cad-to-dagmc 0.8.2__tar.gz → 0.9.1__tar.gz

{cad_to_dagmc-0.8.2 → cad_to_dagmc-0.9.1}/.github/workflows/ci_with_benchmarks.yml

@@ -19,32 +19,47 @@ on:
 jobs:
   testing:
     runs-on: ubuntu-latest
+
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: install dependencies and run CSG / DAMGC benchmarks
-        env:
-          OPENMC_CROSS_SECTIONS: /home/runner/work/cad_to_dagmc/cad_to_dagmc/cross_sections.xml
-        shell: bash
+      - name: Install system packages
         run: |
-          wget -O Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
-          bash Miniforge3.sh -b -p "${HOME}/conda"
-          source "${HOME}/conda/etc/profile.d/conda.sh"
-          source "${HOME}/conda/etc/profile.d/mamba.sh"
-          sudo apt-get --allow-releaseinfo-change update
           sudo apt-get update -y
           sudo apt-get upgrade -y
           sudo apt-get install -y libgl1 libglx-mesa0 libgl1-mesa-dev libglu1-mesa-dev freeglut3-dev libosmesa6 libosmesa6-dev libgles2-mesa-dev libarchive-dev libpangocairo-1.0-0
-          mamba activate
-          mamba install -y -c conda-forge "openmc=0.15.0=dagmc*nompi*" trimesh networkx cadquery gmsh python-gmsh
+
+      - name: Set up Miniforge
+        run: |
+          wget -O Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-$(uname -m).sh"
+          bash Miniforge3.sh -b -p "${HOME}/miniforge"
+          source "${HOME}/miniforge/etc/profile.d/conda.sh"
+          conda init bash
+          conda config --set always_yes yes --set changeps1 no
+          conda update -q conda
+
+      - name: Create and activate Conda environment
+        run: |
+          source "${HOME}/miniforge/etc/profile.d/conda.sh"
+          conda create -n ci-env python=3.11
+          conda activate ci-env
+          conda install -c conda-forge "openmc=0.15.0=dagmc*nompi*" trimesh networkx cadquery gmsh python-gmsh vtk
+          python -m pip install .[tests]
+          python -m pip install git+https://github.com/svalinn/pydagmc
+
+      - name: Run tests
+        shell: bash -l {0}
+        env:
+          OPENMC_CROSS_SECTIONS: /home/runner/work/cad_to_dagmc/cad_to_dagmc/cross_sections.xml
+        run: |
+          source "${HOME}/miniforge/etc/profile.d/conda.sh"
+          conda activate ci-env
           python -m ensurepip --upgrade
           python -m pip install . --no-deps
           python -m pip install openmc_data_downloader
-          openmc_data_downloader -l ENDFB-7.1-NNDC -i Fe56 Be9
+          openmc_data_downloader -l ENDFB-7.1-NNDC -i Fe56 Be9 Al27
           git clone --single-branch -b main --depth 1 https://github.com/fusion-energy/model_benchmark_zoo.git
           cd model_benchmark_zoo
           python -m pip install .[tests]
-          conda env export > environment.yml
-          cat environment.yml
           pytest tests/test_cad_to_dagmc -v

{cad_to_dagmc-0.8.2 → cad_to_dagmc-0.9.1}/.github/workflows/ci_with_conda_install.yml

@@ -31,33 +31,43 @@ jobs:
           sudo apt-get update -y
           sudo apt-get upgrade -y
           sudo apt-get install -y libgl1 libglx-mesa0 libgl1-mesa-dev libglu1-mesa-dev freeglut3-dev libosmesa6 libosmesa6-dev libgles2-mesa-dev libarchive-dev libpangocairo-1.0-0
+      - name: Set up Miniforge
+        run: |
+          wget -O Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-$(uname -m).sh"
+          bash Miniforge3.sh -b -p "${HOME}/miniforge"
+          source "${HOME}/miniforge/etc/profile.d/conda.sh"
+          conda init bash
+          conda config --set always_yes yes --set changeps1 no
+          conda update -q conda
 
