MohidWiki - User contributions [en]

AssimilationPreProcessor

2008-10-03T12:14:10Z

192.168.20.156: /* Input file */

The application '''AssimilationPreProcessor''' performs the calculation of the covariance structure of data in MOHID format HDF5 files while performing EOF Analysis.

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

==Introduction==
AssimilationPreProcessor calculates from fields in HDF5 files the covariance structure to be used as initial state error covariance in sequential data assimilation operations in MOHID Water.

The fields to be analysed are specified through the definition of the state. The state is a set of variables which characterizes the system to be studied at a particular time instant.

These variables can refer to several hydrodynamic and water properties and represent also several spatial locations (or cells) according to the horizontal and vertical grids defined in the HDF5 files. The spatial locations are specific for each property and therefore can be different according to property.

The time instants contained in the input HDF5 files can be selected using a decimation process. This can be used to reduce computational costs of covariance generation and processing and also if subsequent time instants provide very similar data.

Following the state definition the covariance matrix of the state is calculated. This matrix is then processed to be in a form (the covariance structure) suitable to be used in MOHID Water for the initialization of sequential assimilation processes.

Currently, the covariance matrix is processed only only for SEEK filter sequential data assimilation operations. This calculation involves the performance of Empirical Orthogonal Functions (EOF) analysis, as suggested by Pham et al. (1998). Hence, AssimilationPreProcessor can also be used to analyse fields without further use in data assimilation.

If state is composed of several properties with different magnitudes then EOFs can be dominated by the properties with larger magnitude, causing a lack of state variability representation. In this multivariate analysis it is convenient to normalize the states previous to covariance calculation. This is accomplished considering a normalization factor for each property (multiplied to the state value) calculated as the inverse of the average standard deviation of all variables of this property. This is a similar approach to the one of Hoteit (2001), which uses the inverse of the square root of the average of variances of each property.

To reduce the computational costs involved in the EOF analysis the covariance matrix is calculated in the space of the time instants instead of the space of state variables. This implies a lower dimension of the matrix if the number of state variables is larger than the number of time instants considered for covariance calculation.

The EOF Analysis is performed by eigenvalues and eigenvectors decomposition of the covariance matrix, using the power method. The obtained eigenvectors are multiplied by the square root of the respective eigenvalue to obtain the EOF in the time instants space. These are then used together with covariance matrix and eigenvalue to obtain the EOF expansion coefficient.

Finally, the EOF in the time instants space is translated to the state variables space.

Optionally, can be made the reconstruction of the state variables, at the several time instants, using the calculated EOFs and the average state.

''References:''

Hoteit, I., 2001, ''Filtres de Kalman Reduits et Efficaces pour l'Assimilation de Données en Oceanographie'', Ph.D. thesis, Université de Joseph Fourrier - Grenoble I.

Pham, D., J. Verron and M. Roubaud, 1998, "A singular evolutive extended Kalman filter for data assimilation in oceanography", ''Journal of Marine Systems'', 16, pp. 323-340.

'''Typical use:'''

Perform EOF analysis of spatial property fields usable for sequential data assimilation in MOHID Water.

'''Data input requirements:'''

One or more HDF5 files containing spatial fields of hydrodynamic and water properties.

'''Ouput:'''

One HDF5 file with results of EOF analysis (EOFs, eigenvalues, inertia) and the covariance structure, together with general statistics calculated in the processing (e.g. average, standard deviation).

One TimeSeries file with the expansion coeficient is produced for each EOF calculated.

When the state reconstruction is commanded a HDF5 file is produced with the fields used for EOF analysis reconstructed using only the calculated EOFs.

==Input file==

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

(block for each HDF5 file containing data to be analysed; 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 data analysis: yyyy mm dd hh mm ss)
END_TIME : ... (end time for data analysis: yyyy mm dd hh mm ss)

HDF5_MAP_ITEM : ... (time independent map item name in HDF5 file)

3D_HDF5 : 0/1 (0 = 2D HDF5 files, 1 = 3D HDF5 files; 0 = default)

METHOD : 1/... (sequential data assimilation method to which the covariance
structure is intended; 1=SEEK; if the application is intended
for EOF analysis then 1 should be chosen)

NORMALIZATION : 0/1 (0 = no normalization of state; 1 = normalization of state; 0 =
default)

DECIMATION_FACTOR : ... (interval in number of instants not to be considered in the
decimation process; 0 = no decimation; 0 = default)

STATE_RECONSTRUCTION : 0/1 (0 = no reconstruction of state with EOFs estimated; 1 =
reconstruction of state with EOFs estimated; 0 = default)

MAX_BUFFER_SIZE : ... (size in bytes of buffer for expansion coefficient time series;
100000 = default)

OUTPUTFILENAME : ... (path/name of output file (HDF5) with analysis results)

(if METHOD : 1:)
STATECOV_RANK : ... (dimension of the covariance subspace; number of EOFs estimated
if METHOD : 1)

(if STATE_RECONSTRUCTION : 1:)
STATE_OUTPUTFILENAME : ... (path/name of output file (HDF5) with reconstructed state)

(block for each property/parameter which belongs to state definition, may be several)
<beginproperty>
NAME : ... (property name, according with MOHID V4)

UNITS : ... (property units)

DIMENSION : 2D/3D (3D = default)

HDF_GROUP : ... (complete path in HDF5 file to parameter data, according with
MOHID V4)

STATE_WINDOW : ... ... ... ... ... ... (state spatial window limits: ILB (i lower-
left cell), JLB (j lower-left cell), IUB
(i upper-right cell), JUB (j upper-right
cell), KLB (lower layer), KUB (upper layer))

TYPE_ZUV : Z/U/V (type of horizontal grid: Z = cell center, U = cell U faces,
V = cell V faces; Z = default)

(if TYPE_ZUV : Z and (NAME : velocity U or NAME : velocity V)
CONVERT_TO_FACES : 0/1 (0 = not convert to horizontal faces grid; 1 = convert to faces
grid; 0 = default)
<endproperty>

''Remarks:''

- only METHOD : 1 (SEEK) is currently implemented; this should be the option to use in
preprocessing for MOHID Water applications using SEEK and SFEK filters as sequential data
assimilation methods;

- if the application is used to perform EOF analysis then METHOD : 1 must be used;

- in DECIMATION_FACTOR the value should be inserted according with the following example: if 1
out of 6 time instants is to be considered then DECIMATION_FACTOR : 5 must be used;

- if STATE_RECONSTRUCTION : 1 then state is reconstructed for the time instants considered in
the analysis using the number of EOFs defined in STATECOV_RANK;

- the order in which the property blocks appear in the input file is considered to the order
in which the properties appear in state definition;

- in TYPE_ZUV should be indicated the type of grid in which the property fields are available
in input HDF5 files, which is usually Z; if input HDF5 files containing hydrodynamic
properties are generated in MOHID Water simulations with the OUTPUT_FACES keyword selected
in Hydrodynamic_#.dat file then U or V types can be selected;

- if EOFs are intended to be produced to use in SEEK/SFEK filters initialization and velocity
U/velocity V properties are considered for state definition then the properties must be
specified in state definition as having type U or V grid: this can be made indicating in
TYPE_ZUV if velocities are present in input HDF5 files in faces grids or if otherwise by
selecting CONVERT_TO_FACES : 1.

