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Table of Contents |
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FAST
FAST is a two-dimensional model for wave propagation, long waves and mean flow, sediment transport and morphological changes of the nearshore area, beaches, dunes and backbarrier during stormstsunami calculations.
FAST Module Adapter
This page describes the FAST module adapter, its functions, and provides an example for configuring a FAST run in FEWS. It only has a pre adapter since
FAST
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adapter
Model pre- adapter for running a FAST model from Delft-FEWS.
Class namenames:
nl.deltares.FASTfast.FASTPreAdapter
Properties
No specific properties need to be configured for a model run.
There is however extra functionality provided via the properties but this is not needed if the model is setup correctly.
Configured properties starting with "PARAM_" will be added or replaced literally without "PARAM_" (and in lower case) in the params.txt file which defines the parameters for an FAST model run.
This functionality should only be used as a debug option and only by someone that understands the FAST properties in params.txt. To setup a model make sure you use a correctly configured params.txt so this functionality is not needed.
FastPreAdapter
nl.deltares.fast.FastPostAdapter
Notes for users
FastPreAdapter
- For all files that are written by this adapter, if the file to be written already exists, then it will be overwritten.
- This program writes log messages to log file called Fast_Pre_Adapter.log.
- This program uses the information in the specified netcdf run file as input and uses this information to do the following:
- Replace the tag $WAVE_HEIGHT$ in template file (cil0_30mv3_TEMPLATE.xyz) with a wave height value from the exported netcdf file from FEWS.
FastPostAdapter
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- For all files that are written by this adapter, if the file to be written already exists, then it will be overwritten.
- This program writes log messages to a log file called FASTFast_Post_Adapter.log.
- This program does not make use of a template file, parameters are automatically added and replaced in params.txt without the use of tags.
- This program uses the information in the specified netcdf run file as input and uses this information to do the following actions:
- Create the water level input file: zs0file.txt
- Create the SWAN spectrum input files bcfile.txt and bc.timeXXX.sp2
- Replace or add the parameters 'tstart' and 'tstop' in params.txt
System requirements
- Converts model output (cil0_30mv3_out.asc) in esri grid format to fews netcdf grid format for T0.
System requirements
- The model needs Matlab Compiler runtime 2013b x64 v8.2 to be installed
- The adapter needs Java version 1.7 or higher.
- The adapter needs the following Java libraries:
- castor-0.9.5.jar
- commons-
- This program needs Java version 1.7 or higher.
- This program needs the following Java libraries:
- castor-0.9.5.jar
- commons-httpclient-3.0.1.jar
- Delft_Util.jar
- fews-FAST-adapter.jar
- log4j-1.2.14.jar
- netcdf-4.2.jar
- slf4j-api-1.5.6.jar
- slf4j-log4j12-1.5.6.jar
- xercesImpl.jar
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A complete example model run configuration file can be found here: FASTAdapterRunFastAdapterRun.xml
Information how to prepare a FEWS environment to be able to use the FEWS model adapter can be found here: FAST FEWS setup
Start up activities
Start up activities
As a first activity As a first activity it can be useful to delete all files present in the workDir, if for example it would be filled with files from a previous run.
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<startUpActivities>
<purgeActivity>
<filter>workDir*</filter>
</purgeActivity>
</startUpActivities>
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The first steps in the general adapter run are the data set, netcdf and run file export activities. The <exportDataSetActivity> will extract a zip file with the module instance id as file name located in "Config\ModuleDataSetFiles\" of the FEWS environment to the workdir. The <exportNetcdfActivity> 's will be a netcdf file (bcfile.nc) containing Swan wave spectra over time and a netcdf file (zs0file.nc) containing water level over timewhich can have any name containing a variable called wave_height. The <exportNetcdfRunFileActivity> will be a netcdf run file that contains information needed by the pre adapter. The information will be automatically filled by the general adapter but properties can be configured as extra information. For example properties starting with "PARAM_" will be added or replaced literally without "PARAM_" (and in lower case) in the params.txt file which defines the parameters for an FAST model run. An example is given in the config below as <string key="PARAM_OUTPUTFORMAT" value="netcdf"/> this adds or replaces parameter 'outputformat' in params.txt and assigns the value 'netcdf'. All parameters should however be already correctly set in params.txt so these property should not be necessary..
