MohidWiki - User contributions [en]

Petzold phase - function

2008-11-14T17:13:22Z

192.168.20.171:

== Petzold total angular scattering function - Values for scattering b ==

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Continuous

2008-04-14T14:45:44Z

192.168.20.171: /* Syntax */

==Overview==
[[CONTINUOUS]] is the keyword that allows to pursue calculus from a previous run. It relies on the ''.fin'' and ''.fin5'' files that are created at the end of each run, or at the time intervals determined by the keyword [[RESTART_FILE_OUTPUT_TIME]]. In some modules, another keyword is used: [[OLD]].

==Usage==
Make sure the above keyword is placed correctly in the ''hydrodynamic.dat'' and the ''turbulence.dat''. (Other files may be required for this. Also, in some cases, in some files this may not be required.)
*In the Mohid GUI create a new run within the run you wish to continue. This will create a new run with an identical configuration of the previous run.
*Edit the ''model.dat'' and change the time. Make sure the starting time matches the previous run ending time.

===Syntax===
*Add the following keyword to the ''hydrodynamic.dat'' and the ''turbulence.dat'' files
CONTINUOUS : 1
*Add the following keyword to each property of the ''waterproperties.dat'' or ''lagrangian.dat'':
OLD : 1
*Make sure you deactivate the [[SLOWSTART]] and the [[RAMP]] options.
*If you're not using the GUI then add these lines to the nomfich.dat files
AIRW_INI : ../../Simulation/res/InterfaceWaterAir_1.fin
BOT_INI : ../../Simulation/res/InterfaceSedimentWater_1.fin
IN_CNDI : ../../Simulation/res/Hydrodynamic_1.fin
EUL_INI : ../../Simulation/res/WaterProperties_1.fin
TURB_INI : ../../Simulation/res/GOTM_1.fin

===Modules===
Here's the list of modules affected by this keyword
*[[Module Hydrodynamic]]
*[[Module Turbulence]]
*[[Module WaterProperties]]
*[[Module InterfaceSedimentWater]]
*[[Module InterfaceWaterAir]]

==How to restart from a crashed run==
*Get the last .fin saved date in the file Error_and_Messages_x.log. It should be something like this:
WARNING INTERNAL Hydrodynamic restart file saved 1998: 1: 1: 0: 0: 0
*Create a new run inside the run that has crashed with the starting time exactly like the saved .fin file.
*Open the new run's nomfich_x.dat file and make sure that the keywords IN_CNDI, EUL_INI, BOT_INI, TURB_INI point to the previous(crashed) run .fin files.
**IN_CNDI
**EUL_INI (if running with water properties)
**BOT_INI (if running with interface sediment-water properties)
**TURB_INI(if running with [[Module GOTM|GOTM turbulence module]])
*Run the new run

== Advanced options ==
In the ''hydrodynamic.dat'' file you must take care about some options when you want to start your simulations from a previous run, namely remove all features where ramp options are used.

* When using a ramp period for wind forcing change from '''WIND : 2''' to '''WIND : 1''' and remove keyword [[WIND_SMOOTH_PERIOD]] from the data file.
* When using a slow start in imposing tide, i.e., if in the previous run the [[SLOWSTART]] keyword is activated then remove it from the data file.
* When using a cold period in the Flather boundary condition, i.e. if in the previous run the [[FLATHER_COLD_PERIOD]] keyword is activated then remove it.
* When using baroclinic ramp period, i.e. if the [[RAMP]] option was on in the previous run ('''RAMP : 1''') set it to '''RAMP : 0'''. Remove keyword [[INERTIAL_PERIODS]] from the data file.

In the ''assimilation.dat'' input data file you must also remove any feature regarding ramping options. If in the previous run you're using keywords [[COLD_RELAX_PERIOD]] and [[COLD_ORDER]] then remove it from the data file.

==See also==
*[[RESTART_FILE_OUTPUT_TIME]]
*[[RESTART_FILE_OVERWRITE]]

[[Category:keywords]]

Module BoxDif

2008-04-11T17:22:52Z

192.168.20.171: /* Input */

== Overview ==
Module BoxDif has two main purposes: initialise properties fields within predefined [[boxes]], enabling a better approximation for the initial condition; integrate values in time and space inside and between boxes, allowing computing global and zone budgets for almost every modelled variables.

The module is prepared to perform these operations for both 2D and 3D domains, allowing coupling it straightforwardly to the other modules.

Boxes can be drawn over the domain using [[Mohid GIS]], by visually defining them as polygons and exporting them as boxes. By default Box 0 (zero) is always created, corresponding to the box containing all the points that were not included in the boxes definition. This way if box integration is requested and no boxes are defined, the output will be the integration of the entire domain.

The boxes definition is accomplished by verifying in which box is every single cell in which the domain in divided. Every cell is considered to be defined as a point, relative to the centre of the cell.

== Input ==
Use this keyword in the [[ModuleHydrodynamic]] and/or [[ModuleWaterProperties]] to activate the boxes integration in [[MohidWater]]:
BOXFLUXES : ..\..\GeneralData\Boxes\TagusBoxes_Nivel2.dat

Also in every property desired to output box fluxes insert
BOX_TIME_SERIE : 1

See [[Boxes]] to define the boxes in a file.

