Merge pull request #57 from fusion-energy/adding_3d_mesh_export_option

allowing export_gmsh_mesh_file to support 3d volume mesh exporting

.github/workflows/ci_with_benchmarks.yml

@@ -37,7 +37,7 @@ jobs:
           sudo apt-get upgrade -y
           sudo apt-get install -y libgl1-mesa-glx libgl1-mesa-dev libglu1-mesa-dev freeglut3-dev libosmesa6 libosmesa6-dev libgles2-mesa-dev libarchive-dev libpangocairo-1.0-0
           mamba activate
-          mamba install -y -c cadquery -c conda-forge moab gmsh python-gmsh cadquery=master "openmc=0.13.3=dagmc*nompi*"
+          mamba install -y -c conda-forge moab gmsh python-gmsh cadquery=2.4.0 "openmc=0.14.0=dagmc*nompi*"
           python -m pip install --upgrade pip
           python -m pip install cad_to_dagmc openmc_data_downloader
           openmc_data_downloader -l ENDFB-7.1-NNDC -i Fe56 Be9

.github/workflows/ci_with_install.yml

@@ -1,9 +1,4 @@
 
-# This CI will launch a Docker image that contains all the dependencies required
-# within that image the pytest test suite is run 
-# container:
-#       image: continuumio/miniconda3:23.3.1-0
-
 name: CI with install
 
 on:
@@ -40,11 +35,13 @@ jobs:
           sudo apt-get upgrade -y
           sudo apt-get install -y libgl1-mesa-glx libgl1-mesa-dev libglu1-mesa-dev freeglut3-dev libosmesa6 libosmesa6-dev libgles2-mesa-dev libarchive-dev libpangocairo-1.0-0
           mamba activate
-          mamba install -y -c cadquery -c conda-forge moab gmsh python-gmsh cadquery=master
+          mamba create --name cad_to_dagmc python=3.12
+          mamba activate cad_to_dagmc
+          mamba install -y -c conda-forge moab gmsh python-gmsh ocp=7.7.2.0 cadquery=2.4.0
           python -m pip install --upgrade pip 
           python -m pip install .
           python -c "import cad_to_dagmc"
-          mamba install -y -c conda-forge "openmc=0.13.3=dagmc*nompi*"
+          mamba install -y -c conda-forge "openmc=0.14.0=dagmc*nompi*"
           python -m pip install .[tests]
           pytest tests -v
           cd examples
@@ -53,7 +50,8 @@ jobs:
           python cadquery_compound.py
           python cadquery_object_and_stp_file.py
           python cadquery_text.py
-          python curved_cadquery_object.py
+          python curved_cadquery_object_to_dagmc_surface_mesh.py
+          python curved_cadquery_object_to_dagmc_volume_mesh.py
           python multiple_cadquery_objects.py
           python multiple_stp_files.py
           python single_stp_file_multiple_volumes.py

.github/workflows/ci_with_pip_install.yml

@@ -0,0 +1,57 @@
+
+name: CI with pip install
+
+on:
+  pull_request:
+    branches:
+      - main
+    paths-ignore:
+      - 'docs/**'
+      - '.gitignore'
+      - '*.md'
+      - 'CITATION.cff'
+      - 'LICENSE.txt'
+      - 'readthedocs.yml'
+  push:
+    branches:
+      - main
+
+jobs:
+  testing:
+    runs-on: ubuntu-latest
+    container:
+      image: openmc/openmc:develop-dagmc
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: install non pypi dependencies
+        shell: bash
+        run: |
+          apt-get --allow-releaseinfo-change update
+          apt-get update -y
+          apt-get upgrade -y
+          apt-get install -y libgl1-mesa-glx libgl1-mesa-dev libglu1-mesa-dev freeglut3-dev libosmesa6 libosmesa6-dev libgles2-mesa-dev libarchive-dev libpangocairo-1.0-0 libxcursor-dev libxft2 libxinerama-dev 
+          apt install python3
+          apt install python3-pip
+          python -m pip install --upgrade pip 
+          python -m pip install gmsh
+          python -m pip install cadquery-ocp==7.7.2
+          python -m pip install cadquery==2.4.0
+          python -m pip install .
+          python -c "import cad_to_dagmc"
+          python -m pip install .[tests]
+          pytest tests -v
+          cd examples
+          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 curved_cadquery_object_to_dagmc_volume_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

examples/cadquery_assembly.py

@@ -10,5 +10,5 @@
 assembly.add(result2)
 
 my_model = CadToDagmc()
-my_model.add_cadquery_object(assembly, material_tags=["mat1", "mat2"])
-my_model.export_dagmc_h5m_file(min_mesh_size=0.5, max_mesh_size=1.0)
+my_model.add_cadquery_object(assembly)
+my_model.export_dagmc_h5m_file(min_mesh_size=0.5, max_mesh_size=1.0, material_tags=["mat1", "mat2"])

