MohidWiki - User contributions [en]

Mohid Ocean Downscalling

2013-05-28T17:33:17Z

MSMalhadas: /* External fields assimilation */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

RADIATION : 2
LOCAL_SOLUTION : 2
!OBC from submodel

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895

OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run

TYPE_ZUV : z
INITIALIZATION_METHOD : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
!Read the 3D salinity fields interpolated to MOHID grid from HDF5 file

ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 4
!Assumes null gradient at the open boundary

OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895

OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run

TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 5
!OBC are from Submodel

SUBMODEL : 1

SUBMODEL_INI : 1
!Allows to initializate the fields from submodel
!Change to SUBMODEL_INI : 0 to continued the calculus from the spin-up run or remove it

SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5
SUBMODEL : 1
SUBMODEL_INI : 1
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

==External fields assimilation==

Assimilation of a 3D external solution salinity and temperature are imposed in [[Module Assimilation|Assimilation]] module of MOHID. These differs from Level 1 to Level n of nested aplications. In level that external 3D fields are assimilated must be activated the cold relax period for assimilating the 3D salinity, temperature, velocity U and V.

===Level 1===

Sample of Assimilation file:

OUTPUT_TIME : 0 864000.

<beginproperty>
NAME : water level
UNITS : m
DIMENSION : 2D
OUTPUT_HDF : 1
<<begin_field>>
DEFAULTVALUE : 0
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : z
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : velocity U
UNITS : m/s
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000
<<begin_field>>
DEFAULTVALUE : 0
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : u
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : velocity V
UNITS : m/s
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000
<<begin_field>>
DEFAULTVALUE : 0
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : v
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000
<<begin_field>>
DEFAULTVALUE : 18
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : z
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : salinity
UNITS : ºC
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000
<<begin_field>>
DEFAULTVALUE : 36
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : z
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

===Level 2===

Sample of Assimilation file:

OUTPUT_TIME : 0 864000.

<beginproperty>
NAME : water level
UNITS : m
DIMENSION : 2D
OUTPUT_HDF : 1
<<begin_field>>
DEFAULTVALUE : 0
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : z
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : velocity U
UNITS : m/s
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000
<<begin_field>>
DEFAULTVALUE : 0
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : u
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : velocity V
UNITS : m/s
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000
<<begin_field>>
DEFAULTVALUE : 0
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : v
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000
<<begin_field>>
DEFAULTVALUE : 0
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : z
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : salinity
UNITS : ºC
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000
<<begin_field>>
DEFAULTVALUE : 0
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : z
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T17:29:42Z

MSMalhadas: /* Assimilation 3D external Fields */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

RADIATION : 2
LOCAL_SOLUTION : 2
!OBC from submodel

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895

OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run

TYPE_ZUV : z
INITIALIZATION_METHOD : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
!Read the 3D salinity fields interpolated to MOHID grid from HDF5 file

ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 4
!Assumes null gradient at the open boundary

OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895

OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run

TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 5
!OBC are from Submodel

SUBMODEL : 1

SUBMODEL_INI : 1
!Allows to initializate the fields from submodel
!Change to SUBMODEL_INI : 0 to continued the calculus from the spin-up run or remove it

SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5
SUBMODEL : 1
SUBMODEL_INI : 1
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

==External fields assimilation==

To perform assimilation of a 3D external solution for salinity, temperature, velocity U and velocity V and 2D external solution of water level the variables must be prescribed in assimila

===Level 1===

Sample of Assimilation file:

OUTPUT_TIME : 0 864000.

<beginproperty>
NAME : water level
UNITS : m
DIMENSION : 2D
OUTPUT_HDF : 1
<<begin_field>>
DEFAULTVALUE : 0
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : z
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : velocity U
UNITS : m/s
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000
<<begin_field>>
DEFAULTVALUE : 0
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : u
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : velocity V
UNITS : m/s
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000
<<begin_field>>
DEFAULTVALUE : 0
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : v
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000
<<begin_field>>
DEFAULTVALUE : 18
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : z
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : salinity
UNITS : ºC
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000
<<begin_field>>
DEFAULTVALUE : 36
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : z
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

===Level 2===

Sample of Assimilation file:

OUTPUT_TIME : 0 864000.

