Set up a rectangular regional CESM-MOM6 run

Set up a rectangular regional CESM-MOM6 run#

A typical workflow of utilizing CrocoDash consists of four main steps:

  1. Generate a regional MOM6 domain.

  2. Create the CESM case.

  3. Prepare ocean forcing data.

  4. Build and run the case.

SECTION 1: Generate a regional MOM6 domain#

We begin by defining a regional MOM6 domain using CrocoDash. To do so, we first generate a horizontal grid. We then generate the topography by remapping an existing bathymetric dataset to our horizontal grid. Finally, we define a vertical grid.

Step 1.1: Horizontal Grid#

from CrocoDash.grid import Grid

grid = Grid(
  resolution = 0.01,
  xstart = 278.0,
  lenx = 1.0,
  ystart = 7.0,
  leny = 1.0,
  name = "panama1",
)

Step 1.2: Topography#

from CrocoDash.topo import Topo

topo = Topo(
    grid = grid,
    min_depth = 9.5,
)

bathymetry_path='s3://crocodile-cesm/CrocoDash/data/gebco/GEBCO_2024.zarr/'

topo.interpolate_from_file(
    file_path = bathymetry_path,
    longitude_coordinate_name="lon",
    latitude_coordinate_name="lat",
    vertical_coordinate_name="elevation"
)

If bathymetry setup fails, rerun this function with write_to_file = True

Begin regridding bathymetry...

Original bathymetry size: 1.85 Mb
Regridded size: 0.24 Mb
Automatic regridding may fail if your domain is too big! If this process hangs or crashes,make sure function argument write_to_file = True and,open a terminal with appropriate computational and resources try calling ESMF directly in the input directory None via

`mpirun -np NUMBER_OF_CPUS ESMF_Regrid -s bathymetry_original.nc -d bathymetry_unfinished.nc -m bilinear --src_var depth --dst_var depth --netcdf4 --src_regional --dst_regional`

For details see https://xesmf.readthedocs.io/en/latest/large_problems_on_HPC.html

Afterwards, we run the 'expt.tidy_bathymetry' method to skip the expensive interpolation step, and finishing metadata, encoding and cleanup.

Regridding successful! Now calling `tidy_bathymetry` method for some finishing touches...
setup bathymetry has finished successfully.
Tidy bathymetry: Reading in regridded bathymetry to fix up metadata...done. Filling in inland lakes and channels... 

topo.depth.plot()

<matplotlib.collections.QuadMesh at 0x7f0ece942cd0>
../../_images/512e3b4dfe38912c58dd093848bb2dacf023eabcb26d70c2b88f1bf943e94e18.png 
# Erase Pacific & Canada Bays
%matplotlib ipympl
from CrocoDash.topo_editor import TopoEditor
topo.depth["units"] = "m"
TopoEditor(topo)

Step 1.3: Vertical Grid#

from CrocoDash.vgrid import VGrid

vgrid  = VGrid.hyperbolic(
    nk = 75,
    depth = topo.max_depth,
    ratio=20.0
)

print(vgrid.dz)

[ 3.65535122  3.67844102  3.7057838   3.73815846  3.77648469  3.82184774
  3.87552721  3.93903041  4.01413088  4.10291266  4.20782073  4.33171814
  4.47794994  4.65041395  4.85363759  5.0928596   5.37411432  5.70431463
  6.09132815  6.54403859  7.07238132  7.68733883  8.40087798  9.2258073
 10.17552982 11.26366612 12.50352475 13.90740505 15.48573221 17.24604754
 19.19190787 21.32178462 23.62808815 26.09646895 28.70555098 31.42722598
 34.22757583 37.06840024 39.90922464 42.70957449 45.43124949 48.04033152
 50.50871232 52.81501585 54.9448926  56.89075293 58.65106826 60.22939542
 61.63327572 62.87313435 63.96127066 64.91099317 65.73592249 66.44946164
 67.06441915 67.59276188 68.04547232 68.43248585 68.76268615 69.04394087
 69.28316289 69.48638652 69.65885053 69.80508234 69.92897974 70.03388781
 70.12266959 70.19777006 70.26127326 70.31495273 70.36031578 70.39864201
 70.43101667 70.45835946 70.48144925]

import matplotlib.pyplot as plt
plt.close()
# Create the plot
for depth in vgrid.z:
    plt.axhline(y=depth, linestyle='-')  # Horizontal lines

plt.ylim(max(vgrid.z) + 10, min(vgrid.z) - 10)  # Invert y-axis so deeper values go down
plt.ylabel("Depth")
plt.title("Vertical Grid")
plt.show()

SECTION 2: Create the CESM case#

After generating the MOM6 domain, the next step is to create a CESM case using CrocoDash. This process is straightforward and involves instantiating the CrocoDash Case object. The Case object requires the following inputs:

  • CESM Source Directory: A local path to a compatible CESM source copy.

