Mohid Swan
From MohidWiki
In this wiki it would be commented how to implement the Swan model into the Mohid modelling software.
Contents
Software Needed
In addition to the Mohid model it will be needed the following software to achive the goal.
For Maretequers, the software (with configuration examples) and user manuals can be found internally here
\\neptuno\Software\Swan
To get an example of the whole data pre-processing, look internally, here
\\neptuno\Software\MOHID\Mohid Swan
Bathymetry
To create a SWAN bathymetry, one may convert a MOHID bathymetry (grid data file) using the matlab script found in the \\neptuno\Software\MOHID\Mohid Swan\MohidGriddataToSWAN folder. In Matlab, select the script folder as the working directory then type at the matlab prompt:
> MohidBatim2SWAN.m
Then follow the GUI instructions. It should create a SWAN bathymetry file (.sty).
The bathymetry should be visualised using notepad or a software called sigma that needs to be localed in the root directory c:\
Sigma -> Task File -> Show so far -> Linha CGWID
Boundary Conditions
The Swan model would need of wind, tide and deep-Ocean swell as boundary conditions.
Wind
Wind vectors should also be provided from other model results (i.e. MOHID, MM5 or WRF) and then converted to the SWAN format using ConvertToHDF5 using the option "ConvertHDF5ToSWANorMOHID" that will provide a hourly file with values for x and y directions, be aware of the file size.
One way to extract winds to force the SWAN, is to use the wind velocity present in the Atmosphere_x.hdf5 file, coming from a 2D MOHID simulation pre-made for the study region.
An alternative way is to use MM5 HDF5 Mohid results and then glue and interpolate them to the MOHID model(s) grid(s) (which is(are) the same as SWAN's). To perform standard glue and interpolate operations with ConvertToHDF5, please refer to the ConvertToHDF5 wiki ...
ConvertToHDF5 configuration
Here's the ConvertToHdf5 configuration file ConvertToHDF5Action.dat for the action CONVERT FROM HDF5 TO SWAN OR MOHID to use (notice that there are two beginfile/endfile blocks, one for X direction, and another for the Y direction):
<begin_file> ACTION : CONVERT FROM HDF5 TO SWAN OR MOHID INPUTFILENAME : Atmosphere_1.hdf5 INPUT_GRID_FILENAME : ../../Batim/MOHID/BatimSO.dat <<beginproperty>> wind velocity X <<endproperty>> START : 2011 04 04 0 0 0 END : 2011 04 07 0 0 0 OUTPUT_TIME : 0 3600 OUTPUT_OPTION : 1 <end_file> <begin_file> ACTION : CONVERT FROM HDF5 TO SWAN OR MOHID INPUTFILENAME : Atmosphere_1.hdf5 INPUT_GRID_FILENAME : ../../Batim/MOHID/BatimSO.dat <<beginproperty>> wind velocity Y <<endproperty>> START : 2011 04 04 0 0 0 END : 2011 04 07 0 0 0 OUTPUT_TIME : 0 3600 OUTPUT_OPTION : 1 <end_file>
Note that this configuration will produce hourly outputs. This will generate one .txt file per time instant.
Criating a wind.ini SWAN input file
The SWAN input file is a wind.ini file that contains the listing of the wind .txt files created in the subsection above. Example:
Wind/windX_20110404000000.txt Wind/windX_20110404010000.txt Wind/windX_20110404020000.txt Wind/windX_20110404030000.txt Wind/windX_20110404040000.txt Wind/windX_20110404050000.txt Wind/windY_20110404000000.txt Wind/windY_20110404010000.txt Wind/windY_20110404020000.txt Wind/windY_20110404030000.txt Wind/windY_20110404040000.txt Wind/windY_20110404050000.txt
Notice how there are first the X-direction files and then, after, come the Y-direction files.
Troubleshoot
Q: The conversion won't work or the SWAN model won't run because of the winds.