<beginproperty>
NAME : water level
UNITS : m
DIMENSION : 2D
OUTPUT_HDF : 1
<<begin_field>>
DEFAULTVALUE : 0
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : z
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : velocity U
UNITS : m/s
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000
<<begin_field>>
DEFAULTVALUE : 0
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : u
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : velocity V
UNITS : m/s
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000
<<begin_field>>
DEFAULTVALUE : 0
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : v
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000
<<begin_field>>
DEFAULTVALUE : 0
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : z
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : salinity
UNITS : ºC
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000
<<begin_field>>
DEFAULTVALUE : 0
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : z
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T17:19:23Z

MSMalhadas: /* Assimilation 3D external Fields */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

RADIATION : 2
LOCAL_SOLUTION : 2
!OBC from submodel

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895

OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run

TYPE_ZUV : z
INITIALIZATION_METHOD : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
!Read the 3D salinity fields interpolated to MOHID grid from HDF5 file

ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 4
!Assumes null gradient at the open boundary

OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895

OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run

TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 5
!OBC are from Submodel

SUBMODEL : 1

SUBMODEL_INI : 1
!Allows to initializate the fields from submodel
!Change to SUBMODEL_INI : 0 to continued the calculus from the spin-up run or remove it

SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5
SUBMODEL : 1
SUBMODEL_INI : 1
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

==Assimilation 3D external Fields==

OUTPUT_TIME : 0 864000.

<beginproperty>
NAME : water level
UNITS : m
DIMENSION : 2D
OUTPUT_HDF : 1
<<begin_field>>
DEFAULTVALUE : 0
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : z
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : velocity U
UNITS : m/s
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000

<<begin_field>>
DEFAULTVALUE : 0
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : u
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : velocity V
UNITS : m/s
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000

<<begin_field>>
DEFAULTVALUE : 0
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : v
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000

<<begin_field>>
DEFAULTVALUE : 18
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : z
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : salinity
UNITS : ºC
DIMENSION : 3D
OUTPUT_HDF : 1
COLD_RELAX_PERIOD : 432000

<<begin_field>>
DEFAULTVALUE : 36
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : z
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T17:17:23Z

MSMalhadas:

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

RADIATION : 2
LOCAL_SOLUTION : 2
!OBC from submodel

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895

OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run

TYPE_ZUV : z
INITIALIZATION_METHOD : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
!Read the 3D salinity fields interpolated to MOHID grid from HDF5 file

ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 4
!Assumes null gradient at the open boundary

OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895

OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run

TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 5
!OBC are from Submodel

SUBMODEL : 1

SUBMODEL_INI : 1
!Allows to initializate the fields from submodel
!Change to SUBMODEL_INI : 0 to continued the calculus from the spin-up run or remove it

SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5
SUBMODEL : 1
SUBMODEL_INI : 1
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

==Assimilation 3D external Fields==

OUTPUT_TIME : 0 864000.

<beginproperty>
NAME : water level
UNITS : m
DIMENSION : 2D
OUTPUT_HDF : 1
<<begin_field>>
DEFAULTVALUE : 0
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : z
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : velocity U
UNITS : m/s
DIMENSION : 3D
OUTPUT_HDF : 1
<<begin_field>>
DEFAULTVALUE : 0
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : u
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : velocity V
UNITS : m/s
DIMENSION : 3D
OUTPUT_HDF : 1
<<begin_field>>
DEFAULTVALUE : 0
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : v
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DIMENSION : 3D
OUTPUT_HDF : 1
<<begin_field>>
DEFAULTVALUE : 18
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : z
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

<beginproperty>
NAME : salinity
UNITS : ºC
DIMENSION : 3D
OUTPUT_HDF : 1
<<begin_field>>
DEFAULTVALUE : 36
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
TYPE_ZUV : z
<<end_field>>
<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : z
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : Sponge
SPONGE_OUT : 1e5
<<end_coef>>
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T16:48:43Z

MSMalhadas: /* Level 2 */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

RADIATION : 2
LOCAL_SOLUTION : 2
!OBC from submodel

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895

OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run

TYPE_ZUV : z
INITIALIZATION_METHOD : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
!Read the 3D salinity fields interpolated to MOHID grid from HDF5 file

ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 4
!Assumes null gradient at the open boundary

OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895

OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run

TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 5
!OBC are from Submodel

SUBMODEL : 1

SUBMODEL_INI : 1
!Allows to initializate the fields from submodel
!Change to SUBMODEL_INI : 0 to continued the calculus from the spin-up run or remove it

SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5
SUBMODEL : 1
SUBMODEL_INI : 1
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T16:47:32Z

MSMalhadas: /* Initial conditions and Spin up */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

RADIATION : 2
LOCAL_SOLUTION : 2
!OBC from submodel

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
!Read the 3D salinity fields interpolated to MOHID grid from HDF5 file
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4
!Assumes null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
!Read the 3D salinity fields interpolated to MOHID grid from HDF5 file
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4
!Assumes null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895

OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run

TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 5
!OBC are from Submodel

SUBMODEL : 1

SUBMODEL_INI : 1
!Allows to initializate the fields from submodel
!Change to SUBMODEL_INI : 0 to continued the calculus from the spin-up run or remove it

SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5
SUBMODEL : 1
SUBMODEL_INI : 1
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T16:41:28Z

