coastal_ian_hsofs_schism #100

janahaddad · 2024-05-21T20:22:01Z

No description provided.

yunfangsun · 2024-05-23T02:07:37Z

When I am using pyschism to produce the bctides.in by using the following code

config = pyschism.driver.ModelConfig(
    hgrid=hgrid,
    fgrid=fgrid,
    flags=[[3,3,0,0] for i in hgrid.boundaries.open.itertuples()],
    constituents = 'major',
    database = 'tpxo',
#    nws=atmospheric,
    )

It gave me the following error:

---------------------------------------------------------------------------
QhullError                                Traceback (most recent call last)
Cell In[1], line 65
     38 config = pyschism.driver.ModelConfig(
     39     hgrid=hgrid,
     40     fgrid=fgrid,
   (...)
     47 #    nws=atmospheric,
     48     )
     53 coldstart = config.coldstart(
     54     start_date=datetime(2022,9,15) ,
     55     end_date=datetime(2022,10,7),       
   (...)
     62     dahv=True,
     63     )
---> 65 coldstart.write(Path('/work2/noaa/nos-surge/yunfangs/hurricane_ian/hsofs/new'), overwrite=True)

File /work2/noaa/nos-surge/yunfangs/conda/envs/new_sim/lib/python3.10/site-packages/pyschism/driver.py:384, in ModelDriver.write(self, output_directory, overwrite, hgrid, vgrid, fgrid, param, bctides, nws, stations, use_param_template, albedo, diffmax, diffmin, watertype, windrot, shapiro, fluxflag, tvdflag, elev_ic, temp_ic, salt_ic, hydrology)
    381 obj_write(elev_ic, self.elev_ic, "elev.ic", overwrite)
    382 obj_write(stations, self.stations, "station.in", overwrite)
--> 384 self.config.forcings.write(
    385     self, output_directory, overwrite,
    386 )
    388 MakefileDriver(self.server_config, hotstart=self.hotstart).write(
    389     self.outdir [/](https://hercules-ood.hpc.msstate.edu/node/hercules-02-01/60314/lab/workspaces/auto-I/tree/Untitled.ipynb) "Makefile", overwrite
    390 )

File /work2/noaa/nos-surge/yunfangs/conda/envs/new_sim/lib/python3.10/site-packages/pyschism/driver.py:52, in ModelForcings.write(self, driver, output_directory, overwrite)
     44 def write(
     45     self,
     46     driver: "ModelDriver",
     47     output_directory,
     48     overwrite,
     49 ):
     51     if self.bctides is not None:
---> 52         self.bctides.write(
     53             output_directory,
     54             start_date=driver.param.opt.start_date,
     55             rnday=driver.param.core.rnday,
     56             overwrite=True,
     57         )
     59     if self.nws is not None:
     60         if isinstance(self.nws, NWS2):

File /work2/noaa/nos-surge/yunfangs/conda/envs/new_sim/lib/python3.10/site-packages/pyschism/forcing/bctides/bctides.py:265, in Bctides.write(self, output_directory, start_date, rnday, overwrite)
    263     raise IOError("path exists and overwrite is False") 
    264 with open(bctides, "w") as f:
--> 265     f.write(str(self))

File /work2/noaa/nos-surge/yunfangs/conda/envs/new_sim/lib/python3.10/site-packages/pyschism/forcing/bctides/bctides.py:139, in Bctides.__str__(self)
    137 f.append(f"{constituent}")
    138 vertices = self.hgrid.get_xy(crs=self.hgrid.crs)[boundary.indexes, :]
--> 139 amp, phase = self.tides.get_elevation(constituent, vertices)
    140 for i in range(len(boundary.indexes)):
    141     f.append(f"{amp[i]: .6f} {phase[i]: .6f}")

File /work2/noaa/nos-surge/yunfangs/conda/envs/new_sim/lib/python3.10/site-packages/pyschism/forcing/bctides/tides.py:141, in Tides.get_elevation(self, constituent, vertices)
    135     return amps, phases
    137 # if vertices is None:
    138     # raise ValueError(
    139     #     'Argument vertices must not be None for tidal constituent '
    140     #     f'{constituent}.')
--> 141 return self.tidal_database.get_elevation(constituent, vertices)

File /work2/noaa/nos-surge/yunfangs/conda/envs/new_sim/lib/python3.10/site-packages/pyschism/forcing/bctides/tpxo.py:43, in TPXO.get_elevation(self, constituent, vertices)
     40 def get_elevation(self, constituent, vertices):
     41     logger.info('Querying TPXO for elevation constituent '
     42                 f'{constituent}.')
---> 43     amp = self._get_interpolation(
     44         'elevation', 'ha', constituent, vertices)
     45     phase = self._get_interpolation(
     46         'elevation', 'hp', constituent, vertices)
     47     return amp, phase

File /work2/noaa/nos-surge/yunfangs/conda/envs/new_sim/lib/python3.10/site-packages/pyschism/forcing/bctides/tpxo.py:162, in TPXO._get_interpolation(self, phys_var, ncvar, constituent, vertices)
    160 mask2 = np.ma.masked_where(zi != 0., zi)
    161 iidx = np.where(np.logical_and(mask1, mask2))
--> 162 values = griddata(
    163     (xi[iidx], yi[iidx]),
    164     zi[iidx],
    165     (xo, yo),
    166     method='linear',
    167     fill_value=np.nan,
    168 )
    169 nan_idxs = np.where(np.isnan(values))
    170 values[nan_idxs] = griddata(
    171     (xi[iidx], yi[iidx]),
    172     zi[iidx],
    173     (xo[nan_idxs], yo[nan_idxs]),
    174     method='nearest',
    175 )

File /work2/noaa/nos-surge/yunfangs/conda/envs/new_sim/lib/python3.10/site-packages/scipy/interpolate/_ndgriddata.py:323, in griddata(points, values, xi, method, fill_value, rescale)
    321     return ip(xi)
    322 elif method == 'linear':
--> 323     ip = LinearNDInterpolator(points, values, fill_value=fill_value,
    324                               rescale=rescale)
    325     return ip(xi)
    326 elif method == 'cubic' and ndim == 2:

File interpnd.pyx:326, in scipy.interpolate.interpnd.LinearNDInterpolator.__init__()

File interpnd.pyx:92, in scipy.interpolate.interpnd.NDInterpolatorBase.__init__()

File interpnd.pyx:330, in scipy.interpolate.interpnd.LinearNDInterpolator._calculate_triangulation()

File _qhull.pyx:1817, in scipy.spatial._qhull.Delaunay.__init__()

File _qhull.pyx:343, in scipy.spatial._qhull._Qhull.__init__()

QhullError: QH6013 qhull input error: input is less than 3-dimensional since all points have the same x coordinate 299.3

While executing:  | qhull d Qt Qbb Qz Qc Q12
Options selected for Qhull 2019.1.r 2019/06/21:
  run-id 879129230  delaunay  Qtriangulate  Qbbound-last  Qz-infinity-point
  Qcoplanar-keep  Q12-allow-wide  _pre-merge  _zero-centrum  Qinterior-keep
  Pgood  _max-width 0.5  Error-roundoff 4.2e-13  _one-merge 2.9e-12
  Visible-distance 8.3e-13  U-max-coplanar 8.3e-13  Width-outside 1.7e-12
  _wide-facet 5e-12  _maxoutside 3.3e-12

Do you have any suggestions for fix this error?

Thank you very much!

SorooshMani-NOAA · 2024-05-23T13:04:00Z

As afar as I remember this happens when there's a segment of the open boundary which is dry, so when trying to interpolate values from TPXO it encounters nans and masks them hence causing interpolation problem.

My suggestion is to find those instances of open boundary nodes and make them land boundary.

yunfangsun · 2024-05-28T16:30:26Z

Hi @SorooshMani-NOAA ,

I have fixed the dry point problem and made the input files without any error messages, and when I try to run it on Hercules, SCHISM log gave me the following error message:

0: ABORT: AQUIRE_HGRID: nvel_global /= total # of land bnd nodes 62972 55274

Do you have any experience with this error?

Thank you very much!

SorooshMani-NOAA · 2024-05-28T16:56:51Z

@yunfangsun did you manually modify the grid? Maybe you removed it from the ocean boundary but didn't add it to the land boundary?

yunfangsun · 2024-05-28T21:59:31Z

Thank you @SorooshMani-NOAA

And @pvelissariou1 suggested that: try to remove ADCIRC mesh's levies manually. The levies using a different tag, such as look for ibtype 3,4,5 in the file, for example something like: 5 24 = Number of nodes for land boundary 2. and also check grid_subs.F90 for the mesh read. I have removed 7696 nodes, but SCHISM gives me a new error: 499: ABORT: Incomplete ball 6

And for ocsmesh auto_generate(-10), it gave the following, which seems can't generate correct boundaries:

And now I will try to do it manually by SMS

https://github.com/noaa-ocs-modeling/SurgeTeamCoordination/issues/390#issuecomment-2130285790

SorooshMani-NOAA · 2024-05-29T12:45:14Z

To me it still seems like an issue with manual boundary modification. I'm not familiar with SMS, but you can specify polygons in OCSMesh to setup boundary manually as well. First call the auto_generate and then call set_open or set_land with polygons on the boundaries of interest.

yunfangsun · 2024-05-30T01:59:44Z

Thank you @SorooshMani-NOAA

Firstly I compared the hsofs mesh with the levies removed as @pvelissariou1 suggested.

The original hsofs boundaries are as follows:

And the boundaries with levies removed are as follows:

The difference between the twos is as follows:

It is located at the mississippi river estuary.

And it should not be removed from the mesh.

Then I use ocsmesh set_open and set_land to manually reset the boundaries as follows:

With this gr3 file, SCHISM could smoothly run

yunfangsun · 2024-06-04T19:04:33Z

From @pvelissariou1 When compiling SCHISM standalone or coupled, in order to build the utilities as well (required) the following option/flag needs to be passed to cmake from the commandline: -DBUILD_TOOLS=ON.
An example of a complete command (ufs-coastal) is:
compile.sh hercules "-DAPP=CSTLS -DUSE_ATMOS=ON -DNO_PARAMETIS=OFF -DOLDIO=ON -DBUILD_TOOLS=ON" coastalS intel YES NO
This option is only available in my cmmb branch of ufs-coastal (will merge to feature/coastal_app when Ufuk comes back).
git clone --recurse-submodules https://github.com/oceanmodeling/ufs-coastal.git -b cmmb

This will create the build_fv3_coastalS folder and compile SCHISM. The UFS executable will be something like: fv3_coastalS.exe

To find all the utility executables in the build_fv3_coastalS run:
find . -type f -executable | grep -v CMakeFiles | xargs

I suggest creating a "bin" directory outside the build_fv3_coastalS and copy all executables to the "bin" directory.
(all the above need to be fixed to avoid this manual approach).

In ufs-coastal the actual model executable is not built (if needed we can add this capability in the future). The UFS executable (fv3_coastalS.exe) contains CDEPS, CMEPS and SCHISM and it can be run through UFS by calling only the SCHISM model.

However, when I use the compile.sh hercules "-DAPP=CSTLS -DUSE_ATMOS=ON -DNO_PARAMETIS=OFF -DOLDIO=ON -DBUILD_TOOLS=ON" coastalS intel YES NO for the cmmb branch, I got the following error:
CMake Error at SCHISM-interface/CMakeLists.txt:86 (add_subdirectory):
The binary directory

/work2/noaa/nos-surge/yunfangs/ufs-coastal_cmmb/tests/build_fv3_coastalS/SCHISM-interface/SCHISM/src/Utility

is already used to build a source directory. It cannot be used to build
source directory

/work2/noaa/nos-surge/yunfangs/ufs-coastal_cmmb/SCHISM-interface/SCHISM/src/Utility

Specify a unique binary directory name.
@pvelissariou1 could you please take a look at it?

pvelissariou1 · 2024-06-04T19:21:20Z

@yunfangsun Make sure when building SCHISM in ufs-coastal that you don't supply the BLD_STANDALONE option. I have compiled SCHISM with the command:
compile.sh hercules "-DAPP=CSTLS -DUSE_ATMOS=ON -DNO_PARAMETIS=ON -DOLDIO=ON -DBUILD_TOOLS=ON" coastalS intel YES NO and everything compiled as expected.
NOTE: It is -DNO_PARAMETIS=ON and not -DNO_PARAMETIS=OFF (my bad).

