cad-to-dagmc 0.7.3__tar.gz → 0.9.3__tar.gz

{cad_to_dagmc-0.7.3 → cad_to_dagmc-0.9.3}/.github/workflows/ci_with_benchmarks.yml

@@ -19,32 +19,48 @@ 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 "${HOME}/miniforge/etc/profile.d/conda.sh"
+          conda create -n ci-env python=3.11
+          conda activate ci-env
+          conda install -c conda-forge "openmc=0.15.0=dagmc*nompi*" trimesh networkx cadquery gmsh python-gmsh vtk
+          python -m pip install .[tests]
+          python -m pip install git+https://github.com/svalinn/pydagmc
+          python -m pip install git+https://github.com/jmwright/cadquery-direct-mesh-plugin
+
+      - name: Run tests
+        shell: bash -l {0}
+        env:
+          OPENMC_CROSS_SECTIONS: /home/runner/work/cad_to_dagmc/cad_to_dagmc/cross_sections.xml
+        run: |
+          source "${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-0.9.3/.github/workflows/ci_with_conda_install.yml

@@ -0,0 +1,91 @@
+
+# This CI does includes particle transport tests as openmc is installed
+
+name: CI with Conda 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
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install system packages
+        run: |
+          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 "${HOME}/miniforge/etc/profile.d/conda.sh"
+          conda init bash
+          conda config --set always_yes yes --set changeps1 no
+          conda update -q conda
+
+      - name: Create and activate Conda environment
+        run: |
+          source "${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
+          python -m pip install git+https://github.com/jmwright/cadquery-direct-mesh-plugin
+  
+      - 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
+          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/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
+          python examples/surface_mesh/single_stp_file_multiple_volumes.py
+          python examples/surface_mesh/single_stp_file.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
+          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-0.7.3 → cad_to_dagmc-0.9.3}/.github/workflows/ci_with_pip_install.yml

@@ -36,26 +36,30 @@ jobs:
           apt-get install -y libblas-dev liblapack-dev libgl1 libglx-mesa0 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 make cmake libeigen3-dev
           apt install python3
           apt install python3-pip
-          python -m pip install --upgrade pip
-          git clone --single-branch -b master --depth 1 https://bitbucket.org/fathomteam/moab/
-          cd moab
-          python -m pip install . --config-settings=cmake.args=-DENABLE_HDF5=ON
-          cd ..
+          python -m pip install --extra-index-url https://shimwell.github.io/wheels moab
           python -c "import pymoab"
           python -m pip install .[tests]
+          python -m pip install git+https://github.com/svalinn/pydagmc
+          python -m pip install git+https://github.com/jmwright/cadquery-direct-mesh-plugin
           python -c "import cad_to_dagmc"
           pytest -v tests
           python examples/surface_mesh/cadquery_assembly.py
+          python examples/surface_mesh/cadquery_assembly_with_scaled_geometry.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/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_stp_file_multiple_volumes.py
           python examples/surface_mesh/single_cadquery_object.py
+          python examples/surface_mesh/single_stp_file_multiple_volumes.py
           python examples/surface_mesh/single_stp_file.py
-          python examples/surface_mesh/from_gmsh_mesh_file.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/surface_mesh/cadquery_assembly_with_scaled_geometry.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_and_unstructured_mesh/unstructured_mesh_with_conformal_surface_mesh.py

{cad_to_dagmc-0.7.3 → cad_to_dagmc-0.9.3}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: cad_to_dagmc
-Version: 0.7.3
+Version: 0.9.3
 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
@@ -14,12 +14,14 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: trimesh
 Requires-Dist: networkx
-Requires-Dist: cadquery>=2.4.0
-Requires-Dist: numpy<=1.26.4
+Requires-Dist: cadquery>=2.5.2
+Requires-Dist: numpy
 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)
@@ -35,23 +37,36 @@ Requires-Dist: vtk; extra == "tests"
 [![PyPI](https://img.shields.io/pypi/v/cad_to_dagmc?color=brightgreen&label=pypi&logo=grebrightgreenen&logoColor=green)](https://pypi.org/project/cad_to_dagmc/)
 
 
-A minimal package that converts CAD geometry to [DAGMC](https://github.com/svalinn/DAGMC/) h5m files
+A minimal package that converts CAD geometry to [DAGMC](https://github.com/svalinn/DAGMC/) (h5m) files, [unstructured mesh](https://docs.openmc.org/en/latest/pythonapi/generated/openmc.UnstructuredMesh.html) files (vtk) and Gmsh (msh) files ready for use in neutronics simulations.
 