MSMalhadas: /* Level 2 */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

RADIATION : 2
LOCAL_SOLUTION : 2
!OBC from submodel

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
!Read the 3D salinity fields interpolated to MOHID grid from HDF5 file
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4
!Assumes null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
!Read the 3D salinity fields interpolated to MOHID grid from HDF5 file
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4
!Assumes null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T16:40:51Z

MSMalhadas: /* Level 2 */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

RADIATION : 2
LOCAL_SOLUTION : 2
!OBC from submodel

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
!Read the 3D salinity fields interpolated to MOHID grid from HDF5 file
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4
!Assumes null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
!Read the 3D salinity fields interpolated to MOHID grid from HDF5 file

ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4
!Assumes null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T16:39:36Z

MSMalhadas: /* Level 2 */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

RADIATION : 2
LOCAL_SOLUTION : 2
!OBC from submodel

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895

OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run

TYPE_ZUV : z
INITIALIZATION_METHOD : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
!Read the 3D salinity fields interpolated to MOHID grid from HDF5 file

ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 4
!Assumes null gradient at the open boundary

OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.

OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run

TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
!Read the 3D salinity fields interpolated to MOHID grid from HDF5 file

ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 4
!Assumes null gradient at the open boundary

OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T16:38:30Z

MSMalhadas: /* Level 2 */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

RADIATION : 2
LOCAL_SOLUTION : 2
!OBC from submodel

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>

NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895

OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run

TYPE_ZUV : z
INITIALIZATION_METHOD : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
!Read the 3D salinity fields interpolated to MOHID grid from HDF5 file

ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 4
!Assumes null gradient at the open boundary

OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.

OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run

TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
!Read the 3D salinity fields interpolated to MOHID grid from HDF5 file

ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 4
!Assumes null gradient at the open boundary

OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1

<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T16:36:57Z

MSMalhadas: /* Level 2 */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

RADIATION : 2
LOCAL_SOLUTION : 2
!OBC from submodel

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>

NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895

OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run

TYPE_ZUV : z
INITIALIZATION_METHOD : HDF
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
!Read the 3D salinity fields interpolated to MOHID grid from HDF5 file

ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 4
!Assumes null gradient at the open boundary

OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.

OLD : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to OLD: 1 to continued the calculus from the spin-up run

TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
!Read the 3D salinity fields interpolated to MOHID grid from HDF5 file

ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 4
!Assumes null gradient at the open boundary

OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1

<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T16:29:51Z

MSMalhadas: /* Level 2 */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

RADIATION : 2
LOCAL_SOLUTION : 2
!OBC from submodel

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>

NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895

OLD : 0
!Change it to OLD: 1 in the continuous run

TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 4
!Null gradient at the open boundary

OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.

OLD : 0
!Change it to OLD: 1 in the continuous run

TYPE_ZUV : z

INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5

ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 4
!Null gradient at the open boundary

OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1

<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T16:29:14Z

MSMalhadas: /* Level 2 */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

RADIATION : 2
LOCAL_SOLUTION : 2
!OBC from submodel

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895

OLD : 0
!Change it to OLD: 1 in the continuous run

TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 4
!Null gradient at the open boundary

OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.

OLD : 0
!Change it to OLD: 1 in the continuous run

TYPE_ZUV : z

INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5

ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1

BOUNDARY_CONDITION : 4
!Null gradient at the open boundary

OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T16:27:28Z

MSMalhadas: /* Level 3 to Level n */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

RADIATION : 2
LOCAL_SOLUTION : 2
!OBC from submodel

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T16:26:27Z

MSMalhadas: /* Level 3 to Level n */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

RADIATION : 2
LOCAL_SOLUTION : 2
!OBC from submodel (in this case Level 2)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T16:25:43Z

MSMalhadas: /* Level 3 to Level n */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

RADIATION : 2
LOCAL_SOLUTION : 2
!OBC from submodel (in this case Level 2)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T16:24:39Z

MSMalhadas: /* Level 3 to Level n */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

RADIATION : 2
LOCAL_SOLUTION : 2
!OBC from submodel (in this case Level 2)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T16:23:19Z

MSMalhadas: /* Level 2 */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T16:22:53Z

MSMalhadas: /* Level 2 */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T16:21:54Z

MSMalhadas: /* Level 2 */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T16:21:18Z

MSMalhadas:

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued the calculus from the spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued the calculus from the spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T16:19:27Z

MSMalhadas:

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run, remove it to continued calculus from spin-up run

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords is only used in spin-up run, remove it to continued calculus from spin-up run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to continued the calculus from the spin-up run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1
!Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7
!OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)

SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

SUBMODEL_FATHER_HOT_START : 1
!Allows to start from water level of submodel (should be 1 in spin-up run)
!Change it to SUBMODEL_FATHER_HOT_START : 0 to continued the calculus from the spin-up run

EXTERNAL_BAROTROPIC_2D : 0
!Allows to calculate barotropic velocities from velocity U and V of the 3D external solution