  • Case Name: A unique name for the CESM case.

  • Input Directory: The directory where all necessary input files will be written.

  • MOM6 Domain Objects: The horizontal grid, topography, and vertical grid created in the previous section.

  • Project ID: (Optional) A project ID, if required by the machine.

Step 2.1: Specify case name and directories:#

Begin by specifying the case name and the necessary directory paths. Ensure the CESM root directory points to your own local copy of CESM. Below is an example setup:

from pathlib import Path

# CESM case (experiment) name
casename = "panama-not"

# CESM source root (Update this path accordingly!!!)
cesmroot ="/home/runner/work/CrocoGallery/CrocoGallery/CESM/"

# Place where all your input files go 
inputdir = Path.home() / "croc_input" / casename
    
# CESM case directory
caseroot = Path.home() / "croc_cases" / casename

Step 2.2: Create the Case#

To create the CESM case, instantiate the Case object as shown below. This will automatically set up the CESM case based on the provided inputs: The cesmroot argument specifies the path to your local CESM source directory. The caseroot argument defines the directory where the case will be created. CrocoDash will handle all necessary namelist modifications and XML changes to align with the MOM6 domain objects generated earlier.

from CrocoDash.case import Case
import os
os.environ["CIME_MACHINE"] = "ubuntu-latest"
case = Case(
    cesmroot = cesmroot,
    caseroot = caseroot,
    inputdir = inputdir,
    ocn_grid = grid,
    ocn_vgrid = vgrid,
    ocn_topo = topo,
    project = 'NCGD0011',
    override = True,
    machine = "ubuntu-latest",
    compset = "1850_DATM%JRA_SLND_SICE_MOM6_SROF_SGLC_SWAV"
)

WARNING:  cime_interface:CIME_OUTPUT_ROOT doesn't exist. Creating it at /home/runner/cesm/scratch

ERROR:  cime_interface:DIN_LOC_ROOT doesn't exist: /home/runner/cesm/inputdata

INFO:  csp_solver:CspSolver initialized.

Creating case...

• Updating ccs_config/modelgrid_aliases_nuopc.xml file to include the new resolution "panama-not" consisting of the following component grids.
 atm grid: "TL319", lnd grid: "TL319", ocn grid: "panama1".

• Updating ccs_config/component_grids_nuopc.xml file to include newly generated ocean grid "panama1" with the following properties:
 nx: 100, ny: 100. ocean mesh: /home/runner/croc_input/panama-not/ocnice/ESMF_mesh_panama1_249ef7.nc.

Running the create_newcase tool with the following command:

/home/runner/work/CrocoGallery/CrocoGallery/CESM/cime/scripts/create_newcase --compset 1850_DATM%JRA_SLND_SICE_MOM6_SROF_SGLC_SWAV --res panama-not --case /home/runner/croc_cases/panama-not --machine ubuntu-latest --run-unsupported --project NCGD0011 

The create_newcase command was successful.

Navigating to the case directory:

cd /home/runner/croc_cases/panama-not

Apply NTASK grid xml changes:

./xmlchange NTASKS_OCN=128

Running the case.setup script with the following command:

./case.setup

Adding parameter changes to user_nl_mom:

  ! Custom Horizonal Grid, Topography, and Vertical Grid
  INPUTDIR = /home/runner/croc_input/panama-not/ocnice
  TRIPOLAR_N = False
  REENTRANT_X = False
  REENTRANT_Y = False
  NIGLOBAL = 100
  NJGLOBAL = 100
  GRID_CONFIG = mosaic
  GRID_FILE = ocean_hgrid_panama1_249ef7.nc
  TOPO_CONFIG = file
  TOPO_FILE = ocean_topog_panama1_249ef7.nc
  MAXIMUM_DEPTH = 2780.130017656834
  MINIMUM_DEPTH = 9.5
  NK = 75
  COORD_CONFIG = none
  ALE_COORDINATE_CONFIG = FILE:ocean_vgrid_panama1_249ef7.nc
  REGRIDDING_COORDINATE_MODE = Z*

  ! Timesteps (based on grid resolution)
  DT = 25.0
  DT_THERM = 100.0

INFO:	stage:SUCCESS: All stages are complete.