-cad-to-dagmc can create:
+cad-to-dagmc can create DAGMC compatible:
 - surface meshes / faceted geometry / triangular meshes
 - unstructured mesh / tetrahedral meshes / volume meshes
 
-cad-to-dagmc can convert:
+cad-to-dagmc can convert the following in to DAGMC compatible meshes:
 - STEP files
-- CadQuery objects (in memory)
+- 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
+- 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)
+- Ability to tag the DAGMC implicit complement material using the ```implicit_complement_material_tag``` argument
+- Selected different Gmesh mesh algorithms (defaults to 1) using the ```mesh_algorithm``` argument
+- Pass CadQuery objects in memory for fast transfer of geometry using the ```method``` argument
+- Easy to install with [pip](https://pypi.org/project/cad-to-dagmc/) and [Conda/Mamba](https://anaconda.org/conda-forge/cad_to_dagmc)
+- Well tested both with [CI unit tests](https://github.com/fusion-energy/cad_to_dagmc/tree/main/tests), integration tests and the CSG [Model Benchmark Zoo](https://github.com/fusion-energy/model_benchmark_zoo).
+- Compatible with [Paramak](https://github.com/fusion-energy/paramak) geometry for fusion simulations.
 
-cad-to-dagmc aims to produce DAGMC compatible h5m files from CAD geometry is intended to convert [STEP](http://www.steptools.com/stds/step/) files or [CadQuery](https://cadquery.readthedocs.io) objects to a [DAGMC](https://github.com/svalinn/DAGMC/) compatible h5m file.
-
-The resulting DAGMC geometry can then be used for simulations in [OpenMC](https://github.com/openmc-dev/openmc/) or [other supported codes](https://svalinn.github.io/DAGMC/).
-
-This package is tested with [pytest tests](https://github.com/fusion-energy/cad_to_dagmc/tree/main/tests) and also the DAGMC geometry made with this package is compared to simulation carried out with native constructive solid geometry, see [Model Benchmark Zoo](https://github.com/fusion-energy/model_benchmark_zoo) for more details.
-
-Also checkout these other software projects that also create DAGMC geometry [CAD-to-OpenMC](https://github.com/openmsr/CAD_to_OpenMC), [Stellarmesh](https://github.com/Thea-Energy/stellarmesh) and [Coreform Cubit](https://coreform.com/products/coreform-cubit/)
 
 # Installation options
 
@@ -117,21 +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.
-
-```
-git clone  master https://bitbucket.org/fathomteam/moab/
-cd moab
-```
+Then install MOAB, currently available from the repo.
 
-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```
@@ -146,7 +150,7 @@ You may also want to install OpenMC with DAGMC to make use of the h5m geometry f
 
 To install OpenMC you can run ```mamba install -c conda-forge openmc``` however this more specific command makes sure the latest version of OpenMC which contains DAGMC is chosen by conda / mamba
 ```bash
-mamba install -c conda-forge -y "openmc=0.14.0=dagmc*nompi*"
+mamba install -c conda-forge -y "openmc=0.15.0=dagmc*nompi*"
 ```
 
 It might not be possible to install OpenMC and cad-to-dagmc in the same conda/mamba python environment so you may have to create a new conda/mamba environment and install OpenMC there.
@@ -160,15 +164,15 @@ The package requires newer versions of Linux. For example the package does not w
 
 The package requires newer versions of pip. It is recommended to ensure that your version of pip is up to date. This can be done with ```python -m pip install --upgrade pip```
 
-Installing one of the package dependancies (gmsh) with pip appears to result in errors when passing cad objects in memory between cadquery / ocp and gmsh. The default method of passing cad objects is via file so this should not impact most users. The conda install gmsh appears to work fine with in memory passing of cad objects as the version of OCP matches between Gmsh and CadQuery.
+Installing one of the package dependancies (Gmsh) with pip appears to result in errors when passing cad objects in memory between cadquery / ocp and gmsh. The default method of passing cad objects is via file so this should not impact most users. The conda install gmsh appears to work fine with in memory passing of cad objects as the version of OCP matches between Gmsh and CadQuery.
 