RAMP : 1
RAMP_PERIOD : 259200
!Start with baroclinic force null and only after a specific period specified (seconds) the total force is compute
!This keyword is only used in spin-up run, remove it to continued calculus from spin-up run

WIND : 2
WIND_SMOOTH_PERIOD : 259200
!Start wind with a ramp period for wind forcing in order to allow a slowly adjustement
!Both keywords are used only in the spin-up run
!Remove both keywords and include WIND: 1 to continued the calculus from the spin-up run

ATM_PRESSURE : 1
ATM_PERIOD : 259200
!Connect pressure forcing slowly for the prescribe period of time
!ATM_PERIOD keyword is used only in te spin-up run, remove it to continued the calculus from the spin-up run

FLATHER_COLD_PERIOD : 432000
!Allows the relaxation of water level solution for a period of time
!This keyword is only used in spin-up run, remove it to continued calculus from spin-up run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:59:08Z

MSMalhadas: /* Level 1 */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!This keyword is only used in spin-up run. To make continued calculus remove it

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to make a continued calculations from spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords should be only enabled in the spin-up run. To make continued calculations remove it

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!The coefficient is calculated by BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:56:00Z

MSMalhadas: /* Level 1 */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!Connect the tide slowly during the time period (seconds) considered above
!For calculating the calculus if in the previous run this keyword is activated then remove it (should only be in spin-up run)

CONTINUOUS : 0
!Allows to pursue calculus from a previous run (should be 0 in spin-up run)
!Change to CONTINUOUS: 1 to make a continued calculations from spin-up run

INITIAL_ELEVATION : 1
INITIAL_ELEVATION_VALUE : 1.8
!Impose an initial elevation value of 1.8 m(must be in accordance with mean water leve value of the area)
!These keywords should be only enabled in the spin-up run. To make continued calculations remove it

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9
!BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:43:55Z

MSMalhadas: /* Level 1 */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!This keyword connect the tide slowly during the time period (seconds) considered above
!For calculating the calculus if in the previous run this keyword is activated then remove it

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:43:29Z

MSMalhadas: /* Level 1 */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400
!This keyword connect the tide slowly during the time period (seconds) considered above. For calculating the calculus if in the previous run this keyword is activated then remove it

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:32:47Z

MSMalhadas: /* GFS to MOHID */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:32:28Z

MSMalhadas: /* RTOFS to MOHID */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

INTERPOLATION3D : 1
!3D vertical interpolation

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:31:51Z

MSMalhadas: /* MyOcean to MOHID */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!1-bilinear and 3-triangulation

INTERPOLATION3D : 1
!Interpolation 3D in vertical

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1
!2D horizontal interpolation 1-bilinear and 3-Triangulation

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
!3D vertical interpolation

POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:29:41Z

MSMalhadas: /* RTOFS to MOHID */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1
!1-bilinear and 3-triangulation

INTERPOLATION3D : 1
!Interpolation 3D in vertical

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:28:40Z

MSMalhadas: /* GFS to MOHID */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0
!No interpolation 3D in vertical

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:27:47Z

MSMalhadas: /* RTOFS to MOHID */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>

<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:27:19Z

MSMalhadas: /* GFS to MOHID */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>
<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:27:01Z

MSMalhadas: /* MyOcean and RTOFS */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000
<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>
<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:26:42Z

MSMalhadas: /* NOAA/GFS */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>

<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000
<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>
<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:26:17Z

MSMalhadas: /* Bathymetry transition */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000
<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>
<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:25:55Z

MSMalhadas: /* Bathymetry transition */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>

!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2

<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000
<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>
<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:25:04Z

MSMalhadas: /* MyOcean to MOHID */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>
!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2
<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000
<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>
<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat
!The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat
!The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:23:19Z

MSMalhadas: /* MyOcean to MOHID */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>
!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2
<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000
<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>
<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat !The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat !The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:23:03Z

MSMalhadas: /* MyOcean to MOHID */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>
!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2
<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000
<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>
<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat !The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat !The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:22:31Z

MSMalhadas: /* MyOcean to MOHID */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>
!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2
<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000
<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>
<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5
NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat !The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat !The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4

<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:20:48Z

MSMalhadas: /* MyOcean and RTOFS */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>
!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2
<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000
<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>
<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat !The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat !The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4
<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:19:52Z

MSMalhadas: /* Bathymetry transition */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>
!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2
<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000
<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>
<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat !The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat !The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4
<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:19:27Z

MSMalhadas: /* Bathymetry transition */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>
!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2
<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000
<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>
<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat !The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat !The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4
<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:18:39Z

MSMalhadas: /* RTOFS to MOHID */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>
!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2
<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000
<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>
<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat !The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat !The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4
<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:18:17Z

MSMalhadas: /* RTOFS to MOHID */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>
!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2
<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000
<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>
<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat !The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat !The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4
<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:17:26Z

MSMalhadas: /* GFS to MOHID */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>
!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2
<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000
<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>
<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat !The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat !The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4
<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:17:08Z

MSMalhadas: /* GFS to MOHID */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>
!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2
<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000
<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>
<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat !The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat !The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4
<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:16:52Z

MSMalhadas: /* GFS to MOHID */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>
!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2
<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000
<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>
<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat !The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat !The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4
<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;

Mohid Ocean Downscalling

2013-05-28T15:16:34Z

MSMalhadas: /* GFS to MOHID */

== Download ==

The area extracted from NOAA/GFS and MyOcean/RTOFS must be bigger than that the area of MOHID level domain choosen to impose the surface and ocean boundary conditions.