The instructions will change slightly in a few days as I will fix the confict issues between BLD_STANDALONE and BUILD_TOOLS.

yunfangsun · 2024-06-05T19:13:53Z

Hi @SorooshMani-NOAA ,

I am using PySchism to generate the input files for SCHISM, the atmosphere forcing is ERA5, which is downloaded to sflux folder, and there is no windrot_geo2proj.gr3 file generated, could I know where I need to modify to generate the windrot_geo2proj.gr3, thank you

My setting is as follows:

hgrid = pyschism.mesh.Hgrid.open('hsofs/hsofs.gr3', crs=4326)

dramp = timedelta(days=8.)

fgrid = pyschism.mesh.ManningsN.linear_with_depth(
    hgrid,
    min_value=0.02, max_value=0.05,
    min_depth=-1.0, max_depth=-3.0)


config = pyschism.driver.ModelConfig(
    hgrid=hgrid,
    fgrid=fgrid,
#    iettype=pyschism.forcing.bctides.iettype.Iettype3(database="tpxo"),
#    ifltype=pyschism.forcing.bctides.ifltype.Ifltype3(database="tpxo"),

    flags=[[3,3,0,0] for i in hgrid.boundaries.open.itertuples()],
    constituents = 'major',
    database = 'tpxo',
#    nws=atmospheric,
    #nws=NWS2(ERA5()),
    )




coldstart = config.coldstart(
    start_date=datetime(2022,9,15) ,
    end_date=datetime(2022,10,2),       
    timestep=timedelta(seconds=150),
    dramp=dramp,
    dramp_ss=dramp,
    drampwind=dramp,
    nspool=timedelta(hours=1),
    elev=True,
    dahv=True,
    )

coldstart.write(Path('hsofs'), overwrite=True)

SorooshMani-NOAA · 2024-06-05T23:50:43Z

@yunfangsun in the script you shared I don't see where you get the ERA5 files. Are you downloading them separately? The ERA5 part is commented in your script. In an example I have somewhere I do this to write ERA5 files:

era5 = ERA5()
era5.write(
   outdir=schism_dir / "sflux",
   start_date=start_date,
   rnday=rnday.total_seconds() / timedelta(days=1).total_seconds(),
   air=True, rad=True, prc=True,
   bbox=atm_bbox,
   overwrite=True)

and this to write the rotation file:

windrot = gridgr3.Windrot.default(hgrid)
windrot.write(schism_dir / "windrot_geo2proj.gr3", overwrite=True)

Last time I used ERA5, it didn't support NWS2 object creation (unlike GFS and HRRR) so I had to call it explicitly like above. I hope this helps

yunfangsun · 2024-06-06T01:35:48Z

Hi @SorooshMani-NOAA

Thank you very much! It helps a lot

yunfangsun · 2024-06-06T14:23:34Z

Hi @pvelissariou1 ,

With the compile.sh hercules "-DAPP=CSTLS -DUSE_ATMOS=ON -DNO_PARAMETIS=ON -DOLDIO=ON -DBUILD_TOOLS=ON" coastalS intel YES NO, now I can finish the schsim alone simulation within UFS, however, when I take a look at the results, the wind forcings are not read into SCHISM, all the wind_speed outputs are 0.0.

And I have already changed nws = 2 in the namelist, it doesn't help. do you have any suggestions about this error?

Thank you!

pvelissariou1 · 2024-06-06T14:59:05Z

@yunfangsun The combination nws=2 and USE_ATMOS used when you couple with an atmospheric model. Is this what are you trying to do? If this is not the case then you need to remove the -DUSE_ATMOS flag from compilation. If nws=2 , SCHISM takes the atm. inputs from the sflux* files. I thing, for more details you can check the file schism/sample_inputs/param.nml

yunfangsun · 2024-06-06T15:15:36Z

Hi @pvelissariou1 ,
In this case, I am not coupling with atmos,it is using SCHSIM alone inside UFS-coastal, SCHISM should be directly reading from sflux files, and for the parm.nml, I have run the SCHISM alone outside of UFS, it read the same sflux files, and for the SCHISM inside UFS, the settings are identical, but it didn't read from atmospheric forcings from sflux

pvelissariou1 · 2024-06-06T15:18:31Z

@yunfangsun Did you compile with the USE_ATMOS ON? I guess you are using the pschism* executable instead the fv3* executable

yunfangsun · 2024-06-06T15:21:37Z

Hi @pvelissariou1

I am using compile.sh hercules "-DAPP=CSTLS -DUSE_ATMOS=ON -DNO_PARAMETIS=ON -DOLDIO=ON -DBUILD_TOOLS=ON" coastalS intel YES NO

And using srun --label -n 800 ./fv3_coastalS.exe to run the simulation

pvelissariou1 · 2024-06-06T15:27:15Z

@yunfangsun As I mentioned before, try to use:
compile.sh hercules "-DAPP=CSTLS -DNO_PARAMETIS=OFF -DOLDIO=ON -DBUILD_TOOLS=ON" coastalS intel YES NO
Use the buildcoastalS/bin/pschism* executable when running the simulation instead of the fv3_coastalS.exe executable. This should make a difference. (the fv3_coastalS.exe might work as well, but I haven't checked it)

janahaddad · 2024-06-06T15:36:55Z

I'm following along and may have missed a step, but could it be that @yunfangsun is using the default branch version, and @pvelissariou1 has added the BUILD_TOOLS option in cmmb branch? Meanwhile, the default (feature/coastal_app) branch is more recently sync'd with upstream, and has recent changes made by Ufuk on top of that.

If I'm correct, this seems like a recipe for confusion...

yunfangsun · 2024-06-06T15:41:01Z

@janahaddad @pvelissariou1

For the most recent cmmb branch, I have the following error when using compile.sh hercules "-DAPP=CSTLS -DNO_PARAMETIS=OFF -DOLDIO=ON -DBUILD_TOOLS=ON" coastalS intel YES NO



-lm -L/work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.5.1/envs/unified-env/install/intel/2021.9.0/netcdf-c-4.9.2-blbiwxx/lib -lnetcdf
CMake Error at SCHISM-interface/CMakeLists.txt:84 (add_subdirectory):
  add_subdirectory given source "SCHISM/src" which is not an existing
  directory.


CMake Error at SCHISM-interface/CMakeLists.txt:126 (set_target_properties):
  set_target_properties Can not find target to add properties to: core


CMake Error at SCHISM-interface/CMakeLists.txt:127 (target_include_directories):
  Cannot specify include directories for target "core" which is not built by
  this project.


CMake Error at SCHISM-interface/CMakeLists.txt:126 (set_target_properties):
  set_target_properties Can not find target to add properties to: hydro


CMake Error at SCHISM-interface/CMakeLists.txt:127 (target_include_directories):
  Cannot specify include directories for target "hydro" which is not built by
  this project.


CMake Error at SCHISM-interface/CMakeLists.txt:141 (install):
  install TARGETS given target "metis" which does not exist.


-- Configuring incomplete, errors occurred!
See also "/work2/noaa/nos-surge/yunfangs/cmmb/ufs-coastal_cmmb/tests/build_fv3_coastalS/CMakeFiles/CMakeOutput.log".

pvelissariou1 · 2024-06-06T15:42:11Z

@janahaddad , @yunfangsun The changes I made are in the cmmb branch, which has the very latest SCHISM commit merged + my modifications. Need to use this branch for the time being. I believe, I have mentioned this before. SCHISM compiled standalone (outside ufs-coastal) and standalone (compiled inside ufs-coastal) should give exactly the same results.

pvelissariou1 · 2024-06-06T15:44:36Z

@yunfangsun , @janahaddad Let me reclone ufs-coastal and recompile schism on hercules to see if I get any errors. Stand by....

pvelissariou1 · 2024-06-06T16:12:43Z

I think the cmmb branch is corrupted. Let me fix it ...

pvelissariou1 · 2024-06-06T20:10:51Z

@yunfangsun , @janahaddad , @saeed-moghimi-noaa I updated/fixed the ufs-coastal cmmb branch. SCHISM points to the schism repo cmmb branch. That branch is fully syncronized with the master branch and includes my updates as well. Clone ufs-coastal:
git clone -recurse-submodules https://github.com/oceanmodeling/ufs-coastal.git -b cmmb
I compiled SCHISM in ufs-coastal on hercules using:
compile.sh hercules "-DAPP=CSTLS -DNO_PARMETIS=OFF -DOLDIO=ON -DBUILD_TOOLS=ON" coastalS intel YES NO
The compilation completed without errors and the executables are:
/work/noaa/nosofs/pvelissa/ufs-coastal-cmmb-06062024/tests/fv3_coastalS.exe to be used under UFS
Utilities in: /work/noaa/nosofs/pvelissa/ufs-coastal-cmmb-06062024/tests/build_fv3_coastalS/bin
pschism: /work/noaa/nosofs/pvelissa/ufs-coastal-cmmb-06062024/tests/build_fv3_coastalS/bin/pschism_OLDIO_BUILD_TOOLS_TVD-VL

NOTE: This is the latest version(commit) of SCHISM, please check the SCHISM/sample_inputs/param.nml for changes and recent updates. Soroosh has documented these (in his github issue) when I helped him to compile the latest version of SCHISM.

SorooshMani-NOAA · 2024-06-06T20:24:49Z

I suggest working on commit hash instead of branch name ... so that everyone works on a given commit until you tell us to use a newer one later. Working based on dynamic branch names makes it much harder to track down issues.

yunfangsun · 2024-06-06T20:43:10Z

Hi @pvelissariou1 ,

Thank you! Now I can compile the cmmb branch of ufs-coastal, and I have updated the param.nml (many changes from the previous version)

Although I have turned off the vegetation model by setting iveg=1, it always gives me the following error:

333:  333: ABORT: INIT: nbins_veg_vert<=0
618:  618: ABORT: INIT: nbins_veg_vert<=0
 72:   72: ABORT: INIT: nbins_veg_vert<=0
438:  438: ABORT: INIT: nbins_veg_vert<=0
203:  203: ABORT: INIT: nbins_veg_vert<=0

I will look into the name list to see if extra modifications are needed.

saeed-moghimi-noaa · 2024-06-06T20:55:41Z

@feiye-vims @josephzhang8
Any idea about the error that @yunfangsun is getting. Thanks.

josephzhang8 · 2024-06-06T20:58:09Z

Ah.. he's using the new version. Just add

nbins_veg_vert=1

in CORE/ section of param.nml.

yunfangsun · 2024-06-06T21:03:29Z

@josephzhang8

Thank you, I have just changed it to nbins_veg_vert=1, then a new error message comes out:

 20: forrtl: severe (18): too many values for NAMELIST variable, unit 15, file /work2/noaa/nos-surge/yunfangs/stmp/yunfangs/FV3_RT/rt_test/coastal_ian_hsofs_sch_intel/.//param.nml, line 732, position 25
 20: Image              PC                Routine            Line        Source
 20: fv3_coastalS.exe   0000000001F9B48D  Unknown               Unknown  Unknown
 20: fv3_coastalS.exe   0000000001D4A73B  schism_init_              514  schism_init.F90
 20: fv3_coastalS.exe   0000000001CE83C8  schism_nuopc_cap_         345  schism_nuopc_cap.F90
 20: fv3_coastalS.exe   0000000000B85174  Unknown               Unknown  Unknown
 20: fv3_coastalS.exe

And in the param.nml, line 732, position 25, the setting is using the default values:

  iveg = 0 !on/off flag
  veg_vert_z = 0.,0.5,1. ![m] starting from 0.
  veg_vert_scale_cd = 1.,1.,1. !scaling [-]
  veg_vert_scale_N = 1.,1.,1. !scaling [-]
  veg_vert_scale_D = 1.,1.,1. !scaling [-]

Could you please advise how to modify this part?