==Sample==
<BeginHDF5File>
NAME : Hydrodynamic_3.hdf5
<EndHDF5File>

<BeginHDF5File>
NAME : Hydrodynamic_4.hdf5
<EndHDF5File>

<BeginHDF5File>
NAME : Hydrodynamic_5.hdf5
<EndHDF5File>

<BeginHDF5File>
NAME : Hydrodynamic_6.hdf5
<EndHDF5File>

START_TIME : 1972 11 1 0 0 0
END_TIME : 1972 11 10 0 0 0

HDF5_MAP_ITEM : WaterPoints3D

3D_HDF5 : 1

METHOD : 1

STATECOV_RANK : 50

OUTPUTFILENAME : InitialCovWrongModel_Nov72Dez72_Sampling1h.hdf5

NORMALIZATION : 1

DECIMATION_FACTOR : 0

STATE_RECONSTRUCTION : 1

STATE_OUTPUTFILENAME : RecStateWrongModel_Nov72Dez72_Sampling1h.hdf5

<beginproperty>
NAME : velocity U
UNITS : m/s
DIMENSION : 3D

HDF_GROUP : /Results/FacesVelocityU

STATE_WINDOW : 1 162 1 162 1 1

TYPE_ZUV : U
CONVERT_TO_FACES : 0
<endproperty>

<beginproperty>
NAME : velocity V
UNITS : m/s
DIMENSION : 3D

HDF_GROUP : /Results/FacesVelocityV

STATE_WINDOW : 1 162 1 162 1 1

TYPE_ZUV : V
CONVERT_TO_FACES : 0
<endproperty>

<beginproperty>
NAME : water level
UNITS : m
DIMENSION : 2D

HDF_GROUP : /Results/water level

STATE_WINDOW : 1 162 1 162

TYPE_ZUV : Z
<endproperty>

ConvertToHDF5

2008-10-02T10:03:48Z

192.168.20.156: /* INTERPOLATE GRIDS */

The '''ConvertToHDF5''' is an application which allows the making of several operations, called '''actions''', involving HDF5 files: conversion of data in other formats (e.g. NETCDF) to HDF5, grid interpolation, concatenation of several files.

Running options for this application are specified by the user in a input file named [[ConvertToHDF5#Input file (ConvertToHDF5Action.dat)|'''ConvertToHDF5Action.dat''']]. Several actions can be specified in the same input file, being processed sequentially by the ConvertToHDF5 application.

==Introduction==
The operations involving HDF5 files performed by ConvertToHDF5, specified individually by an action, can be organized in [[#file management|file management]], [[#grid interpolation|grid interpolation]] and [[#format conversion|format conversion]]. These types and the respective actions are detailed in the next sections.

The input file specification for each action can be found bellow in the [[#Input file (ConvertToHDF5Action.dat)|Input file (ConvertToHDF5Action.dat)]] section.

===File management===

====Glue files====
This action consists in joining or glue in a single HDF5 file two or more HDF5 files having the same HDF5 data groups and referring to time periods which come in sequence. Both sets of 2D and 3D HDF5 files can be glued.

'''Typical use:'''

Glue MOHID Water results files from several runs produced in continuous running of the model, for storage space economy reasons. Can be used to join data from other origins (e.g. results of meteorological models) as long as the HDF5 format is the one supported by MOHID Water.

'''Data input requirements:'''

HDF5 files to be glued. "Grid" and "Results" data groups should be equal in all these files.

'''Output:'''

HDF5 file with glued "Results" data. "Residual" and "Statistics" HDF5 data groups are not copied to the output file since they are time period specific (different values potentially occour in each file). General statistics can be calculated for the glued HDF5 file data using tool [[HDF5Statistics]].

'''ConvertToHDF5 action:''' [[#GLUES HDF5 FILES|GLUES HDF5 FILES]].

===Grid interpolation===

====Interpolate files====
This action performs the conversion of one HDF5 file data existing in one 2D or 3D spatial grid to another 2D or 3D spatial grid, creating a new HDF5 file. The interpolation is performed only for the data located a time window specified by the user.

The HDF5 file containing data to be interpolated is called the '''father file'''.

In case of 3D interpolation the application conducts first the horizontal grid interpolation
(keeping father geometry) and only after it conducts the vertical interpolation (from father geometry to new geometry).

Several types of 2D interpolation are available for use: bilinear, spline 2D and triangulation.
For vertical interpolation (used in 3D interpolation) can be supplied several polinomial degrees for interpolation.

'''Typical use:'''

Obtain an HDF5 file with data for forcing or providing initial conditions for a MOHID Water model, e.g. a meteorological forcing file.

'''Data input requirements:'''

For 2D/3D interpolation:

- father HDF5 file;

- father horizontal data grid, in a grid data file in the format supported by MOHID;

- new horizontal data grid, in a grid data file in the format supported by MOHID;

For 3D interpolation also needed:

- father vertical geometry, in a geometry file in the format supported by MOHID;

- new vertical geometry, in a geometry file in the format supported by MOHID;

- auxiliary horizontal data grid, in a grid data file in the format supported by MOHID; this file is used for horizontal grid interpolation in 3D interpolation operations.

'''Ouput:'''

HDF5 file with interpolated data. In case of 3D interpolation also produced an auxiliary HDF5 file with the result of the horizontal grid interpolation, which can be inspected to check if this operation is well performed.

'''ConvertToHDF5 action:''' [[#INTERPOLATE GRIDS|INTERPOLATE GRIDS]].

====Patch files====
This action consists in performing an interpolation of HDF5 data between grids, as in action [[#Interpolate files|Interpolate files]], but considering more than one HDF5 file as containing data to be interpolated to the new grid and a priority scale. The interpolation is performed only for the data located in the time window specified by the user. The present version of this action operates only on 2D data.

Each HDF5 file containing data to be interpolated is called a '''father file''' and has an user-attributed '''priority level''' to be respected in the interpolation process: for each new grid cell the ConvertToHDF5 application will look for data first on the Level 1 father file and only in the case this data is inexistent will it look for data in Level 2 file, proceeding in looking for higher level files if no data is found subsequentely.

'''Typical use:'''

To obtain an HDF5 file with data from several HDF5 files each containing data with different spatial resolution and only for a specific part of the new grid. This is, for instance, the case when one is preparing a best resolution meteorological HDF5 file for forcing MOHID Water from several meteorological model domains, having different spatial resolution and span, since the best resolution data is not available for all new grid cells.