examples/cadquery_compound.py

@@ -24,5 +24,5 @@
 compound_of_shapes = cq.Compound.makeCompound([cq_shape_1.val(), cq_shape_2.val()])
 
 my_model = CadToDagmc()
-my_model.add_cadquery_object(object=compound_of_shapes, material_tags=["mat1", "mat2"])
-my_model.export_dagmc_h5m_file(max_mesh_size=0.2, min_mesh_size=0.1)
+my_model.add_cadquery_object(object=compound_of_shapes)
+my_model.export_dagmc_h5m_file(max_mesh_size=0.2, min_mesh_size=0.1, material_tags=["mat1", "mat2"])

examples/cadquery_object_and_stp_file.py

@@ -4,6 +4,13 @@
 result = cq.Workplane("XY").moveTo(10, 0).box(3, 3, 0.5).edges("|Z").fillet(0.125)
 
 my_model = CadToDagmc()
-my_model.add_cadquery_object(object=result, material_tags=["mat1"])
-my_model.add_stp_file(filename="single_cube.stp", material_tags=["mat2"], scale_factor=0.1)
-my_model.export_dagmc_h5m_file(max_mesh_size=0.2, min_mesh_size=0.1)
+
+my_model.add_cadquery_object(result)
+
+my_model.add_stp_file(filename="single_cube.stp", scale_factor=0.1)
+
+my_model.export_dagmc_h5m_file(
+    max_mesh_size=0.2,
+    min_mesh_size=0.1,
+    material_tags=["mat1", "mat2"],
+)

examples/cadquery_text.py

@@ -5,8 +5,12 @@
 
 
 my_model = CadToDagmc()
-my_model.add_cadquery_object(
-    object=text,
+my_model.add_cadquery_object(object=text)
+
+my_model.export_dagmc_h5m_file(
+    filename="cadquery_text.h5m",
+    max_mesh_size=0.2,
+    min_mesh_size=0.1,
     material_tags=[
         "mat1",
         "mat2",
@@ -15,5 +19,3 @@
         "mat5",
     ],  # 5 volumes one for each letter
 )
-
-my_model.export_dagmc_h5m_file(filename="cadquery_text.h5m", max_mesh_size=0.2, min_mesh_size=0.1)

examples/curved_cadquery_object.py → examples/curved_cadquery_object_to_dagmc_surface_mesh.py

@@ -39,11 +39,11 @@ def gear(t, r1=4, r2=1):
 
 my_model = CadToDagmc()
 
-my_model.add_cadquery_object(
-    result,
-    material_tags=["mat1"],
-)
+my_model.add_cadquery_object(result)
 
 my_model.export_dagmc_h5m_file(
-    filename="cadquery_objects_and_stp_files.h5m", max_mesh_size=1, min_mesh_size=0.1
+    filename="cadquery_objects_and_stp_files.h5m",
+    max_mesh_size=1,
+    min_mesh_size=0.1,
+    material_tags=["mat1"],
 )

examples/multiple_cadquery_objects.py

@@ -7,6 +7,6 @@
 box_with_round_corners = cq.Workplane("XY").box(2, 1, 1)
 
 my_model = CadToDagmc()
-my_model.add_cadquery_object(box, material_tags=["mat1"])
-my_model.add_cadquery_object(box_with_round_corners, material_tags=["mat2"])
-my_model.export_dagmc_h5m_file()
+my_model.add_cadquery_object(box)
+my_model.add_cadquery_object(box_with_round_corners)
+my_model.export_dagmc_h5m_file(material_tags=["mat1", "mat2"])

examples/multiple_stp_files.py

@@ -1,9 +1,12 @@
 from cad_to_dagmc import CadToDagmc
 
 my_model = CadToDagmc()
-my_model.add_stp_file("two_connected_cubes.stp", material_tags=["mat1", "mat2"])
-my_model.add_stp_file("single_sphere.stp", material_tags=["mat3"])
+my_model.add_stp_file("two_connected_cubes.stp")
+my_model.add_stp_file("single_sphere.stp")
 
 my_model.export_dagmc_h5m_file(
-    max_mesh_size=1, min_mesh_size=0.5, implicit_complement_material_tag="air"
+    max_mesh_size=1,
+    min_mesh_size=0.5,
+    implicit_complement_material_tag="air",
+    material_tags=["mat1", "mat2", "mat3"],
 )

examples/single_cadquery_object.py

@@ -4,5 +4,5 @@
 result = sphere = cq.Workplane().moveTo(100, 0).sphere(5)
 
 my_model = CadToDagmc()
-my_model.add_cadquery_object(result, material_tags=["mat1"])
-my_model.export_dagmc_h5m_file()
+my_model.add_cadquery_object(result)
+my_model.export_dagmc_h5m_file(material_tags=["mat1"])