Thank you!

josephzhang8 · 2024-06-06T21:08:14Z

I didn't know you added this part also. Change

nbins_veg_vert=2

pvelissariou1 · 2024-06-06T21:14:26Z

@yunfangsun You need to specify both as Joseph mentioned. It is already documented in the github issues related to SCHISM. @josephzhang8 I have submitted a PR on how to build SCHISM in and outside ufs-coastal. Waiting your approval.

josephzhang8 · 2024-06-06T21:15:54Z

Thx @pvelissariou1 for the reminder. I'm just out of meetings and will look at PR now... thx

pvelissariou1 · 2024-06-06T21:18:53Z

@josephzhang8 Thank you very much Joseph.

yunfangsun · 2024-06-06T21:34:08Z

Thank you @pvelissariou1 @josephzhang8

@pvelissariou1 I see schism-dev/pyschism#126

Now I have a new error message:

  0: forrtl: No such file or directory
  0: forrtl: severe (29): file not found, unit 32, file /work2/noaa/nos-surge/yunfangs/stmp/yunfangs/FV3_RT/rt_test/coastal_ian_hsofs_sch_intel/.//tvd.prop
  0: Image              PC                Routine            Line        Source
  0: fv3_coastalS.exe   0000000001F89C25  Unknown               Unknown  Unknown
  0: fv3_coastalS.exe   0000000001D63586  schism_init_             3856  schism_init.F90
  0: fv3_coastalS.exe   0000000001CE83C8  schism_nuopc_cap_         345  schism_nuopc_cap.F90
  0: fv3_coastalS.exe   0000000000B85174  Unknown               Unknown  Unknown
  0: fv3_coastalS.exe   0000000000B890EF  Unknown               Unknown  Unknown
  0: fv3_coastalS.exe   0000000000CFFD17  Unknown               Unknown  Unknown

Could I know where I can turn off the usage of tvd.prop
And my param.nml is as follows:


!parameter inputs via namelist convention.
!(1) Use ' ' (single quotes) for chars;
!(2) integer values are fine for real vars/arrays;
!(3) if multiple entries for a parameter are found, the last one wins - please avoid this
!(4) array inputs follow column major (like FORTRAN) and can spill to multiple lines. 
!    Values can be separated by commas or spaces.
!(5) space allowed before/after '='

&CORE
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
! Core (mandatory) parameters; no defaults
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
! Pre-processing option. Useful for checking grid errors etc. Need to use 1 
! core only for compute (plus necessary scribe cores). Under scribe I/O, the 
! code (the scribe part) will hang but the outputs will be there. Just kill 
! the job.
  ipre = 0 !Pre-processor flag (1: on; 0: off)

! Baroclinic/barotropic option. If ibc=0 (baroclinic model), ibtp is not used.
  ibc = 0 !Baroclinic option
  ibtp = 1 

  rnday = 17 !total run time in days
  dt = 150. !Time step in sec

! Grid for WWM (USE_WWM)
  msc2 = 24     !same as msc in .nml ... for consitency check between SCHISM and WWM
  mdc2 = 30     !same as mdc in .nml

! Define # of tracers in tracer modules (if enabled)
  ntracer_gen = 2 !user defined module (USE_GEN)
  ntracer_age = 4 !age calculation (USE_AGE). Must be =2*N where N is # of age tracers
  sed_class = 5 !SED3D (USE_SED)
  eco_class = 27 !EcoSim (USE_ECO): must be between [25,60]

! # of vertical bins in vegetation module (used only if iveg/=0)
  nbins_veg_vert = 2

! Global output controls
  nspool = 24 !output step spool
  ihfskip = 9792 !stack spool; every ihfskip steps will be put into 1_*, 2_*, etc...
/

&OPT
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
! Optional parameters. The values shown below are default unless otherwise noted
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
!-----------------------------------------------------------------------
! Optional offline partitioning using NO_PARMETIS. If on, need partition.prop (like global_to_local.prop).
!-----------------------------------------------------------------------


!-----------------------------------------------------------------------
! 2nd pre-proc flag. If ipre2/=0, code will output some diagnotic outputs and stop.
! These outputs are: drag coefficients (Cdp)
!-----------------------------------------------------------------------
  ipre2 = 0

!-----------------------------------------------------------------------
! Option to only solve tracer transport (and bypass most b-tropic solver)
! Usage: turn the flag on ('1' or '2') and turn on your tracer modules and make sure
! (1) your inputs are consistent with the original hydro-only run (with additional tracers
! of course); (2) hydro-only run results are in hydro_out/schout*.nc, which must
! have 'hvel_side' (not normal hvel), 'elev', 'diffusivity', 'temp_elem', 'salt_elem' (for
! new scribe outputs, use corresponding files/var names); (3) dt above is 
! multiple of _output_ step used in the original hydro-only run 
! (as found in in hydro_out/schout*.nc); e.g. dt = 1 hour. (4). When itransport_only=2,
! additional variables ('totalSuspendedLoad','sedBedStress') are needed.
! Hotstart should work also, but you'd probably not use an aggressively large dt especially
! when air-sea exchange is involved.
!-----------------------------------------------------------------------
  itransport_only = 0

!-----------------------------------------------------------------------
! Option to add self-attracting and loading tide (SAL) into tidal potential 
! (usually for basin-scale applications). 
! If iloadtide=0, no SAL.
! If iloadtide=1, needs inputs: loadtide_[FREQ].gr3, 
! where [FREQ] are freq names (shared with tidal potential, in upper cases) 
! and the _two_ 'depths' inside are amplitude (m) and phases (degrees behind GMT), 
! interpolated from global tide model (e.g. FES2014). In this option, SAL is 
! lumped into tidal potential so it shares some parameters with tidal potential 
! in bctides.in (cut-off depth, frequencies).
! If iloadtide=2 or 3, use a simple scaling for gravity approach (in this option,
! SAL is applied everywhere and does not share parameters with tidal potential).
! For iloadtide=2, a const scaling (1-loadtide_coef) is used; for iloadtide=3, the scaling is 
! dependent on depth (Stepanov & Hughes 2004) with max of loadtide_coef.
!-----------------------------------------------------------------------
  iloadtide = 0
  loadtide_coef = 0.1 !only used if iloadtide=2,3 (for '3', the default should be 0.12)

! Starting time
  start_year = 2022 !int
  start_month = 9 !int
  start_day = 15 !int
  start_hour = 0 !double
  utc_start = 0 !double

!-----------------------------------------------------------------------
! Coordinate option: 1: Cartesian; 2: lon/lat (hgrid.gr3=hgrid.ll in this case,
! and orientation of element is outward of earth)
! Notes for lon/lat: make sure hgrid.ll and grid in sflux are consistent in 
! longitude range!
!-----------------------------------------------------------------------
  ics = 2 !Coordinate option

!-----------------------------------------------------------------------
! Hotstart option. 0: cold start; 1: hotstart with time reset to 0; 2: 
! continue from the step in hotstart.nc
!-----------------------------------------------------------------------
  ihot = 0

!-----------------------------------------------------------------------
! Equation of State type used
! ieos_type=0: UNESCO 1980 (nonlinear); =1: linear function of T ONLY, i.e. 
! \rho=eos_b+eos_a*T, where eos_a<=0 in kg/m^3/C
!-----------------------------------------------------------------------
  ieos_type = 0
  ieos_pres = 0 !used only if ieos_type=0. 0: without pressure effects 
  eos_a = -0.1 !needed if ieos_type=1; should be <=0 
  eos_b = 1001. !needed if ieos_type=1

!-----------------------------------------------------------------------
! Main ramp option
!-----------------------------------------------------------------------
!  nramp = 1 !ramp-up option (1: on; 0: off)
  dramp = 8. !ramp-up period in days for b.c. etc (no ramp-up if <=0)

!  nrampbc = 0 !ramp-up flag for baroclinic force
  drampbc = 8. !ramp-up period in days for baroclinic force

!-----------------------------------------------------------------------
! Method for momentum advection. 0: ELM; 1: upwind (not quite working yet)
!-----------------------------------------------------------------------
  iupwind_mom = 0

!-----------------------------------------------------------------------
! Methods for computing velocity at nodes. 
! If indvel=0, conformal linear shape function is used; if indvel=1, averaging method is used.
! For indvel=0, a stabilization method is needed (see below). 
!-----------------------------------------------------------------------
  indvel = 0 
 
!-----------------------------------------------------------------------
! 2 stabilization methods, mostly for indvel=0.
! (1) Horizontal viscosity option. ihorcon=0: no viscosity is used; =1: Lapacian;
! =2: bi-harmonic. If ihorcon=1, horizontal viscosity _coefficient_ (<=1/8, related
! to diffusion number) is given in hvis_coef0, and the diffusion # 
! is problem dependent; [0.001-1/8] seems to work well.
! If ihorcon=2, diffusion number is given by hvis_coef0 (<=0.025).
! If indvel=1, no horizontal viscosity is needed. 
! (2) Shapiro filter (see below)
!
! For non-eddying regime applications (nearshore, estuary, river), an easiest option is: 
!  indvel=0, ishapiro=1 (shapiro0=0.5), ihorcon=inter_mom=0.
! For applications that include eddying regime, refer to the manual.
!-----------------------------------------------------------------------
  ihorcon = 0
  hvis_coef0 = 0.025 !const. diffusion # if ihorcon/=0; <=0.025 for ihorcon=2, <=0.125 for ihorcon=1
!  cdh = 0.01 !needed only if ihorcon/=0; land friction coefficient - not active yet

!-----------------------------------------------------------------------
! 2nd stabilization method via Shapiro filter. This should normally be used 
! if indvel=0. ishapiro=0: off; =1: constant filter strength in shapiro0; =-1:
! variable filter strength specified in shapiro.gr3; =2: variable filter strength specified
! as a Smagorinsky-like filter, with the coefficient specified in shapiro.gr3.
! To transition between eddying/non-eddying regimes, use
! indvel=0, ihorcon/=0, and ishapiro=-1 (requiring shapiro.gr3) or 2 (Smagorinsky-like filter).
!-----------------------------------------------------------------------
  ishapiro = 1 !options
  niter_shap = 1 !needed if ishapiro/=0: # of iterations with Shapiro filter
  !shapiro0: Shapiro filter strength, needed only if ishapiro=1 
  !If ishapiro=1, shapiro0 is the filter strength (max is 0.5).
  !If ishapiro=2, the coefficient in tanh() is specified in shapiro.gr3. Experiences so far suggest 100 to 1.e3
  !If ishapiro=-1, the filter strength is directly read in from shapiro.gr3
  shapiro0 = 0.5 !needed only if ishapiro=1

!-----------------------------------------------------------------------
! Implicitness factor (0.5<thetai<=1).
!-----------------------------------------------------------------------
  thetai = 0.6 