-      - name: Set up Conda
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          activate-environment: ci-env
-          miniforge-version: latest
-          channels: conda-forge
-
-      - name: install dependencies
-        shell: bash -l {0}
+      - name: Create and activate Conda environment
         run: |
-          conda install -y -c conda-forge "openmc=0.15.0=dagmc*nompi*" trimesh networkx cadquery gmsh python-gmsh vtk
+          source "${HOME}/miniforge/etc/profile.d/conda.sh"
+          conda create -n ci-env python=3.11
+          conda activate ci-env
+          conda install -c conda-forge "openmc=0.15.0=dagmc*nompi*" trimesh networkx cadquery gmsh python-gmsh vtk
           python -m pip install .[tests]
-
+          python -m pip install git+https://github.com/svalinn/pydagmc
+  
       - name: Test import
         shell: bash -l {0}
         run: |
+          source "${HOME}/miniforge/etc/profile.d/conda.sh"
+          conda activate ci-env
           python -c "import cad_to_dagmc"
 
       - name: Run tests
         shell: bash -l {0}
         run: |
+          source "${HOME}/miniforge/etc/profile.d/conda.sh"
+          conda activate ci-env
           pytest -v tests
 
       - name: Run examples
         shell: bash -l {0}
         run: |
+          source "${HOME}/miniforge/etc/profile.d/conda.sh"
+          conda activate ci-env
           python examples/surface_mesh/cadquery_assembly.py
           python examples/surface_mesh/cadquery_assembly_with_scaled_geometry.py
           python examples/surface_mesh/cadquery_compound.py
@@ -65,6 +75,8 @@ jobs:
           python examples/surface_mesh/cadquery_text.py
           python examples/surface_mesh/curved_cadquery_object_to_dagmc_surface_mesh.py
           python examples/surface_mesh/from_gmsh_mesh_file.py
+          python examples/surface_mesh/from_gmsh_mesh_file_with_tags.py
+          python examples/surface_mesh/from_gmsh_object_with_tag.py
           python examples/surface_mesh/multiple_cadquery_objects.py
           python examples/surface_mesh/multiple_stp_files.py
           python examples/surface_mesh/single_cadquery_object.py

{cad_to_dagmc-0.8.2 → cad_to_dagmc-0.9.1}/.github/workflows/ci_with_pip_install.yml

@@ -43,6 +43,7 @@ jobs:
           cd ..
           python -c "import pymoab"
           python -m pip install .[tests]
+          python -m pip install git+https://github.com/svalinn/pydagmc
           python -c "import cad_to_dagmc"
           pytest -v tests
           python examples/surface_mesh/cadquery_assembly.py
@@ -56,6 +57,8 @@ jobs:
           python examples/surface_mesh/single_cadquery_object.py
           python examples/surface_mesh/single_stp_file.py
           python examples/surface_mesh/from_gmsh_mesh_file.py
+          python examples/surface_mesh/from_gmsh_mesh_file_with_tags.py
+          python examples/surface_mesh/from_gmsh_object_with_tag.py
           python examples/unstrucutred_volume_mesh/curved_cadquery_object_to_dagmc_volume_mesh.py
           python examples/unstrucutred_volume_mesh/simulate_unstrucutred_volume_mesh_with_openmc.py
           python examples/unstrucutred_volume_mesh/different_resolution_meshes.py

{cad_to_dagmc-0.8.2 → cad_to_dagmc-0.9.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: cad_to_dagmc
-Version: 0.8.2
+Version: 0.9.1
 Summary: Converts CAD files to a DAGMC h5m file
 Author-email: Jonathan Shimwell <mail@jshimwell.com>
 Project-URL: Homepage, https://github.com/fusion-energy/cad_to_dagmc
@@ -20,6 +20,8 @@ Requires-Dist: gmsh
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: vtk; extra == "tests"
+Requires-Dist: assembly-mesh-plugin; extra == "tests"
+Dynamic: license-file
 
 
 [![N|Python](https://www.python.org/static/community_logos/python-powered-w-100x40.png)](https://www.python.org)
@@ -43,13 +45,17 @@ cad-to-dagmc can create DAGMC compatible:
 
 cad-to-dagmc can convert the following in to DAGMC compatible meshes:
 - STEP files
-- CadQuery objects (in memory)
-- Gmsh meshes
+- CadQuery objects (optionally use names as material tags)
+- Gmsh meshes (optionally use physical groups as material tags)
 
