cad-to-dagmc 0.9.0__tar.gz → 0.9.2__tar.gz

{cad_to_dagmc-0.9.0 → cad_to_dagmc-0.9.2}/.github/workflows/ci_with_benchmarks.yml

@@ -19,25 +19,42 @@ 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
@@ -45,7 +62,4 @@ jobs:
           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]
-          pip install git+https://github.com/svalinn/pydagmc
-          conda env export > environment.yml
-          cat environment.yml
           pytest tests/test_cad_to_dagmc -v

{cad_to_dagmc-0.9.0 → cad_to_dagmc-0.9.2}/.github/workflows/ci_with_conda_install.yml

@@ -31,34 +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
@@ -78,3 +87,4 @@ jobs:
           python examples/unstrucutred_volume_mesh/different_resolution_meshes.py
           python examples/surface_mesh/different_resolution_meshes.py
           python examples/surface_mesh/cadquery_assembly_with_scaled_geometry.py
+          python examples/surface_and_unstructured_mesh/unstructured_mesh_with_conformal_surface_mesh.py

{cad_to_dagmc-0.9.0 → cad_to_dagmc-0.9.2}/.github/workflows/ci_with_pip_install.yml

@@ -63,4 +63,5 @@ jobs:
           python examples/unstrucutred_volume_mesh/simulate_unstrucutred_volume_mesh_with_openmc.py
           python examples/unstrucutred_volume_mesh/different_resolution_meshes.py
           python examples/surface_mesh/different_resolution_meshes.py
-          python examples/surface_mesh/cadquery_assembly_with_scaled_geometry.py
+          python examples/surface_mesh/cadquery_assembly_with_scaled_geometry.py
+          python examples/surface_and_unstructured_mesh/unstructured_mesh_with_conformal_surface_mesh.py

{cad_to_dagmc-0.9.0 → cad_to_dagmc-0.9.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cad_to_dagmc
-Version: 0.9.0
+Version: 0.9.2
 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
@@ -55,6 +55,8 @@ Cad-to-dagmc offers a wide range of features including.
 - 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
+- Unstructured mesh that share the same coordinates as the surface mesh.
+- Volume mesh allows selecting individual volumes in the geometry.
 - 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)
@@ -130,21 +132,10 @@ 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-0.9.0 → cad_to_dagmc-0.9.2}/README.md

@@ -30,6 +30,8 @@ Cad-to-dagmc offers a wide range of features including.
 - 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
+- Unstructured mesh that share the same coordinates as the surface mesh.
+- Volume mesh allows selecting individual volumes in the geometry.
 - 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)
@@ -105,21 +107,10 @@ 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-0.9.2/examples/surface_and_unstructured_mesh/unstructured_mesh_with_conformal_surface_mesh.py

@@ -0,0 +1,104 @@
+# 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
+import openmc
+
+
+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"])
+
+dagmc_filename, umesh_filename = model.export_dagmc_h5m_file(
+    filename="surface_mesh_conformal.h5m",
+    set_size={
+        1: 0.9,
+        2: 0.1,
+        3: 0.9,
+    },
+    unstructured_volumes=[2],
+    umesh_filename="volume_mesh_conformal.vtk",  #
+)
+
+
+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_filename, 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=dagmc_filename)
+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-0.9.0 → cad_to_dagmc-0.9.2}/examples/surface_mesh/from_gmsh_object_with_tag.py

@@ -1,7 +1,7 @@
 import cadquery as cq
 import cad_to_dagmc
 import gmsh
-import assembly_mesh_plugin.plugin
+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)

{cad_to_dagmc-0.9.0 → cad_to_dagmc-0.9.2}/src/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.9.0'
-__version_tuple__ = version_tuple = (0, 9, 0)
+__version__ = version = '0.9.2'
+__version_tuple__ = version_tuple = (0, 9, 2)

{cad_to_dagmc-0.9.0 → cad_to_dagmc-0.9.2}/src/cad_to_dagmc/core.py

@@ -1,4 +1,5 @@
 from pathlib import Path
+from typing import Iterable
 import cadquery as cq
 import gmsh
 import numpy as np
@@ -6,6 +7,7 @@ from cadquery import importers
 from pymoab import core, types
 import tempfile
 import warnings
+from typing import Iterable
 from cad_to_dagmc import __version__
 
 
@@ -234,15 +236,14 @@ def init_gmsh():
     return gmsh
 
 
-def mesh_brep(
+def set_sizes_for_mesh(
     gmsh,
     min_mesh_size: float | None = None,
     max_mesh_size: float | None = None,
     mesh_algorithm: int = 1,
-    dimensions: int = 2,
     set_size: dict[int, float] | None = None,
 ):
-    """Creates a conformal surface meshes of the volumes in a Brep file using Gmsh.
+    """Sets up the mesh sizes for each volume in the mesh.
 