!-----------------------------------------------------------------------
! If WWM is used, set coupling/decoupling flag 'icou_elfe_wwm'. 
! No effects if USE_WWM is distabled in Makefile.
! Note that all these parameters must be present in this file (even when not used).
!       0: no elevation and no currents in wwm, no wave force in SCHISM (but wave turbulecne, WBL etc are still in SCHISM);
!       1: full coupled (elevation, vel, and wind are all passed to WWM); 
!       2: elevation and currents in wwm, no wave force in SCHISM;  
!       3: no elevation and no currents in wwm, wave force in SCHISM;
!       4: elevation but no currents in wwm, wave force in SCHISM;
!       5: elevation but no currents in wwm, no wave force in SCHISM;
!       6: no elevation but currents in wwm, wave force in SCHISM;
!       7: no elevation but currents in wwm, no wave force in SCHISM;
! If WWM is used and RADFLAG='VOR' in wwminput.nml, some parameters (fwvor_*)
! are added to take into account (1) or not (0) the different terms in vortex
! force expression.
! To get SCHISM-only result withno feedback from WWM, compile without WWM.
!-----------------------------------------------------------------------
  icou_elfe_wwm = 0 
  nstep_wwm = 1  !call WWM every this many time steps 
  iwbl = 0 !wave boundary layer formulation (used only if USE_WMM and 
           !icou_elfe_wwm/=0 and nchi=1. If icou_elfe_wwm=0, set iwbl=0): 
           !1-modified Grant-Madsen formulation; 2-Soulsby (1997)
  hmin_radstress = 1. !min. total water depth used only in radiation stress calculation [m]
!  nrampwafo = 0       !ramp-up option for the wave forces (1: on; 0: off)
  drampwafo = 0.      !ramp-up period in days for the wave forces (no ramp-up if <=0)
  turbinj = 0.15      !% of depth-induced wave breaking energy injected in turbulence 
                      !(default: 0.15 (15%), as proposed by Feddersen, 2012)
  turbinjds = 1.0     !% of wave energy dissipated through whitecapping injected in turbulence 
                      !(default: 1 (100%), as proposed by Paskyabi et al. 2012)
  alphaw = 0.5        !for itur=4 : scaling parameter for the surface roughness z0s = alphaw*Hm0. 
                      !If negative z0s = abs(alphaw) e.g. z0s=0.2 m (Feddersen and Trowbridge, 2005)
                         ! Vortex Force terms (off/on:0/1)
  fwvor_advxy_stokes = 1 !  --> Stokes drift advection (xy), Coriolis
  fwvor_advz_stokes = 1  !  --> Stokes drift advection (z) , Coriolis
  fwvor_gradpress = 1    !  --> Pressure term
  fwvor_breaking = 1     !  --> Wave breaking
  fwvor_streaming = 1    !  --> Wave streaming (works with iwbl /= 0)
  fwvor_wveg = 0         !  --> Wave dissipation by vegetation acceleration term
  fwvor_wveg_NL = 0      !  --> Non linear intrawave vegetation force (see Dean and Bender, 2006 or van Rooijen et al., 2016 for details) 
  cur_wwm = 0            ! Coupling current in WWM
                         ! 0: surface layer current
                         ! 1: depth-averaged current
                         ! 2: computed according to Kirby and Chen (1989)
  wafo_obcramp = 0       ! Ramp on wave forces at open boundary (1: on / 0: off)
                         !  --> this option requires the input file wafo_ramp.gr3
                         !      which defines the ramp value (between 0 and 1)
                         !      at nodes over the whole domain

!-----------------------------------------------------------------------
! Bed deformation option (0: off; 1: vertical deformation only; 2: 3D bed deformation). 
! If imm=1, bdef.gr3 is needed; if imm=2, user needs to update depth info etc
! in the code (not working for ics=2 yet).
!-----------------------------------------------------------------------
  imm = 0
  ibdef = 10 !needed if imm=1; # of steps used in deformation

!-----------------------------------------------------------------------
! Reference latitude for beta-plane approximation when ncor=1 (not used if ics=2)
!-----------------------------------------------------------------------
  slam0 = -124  !lon - not really used
  sfea0 = 45 !lat

!-----------------------------------------------------------------------
! Option to deal with under resolution near steep slopes in deeper depths
! 0: use h[12,_bcc below; /=0: use hw_* below
!-----------------------------------------------------------------------
  iunder_deep = 0 

!-----------------------------------------------------------------------
! Baroclinicity calculation in off/nearshore with iunder_deep=ibc=0. 
! The 'below-bottom' gradient
! is zeroed out if h>=h2_bcc (i.e. like Z) or uses const extrap
! (i.e. like terrain-following) if h<=h1_bcc(<h2_bcc) (and linear
! transition in between based on local depth)
!-----------------------------------------------------------------------
  h1_bcc = 50. ![m]
  h2_bcc = 100. ![m]; >h1_bcc

!-----------------------------------------------------------------------
! Hannah-Wright-like ratio & depth used to account for under-resolution
! in a b-clinic model. Used only if ibc=0 and iunder_deep/=0.
! The b-clinic force at prism centers is calculated with a reconstruction
! method in horizontal that has a stencil of an element and its adjacent elements.
! If the depths change is too much between the elem and its adjacent elem
! the under-resolution occurs (with steep bottom slope) and b-clinic force
! needs to be zeroed out below the (higher) bottom, specifically, if
! max(2 depths)>=hw_depth and abs(diff(2 depths))>=hw_ratio*max(2 depths).
!-----------------------------------------------------------------------
  hw_depth = 1.e6 !threshold depth in [m]
  hw_ratio = 0.5 !ratio

!-----------------------------------------------------------------------
! Hydraulic model option. If ihydraulics/=0, hydraulics.in 
! is required. This option cannot be used with non-hydrostatic model.
!-----------------------------------------------------------------------
  ihydraulics = 0

!-----------------------------------------------------------------------
! Point sources/sinks option (0: no; 1: ASCII inputs; -1: netcdf). 
! If =1, needs source_sink.in (list of elements),
! vsource,th, vsink.th, and msource.th (the source/sink values must be single precision). 
! If =-1, all info is in source.nc
! and each type of volume/mass source/sink can have its own time step and
! # of records.
! Source/sinks can be specified at an elem more
! than once, and the code will accumulate the volumes; for mass conc, 
! values are applied at _net_ source elem (no summation for conc).

! If USE_NWM_BMI is on with if_source/=0, some parts of the reading and some b.c. will be bypassed (but the inputs
! will still be needed).
!-----------------------------------------------------------------------
  if_source = 0
!  nramp_ss = 1 !needed if if_source=1; ramp-up flag for source/sinks
  dramp_ss = 2 !needed if if_source/=0; ramp-up period in days for source/sinks (no ramp-up if <=0)

!----------------------------------------------------------------------
! Specify vertical level to inject source concentration for each tracer _module_.
! Code will extrapolate below bottom/above surface unless level 0 is specified. In
! the latter case, the incoming tracer mass will be distributed across all vertical layers - 
! this approach works best in shallow waters. 
! NOTE: AGE module has its own way of injecting age tracers, so make sure the age concentrations
!  are all -9999. in msource.th so as to not interfere!
!----------------------------------------------------------------------
  lev_tr_source(1) = -9 !T
  lev_tr_source(2) = -9 !S
  lev_tr_source(3) = -9 !GEN
  lev_tr_source(4) = -9 !AGE: set -9999. in msource's AGE section
  lev_tr_source(5) = -9 !SED3D
  lev_tr_source(6) = -9 !EcoSim
  lev_tr_source(7) = -9 !ICM
  lev_tr_source(8) = -9 !CoSINE
  lev_tr_source(9) = -9 !Feco
  lev_tr_source(10) = -9 !TIMOR
  lev_tr_source(11) = -9 !FABM
  lev_tr_source(12) = -9 !DVD

!----------------------------------------------------------------------
! Specify level #'s if age module is invoked (USE_AGE), for 1st half of tracers only
!----------------------------------------------------------------------
  level_age = 9, -999 !default: -999 (all levels)

!-----------------------------------------------------------------------
! Horizontal diffusivity option. if ihdif=1, horizontal diffusivity is given in hdif.gr3
!-----------------------------------------------------------------------
  ihdif = 0 

!-----------------------------------------------------------------------
! Bottom friction. 
!           nchi=0: drag coefficients specified in drag.gr3; nchi=-1: Manning's 
!           formulation (even for 3D prisms) with n specified in manning.gr3. 
!           nchi=1: bottom roughness (in meters) specified in rough.gr3 (and in this case, negative
!           or 0 depths in rough.gr3 indicate time-independent Cd, not roughness!).
!           Cd is calculated using the log law, when dzb>=dzb_min; when dzb<dzb_min,
!           Cd=Cdmax, where Cdmax=Cd(dzb=dzb_min).
!           If iwbl/=0, nchi must =1.
!-----------------------------------------------------------------------
  nchi = -1 
  dzb_min = 0.5 !needed if nchi=1; min. bottom boundary layer thickness [m].
!  dzb_decay = 0. !needed if nchi=1; a decay const. [-]. should =0
  hmin_man = 1. !needed if nchi=-1: min. depth in Manning's formulation [m]

!-----------------------------------------------------------------------
! Coriolis. If ncor=-1, specify "rlatitude" (in degrees); if ncor=0,
! specify Coriolis parameter in "coricoef"; if ncor=1, model uses
! lat/lon in hgrid.ll for beta-plane approximation if ics=1, and in this case,
! the latitude specified in CPP projection ('sfea0') is used. If ncor=1 and ics=2,
! Coriolis is calculated from local latitude, and 'sfea0' is not used.
!-----------------------------------------------------------------------
  ncor = 1 !should usually be 1 if ics=2
  rlatitude = 46 !if ncor=-1
  coricoef = 0 !if ncor=0

!-----------------------------------------------------------------------
! Elevation initial condition flag for cold start only. For hotstart, set this to 0
! (and elev will be read in from hotstart.nc).
! If ic_elev=1, elev.ic (in *.gr3 format) is needed
! to specify the initial elevations; otherwise elevation is initialized to 0 everywhere 
!-----------------------------------------------------------------------
  ic_elev = 0

!-----------------------------------------------------------------------
! Elevation boundary condition ramp-up flag. =0: ramp up from 0; =1: ramp up from
! elev. values read in from elev.ic or hotstart.nc - if neither is present, from 0.
! This flag is mainly used to start the simulation from non-zero elev.
! The ramp-up period is 'dramp' (so if dramp=0, full strength is applied).
!-----------------------------------------------------------------------
  nramp_elev = 0

!-----------------------------------------------------------------------
! Optional inverse barometric effects on the elev. b.c.
! If inv_atm_bnd=1, the elev.'s at boundary are corrected by the difference
! between the actual atmos. pressure and a reference pressure (prmsl_ref below)
!-----------------------------------------------------------------------
  inv_atm_bnd = 0 !0: off; 1: on
  prmsl_ref = 101325. !reference atmos. pressure on bnd [Pa]

!-----------------------------------------------------------------------
! Initial condition for T,S. This value only matters for ihot=0 (cold start).
! If flag_ic(1:2)=1, the initial T,S field is read in from temp.ic and salt.ic (horizontally varying).
! If flag_ic(1:2)=2, the initial T,S field is read in from ts.ic (vertical varying).
! If ihot=0 && flag_ic(1:2)=2 || ibcc_mean=1, ts.ic is used for removing mean density profile.
! flag_ic(1) must =flag_ic(2)
!-----------------------------------------------------------------------
  flag_ic(1) = 1 !T
  flag_ic(2) = 1 !S

! initial conditions for other tracers.
! 1: needs inputs [MOD]_hvar_[1,2,...].ic ('1...' is tracer id); format of each file is similar to salt.ic;
!    i.e. horizontally varying i.c. is used for each tracer.
! 2: needs [MOD]_vvar_[1,2,...].ic. Format of each file (for each tracer in tis MOD) is similar to ts.ic
!    (i.e. level #, z-coord., tracer value). Verically varying i.c. is used for each tracer.
! 0: model sets own i.c. (EcoSim; TIMOR)
  flag_ic(3) = 1 !GEN (user defined module)
!  flag_ic(4) = 1 !Age i.c. flag set inside code
  flag_ic(5) = 1 !SED3D
  flag_ic(6) = 1 !EcoSim
  flag_ic(7) = 1 !ICM
  flag_ic(8) = 1 !CoSINE
  flag_ic(9) = 1 !FIB
  flag_ic(10) = 1 !TIMOR
  flag_ic(11) = 1 !FABM
  flag_ic(12) = 0 !DVD (must=0)

!-----------------------------------------------------------------------
! Settling vel [m/s] for GEN module (positive downward)
!-----------------------------------------------------------------------
  gen_wsett = 0 !1.e-4

!-----------------------------------------------------------------------
! Mean T,S profile option. If ibcc_mean=1 (or ihot=0 and flag_ic(1)=2), mean profile
! is read in from ts.ic, and will be removed when calculating baroclinic force.
! No ts.ic is needed if ibcc_mean=0.
!-----------------------------------------------------------------------
  ibcc_mean = 0 

!-----------------------------------------------------------------------
! Max. horizontal velocity magnitude, used mainly to prevent problem in 
! bulk aerodynamic module
!-----------------------------------------------------------------------
  rmaxvel = 5.