'''Data input requirements:'''

The new horizontal data grid, in a grid data file in the format supported by MOHID, and for each father file:

- level of priority: 1 = maximum priority, priority decreases with increasing level value;

- data grid, in the form of a grid data file in the format supported by MOHID.

'''Ouput:'''

HDF5 file with patched data.

'''ConvertToHDF5 action:''' [[#PATCH HDF5 FILES|PATCH HDF5 FILES]].

===Format conversion===

====Meteorological model data====
Mohid does not simulate explicitly the atmosphere, but needs information about atmospheric properties in time and space. This requires that atmospheric properties are supplied to MOHID Water in supported formats. These formats can be derived from meteorological data in HDF5 format. Because the results of meteorological models are accessed in different formats conversion is required.

The formats currently convertible to HDF5 in ConvertToHDF5 include the MM5 and the ERA40. These are succintly detailed in the next sections.

=====''ERA40''=====
This format refers to the European Centre for Medium-Range Weather Forecasts (ECMWF) 40 years re-analysises results, acessed by site http://data.ecmwf.int/data/d/era40_daily/. This data is available for several meteorological variables with maximum 6 hour periodicity for days in the period from 1957-09-01 to 2002-08-31.

ERA40 data files are supplied by ECMWF in a NetCDF format and with an user-costumized time window, periodicity (time step range from 6 hours to a day) and meteorological properties set. The ERA40 meteorological properties which are recognized by MOHID are presented bellow together with the correspondent MOHID name:

---ERA40 NAME--- ---MOHID NAME---
sshf sensible heat
slhf latent heat
msl atmospheric pressure
tcc cloud cover
p10u wind velocity X
p10v wind velocity Y
p2t air temperature
ewss wind stress X
nsss wind stress Y

The standard ConvertToHDF5 action is to convert to HDF5 the data referring to all MOHID Water recognized property available in the ERA40 file, producing an individual HDF5 file for each property. The name of each HDF5 file generated includes the ERA40 meteorological property identificator correspondent to the data contained.

Alternatively, ConvertToHDF5 can copy to a single ASCII file the heading information concerning each meteorological variable considered in the original ERA40 file.

'''Typical use:'''

Obtain an HDF5 file with data suitable for being used for forcing MOHID Water models.

'''Data input requirements:'''

ERA40 NetCDF file.

'''Output:'''

One HDF5 file for each meteorological property contained in the original NetCDF file.

'''ConvertToHDF5 action:''' [[#CONVERT ERA40 FORMAT|CONVERT ERA40 FORMAT]].

=====''MM5''=====
This format relates to the Fifth-Generation NCAR / Penn State Mesoscale Model (MM5) output files format. Almost every atmospheric property needed by MOHID Water is present in MM5 output files, enabling to run prediction simulations with MOHID Water when access to MM5 prevision files is available.

The ConvertToHDF5 action converts MM5 results files from the original format to HDF5 format, allowing the easy use of these results in the MOHID framework. Conversion is only performed for the MM5 properties and the time window specified by the user.

Besides the conversion, the application can calculate some properties not contained in
the MM5 files using the available information: these are windstress, relative humidity and precipitation.

For conversion to be completed it is required the horizontal grid information of MM5 results which is available in special TERRAIN files.

'''Typical use:'''

Produce HDF5 meteorological data usable for forcing MOHID Water models.

'''Data input requirements:'''

MM5 results file to convert and MM5 TERRAIN file. The TERRAIN file supplies the MM5 results grid information.

'''Ouput:'''

An HDF5 file with MM5 results and a grid data file in MOHID format with the MM5 grid information.
This last file can be used to interpolate the MM5 data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]), for instance to produce an HDF5 file suitable for forcing MOHID Water models.

'''Compilation:'''

Caution! The ConvertToHDF5 executable must be compiled with the [[Big-endian little-endian|Big-Endian]] option set (see compatibility in the project's settings).

'''ConvertToHDF5 action:''' [[#CONVERT MM5 FORMAT|CONVERT MM5 FORMAT]].

=====''Aladin''=====
This format relates to Aladin meteorological model results. Some of the atmospheric property needed by MOHID Water is present in Aladin output files, enabling to run prediction simulations with MOHID Water when access to Aladin prevision files is available.

The ConvertToHDF5 action converts Aladin results files from the original format to HDF5 format, allowing the easy use of these results in the MOHID framework. Conversion is only performed for the MM5 properties and the time window specified by the user.

'''Typical use:'''

Produce HDF5 meteorological data usable for forcing MOHID Water models.

'''Data input requirements:'''

Aladin netcdf results file to convert.

'''Ouput:'''

An HDF5 file with Aladin results and a grid data file in MOHID format with the Aladin grid pseudo-information: a fake orography is created of 100 m depth.
This last file can be used to interpolate the Aladin data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]), for instance to produce an HDF5 file suitable for forcing MOHID Water models.

'''Compilation:'''

Caution! The ConvertToHDF5 executable must be compiled with the [[Big-endian little-endian|Big-Endian]] option set (see compatibility in the project's settings).

'''ConvertToHDF5 action:''' [[#CONVERT ALADIN FORMAT|CONVERT ALADIN FORMAT]].

====Ocean model data====
Ocean model data, available in diverse formats, can be used by MOHID Water to specify boundary (open ocean boundary and surface), initial conditions or for validation. These uses require that the model data is in HDF5 format and conversion is therefore needed.

Currently the large scale ocean models formats convertible into HDF5 by ConvertToHDF5 includes MERCATOR.

=====''MERCATOR''=====
MERCATOR data files are supplied in a NetCDF format and with an user-costumized spatial window and periodicity. Water level and water properties (temperature and salinity) data is available in type T files, velocity component u data is available in type U files and velocity component v data is available in type V files. The type of data of a specific MERCATOR file is generally indicated in the file name.

The standard ConvertToHDF5 action is to convert to HDF5 the data referring to temperature, salinity, water level, component u of velocity and component v of velocity.

'''Typical use:'''

Obtain HDF5 MERCATOR data usable for forcing or validation of MOHID Water models.

'''Data input requirements:'''

NetCDF MERCATOR results data files and NetCDF MERCATOR grid data files. It should be provided one grid data file of each type: T, U and V. These are generally provided by the MERCATOR services together with the results files.

'''Ouput:'''

One HDF5 file containing all properties contained in the recognized set of properties (temperature, salinity, water level, velocity u and velocity v) and the correspondent grid data and geometry files, containing respectively the horizontal grid and the vertical discretization of the HDF5 file. The grid data and geometry files can be used afterwards to interpolate the MERCATOR data to another grid and geometry (see [[#Interpolate files|Interpolate files]]).