===NOOA/GFS===

To download GFS model solution go to http://nomads.ncdc.noaa.gov/cgi-bin/ncdc-ui/define-collection.pl?model_sys=gfs4&model_name=gfs&grid_name=4. Then select date range(Ex.: 2013 April 15 To 2013 April 20), select cycles (Ex.: 0000), select forecast hours (Ex.: 003 006 009 012 015 018 021 024). Press Submit Data request button and Press Selected Files for FTP. On the Filename Filter Type “*.grb2” and press Select files button. Then select the levels desired and at FTP Information, type your email and press the start FTP button. This will place the files in the ftp for download.

NOTES : This is a 24 hour period with all the necessary properties for Mohid, the best forecast for each day in the range. The 000 output is neglected because some properties are 3 hour average, for instance “downward solar radiation” isn’t present. For this 000 is subtracted and the 024 added.

===MyOcean===

To download my ocean solution go to http://www.myocean.eu/. and click in ACCES THE CATALOGUE. In block 1 choose "Global Ocean", in 2 the parameters and in 3 choose forecast products. After fill all the blocks click search and in the next web page choose DATA ACCES and then GO. Prescribe the user name and password and then choose the dates and area of interest.

===RTOFS===

To download te RTOFS global model solution go to http://polar.ncep.noaa.gov/global/data_access.shtml or http://nomads.ncep.noaa.gov:9090/dods/rtofs. The download in the second one is made via opendap. select the product and thenclick in download data.

== Conversion ==

=== Bathymetry transition ===

Running tool SmoothBathymNesting.exe

Example of the input file SmoothBathymNesting.dat

!File [[Bathymetry| bathymetry]] of the external 3D solution
FATHER_BATIM : Father.dat

!Bathymetry File of MOHID solution
SON_BATIM : Son.dat

!New Bathymetry File
NEW_SON_BATIM : NewSon.dat

<begin_coef>
!Name of generic property
NAME : generic property

!Type of initialization used
INITIALIZATION_METHOD : sponge

!0-external 3D solution, 1-MOHID solution
DEFAULTVALUE : 1

!sponge output
SPONGE_OUT : 0

!sponge cells number
SPONGE_CELLS : 10

!1-exponential, 2-linear
SPONGE_EVOLUTION : 2
<end_coef>

=== Grib-Netcdf-Hdf5 ===

==== NOAA/GFS ====

STEP 1: Grib to NetCDF

To convert grib files to NetCDF files create a batch file and write the follow comand line "java -Xmx1024m -classpath netcdfAll-4.3.jar ucar.nc2.dataset.NetcdfDataset -in gfs_4_20130415_0000_003.grb2 -out gfs_4_20130415_0000_003.nc > NCDumpLog.txt". The input file must be in the same folder of batch file.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : outfile.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : outfile.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
NETCDF_NAME_MAPPING : Temperature_height_above_ground
MAPPING_LIMIT : -10000
<<end_grid>>

PROPERTIES_NUMBER : 8

<<begin_field>>
NETCDF_NAME : u-component_of_wind_height_above_ground
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : v-component_of_wind_height_above_ground
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : Temperature_height_above_ground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_field>>
NETCDF_NAME : Total_precipitation_surface_3_Hour_Accumulation
NAME : precipitation
UNITS : mm/h
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Relative_humidity_height_above_ground
NAME : relative humidity
UNITS : -
DESCRIPTION : MOHID
DIM : 2
MULTIPLY_FACTOR : 0.01
<<end_field>>

<<begin_field>>
NETCDF_NAME : Downward_Short-Wave_Radiation_Flux_surface_3_Hour_Average
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : Pressure_reduced_to_MSL_msl
NAME : atmospheric pressure
UNITS : pa
DESCRIPTION : Malaca
DIM : 2
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

==== MyOcean and RTOFS ====

STEP 1: Grib to NetCDF

In case of download grib data use the same sample than that the one prescribed in GFS. If the data downloaded is already in NETCDF than go to Step 2.