     Args:
         occ_shape: the occ_shape of the Brep file to convert
@@ -252,8 +253,6 @@ def mesh_brep(
             into gmsh.option.setNumber("Mesh.MeshSizeMax", max_mesh_size)
         mesh_algorithm: The Gmsh mesh algorithm number to use. Passed into
             gmsh.option.setNumber("Mesh.Algorithm", mesh_algorithm)
-        dimensions: The number of dimensions, 2 for a surface mesh 3 for a
-            volume mesh. Passed to gmsh.model.mesh.generate()
         set_size: a dictionary of volume ids (int) and target mesh sizes
             (floats) to set for each volume, passed to gmsh.model.mesh.setSize.
 
@@ -279,25 +278,42 @@ def mesh_brep(
         volumes = gmsh.model.getEntities(3)
         available_volumes = [volume[1] for volume in volumes]
         print("volumes", volumes)
-        for volume_id, size in set_size.items():
-            if volume_id in available_volumes:
-                size = set_size[volume_id]
-                if isinstance(size, dict):
-                    # TODO face specific mesh sizes
-                    pass
-                else:
-                    boundaries = gmsh.model.getBoundary(
-                        [(3, volume_id)], recursive=True
-                    )  # dim must be set to 3
-                    print("boundaries", boundaries)
-                    gmsh.model.mesh.setSize(boundaries, size)
-                    print(f"Set size of {size} for volume {volume_id}")
-            else:
+
+        # Ensure all volume IDs in set_size exist in the available volumes
+        for volume_id in set_size.keys():
+            if volume_id not in available_volumes:
                 raise ValueError(
                     f"volume ID of {volume_id} set in set_sizes but not found in available volumes {volumes}"
                 )
 
-    gmsh.model.mesh.generate(dimensions)
+        # Step 1: Preprocess boundaries to find shared surfaces and decide mesh sizes
+        boundary_sizes = {}  # Dictionary to store the mesh size and count for each boundary
+        for volume_id, size in set_size.items():
+            boundaries = gmsh.model.getBoundary(
+                [(3, volume_id)], recursive=True
+            )  # dim must be set to 3
+            print(f"Boundaries for volume {volume_id}: {boundaries}")
+
+            for boundary in boundaries:
+                boundary_key = (boundary[0], boundary[1])  # (dimension, tag)
+                if boundary_key in boundary_sizes:
+                    # If the boundary is already processed, add the size to the list
+                    boundary_sizes[boundary_key]["total_size"] += size
+                    boundary_sizes[boundary_key]["count"] += 1
+                else:
+                    # Otherwise, initialize the boundary with the current size
+                    boundary_sizes[boundary_key] = {"total_size": size, "count": 1}
+
+        # Step 2: Calculate the average size for each boundary
+        averaged_boundary_sizes = {
+            boundary: data["total_size"] / data["count"]
+            for boundary, data in boundary_sizes.items()
+        }
+
+        # Step 3: Apply mesh sizes to all boundaries
+        for boundary, size in averaged_boundary_sizes.items():
+            gmsh.model.mesh.setSize([boundary], size)
+            print(f"Set mesh size {size} for boundary {boundary}")
 
     return gmsh
 
@@ -615,11 +631,13 @@ class CadToDagmc:
         scale_factor: float = 1.0,
         imprint: bool = True,
         set_size: dict[int, float] | None = None,
+        volumes: Iterable[int] | None = None,
     ):
         """
-        Exports an unstructured mesh file in VTK format for use with openmc.UnstructuredMesh.
-        Compatible with the MOAB unstructured mesh library. Example useage
-        openmc.UnstructuredMesh(filename="umesh.vtk", library="moab")
+        Exports an unstructured mesh file in VTK format for use with
+        openmc.UnstructuredMesh. Compatible with the MOAB unstructured mesh
+        library. Example useage openmc.UnstructuredMesh(filename="umesh.vtk",
+        library="moab").
 
         Parameters:
         -----------
@@ -648,6 +666,8 @@ class CadToDagmc:
                 and this can save time.
             set_size: a dictionary of volume ids (int) and target mesh sizes
                 (floats) to set for each volume, passed to gmsh.model.mesh.setSize.
+            volumes: a list of volume ids (int) to include in the mesh. If left
+                as default (None) then all volumes will be included.
 
