Merge pull request #8 from fusion-energy/develop

updated docs and targeting develop branch on DAGMC repo

Dockerfile

@@ -126,7 +126,7 @@ RUN git clone --single-branch --branch main https://github.com/pshriwise/double-
 RUN mkdir DAGMC && \
     cd DAGMC && \
     # git clone --single-branch --branch 3.2.0 --depth 1 https://github.com/svalinn/DAGMC.git && \
-    git clone --single-branch --branch 9b59a53311e94b8a49c8405d730aeef84f4ca3e2 --depth 1 https://github.com/svalinn/DAGMC.git && \
+    git clone --single-branch --branch develop --depth 1 https://github.com/svalinn/DAGMC.git && \
     mkdir build && \
     cd build && \
     cmake ../DAGMC -DBUILD_TALLY=ON \

docs/source/example_neutronics_simulations.rst

@@ -2,18 +2,7 @@ Examples - Neutronics Simulations
 =================================
 
 These are minimal examples of neutronics simulations that demonstrate the core
-functionality of the neutronics features. In general it easy to export geomtry
-in h5m format for use in DAGMC enabled simulations. There are two options for
-this export. The Trelis method of converting geometry imprints and merges
-surfaces while the PyMoab converts the geoemtry without imprinting and merging
-surfaces.
-
-The resulting h5m files can be used in DAGMC enabled neutronics codes such as
-OpenMC and MCNP. There is also a class (NeutronicsModel) that facilitates
-adding tallies, materials and a source to the geoemtry to create a complete
-OpenMC neutronics model which can be simulated. The simulated results are also
-extracted from the statepoint.h5 file that OpenMC produces and converted to
-vtk, png and JSON files depending on the tally.
+functionality of the neutronics features.
 
 
 ball_reactor.ipynb

docs/source/index.rst

@@ -8,8 +8,8 @@ generating using the `Paramak <https://github.com/fusion-energy/paramak>`_
    :maxdepth: 1
 
    install
-   paramak_neutronics.neutronics_model
    example_neutronics_simulations
+   paramak_neutronics.neutronics_model
    tests
 
 History
@@ -20,31 +20,33 @@ neutronics simulations of fusion reactors.
 
 The Paramak-neutronics source code is distributed with a permissive open-source
 license (MIT) and is available from the GitHub repository 
-`https://github.com/fusion-energy/paramak <https://github.com/fusion-energy/paramak>`_
+`https://github.com/fusion-energy/paramak-neutronics <https://github.com/fusion-energy/paramak-neutronics>`_
 
 
 Features
 --------
 
-In general Paramak-neutronics takes a Paramak.Reactor or Paramak.Shape object and
-allows tallies to be easily added and processes the results for ease of access.
+In general Paramak-neutronics takes a Paramak.Reactor or Paramak.Shape object
+and allows tallies, materials and a source term to be easily added to create
+a complete neutronics model. The Paramal-neutronics package will also post
+processes the results of the neutronics simulation to allow easy access to the
+outputs. The simulated results are extracted from the statepoint.h5 file that
+OpenMC produces and converted to vtk, png and JSON files depending on the tally.
 
-The Paramak supports automated neutronics model creation and subsequent
-simulation. 
+The Paramak supports automated geometry creation and the Paramak-neutronics
+allows subsequent neutronics simulations to be carried out on the geometry.
 
-The neutronics models created are DAGMC models and are therefore compatible 
-with a suite of neutronics codes (MCNP, Fluka, Geant4, OpenMC).
+The neutronics geometry created by the Paramak are DAGMC models (h5m files) and
+are therefore compatible  with a suite of neutronics codes (MCNP, Fluka,
+Geant4, OpenMC).
 
 The automated simulations supported within the paramak are via OpenMC however
 one could also carry out simulations in other neutronics codes using the
-dagmc.h5m file created. Moab can be used to inspect the dagmc.h5 file and file
-the material tag names.
+h5m file created by the Parmaak.
 
-.. code-block:: bash
 
-   mbsize -ll dagmc.h5m | grep 'mat:'
-
-The creation of the dagmc.h5m file can be carried out via three routes.
+The creation of the dagmc.h5m file using the Paramak can be carried out via
+two routes:
 
 Option 1. Use of `PyMoab <https://bitbucket.org/fathomteam/moab>`_ which is
 distributed with MOAB. Thus method can not imprint or merge the surfaces of the
@@ -53,28 +55,25 @@ components or components that touch on flat surfaces. Curved surfaces converted
 via this method can potentially overlap and cause errors with the particle
 tracking.
 
