Merge pull request #61 from fusion-energy/geting_um_mesh_working_in_ci

get umesh example working in CI

.github/workflows/ci_with_install.yml

@@ -46,29 +46,25 @@ jobs:
           pytest -v tests/test_loading_from_file_vs_shape_object.py
           pytest -v tests/test_python_api.py
           pytest -v tests/test_version.py
-          cd examples/surface_mesh
-          python create_stp_files_for_examples.py
-          python cadquery_assembly.py
-          python cadquery_compound.py
-          python cadquery_object_and_stp_file.py
-          python cadquery_text.py
-          python curved_cadquery_object_to_dagmc_surface_mesh.py
-          python multiple_cadquery_objects.py
-          python multiple_stp_files.py
-          python single_stp_file_multiple_volumes.py
-          python single_cadquery_object.py
-          python single_stp_file.py
-          cd ../..
-          cd examples/unstrucutred_volume_mesh
-          python curved_cadquery_object_to_dagmc_volume_mesh.py
-          cd ../..
+          python examples/surface_mesh/create_stp_files_for_examples.py
+          python examples/surface_mesh/cadquery_assembly.py
+          python examples/surface_mesh/cadquery_compound.py
+          python examples/surface_mesh/cadquery_object_and_stp_file.py
+          python examples/surface_mesh/cadquery_text.py
+          python examples/surface_mesh/curved_cadquery_object_to_dagmc_surface_mesh.py
+          python examples/surface_mesh/multiple_cadquery_objects.py
+          python examples/surface_mesh/multiple_stp_files.py
+          python examples/surface_mesh/single_stp_file_multiple_volumes.py
+          python examples/surface_mesh/single_cadquery_object.py
+          python examples/surface_mesh/single_stp_file.py
+          python examples/unstrucutred_volume_mesh/curved_cadquery_object_to_dagmc_volume_mesh.py
           pytest -v tests/test_model_creation_for_transport.py
           mamba activate base
           mamba create -y --name openmc python=3.10
           mamba activate openmc
           mamba install -y -c conda-forge "openmc=0.14.0=dagmc*nompi*"
           python -m pip install pytest
+          python -m pip install vtk
           pytest -v tests/test_h5m_in_simulation.py
           pytest -v tests/test_h5m_in_transport.py
-          cd examples/unstrucutred_volume_mesh
-          python simulate_unstrucutred_volume_mesh_with_openmc.py
+          python examples/unstrucutred_volume_mesh/simulate_unstrucutred_volume_mesh_with_openmc.py

examples/unstrucutred_volume_mesh/simulate_unstrucutred_volume_mesh_with_openmc.py

@@ -3,26 +3,29 @@
 
 import openmc
 
+with open("cross_sections.xml", "w") as file:
+    file.write(
+        """
+        <?xml version='1.0' encoding='UTF-8'?>
+        <cross_sections>
+        <library materials="H1" path="tests/ENDFB-7.1-NNDC_H1.h5" type="neutron"/>
+        </cross_sections>
+        """
+    )
+openmc.config["cross_sections"] = "cross_sections.xml"
+
 umesh = openmc.UnstructuredMesh("umesh.h5m", library="moab")
 mesh_filter = openmc.MeshFilter(umesh)
-tally = openmc.Tally(name="t1")
+tally = openmc.Tally(name="unstrucutred_mesh_tally")
 tally.filters = [mesh_filter]
 tally.scores = ["flux"]
 tally.estimator = "tracklength"
 my_tallies = openmc.Tallies([tally])
 
 
 mat1 = openmc.Material()
-mat1.add_element("Pb", 84.2, percent_type="ao")
-mat1.add_element(
-    "Li",
-    15.8,
-    percent_type="ao",
-    enrichment=50.0,
-    enrichment_target="Li6",
-    enrichment_type="ao",
-)
-mat1.set_density("g/cm3", 11)
+mat1.add_nuclide("H1", 1, percent_type="ao")
+mat1.set_density("g/cm3", 0.001)
 my_materials = openmc.Materials([mat1])
 
 surf1 = openmc.Sphere(r=500, boundary_type="vacuum")
@@ -33,16 +36,14 @@
 
 my_geometry = openmc.Geometry([cell1])
 
-
 my_settings = openmc.Settings()
 my_settings.batches = 10
 my_settings.inactive = 0
 my_settings.particles = 5000
 my_settings.run_mode = "fixed source"
 
 # Create a DT point source
-my_source = openmc.Source()
-# my_source = openmc.IndependentSource()
+my_source = openmc.IndependentSource()
 my_source.space = openmc.stats.Point((0, 0, 0))
 my_source.angle = openmc.stats.Isotropic()
 my_source.energy = openmc.stats.Discrete([14e6], [1])
@@ -53,12 +54,16 @@
 
 sp = openmc.StatePoint(sp_filename)
 
-tally_result = sp.get_tally(name="t1")
-
+tally_result = sp.get_tally(name="unstrucutred_mesh_tally")
 
+# normally with regular meshes I would get the mesh from the tally
+# but with unstrucutred meshes the tally does not contain the mesh
+# however we can get it from the statepoint file
 # umesh = tally_result.find_filter(openmc.MeshFilter)
 umesh_from_sp = sp.meshes[1]
 
+# these trigger internal code in the mesh object so that its centroids and volumes become known.
+# centroids and volumes are needed for the get_values and write_data_to_vtk steps
 centroids = umesh_from_sp.centroids
 mesh_vols = umesh_from_sp.volumes
 

tests/test_h5m_in_simulation.py

@@ -6,7 +6,7 @@
 
 
 def transport_particles_on_h5m_geometry(
-    h5m_filename,
+    h5m_filename: str,
     material_tags,
 ):
     """A function for testing the geometry file with particle transport in DAGMC OpenMC"""

tests/test_h5m_in_transport.py

@@ -91,6 +91,7 @@ def transport_particles_on_h5m_geometry(
     settings.inactive = 0
     settings.run_mode = "fixed source"
     settings.source = my_source
+    settings.photon_transport = False
 
     # adds a tally to record the heat deposited in entire geometry
     cell_tally = openmc.Tally(name="flux")