 Cad-to-dagmc offers a wide range of features including.
+- Compatibly with [assembly-mesh-plugin](https://github.com/CadQuery/assembly-mesh-plugin) (see examples)
+- Access to the Gmsh mesh to allow user to define full set of mesh parameters
+- Option to use Gmsh physical groups as material tags
 - Geometry scaling with ```scale_factor``` argument
 - Model wide mesh size parameters with ```min_mesh_size``` and ```max_mesh_size``` arguments
 - Volume specific mesh sizing parameters with the ```set_size``` argument
+- Volume mesh selected volumes in the geometry (helps ensure conformal volume and surface mesh).
 - Parallel meshing to quickly mesh the geometry using multiple CPU cores
 - Imprint and merging of CAD geometry, or disable with the ```imprint``` argument
 - Add geometry from multiple sources ([STEP](http://www.steptools.com/stds/step/) files, [CadQuery](https://cadquery.readthedocs.io) objects and [Gmsh](https://gmsh.info/) meshes)
@@ -125,21 +131,10 @@ First ensure hdf5 is installed as this is needed by MOAB pip install command
 sudo apt-get install libhdf5-dev
 ```
 
-Then clone the latest version of MOAB and cd into the moab directory.
+Then install MOAB, currently available from the repo.
 
 ```
-git clone  master https://bitbucket.org/fathomteam/moab/
-cd moab
-```
-
-Ensure pip is up to date as a new version is needed
-```
-python -m pip install --upgrade pip
-```
-
-Run the pip install command with cmake arguments.
-```
-pip install . --config-settings=cmake.args=-DENABLE_HDF5=ON
+pip install git+https://bitbucket.org/fathomteam/moab/
 ```
 
 Then you can install the cad_to_dagmc package with ```pip```

{cad_to_dagmc-0.8.2 → cad_to_dagmc-0.9.1}/README.md

@@ -20,13 +20,17 @@ cad-to-dagmc can create DAGMC compatible:
 
 cad-to-dagmc can convert the following in to DAGMC compatible meshes:
 - STEP files
-- CadQuery objects (in memory)
-- Gmsh meshes
+- CadQuery objects (optionally use names as material tags)
+- Gmsh meshes (optionally use physical groups as material tags)
 
 Cad-to-dagmc offers a wide range of features including.
+- Compatibly with [assembly-mesh-plugin](https://github.com/CadQuery/assembly-mesh-plugin) (see examples)
+- Access to the Gmsh mesh to allow user to define full set of mesh parameters
+- Option to use Gmsh physical groups as material tags
 - Geometry scaling with ```scale_factor``` argument
 - Model wide mesh size parameters with ```min_mesh_size``` and ```max_mesh_size``` arguments
 - Volume specific mesh sizing parameters with the ```set_size``` argument
+- Volume mesh selected volumes in the geometry (helps ensure conformal volume and surface mesh).
 - Parallel meshing to quickly mesh the geometry using multiple CPU cores
 - Imprint and merging of CAD geometry, or disable with the ```imprint``` argument
 - Add geometry from multiple sources ([STEP](http://www.steptools.com/stds/step/) files, [CadQuery](https://cadquery.readthedocs.io) objects and [Gmsh](https://gmsh.info/) meshes)
@@ -102,21 +106,10 @@ First ensure hdf5 is installed as this is needed by MOAB pip install command
 sudo apt-get install libhdf5-dev
 ```
 
-Then clone the latest version of MOAB and cd into the moab directory.
+Then install MOAB, currently available from the repo.
 
 ```
-git clone  master https://bitbucket.org/fathomteam/moab/
-cd moab
-```
-
-Ensure pip is up to date as a new version is needed
-```
-python -m pip install --upgrade pip
-```
-
-Run the pip install command with cmake arguments.
-```
-pip install . --config-settings=cmake.args=-DENABLE_HDF5=ON
+pip install git+https://bitbucket.org/fathomteam/moab/
 ```
 
