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included a min_depth parameter and overwite this in MOM_input #185

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included a min_depth parameter and overwite this in MOM_input #185

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included a min_depth parameter and overwite this in MOM_input
ashjbarnes Aug 28, 2024
0523f1d
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ashjbarnes Aug 28, 2024
14023d0
Merge branch 'main' into override-min-depth
navidcy Sep 6, 2024
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17 changes: 14 additions & 3 deletions regional_mom6/regional_mom6.py
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Original file line number Diff line number Diff line change
Expand Up @@ -485,6 +485,7 @@ def __init__(
self.repeat_year_forcing = repeat_year_forcing
self.ocean_mask = None
self.layout = None # This should be a tuple. Leaving in a dummy 'None' makes it easy to remind the user to provide a value later on.
self.min_depth = 0.0 # Minimum depth. Shallower water will be masked out. This value is overwritten when running "setup_bathymetry" method.
if read_existing_grids:
try:
self.hgrid = xr.open_dataset(self.mom_input_dir / "hgrid.nc")
Expand Down Expand Up @@ -1356,7 +1357,7 @@ def tidy_bathymetry(
## REMOVE INLAND LAKES

min_depth = self.vgrid.zi[minimum_layers]

self.min_depth = min_depth
ocean_mask = bathymetry.copy(deep=True).depth.where(
bathymetry.depth <= min_depth, 1
)
Expand Down Expand Up @@ -1698,7 +1699,7 @@ def setup_run_directory(

print("Number of CPUs required: ", ncpus)

## Modify the input namelists to give the correct layouts
## Modify the MOM_layout file to have correct horizontal dimensions and CPU layout
# TODO Re-implement with package that works for this file type? or at least tidy up code
with open(self.mom_run_dir / "MOM_layout", "r") as file:
lines = file.readlines()
Expand All @@ -1716,10 +1717,20 @@ def setup_run_directory(

if "NJGLOBAL" in lines[jj]:
lines[jj] = f"NJGLOBAL = {self.hgrid.ny.shape[0]//2}\n"

with open(self.mom_run_dir / "MOM_layout", "w") as f:
f.writelines(lines)

# Overwrite values pertaining to vertical structure in the MOM_input file
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@navidcy navidcy Aug 29, 2024 •
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I was just wondering: does the new thing here is that first we f.writelines(lines) and then we ensure that if something was there already we overwrite it?

with open(self.mom_run_dir / "MOM_input", "r") as file:
lines = file.readlines()
for jj in range(len(lines)):
if "MINIMUM_DEPTH" in lines[jj]:
lines[jj] = f'MINIMUM_DEPTH = "{self.min_depth}"\n'
if "NK =" in lines[jj]:
lines[jj] = f"NK = {len(self.vgrid.zl.values)}\n"
with open(self.mom_run_dir / "MOM_input", "w") as f:
f.writelines(lines)

## If using payu to run the model, create a payu configuration file
if not using_payu and os.path.exists(f"{self.mom_run_dir}/config.yaml"):
os.remove(f"{self.mom_run_dir}/config.yaml")
Expand Down
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