!-----------------------------------------------------------------------
!  Following parameters control backtracking
!-----------------------------------------------------------------------
!-----------------------------------------------------------------------
!  min. vel for invoking btrack and for abnormal exit in quicksearch
!-----------------------------------------------------------------------
  velmin_btrack = 1.e-4
!-----------------------------------------------------------------------
! Nudging factors for starting side/node - add noise to avoid underflow
! The starting location is nudged to: old*(1-btrack_nudge)+btrack_nudge*centroid
! Suggested value: btrack_nudge=9.013e-3
!-----------------------------------------------------------------------
  btrack_nudge= 9.013e-3 

!-----------------------------------------------------------------------
! Behavior when trajectory hits open bnd. If ibtrack_openbnd=0, slide with
! tangential vel; otherwise, stop and exit btrack 
!-----------------------------------------------------------------------
!  ibtrack_openbnd = 1 !hardwired

!-----------------------------------------------------------------------
! Wetting and drying. 
! - if ihhat=1, \hat{H} is made non-negative to enhance robustness near 
! wetting and drying; if ihhat=0, no retriction is imposed for this quantity. 
! - inunfl=0 is used for normal cases and inunfl=1 is used for more accurate wetting
! and drying if grid resolution is sufficiently fine.
! - if shorewafo=1, we impose radiation stress R_s = g*grad(eta) (balance between radiation stress
! gradients and the barotropic gradients) at the numerical shoreline (boundary between
! dry and wet elements). This option ensures that the shallow depth in dry elements does not
! create unphysical and very high wave forces at the shoreline (advised for morphodynamics runs).
!-----------------------------------------------------------------------
  ihhat = 1 
  inunfl = 0
  h0 = 0.01     !min. water depth for wetting/drying [m]
  shorewafo = 0 !Matters only if USE_WWM

!-----------------------------------------------------------------------
! Solver options
! USE_PETSC controls the solver type. If it's diabled, the default JCG 
! solver is used. If it's enabled, use PetSc lib. Some of the parameters
! have different meanings under these 2 options. Also with PetSc one can
! use cmd line options to choose solver etc.
!-----------------------------------------------------------------------
  moitn0 = 50 !output spool for solver info; used only with JCG
  mxitn0 = 1500 !max. iteration allowed
  rtol0 = 1.e-12 !error tolerance

!-----------------------------------------------------------------------
! Advection (ELM) option. If nadv=1, backtracking is done using Euler method; 
! nadv=2, using 2nd order Runge-Kutta; if nadv=0, advection in momentum 
! is turned off/on in adv.gr3 (the depths=0,1, or 2 also control methods 
! in backtracking as above). dtb_max/min are the max/min steps allowed -
! actual step is calculated adaptively based on local gradient.
!-----------------------------------------------------------------------
  nadv = 1
  dtb_max = 30. !in sec
  dtb_min = 10.

!-----------------------------------------------------------------------
! If inter_mom=0, linear interpolation is used for velocity at foot of char. line.
! If inter_mom=1 or -1, Kriging is used, and the choice of covariance function is
! specified in 'kr_co'. If inter_mom=1, Kriging is applied to whole domain;
! if inter_mom=-1, the regions where Kriging is used is specified in krvel.gr3 
! (depth=0: no kriging; depth=1: with kriging). 
!-----------------------------------------------------------------------
  inter_mom = 0 
  kr_co = 1 !not used if inter_mom=0

!-----------------------------------------------------------------------
! Tracer transport method. TVD or WENO method requires tvd.prop.
! TVD or WENO method is used on an element/prism if the total depth (at all nodes of the elem.)>=h_tvd and the flag in
! tvd.prop = 1 for the elem; otherwise upwind is used for efficiency. 
! itr_met=3 (horizontal TVD) or 4 (horizontal WENO): implicit TVD in the vertical dimension. 
! Also if itr_met==3 and h_tvd>=1.e5, some parts of the code are bypassed for efficiency.
! Controls for WENO are not yet in place.
!-----------------------------------------------------------------------
  itr_met = 3 
  h_tvd = 5. !cut-off depth (m) 
  !If itr_met=3 or 4, need the following 2 tolerances of convergence. The convergence
  !is achieved when sqrt[\sum_i(T_i^s+1-T_i^s)^2]<=eps1_tvd_imp*sqrt[\sum_i(T_i^s)^2]+eps2_tvd_imp
  eps1_tvd_imp = 1.e-4 !suggested value is 1.e-4, but for large suspended load, need to use a smaller value (e.g. 1.e-9)
  eps2_tvd_imp = 1.e-14  

  !Optional hybridized ELM transport for efficiency
  ielm_transport = 0 !1: turn on 
  max_subcyc = 10 !used only if ielm_transport/=0. Max # of subcycling per time step in transport allowed

  !if itr_met = 4, the following parameters are needed
  !if itr_met=4 and ipre=1, diagnostic outputs are generated for weno accuracy and stencil quality, 
  !  see subroutine weno_diag in src/Hydro/misc_subs.F90 for details
  ip_weno = 2   !order of accuracy: 0- upwind; 1- linear polynomial, 2nd order; 2- quadratic polynomial, 3rd order
  courant_weno=0.5 !Courant number for weno transport
  nquad = 2  !number of quad points on each side, nquad= 1 or 2
  ntd_weno = 1 !order of temporal discretization: (1) Euler (default); (3): 3rd-order Runge-Kutta (only for benchmarking)

  epsilon1 = 1.e-15   !coefficient of 2nd-order weno smoother (larger values are more prone to numerical dispersion)
  i_epsilon2 = 1      !switch for the specification method of 3rd-order weno smoother coefficient
                      !(1) spatially uniform, set by the parameter epsilon2 below;
                      !(2) spatially varying, set by the input file epsilon2.gr3,
                      !    Important:
                      !      Provide log10(epsilon2) in epsilon2.gr3, e.g.,
                      !      if epsilon2=10^(-6) or 1e-6, then write the z value should be -6 in epsilon2.gr3.
                      !      This is mainly for the convenience of visualization.
  epsilon2 = 1.e-10   !used when i_epsilon2 = 1
                      !spatially uniform coefficient of 3rd-order weno smoother
                      !(larger values are more prone to numerical dispersion,
                      ! 1.e-10 should be fairly safe, recommended values: 1.e-8 ~ 1.e-6)
  i_prtnftl_weno = 0 !option for writing nonfatal errors on invalid temp. or salinity for density: (0) off; (1) on.

  !Inactive at the moment:
  epsilon3 = 1.e-25  !Second coefficient of 3rd-order weno smoother (inactive at the moment)
  !Elad filter has not been implemented yet; preliminary tests showed it might not be necessary
  ielad_weno = 0      !ielad, if ielad=1, use ELAD method to suppress dispersion (inactive at the moment)
  small_elad = 1.e-4  !small (inactive at the moment)

!-----------------------------------------------------------------------
! Atmos. option. Use nws=2 and USE_ATMOS for coupling with atmospheric model.
! If nws=0, no atmos. forcing is applied. If nws=1, atmos.
! variables are read in from wind.th. If nws=2, atmos. variables are
! read in from sflux_ files.
! If nws=4, ascii format is used for wind and atmos. pressure at each node (see source code).
! If nws=-1 (requires USE_PAHM), use Holland parametric wind model (barotropic only with wind and atmos. pressure).
!  In this case, the Holland model is called every step so wtiminc is not used. An extra 
!  input file is needed: hurricane-track.dat, in addition to a few parameters below.
!
! Stress calculation:
! If nws=2, ihconsv=1 and iwind_form=0, the stress is calculated from heat exchange
! routine; in this case USE_ATMOS cannot be on.
! Otherwise if iwind_form=-1, the stress is calculated from Pond & Pichard formulation;
! if iwind_form=1, Hwang (2018) formulation (Cd tapers off at high wind).
! If WWM is enabled and icou_elfe_wwm>0 and iwind_form=-2 or -3, stress is overwritten by WWM:
! If iwind_form=-2, stress=rho_air*ufric^2; scaled by rho_water
! If iwind_form=-3, the stress is calculated according to the param. of Donelan et al. (1993) based on the wave age.
! In all cases, if USE_ICE the stress in ice-covered portion is calculated by ICE routine.
!-----------------------------------------------------------------------
  nws = 0 
  wtiminc = 150. !time step for atmos. forcing. Default: same as dt
!  nrampwind = 1 !ramp-up option for atmos. forcing
  drampwind = 8. !ramp-up period in days for wind (no ramp-up if <=0)
  iwindoff = 0 !needed only if nws/=0; '1': needs windfactor.gr3
  iwind_form = 1 !needed if nws/=0
  model_type_pahm=10 !only used if nws=-1: hurricane model type (1: Holland; 10: GAHM)

!-----------------------------------------------------------------------
! Heat and salt exchange using Zeng's (default) or Fairall (USE_BULK_FAIRALL) scheme.
! isconsv=1 needs ihconsv=1; ihconsv=1 needs nws=2.
! If isconsv=1, need to compile with precip/evap module turned on.
! If at least one of ihconsv and isconsv is set to 1,
! locally turning off air-sea exchange in shallow waters (<0.25 m) is recommended.
! Options for locally turning off heat/salt exchange are specified by
! i_hmin_airsea_ex, i_hmin_salt_ex respectively:
!   0: not turned off locally;
!   1: locally turned off, based on grid depth, i.e.,
!      off when the local grid depth (z in hgrid) < hmin_airsea_ex or hmin_salt_ex;
!   2 (recommended): locally turned off, based on local total water depth, i.e.,
!      off when the local total water depth < hmin_airsea_ex or hmin_salt_ex,
! hmin_airsea_ex, hmin_salt_ex:
!   0.2 m is recommended for both "1" and "2"
!-----------------------------------------------------------------------
  ihconsv = 0 !heat exchange option
  isconsv = 0 !evaporation/precipitation model
  i_hmin_airsea_ex = 2 ! no effect if ihconsv=0 
  hmin_airsea_ex = 0.2 ![m], no effect if ihconsv=0 
  i_hmin_salt_ex = 2 ! no effect if isconsv=0 
  hmin_salt_ex = 0.2 ![m], no effect if isconsv=0 
  iprecip_off_bnd = 0 !if /=0, precip will be turned off near land bnd

!-----------------------------------------------------------------------
! Option to add a sediment layer for the buffer effect on temperature
! stemp_stc=0 recovers previous results
!-----------------------------------------------------------------------
  stemp_stc  = 0.0   !heat transfer coefficient W.m-2.K-1
  stemp_dz(1)= 1.0   !equivalent sediment buffer depth (m) for heat into sediment
  stemp_dz(2)= 1.0   !equivalent sediment buffer depth (m) for heat out of sediment

!-----------------------------------------------------------------------
! Turbulence closure.
!-----------------------------------------------------------------------
  itur = 3 !Default: 0
  dfv0 = 1.e-2 !needed if itur=0
  dfh0 = 1.e-4 !needed if itur=0
  mid = 'KL' !needed if itur=3,5. Use KE if itur=5 
  stab = 'KC' !needed if itur=3 or 5. Use 'GA' if turb_met='MY'; otherwise use 'KC'. 
  xlsc0 = 0.1 !needed if itur=3 or 5. Scale for surface & bottom mixing length (>0)

!-----------------------------------------------------------------------
! Sponge layer for elevation and vel.
! If inu_elev=0, no relaxation is applied to elev.
! If inu_elev=1, relax. constants (in 1/sec, i.e. relax*dt<=1) are specified in elev_nudge.gr3
! and applied to eta=0 (thus a depth=0 means no relaxation).
! Similarly for inu_uv (with input uv_nudge.gr3)
!-----------------------------------------------------------------------
  inu_elev = 0
  inu_uv = 0