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<exportActivities>
<exportDataSetActivity>
<moduleInstanceId>Run_FAST</moduleInstanceId>
</exportDataSetActivity>
<exportNetcdfActivity>
<exportFile>wave_height.nc</exportFile>
<timeSeriesSets>
<timeSeriesSet>
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xml | xml | |||||
title | export activities | <exportActivities> <exportDataSetActivity> <moduleInstanceId>Run_FAST</moduleInstanceId> <<valueType>scalar</exportDataSetActivity>valueType> <exportNetcdfActivity><parameterId>WaveHeight</parameterId> <exportFile>bcfile.nc</exportFile> <locationId>Dummy</locationId> <timeSeriesSets> <timeSeriesSet><timeSeriesType>external historical</timeSeriesType> <moduleInstanceId>Run_FAST</moduleInstanceId><timeStep unit="hour"/> <valueType>scalar</valueType><relativeViewPeriod unit="hour" start="0" end="0"/> <parameterId>EnDens<<readWriteMode>add originals</parameterId>readWriteMode> <domainParameterId>AFREQ<</domainParameterId>timeSeriesSet> <domainParameterId>NDIR</domainParameterId></timeSeriesSets> </exportNetcdfActivity> <locationId>Dummy</locationId><exportNetcdfRunFileActivity> <timeSeriesType>external historical</timeSeriesType><description>This run file is passed as argument to FastPreAdapter</description> <timeStep unit="hour"/><exportFile>run.nc</exportFile> <relativeViewPeriod unit="hour" start="-24" end</exportNetcdfRunFileActivity> </exportActivities> |
Execute activities
The next steps are the execute activities.
The first will be the pre adapter.
The second execute activity will be the module run.
The third execute activity will be the post adapter.
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<executeActivities> <executeActivity> <command>="0"/> <readWriteMode>add originals</readWriteMode> <synchLevel>1</synchLevel><className>nl.deltares.fast.FastPreAdapter</className> <<binDir>adapter\bin</timeSeriesSet>binDir> </timeSeriesSets>command> </exportNetcdfActivity><arguments> <exportNetcdfActivity> <exportFile>zs0file<argument>run.nc</exportFile>argument> <timeSeriesSets></arguments> <timeSeriesSet><logFile> <moduleInstanceId>Run_FAST</moduleInstanceId><file>Fast_Pre_Adapter.log</file> <valueType>scalar</valueType><errorLinePattern>ERROR*</errorLinePattern> <parameterId>H_mean</parameterId><warningLinePattern>WARN*</warningLinePattern> <locationId>Dummy</locationId><infoLinePattern>INFO*</infoLinePattern> <timeSeriesType>external historical</timeSeriesType><debugLinePattern>DEBUG*</debugLinePattern> <timeStep unit="minute" multiplier="10"/></logFile> <relativeViewPeriod unit="hour" start="-24" end="0"/><timeOut>99999999</timeOut> <ignoreDiagnostics>true</ignoreDiagnostics> </executeActivity> <executeActivity> <readWriteMode>add originals</readWriteMode><command> <<executable>FASTrun.exe</timeSeriesSet>executable> </timeSeriesSets>command> </exportNetcdfActivity><arguments> <exportNetcdfRunFileActivity><argument>cil0b2</argument> <description>This run file is passed as argument to FASTPreAdapter</description> <argument>cil0_30mv3</argument> <exportFile>run.nc<</exportFile>arguments> <properties><timeOut>99999999</timeOut> <string key="PARAM_OUTPUTFORMAT" value="netcdf"/><ignoreDiagnostics>true</ignoreDiagnostics> </properties>executeActivity> </exportNetcdfRunFileActivity><executeActivity> </exportActivities> |
Execute activities
The next steps are the execute activities.
The first will be the pre adapter. This program will read the run.nc input file and use the contents for instructions on which directory and files should be used to convert to the correct FAST input format. The Pre adapter generates a log file called FAST.log, which can be read into FEWS by coupling line patterns to FEWS log messages.
The second execute activity will be the module run. FAST generates different log files with different meaning, in the configuration below, all line from XBerror.txt are coupled to error messages in FEWS, all lines from XBwaring.txt are coupled to info messages in FEWS and all lines in XBlog.txt are coupled to debug messages in FEWS.
