Develop combine

.gitignore

@@ -35,11 +35,14 @@ coverage.xml
 # neutronics simulation files
 *.h5
 *.out
+*.vtk
 
 # 2D and 3D images of the model
 *.svg
 *.png
 *.vtk
+*.jpg
+*.xcf
 
 # sphinx built documetation
 docs/build/

Dockerfile

@@ -105,7 +105,7 @@ RUN if [ "$include_neutronics" = "true" ] ; \
     mkdir build ; \
     cd build ; \
     cmake .. -DCMAKE_INSTALL_PREFIX=.. \
-        -DEMBREE_ISPC_SUPPORT=OFF ; \
+             -DEMBREE_ISPC_SUPPORT=OFF ; \
     make -j"$compile_cores" ; \
     make -j"$compile_cores" install ; \
     fi
@@ -119,19 +119,20 @@ RUN if [ "$include_neutronics" = "true" ] ; \
     git clone  --single-branch --branch develop https://bitbucket.org/fathomteam/moab/ ; \
     cd build ; \
     cmake ../moab -DENABLE_HDF5=ON \
-                -DENABLE_NETCDF=ON \
-                -DBUILD_SHARED_LIBS=OFF \
-                -DENABLE_FORTRAN=OFF \
-                -DCMAKE_INSTALL_PREFIX=/MOAB ; \
+                  -DENABLE_NETCDF=ON \
+                  -DENABLE_FORTRAN=OFF \
+                  -DENABLE_BLASLAPACK=OFF \
+                  -DBUILD_SHARED_LIBS=OFF \
+                  -DCMAKE_INSTALL_PREFIX=/MOAB ; \
     make -j"$compile_cores" ; \
     make -j"$compile_cores" install ; \
     rm -rf * ; \
-    cmake ../moab -DBUILD_SHARED_LIBS=ON \
-                -DENABLE_HDF5=ON \
-                -DENABLE_PYMOAB=ON \
-                -DENABLE_BLASLAPACK=OFF \
-                -DENABLE_FORTRAN=OFF \
-                -DCMAKE_INSTALL_PREFIX=/MOAB ; \
+    cmake ../moab -DENABLE_HDF5=ON \
+                  -DENABLE_PYMOAB=ON \
+                  -DENABLE_FORTRAN=OFF \
+                  -DBUILD_SHARED_LIBS=ON \
+                  -DENABLE_BLASLAPACK=OFF \
+                  -DCMAKE_INSTALL_PREFIX=/MOAB ; \
     make -j"$compile_cores" ; \
     make -j"$compile_cores" install ; \
     cd pymoab ; \
@@ -146,10 +147,9 @@ RUN if [ "$include_neutronics" = "true" ] ; \
     cd double-down ; \
     mkdir build ; \
     cd build ; \
-    cmake .. -DCMAKE_INSTALL_PREFIX=.. \
-        -DMOAB_DIR=/MOAB \
-        -DEMBREE_DIR=/embree/lib/cmake/embree-3.12.1 \
-        -DEMBREE_ROOT=/embree/lib/cmake/embree-3.12.1 ; \
+    cmake .. -DMOAB_DIR=/MOAB \
+             -DCMAKE_INSTALL_PREFIX=.. \
+             -DEMBREE_DIR=/embree/lib/cmake/embree-3.12.1 ; \
     make -j"$compile_cores" ; \
     make -j"$compile_cores" install ; \
     fi
@@ -162,10 +162,10 @@ RUN if [ "$include_neutronics" = "true" ] ; \
     mkdir build ; \
     cd build ; \
     cmake ../dagmc -DBUILD_TALLY=ON \
-        -DCMAKE_INSTALL_PREFIX=/dagmc/ \
-        -DMOAB_DIR=/MOAB \
-        -DBUILD_STATIC_LIBS=OFF \
-        -DBUILD_STATIC_EXE=OFF ; \
+                   -DMOAB_DIR=/MOAB \
+                   -DBUILD_STATIC_EXE=OFF \
+                   -DBUILD_STATIC_LIBS=OFF \
+                   -DCMAKE_INSTALL_PREFIX=/dagmc/ ; \
     make -j"$compile_cores" install ; \
     rm -rf /DAGMC/dagmc /DAGMC/build ; \
     fi
@@ -176,9 +176,10 @@ RUN if [ "$include_neutronics" = "true" ] ; \
     cd /opt/openmc ; \
     mkdir build ; \
     cd build ; \
-    cmake -Doptimize=on -Ddagmc=ON \
-        -DDAGMC_DIR=/DAGMC/ \
-        -DHDF5_PREFER_PARALLEL=on ..  ; \
+    cmake -Doptimize=on \
+          -Ddagmc=ON \
+          -DDAGMC_DIR=/DAGMC/ \
+          -DHDF5_PREFER_PARALLEL=on ..  ; \
     make -j"$compile_cores" ; \
     make -j"$compile_cores" install ; \
     cd ..  ; \
@@ -191,9 +192,9 @@ ENV OPENMC_CROSS_SECTIONS=/root/nndc_hdf5/cross_sections.xml
 # Copies over the Paramak code from the local repository
 