!-----------------------------------------------------------------------
! Nudging options for tracers. If inu_[MOD]=0, no nudging is used. If inu_tr=1,
! nudge to initial condition according to relaxation constants specified.
! If inu_tr=2, nudge to values in [MOD]_nu.nc (with step 'step_nu_tr').
! The relaxation constants = [horizontal relax (specified in [MOD]_nudge.gr3) + or x
! vertical relax] times dt, where vertical relax is a linear function of 
! vnh[1,2] and vnf[1,2], and [MOD] are tracer model names. 'nu_sum_mult' decides
! '+' or 'x' in the calculation of final relax.
! Code will ignore junk values (<=-99) inside [MOD]_nu.nc, so 1 way to avoid 
! nudging for a tracer is to set its nudged values to -9999
!-----------------------------------------------------------------------
  inu_tr(1) = 0 !T
  inu_tr(2) = 0 !S
  inu_tr(3) = 0 !GEN
  inu_tr(4) = 0 !Age
  inu_tr(5) = 0 !SED3D
  inu_tr(6) = 0 !EcoSim 
  inu_tr(7) = 0 !ICM 
  inu_tr(8) = 0 !CoSINE 
  inu_tr(9) = 0 !FIB
  inu_tr(10) = 0 !TIMOR 
  inu_tr(11) = 0 !FABM 
  inu_tr(12) = 0 !DVD (must=0)

  nu_sum_mult=1 !1: final relax is sum of horizontal&vertical; 2: product
  vnh1 = 400 !vertical nudging depth 1
  vnf1 = 0. !vertical relax \in [0,1]
  vnh2 = 500 !vertical nudging depth 2 (must >vnh1)
  vnf2 = 0. !vertical relax

  step_nu_tr = 86400. !time step [sec] in all [MOD]_nu.nc (for inu_[MOD]=2)

!-----------------------------------------------------------------------
! Cut-off depth for cubic spline interpolation near bottom when computing horizontal gradients
! e.g. using hgrad_nodes() (radiation stress, and gradients of qnon and qhat in non-hydro model). 
! If depth > h_bcc1 ('deep'),
! a min. (e.g. max bottom z-cor for the element) is imposed in the spline and so a more
! conservative method is used without extrapolation beyond bottom; 
! otherwise constant extrapolation below bottom is used.
!-----------------------------------------------------------------------
  h_bcc1 = 100. !h_bcc1

!-----------------------------------------------------------------------
! Dimensioning parameters for inter-subdomain btrack. 
! If error occurs like 'bktrk_subs: overflow' or 'MAIN: nbtrk > mxnbt'
! gradually increasing these will solve the problem
!-----------------------------------------------------------------------
  s1_mxnbt = 0.5
  s2_mxnbt = 3.5

!-----------------------------------------------------------------------
! Flag for harmonic analysis for elevation. If used , need to turn on USE_HA
! in Makefile, and input harm.in. Otherwise set it to 0. Hotstart ihot=2 is not working with HA
! Outputs are harme_* and use combine_outHA to combine.
!-----------------------------------------------------------------------
  iharind = 0

!-----------------------------------------------------------------------
! Conservation check option. If iflux/=0, some fluxes are computed
! in regions specified in fluxflag.prop (regional number from -1 to an arbitrary integer)
! in output flux.out, positive means flux from region n to region n-1 (n>=1).
! Output file flux.out will be appended on ihot=2.
! iflux=1: basic output; =2: more elaborate outputs
!-----------------------------------------------------------------------
  iflux = 0

!-----------------------------------------------------------------------
! Test flags for debugging. These flags should be turned off normally.
!-----------------------------------------------------------------------
! Williamson test #5 (zonal flow over an isolated mount); if
! on, ics must =2
!-----------------------------------------------------------------------
  izonal5 = 0 !"0" - no test; otherwise on

!-----------------------------------------------------------------------
! Rotating Gausshill test with stratified T,S (1: on; 0: off)
! Surface T,S read in from *.ic; code generates stratification
!-----------------------------------------------------------------------
  ibtrack_test = 0

!-----------------------------------------------------------------------
! Rouse profile test (1: on; 0: off)
! If on, must turn on USE_TIMOR
!-----------------------------------------------------------------------
  irouse_test = 0

!-----------------------------------------------------------------------
! Flag to choose FIB model for bacteria decay (used with USE_FIB)
! flag_fib = 1 - Constant decay rate (/day) in .gr3 format
!                (kkfib_1.gr3 and kkfib_2.gr3)
! flag_fib = 2 - Decay rate computed from Canteras et al., 1995
! flag_fib = 3 - Decay rate computed from Servais et al., 2007
!----------------------------------------------------------------------
  flag_fib = 1

!----------------------------------------------------------------------
! Marsh model parameters (only if USE_MARSH is on)
!----------------------------------------------------------------------
  slr_rate = 120. !sea-level rise rate in mm/yr, times morphological acceleration if used

!----------------------------------------------------------------------
! Vegetation model
! If iveg=1, need 4 extra inputs: (1) veg_D.gr3 (depth is stem diameter in meters);
! (2) veg_N.gr3 (depth is # of stems per m^2);
! (3) veg_h.gr3 (height of canopy in meters);
! (4) veg_cd.gr3 (drag coefficient).
! The vertical scaling is given by veg_vert_scale_[cd,N,D](1:nbins_veg_vert+1) below.
! veg_vert_z(:) specify the distance from bed for each bin (ascending order starting from 0).

! If one of these depths=0 at a node, the code will set all to 0. 
! If USE_MARSH is on and iveg=1, all .gr3 must have constant depths!
!----------------------------------------------------------------------
  iveg = 0 !on/off flag
  veg_vert_z = 0.,0.5,1. ![m] starting from 0.
  veg_vert_scale_cd = 1.,1.,1. !scaling [-]
  veg_vert_scale_N = 1.,1.,1. !scaling [-]
  veg_vert_scale_D = 1.,1.,1. !scaling [-]

!----------------------------------------------------------------------
! Coupling step with ICE module.
!----------------------------------------------------------------------
  nstep_ice = 1 !call ice module every nstep_ice steps of SCHISM


!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
! Physical constants
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
!-----------------------------------------------------------------------
! Earth's radii at pole and equator (to define an ellipsoid)
!-----------------------------------------------------------------------
  rearth_pole = 6378206.4
  rearth_eq = 6378206.4

!-----------------------------------------------------------------------
! Specific heat of water (C_p) in J/kg/K
!-----------------------------------------------------------------------
  shw = 4184.d0

!-----------------------------------------------------------------------
! Reference water density for Boussinesq approximation
!-----------------------------------------------------------------------
  rho0 = 1000.d0 !kg/m^3

!-----------------------------------------------------------------------
! Fraction of vertical flux closure adjustment applied at surface, then subtracted
! from all vertical fluxes. This is currently done for T,S only
! 0.0 <= vclose_surf_frac < 1.0
! 1: fully from surface (i.e. no correction as before); 0: fully from bottom 
!-----------------------------------------------------------------------
  vclose_surf_frac=1.0

!-----------------------------------------------------------------------
! Option to enforce strict mass conservation for each tracer model (only works with itr_met=3,4)
! At moment the scheme has not accounted for bottom 'leaking' (e.g. in SED), 
! so iadjust_mass_consv0(5) must =0
!-----------------------------------------------------------------------
  iadjust_mass_consv0(1)=0 !T
  iadjust_mass_consv0(2)=0 !S
  iadjust_mass_consv0(3)=0 !GEN
  iadjust_mass_consv0(4)=0 !AGE
  iadjust_mass_consv0(5)=0 !SED3D (code won't allow non-0 for this module)
  iadjust_mass_consv0(6)=0 !EcoSim
  iadjust_mass_consv0(7)=0 !ICM
  iadjust_mass_consv0(8)=0 !CoSiNE
  iadjust_mass_consv0(9)=0 !Feco
  iadjust_mass_consv0(10)=0 !TIMOR
  iadjust_mass_consv0(11)=0 !FABM
  iadjust_mass_consv0(12)=0 !DVD (must=0)

! For ICM, impose mass conservation for depths larger than a threshold by considering prism 
! volume change from step n to n+1. rinflation_icm is the max ratio btw H^{n+1} and H^n allowed.
  h_massconsv = 2. ![m]
  rinflation_icm = 1.e-3

/

&SCHOUT
!-----------------------------------------------------------------------
! Output section - all optional. Values shown are default unless otherwise stated,
! and default for most global outputs is off
!-----------------------------------------------------------------------

!-----------------------------------------------------------------------
! Main switch to control netcdf. If =0, SCHISM won't output nc files 
! at all (useful for other programs like ESMF to output)
!-----------------------------------------------------------------------
  nc_out = 1

!-----------------------------------------------------------------------
! UGRID option for _3D_ outputs under scribed IO (out2d*.nc always has meta
! data info). If iof_ugrid/=0, 3D outputs will also have UGRID metadata (at
! the expense of file size). 
!-----------------------------------------------------------------------
  iof_ugrid = 0

!-----------------------------------------------------------------------
! Option for hotstart outputs
!-----------------------------------------------------------------------
  nhot = 1 !1: output *_hotstart every 'nhot_write' steps
  nhot_write = 9792 !must be a multiple of ihfskip if nhot=1

!-----------------------------------------------------------------------
! Station output option. If iout_sta/=0, need output skip (nspool_sta) and
! a station.in. If ics=2, the cordinates in station.in must be in lon., lat,
! and z (positive upward; not used for 2D variables). 
!-----------------------------------------------------------------------
  iout_sta = 0
  nspool_sta = 10 !needed if iout_sta/=0; mod(nhot_write,nspool_sta) must=0

!-----------------------------------------------------------------------
! Global output options
! The variable names that appear in nc output are shown in {}
!-----------------------------------------------------------------------
  iof_hydro(1) = 1 !0: off; 1: on - elev. [m]  {elevation}  2D
  iof_hydro(2) = 0 !air pressure [Pa]  {airPressure}  2D
  iof_hydro(3) = 0 !air temperature [C] {airTemperature}  2D
  iof_hydro(4) = 0 !Specific humidity [-] {specificHumidity}  2D
  iof_hydro(5) = 0 !Net downward solar (shortwave) radiation after albedo [W/m/m] {solarRadiation}  2D
  iof_hydro(6) = 0 !sensible flux (positive upward) [W/m/m]  {sensibleHeat}  2D
  iof_hydro(7) = 0 !latent heat flux (positive upward) [W/m/m] {latentHeat}  2D
  iof_hydro(8) = 0 !upward longwave radiation (positive upward) [W/m/m] {upwardLongwave}  2D
  iof_hydro(9) = 0 !downward longwave radiation (positive downward) [W/m/m] {downwardLongwave}  2D
  iof_hydro(10) = 0 !total flux=-flsu-fllu-(radu-radd) [W/m/m] {totalHeat}  2D
  iof_hydro(11) = 0 !evaporation rate [kg/m/m/s] {evaporationRate}  2D
  iof_hydro(12) = 0 !precipitation rate [kg/m/m/s] {precipitationRate}  2D
  iof_hydro(13) = 0 !Bottom stress vector [kg/m/s^2(Pa)] {bottomStressX,Y}  2D vector
  iof_hydro(14) = 1 !wind velocity vector [m/s] {windSpeedX,Y}  2D vector
  iof_hydro(15) = 0 !wind stress vector [m^2/s/s] {windStressX,Y}  2D vector
  iof_hydro(16) = 1 !depth-averaged vel vector [m/s] {depthAverageVelX,Y}  2D vector
  iof_hydro(17) = 0 !vertical velocity [m/s] {verticalVelocity}  3D
  iof_hydro(18) = 0 !water temperature [C] {temperature}  3D
  iof_hydro(19) = 0 !water salinity [PSU] {salinity}  3D
  iof_hydro(20) = 0 !water density [kg/m^3] {waterDensity}  3D
  iof_hydro(21) = 0 !vertical eddy diffusivity [m^2/s] {diffusivity}  3D
  iof_hydro(22) = 0 !vertical eddy viscosity [m^2/s] {viscosity}  3D
  iof_hydro(23) = 0 !turbulent kinetic energy {turbulentKineticEner}   3D
  iof_hydro(24) = 0 !turbulent mixing length [m] {mixingLength}  3D
!  iof_hydro(25) = 1 !z-coord {zCoordinates} 3D - this flag should be on for visIT etc
  iof_hydro(26) = 1 !horizontal vel vector [m/s] {horizontalVelX,Y} 3D vector
  iof_hydro(27) = 0 !horizontal vel vector defined @side [m/s] {horizontalSideVelX,Y} 3D vector
  iof_hydro(28) = 0 !vertical vel. @elem [m/s] {verticalVelAtElement} 3D
  iof_hydro(29) = 0 !T @prism centers [C] {temperatureAtElement} 3D
  iof_hydro(30) = 0 !S @prism centers [PSU] {salinityAtElement} 3D
  iof_hydro(31) = 0 !Barotropic pressure gradient force vector (m.s-2) @side centers  {pressure_gradient} 2D vector