A: The Atmosphere_x.hdf5 of the MOHID results needs to be edited and changed (using HDFView). 1 - The MappingPoints2D data needs to be renamed to WaterPoints in the GRID/ group. 2 - The first instant of Time is could be wrong; it could display an offset of one dt. The time instant data should be edited and the offset should be removed. Example: Once, the first time instant in the HDF5 atmosphere_x file would read 2006 10 15 17 00 20 when it should read instead 2006 10 15 17 00 00.
Q: The SWAN won't run because it can't find a wind text file, whose name in the log is a few characters short.
A: The path and filenames to the wind text files found in the wind.ini file exceed the maximum allowed number of characters in a single line. Try reducing the number of characters, by renaming the wind.ini file and/or by renaming its files.
Tide
The tide sould be obtained from other models (i.e. PCOMS), or calculated (i.e. Tideprev) and interpolated to the user domain grid.
For the interpolation method between the source grid and the user domain grid, the user is recommended to use the ConvertToHdf5 tool with the INTERPOLATE action. Please refer to this wiki.
Alternatively, the user domain model could be pre-run with tide only and outputs be given with the same time-period and same frequency as the wind's. Thus the user would only need to use the water level results from the hydrodynamic_x.hdf5 file.
Then, the tide should be converted into SWAN input file for tide, using the CONVERT FROM HDF5 TO SWAN OR MOHID action method of the ConvertToHDF5 tool. Here's the input configuration to copy/paste/edit in the ConvertToHdf5Action.dat file:
<begin_file> ACTION : CONVERT FROM HDF5 TO SWAN OR MOHID INPUTFILENAME : Hydrodynamic_x.hdf5 INPUT_GRID_FILENAME : Batim/MOHID/BatimSO.dat <<beginproperty>> water level <<endproperty>> START : 2011 04 04 0 0 0 END : 2011 04 05 0 0 0 OUTPUT_TIME : 0 3600 OUTPUT_OPTION : 1 <end_file>
Criating a WaterLevel.ini SWAN input file
The SWAN input file is a WaterLevel.ini file that contains the listing of the waterlevel .txt files created in the subsection above. Example:
Wlevel/WL_20110404000000.txt Wlevel/WL_20110404010000.txt Wlevel/WL_20110404020000.txt Wlevel/WL_20110404030000.txt Wlevel/WL_20110404040000.txt Wlevel/WL_20110404050000.txt
Swell
The swell can be read from a global wave model, such as WaveWatch III.
Alternatively, a constant swell can be imposed at each of the lateral open boundaries of the user domain (North, South, East or West sides). This is defined and examplified in the SWAN configuration file sample below in this wiki article.
The North position must be defined (ex: 90º) and the orientation is direct (or anti-clockwise).
SWAN Model Input
Please refer to sample input file in the subsection below for a reference input file. This section will only describe the parts that the user NEEDS to edit. For more information, please refer to the SWAN user manual.
Sect 3 CGRID is the origin, starting from the lower left corner 0 -> Rotation (0 no inclination) 1.3 -> Grid step x in degrees 2 -> Grid step y in degrees 130 -> cells -1 in X direction 200 -> cells -1 in Y direction CIR -> Whole circle of directions 36 -> Number of directions 0.04 -> Minimum frequency 0.5 -> Maximum frequency 50 -> Number of frequencies -1 (in total then 51)
Sect 4 Equal to Sect 3 but define the grid resolution instead of the number of cells, for each direction, (ex: dx = 0.01 = dy) wlevel.in wind.in
Sect 5
WavewatchIII
BOUN (boundary) SIDE W CONST PAS 5 10 210 30
H T Dir Dispersion
Sect 6 Physics Do not change
Sect 8 Time series To obtain a window it should be edited NGRID Indicating the lower left cell for the new grid, the size of the grid in x and y and the number of cells SUBG Indicates the subgrid and in should be provided the lower left corner of the father grid
Sect 10 It makes the domain 4 times and when reach the 98% probability then stops. Defines the initial and final date It should be defined a day as the initial date
Excerpt from word manual
On the contrary of STWAVE there was not introduced any modifications to the original code and so the files format does not follows the “MOHID standard”. In this case it will be necessary to provide the bathymetry in SWAN format. Besides the bathymetric data file it is necessary to provide a file with the computational conditions usually named INPUT. The basic philosophy still lies in the definition ok keywords o specify the model options. For learning more about the different computational options please make use of the user manual. Here, for reference, it is presented an example of an INPUT file.