 Then you can install the cad_to_dagmc package with ```pip```

cad_to_dagmc-0.9.1/examples/surface_and_unstructured_mesh/unstructured_mesh_with_conformal_surface_mesh.py

@@ -0,0 +1,107 @@
+# This example makes 3 CAD half spheres
+# Meshes the 3 volumes with different resolutions
+# exports the mesh to a DAGMC unstructured VTK file and a DAGMC h5m file
+# The outer surface of the volume mesh should match the surface of the surface
+# mesh as the same mesh parameters were used in both the surface and volume mesh.
+# Additionally only volume 2 is volume meshed, while all three volumes are surface meshed
+
+
+import cadquery as cq
+from cad_to_dagmc import CadToDagmc
+
+box_cutter = cq.Workplane("XY").moveTo(0, 5).box(20, 10, 20)
+inner_sphere = cq.Workplane("XY").sphere(6).cut(box_cutter)
+middle_sphere = cq.Workplane("XY").sphere(6.1).cut(box_cutter).cut(inner_sphere)
+outer_sphere = cq.Workplane("XY").sphere(10).cut(box_cutter).cut(inner_sphere).cut(middle_sphere)
+
+assembly = cq.Assembly()
+assembly.add(inner_sphere, name="inner_sphere")
+assembly.add(middle_sphere, name="middle_sphere")
+assembly.add(outer_sphere, name="outer_sphere")
+
+
+model = CadToDagmc()
+model.add_cadquery_object(assembly, material_tags=["mat1", "mat2", "mat3"])
+
+
+h5m_file = model.export_dagmc_h5m_file(
+    filename="different_resolution_meshes.h5m",
+    set_size={1: 0.9, 2: 0.1, 3: 0.9},
+)
+
+vtk_file = model.export_unstructured_mesh_file(
+    filename="umesh.vtk",
+    set_size={1: 0.9, 2: 0.1, 3: 0.9},
+    volumes=[2],  # only mesh volume 2 out of the three volumes
+)
+
+
+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(vtk_file, library="moab")
+mesh_filter = openmc.MeshFilter(umesh)
+tally = openmc.Tally(name="unstructured_mesh_tally")
+tally.filters = [mesh_filter]
+tally.scores = ["flux"]
+my_tallies = openmc.Tallies([tally])
+
+
+mat1 = openmc.Material(name="mat1")
+mat1.add_nuclide("H1", 1, percent_type="ao")
+mat1.set_density("g/cm3", 0.001)
+mat2 = openmc.Material(name="mat2")
+mat2.add_nuclide("H1", 1, percent_type="ao")
+mat2.set_density("g/cm3", 0.002)
+mat3 = openmc.Material(name="mat3")
+mat3.add_nuclide("H1", 1, percent_type="ao")
+mat3.set_density("g/cm3", 0.003)
+my_materials = openmc.Materials([mat1, mat2, mat3])
+
+dag_univ = openmc.DAGMCUniverse(filename=h5m_file)
+bound_dag_univ = dag_univ.bounded_universe()
+my_geometry = openmc.Geometry(root=bound_dag_univ)
+
+
+my_settings = openmc.Settings()
+my_settings.batches = 10
+my_settings.particles = 5000
+my_settings.run_mode = "fixed source"
+
+# Create a DT point source
+my_source = openmc.IndependentSource()
+my_source.space = openmc.stats.Point(my_geometry.bounding_box.center)
+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="unstructured_mesh_tally")
+
+# normally with regular meshes I would get the mesh from the tally
+# but with unstructured 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
+
+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})

{cad_to_dagmc-0.8.2 → cad_to_dagmc-0.9.1}/examples/surface_mesh/from_gmsh_mesh_file.py

@@ -1,11 +1,12 @@
 # this file makes a GMESH mesh file from a Step file
 # then loads up the GMESH file and converts it to a DAGMC file
 
-
-# making the GMESH file
 from cad_to_dagmc import CadToDagmc
 import cadquery as cq
+import cad_to_dagmc
+import openmc
 