 
         Returns:
@@ -672,17 +692,30 @@ class CadToDagmc:
 
         gmsh = init_gmsh()
 
-        gmsh, _ = get_volumes(gmsh, imprinted_assembly, method=method, scale_factor=scale_factor)
+        gmsh, volumes_in_model = get_volumes(
+            gmsh, imprinted_assembly, method=method, scale_factor=scale_factor
+        )
 
-        gmsh = mesh_brep(
+        gmsh = set_sizes_for_mesh(
             gmsh=gmsh,
             min_mesh_size=min_mesh_size,
             max_mesh_size=max_mesh_size,
             mesh_algorithm=mesh_algorithm,
-            dimensions=3,
             set_size=set_size,
         )
 
+        if volumes:
+            for volume_id in volumes_in_model:
+                if volume_id[1] not in volumes:
+                    gmsh.model.occ.remove([volume_id], recursive=True)
+            gmsh.option.setNumber("Mesh.SaveAll", 1)
+            gmsh.model.occ.synchronize()
+            # Clear the mesh
+            gmsh.model.mesh.clear()
+            gmsh.option.setNumber("Mesh.SaveElementTagType", 3)  # Save only volume elements
+
+        gmsh.model.mesh.generate(3)
+
         # makes the folder if it does not exist
         if Path(filename).parent:
             Path(filename).parent.mkdir(parents=True, exist_ok=True)
@@ -695,7 +728,7 @@ class CadToDagmc:
 
         gmsh.finalize()
 
-        return gmsh
+        return filename
 
     def export_gmsh_mesh_file(
         self,
@@ -751,15 +784,16 @@ class CadToDagmc:
 
         gmsh, _ = get_volumes(gmsh, imprinted_assembly, method=method, scale_factor=scale_factor)
 
-        gmsh = mesh_brep(
+        gmsh = set_sizes_for_mesh(
             gmsh=gmsh,
             min_mesh_size=min_mesh_size,
             max_mesh_size=max_mesh_size,
             mesh_algorithm=mesh_algorithm,
-            dimensions=dimensions,
             set_size=set_size,
         )
 
+        gmsh.model.mesh.generate(dimensions)
+
         # makes the folder if it does not exist
         if Path(filename).parent:
             Path(filename).parent.mkdir(parents=True, exist_ok=True)
@@ -785,6 +819,8 @@ class CadToDagmc:
         scale_factor: float = 1.0,
         imprint: bool = True,
         set_size: dict[int, float] | None = None,
+        unstructured_volumes: Iterable[int] | None = None,
+        umesh_filename: str = "umesh.vtk",
     ) -> str:
         """Saves a DAGMC h5m file of the geometry
 
@@ -813,9 +849,13 @@ class CadToDagmc:
                 and this can save time.
             set_size: a dictionary of volume ids (int) and target mesh sizes
                 (floats) to set for each volume, passed to gmsh.model.mesh.setSize.
+            unstructured_volumes: a list of volume ids to be saved in as an
+                unstructured mesh file.
+            umesh_filename: the filename to use for the optional unstructured
+                mesh file. Only used if unstructured_volumes is not empty.
 
         Returns:
-            str: the DAGMC filename saved
+            str: the filenames(s) for the files created.
         """
 
         assembly = cq.Assembly()
@@ -852,7 +892,7 @@ class CadToDagmc:
             gmsh, imprinted_assembly, method=method, scale_factor=scale_factor
         )
 
-        gmsh = mesh_brep(
+        gmsh = set_sizes_for_mesh(
             gmsh=gmsh,
             min_mesh_size=min_mesh_size,
             max_mesh_size=max_mesh_size,
@@ -860,19 +900,39 @@ class CadToDagmc:
             set_size=set_size,
         )
 
-        dims_and_vol_ids = volumes
+        gmsh.model.mesh.generate(2)
 
         vertices, triangles_by_solid_by_face = mesh_to_vertices_and_triangles(
-            dims_and_vol_ids=dims_and_vol_ids
+            dims_and_vol_ids=volumes
         )
 