INPUT
$-------- Section 1. Start
PROJECT 'Quarteira' '01' Title and run ID SET 2 90 0.05 200 1 9.81 1 0 5 water level, north, depmin, max messages, warnings, gravity, output based n energy, nautical, power of high frequency tail
MODE TWOD mode twodimensional
$-------- Section 3. Model Description
CGRID REG 185000 -8000 0 29900 22450 299 449 CIR 36 0.05 1 50 Computational grid regular, Xorig, Yorig, X axis direction, domain length in X direction, domain length in Y direction, grid cells in X direction, grid cells in Y direction, spectral directions cover the full circle, number of meshes in -space (in this case it means that we are considering 10º divisons; 360/36), lower frequency, higher frequency, number of frequencies
$-------- Section 4. Input
INPGRID BOT REG 185000 -8000 0 299 449 100 50 EXCEPTION -99 READ BOT 1 'd/450x300_Swan_Ref.bty' 1 0 FREE WIND 0.1 0 Grid coordinates: referred to the bottom, regular, Xorig, Yorig, X axis direction, grid cells in X direction, grid cells in Y direction, DX, DY, Ignore points -99 Bathymetry file: data sign, filename, read mode, header lines, free format reading Wind characteristics: Velocity, direction
$-------- Section 5. Boundary/Initial Conditions
BOUN SHAPE JON 1 PEAK DSPR DEGREES BOUN SIDE E CONST PAR 7.5 16 45 30 BOUN SIDE S CONST PAR 7.5 16 45 30 BOUN SIDE W CONST PAR 7.5 16 45 30 Boundary conditions: Jonswap spectrum, gamma parameter, peak period, directional distribution, degrees Wave characteristics in the boundaries (E,S,W). spectral parameters (PAR), Hs, Tp, Dir, directional spreading.
$-------- Section 6. Physics
GEN3 KOM 2.36e-5 3.02e-3 QUAD 2 AGROW 0.0015 SETUP 0 BREAKING CONSTANT 1.0 0.73 FRICTION JON 0.067 TRIAD
Komen exponential growth, rate of whitecapping dissipation, wave steepness, Quadruplets, fully implicit computation, Cavaleri and Malanotte grow terms, Cavaleri and Malanotte coefficient Setup computation activated. 0 denotes that no constant is added. Breaking constant, alpha and gamma coefficients. Frction: Jonswap type, Jonswap coefficient Triad wave-wave interaction activated
$-------- Section 9. Output BLOCK 'COMPGRID' NOHEAD 'o/S' LAY 3 SETUP 1 BLOCK 'COMPGRID' NOHEAD 'o/H' LAY 3 HS 1 BLOCK 'COMPGRID' NOHEAD 'o/T' LAY 3 PER 1 BLOCK 'COMPGRID' NOHEAD 'o/F' LAY 3 FOR 1 BLOCK 'COMPGRID' NOHEAD 'o/D' LAY 3 DIR 1 BLOCK 'COMPGRID' NOHEAD 'o/W' LAY 3 WIND 1
These are the spatial distribution of the variables that will be written in the computational grid format. Noheaders will be added. Layout type 3, $ TABLE 'COMPGRID' NOHEAD 'o/data.tbl' XP YP DEP HS DIR SETUP FOR WIND TABLE 'COMPGRID' NOHEAD 'o/dataS.tbl' XP YP SETUP TABLE 'COMPGRID' NOHEAD 'o/dataF.tbl' XP YP FOR
Writes on a table the selected variables. A program named READSWANRES was set up to write these variables in a “MOHID standard format”
$-------- Section 10. Run NUM ACCUR 0.02 0.02 0.02 98 30 COMPUTE STOP
Numerics: criterion for terminating the iterative procedure: fraction of the wave height change, fraction of the average significant wave height, fraction the mean wave period, fraction of the points to met the conditions, maximum number of iterations for stationary computations
Sample input file
This sample input file configures the SWAN to run forced with tide, wind and a constant swell of 5m and 210º in direction (with a 30º of dispersion) coming in from the South and West boundaries of the domain. It runs for 5 hours and demands hourly results in table format.