 
-# Usage - creation of DAGMC h5m files
+# Usage
 
-For examples see the [examples folder](https://github.com/fusion-energy/cad_to_dagmc/tree/main/examples)
+For examples showing creation of DAGMC h5m files, vtk files and usage within OpenMC transport code see the [examples folder](https://github.com/fusion-energy/cad_to_dagmc/tree/main/examples)
 
-# Usage - simulation with transport code
+For more examples see the CAD tasks in the [neutronics-workshop](https://github.com/fusion-energy/neutronics-workshop) and [model benchmark zoo](https://github.com/fusion-energy/model_benchmark_zoo)
 
-For examples see the [examples folder](https://github.com/fusion-energy/cad_to_dagmc/tree/main/examples)
+# Related software
 
-For more examples see the CAD tasks in the [neutronics-workshop](https://github.com/fusion-energy/neutronics-workshop) and [model benchmark zoo](https://github.com/fusion-energy/model_benchmark_zoo)
+Also checkout these other software projects that also create DAGMC geometry [CAD-to-OpenMC](https://github.com/openmsr/CAD_to_OpenMC), [Stellarmesh](https://github.com/Thea-Energy/stellarmesh) and [Coreform Cubit](https://coreform.com/products/coreform-cubit/).

{cad_to_dagmc-0.7.3 → cad_to_dagmc-0.9.3}/README.md

@@ -12,23 +12,36 @@
 [![PyPI](https://img.shields.io/pypi/v/cad_to_dagmc?color=brightgreen&label=pypi&logo=grebrightgreenen&logoColor=green)](https://pypi.org/project/cad_to_dagmc/)
 
 
-A minimal package that converts CAD geometry to [DAGMC](https://github.com/svalinn/DAGMC/) h5m files
+A minimal package that converts CAD geometry to [DAGMC](https://github.com/svalinn/DAGMC/) (h5m) files, [unstructured mesh](https://docs.openmc.org/en/latest/pythonapi/generated/openmc.UnstructuredMesh.html) files (vtk) and Gmsh (msh) files ready for use in neutronics simulations.
 
-cad-to-dagmc can create:
+cad-to-dagmc can create DAGMC compatible:
 - surface meshes / faceted geometry / triangular meshes
 - unstructured mesh / tetrahedral meshes / volume meshes
 
-cad-to-dagmc can convert:
+cad-to-dagmc can convert the following in to DAGMC compatible meshes:
 - STEP files
-- CadQuery objects (in memory)
+- 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
+- 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)
+- Ability to tag the DAGMC implicit complement material using the ```implicit_complement_material_tag``` argument
+- Selected different Gmesh mesh algorithms (defaults to 1) using the ```mesh_algorithm``` argument
+- Pass CadQuery objects in memory for fast transfer of geometry using the ```method``` argument
+- Easy to install with [pip](https://pypi.org/project/cad-to-dagmc/) and [Conda/Mamba](https://anaconda.org/conda-forge/cad_to_dagmc)
+- Well tested both with [CI unit tests](https://github.com/fusion-energy/cad_to_dagmc/tree/main/tests), integration tests and the CSG [Model Benchmark Zoo](https://github.com/fusion-energy/model_benchmark_zoo).
+- Compatible with [Paramak](https://github.com/fusion-energy/paramak) geometry for fusion simulations.
 
-cad-to-dagmc aims to produce DAGMC compatible h5m files from CAD geometry is intended to convert [STEP](http://www.steptools.com/stds/step/) files or [CadQuery](https://cadquery.readthedocs.io) objects to a [DAGMC](https://github.com/svalinn/DAGMC/) compatible h5m file.
-
-The resulting DAGMC geometry can then be used for simulations in [OpenMC](https://github.com/openmc-dev/openmc/) or [other supported codes](https://svalinn.github.io/DAGMC/).
-
-This package is tested with [pytest tests](https://github.com/fusion-energy/cad_to_dagmc/tree/main/tests) and also the DAGMC geometry made with this package is compared to simulation carried out with native constructive solid geometry, see [Model Benchmark Zoo](https://github.com/fusion-energy/model_benchmark_zoo) for more details.
-
-Also checkout these other software projects that also create DAGMC geometry [CAD-to-OpenMC](https://github.com/openmsr/CAD_to_OpenMC), [Stellarmesh](https://github.com/Thea-Energy/stellarmesh) and [Coreform Cubit](https://coreform.com/products/coreform-cubit/)
 
 # Installation options
 
@@ -94,21 +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.
-
-```
-git clone  master https://bitbucket.org/fathomteam/moab/
-cd moab
-```
+Then install MOAB, currently available from the repo.
 