!-----------------------------------------------------------------------
! Outputs from optional modules. Only uncomment these if the USE_* is on
!-----------------------------------------------------------------------
!-----------------------------------------------------------------------
! Outputs from DVD (USE_DVD must be on in Makefile)
!-----------------------------------------------------------------------
!  iof_dvd(1) = 1 !num mixing for S (PSU^2/s) {DVD_1}   3D elem

!-----------------------------------------------------------------------
! Outputs from WWM (USE_WWM must be on in Makefile)
!-----------------------------------------------------------------------
!  iof_wwm(1)  = 0 !sig. height (m) {sigWaveHeight}   2D
!  iof_wwm(2)  = 0 !Mean average period (sec) - TM01 {meanWavePeriod}  2D
!  iof_wwm(3)  = 0 !Zero down crossing period for comparison with buoy (s) - TM02 {zeroDowncrossPeriod}  2D
!  iof_wwm(4)  = 0 !Average period of wave runup/overtopping - TM10 {TM10}  2D
!  iof_wwm(5)  = 0 !Mean wave number (1/m) {meanWaveNumber}  2D
!  iof_wwm(6)  = 0 !Mean wave length (m) {meanWaveLength}  2D
!  iof_wwm(7)  = 0 !Mean average energy transport direction (degr) - MWD in NDBC? {meanWaveDirection}  2D
!  iof_wwm(8) = 0 !Mean directional spreading (degr) {meanDirSpreading}  2D
!  iof_wwm(9) = 0 !Discrete peak period (sec) - Tp {peakPeriod}  2D
!  iof_wwm(10) = 0 !Continuous peak period based on higher order moments (sec) {continuousPeakPeriod}  2D
!  iof_wwm(11) = 0 !Peak phase vel. (m/s) {peakPhaseVel}  2D
!  iof_wwm(12) = 0 !Peak n-factor {peakNFactor}   2D
!  iof_wwm(13) = 0 !Peak group vel. (m/s) {peakGroupVel}   2D
!  iof_wwm(14) = 0 !Peak wave number {peakWaveNumber}  2D
!  iof_wwm(15) = 0 !Peak wave length {peakWaveLength}  2D
!  iof_wwm(16) = 0 !Peak (dominant) direction (degr) {dominantDirection}  2D
!  iof_wwm(17) = 0 !Peak directional spreading {peakSpreading}  2D
!  iof_wwm(18) = 0 !Discrete peak direction (radian?) {discretePeakDirectio}  2D
!  iof_wwm(19) = 0 !Orbital vel. (m/s) {orbitalVelocity}  2D
!  iof_wwm(20) = 0 !RMS Orbital vel. (m/s) {rmsOrbitalVelocity}  2D
!  iof_wwm(21) = 0 !Bottom excursion period (sec?) {bottomExcursionPerio}  2D
!  iof_wwm(22) = 0 !Bottom wave period (sec) {bottomWavePeriod}  2D
!  iof_wwm(23) = 0 !Uresell number based on peak period {UresellNumber}  2D
!  iof_wwm(24) = 0 !Friction velocity (m/s?) {frictionalVelocity}  2D
!  iof_wwm(25) = 0 !Charnock coefficient {CharnockCoeff}  2D
!  iof_wwm(26) = 0 !Rougness length {rougnessLength}  2D

!  iof_wwm(27) = 0 !Roller energy dissipation rate (W/m²) @nodes {Drol} 2D
!  iof_wwm(28) = 0 !Total wave energy dissipation rate by depth-induced breaking (W/m²) @nodes {wave_sbrtot}  2D
!  iof_wwm(29) = 0 !Total wave energy dissipation rate by bottom friction (W/m²) @nodes {wave_sbftot} 2D
!  iof_wwm(30) = 0 !Total wave energy dissipation rate by whitecapping (W/m²) @nodes {wave_sdstot} 2D
!  iof_wwm(31) = 0 !Total wave energy dissipation rate by vegetation (W/m²) @nodes {wave_svegtot} 2D
!  iof_wwm(32) = 0 !Total wave energy input rate from atmospheric forcing (W/m²) @nodes {wave_sintot} 2D
!  iof_wwm(33) = 0 !WWM_energy vector {waveEnergyDirX,Y}  2D vector

!  iof_wwm(34) = 0 !Vertical Stokes velocity (m.s-1) @sides and whole levels {stokes_wvel}  3D
!  iof_wwm(35) = 0 !Wave force vector (m.s-2) computed by wwm @side centers and whole levels {waveForceX,Y}   3D vector

!  iof_wwm(36) = 0 !Horizontal Stokes velocity (m.s-1) @nodes and whole levels {stokes_hvel} 3D vector
!  iof_wwm(37) = 0 !Roller contribution to horizontal Stokes velocity (m.s-1) @nodes and whole levels {roller_stokes_hvel} 3D vector 

!-----------------------------------------------------------------------
! Tracer module outputs. In most cases, actual # of outputs depends on # of tracers used
!-----------------------------------------------------------------------
! Outputs for user-defined tracer module (USE_GEN)
!-----------------------------------------------------------------------
!  iof_gen(1) = 0 !1st tracer {GEN_1}  3D
!  iof_gen(2) = 0 !2nd tracer {GEN_2}  3D

!-----------------------------------------------------------------------
! Outputs for (age). Indices from "1" to "ntracer_age/2"; [days]
!-----------------------------------------------------------------------
!  iof_age(1) = 0 !{AGE_1}  3D
!  iof_age(2) = 0 !{AGE_2}  3D

!-----------------------------------------------------------------------
! Specific outputs in SED3D (USE_SED must be on in Makefile;
! otherwise these are not needed)
!-----------------------------------------------------------------------
!  iof_sed(1) = 0 ! total bed thickness @elem (m) {sedBedThickness}  2D
!  iof_sed(2) = 0 ! total bed age over all layers @elem (sec) {sedBedAge}  2D
!  iof_sed(3) = 0 ! Sediment transport roughness length @elem (m) (sedTransportRough) {z0st}  2D
!  iof_sed(4) = 0 !current-ripples roughness length @elem (m) (sedRoughCurrentRippl) {z0cr}  2D
!  iof_sed(5) = 0 !sand-waves roughness length (m) @elem (z0sw_elem) {sedRoughSandWave}  2D
!  iof_sed(6) = 0 !wave-ripples roughness length @elem (m) (z0wr_elem) {sedRoughWaveRipple}  2D

!  iof_sed(7) = 0 !bottom depth _change_ from init. condition (m) {sedDepthChange}  2D
!  iof_sed(8) = 0 ! Bed median grain size in the active layer (mm) {sedD50}  2D
!  iof_sed(9) = 0 ! Bottom shear stress (Pa) {sedBedStress}  2D
!  iof_sed(10) = 0 ! Bottom roughness lenghth (mm) {sedBedRoughness}  2D
!  iof_sed(11) = 0 ! sediment porosity in the top layer (-) {sedPorocity}  2D
!  iof_sed(12) = 0 ! erosion flux for suspended transport (kg/m/m/s) {sedErosionalFlux}  2D
!  iof_sed(13) = 0 ! deposition flux for suspended transport (kg/m/m/s) {sedDepositionalFlux}  2D
!  iof_sed(14) = 0 ! Bedload transport rate vector due to wave acceleration (kg/m/s) {sedBedloadTransportX,Y}  2D vector

!  Example of using 2 classes
!  iof_sed(15) = 0 !Bedload transport rate _vector_ (kg.m-1.s-1) for 1st tracer (one output per class) {sedBedload[X,Y]_1}  2D vector
!  iof_sed(16) = 0 !Bedload transport of 2nd class {sedBedFraction_[X,Y]_2}  2D vector
!  iof_sed(17) = 0 !Bed fraction 1st tracer (one output per class) [-] {sedBedFraction_1}   2D
!  iof_sed(18) = 0 !Bed fraction of 2nd class {sedBedFraction_2}   2D

!  iof_sed(19) = 0 !conc. of 1st class (one output need by each class) [g/L] {sedConcentration_1}   3D
!  iof_sed(20) = 0 !conc. of 2nd class {sedConcentration_2}   3D

!  iof_sed(21) = 0 !total suspended concentration (g/L) {totalSuspendedLoad}  3D

!-----------------------------------------------------------------------
! EcoSim outputs 
!-----------------------------------------------------------------------
!  iof_eco(1) = 0 {ECO_1}  3D

!-----------------------------------------------------------------------
! ICM outputs 
!-----------------------------------------------------------------------
!  !core Module
!  iof_icm_core(1)  = 1 !PB1
!  iof_icm_core(2)  = 1 !PB2
!  iof_icm_core(3)  = 1 !PB3
!  iof_icm_core(4)  = 1 !RPOC
!  iof_icm_core(5)  = 1 !LPOC
!  iof_icm_core(6)  = 1 !DOC
!  iof_icm_core(7)  = 1 !RPON
!  iof_icm_core(8)  = 1 !LPON
!  iof_icm_core(9)  = 1 !DON
!  iof_icm_core(10) = 1 !NH4
!  iof_icm_core(11) = 1 !NO3
!  iof_icm_core(12) = 1 !RPOP
!  iof_icm_core(13) = 1 !LPOP
!  iof_icm_core(14) = 1 !DOP
!  iof_icm_core(15) = 1 !PO4
!  iof_icm_core(16) = 1 !COD
!  iof_icm_core(17) = 1 !DOX
!
!  !silica module
!  iof_icm_silica(1) = 1 !SU
!  iof_icm_silica(2) = 1 !SA
!
!  !zooplankton module
!  iof_icm_zb(1)  = 1 !ZB1
!  iof_icm_zb(2)  = 1 !ZB2
!
!  !pH model
!  iof_icm_ph(1) = 1 !TIC
!  iof_icm_ph(2) = 1 !ALK
!  iof_icm_ph(3) = 1 !CA
!  iof_icm_ph(4) = 1 !CACO3
!
!  !CBP model
!  iof_icm_cbp(1) = 1 !SRPOC
!  iof_icm_cbp(2) = 1 !SRPON
!  iof_icm_cbp(3) = 1 !SRPOP
!  iof_icm_cbp(4) = 1 !PIP
!
!  !SAV model
!  !-------------------------------------------------------------
!  !stleaf/ststem/stroot: leaf/stem/root biomass @elem [gC/m^2]
!  !sht: canopy height @elem [m]
!  !-------------------------------------------------------------
!  iof_icm_sav    = 1
!
!  !VEG model
!  !-------------------------------------------------------------
!  !vtleaf/vtstem/vtroot(1:3): leaf/stem/root biomass for 3 groups [gC/m^2]
!  !vht(1:3): canopy height group 1-3 [m]
!  !-------------------------------------------------------------
!  iof_icm_veg     = 1
!
!  !SFM model
!  !-------------------------------------------------------------
!  !bPOC(3),bPON(3),bPOP(3),bNH4,bNO3,bPO4,bH2S,bCH4,bPOS,bSA: sediment concs. (g.m-3)
!  !SOD/JNH4/JNO3/JPO4/JSA/JCOD: sediment fluxes   (g.m-2.day-1)
!  !bstc: surface transfer coeff. (m/day)
!  !bSTR: benthic stress      (day)
!  !bThp: consective days of hypoxia (day)
!  !bTox: consective days of oxic condition after hypoxia (day)
!  !-------------------------------------------------------------
!  iof_icm_sed      = 1
!
!  !Benthic Algae model
!  iof_icm_ba       = 1 !BA    (g[C].m-2)

!  !clam model
!  !-------------------------------------------------------------
!  !clam biomass(1:nclam) (g[C]/m^2)
!  !-------------------------------------------------------------
!  iof_icm_clam     = 1
!
!  !ICM Debug Outputs (need coding, for developers)
!  iof_icm_dbg      = 1 !2D/3D ICM debug variables
           