Case created successfully at /home/runner/croc_cases/panama-not.

To further customize, build, and run the case, navigate to the case directory in your terminal. To create another case, restart the notebook.

Section 3: Prepare ocean forcing data#

We need to cut out our ocean forcing. The package expects an initial condition and one time-dependent segment per non-land boundary. Naming convention is "east_unprocessed" for segments and "ic_unprocessed" for the initial condition.

In this notebook, we are forcing with the Copernicus Marine “Glorys” reanalysis dataset. There’s a function in the CrocoDash package, called configure_forcings, that generates a bash script to download the correct boundary forcing files for your experiment. First, you will need to create an account with Copernicus, and then call copernicusmarine login to set up your login details on your machine. Then you can run the get_glorys_data.sh bash script.

Step 3.1 Configure Initial Conditions and Forcings#

case.configure_forcings(
    date_range = ["2020-01-01 00:00:00", "2020-01-09 00:00:00"],
    function_name="get_glorys_data_from_cds_api"
)

INFO - 2025-08-04T21:44:09Z - Selected dataset version: "202311"

INFO:copernicusmarine:Selected dataset version: "202311"

INFO - 2025-08-04T21:44:09Z - Selected dataset part: "default"

INFO:copernicusmarine:Selected dataset part: "default"

INFO - 2025-08-04T21:44:18Z - Starting download. Please wait...

INFO:copernicusmarine:Starting download. Please wait...

---------------------------------------------------------------------------
KeyboardInterrupt                         Traceback (most recent call last)
Input In [12], in <cell line: 0>()
----> 1 case.configure_forcings(
      2     date_range = ["2020-01-01 00:00:00", "2020-01-09 00:00:00"],
      3     function_name="get_glorys_data_from_cds_api"
      4 )

File ~/work/CrocoGallery/CrocoGallery/CrocoDash/CrocoDash/case.py:327, in Case.configure_forcings(self, date_range, boundaries, tidal_constituents, tpxo_elevation_filepath, tpxo_velocity_filepath, product_name, function_name, too_much_data, chl_processed_filepath)
    323 self.ProductFunctionRegistry.load_functions()
    324 assert (
    325     tb.category_of_product(product_name) == "forcing"
    326 ), "Data product must be a forcing product"
--> 327 if not self.ProductFunctionRegistry.validate_function(
    328     product_name, function_name
    329 ):
    330     raise ValueError("Selected Product or Function was not valid")
    331 self.forcing_product_name = product_name.lower()

File ~/work/CrocoGallery/CrocoGallery/CrocoDash/CrocoDash/raw_data_access/driver.py:101, in ProductFunctionRegistry.validate_function(self, product, func_name)
     99     return False
    100 try:
--> 101     res = func(*test_args)
    102 except Exception as e:
    103     logger.error(f"Error running function: {e}")

File ~/work/CrocoGallery/CrocoGallery/CrocoDash/CrocoDash/raw_data_access/datasets/glorys.py:83, in get_glorys_data_from_cds_api(dates, lat_min, lat_max, lon_min, lon_max, output_dir, output_file, dataset_varnames)
     81 end_datetime = dates[-1]
     82 dataset_id = "cmems_mod_glo_phy_my_0.083deg_P1D-m"
---> 83 response = copernicusmarine.subset(
     84     dataset_id=dataset_id,
     85     minimum_longitude=lon_min - 1,
     86     maximum_longitude=lon_max + 1,
     87     minimum_latitude=lat_min - 1,
     88     maximum_latitude=lat_max + 1,
     89     start_datetime=start_datetime,
     90     end_datetime=end_datetime,
     91     variables=dataset_varnames,
     92     output_directory=output_dir,
     93     output_filename=output_file,
     94 )
     95 return response

File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/copernicusmarine/core_functions/deprecated_options.py:78, in deprecated_python_option.<locals>.deco.<locals>.wrapper(*args, **kwargs)
     75 @functools.wraps(f)
     76 def wrapper(*args, **kwargs):
     77     rename_kwargs(f.__name__, kwargs, aliases)
---> 78     return f(*args, **kwargs)

File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/copernicusmarine/python_interface/exception_handler.py:13, in log_exception_and_exit.<locals>.wrapper(*args, **kwargs)
     10 @wraps(function)
     11 def wrapper(*args, **kwargs):
     12     try:
---> 13         return function(*args, **kwargs)
     14     except click.Abort:
     15         print("Abort")