STEP 2: NetCDF to HDF5

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : 20130416_rtofs_glo_3dz_nowcast_daily.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : rtofs_glo_3dz_nowcast_daily.nc

WINDOW_OUT : 1173 1323 1428 1643
!is optional but usefull to generate smaller area for interpolation. In case of already extracted a small area durin the download data then change to WINDOW_OUT : 0.

<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : lat
NETCDF_NAME_LONG : lon
STARTS_180W : 0
NETCDF_NAME_MAPPING : temperature
MAPPING_LIMIT : 1.2676506E29
MAPPING_INSTANT : 2
NETCDF_NAME_DEPTH : lev
INVERT_LAYER_ORDER : 1
BATHYM_FROM_MAP : 1
BATHYM_FILENAME : Batim_rtofs_glo_3dz_nowcast_daily.dat
<<end_grid>>

PROPERTIES_NUMBER : 5

<<begin_field>>
NETCDF_NAME : temperature
NAME : temperature
UNITS : ºC
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : salinity
NAME : salinity
UNITS : psu
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : u
NAME : velocity U
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : v
NAME : velocity V
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
<<end_field>>

<<begin_field>>
NETCDF_NAME : velocity_modulus
NAME : velocity modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 3
VECTOR_INTENSITY : 1
VECTOR_X : velocity U
VECTOR_Y : velocity V
<<end_field>>

<<begin_input_files>>
!path to the input files
<<end_input_files>>
<end_file>

== Interpolation ==

Vertical discretization of RTOFS and MyOcean model solutions correspond to the depth of the center of the cell. Since MOHID [[Module Geometry | geometry]] must be provided in thickness the depths must be convertes to top of the faces cell and then to thickness layers. In order to avoid this the new method of interpolating grids allow to provide the depth of the center of the cells in ConvertToHDF5.dat instead to use a thickness calculated baing on the centers depth. Th both samples are provided bellow.

=== GFS to MOHID ===

This example perform linear horizontally interpolation (e.g., 2D) between GFS grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Sample of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
!Option 1 is bilinear and 3 triangulation

INTERPOLATION3D : 0

FATHER_FILENAME : ..\outdata\GFS_2011010100_2011011621.hdf5
FATHER_GRID_FILENAME : batim\GFS.dat

OUTPUTFILENAME : ..\outdata\Batim_Caribe_Colombia_5km.hdf5
NEW_GRID_FILENAME : batim\Batim_Caribe_Colombia_5km_GFS.dat

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000
<end_file>

=== RTOFS to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between RTOFS grid data and MOHID. In this sample is provided the depth of the centers cells in the file.dat.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>
ACTION : INTERPOLATE GRIDS

DO_NOT_BELIEVE_MAP : 1

TYPE_OF_INTERPOLATION : 1

INTERPOLATION3D : 1

START : 2013 04 13 0 0 0
END : 2013 04 18 0 0 0

FATHER_FILENAME : ..\work\20130410_rtofs_glo_3dz_nowcast_daily.hdf5
FATHER_GRID_FILENAME : ..\work\batim\Batim_RTOFS.dat

OUTPUTFILENAME : ..\work\Level2_RTOFS_13_18_04_2013.hdf5
NEW_GRID_FILENAME : ..\work\batim\Level2_.new

EXTRAPOLATE_2D : 4
EXTRAPOLATE_LIMIT : -10000

FATHER_GEOMETRY : ..\work\Geometry_RTOFS.dat
!A "false" geometry must be provide, but in reality uses the depths in the file.dat

NEW_GEOMETRY : ..\work\Geometry_1.dat
!MOHID geometry with thicknes layers

<<BeginDepths>>
0.0
10.0
20.0
30.0
50.0
75.0
100.0
125.0
150.0
200.0
250.0
300.0
400.0
500.0
600.0
700.0
800.0
900.0
1000.0
1100.0
1200.0
1300.0
1400.0
1500.0
1750.0
2000.0
2500.0
3000.0
3500.0
4000.0
4500.0
5000.0
5500.0
<<EndDepths>>
<end_file>

=== MyOcean to MOHID ===

This example perform 2D horizontal and 3D vertical interpolation between MyOcean grid data and MOHID.

Running tool [[ConvertToHDF5|ConversionHDF5.exe]]

Example of the file ConvertToHDF5.dat

<begin_file>

ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : ..\conv\MyOcean3D.hdf5
FATHER_GRID_FILENAME : ..\conv\MyOceanMaxDepth.dat

OUTPUTFILENAME : Level2_MyOcean_13-04_27-04_2013.hdf5

START : 2013 04 12 12 0 0
END : 2013 04 27 12 0 0

NEW_GRID_FILENAME : Level2_.new

FATHER_GEOMETRY : ..\conv\MyOceanGeometry.dat !The geometry corresponds to thickness layers calculated basing on depth centers cells

NEW_GEOMETRY : geometry_1.dat !The geometry corresponds to thickness layers converting the depth centers cells in faces top and then in thickness

