cad-to-dagmc 0.6.2__tar.gz → 0.9.3__tar.gz

{cad_to_dagmc-0.6.2 → cad_to_dagmc-0.9.3}/.github/workflows/black.yml

@@ -13,11 +13,11 @@ jobs:
   black:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         ref: ${{ github.head_ref }}
     - name: Setup Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: 3.x
     - name: Install black
@@ -27,6 +27,6 @@ jobs:
     - name: Run black
       run: |
         black --line-length 100 .
-    - uses: stefanzweifel/git-auto-commit-action@v4
+    - uses: stefanzweifel/git-auto-commit-action@v5
       with:
         commit_message: "[skip ci] Apply formatting changes"

cad_to_dagmc-0.9.3/.github/workflows/ci_with_benchmarks.yml

@@ -0,0 +1,66 @@
+
+name: CI with model benchmark zoo
+
+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: 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 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]
+          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-0.9.3/.github/workflows/ci_with_pip_install.yml

@@ -0,0 +1,65 @@
+
+# This CI does not currently include particle transport tests as openmc is not installed
+
+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 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 --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_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-0.6.2 → cad_to_dagmc-0.9.3}/.gitignore

@@ -137,3 +137,4 @@ dmypy.json
 *.stp
 src/_version.py
 *.msh
+*.step

cad_to_dagmc-0.9.3/CITATION.cff

@@ -0,0 +1,10 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Shimwell"
+  given-names: "Jonathan"
+  orcid: "https://orcid.org/0000-0001-6909-0946"
+title: "CAD to DAGMC. Convert CAD geometry (STP files) or Cadquery assemblies to DAGMC h5m files"
+version: 0.7.0
+date-released: 2024-4-14
+url: "https://github.com/fusion-energy/cad_to_dagmc"

{cad_to_dagmc-0.6.2 → 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: 0.6.2
+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
@@ -14,15 +14,21 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: trimesh
 Requires-Dist: networkx
-Requires-Dist: cadquery>=2.4.0
+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)
 
-[![CI with install](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_install.yml/badge.svg?branch=main)](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_install.yml) Testing package and running examples
+[![CI with Conda install](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_conda_install.yml/badge.svg)](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_conda_install.yml) Testing package and running examples with dependencies installed via Conda
+
+[![CI with pip install](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_pip_install.yml/badge.svg)](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_pip_install.yml) Testing package and running examples with dependencies installed vua PIP
 
 [![CI with model benchmark zoo](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_benchmarks.yml/badge.svg?branch=main)](https://github.com/fusion-energy/cad_to_dagmc/actions/workflows/ci_with_benchmarks.yml) Testing with [Model Benchmark Zoo](https://github.com/fusion-energy/model_benchmark_zoo)
 
@@ -31,32 +37,44 @@ 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)
-
-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/).
+- 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.
 
-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
 
-- Install using Mamba and pip
-- Install using Conda and pip
+- Install using Mamba
+- Install using Conda
 - Install using pip and source compilations
 
-
-## Install using Mamba and pip
+## Install using Mamba
 
 In principle, installing any Conda/Mamba distribution will work. A few Conda/Mamba options are:
 - [Miniforge](https://github.com/conda-forge/miniforge) (recommended as it includes mamba)
@@ -65,7 +83,7 @@ In principle, installing any Conda/Mamba distribution will work. A few Conda/Mam
 
 This example assumes you have installed the Miniforge option or separately have installed Mamba with ```conda install -c conda-forge mamba -y```
 
-Create a new conda environment, I've chosen Python 3.10 here but newer versions are
+Create a new environment, I've chosen Python 3.10 here but newer versions are
 also supported.
 ```bash
 mamba create --name new_env python=3.10 -y
@@ -76,27 +94,20 @@ Activate the environment
 mamba activate new_env
 ```
 
-Install the dependencies
-```bash
-mamba install -y -c conda-forge "moab>=5.3.0" gmsh python-gmsh
-```
-
-Then you can install the cad_to_dagmc package with ```pip```
+Then you can install the cad_to_dagmc package
 ```bash
-pip install cad_to_dagmc
+mamba install -y -c conda-forge cad_to_dagmc
 ```
 
-
-## Install using Conda and pip
+## Install using Conda
 
 In principle, installing any Conda/Mamba distribution will work. A few Conda/Mamba options are:
 - [Miniforge](https://github.com/conda-forge/miniforge) (recommended as it includes mamba)
 - [Anaconda](https://www.anaconda.com/download)
 - [Miniconda](https://docs.conda.io/en/latest/miniconda.html)
 
-This example uses Conda to install some dependencies that are not available via PyPi.
-
-Create a new conda environment
+Create a new environment, I've chosen Python 3.10 here but newer versions are
+also supported.
 ```bash
 conda create --name new_env python=3.10 -y
 ```
@@ -106,23 +117,26 @@ Activate the environment
 conda activate new_env
 ```
 
-Install the dependencies
+Then you can install the cad_to_dagmc package
 ```bash
-conda install -y -c conda-forge "moab>=5.3.0" gmsh python-gmsh
-```
-
-Then you can install the cad_to_dagmc package with ```pip```
-```bash
-pip install cad_to_dagmc
+conda install -y -c conda-forge cad_to_dagmc
 ```
 
 ## Install using pip and source compilations
 
-It should possible to avoid the use of conda and installing using pip and compiling from source.
+It is also possible to avoid the use of conda/mamba and installing using pip.
 
-First compile MOAB (and install Pymoab) from source
+First ensure hdf5 is installed as this is needed by MOAB pip install command
 
-Then install gmsh from source (installing from pip appears to cause conflicts with the open cascade used in ocp and cadquery)
+```
+sudo apt-get install libhdf5-dev
+```
+
+Then install MOAB, currently available from the repo.
+
+```
+pip install git+https://bitbucket.org/fathomteam/moab/
+```
 
 Then you can install the cad_to_dagmc package with ```pip```
 
@@ -130,13 +144,13 @@ Then you can install the cad_to_dagmc package with ```pip```
 pip install cad_to_dagmc
 ```
 