File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/copernicusmarine/python_interface/subset.py:154, in subset(dataset_id, dataset_version, dataset_part, username, password, variables, minimum_longitude, maximum_longitude, minimum_latitude, maximum_latitude, minimum_depth, maximum_depth, vertical_axis, start_datetime, end_datetime, coordinates_selection_method, output_filename, file_format, service, request_file, output_directory, credentials_file, motu_api_request, overwrite, skip_existing, dry_run, disable_progress_bar, staging, netcdf_compression_level, netcdf3_compatible, chunk_size_limit)
    151 start_datetime = homogenize_datetime(start_datetime)
    152 end_datetime = homogenize_datetime(end_datetime)
--> 154 return subset_function(
    155     dataset_id,
    156     dataset_version,
    157     dataset_part,
    158     username,
    159     password,
    160     variables,
    161     minimum_longitude,
    162     maximum_longitude,
    163     minimum_latitude,
    164     maximum_latitude,
    165     minimum_depth,
    166     maximum_depth,
    167     vertical_axis,
    168     start_datetime,
    169     end_datetime,
    170     coordinates_selection_method,
    171     output_filename,
    172     file_format,
    173     service,
    174     request_file,
    175     output_directory,
    176     credentials_file,
    177     motu_api_request,
    178     overwrite,
    179     skip_existing,
    180     dry_run,
    181     disable_progress_bar,
    182     staging,
    183     netcdf_compression_level,
    184     netcdf3_compatible,
    185     chunk_size_limit,
    186 )

File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/copernicusmarine/core_functions/subset.py:184, in subset_function(dataset_id, force_dataset_version, force_dataset_part, username, password, variables, minimum_longitude, maximum_longitude, minimum_latitude, maximum_latitude, minimum_depth, maximum_depth, vertical_axis, start_datetime, end_datetime, coordinates_selection_method, output_filename, file_format, force_service, request_file, output_directory, credentials_file, motu_api_request, overwrite, skip_existing, dry_run, disable_progress_bar, staging, netcdf_compression_level, netcdf3_compatible, chunk_size_limit)
    174 if retrieval_service.service_name in [
    175     CopernicusMarineServiceNames.GEOSERIES,
    176     CopernicusMarineServiceNames.TIMESERIES,
    177     CopernicusMarineServiceNames.OMI_ARCO,
    178     CopernicusMarineServiceNames.STATIC_ARCO,
    179 ]:
    180     if (
    181         retrieval_service.service_format
    182         == CopernicusMarineServiceFormat.ZARR
    183     ):
--> 184         response = download_zarr(
    185             username,
    186             password,
    187             subset_request,
    188             retrieval_service.dataset_id,
    189             disable_progress_bar,
    190             retrieval_service.dataset_valid_start_date,
    191             retrieval_service.service,
    192             None if chunk_size_limit == 0 else chunk_size_limit,
    193         )
    194 else:
    195     raise ServiceNotSupported(retrieval_service.service_name)

File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/copernicusmarine/download_functions/download_arco_series.py:237, in download_zarr(username, password, subset_request, dataset_id, disable_progress_bar, dataset_valid_start_date, service, chunk_size_limit)
    230 output_directory = (
    231     subset_request.output_directory
    232     if subset_request.output_directory
    233     else pathlib.Path(".")
    234 )
    235 variables = subset_request.variables
--> 237 response = download_dataset(
    238     username=username,
    239     password=password,
    240     dataset_id=dataset_id,
    241     geographical_parameters=geographical_parameters,
    242     temporal_parameters=temporal_parameters,
    243     depth_parameters=depth_parameters,
    244     coordinates_selection_method=subset_request.coordinates_selection_method,
    245     dataset_url=dataset_url,
    246     output_directory=output_directory,
    247     output_filename=subset_request.output_filename,
    248     file_format=subset_request.file_format,
    249     variables=variables,
    250     disable_progress_bar=disable_progress_bar,
    251     overwrite=subset_request.overwrite,
    252     netcdf_compression_level=subset_request.netcdf_compression_level,
    253     netcdf3_compatible=subset_request.netcdf3_compatible,
    254     dry_run=subset_request.dry_run,
    255     service=service,
    256     chunk_size_limit=chunk_size_limit,
    257     skip_existing=subset_request.skip_existing,
    258 )
    259 return response