 RUN if [ "$include_neutronics" = "true" ] ; \
-    then pip install neutronics_material_maker ; \
+    then pip install vtk ; \
     pip install parametric_plasma_source ; \
-    pip install vtk ; \
+    pip install neutronics_material_maker ; \
     fi
 
 COPY requirements.txt requirements.txt

DockerfileDependencies

@@ -106,7 +106,7 @@ RUN if [ "$include_neutronics" = "true" ] ; \
     mkdir build ; \
     cd build ; \
     cmake .. -DCMAKE_INSTALL_PREFIX=.. \
-        -DEMBREE_ISPC_SUPPORT=OFF ; \
+             -DEMBREE_ISPC_SUPPORT=OFF ; \
     make -j"$compile_cores" ; \
     make -j"$compile_cores" install ; \
     fi
@@ -120,24 +120,20 @@ RUN if [ "$include_neutronics" = "true" ] ; \
     git clone  --single-branch --branch develop https://bitbucket.org/fathomteam/moab/ ; \
     cd build ; \
     cmake ../moab -DENABLE_HDF5=ON \
-                -DENABLE_NETCDF=ON \
-                -DBUILD_SHARED_LIBS=OFF \
-                -DENABLE_FORTRAN=OFF \
-                -DCMAKE_INSTALL_PREFIX=/MOAB ; \
+                  -DENABLE_NETCDF=ON \
+                  -DBUILD_SHARED_LIBS=OFF \
+                  -DENABLE_FORTRAN=OFF \
+                  -DENABLE_BLASLAPACK=OFF ; \
     make -j"$compile_cores" ; \
     make -j"$compile_cores" install ; \
     rm -rf * ; \
     cmake ../moab -DBUILD_SHARED_LIBS=ON \
-                -DENABLE_HDF5=ON \
-                -DENABLE_PYMOAB=ON \
-                -DENABLE_BLASLAPACK=OFF \
-                -DENABLE_FORTRAN=OFF \
-                -DCMAKE_INSTALL_PREFIX=/MOAB ; \
+                  -DENABLE_HDF5=ON \
+                  -DENABLE_PYMOAB=ON \
+                  -DENABLE_FORTRAN=OFF \
+                  -DENABLE_BLASLAPACK=OFF ; \
     make -j"$compile_cores" ; \
     make -j"$compile_cores" install ; \
-    cd pymoab ; \
-    bash install.sh ; \
-    python setup.py install ; \
     fi
 
 
@@ -148,9 +144,8 @@ RUN if [ "$include_neutronics" = "true" ] ; \
     mkdir build ; \
     cd build ; \
     cmake .. -DCMAKE_INSTALL_PREFIX=.. \
-        -DMOAB_DIR=/MOAB \
-        -DEMBREE_DIR=/embree/lib/cmake/embree-3.12.1 \
-        -DEMBREE_ROOT=/embree/lib/cmake/embree-3.12.1 ; \
+             -DMOAB_DIR=/usr/local \
+             -DEMBREE_DIR=/embree/lib/cmake/embree-3.12.1 ; \
     make -j"$compile_cores" ; \
     make -j"$compile_cores" install ; \
     fi
@@ -163,10 +158,10 @@ RUN if [ "$include_neutronics" = "true" ] ; \
     mkdir build ; \
     cd build ; \
     cmake ../dagmc -DBUILD_TALLY=ON \
-        -DCMAKE_INSTALL_PREFIX=/dagmc/ \
-        -DMOAB_DIR=/MOAB \
-        -DBUILD_STATIC_LIBS=OFF \
-        -DBUILD_STATIC_EXE=OFF ; \
+                   -DCMAKE_INSTALL_PREFIX=/dagmc/ \
+                   -DMOAB_DIR=/usr/local \
+                   -DBUILD_STATIC_LIBS=OFF \
+                   -DBUILD_STATIC_EXE=OFF ; \
     make -j"$compile_cores" install ; \
     rm -rf /DAGMC/dagmc /DAGMC/build ; \
     fi
@@ -177,9 +172,10 @@ RUN if [ "$include_neutronics" = "true" ] ; \
     cd /opt/openmc ; \
     mkdir build ; \
     cd build ; \
-    cmake -Doptimize=on -Ddagmc=ON \
-        -DDAGMC_DIR=/DAGMC/ \
-        -DHDF5_PREFER_PARALLEL=on ..  ; \
+    cmake -Doptimize=on \
+          -Ddagmc=ON \
+          -DDAGMC_DIR=/DAGMC/ \
+          -DHDF5_PREFER_PARALLEL=on ..  ; \
     make -j"$compile_cores" ; \
     make -j"$compile_cores" install ; \
     cd ..  ; \
@@ -189,12 +185,10 @@ RUN if [ "$include_neutronics" = "true" ] ; \
 