-        gmsh.finalize()
-
-        # checks and fixes triangle fix_normals within vertices_to_h5m
-        return vertices_to_h5m(
+        dagmc_filename = vertices_to_h5m(
             vertices=vertices,
             triangles_by_solid_by_face=triangles_by_solid_by_face,
             material_tags=material_tags_in_brep_order,
             h5m_filename=filename,
             implicit_complement_material_tag=implicit_complement_material_tag,
         )
+
+        if unstructured_volumes:
+            # remove all the unused occ volumes, this prevents them being meshed
+            for volume_dim, volume_id in volumes:
+                if volume_id not in unstructured_volumes:
+                    gmsh.model.occ.remove([(volume_dim, volume_id)], recursive=True)
+            gmsh.option.setNumber("Mesh.SaveAll", 1)
+            gmsh.model.occ.synchronize()
+
+            # removes all the 2D groups so that 2D faces are not included in the vtk file
+            all_2d_groups = gmsh.model.getPhysicalGroups(2)
+            for entry in all_2d_groups:
+                gmsh.model.removePhysicalGroups([entry])
+
+            gmsh.model.mesh.generate(3)
+            gmsh.option.setNumber("Mesh.SaveElementTagType", 3)  # Save only volume elements
+            gmsh.write(umesh_filename)
+
+            gmsh.finalize()
+
+            return dagmc_filename, umesh_filename
+        else:
+            return dagmc_filename

{cad_to_dagmc-0.9.0 → cad_to_dagmc-0.9.2}/src/cad_to_dagmc.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cad_to_dagmc
-Version: 0.9.0
+Version: 0.9.2
 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
@@ -55,6 +55,8 @@ Cad-to-dagmc offers a wide range of features including.
 - 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
+- Unstructured mesh that share the same coordinates as the surface mesh.
+- Volume mesh allows selecting individual volumes in the geometry.
 - 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)
@@ -130,21 +132,10 @@ 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-0.9.0 → cad_to_dagmc-0.9.2}/src/cad_to_dagmc.egg-info/SOURCES.txt

@@ -8,6 +8,7 @@ pyproject.toml
 .github/workflows/ci_with_conda_install.yml
 .github/workflows/ci_with_pip_install.yml
 .github/workflows/python-publish.yml
+examples/surface_and_unstructured_mesh/unstructured_mesh_with_conformal_surface_mesh.py
 examples/surface_mesh/cadquery_assembly.py
 examples/surface_mesh/cadquery_assembly_with_scaled_geometry.py
 examples/surface_mesh/cadquery_compound.py

{cad_to_dagmc-0.9.0 → cad_to_dagmc-0.9.2}/tests/test_h5m_in_transport.py

@@ -22,6 +22,7 @@ def transport_particles_on_h5m_geometry(
     material_tags: list,
     nuclides: list = None,
     cross_sections_xml: str = None,
+    vtk_filename: str = None,
 ):
     """A function for testing the geometry file with particle transport in
     DAGMC OpenMC. Requires openmc and either the cross_sections_xml to be
@@ -102,10 +103,16 @@ def transport_particles_on_h5m_geometry(
     # adds a tally to record the heat deposited in entire geometry
     cell_tally = openmc.Tally(name="flux")
     cell_tally.scores = ["flux"]
-
-    # groups the two tallies
     tallies = openmc.Tallies([cell_tally])
 
+    if vtk_filename:
+        umesh_tally = openmc.Tally(name="unstructured_mesh_tally")
+        umesh = openmc.UnstructuredMesh(vtk_filename, library="moab")
+        mesh_filter = openmc.MeshFilter(umesh)
+        umesh_tally.filters = [mesh_filter]
+        umesh_tally.scores = ["flux"]
+        tallies.append(umesh_tally)
+
     # builds the openmc model
     my_model = openmc.Model(
         materials=materials, geometry=geometry, settings=settings, tallies=tallies
@@ -255,3 +262,40 @@ def test_h5m_with_multi_volume_touching():
             material_tags=mat_tags,
             nuclides=["H1"] * len(mat_tags),
         )
+
+
+@pytest.mark.skipif(openmc is None, reason="openmc tests only required for CI")
+def test_umesh_with_volumes():
+    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()
+    mat_tags = ["mat1", "mat2", "mat3"]
+    model.add_cadquery_object(assembly, material_tags=mat_tags)
+
+    h5m_file = model.export_dagmc_h5m_file(
+        filename="dagmc.h5m",
+        set_size={1: 0.9, 2: 0.1, 3: 0.9},
+    )
+
+    vtk_file = model.export_unstructured_mesh_file(
+        filename="umesh_vol_1.vtk",
+        set_size={1: 0.9, 2: 0.1, 3: 0.9},
+        volumes=[1],  # only mesh volume 2 out of the three volumes
+    )
+
+    transport_particles_on_h5m_geometry(
+        h5m_filename=h5m_file,
+        material_tags=mat_tags,
+        nuclides=["H1"] * len(mat_tags),
+        vtk_filename=vtk_file,
+    )