File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/copernicusmarine/download_functions/download_arco_series.py:174, in download_dataset(username, password, dataset_id, geographical_parameters, temporal_parameters, depth_parameters, coordinates_selection_method, dataset_url, output_directory, output_filename, file_format, variables, disable_progress_bar, netcdf_compression_level, netcdf3_compatible, service, dry_run, overwrite, chunk_size_limit, skip_existing)
    172 else:
    173     with TqdmCallback():
--> 174         _save_dataset_locally(
    175             dataset,
    176             output_path,
    177             netcdf_compression_level,
    178             netcdf3_compatible,
    179         )
    180 logger.info(f"Successfully downloaded to {output_path}")
    181 if overwrite:

File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/copernicusmarine/download_functions/download_arco_series.py:499, in _save_dataset_locally(dataset, output_path, netcdf_compression_level, netcdf3_compatible)
    497     _download_dataset_as_zarr(dataset, output_path)
    498 else:
--> 499     _download_dataset_as_netcdf(
    500         dataset,
    501         output_path,
    502         netcdf_compression_level,
    503         netcdf3_compatible,
    504     )

File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/copernicusmarine/download_functions/download_arco_series.py:551, in _download_dataset_as_netcdf(dataset, output_path, netcdf_compression_level, netcdf3_compatible)
    549 xarray_download_format = "NETCDF3_CLASSIC" if netcdf3_compatible else None
    550 engine = "h5netcdf" if not netcdf3_compatible else "netcdf4"
--> 551 return dataset.to_netcdf(
    552     output_path,
    553     mode="w",
    554     encoding=encoding,
    555     format=xarray_download_format,
    556     engine=engine,
    557 )

File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/xarray/core/dataset.py:2310, in Dataset.to_netcdf(self, path, mode, format, group, engine, encoding, unlimited_dims, compute, invalid_netcdf)
   2307     encoding = {}
   2308 from xarray.backends.api import to_netcdf
-> 2310 return to_netcdf(  # type: ignore  # mypy cannot resolve the overloads:(
   2311     self,
   2312     path,
   2313     mode=mode,
   2314     format=format,
   2315     group=group,
   2316     engine=engine,
   2317     encoding=encoding,
   2318     unlimited_dims=unlimited_dims,
   2319     compute=compute,
   2320     multifile=False,
   2321     invalid_netcdf=invalid_netcdf,
   2322 )

File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/xarray/backends/api.py:1324, in to_netcdf(dataset, path_or_file, mode, format, group, engine, encoding, unlimited_dims, compute, multifile, invalid_netcdf)
   1321 if multifile:
   1322     return writer, store
-> 1324 writes = writer.sync(compute=compute)
   1326 if isinstance(target, BytesIO):
   1327     store.sync()

File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/xarray/backends/common.py:256, in ArrayWriter.sync(self, compute, chunkmanager_store_kwargs)
    253 if chunkmanager_store_kwargs is None:
    254     chunkmanager_store_kwargs = {}
--> 256 delayed_store = chunkmanager.store(
    257     self.sources,
    258     self.targets,
    259     lock=self.lock,
    260     compute=compute,
    261     flush=True,
    262     regions=self.regions,
    263     **chunkmanager_store_kwargs,
    264 )
    265 self.sources = []
    266 self.targets = []

File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/xarray/core/daskmanager.py:211, in DaskManager.store(self, sources, targets, **kwargs)
    203 def store(
    204     self,
    205     sources: DaskArray | Sequence[DaskArray],
    206     targets: Any,
    207     **kwargs,
    208 ):
    209     from dask.array import store
--> 211     return store(
    212         sources=sources,
    213         targets=targets,
    214         **kwargs,
    215     )

File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/dask/array/core.py:1227, in store(***failed resolving arguments***)
   1224 if not return_stored:
   1225     import dask
-> 1227     dask.compute(arrays, **kwargs)
   1228     return None
   1229 else:

File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/dask/base.py:681, in compute(traverse, optimize_graph, scheduler, get, *args, **kwargs)
    678     expr = expr.optimize()
    679     keys = list(flatten(expr.__dask_keys__()))
--> 681     results = schedule(expr, keys, **kwargs)
    683 return repack(results)

File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/queue.py:171, in Queue.get(self, block, timeout)
    169 elif timeout is None:
    170     while not self._qsize():
--> 171         self.not_empty.wait()
    172 elif timeout < 0:
    173     raise ValueError("'timeout' must be a non-negative number")