'''ConvertToHDF5 action:''' [[#CONVERT MERCATOR FORMAT|CONVERT MERCATOR FORMAT]].

====Climatological data====
Climatological data can be used in MOHID Water to specify boundary (open ocean boundary and surface), initial conditions or for validation, in case more realistic data (measurements or model) data is unavailable. This data is generally supplied by producers in formats not readly usable by MOHID Water which justifies the existence of a conversion tool.

Two climatological data format conversions are implemented in ConvertToHDF5: Levitus ocean data and Hellerman Rosenstein meteorological data.

=====''Levitus''=====
The Levitus climatology provides results for water temperature and salinity.
The ConvertToHDF5 action converts the climatological data for the properties and spatial window requested by the user.
Typically, it requires 3 steps to complete the task:

- convert levitus format

- extrapolate the data to the whole levitus domain(required to avoid uncoincidental coastlines)

- interpolate with the model grid(bathymetry)

'''Typical use:'''

Obtain climatological data in HDF5 format to use as boundary forcing and/or initial condition specification in MOHID Water models.

'''Data input requirements:'''

Levitus climatological data files, one per property and per time period (e.g a month).

'''Ouput:'''

HDF5 file with Levitus climatological data, grid data file with the horizontal
grid of the data and a geometry file with vertical discretization of the data (MOHID formats).
The grid data and the geometry files can be used to interpolate the climatological data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]).

'''ConvertToHDF5 action:''' [[#CONVERT LEVITUS FORMAT|CONVERT LEVITUS FORMAT]].

=====''Hellerman Rosenstein''=====
This is a meteorological climatology providing wind stress. There is a file per wind stress component. Since the data refer to surface values it is a 2D field.

The ConvertToHDF5 action converts the climatological data for the properties and spatial window provided by the user.

'''Typical use:'''

Obtain climatological data in HDF5 format to use as meteorological forcing in MOHID Water models.

'''Data input requirements:'''

Hellerman Rosenstein climatological data ASCII files, one per wind stress component.

'''Ouput:'''

HDF5 file with Hellerman Rosenstein climatological data and grid data file with the horizontal
grid of the climatological data. This grid data file can be used to interpolate the climatological data from the original horizontal grid to a new grid (see [[#Interpolate files|Interpolate files]]).

'''ConvertToHDF5 action:''' [[#CONVERT HELLERMAN ROSENSTEIN ASCII|CONVERT HELLERMAN ROSENSTEIN ASCII]].

=====''World Ocean Atlas 2005''=====
The World Ocean Atlas (WOA) 2005 climatology provides results for water temperature, salinity and several water quality and biology properties.

Description, Action and Input Files are described in a separate page: [[ConvertToHDF5 WOA2005]].

==Input file (ConvertToHDF5Action.dat)==
===General structure===
<begin_file> (block containing instructions for running a specific action)
ACTION : ... (intended action)
... (action specific instructions)
<end_file>

<begin_file>
ACTION : ...
...
<end_file>

===GLUES HDF5 FILES===
<begin_file>
ACTION : GLUES HDF5 FILES

3D_FILE : 0/1 (0 = 2D file, 1 = 3D file)

TIME_GROUP : ... (Default="Time". Other option: "SurfaceTime".)

BASE_GROUP : ... (Default="Results". Other options: "Residual", "SurfaceResults".)

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)

(block of HDF5 data files)
<<begin_list>>
... (path/name of HDF5 file with data to be included in glue, one per line, at least two files)
...
<<end_list>>
<end_file>

===INTERPOLATE GRIDS===
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : ... (type of horizontal interpolation: 1 = Bilinear, 2 = Spline2D,
3 = Triangulation)

INTERPOLATION_WINDOW : ... ... ... ... (2D spatial window to consider for interpolation:
Xmin Ymin Xmax Ymax; default = all domain)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

INTERPOLATION3D : 0/1 (0 = 2D interpolation, 1 = 3D interpolation)

FATHER_FILENAME : ... (path/name of input HDF5 file with data to be interpolated)
FATHER_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization of input HDF5 file)

OUTPUTFILENAME : ... (path/name of output HDF5 file to be created)
NEW_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization intended for output HDF5 file)

EXTRAPOLATE_2D : 0/1/2/3/4/5 (2D extrapolation: 0=no extrapolation, 1=medium
triangulation, 2=high triangulation,
3=nearest neighbour, 4=nearest cell,
5=constant value)

EXTRAPOLATE_VALUE : ... (name of the value to extrapolate to when EXTRAPOLATE_2D is
set to constant value (5))

DO_NOT_BELIEVE_MAP : 0/1 (0=consider input HDF5 file map, 1=do not consider input HDF5
file map)

BASE_GROUP : ... (name of base group of HDF5 variables containing data to be
interpolated; default is "/Results")

(if INTERPOLATION3D : 1 also required:)
FATHER_GEOMETRY : ... (path/name of file (MOHID format) with vertical discretization
of input HDF5 file)
NEW_GEOMETRY : ... (path/name of file (MOHID format) with vertical discretization
intended for output HDF5 file)
POLI_DEGREE : 1/... (degree of vertical interpolation: 1=linear, ...)

AUX_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization intended for auxiliar output HDF5 file;
default is file provided in NEW_GRID_FILENAME)

AUX_OUTPUTFILENAME : ... (path/name of auxiliar output HDF5 file to contain result
of horizontal grid interpolation)
<end_file>

''Remarks:''

- the file indicated in AUX_GRID_FILENAME can be different from the one indicated in
NEW_GRID_FILENAME in terms of bathymetry, while the horizontal grid should be, commonly, the
same: this altered bathymetry can be used to extend the water column in the original data so
that the process of vertical interpolation is done easily;

- in case of INTERPOLATION3D : 1, ConvertToHDF5 can generate new versions of bathymetry which
are consistent with the geometry definition (extension is '.new'); there are possibly three
bathymetry changes referring to father grid, new grid and aux grid (the same bathymetry is
not altered twice); although initially new and aux grid are the same they can result
different because of bathymetry changes;

- in case the new geometry is 2D and father geometry is 3D then POLI_DEGREE : 1
(linear interpolation) should be used;

- EXTRAPOLATE_2D : 1/2/3/4/5 should be considered if it is expected that the coast line is not
coincidental in the father and new grids, to avoid lack of data in the interpolation
process; extrapolation is performed for all cells even the land cells;

- in case of DO_NOT_BELIEVE_MAP : 1 the application generates a map based on cells where
interpolation results are available; this causes that if EXTRAPOLATE_2D : 1/2/3/4/5 is used
the AUX_GRID_FILENAME should not have land cells in order for the new map to be concurrent
with the result of extrapolation and avoid errors generation, specially if INTERPOLATION3D :
1 is considered.