+# making the gmsh file just so we have one for the example
 result1 = cq.Workplane("XY").box(10.0, 10.0, 5.0)
 result2 = cq.Workplane("XY").moveTo(10, 0).box(10.0, 10.0, 5.0)
 assembly = cq.Assembly()
@@ -17,18 +18,15 @@ geometry = CadToDagmc()
 geometry.add_stp_file("two_connected_cubes.stp")
 geometry.export_gmsh_mesh_file(filename="example_gmsh_mesh.msh")
 
-# converting the mesh file to a DAGMC file
-from cad_to_dagmc import MeshToDagmc
 
-mesh = MeshToDagmc(filename="example_gmsh_mesh.msh")
+# converting the mesh file to a DAGMC file
 
-mesh.export_dagmc_h5m_file(
+cad_to_dagmc.export_gmsh_file_to_dagmc_h5m_file(
+    gmsh_filename="example_gmsh_mesh.msh",
     material_tags=["mat1", "mat2"],
-    filename="dagmc.h5m",
+    dagmc_filename="dagmc.h5m",
 )
 
-# making use of the DAGMC file in OpenMC
-import openmc
 
 openmc.config["cross_sections"] = "cross_sections.xml"
 

cad_to_dagmc-0.9.1/examples/surface_mesh/from_gmsh_mesh_file_with_tags.py

@@ -0,0 +1,44 @@
+# this file makes a GMESH mesh file that contains 3D physical groups.
+# these groups are then used as the material tags in the DAGMC file.
+
+
+# making the GMESH file
+import cad_to_dagmc
+import openmc
+
+
+# converting the mesh file to a DAGMC file
+
+cad_to_dagmc.export_gmsh_file_to_dagmc_h5m_file(
+    gmsh_filename="examples/surface_mesh/tagged_mesh.msh",
+    # no need to specify material tags as the mesh file already has physical
+    # groups which are used as material tags
+    # material_tags=["shell", "insert"],
+    dagmc_filename="dagmc.h5m",
+)
+
+# making use of the DAGMC file in OpenMC
+
+openmc.config["cross_sections"] = "cross_sections.xml"
+
+mat1 = openmc.Material(name="shell")
+mat1.add_nuclide("H1", 1, percent_type="ao")
+mat1.set_density("g/cm3", 0.001)
+
+mat2 = openmc.Material(name="insert")
+mat2.add_nuclide("H1", 1, percent_type="ao")
+mat2.set_density("g/cm3", 0.002)
+
+materials = openmc.Materials([mat1, mat2])
+
+universe = openmc.DAGMCUniverse("dagmc.h5m").bounded_universe()
+geometry = openmc.Geometry(universe)
+
+my_settings = openmc.Settings()
+my_settings.batches = 10
+my_settings.inactive = 0
+my_settings.particles = 500
+my_settings.run_mode = "fixed source"
+
+model = openmc.Model(geometry=geometry, materials=materials, settings=my_settings)
+model.run()

cad_to_dagmc-0.9.1/examples/surface_mesh/from_gmsh_object_with_tag.py

@@ -0,0 +1,26 @@
+import cadquery as cq
+import cad_to_dagmc
+import gmsh
+import assembly_mesh_plugin
+
+box_shape1 = cq.Workplane("XY").box(50, 50, 50)
+box_shape2 = cq.Workplane("XY").moveTo(0, 50).box(50, 50, 100)
+
+assembly = cq.Assembly()
+assembly.add(box_shape1, name="first_material")
+assembly.add(box_shape2, name="second_material")
+
+# getTaggedGmsh initializes gmsh and creates a mesh object ready for meshing
+assembly.getTaggedGmsh()
+# Here you can set the mesh parameters
+# In this case, we set the minimum and maximum mesh size
+# but you can set any other Gmsh parameters
+# Remember that the gmsh has physical groups if you want to use them when meshing
+gmsh.option.setNumber("Mesh.MeshSizeMax", 4.2)
+gmsh.model.mesh.generate(2)  # for DAGMC surface mesh we just need a 2D surface mesh
+
+cad_to_dagmc.export_gmsh_object_to_dagmc_h5m_file(filename="dagmc_from_gmsh_object.h5m")
+
+# finalize the GMSH API after using export_gmsh_object_to_dagmc_h5m_file
+# and getTaggedGmsh as these both need access to the GMSH object.
+gmsh.finalize()