File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/threading.py:327, in Condition.wait(self, timeout)
    325 try:    # restore state no matter what (e.g., KeyboardInterrupt)
    326     if timeout is None:
--> 327         waiter.acquire()
    328         gotit = True
    329     else:

KeyboardInterrupt:

Step 3.3: Process forcing data#

In this final step, we call the process_forcings method of CrocoDash to cut out and interpolate the initial condition as well as all boundaries. CrocoDash also updates MOM6 runtime parameters and CESM xml variables accordingly.

case.process_forcings()

INFO:regional_mom6.regridding:Getting t points..
INFO:regional_mom6.regridding:Creating Regridder
INFO:regional_mom6.regridding:Creating Regridder
INFO:regional_mom6.regridding:Creating Regridder

Setting up Initial Conditions
Regridding Velocities... 

INFO:regional_mom6.rotation:Getting rotation angle
INFO:regional_mom6.rotation:Calculating grid rotation angle
INFO:regional_mom6.regridding:Getting u points..
INFO:regional_mom6.regridding:Getting v points..

Done.
Regridding Tracers... Done.
Regridding Free surface... Done.
Saving outputs... 

INFO:regional_mom6.regridding:Creating coordinates of the boundary q/u/v points
INFO:regional_mom6.regridding:Creating Regridder
INFO:regional_mom6.rotation:Getting rotation angle
INFO:regional_mom6.rotation:Calculating grid rotation angle
INFO:regional_mom6.regridding:Creating coordinates of the boundary q/u/v points
INFO:regional_mom6.regridding:Filling in missing data horizontally, then vertically
INFO:regional_mom6.regridding:Adding time dimension
INFO:regional_mom6.regridding:Renaming vertical coordinate to nz_... in salt_segment_001
INFO:regional_mom6.regridding:Replacing old depth coordinates with incremental integers
INFO:regional_mom6.regridding:Adding perpendicular dimension to salt_segment_001
INFO:regional_mom6.regridding:Renaming vertical coordinate to nz_... in temp_segment_001
INFO:regional_mom6.regridding:Replacing old depth coordinates with incremental integers
INFO:regional_mom6.regridding:Adding perpendicular dimension to temp_segment_001
INFO:regional_mom6.regridding:Renaming vertical coordinate to nz_... in u_segment_001
INFO:regional_mom6.regridding:Replacing old depth coordinates with incremental integers
INFO:regional_mom6.regridding:Adding perpendicular dimension to u_segment_001
INFO:regional_mom6.regridding:Renaming vertical coordinate to nz_... in v_segment_001
INFO:regional_mom6.regridding:Replacing old depth coordinates with incremental integers
INFO:regional_mom6.regridding:Adding perpendicular dimension to v_segment_001
INFO:regional_mom6.regridding:Adding perpendicular dimension to eta_segment_001
WARNING:regional_mom6.regridding:All NaNs filled b/c bathymetry wasn't provided to the function. Add bathymetry_path to the segment class to avoid this
INFO:regional_mom6.regridding:Generating encoding dictionary
INFO:regional_mom6.regridding:Creating coordinates of the boundary q/u/v points
INFO:regional_mom6.regridding:Creating Regridder
INFO:regional_mom6.rotation:Getting rotation angle
INFO:regional_mom6.rotation:Calculating grid rotation angle
INFO:regional_mom6.regridding:Creating coordinates of the boundary q/u/v points
INFO:regional_mom6.regridding:Filling in missing data horizontally, then vertically
INFO:regional_mom6.regridding:Adding time dimension
INFO:regional_mom6.regridding:Renaming vertical coordinate to nz_... in salt_segment_002
INFO:regional_mom6.regridding:Replacing old depth coordinates with incremental integers
INFO:regional_mom6.regridding:Adding perpendicular dimension to salt_segment_002
INFO:regional_mom6.regridding:Renaming vertical coordinate to nz_... in temp_segment_002
INFO:regional_mom6.regridding:Replacing old depth coordinates with incremental integers
INFO:regional_mom6.regridding:Adding perpendicular dimension to temp_segment_002
INFO:regional_mom6.regridding:Renaming vertical coordinate to nz_... in u_segment_002
INFO:regional_mom6.regridding:Replacing old depth coordinates with incremental integers
INFO:regional_mom6.regridding:Adding perpendicular dimension to u_segment_002
INFO:regional_mom6.regridding:Renaming vertical coordinate to nz_... in v_segment_002
INFO:regional_mom6.regridding:Replacing old depth coordinates with incremental integers
INFO:regional_mom6.regridding:Adding perpendicular dimension to v_segment_002
INFO:regional_mom6.regridding:Adding perpendicular dimension to eta_segment_002
WARNING:regional_mom6.regridding:All NaNs filled b/c bathymetry wasn't provided to the function. Add bathymetry_path to the segment class to avoid this
INFO:regional_mom6.regridding:Generating encoding dictionary
INFO:regional_mom6.regridding:Creating coordinates of the boundary q/u/v points
INFO:regional_mom6.regridding:Creating Regridder
INFO:regional_mom6.rotation:Getting rotation angle
INFO:regional_mom6.rotation:Calculating grid rotation angle