!-----------------------------------------------------------------------
! CoSINE outputs: all 3D
!-----------------------------------------------------------------------
!  iof_cos(1)  = 0 !NO3 (uM)
!  iof_cos(2)  = 0 !SiO4(uM)
!  iof_cos(3)  = 0 !NH4 (uM)
!  iof_cos(4)  = 0 !S1  (uM)
!  iof_cos(5)  = 0 !S2  (uM)
!  iof_cos(6)  = 0 !Z1  (uM)
!  iof_cos(7)  = 0 !Z2  (uM)
!  iof_cos(8)  = 0 !DN  (uM) 
!  iof_cos(9)  = 0 !DSi (uM) 
!  iof_cos(10) = 0 !PO4 (uM) 
!  iof_cos(11) = 0 !DOX (uM) 
!  iof_cos(12) = 0 !CO2 (uM) 
!  iof_cos(13) = 0 !ALK (uM) 

!-----------------------------------------------------------------------
! Fecal indicating bacteria module
!-----------------------------------------------------------------------
!  iof_fib(1) = 0 ! {FIB_1}  3D

!-----------------------------------------------------------------------
! Specific outputs in SED2D (USE_SED2D must be on in Makefile;
! otherwise these are not needed) - not implemented yet
!-----------------------------------------------------------------------
!  iof_sed2d(1)  = 0 !bottom depth _change_ from init. condition (m) {SED2D_depth_change}
!  iof_sed2d(2)  = 0 !drag coefficient used in transport formulae SED2D_Cd{}
!  iof_sed2d(3) = 0 !Courant number (b.qtot.dt / h.dx) {SED2D_cflsed}
!  iof_sed2d(4)    = 0 !Top layer d50 (m) {SED2D_d50}
!  iof_sed2d(5)   = 0 !total transport rate vector (kg/m/s) {SED2D_total_transport}
!  iof_sed2d(6)   = 0 !suspended tranport rate vector (kg/m/s) {SED2D_susp_load}
!  iof_sed2d(7)   = 0 !bedload transport rate vector (kg/m/s) {SED2D_bed_load}
!  iof_sed2d(8)    = 0 !time averaged total transport rate vector (kg/m/s) {SED2D_average_transport}
!  iof_sed2d(9)  = 0 !bottom slope vector (m/m); negative uphill {SED2D_bottom_slope}
!  iof_sed2d(10) = 0 !Total roughness length @elem (m) (z0eq) {z0eq}
!  iof_sed2d(11) = 0 !current-ripples roughness length @elem (m) (z0cr) {z0cr}
!  iof_sed2d(12) = 0 !sand-waves roughness length @elem (m) (z0sw) {z0sw}
!  iof_sed2d(13) = 0 !wave-ripples roughness length @elem (m) (z0wr) {z0wr}
 
!-----------------------------------------------------------------------
!  marsh flags (USE_MARSH on)
!-----------------------------------------------------------------------
!  iof_marsh(1) = 0 ! {marshFlag}  2D elem

!-----------------------------------------------------------------------
! Ice module outputs (if USE_ICE is on)
!-----------------------------------------------------------------------
!  iof_ice(1)= 0 !divergence @ elem ('Delta') [1/sec] {iceStrainRate}  2D
!  iof_ice(2)= 0 !ice advective velcoity vector [m/s] {iceVelocityX,Y}  2D vector
!  iof_ice(3)= 0 !net heat flux to ocean (>0 warm up SST) [W/m/m] {iceNetHeatFlux}  2D
!  iof_ice(4)= 0 !net fresh water flux to ocean (>0 freshens up SSS) [kg/s/m/m] {iceFreshwaterFlux}  2D
!  iof_ice(5)= 0 !ice temperature [C] at air-ice interface {iceTopTemperature}  2D

!  iof_ice(6)= 0 !ice volume [m] {iceTracer_1}   2D
!  iof_ice(7)= 0 !ice concentration [-] {iceTracer_2}  2D
!  iof_ice(8)= 0 !snow volume [m] {iceTracer_3}  2D

!-----------------------------------------------------------------------
! Analysis module outputs (USE_ANALYSIS)
!-----------------------------------------------------------------------
!  iof_ana(1) = 0 !min time step at each element over all subcycles in horizontal transport solver [s]   {minTransportTimeStep}  2D
!  iof_ana(2) = 0 !x-component of \nabla air_pres /\rho_0 [m/s/s] {airPressureGradientX}  2D
!  iof_ana(3) = 0 !y-component of \nabla air_pres /\rho_0 [m/s/s] {airPressureGradientY}  2D
!  iof_ana(4) = 0  !\alpha*g*\nabla \Psi [m/s/s] (gradient of tidal potential) {tidePotentialGradX}  2D
!  iof_ana(5) = 0  !\alpha*g*\nabla \Psi [m/s/s] {tidePotentialGradY}  2D
!  iof_ana(6) = 0 !\nabla \cdot (\mu \nabla u) [m/s/s] (horizontal momentum mixing) {horzontalViscosityX}  3D side
!  iof_ana(7) = 0 !\nabla \cdot (\mu \nabla v) [m/s/s] {horzontalViscosityY}   3D side
!  iof_ana(8) = 0 !-g/rho0* \int_z^\eta dr_dx dz  [m/s/s] (b-clinic gradient) {baroclinicForceX}  3D side
!  iof_ana(9) = 0 !-g/rho0* \int_z^\eta dr_dy dz  [m/s/s] {baroclinicForceY}  3D side
!  iof_ana(10) = 0 !d (\nu du/dz)/dz [m/s/s] - no vegetation effects (vertical momentum mixing) {verticalViscosityX}  3D side
!  iof_ana(11) = 0 !d (\nu dv/dz)/dz [m/s/s] - no vegetation effects {verticalViscosityY}  3D side
!  iof_ana(12) = 0 !(u \cdot \nabla) u [m/s/s] (momentum advection) {mommentumAdvectionX}  3D side
!  iof_ana(13) = 0 !(u \cdot \nabla) u [m/s/s] {mommentumAdvectionY}  3D side
!  iof_ana(14) = 0 !gradient Richardson number [-] {gradientRichardson}   3D
/

josephzhang8 · 2024-06-06T21:38:22Z

You set ibc=0 (baroclinic model) so it requires tvd.prop.
Were you trying to do b-tropic model? If so you need to change this and a few other parameters.

yunfangsun · 2024-06-06T22:14:45Z

Thank you @josephzhang8 ,
I am running barotropic case and have changed to ibc=1, it could run.

Hi @pvelissariou1 , with the compilation of compile.sh hercules "-DAPP=CSTLS -DNO_PARMETIS=OFF -DOLDIO=ON -DBUILD_TOOLS=ON" coastalS intel YES NO, it still can't directly read wind file from sflux, the wind speed outputs are still 0.0

yunfangsun · 2024-06-06T22:44:05Z

Hi @pvelissariou1

The problem is solved by changing nws=2

janahaddad · 2024-06-07T18:19:35Z

@yunfangsun , @janahaddad , @saeed-moghimi-noaa I updated/fixed the ufs-coastal cmmb branch. SCHISM points to the schism repo cmmb branch. That branch is fully syncronized with the master branch and includes my updates as well. Clone ufs-coastal: git clone -recurse-submodules https://github.com/oceanmodeling/ufs-coastal.git -b cmmb I compiled SCHISM in ufs-coastal on hercules using: compile.sh hercules "-DAPP=CSTLS -DNO_PARMETIS=OFF -DOLDIO=ON -DBUILD_TOOLS=ON" coastalS intel YES NO The compilation completed without errors and the executables are: /work/noaa/nosofs/pvelissa/ufs-coastal-cmmb-06062024/tests/fv3_coastalS.exe to be used under UFS Utilities in: /work/noaa/nosofs/pvelissa/ufs-coastal-cmmb-06062024/tests/build_fv3_coastalS/bin pschism: /work/noaa/nosofs/pvelissa/ufs-coastal-cmmb-06062024/tests/build_fv3_coastalS/bin/pschism_OLDIO_BUILD_TOOLS_TVD-VL

NOTE: This is the latest version(commit) of SCHISM, please check the SCHISM/sample_inputs/param.nml for changes and recent updates. Soroosh has documented these (in his github issue) when I helped him to compile the latest version of SCHISM.

thanks for resyncing with the feature/coastal-app first @pvelissariou1 . Seems like that's a best practice to use moving forward for any "non-default" branch such as the cmmb branch. That's one thing for us to discuss this afternoon

saeed-moghimi-noaa · 2024-06-07T20:05:49Z

@pvelissariou1 Please add the hash of the cmmb branch that working here. Thanks

pvelissariou1 · 2024-06-07T21:22:51Z

Here is the hash: 38d9501fda5ac5849055e29978f6b4326b26c5f1 (38d9501) schism/master

saeed-moghimi-noaa · 2024-06-07T21:26:00Z

Here is the hash: 38d9501fda5ac5849055e29978f6b4326b26c5f1 (38d9501) schism/master

Please add a git command line on how to clone it (which repo and so on). Thanks

pvelissariou1 · 2024-06-07T22:25:12Z

Working schism version/commit (standalone/ufs-coastal) as of 06/07/2024
Hash: 38d9501fda5ac5849055e29978f6b4326b26c5f1 (38d9501)

How to get/clone this commit locally

Approach 1: Download the zip archive
wget https://github.com/schism-dev/schism/archive/38d9501fda5ac5849055e29978f6b4326b26c5f1.zip

Approach 2: Clone the repo and checkout the specific commit into a branch

git clone -n https://github.com/schism-dev/schism.git schism
cd schism  (only the .git folder is present)
git checkout -b 38d9501 38d9501

Approach 3: Clone the repo and checkout the specific commit

git clone -n https://github.com/schism-dev/schism.git schism
cd schism  (only the .git folder is present)
git checkout 38d9501

pvelissariou1 · 2024-06-08T02:24:51Z

@yunfangsun , @Armaghan-NOAA , @janahaddad , @saeed-moghimi-noaa I have updated the ufs-coastal (cmmb branch) so the SCHISM submodule pointer points to SCHISM (master) - commit: 38d9501.
git clone --recurse-submodules https://github.com/oceanmodeling/ufs-coastal.git -b cmmb [local_dir_name]
As agreed, this commit will be removed upon merging with feature/coastal_app. For the time being let's use this branch for our SCHISM compilations.
The only update (if any) in the next weeks will be related to PaHM.

saeed-moghimi-noaa · 2024-06-10T13:25:25Z

@yunfangsun , @Armaghan-NOAA , @janahaddad , @saeed-moghimi-noaa I have updated the ufs-coastal (cmmb branch) so the SCHISM submodule pointer points to SCHISM (master) - commit: 38d9501. git clone --recurse-submodules https://github.com/oceanmodeling/ufs-coastal.git -b cmmb [local_dir_name] As agreed, this commit will be removed upon merging with feature/coastal_app. For the time being let's use this branch for our SCHISM compilations. The only update (if any) in the next weeks will be related to PaHM.

Thanks Takis, Highly appreciated.

yunfangsun · 2024-06-13T13:53:38Z

The case is now finished in /work2/noaa/nos-surge/yunfangs/hurricane_ian/ufs_sch_hsofs

janahaddad · 2024-09-26T14:17:15Z

@mansurjisan see here

janahaddad mentioned this issue May 21, 2024

SCHISM+WW3 H. Ian testing-suite: Phase 1 #92

Open

29 tasks

janahaddad changed the title ~~HSOFS mesh~~ coastal_ian_hsofs_schism May 21, 2024

yunfangsun mentioned this issue Jun 10, 2024

ufs-weather-model Hash: 38d9501fda5ac5849055e29978f6b4326b26c5f1 (38d9501) regression tests for SCHISM #107

Closed

yunfangsun closed this as completed Jun 13, 2024

janahaddad added this to ufs-coastal project Nov 15, 2024

janahaddad moved this to Done in ufs-coastal project Nov 15, 2024

coastal_ian_hsofs_schism #100

coastal_ian_hsofs_schism #100

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