{cad_to_dagmc-0.9.0 → cad_to_dagmc-0.9.2}/tests/test_mesh_to_dagmc.py

@@ -2,7 +2,7 @@ import gmsh
 from test_python_api import get_volumes_and_materials_from_h5m
 from test_h5m_in_transport import transport_particles_on_h5m_geometry
 import cadquery as cq
-import assembly_mesh_plugin.plugin
+import assembly_mesh_plugin
 import gmsh
 import pydagmc
 import math
@@ -47,7 +47,7 @@ def test_mesh_to_dagmc_with_mesh_object():
         2: "mat:insert",
     }
 
-    model = pydagmc.DAGModel(test_h5m_filename)
+    model = pydagmc.Model(test_h5m_filename)
     v1 = model.volumes_by_id[1]  # get volume by id number 1
     v2 = model.volumes_by_id[2]  # get volume by id number 2
     assert len(model.volumes_by_id) == 2
@@ -89,7 +89,7 @@ def test_mesh_to_dagmc_with_cadquery_object():
         1: "mat:firstmat",
         2: "mat:aluminum",
     }
-    model = pydagmc.DAGModel(test_h5m_filename)
+    model = pydagmc.Model(test_h5m_filename)
     v1 = model.volumes_by_id[1]  # get volume by id number 1
     v2 = model.volumes_by_id[2]  # get volume by id number 2
     assert len(model.volumes_by_id) == 2

{cad_to_dagmc-0.9.0 → cad_to_dagmc-0.9.2}/tests/test_python_api.py

@@ -333,3 +333,89 @@ def test_two_box_scaling_factor_when_adding_cq_object(
     assert width_x == expected_x_width
     assert width_y == expected_y_width
     assert width_z == expected_z_width
+
+
+def test_unstructured_mesh_export_with_surface_mesh():
+
+    box_set_size_course_mesh = cq.Workplane().box(1, 1, 2)
+    box_set_size_fine_mesh = cq.Workplane().moveTo(1, 0.5).box(1, 1, 1.5)
+    box_set_global_mesh = cq.Workplane().moveTo(2, 1).box(1, 1, 1)
+
+    assembly = cq.Assembly()
+    assembly.add(box_set_size_course_mesh, color=cq.Color(0, 0, 1))
+    assembly.add(box_set_size_fine_mesh, color=cq.Color(0, 1, 0))
+    assembly.add(box_set_global_mesh, color=cq.Color(1, 0, 0))
+
+    model = CadToDagmc()
+    model.add_cadquery_object(assembly, material_tags=["mat1", "mat2", "mat3"])
+
+    dag_filename, umesh_filename = model.export_dagmc_h5m_file(
+        filename="conformal-surface-mesh2.h5m",
+        min_mesh_size=0.01,
+        max_mesh_size=10,
+        set_size={
+            1: 0.5,
+            2: 0.4,
+            3: 0.4,
+        },
+        unstructured_volumes=[2],
+        umesh_filename="conformal-volume-mesh2.vtk",
+    )
+    assert Path("conformal-surface-mesh2.h5m").is_file()
+    assert Path("conformal-volume-mesh2.vtk").is_file()
+    assert Path(dag_filename).is_file()
+    assert Path(umesh_filename).is_file()
+    # TODO check the volume mesh outer surface is the same as the surface mesh volume 2 surface
+
+
+def test_unstructured_mesh_with_volumes():
+
+    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"])
+
+    filename = model.export_dagmc_h5m_file(
+        filename="dagmc.h5m",
+        set_size={1: 0.9, 2: 0.1, 3: 0.9},
+    )
+    assert Path(filename).is_file()
+
+    filename = model.export_unstructured_mesh_file(
+        filename="umesh_vol_1.vtk",
+        set_size={1: 0.9, 2: 0.1, 3: 0.9},
+        volumes=[1],  # only mesh volume 2 out of the three volumes
+    )
+    assert Path(filename).is_file()
+
+    filename = model.export_unstructured_mesh_file(
+        filename="umesh_vol_2.vtk",
+        set_size={1: 0.9, 2: 0.1, 3: 0.9},
+        volumes=[2],  # only mesh volume 2 out of the three volumes
+    )
+    assert Path(filename).is_file()
+
+    filename = model.export_unstructured_mesh_file(
+        filename="umesh_vol_3.vtk",
+        set_size={1: 0.9, 2: 0.1, 3: 0.9},
+        volumes=[3],  # only mesh volume 2 out of the three volumes
+    )
+    assert Path(filename).is_file()
+
+    filename = model.export_unstructured_mesh_file(
+        filename="umesh_vol_1_2.vtk",
+        set_size={1: 0.9, 2: 0.1, 3: 0.9},
+        volumes=[1, 2],  # only mesh volume 2 out of the three volumes
+    )
+
+    assert Path(filename).is_file()