INTERPOLATION3D : 1
POLI_DEGREE : 1
DO_NOT_BELIEVE_MAP : 0
EXTRAPOLATE_2D : 4
<end_file>

== Boundary Conditions==

===Open boundary ===

Open boundary conditions are imposed in [[Module Hydrodynamic|hydrodynamic]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model usualy forced only with tide (no wind in atmosphere and InterfaceWaterAir module) with a slow connection. From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the OBC are resolved by imposing a Flow Relaxation Scheme (FRS) similar to the one presented by Marchesiello et al. (2001). The FRS is applied to temperature (T), salinity (S) and velocities (U, V) (Martinsen and Engedahl, 1987) being combined with a radiation scheme from Flather (1976) for the barotropic mode. The barotropic forces are turned on and the wind stress and atmospheric pressure terms imposed and connected slowly.

====Level 1====

Sample of the hydrodynamic file:

BAROCLINIC : 0

SLOWSTART : 86400 !Connection of the tide slowly. Remove it in the continuous run

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

INITIAL_ELEVATION : 1 !Remove it in the continuous run
INITIAL_ELEVATION_VALUE : 1.8 !Remove it in the continuous run

TIDE : 1
TIDEPOTENTIAL : 1

DATA_ASSIMILATION : 0
BRFORCE : 0
SUBMODEL : 0

WIND : 0
ATM_PRESSURE : 0

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 21600

====Level 2====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1 !Activate the [[InvertedBarometer|Inverted Barometer]] method

RADIATION : 2
LOCAL_SOLUTION : 7 !OBC from submodel (Level 1) + field (MyOcean or RTOFS) + gauges (pressure effect from inverted barometer effect)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1
SUBMODEL_FATHER_HOT_START : 1 !Change it to SUBMODEL_FATHER_HOT_START : 0 in the continuous runs

EXTERNAL_BAROTROPIC_2D : 0

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous runs
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

FLATHER_COLD_PERIOD : 432000 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e9 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

====Level 3 to Level n====

Sample of the hydrodynamic file:

BAROCLINIC : 1
BAROCLINIC_POLIDEGREE : 1

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

CONTINUOUS : 0 !Change to CONTINUOUS: 1 in the continuous run

TIDE : 0
TIDEPOTENTIAL : 1
DATA_ASSIMILATION : 1
BRFORCE : 1
ATM_PRESSURE : 1

IMPOSE_INVERTED_BAROMETER : 1

RADIATION : 2
LOCAL_SOLUTION : 2 !OBC from submodel (Level 2)
SUBMODEL : 1
MISSING_NULL : 1
SUBMODEL_EXTRAPOLATE : 1

RAMP : 1 !Start with baroclinic force null and only after a specific period the total force is compute. Remove it in the continuous run
RAMP_PERIOD : 259200 !Remove it in the continuous run

WIND : 2 !Using a ramp period for wind forcing. Change it to WIND: 1 in the continuous run
WIND_SMOOTH_PERIOD : 259200 !Remove it in the continuous run

ATM_PRESSURE : 1 !Connect pressure forcing slowly for a period of time.
ATM_PERIOD : 259200 !Remove it in the continuous run

BIHARMONIC : 1
BIHARMONIC_COEF : 2e7 !BIHARMONIC_COEF = Dx^3/100

RESIDUAL : 1
ENERGY : 1

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

===Surface===

To impose surface boundary conditions (e.g., wind stress, solar radiation, temperature, pressure etc.) in [[Module Atmosphere|atmosphere module]] an example of the file is provided below.

Sample of the atmosphere file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : air temperature
UNITS : ºC
DESCRIPTION : Temperature interpolated from GFS model field
DEFAULTVALUE : 15.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : solar radiation
UNITS : W/m^2
DESCRIPTION : Solar radiation interpolated from GFS model field
DEFAULTVALUE : 0.0
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
TIME_SERIE : 0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : Atmospheric pressure interpolated from GFS model field
DEFAULTVALUE : 0.
FILE_IN_TIME : HDF
FILENAME : ..\..\..\GeneralData\GFS\Abril2013\Level2_10-04-2013_25-04-2013.hdf5
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : relative humidity
UNITS : fraction
DESCRIPTION : Constant value
DEFAULTVALUE : 0.55
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : cloud cover
UNITS : %
DESCRIPTION : Constant value
DEFAULTVALUE : 50.
TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==Ocean-Atmosphere Heat Fluxes==

Sensible/latent heat is computed in [[Module InterfaceWaterAir|Module InterfaceWaterAir]] based in the atmospheric parameters (e.g.,wind stress, solar radiation, temperature, pressure etc.) prescribed in the atmosphere module. An example of the file is provided below.

Sample of the InterfaceWaterAir file.

OUTPUT_TIME : 0. 3600.