-## Install with transport code (e.g OpenMC)
+## Install with OpenMC or other particle transport codes
 
 You may also want to install OpenMC with DAGMC to make use of the h5m geometry files produced in simulations. However you could also use other supported particle transport codes such as MCNP, FLUKA and others [link to DAGMC documentation](https://svalinn.github.io/DAGMC/).
 
 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.
@@ -144,36 +158,21 @@ It might not be possible to install OpenMC and cad-to-dagmc in the same conda/ma
 Another option would be to [install OpenMC from source](https://docs.openmc.org/en/stable/quickinstall.html) which would also need compiling with MOAB and DAGMC options.
 
 
-
 # Known incompatibilities
 
 The package requires newer versions of Linux. For example the package does not work on Ubuntu 18.04 or older.
 
 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 occational errors when passing cad objects between cadquery / ocp and gmsh. The conda install gmsh appears to work fine.
+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 - with OpenMC
 
-You may also want to install OpenMC with DAGMC to make use of the h5m geometry files produced in simulations. However you could also use other supported particle transport codes such as MCNP, FLUKA and others supported by [DAGMC](https://svalinn.github.io/DAGMC/).
+# Usage
 
-You can run ```mamba install -c conda-forge openmc``` however this may choose to install OpenMC without DAGMC included.
+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)
 
-You can be more specific with conda/mamba commands to make 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*"
-```
-
-You could also [install OpenMC from source](https://docs.openmc.org/en/stable/quickinstall.html) which might be prefered as it can be tricky for the conda enviroment to get resolved.
-
-
-
-# Usage - creation of DAGMC h5m files
-
-For examples 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/README.md

@@ -0,0 +1,153 @@
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+
+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 DAGMC compatible:
+- surface meshes / faceted geometry / triangular meshes
+- unstructured mesh / tetrahedral meshes / volume meshes
+
+cad-to-dagmc can convert the following in to DAGMC compatible meshes:
+- STEP files
+- 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.
+
+
+# Installation options
+
+- Install using Mamba
+- Install using Conda
+- Install using pip and source compilations
+
+## Install using Mamba
+
+In principle, installing any Conda/Mamba distribution will work. A few Conda/Mamba options are:
+- [Miniforge](https://github.com/conda-forge/miniforge) (recommended as it includes mamba)
+- [Anaconda](https://www.anaconda.com/download)
+- [Miniconda](https://docs.conda.io/en/latest/miniconda.html)
+
+This example assumes you have installed the Miniforge option or separately have installed Mamba with ```conda install -c conda-forge mamba -y```
+
+Create a new environment, I've chosen Python 3.10 here but newer versions are
+also supported.
+```bash
+mamba create --name new_env python=3.10 -y
+```
+
+Activate the environment
+```bash
+mamba activate new_env
+```
+
+Then you can install the cad_to_dagmc package
+```bash
+mamba install -y -c conda-forge cad_to_dagmc
+```
+
+## Install using Conda
+
+In principle, installing any Conda/Mamba distribution will work. A few Conda/Mamba options are:
+- [Miniforge](https://github.com/conda-forge/miniforge) (recommended as it includes mamba)
+- [Anaconda](https://www.anaconda.com/download)
+- [Miniconda](https://docs.conda.io/en/latest/miniconda.html)
+
+Create a new environment, I've chosen Python 3.10 here but newer versions are
+also supported.
+```bash
+conda create --name new_env python=3.10 -y
+```
+
+Activate the environment
+```bash
+conda activate new_env
+```
+
+Then you can install the cad_to_dagmc package
+```bash
+conda install -y -c conda-forge cad_to_dagmc
+```
+
+## Install using pip and source compilations
+
+It is also possible to avoid the use of conda/mamba and installing using pip.
+
+First ensure hdf5 is installed as this is needed by MOAB pip install command
+
+```
+sudo apt-get install libhdf5-dev
+```
+
+Then install MOAB, currently available from the repo.
+
+```
+pip install git+https://bitbucket.org/fathomteam/moab/
+```
+
+Then you can install the cad_to_dagmc package with ```pip```
+
+```bash
+pip install cad_to_dagmc
+```
+
+## Install with OpenMC or other particle transport codes
+
+You may also want to install OpenMC with DAGMC to make use of the h5m geometry files produced in simulations. However you could also use other supported particle transport codes such as MCNP, FLUKA and others [link to DAGMC documentation](https://svalinn.github.io/DAGMC/).
+
+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=0.15.0=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.
+
+Another option would be to [install OpenMC from source](https://docs.openmc.org/en/stable/quickinstall.html) which would also need compiling with MOAB and DAGMC options.
+
+
+# Known incompatibilities
+
+The package requires newer versions of Linux. For example the package does not work on Ubuntu 18.04 or older.
+
+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.
+
+
+# Usage
+
+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)
+
+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)
+
+# Related software
+
+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/).