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Add the option to provide a separate file for the mesh to the extract_subdomain script #268

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Merged
adperezm merged 3 commits into from
Jun 8, 2026
Merged

Add the option to provide a separate file for the mesh to the extract_subdomain script #268

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253680c
Add optional mesh file argument to extract_subdomain script
timofeymukha Jun 4, 2026
85b6a17
Merge branch 'feature/boudnary_edges' of https://github.com/ExtremeFL…
timofeymukha Jun 4, 2026
d3e0a3c
Merge develop
timofeymukha Jun 4, 2026
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14 changes: 11 additions & 3 deletions pysemtools/cli/extract_subdomain.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ def main():
--------
To use this script, run it with MPI using the following command:

>>> mpirun -n <num_processes> python pysemtools_extract_subdomain --input_file <input.fld> --output_file <output.fld> --bounds=<xmin,xmax,ymin,ymax,zmin,zmax> [--fields=<field1,field2,...>]
>>> mpirun -n <num_processes> python pysemtools_extract_subdomain --input_file <input.fld> --output_file <output.fld> --bounds=<xmin,xmax,ymin,ymax,zmin,zmax> [--fields=<field1,field2,...>] [--mesh_file=<mesh.fld>]

Replacing the placeholders with actual values. Observe that you have to remove the angle brackets.
'''
Expand All @@ -59,6 +59,9 @@ def main():
parser.add_argument(
"--input_file", type=str, required=True, help="Path to the field file"
)
parser.add_argument(
"--mesh_file", type=str, required=False, help="Path to the mesh file"
)
parser.add_argument(
"--output_file",
type=str,
Expand All @@ -69,7 +72,7 @@ def main():
"--bounds",
type=parse_bounds,
required=True,
help="Comma-separated list of 6 floats",
help="Comma-separated list of 6 floats, use format --bounds=-1.0,2.0,-1,1,0,0.1",
)
parser.add_argument(
"--fields",
Expand All @@ -88,7 +91,12 @@ def main():
fld = FieldRegistry(comm)

# Read
pynekread(args.input_file, comm, data_dtype=np.single, msh=mesh, fld=fld)
if not args.mesh_file:
pynekread(args.input_file, comm, data_dtype=np.single, msh=mesh, fld=fld)
else:
pynekread(args.mesh_file, comm, data_dtype=np.single, msh=mesh)
pynekread(args.input_file, comm, data_dtype=np.single, fld=fld)


fields = args.fields
if not fields:
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