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<executeActivities>
<executeActivity>
<command>
<className>nl.deltares.FAST.FASTPreAdapter</className>
<binDir>adapter\bin</binDir>
</command>
<arguments>
<argument>run.nc</argument>
</arguments>
<logFile>
<file>FAST.log</file>
<errorLinePattern>ERROR*</errorLinePattern>
<warningLinePattern>WARN*</warningLinePattern>
<infoLinePattern>INFO*</infoLinePattern>
<debugLinePattern>DEBUG*</debugLinePattern>
</logFile>
<timeOut>99999999</timeOut>
</executeActivity>
<executeActivity>
<command>
<executable>FAST.exe</executable>
</command>
<logFile>
<file>XBerror.txt</file>
<errorLinePattern>*</errorLinePattern>
</logFile>
<logFile>
<file>XBwarning.txt</file>
<infoLinePattern>*</infoLinePattern>
</logFile>
<logFile>
<file>XBlog.txt</file>
<debugLinePattern>*</debugLinePattern>
</logFile>
<timeOut>99999999</timeOut>
</executeActivity>
</executeActivities>
Wave spectrum conversion
"bcfile.nc" will be used to write the wave spectra into the following format:
- bcfile.txt referencing to wave spectrum files and a time of how long these should be used in each calculation step
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FILELIST
3600.0 1.0 bc.time001.sp2
3600.0 1.0 bc.time002.sp2
3600.0 1.0 bc.time003.sp2
3600.0 1.0 bc.time004.sp2
3600.0 1.0 bc.time005.sp2
3600.0 1.0 bc.time006.sp2
3600.0 1.0 bc.time007.sp2
3600.0 1.0 bc.time008.sp2
3600.0 1.0 bc.time009.sp2
3600.0 1.0 bc.time010.sp2
- bc.time001.sp2 containing a wave spectrum
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SWAN 1 Swan standard spectral file, version
$ Data exported by FEWS for SWAN
$ Project: ; run number:
TIME time-dependent data
1 time coding option
LONLAT locations in spherical coordinates
1 number of locations
4.6019540 52.6194688
AFREQ 1/s
25 number of frequencies
0.0500
0.0566
0.0642
...
0.7791
0.8827
1.0000
NDIR degrees
36 number of directions
265.0000
255.0000
245.0000
...
-65.0000
-75.0000
-85.0000
QUANT
1 number of quantities in table
EnDens id
m unit
-0.9900E+02 exception value
20010101.000000 date and time
FACTOR
0.0011500214
0 0 0 0 0 0 0 0 0 0 ... 0 0 0
0 0 0 0 0 0 0 0 0 0 ... 0 0 0
0 0 0 0 0 0 0 0 0 0 ... 0 0 0
1 1 0 0 0 0 0 0 0 0 ... 0 0 1
40 27 9 3 3 3 2 0 0 0 ... 2 9 28
610 294 70 17 24 31 17 0 0 0 ... 67 303 626
4916 1621 268 57 119 193 145 23 0 1 ... 1780 5295 7229
13782 3341 415 94 287 659 803 340 0 6 ... 14433 28039 27099
14186 2446 257 68 290 982 1874 1407 5 3 ... 52381 62127 39577
10369 1638 231 37 90 431 1241 1598 227 0 ... 99999 80353 37089
8225 1923 361 54 17 70 324 770 448 0 ... 77305 54223 24535
6742 1962 381 88 21 6 30 143 211 0 ... 42814 28100 15442
5744 2480 622 147 34 5 1 8 30 0 ... 27283 16631 9808
4448 2618 1011 228 41 6 0 0 2 2 ... 15103 9139 6001
2853 2150 977 217 34 5 1 0 0 0 ... 8682 5250 3507
1818 1588 752 160 20 4 1 0 0 0 ... 4838 2895 2116
1064 927 597 168 23 3 0 0 0 0 ... 2374 1383 1151
517 534 423 142 23 2 0 0 0 0 ... 1182 789 561
243 299 202 87 17 1 0 0 0 0 ... 756 329 262
137 112 87 51 12 1 0 0 0 0 ... 243 98 120
86 40 34 18 5 1 0 0 0 0 ... 137 117 142
55 21 8 4 2 0 0 0 0 0 ... 137 123 87
24 13 3 1 0 0 0 0 0 0 ... 83 74 62
6 7 1 0 0 0 0 0 0 0 ... 58 27 16
6 3 0 0 0 0 0 0 0 0 ... 39 20 10
Water level conversion
In this example "zs0file.nc" will be used to write the time dependent water levels to a file named "zs0file.txt". The first column specifies the time (meaning defined in "PARAM_TUNITS") and the second column water level. For now the adapter only supports the water level as a single boundary condition but FAST has to possibility to also use 2 or 4 resulting in 1 or 3 extra columns.