examples/single_stp_file.py

@@ -1,5 +1,5 @@
 from cad_to_dagmc import CadToDagmc
 
 my_model = CadToDagmc()
-my_model.add_stp_file("spline_extrude.stp", material_tags=["mat1"])
-my_model.export_dagmc_h5m_file()
+my_model.add_stp_file("spline_extrude.stp")
+my_model.export_dagmc_h5m_file(material_tags=["mat1"])

examples/single_stp_file_multiple_volumes.py

@@ -2,5 +2,5 @@
 
 my_model = CadToDagmc()
 # the d and c from the word dagmc would be tagged with one material and the agm are tagged with another material
-my_model.add_stp_file("text_dagmc.stp", material_tags=["mat1", "mat2", "mat2", "mat2", "mat1"])
-my_model.export_dagmc_h5m_file()
+my_model.add_stp_file("text_dagmc.stp")
+my_model.export_dagmc_h5m_file(material_tags=["mat1", "mat2", "mat2", "mat2", "mat1"])

examples/unsructured_volume_mesh/curved_cadquery_object_to_dagmc_volume_mesh.py

@@ -0,0 +1,62 @@
+from cad_to_dagmc import CadToDagmc
+import cadquery as cq
+from math import sin, cos, pi, floor
+
+
+# define the generating function
+def hypocycloid(t, r1, r2):
+    return (
+        (r1 - r2) * cos(t) + r2 * cos(r1 / r2 * t - t),
+        (r1 - r2) * sin(t) + r2 * sin(-(r1 / r2 * t - t)),
+    )
+
+
+def epicycloid(t, r1, r2):
+    return (
+        (r1 + r2) * cos(t) - r2 * cos(r1 / r2 * t + t),
+        (r1 + r2) * sin(t) - r2 * sin(r1 / r2 * t + t),
+    )
+
+
+def gear(t, r1=4, r2=1):
+    if (-1) ** (1 + floor(t / 2 / pi * (r1 / r2))) < 0:
+        return epicycloid(t, r1, r2)
+    else:
+        return hypocycloid(t, r1, r2)
+
+
+# create the gear profile and extrude it
+result = (
+    cq.Workplane("XY")
+    .parametricCurve(lambda t: gear(t * 2 * pi, 6, 1))
+    .twistExtrude(15, 90)
+    .faces(">Z")
+    .workplane()
+    .circle(2)
+    .cutThruAll()
+)
+assembly = cq.Assembly()
+assembly.add(result)
+assembly.save("twist.step")
+
+s = cq.Workplane("XY")
+sPnts = [
+    (2.75, 1.5),
+    (2.5, 1.75),
+    (2.0, 1.5),
+    (1.5, 1.0),
+    (1.0, 1.25),
+    (0.5, 1.0),
+    (0, 1.0),
+]
+r = s.lineTo(3.0, 0).lineTo(3.0, 1.0).spline(sPnts, includeCurrent=True).close()
+result2 = r.extrude(-20)
+assembly.add(result2)
+assembly.save("twist_and_extrude.step")
+
+my_model = CadToDagmc()
+
+my_model.add_cadquery_object(result)
+my_model.add_cadquery_object(result2)
+
+my_model.export_unstructured_mesh_file(filename="umesh.h5m", max_mesh_size=1, min_mesh_size=0.1)

examples/unsructured_volume_mesh/simulate_unstrucutred_volume_mesh_with_openmc.py

@@ -0,0 +1,66 @@
+# script assumes that "umesh.h5m" has been created by
+# curved_cadquery_object_to_dagmc_volume_mesh.py has been
+
+import openmc
+
+umesh = openmc.UnstructuredMesh("umesh.h5m", library="moab")
+mesh_filter = openmc.MeshFilter(umesh)
+tally = openmc.Tally(name="t1")
+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)
+my_materials = openmc.Materials([mat1])
+
+surf1 = openmc.Sphere(r=500, boundary_type="vacuum")
+region1 = -surf1
+
+cell1 = openmc.Cell(region=region1)
+cell1.fill = mat1
+
+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.space = openmc.stats.Point((0, 0, 0))
+my_source.angle = openmc.stats.Isotropic()
+my_source.energy = openmc.stats.Discrete([14e6], [1])
+my_settings.source = my_source
+
+model = openmc.model.Model(my_geometry, my_materials, my_settings, my_tallies)
+sp_filename = model.run()
+
+sp = openmc.StatePoint(sp_filename)
+
+tally_result = sp.get_tally(name="t1")
+
+
+# umesh = tally_result.find_filter(openmc.MeshFilter)
+umesh_from_sp = sp.meshes[1]
+
+centroids = umesh_from_sp.centroids
+mesh_vols = umesh_from_sp.volumes
+
+flux_mean = tally_result.get_values(scores=["flux"], value="mean").reshape(umesh_from_sp.dimension)
+umesh_from_sp.write_data_to_vtk(filename="tally.vtk", datasets={"mean": flux_mean})