===PATCH HDF5 FILES===
<begin_file>
ACTION : PATCH HDF5 FILES

TYPE_OF_INTERPOLATION : ... (type of interpolation: 3 = Triangulation, default and only
one implemented)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

(block for each father HDF5 file, should be at least two)
<<begin_father>>
LEVEL : ... (integer priority level: 1 = highest, increase for lower
priority)
FATHER_FILENAME : ... (path/name of input HDF5 file with data to be interpolated)
FATHER_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization of input HDF5 file)
<<end_father>>

OUTPUTFILENAME : ... (path/name of output HDF5 file to be created)
NEW_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization intended for output HDF5 file)
<end_file>

===CONVERT ERA40 FORMAT===
<begin_file>
ACTION : CONVERT ERA40 FORMAT

FILENAME : ... (path/name of ERA40 NetCDF file)
OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
(root of name for all files produced)

CONVERT_TO_ASCII : 0/1 (1 = convert variable heading info for ASCII file; 0 = default)
CONVERT_TO_HDF5 : 0/1 (1 = convert to HDF5 file; 0 = default)
GRIDTO180 : 0/1 (1 = convert grid from [0 360] to [-180 180], 0 = default)

XX_VARIABLE : ... (name of longitude variable in the input file: usual name
is "longitude")
YY_VARIABLE : ... (name of longitude variable in the input file: usual name
is "latitude")
TIME_VARIABLE : ... (name of time variable in the input file: usual name is
"time")
<end_file>

''Remarks:''

- either CONVERT_TO_ASCII : 1 or CONVERT_TO_HDF5 : 1 must be chosen for any action to be
performed by ConvertToHDF5;

- when CONVERT_TO_HDF5 : 1 an HDF5 file is produced for every variable contained in the
original ERA40 file; the name of each file is composed of the name indicated on FILENAME
concatenated with the ERA40 variable identifier;

- to the XX_VARIABLE, YY_VARIABLE and TIME_VARIABLE keywords should generally be
specified "longitude", "latitude" and "time", respectively; the option to
include as keywords was made only to make the application robust to future variable name
changes.

===CONVERT MM5 FORMAT===
<begin_file>
ACTION : CONVERT MM5 FORMAT

FILENAME : ... (path/name of MM5 file)
TERRAIN_FILENAME : ... (path/name of MM5 TERRAIN file)

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data file with horizontal grid of MM5 data
to be created)

COMPUTE_WINDSTRESS : 0/1 (1 = compute and write wind stress field; 0 = default)
COMPUTE_RELATIVE_HUMIDITY : 0/1 (1 = compute and write relative humidity field; 0 = default)
COMPUTE_PRECIPITATION : 0/1 (1 = compute and write precipitation field; 0 = default)
COMPUTE_WINDMODULUS : 0/1 (1 = compute wind modulus; 0 = default)

WRITE_XYZ : 0/1 (1 = write xyz center grid cells; 0 = default)
WRITE_TERRAIN : 0/1 (1 = write MM5 TERRAIN fields; 0 = default)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

(block of MM5 properties to convert)
<<BeginFields>>
... (name of MM5 property to convert do HDF5 format, one per line)
...
<<EndFields>>

<end_file>

''Remarks:''

- the name of each MM5 property to convert in <<BeginFields>>...<<EndFields>> block must
conform to the MOHID designation specified in code of ModuleGlobalData; the correspondence is
the following (see [[Module_InterfaceWaterAir]] for a more detailed explanation).

---MM5 NAME--- ---MOHID NAME---
T2 air temperature
PSTARCRS atmospheric pressure
U10 wind velocity X
V10 wind velocity Y
UST wind shear velocity
LHFLUX latent heat
SWDOWN sensible heat
SWDOWN solar radiation
LWDOWN infrared radiation
SWOUT top outgoing shortwave radiation
LWOUT top outgoing longwave radiation
SOIL T 1 soil temperature layer 1
SOIL T 1 soil temperature layer 2
SOIL T 1 soil temperature layer 3
SOIL T 1 soil temperature layer 4
SOIL T 1 soil temperature layer 5
SOIL T 1 soil temperature layer 6
Q2 2-meter mixing ratio
TSEASFC sea water temperature
PBL HGT PBL height
PBL REGIME PBL regime
RAIN CON accumulated convective precipitation (cm)
RAIN NON accumulated non-convective precipitation (cm)
GROUND T ground temperature
RES TEMP infinite reservoir slab temperature
U wind velocity X_3D
V wind velocity Y_3D
W wind velocity Z_3D
T air temperature_3D
PP atmospheric pressure_3D
Q mixing ratio_3D
CLW cloud water mixing ratio_3D
RNW rain water mixing ratio_3D
ICE cloud ice mixing ratio_3D
SNOW snow mixing ratio_3D
RAD TEND atmospheric radiation tendency_3D

===CONVERT ALADIN FORMAT===
<begin_file>
ACTION : CONVERT ALADIN FORMAT

OUTPUTFILENAME : aladin.hdf5
OUTPUT_GRID_FILENAME : aladin_griddata.dat

!Put here the name of any netcdf file for grid-data generation's sake.
INPUT_GRID_FILENAME : D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKCLOUD_OPASYMP_19723_20088.nc

<<begin_input_files>>
(path to aladin netcdf file)\ALADIN_BULKIR_OPASYMP_19723_20088.nc
...
<<end_input_files>>

<end_file>

''Remarks:''

- the name of each Aladin property to convert in <<begin_input_files>>...<<end_input_files>> block must conform to the following variables

---ALADIN NAME--- ---MOHID NAME---
soclotot CloudCover_
sohumrel RelativeHumidity_
sofluxir NonSolarFlux_
sosspres AtmosphericPressure_
sosolarf SolarRadiation_
sotemair AirTemperature_
sowinmod WindModulus_
sowaprec Precipitation_
sozotaux WindStressX_
sometauy WindStressY_
sowindu10 WindVelocityX_
sowindv10 WindVelocityY_

===CONVERT MERCATOR FORMAT===
<begin_file>
ACTION : CONVERT MERCATOR FORMAT

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data with horizontal discretization to be
created)
OUTPUT_GEOMETRY_FILENAME : ... (path/name of geometry file with vertical discretization to be
created)

INPUT_GRID_FILENAME : ... (path/name of file with horizontal discretization of water
properties and water level data)
INPUT_GRID_FILENAME_U : ... (path/name of file with horizontal discretization of velocity
component U data)
INPUT_GRID_FILENAME_V : ... (path/name of file with horizontal discretization of velocity
component V data)

(block of MERCATOR data files)
<<begin_input_files>>
... (path/name of MERCATOR NetCDF data file, one per line, can be several)
...
<<<end_input_files>>>

<end_file>

===CONVERT LEVITUS FORMAT===
<begin_file>
ACTION : CONVERT LEVITUS FORMAT

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data with horizontal discretization to be
created)
OUTPUT_GEOMETRY_FILENAME : ... (path/name of geometry file with vertical discretization to be
created)