$-------- Section 1. Start PROJECT 'SAndre' '1' SET 0.0 90 0.05 200 1 9.81 1025 0 5 NAUTICAL MODE NONSTAT TWOD COORD SPHE CCM $ $-------- Section 2. General $ $-------- Section 3. Model Description CGRID REG -9.22 37.637 0 0.445 0.615 89 123 CIR 36 0.04 0.5 50 $ $-------- Section 4. Input INPGRID BOTTOM REG -9.22 37.637 0 89 123 0.005 0.005 EXCEPTION -99. READ BOT 1 'batim/Swan/BatimSO.bty' 1 0 FREE $ INPGRID WLEVEL REG -9.22 37.637 0 89 123 0.005 0.005 EXCEPTION -999 & NONSTAT 20110404.000000 1 HR 20110404.050000 READ WLEV 1 SERIES 'WLevel/WLevel.Ini' 1 0 FREE $ INPGRID WX REG -9.22 37.637 0 89 123 0.005 0.005 EXCEPTION -999 & NONSTAT 20110404.000000 1 HR 20110404.050000 $ INPGRID WY REG -9.22 37.637 0 89 123 0.005 0.005 EXCEPTION -999 & NONSTAT 20110404.000000 1 HR 20110404.050000 READ WIND 1 SERIES 'Wind/Wind.ini' 1 0 FREE $ $ $-------- Section 5. Boundary/Initial Conditions $BOUNDNEST3 WWIII 'WW3_Conditions/NBCWW3.nbc' OPEN $ BOUN SHAPE JON 3.3 PEAK DSPR DEGREES BOUN SIDE W CONST PAR 5 10 210 30 BOUN SIDE S CONST PAR 5 10 210 30 $ $-------- Section 6. Physics GEN3 JANSSEN 4.5 0.5 AGROW 0.003 BREAKING CONSTANT FRICTION JONSWAP TRIAD DIFFRACtion $ $-------- Section 7. Numerics $ $-------- Section 8. Output Sets $ TABLE 'COMPGRID' NOHEAD 'Results/20110404.000000.tbl' DEP HS HSWELL PER RTP DIR PDIR FOR WIND & WATLEV OUTPUT 20110404.000000 1 HR $ TABLE 'COMPGRID' NOHEAD 'Results/Time.dat' TIME & OUTPUT 20110404.000000 1 HR $ $-------- Section 10. Run NUM ACCUR 0.02 0.02 0.02 98 30 COMPUTE NONSTAT 20110404.000000 20 MI 20110404.050000 STOP
Running Swan
Open a SWAN shell (terminal) and execute the following commands:
> cd [path to my INPUT_new.nrw file] > swanrun INPUT_new
SWAN Model Output
Use the ReadSwanRes.exe to convert the .tbl file(s) into MOHID HDF5 format file. Edit the ReadSwanResults.dat input file accordingly from the following sample configuration:
../batim/MOHID/BatimSO.dat 20110404.000000.tbl 6
where the second line contains the SWAN output in table format and where the third and last line contains the number of time instants generated by the SWAN (we have 6 hourly instants in this case).
Then, open a dos terminal (dos shell) and type:
> ReadSwanRes
This will execute the program and generate the results.
The ReadSwanRes conversion will yield one hdf5 file per time instant (6 files, in the example above). Thus a final glue action with the ConvertToHdf5 tool will allow to generate a final Waves.hdf5 to which configure MOHID Module Waves. Please refer to the ConvertToHDF5 wiki for samples on how to perform a glue action.
Configuring MOHID to run with the module waves
You can now go check this wiki.