-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```
@@ -123,7 +125,7 @@ You may also want to install OpenMC with DAGMC to make use of the h5m geometry f
 
 To install OpenMC you can run ```mamba install -c conda-forge openmc``` however this more specific command makes sure the latest version of OpenMC which contains DAGMC is chosen by conda / mamba
 ```bash
-mamba install -c conda-forge -y "openmc=0.14.0=dagmc*nompi*"
+mamba install -c conda-forge -y "openmc=0.15.0=dagmc*nompi*"
 ```
 
 It might not be possible to install OpenMC and cad-to-dagmc in the same conda/mamba python environment so you may have to create a new conda/mamba environment and install OpenMC there.
@@ -137,15 +139,15 @@ The package requires newer versions of Linux. For example the package does not w
 
 The package requires newer versions of pip. It is recommended to ensure that your version of pip is up to date. This can be done with ```python -m pip install --upgrade pip```
 
-Installing one of the package dependancies (gmsh) with pip appears to result in errors when passing cad objects in memory between cadquery / ocp and gmsh. The default method of passing cad objects is via file so this should not impact most users. The conda install gmsh appears to work fine with in memory passing of cad objects as the version of OCP matches between Gmsh and CadQuery.
+Installing one of the package dependancies (Gmsh) with pip appears to result in errors when passing cad objects in memory between cadquery / ocp and gmsh. The default method of passing cad objects is via file so this should not impact most users. The conda install gmsh appears to work fine with in memory passing of cad objects as the version of OCP matches between Gmsh and CadQuery.
 
 
-# Usage - creation of DAGMC h5m files
+# Usage
 
-For examples see the [examples folder](https://github.com/fusion-energy/cad_to_dagmc/tree/main/examples)
+For examples showing creation of DAGMC h5m files, vtk files and usage within OpenMC transport code see the [examples folder](https://github.com/fusion-energy/cad_to_dagmc/tree/main/examples)
 
-# Usage - simulation with transport code
+For more examples see the CAD tasks in the [neutronics-workshop](https://github.com/fusion-energy/neutronics-workshop) and [model benchmark zoo](https://github.com/fusion-energy/model_benchmark_zoo)
 
-For examples see the [examples folder](https://github.com/fusion-energy/cad_to_dagmc/tree/main/examples)
+# Related software
 
-For more examples see the CAD tasks in the [neutronics-workshop](https://github.com/fusion-energy/neutronics-workshop) and [model benchmark zoo](https://github.com/fusion-energy/model_benchmark_zoo)
+Also checkout these other software projects that also create DAGMC geometry [CAD-to-OpenMC](https://github.com/openmsr/CAD_to_OpenMC), [Stellarmesh](https://github.com/Thea-Energy/stellarmesh) and [Coreform Cubit](https://coreform.com/products/coreform-cubit/).

cad_to_dagmc-0.9.3/examples/surface_and_unstructured_mesh/unstructured_mesh_with_conformal_surface_mesh.py

@@ -0,0 +1,105 @@
+# 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",
+    meshing_backend="gmsh",
+)
+
+
+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-0.9.3/examples/surface_mesh/different_resolution_meshes.py

@@ -0,0 +1,44 @@
+# This example makes 3 CAD boxes
+# Meshes the 3 volumes with different resolutions
+# exports the mesh to a DAGMC h5m file and GMsh msh file
+import cadquery as cq
+from cad_to_dagmc import CadToDagmc
+
+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))
+
+assembly.export("different_resolution_meshes.step")
+
+# uncomment to see the assembly in a pop up vtk viewer
+# from cadquery import vis
+# vis.show(assembly)
+
+model = CadToDagmc()
+model.add_cadquery_object(assembly, material_tags=["mat1", "mat2", "mat3"])
+
+model.export_dagmc_h5m_file(
+    filename="different_resolution_meshes.h5m",
+    min_mesh_size=0.01,
+    max_mesh_size=10,
+    set_size={
+        1: 0.9,
+        2: 0.1,
+    },  # not volume 3 is not specified in the set_size so it uses only the min max mesh sizes
+)
+
+model.export_gmsh_mesh_file(
+    filename="different_resolution_meshes.msh",
+    dimensions=2,
+    min_mesh_size=0.01,
+    max_mesh_size=10,
+    set_size={
+        1: 0.9,
+        2: 0.1,
+    },  # not volume 3 is not specified in the set_size so it uses only the min max mesh sizes
+)

{cad_to_dagmc-0.7.3 → cad_to_dagmc-0.9.3}/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"