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
REMAIN_CONSTANT : 0
<end_rugosity>

<beginproperty>
NAME : wind shear velocity
UNITS : m/s
DESCRIPTION : Computed wind shear velocity
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress X
UNITS : N/m2
DESCRIPTION : Computed wind stress X
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind stress Y
UNITS : N/m2
DESCRIPTION : Computed wind stress Y
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
TIME_SERIE : 0
DEFAULTVALUE : 0.
DEFINE_CDWIND : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : latent heat
UNITS : W/m^2
DESCRIPTION : Computed latent heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : sensible heat
UNITS : W/m^2
DESCRIPTION : Computed sensible heat
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : surface radiation
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
ALBEDO : 0.05
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : net long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed net long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : downward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed downward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : upward long wave radiation
UNITS : W/m^2
DESCRIPTION : Computed upward long wave radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : non solar flux
UNITS : W/m^2
DESCRIPTION : Computed infrared radiation
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 0
DEFAULTVALUE : 0.
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Initial conditions and Spin up ==

For the spin-up procedure, a methodology based on a slow connection of the forcing terms (baroclinic force, winds tress, atmospheric pressure) is used. This methodology consists of defining an initial condition where the initial fields of salinity and temperature are interpolated from the external 3D solution (MyOcean or RTOFS), a null velocity field is assumed, and a SSH field with null gradient is also considered. A coefficient that varies linearly between 0 and 1 along the “connection” period of 5 days is multiplied by the baroclinic force and wind stress. Because the forces are slowly connected, the velocity reference solution of the OBC also needs to be slowly connected. The nudging term in the momentum equation is multiplied by a coefficient C given by:

<math>C=(Elapsed Time/Connection Period)^4; Elapsed Time<Connection Period</math>

<math>C=1 ; Elapsed Time>=Connection Period</math>

In this way, the velocity field near the boundary also converges slowly to the reference solution. To minimize the perturbations suffered by the initial condition of salinity and temperature along the spin-up period, a relaxation period variable in time was also assumed for these properties. The idea is to assume a relaxation period that increases with time; this way, in the beginning of the run the temperature and salinity fields have a stronger nudging when the external and internal activity is more intense due to the spin-up process. In the end of the spin-up period, the nudging in the model interior (out of the FRS area) is null. For the forces, a connection coefficient was assumed with a linear evolution over 5 days. For the reference solution a quadratic evolution was imposed. For the slow connection of the forcing mechanisms, the methodology followed by Mellor (2004) for the baroclinic force was assumed. This evolution allows, in the first instants, a strong nudging across the entire domain. With time, the model tends to be free except in the flow relaxation scheme area.

Initial conditions of salinity and temperature are imposed in [[Module WaterProperties|WaterProperties]] module of MOHID. These differs from Level 1 to Level n of nested aplications. Level 1 is a 2D barotropic model and does not use the calculus of density fields (no keywords in WaterProperties file). From Level 2 to Level n of nested domains the models are 3D baroclinic (e.g., include th density gradientes efects) and the initial cnditons are prescribed by imposing a densitiy 3D field.

===Level 2===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
INITIALIZATION_METHOD : HDF !3D salinity field interoplated to MOHID grid domain
FILENAME : ..\..\..\GeneralData\MyOcean\Level2_MyOcean_13-04_27-04_2013.hdf5
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 4 !Null gradient at the open boundary
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

===Level 3 to Level n===

Sample of the WaterProperties file:

OUTPUT_TIME : 0 10800
SURFACE_OUTPUT_TIME : 0 900

ADV_METHOD_H : 4
ADV_METHOD_V : 4
TVD_LIMIT_H : 4
TVD_LIMIT_V : 4
VOLUME_RELATION_MAX : 1.3

<beginproperty>
NAME : salinity
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 34.895
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous run
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : MyOcean Interpolated results
DEFAULTVALUE : 16.
OLD : 0 !Change it to OLD: 1 in the continuous run
TYPE_ZUV : z
ADVECTION_DIFFUSION : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 1
BOUNDARY_CONDITION : 5 !Submodel (Level 2)
SUBMODEL : 1
SUBMODEL_INI : 1 !Change it to SUBMODEL_INI: 0 in the continuous runs
SUBMODEL_EXTRAPOLATE : 1
OUTPUT_HDF : 1
OUTPUT_SURFACE_HDF : 1
<endproperty>

== Usual mistakes and known limitations ==

If errors occurs after MOHID project implementation with the procedements provided above then check the following:

1. The ratio between grids can not be higher than 1/5;

2. In the open boundaries cannot exist intertidal areas;

3. To choose the open boundaries delimitation avoid areas with big diferences in topography;

4. Deviate the open boundaries far away from areas with big velocities jets;

5. If noisy is created in the open boundary of large model domain (the ones that simulate the tide only) close some cells in the boundary with land;

6. Check if the interpolations of 3D fields were performed with double precision;