PERIODICITY : ... (periodicity of Levitus data: "monthly"/"annual"; default is
"monthly")

SPATIAL_RESOLUTION : ... (spatial resolution (degrees) of horizontal Levitus grid)

FILL_VALUE : ... (real value identificator for missing data; default is
"-99.999900")

(definition of spatial window to be present in output HDF5 file)
LOWER_LEFT_CORNER : ... ... (longitude and latitude (degrees) of south west corner)
UPPER_RIGHT_CORNER : ... ... (longitude and latitude (degrees) of north east corner)

(block for each water property to be present in output HDF5 file, can be several)
<<beginfield>>
NAME : ... (name of property)
ANNUAL_FILE : ... (path/name of Levitus annual file)

(block of Levitus data files)
<<<begin_input_files>>>
... (path/name of Levitus data file (e.g. a monthly data file), one per line, can be several)
...
<<<end_input_files>>>

<<endfield>>

<end_file>

===CONVERT HELLERMAN ROSENSTEIN ASCII===
<begin_file>
ACTION : CONVERT HELLERMAN ROSENSTEIN ASCII

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data with horizontal discretization to be
created)

PERIODICITY : ... (periodicity of Hellerman Rosenstein data: "monthly")

SPATIAL_RESOLUTION : ... (spatial resolution (degrees) of horizontal Hellerman
Rosenstein grid: default and only allowed value is "2.")

FILL_VALUE : ... (real value identificator for missing data; default is
"-99.999900")

(definition of spatial window to be present in output HDF5 file)
LOWER_LEFT_CORNER : ... ... (longitude and latitude (degrees) of south west corner)
UPPER_RIGHT_CORNER : ... ... (longitude and latitude (degrees) of north east corner)

(block for each Hellerman Rosenstein data file)
<<beginfield>>
NAME : ... (name of property: "wind stress X"/"wind stress Y")
FILE : ... (path/name Hellerman Rosenstein file)
<<endfield>>

<end_file>

==Samples==
All sample files are named ''ConvertToHDF5Action.dat''.

===Glue several MOHID(.hdf5) files===
<begin_file>
ACTION : GLUES HDF5 FILES

OUTPUTFILENAME : SurfaceHydro_OP.hdf5

<<begin_list>>
D:\Projectos\SurfaceHydrodynamic_21.hdf5
D:\Projectos\SurfaceHydrodynamic_22.hdf5
<<end_list>>
<end_file>

===Interpolate 2D MOHID(.hdf5) files to a new grid===
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
FATHER_FILENAME : D:\Projectos\MohidRun\test\res\Lagrangian_1.hdf5
OUTPUTFILENAME : OilSpillThickness_GridRegular.hdf5

START : 2006 6 21 17 22 30
END : 2006 6 22 17 22 0

FATHER_GRID_FILENAME : D:\Projectos\MohidRun\GeneralData\batim\Tagus.dat_A
NEW_GRID_FILENAME : TagusConstSpacing.dat

BASE_GROUP : /Results/Oil/Data_2D
<end_file>

===Interpolate 3D MOHID(.hdf5) files to a new grid===
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
FATHER_FILENAME : D:\Projectos\MohidRun\test\res\Lagrangian_1.hdf5
OUTPUTFILENAME : OilSpillThickness_GridRegular.hdf5

START : 2006 6 21 17 22 30
END : 2006 6 22 17 22 0

FATHER_GRID_FILENAME : D:\Projectos\MohidRun\GeneralData\batim\Tagus.dat_A
NEW_GRID_FILENAME : TagusConstSpacing.dat

BASE_GROUP : /Results/Oil/Data_2D

INTERPOLATION3D : 1
FATHER_GEOMETRY : D:\Projectos\MohidRun\test\data\Geometry_1.dat
NEW_GEOMETRY : TagusGeometry.dat
AUX_GRID_FILENAME : TagusConstSpacing.dat
AUX_OUTPUTFILENAME : Aux_GridRegular.hdf5
<end_file>

===Patch several MOHID(.hdf5) files to a new grid===
<begin_file>
ACTION : PATCH HDF5 FILES

TYPE_OF_INTERPOLATION : 3

START : 2005 2 28 13 0 0
END : 2005 3 1 13 0 0

<<begin_father>>
LEVEL : 3
FATHER_FILENAME : K:\MM5output\2005022812_2005030712\MM5OUT_D1.hdf5
FATHER_GRID_FILENAME : K:\MM5output\2005022812_2005030712\grid1.dat
<<end_father>>

<<begin_father>>
LEVEL : 2
FATHER_FILENAME : K:\MM5output\2005022812_2005030712\MM5OUT_D2.hdf5
FATHER_GRID_FILENAME : K:\MM5output\2005022812_2005030712\grid2.dat
<<end_father>>

<<begin_father>>
LEVEL : 1
FATHER_FILENAME : K:\MM5output\2005022812_2005030712\MM5OUT_D3.hdf5
FATHER_GRID_FILENAME : K:\MM5output\2005022812_2005030712\grid3.dat
<<end_father>>

OUTPUTFILENAME : MM5Forcing.hdf5
NEW_GRID_FILENAME : K:\Simula\GeneralData\Batim\CostaPortuguesa.dat
<end_file>

===Convert an ERA40 file to MOHID(.hdf5)===
<begin_file>
ACTION : CONVERT ERA40 FORMAT

FILENAME : D:\Aplica\ERA40\1971ERA1973.nc
OUTPUTFILENAME : D:\Aplica\ERA40\1971ERA1973T2

CONVERT_TO_ASCII : 0
CONVERT_TO_HDF5 : 1

XX_VARIABLE : longitude
YY_VARIABLE : latitude
TIME_VARIABLE : time
<end_file>

===Convert a MM5 file to MOHID(.hdf5)===
<begin_file>
ACTION : CONVERT MM5 FORMAT

FILENAME : K:\MM5output\DataCenter\Modelos\Meteo_IST\Fev2005\MMOUT_D3
TERRAIN_FILENAME : K:\MM5output\DataCenter\Modelos\Meteo_IST\Fev2005\TERRAIN_D3
OUTPUT_GRID_FILENAME : K:\MM5output\DataCenter\Modelos\Meteo_IST\Fev2005\grid3.dat
OUTPUTFILENAME : K:\MM5output\DataCenter\Modelos\Meteo_IST\Fev2005\MM5_D3.hdf5

COMPUTE_WINDSTRESS : 0
COMPUTE_RELATIVE_HUMIDITY : 1
WRITE_XYZ : 0

<<BeginFields>>
solar radiation
air temperature
wind velocity X
wind velocity Y
sensible heat
latent heat
atmospheric pressure
sea water temperature
<<EndFields>>
<end_file>

