From 253680cd6462e73bd36a3b0f19ffc2321c57af9b Mon Sep 17 00:00:00 2001
From: Timofey Mukha <timofey.mukha@protonmail.com>
Date: Thu, 4 Jun 2026 11:06:32 +0300
Subject: [PATCH 1/2] Add optional mesh file argument to extract_subdomain
 script

---
 pysemtools/cli/extract_subdomain.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/pysemtools/cli/extract_subdomain.py b/pysemtools/cli/extract_subdomain.py
index 0ef4d3b..fd9ede2 100644
--- a/pysemtools/cli/extract_subdomain.py
+++ b/pysemtools/cli/extract_subdomain.py
@@ -32,6 +32,9 @@ 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,
@@ -42,7 +45,7 @@ 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",
@@ -61,7 +64,12 @@ 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:

From d3e0a3c286ed1254fa474017bf231c424a4d63f5 Mon Sep 17 00:00:00 2001
From: Timofey Mukha <timofey.mukha@protonmail.com>
Date: Thu, 4 Jun 2026 11:17:06 +0300
Subject: [PATCH 2/2] Merge develop

---
 pysemtools/cli/extract_subdomain.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pysemtools/cli/extract_subdomain.py b/pysemtools/cli/extract_subdomain.py
index f282011..a0caeb2 100644
--- a/pysemtools/cli/extract_subdomain.py
+++ b/pysemtools/cli/extract_subdomain.py
@@ -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.
     '''