-Option 2. Use of `Trelis <https://www.coreform.com/products/trelis/>`_ by
-Coreform along with the DAGMC
+Option 2. Use of `Cubit <https://cubit.sandia.gov/>`_ or 
+`Cubit Corefoam <https://www.coreform.com/>`_ along with the DAGMC
 `plugin <https://svalinn.github.io/DAGMC/install/plugin.html>`_ / This method
 can support imprinting and merging of shared surfaces between components and is
-therefore suitable for converting more complex CAD geometry to the PyMoab
+therefore suitable for converting more complex CAD geometry than the PyMoab
 method.
 
-Option 3. Use of the `PPP <https://github.com/ukaea/parallel-preprocessor>`_
-and `OCC_Faceter <https://github.com/makeclean/occ_faceter/>`_ . This option
-has not yet been fully demonstrated but is partly included to test the
-promising new method.
 
 To create a model it is also necessary to define the source and the materials
 used. 
 
-For fusion simulations you might want to used the parametric-plasma-source
-`Git repository <https://github.com/open-radiation-sources/parametric-plasma-source>`_ 
-
-Details of the Neutronics Material Maker are available from the
+The Paramak accepts native OpenMC materials and also Neutronics Material Maker
+materials. Further details on the Neutronics Material Maker is avaialbe via online
 `documentation <https://neutronics-material-maker.readthedocs.io/en/latest/>`_ 
-and the `source code repository <https://github.com/ukaea/neutronics_material_maker>`_
-. However openmc.Materials can also be used directly.
+and the `source code repository <https://github.com/fusion-energy/neutronics_material_maker>`_
+.
+
+For magnetic confinment fusion simulations you might want to use the parametric-plasma-source
+`Git repository <https://github.com/open-radiation-sources/parametric-plasma-source>`_ 
 
-The `OpenMC workshop <https://github.com/ukaea/openmc_workshop>`_ also has
+The `OpenMC workshop <https://github.com/fusion-energy/openmc_workshop>`_ also has
 some Paramak with DAGMC and OpenMC based tasks that might be of interest.

docs/source/install.rst

@@ -6,39 +6,46 @@ Installation
 Prerequisites
 -------------
 
-To use the paramak-neutronics module you will need the Python, Paramak, DAGMC and OpenMC installed.
+To use the paramak-neutronics module you will need the Python, Paramak, DAGMC
+and OpenMC installed.
 
-* `Python 3 <https://www.python.org/downloads/>`_
+The recommended method is to install Python 3 using Anaconda or Miniconda
 
-Python 3 and can be installed using Conda or Miniconda (recommended)
-
-* `Anaconda <https://www.anaconda.com/>`_
-* `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_
+* `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_ (preferable to avoid hdf5 conflicts)
+* `Anaconda https://www.anaconda.com/>`_
 
 Once you have Conda or MiniConda installed then CadQuery can be installed
-into a new enviroment and that environment can be activated using Anaconda or Miniconda. 
+into a new enviroment and that environment can be activated using Conda.
 
 First create a new Conda environment.
 
 .. code-block:: python
 
-   conda create -n paramak_env
+   conda create -n my_env
 
 
 Then activated the conda environment, 
 
 .. code-block:: python
 
-   conda activate paramak_env
+   conda activate my_env
+
+Then install CadQuery:
+
+.. code-block:: python
+
+   conda install -c conda-forge -c cadquery cadquery=2.1
 
 
-Then install the paramak-neutronics package 
+Then install the paramak-neutronics package using Pip.
 
 .. code-block:: python
 
-   # conda install not working yet, try pip install paramak-neutronics
-   conda install -c fusion-energy paramak-neutronics
+   pip install paramak-neutronics
 
+To complete the software stack OpenMC, DAGMC, Cubit and the DAGMC/Cubit plugin
+will also need installing. We don't have simple instructions for these packages
+yet but one option is to duplicate the stages in the `Dockerfile <https://github.com/fusion-energy/paramak-neutronics/blob/main/Dockerfile>`_
 
 Docker Image Installation
 -------------------------

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="paramak_neutronics",
-    version="0.0.1",
+    version="0.0.3",
     author="The Paramak Development Team",
     author_email="[email protected]",
     description="Perform neutronics simulations on models generated with the Paramak",