===Convert Mercator-Ocean(.nc) to MOHID(.hdf5)===
<begin_file>
ACTION : CONVERT MERCATOR FORMAT

OUTPUTFILENAME : Psy2v2r1v_R20060628/MercatorR20060628.hdf5
OUTPUT_GRID_FILENAME : Psy2v2r1v_R20060628/MercatorGridR20060628.dat
OUTPUT_GEOMETRY_FILENAME : Psy2v2r1v_R20060628/MercatorGeometryR20060628.dat

INPUT_GRID_FILENAME : GridFiles/ist_meteog-gridT.nc
INPUT_GRID_FILENAME_U : GridFiles/ist_meteog-gridU.nc
INPUT_GRID_FILENAME_V : GridFiles/ist_meteog-gridV.nc

<<begin_input_files>>
Psy2v2r1v_R20060628/ist_meteog-mercatorPsy2v2r1v_T_MEAN_ANA_20060621_R20060628.nc
Psy2v2r1v_R20060628/ist_meteog-mercatorPsy2v2r1v_T_MEAN_ANA_20060622_R20060628.nc
Psy2v2r1v_R20060628/ist_meteog-mercatorPsy2v2r1v_T_MEAN_ANA_20060623_R20060628.nc
<<end_input_files>>
<end_file>

===Convert Levitus format to MOHID(.hdf5) and interpolate grid===
==== Convert ====
First convert the Levitus ASCII format to a raw HDF5 format:
<begin_file>
ACTION : CONVERT LEVITUS FORMAT

OUTPUTFILENAME : Levitus.hdf5
OUTPUT_GRID_FILENAME : LevitusGrid.dat
OUTPUT_GEOMETRY_FILENAME : LevitusGeometry.dat

PERIODICITY : monthly
SPATIAL_RESOLUTION : 0.25
FILL_VALUE : -99.9999

LOWER_LEFT_CORNER : -16.0 31
UPPER_RIGHT_CORNER : 1. 40

<<beginfield>>
NAME : salinity
ANNUAL_FILE : DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s000hr.obj

<<<begin_input_files>>>
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s001
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s002
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s003
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s004
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s005
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s006
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s007
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s008
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s009
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s010
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s011
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s012
<<<end_input_files>>>
<<endfield>>

<<beginfield>>
NAME : temperature
ANNUAL_FILE : DataCenter\DadosBase\Ocean\Levitus\Data\Temp\t000hr.obj

<<<begin_input_files>>>
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t001
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t002
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t003
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t004
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t005
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t006
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t007
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t008
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t009
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t010
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t011
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t012
<<<end_input_files>>>
<<endfield>>
<end_file>

==== Extrapolate ====
Then extrapolate the data (still in the raw HDF5 format):
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : Levitus.hdf5
FATHER_GRID_FILENAME : LevitusGrid.dat

OUTPUTFILENAME : LeviTusAllPointsWithData.hdf5
NEW_GRID_FILENAME : LevitusGrid.dat

START : -9999 1 1 0 0 0
END : -9999 12 1 0 0 0

INTERPOLATION3D : 1
FATHER_GEOMETRY : LevitusGeometry.dat
NEW_GEOMETRY : LevitusGeometry.dat
AUX_GRID_FILENAME : LevitusGrid.dat
AUX_OUTPUTFILENAME : AuxLeviTusAllPointsWithData.hdf5

POLI_DEGREE : 3
DO_NOT_BELIEVE_MAP : 1
EXTRAPOLATE_2D : 2
<end_file>

==== Interpolate ====
Finally, interpolate to the final grid and geometry (same as the [[#Interpolate 3D MOHID(.hdf5) files to a new grid| Interpolate 3D sample]]):
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
FATHER_FILENAME : LeviTusAllPointsWithData.hdf5
OUTPUTFILENAME : CadizMonthlyLevitus.hdf5
FATHER_GRID_FILENAME : LevitusGrid.dat
NEW_GRID_FILENAME : Algarve0.02SigmaSmooth_V3_CartMoreLayers.dat

START : -9999 1 1 0 0 0
END : -9999 12 1 0 0 0

INTERPOLATION3D : 1
FATHER_GEOMETRY : LevitusGeometry.dat
NEW_GEOMETRY : Geometry_1.dat
AUX_OUTPUTFILENAME : AuxCadizMonthlyLevitus.hdf5
AUX_GRID_FILENAME : Aux12km.dat

POLI_DEGREE : 3
DO_NOT_BELIEVE_MAP : 1
<end_file>

Note that the programme may construct a new bathymetry twice. Use this bathymetry only on the AUX_GRID_FILENAME keyword.

===Convert Hellerman Rosenstein ASCII format to MOHID(.hdf5) ===
<begin_file>
ACTION : CONVERT HELLERMAN ROSENSTEIN ASCII

OUTPUTFILENAME : ClimatologicWindStress.hdf5
OUTPUT_GRID_FILENAME : ClimatologicWindStressGrid.dat

PERIODICITY : monthly
SPATIAL_RESOLUTION : 2.
FILL_VALUE : -99.9999

LOWER_LEFT_CORNER : -180 -90
UPPER_RIGHT_CORNER : 180 90

<<beginfield>>
NAME : wind stress X
FILE : D:\Aplica\Dados\Hellerman_Rosenstein\TAUXX.DAT
<<endfield>>

<<beginfield>>
NAME : wind stress Y
FILE : D:\Aplica\Dados\Hellerman_Rosenstein\TAUYY.DAT
<<endfield>>
<end_file>

===Convert ALADIN(.nc) format to MOHID(.hdf5)===
<begin_file>
ACTION : CONVERT ALADIN FORMAT

OUTPUTFILENAME : aladin.hdf5
OUTPUT_GRID_FILENAME : aladin_griddata.dat

!Put here the name of any netcdf file for grid-data generation's sake.
INPUT_GRID_FILENAME : D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKCLOUD_OPASYMP_19723_20088.nc

<<begin_input_files>>
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKIR_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKPRES_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKSOLAR_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKTAIR_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKWIND_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_FLUXPRE_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_STRESSU_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_STRESSV_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_U10_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_V10_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKCLOUD_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKHUMI_OPASYMP_19723_20088.nc
<<end_input_files>>

<end_file>

== OceanColor modules compilation ==
Compiling the [[ConvertToHDF5]] tool with the OceanColor modules is more complicated than one might expect. A solution is proposed here for a release version using the Compaq Visual Fortran 6.6c. The difficulties rise because C code is embedded with a fortran interface and also, extra libraries such as hdf4 are required.