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0.0000000e+000 -2.2000000e-002
6.0000000e+002 2.2000000e-002
1.2000000e+003 6.4999998e-002
1.8000000e+003 1.0800000e-001
2.4000000e+003 1.5200000e-001
3.0000000e+003 1.9400001e-001
3.6000000e+003 2.3700000e-001
4.2000000e+003 2.7900001e-001
4.8000000e+003 3.1999999e-001
5.4000000e+003 3.6100000e-001
6.0000000e+003 4.0099999e-001
6.6000000e+003 4.4100001e-001
7.2000000e+003 4.7900000e-001
7.8000000e+003 5.1700002e-001
8.4000000e+003 5.5400002e-001
9.0000000e+003 5.8999997e-001
9.6000000e+003 6.2400001e-001
1.0200000e+004 6.5700001e-001
1.0800000e+004 6.9000000e-001
1.1400000e+004 7.2000003e-001
1.2000000e+004 7.5000000e-001
1.2600000e+004 7.7800000e-001
1.3200000e+004 8.0500001e-001
1.3800000e+004 8.2999998e-001
1.4400000e+004 8.5299999e-001
1.5000000e+004 8.7500000e-001
1.5600000e+004 8.9499998e-001
1.6200000e+004 9.1399997e-001
1.6800000e+004 9.3000001e-001
1.7400000e+004 9.4599998e-001
1.8000000e+004 9.5899999e-001
Parameter conversion
It is possible to change model parameters as defined in params.txt from FEWS. The pre adapter will convert all run file properties starting with "PARAM_" to FAST parameters in "params.txt". Example: params.txt.
It reads the existing "params.txt" and searches for a line starting with the specified parameter and replaces the whole line with "parameter = value" or adds a new line in the same format when the parameter was not present yet.
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----------------------------------------------------
Grid input
nx = 154
ny = 70
xfile = x.grd
yfile = y.grd
xori = 101627.84
yori = 513562.63
depfile = egmondFAST.dep
----------------------------------------------------
Numerics input
CFL = 0.8
eps = 0.01
----------------------------------------------------
Time input
tstart = 0.
tstop = 36000
----------------------------------------------------
General constants
rho = 1025
g = 9.81
----------------------------------------------------
Boundary condition options
zs0file = zs0file.txt
tideloc = 1
----------------------------------------------------
Wave calculation options
bcfile = bcfile.txt
----------------------------------------------------
Flow calculation options
nuh = 0.1
nuhfac = 1.0
----------------------------------------------------
Sediment transport calculation options
facua = 0.10
D50 = 0.0002
----------------------------------------------------
Morphological calculation options
morfac = 10
morstart = 3600
----------------------------------------------------
Output options
outputformat = netcdf
nglobalvar = 3
tunits = seconds since 2001-01-01
<command>
<className>nl.deltares.fast.FastPostAdapter</className>
<binDir>adapter\bin</binDir>
</command>
<arguments>
<argument>run.nc</argument>
</arguments>
<logFile>
<file>Fast_Post_Adapter.log</file>
<errorLinePattern>ERROR*</errorLinePattern>
<warningLinePattern>WARN*</warningLinePattern>
<infoLinePattern>INFO*</infoLinePattern>
<debugLinePattern>DEBUG*</debugLinePattern>
</logFile>
<timeOut>99999999</timeOut>
<ignoreDiagnostics>true</ignoreDiagnostics>
</executeActivity>
</executeActivities>
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Executing pre adapter
This program will read the run.nc input file and use the contents for instructions on which directory and files should be used to convert to the correct FAST input format.
The Pre adapter generates a log file called fast_pre_adapter.log, which can be read into FEWS by coupling line patterns to FEWS log messages.
