Merge pull request #496 from gprMax/mpi

Small bug fixes and docs update

docs/requirements.txt

@@ -1,5 +1,9 @@
 cython>=0.20
 numpy>=1.9
+colorama
+reframe-hpc
+scipy
+typing_extensions
 
 # Note: beware of https://github.com/readthedocs/sphinx_rtd_theme/issues/1115
 docutils==0.17.1

docs/source/conf.py

@@ -29,6 +29,16 @@ extensions = [
     "sphinx.ext.autosummary",
 ]
 
+autodoc_mock_imports = [
+    "h5py",
+    "humanize",
+    "mpi4py_fft",
+    "mpi4py",
+    "psutil",
+    "terminaltables",
+    "tqdm",
+]
+
 # Figure numbering
 numfig = True
 

docs/source/input_api.rst

@@ -196,6 +196,10 @@ Geometry View
 -------------
 .. autoclass:: gprMax.user_objects.cmds_output.GeometryView
 
+Geometry Objects Read
+----------------------
+.. autoclass:: gprMax.user_objects.cmds_geometry.geometry_objects_read.GeometryObjectsRead
+
 Geometry Objects Write
 ----------------------
 .. autoclass:: gprMax.user_objects.cmds_output.GeometryObjectsWrite

gprMax/contexts.py

@@ -169,10 +169,11 @@ class MPIContext(Context):
 
         requested_mpi_size = np.prod(config.sim_config.mpi)
         if self.comm.size < requested_mpi_size:
-            raise ValueError(
+            logger.error(
                 f"MPI_COMM_WORLD size of {self.comm.size} is too small for requested dimensions of"
                 f" {config.sim_config.mpi}. {requested_mpi_size} ranks are required."
             )
+            exit()
 
         if self.rank >= requested_mpi_size:
             logger.warning(

gprMax/hash_cmds_multiuse.py

@@ -1,5 +1,5 @@
 # Copyright (C) 2015-2025: The University of Edinburgh, United Kingdom
-#                 Authors: Craig Warren, Antonis Giannopoulos, John Hartley, 
+#                 Authors: Craig Warren, Antonis Giannopoulos, John Hartley,
 #                          and Nathan Mannall
 #
 # This file is part of gprMax.
@@ -328,7 +328,10 @@ def process_multicmds(multicmds):
             p2 = (float(tmp[3]), float(tmp[4]), float(tmp[5]))
             dl = (float(tmp[6]), float(tmp[7]), float(tmp[8]))
             filename = tmp[10]
-            fileext = "." + filename.split(".")[-1]
+            if "." in filename:
+                fileext = "." + filename.split(".")[-1]
+            else:
+                fileext = None
 
             try:
                 iterations = int(tmp[9])

gprMax/user_objects/cmds_geometry/geometry_objects_read.py

@@ -1,5 +1,5 @@
 # Copyright (C) 2015-2025: The University of Edinburgh, United Kingdom
-#                 Authors: Craig Warren, Antonis Giannopoulos, John Hartley, 
+#                 Authors: Craig Warren, Antonis Giannopoulos, John Hartley,
 #                          and Nathan Mannall
 #
 # This file is part of gprMax.
@@ -33,6 +33,22 @@ logger = logging.getLogger(__name__)
 
 
 class GeometryObjectsRead(GeometryUserObject):
+    """Allows you to insert pre-defined geometry into a model.
+
+    The geometry is specified using a 3D array of integer numbers stored
+    in a HDF5 file. The integer numbers must correspond to the order of
+    a list of ``#material`` commands specified in a text file.
+
+    Attributes:
+        p1: list of lower left (x,y,z) coordinates in the domain where
+            the lower left corner of the geometry array should be
+            placed.
+        geofile: string path to and filename of the HDF5 file that
+            contains an integer array which defines the geometry.
+        matfile: string path to and filename of the text file that
+            contains ``#material`` commands.
+    """
+
     @property
     def hash(self):
         return "#geometry_objects_read"
@@ -75,7 +91,7 @@ class GeometryObjectsRead(GeometryUserObject):
         free_space = f"#material: 1 0 1 0 free_space{{{matstr}}}\n"
         if materials[0] == pec and materials[1] == free_space:
             materials.pop(0)
-            materials.pop(1)
+            materials.pop(0)
             numexistmaterials -= 2
         elif materials[0] == pec or materials[0] == free_space:
             materials.pop(0)