done setting up initial condition.
Processing south boundary velocity & tracers...Done.
Processing north boundary velocity & tracers...Done.
Processing west boundary velocity & tracers...

INFO:regional_mom6.regridding:Creating coordinates of the boundary q/u/v points
INFO:regional_mom6.regridding:Filling in missing data horizontally, then vertically
INFO:regional_mom6.regridding:Adding time dimension
INFO:regional_mom6.regridding:Renaming vertical coordinate to nz_... in salt_segment_003
INFO:regional_mom6.regridding:Replacing old depth coordinates with incremental integers
INFO:regional_mom6.regridding:Adding perpendicular dimension to salt_segment_003
INFO:regional_mom6.regridding:Renaming vertical coordinate to nz_... in temp_segment_003
INFO:regional_mom6.regridding:Replacing old depth coordinates with incremental integers
INFO:regional_mom6.regridding:Adding perpendicular dimension to temp_segment_003
INFO:regional_mom6.regridding:Renaming vertical coordinate to nz_... in u_segment_003
INFO:regional_mom6.regridding:Replacing old depth coordinates with incremental integers
INFO:regional_mom6.regridding:Adding perpendicular dimension to u_segment_003
INFO:regional_mom6.regridding:Renaming vertical coordinate to nz_... in v_segment_003
INFO:regional_mom6.regridding:Replacing old depth coordinates with incremental integers
INFO:regional_mom6.regridding:Adding perpendicular dimension to v_segment_003
INFO:regional_mom6.regridding:Adding perpendicular dimension to eta_segment_003
WARNING:regional_mom6.regridding:All NaNs filled b/c bathymetry wasn't provided to the function. Add bathymetry_path to the segment class to avoid this
INFO:regional_mom6.regridding:Generating encoding dictionary
INFO:regional_mom6.regridding:Creating coordinates of the boundary q/u/v points
INFO:regional_mom6.regridding:Creating Regridder
INFO:regional_mom6.rotation:Getting rotation angle
INFO:regional_mom6.rotation:Calculating grid rotation angle
INFO:regional_mom6.regridding:Creating coordinates of the boundary q/u/v points
INFO:regional_mom6.regridding:Filling in missing data horizontally, then vertically
INFO:regional_mom6.regridding:Adding time dimension
INFO:regional_mom6.regridding:Renaming vertical coordinate to nz_... in salt_segment_004
INFO:regional_mom6.regridding:Replacing old depth coordinates with incremental integers
INFO:regional_mom6.regridding:Adding perpendicular dimension to salt_segment_004
INFO:regional_mom6.regridding:Renaming vertical coordinate to nz_... in temp_segment_004
INFO:regional_mom6.regridding:Replacing old depth coordinates with incremental integers
INFO:regional_mom6.regridding:Adding perpendicular dimension to temp_segment_004
INFO:regional_mom6.regridding:Renaming vertical coordinate to nz_... in u_segment_004
INFO:regional_mom6.regridding:Replacing old depth coordinates with incremental integers
INFO:regional_mom6.regridding:Adding perpendicular dimension to u_segment_004
INFO:regional_mom6.regridding:Renaming vertical coordinate to nz_... in v_segment_004
INFO:regional_mom6.regridding:Replacing old depth coordinates with incremental integers
INFO:regional_mom6.regridding:Adding perpendicular dimension to v_segment_004
INFO:regional_mom6.regridding:Adding perpendicular dimension to eta_segment_004
WARNING:regional_mom6.regridding:All NaNs filled b/c bathymetry wasn't provided to the function. Add bathymetry_path to the segment class to avoid this
INFO:regional_mom6.regridding:Generating encoding dictionary

Done.
Processing east boundary velocity & tracers...Done.
Adding parameter changes to user_nl_mom:

  ! Initial conditions
  INIT_LAYERS_FROM_Z_FILE = True
  TEMP_SALT_Z_INIT_FILE = init_tracers.nc
  Z_INIT_FILE_PTEMP_VAR = temp
  Z_INIT_ALE_REMAPPING = True
  TEMP_SALT_INIT_VERTICAL_REMAP_ONLY = True
  DEPRESS_INITIAL_SURFACE = True
  SURFACE_HEIGHT_IC_FILE = init_eta.nc
  SURFACE_HEIGHT_IC_VAR = eta_t
  VELOCITY_CONFIG = file
  VELOCITY_FILE = init_vel.nc

  ! Open boundary conditions
  OBC_NUMBER_OF_SEGMENTS = 4
  OBC_FREESLIP_VORTICITY = False
  OBC_FREESLIP_STRAIN = False
  OBC_COMPUTED_VORTICITY = True
  OBC_COMPUTED_STRAIN = True
  OBC_ZERO_BIHARMONIC = True
  OBC_TRACER_RESERVOIR_LENGTH_SCALE_OUT = 3.0E+04
  OBC_TRACER_RESERVOIR_LENGTH_SCALE_IN = 3000.0
  BRUSHCUTTER_MODE = True
  OBC_SEGMENT_001 = "J=0,I=0:N,FLATHER,ORLANSKI,NUDGED,ORLANSKI_TAN,NUDGED_TAN"
  OBC_SEGMENT_001_VELOCITY_NUDGING_TIMESCALES = 0.3, 360.0
  OBC_SEGMENT_001_DATA = "U=file:forcing_obc_segment_001.nc(u),V=file:forcing_obc_segment_001.nc(v),SSH=file:forcing_obc_segment_001.nc(eta),TEMP=file:forcing_obc_segment_001.nc(temp),SALT=file:forcing_obc_segment_001.nc(salt)"
  OBC_SEGMENT_002 = "J=N,I=N:0,FLATHER,ORLANSKI,NUDGED,ORLANSKI_TAN,NUDGED_TAN"
  OBC_SEGMENT_002_VELOCITY_NUDGING_TIMESCALES = 0.3, 360.0
  OBC_SEGMENT_002_DATA = "U=file:forcing_obc_segment_002.nc(u),V=file:forcing_obc_segment_002.nc(v),SSH=file:forcing_obc_segment_002.nc(eta),TEMP=file:forcing_obc_segment_002.nc(temp),SALT=file:forcing_obc_segment_002.nc(salt)"
  OBC_SEGMENT_003 = "I=0,J=N:0,FLATHER,ORLANSKI,NUDGED,ORLANSKI_TAN,NUDGED_TAN"
  OBC_SEGMENT_003_VELOCITY_NUDGING_TIMESCALES = 0.3, 360.0
  OBC_SEGMENT_003_DATA = "U=file:forcing_obc_segment_003.nc(u),V=file:forcing_obc_segment_003.nc(v),SSH=file:forcing_obc_segment_003.nc(eta),TEMP=file:forcing_obc_segment_003.nc(temp),SALT=file:forcing_obc_segment_003.nc(salt)"
  OBC_SEGMENT_004 = "I=N,J=0:N,FLATHER,ORLANSKI,NUDGED,ORLANSKI_TAN,NUDGED_TAN"
  OBC_SEGMENT_004_VELOCITY_NUDGING_TIMESCALES = 0.3, 360.0
  OBC_SEGMENT_004_DATA = "U=file:forcing_obc_segment_004.nc(u),V=file:forcing_obc_segment_004.nc(v),SSH=file:forcing_obc_segment_004.nc(eta),TEMP=file:forcing_obc_segment_004.nc(temp),SALT=file:forcing_obc_segment_004.nc(salt)"

./xmlchange RUN_STARTDATE=2020-01-01

./xmlchange MOM6_MEMORY_MODE=dynamic_symmetric

Case is ready to be built: /Users/manishrv/croc_cases/panama-1

Section 4: Build and run the case#

After completing the previous steps, you are ready to build and run your CESM case. Begin by navigating to the case root directory specified during the case creation. Before proceeding, review the user_nl_mom file located in the case directory. This file contains MOM6 parameter settings that were automatically generated by CrocoDash. Carefully examine these parameters and make any necessary adjustments to fine-tune the model for your specific requirements. While CrocoDash aims to provide a solid starting point, further tuning and adjustments are typically necessary to improve the model for your use case.

Once you have reviewed and modified the parameters as needed, you can build and execute the case using the following commands:

./case.build
./case.submit
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