== Output ==
Two time series files can be generated by Module BoxDif, being distinguished by their extensions.
: *.BXF - Contains time series for fluxes across adjacent boxes
:: Flux_X_Y, where X stands for the section index and Y stands for the vertical index.

: *.BXM - Contains time series for values integration within each defined box
:: Box_Y, where stands for the vertical index.

== Algorithm ==
See [[Module Drawing]]

[[Category:Modules]]
[[Category:MOHID Base 2]]

ModuleHydrodynamic

2008-03-21T11:01:06Z

192.168.20.171:

#REDIRECT [[Module Hydrodynamic]]

HDF5Exporter

2008-02-28T14:09:35Z

192.168.20.171: /* Sample */

The application '''HDF5Exporter''' produces [[Time Series|time series]] from data contained in [[HDF5]] files in MOHID format .

Running options for this application are specified in an [[HDF5Exporter#Input file|input file]] whose path is indicated in a [[nomfich.dat file]].

==Introduction==
HDF5Exporter extracts data contained in one or more HDF5 files subject to the parameter list, time window and locations specified by the user.

The time window specified by the user indicates the intended time series period. The actual time series period results from the intended period subjected to the data availability of the supplied HDF5 files.

Each time series location consists in a grid cell, defined by the cell indentification indexes, and originates by HDF5Exporter an individual time series file. All the time series produced in a HDF5Exporter will have data for the same parameters and time window.

'''Typical use:'''

Extract time series from MOHID Water result files from several runs produced in continuous running of the model.

'''Data input requirements:'''

One or more HDF5 files, in MOHID format, containing data to create time series.

'''Ouput:'''

A time series file, in MOHID format, for each time series location defined by the user in the input file.

==Input file==

The name of the input file must be provided in the [[nomfich.dat file]] in use.

(block for each HDF5 file to extract time series from; may be several, block order is
irrelevant)
<BeginHDF5File>
NAME : ... (path/name of HDF5 file with data to extract time series)
<EndHDF5File>

START_TIME : ... (start time for time series: yyyy mm dd hh mm ss)
END_TIME : ... (end time for time series: yyyy mm dd hh mm ss)

COMPUTE_RESIDUAL : 0/1 (residual appearance in time series: 0 = appears not, 1 =
appears; 1 = default; residual is meanless in time series
produced, should always be 0)

VARIABLE_GRID : 0/1 (use time variable grid: 0 = normal grid, 1 = variable grid;
0 = default)

WATERPOINTS_NAME : ... (time independent map item name in HDF5 file)

(block for each parameter that is requested a time series; may be several)
<BeginParameter>
PROPERTY : ... (parameter/property name)
HDF_GROUP : ... (complete path in HDF5 file to parameter data)
<EndParameter>

(block for each time series location; may be several, one per output time series file)
<BeginTimeSerie>
NAME : ... (path/name of output time series file)

LOCALIZATION_I : ... (time series location latitude cell indentification index, i)
LOCALIZATION_J : ... (time series location longitude cell indentification index, j)
LOCALIZATION_K : ... (time series location vertical cell indentification index, k;
should be 1 in 2D data)

(if VARIABLE_GRID : 1:)
LATITUDE : ... (time series location geographic decimated latitude)
LONGITUDE : ... (time series location geographic decimated longitude)
<EndTimeSerie>

''Remarks:''

- option VARIABLE_GRID : 1 is usually useful when input HDF5 files contain satellite images
data;

- the parameter/property name indicated in PROPERTY keyword should be the one used in MOHID
framework, otherwise a warning message is issued;

- all the time series locations introduced through <BeginTimeSerie>...<EndTimeSerie> blocks
must have valid data in the input HDF5 files for any output files to be produced: if one
input location does not have valid data the application will produce an error and end
without producing output files.

- The time-span of the data files must be included (but not necessarily equal)
in the interval defined by START_TIME and END_TIME.

- The properties MUST be present in the data files, otherwise an error is returned.

==Sample==
<BeginHDF5File>
NAME : K:\Simula\Nivel1CostaPort\Nivel2Tagus\res\WaterProperties_15.hdf5
<EndHDF5File>

<BeginHDF5File>
NAME : K:\Simula\Nivel1CostaPort\Nivel2Tagus\res\WaterProperties_16.hdf5
<EndHDF5File>

<BeginHDF5File>
NAME : K:\Simula\Nivel1CostaPort\Nivel2Tagus\res\WaterProperties_17.hdf5
<EndHDF5File>

START_TIME : 2005 1 31 0 0 0
END_TIME : 2005 3 1 0 0 0

WATERPOINTS_NAME : WaterPoints3D

COMPUTE_RESIDUAL : 0

VARIABLE_GRID : 0

<BeginParameter>
PROPERTY : salinity
HDF_GROUP : /Results/salinity
<EndParameter>

<BeginParameter>
PROPERTY : temperature
HDF_GROUP : /Results/temperature
<EndParameter>

<BeginTimeSerie>
NAME : P1
LOCALIZATION_I : 60
LOCALIZATION_J : 82
LOCALIZATION_K : 33
<EndTimeSerie>

<BeginTimeSerie>
NAME : P2
LOCALIZATION_I : 60
LOCALIZATION_J : 108
LOCALIZATION_K : 33
<EndTimeSerie>

[[Category:Hdf5]]
[[Category:Tools]]