=== Pre-requisites ===

This is a list of prerequisites to successfully compile the tool:
*Compaq Visual Fortran 6.5 with patch 6.6c,
*VS .NET 2003 (Vc7 in particular),
*Hdf5 libraries ('''hdf5.lib''' '''hdf5_fortran.lib''' '''hdf5_hl.lib'''),
*Netcdf libraries ('''netcdf.lib''' '''netcdf_.lib'''),
*Hdf4 libraries ('''hd421.lib''', '''hm421.lib'''),
*szlib, zlib and jpeg libraries ('''szlib.lib''', '''zlib.lib''' and '''libjpeg.lib'''),
*the fortran source files ('''ModuleConvertModisL2.F90 ModuleConvertModisL3.F90 ModuleConvertOceanColorL2.F90'''),
*the C source files and their fortran interface files ('''readL2scan.c readL2Seadas.c''' and '''cdata.f crossp.f fgeonav.f''').

=== CVF IDE configuration ===
# Configure everything as specified in [[Compiling with CVF]].
# Add the source files listed in the prerequisites above to the source files listing.
# Go to '''Tools-->Options...-->Directories'''. There, add the '''$DOTNET2K3/Vc7/bin''' to the '''Executable files''''; the '''$DOTNET2K3/Vc7/include''' and '''$DOTNET2K3/Vc7/PlatformSDK/include''' to the '''Include files'''; and finally, the '''$DOTNET2K3/Vc7/lib''', '''$DOTNET2K3/Vc7/PlatformSDK/lib''' and '''$DOTNET2K3/Vc7/PlatformSDK/bin''' to the '''Library files'''.
# Go to '''Projects-->Settings-->Release-->Link-->Input'''. There, add the following libraries: '''netcdf.lib netcdf_.lib hd421.lib hm421.lib libjpeg.lib'''. (Make sure the hdf5 libraries as well as the szlib and zlib libraries are already mentioned).

=== Troubleshoots ===
'''Q: I get unresolved external references during linkage, but I have all the libraries mentioned above included. What should I do?'''

A: Unresolved external references can come out for two reasons:
#you didn't specified all the libraries required or all the paths for the default libraries or,
#[http://en.wikipedia.org/wiki/Name_decoration name mangling] problems. Use the [[dumpbin]] utility to the libraries to checkout which language convention they are using. If that's the problem then you need to try to get new libraries with the correct naming convention.

That's it, you should now be able to build the [[ConvertToHdf5]] project successfully.

'''Q: I got a message saying the entry point _NF_PUT_ATT_REAL@28 could not be located in netcdf.dll'''

A: copy the file netcdf.dll to the exe folder

== References ==
*[http://www.hdfgroup.org/ HDF5 Homepage]
*[http://www.hdfgroup.org/ HDF4 Homepage]

== Links ==

*[[Module_Atmosphere]]
*[[Module_InterfaceWaterAir]]
*[[Coupling_Water-Atmosphere_User_Manual]]

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

HydrodynamicAnalyser

2008-09-25T17:33:32Z

192.168.20.156:

The application '''HydrodynamicAnalyser''' calculates hydrodynamic properties from hydrodynamic data in one HDF5 file.

Running options for this application are specified in an input file named [[HydrodynamicAnalyser#Input file(HydrodynamicAnalyser.dat)|'''HydrodynamicAnalyser.dat''']]

HDF file

2008-01-31T15:13:54Z

192.168.20.156: /* HDF5 file as atmospheric forcing for MOHID models */

== Overview ==
MOHID uses [[HDF5]] as the file format to store matricial data. These files are used to input data to the model. The model also writes its outputs in this format.
Typically, the HDF5 file is organized in '''groups''' and '''datasets'''. Groups are comparable to folders where the datasets are stored. Datasets refer to the data itself.
In MOHID these files are handled (read and write) by [[Module HDF5]].

== Standard organization of a MOHID HDF5 file ==
MOHID HDF5 files have a typical organization in terms of nomenclature of the groups and in terms of which datasets go into which group. There are normally 3 main groups: '''Grid''', '''Results''' and '''Time''', which will be described below.

=== Grid group ===
The Grid group stores information about the grid and it is required to have the data sets shown in figure below.

[[Image:hdf5gridgroup.png|100px|thumb|center|'''View of a hdf5 file grid group''']]

=== Results group ===
The Results group stores the results. The fields stored in the file must correspond to the modeled domain, that is, they must correspond to the same horizontal and vertical grid.
The name of the fields must be recognized by MOHID (see list of supported names)

[[Image:hdf5resultsgroup.png|100px|thumb|center|'''View of a hdf5 file grid group''']]

=== Time group ===
The Time group stores the dates of each result dataset. Time data set must contain as many instants as the field data sets. If the file is being used as an input for the model then time data set must also contain dates for a period of the same or greater duration of the simulation.

[[Image:hdf5timegroup.png|100px|thumb|center|'''View of a hdf5 file grid group''']]

== HDF5 file as atmospheric forcing for MOHID models ==

One of the ways to provide the atmospheric properties forcing for MOHID models is to get the data from an HDF5 file.

To accomplish its mission this file has to have the data organized in a specific format. Two groups must be present:

- Results: with data for the atmospheric properties referenced with the [[properties_names|'''properties names''']] registered in MOHID [[Module_GlobalData|'''Module GlobalData''']] (so that these names can be recognized by MOHID models);

- Time: time instants of the data.

No Grid group is required because the MOHID model always assumes that the forcing data are in the same grid as the model domain.

If one wants to use atmospheric data from a specific atmospheric model or atmospheric data source as forcing for MOHID models the data must be first converted to MOHID HDF5 file. [[ConvertToHDF5#Format_conversion|'''ConvertToHDF5''']] tool can be used to convert data from some formats and specific modules for converting data from other data sources can also be added to this tool with some extra programming.

Once in MOHID HDF5 file the atmospheric data must be interpolated from the original grid to the model domain grid. For this use the ConvertToHDF5 tool with [[ConvertToHDF5##Grid_interpolation|'''action INTERPOLATE GRIDS''']].

== See also ==
[[Module FillMatrix]]

[[Category:Input Data Formats]]

Mohid Programming

2008-01-28T16:47:10Z

192.168.20.156: /* Related links */

MOHID is programmed in ANSI FORTRAN 95 using an [[Object oriented approach|object oriented approach]] and hierarchical structure which enables consisting of several [[Modules|modules]] to develop several numerical models and [[Mohid Support Tools|support tools]] with a high level of code re-use. To this structure we call [[Mohid Framework]].

Due to the high number of developers programming in MOHID, several [[Programming guidelines|programming guidelines]] have been defined in order to [[Changing the code|change the code]] in a straighforward, systematic and sustentable way.

MOHID is licensed under GPL and the code can be downloaded from the download area. Currently, MOHID has been [[Compiling|compiled]] and run under [[Supported architectures|several architectures]].

== Related links ==

See also [[Parallel processing]], [[Compiling]], [[Profiling]], [[Programming in Fortran issues]]

[[Category:Programming]]