It uses the exported netcdf file to look for the latest non missing value of the wave height to write to cil0_30mv3.xyz by replacing the tag $WAVE_HEIGHT$ in cil0_30mv3_TEMPLATE.xyz:
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108.34958333 -7.83289859 $WAVE_HEIGHT$ 900 1
108.35411600 -7.83289136 $WAVE_HEIGHT$ 900 1
108.35859257 -7.83344007 $WAVE_HEIGHT$ 900 1
108.36302258 -7.83258101 $WAVE_HEIGHT$ 900 1
108.36729527 -7.83112279 $WAVE_HEIGHT$ 900 1
108.37134559 -7.82910962 $WAVE_HEIGHT$ 900 1
108.37528703 -7.82689069 $WAVE_HEIGHT$ 900 1
108.37936617 -7.82496548 $WAVE_HEIGHT$ 900 1
108.38335489 -7.82662508 $WAVE_HEIGHT$ 900 1
108.38745431 -7.82846972 $WAVE_HEIGHT$ 900 1
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By replacing $WAVE_HEIGHT$ with value 5 cil0_30mv3.xyz will be:
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108.34958333 -7.83289859 5.00 900 1
108.35411600 -7.83289136 5.00 900 1
108.35859257 -7.83344007 5.00 900 1
108.36302258 -7.83258101 5.00 900 1
108.36729527 -7.83112279 5.00 900 1
108.37134559 -7.82910962 5.00 900 1
108.37528703 -7.82689069 5.00 900 1
108.37936617 -7.82496548 5.00 900 1
108.38335489 -7.82662508 5.00 900 1
108.38745431 -7.82846972 5.00 900 1
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Executing model run
This activity runs the model (FASTrun.exe) in the workdir containing the model files with the input file names as arguments. The model creates the output file cil0_30mv3_out.asc which contains the grid information for FEWS.
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<executeActivity>
<command>
<executable>FASTrun.exe</executable>
</command>
<arguments>
<argument>cil0b2</argument>
<argument>cil0_30mv3</argument>
</arguments>
<timeOut>99999999</timeOut>
<ignoreDiagnostics>true</ignoreDiagnostics>
</executeActivity>
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Executing post adapter
The post adapter converts model output (cil0_30mv3_out.asc) in esri grid format to fews netcdf grid format for T0. The name of the netcdf file will be the name configured for the netcdf import activity which is stored in the netcdf run file.
The post adapter writes log messages to log file called Fast_Post_Adapter.log which can be read into FEWS by coupling line patterns to FEWS log messages.
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<executeActivity>
<command>
<className>nl.deltares.fast.FastPostAdapter</className>
<binDir>adapter\bin</binDir>
</command>
<arguments>
<argument>run.nc</argument>
</arguments>
<logFile>
<file>Fast_Post_Adapter.log</file>
<errorLinePattern>ERROR*</errorLinePattern>
<warningLinePattern>WARN*</warningLinePattern>
<infoLinePattern>INFO*</infoLinePattern>
<debugLinePattern>DEBUG*</debugLinePattern>
</logFile>
<timeOut>99999999</timeOut>
<ignoreDiagnostics>true</ignoreDiagnostics>
</executeActivity>
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Importing post adapter
Executing model run
The next activity will be executing the FAST model run. This is done by running FAST.exe in the workdir containing the model files.
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<executeActivity>
<command>
<executable>FAST.exe</executable>
</command>
<timeOut>99999999</timeOut>
</executeActivity>
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output
The last part of the general adapter run is importing the FAST output. xboutput.nc contains all parameter, output and grid information of the run. This can be visualized in FEWS after defining the needed parameters, location and grid. How to do this can be found here: FAST FEWS setuppost adapter output.
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<importActivities> <importPiNetcdfActivity><importNetcdfActivity> <importFile>xboutput<importFile>postAdapterOutput.nc</importFile> <timeSeriesSets> <timeSeriesSet> <moduleInstanceId>Run_FAST<XBeach</moduleInstanceId> <valueType>grid</valueType> <parameterId>H_max</parameterId> <locationId>Dummy<<locationId>Fast</locationId> <timeSeriesType>external historical</timeSeriesType> <timeStep unit="hournonequidistant"/> <readWriteMode>add<readWriteMode>read complete originals<forecast</readWriteMode> </timeSeriesSet> </timeSeriesSets> </importPiNetcdfActivity>importNetcdfActivity> </importActivities> |