 ENV OPENMC_CROSS_SECTIONS=/root/nndc_hdf5/cross_sections.xml
 
-# Copies over the Paramak code from the local repository
-
 RUN if [ "$include_neutronics" = "true" ] ; \
-    then pip install neutronics_material_maker ; \
+    then pip install vtk ; \
     pip install parametric_plasma_source ; \
-    pip install vtk ; \
+    pip install neutronics_material_maker ; \
     fi
 
 COPY requirements.txt requirements.txt

README.md

@@ -2,7 +2,7 @@
 [![N|Python](https://www.python.org/static/community_logos/python-powered-w-100x40.png)](https://www.python.org)
 [![CircleCI](https://circleci.com/gh/ukaea/paramak/tree/main.svg?style=svg)](https://circleci.com/gh/ukaea/paramak/tree/main)
 [![codecov](https://codecov.io/gh/ukaea/paramak/branch/main/graph/badge.svg)](https://codecov.io/gh/ukaea/paramak)
-[![PyPI version](https://badge.fury.io/py/paramak.svg)](https://badge.fury.io/py/paramak)
+[![PyPI](https://img.shields.io/pypi/v/paramak?color=green&label=green&logo=green&logoColor=green)](https://pypi.org/project/paramak/)
 [![Documentation Status](https://readthedocs.org/projects/paramak/badge/?version=main)](https://paramak.readthedocs.io/en/main/?badge=main)
 [![dockerhub-publish-stable](https://github.com/ukaea/paramak/workflows/dockerhub-publish-stable/badge.svg)](https://github.com/ukaea/paramak/actions?query=workflow%3Adockerhub-publish-stable)
 [![DOI](https://zenodo.org/badge/269635577.svg)](https://zenodo.org/badge/latestdoi/269635577)

docs/source/conf.py

@@ -43,7 +43,8 @@
 extensions = [
     "sphinx.ext.autodoc",
     "sphinx.ext.coverage",
-    "sphinx.ext.napoleon"]
+    "sphinx.ext.napoleon",
+    "sphinx_autodoc_typehints"]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]

docs/source/index.rst

@@ -15,9 +15,8 @@ straightforward for developers with Python knowledge.
 
 .. raw:: html
 
-    <span style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden; max-width: 100%; height: auto;"> 
       <iframe width="560" height="315" src="https://www.youtube.com/embed/fXboew3U7rw" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
-    </span>
+
 
 .. toctree::
    :maxdepth: 1

docs/source/paramak.parametric_neutronics.rst

@@ -14,14 +14,24 @@ the material tag names. mbsize -ll dagmc.h5m | grep 'mat:'
 
 The creation of the dagmc.h5m file can be carried out via three routes.
 
-Option 1. Use of the `OCC_Faceter <https://github.com/makeclean/occ_faceter/>`_ 
-and the `PPP <https://github.com/ukaea/parallel-preprocessor>`_
+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
+geometry that touch. Therefore this method should only be used for single
+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
+Coreform 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
+method.
 
-Option 3. Use of `PyMoab <https://bitbucket.org/fathomteam/moab>`_ by
-Coreform
+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. 
@@ -34,7 +44,7 @@ Details of the Neutronics Material Maker are available from the
 and the `source code repository <https://github.com/ukaea/neutronics_material_maker>`_
 . However openmc.Materials can also be used directly.
 
-The [UKAEA openmc workshop](https://github.com/ukaea/openmc_workshop) also has
+The `OpenMC workshop <https://github.com/ukaea/openmc_workshop>`_ also has
 some Paramak with DAGMC and OpenMC based tasks that might be of interest.
 
 NeutronicsModel()

examples/example_neutronics_simulations/component_based_mesh_simulation.py

@@ -0,0 +1,69 @@
+"""This example creates a curved center column with a few different sizes.
+The shape is then converted into a neutronics geometry and the heat deposited
+is simulated for a few different sizes of ceter column"""
+
+import matplotlib.pyplot as plt
+import openmc
+import paramak
+
+
+def make_model_and_simulate():
+    simulation_values = []
+    for mid_radius in [60, 70, 80]:
+
+        # makes the component with a few different size mid radius values
+        my_shape = paramak.CenterColumnShieldHyperbola(
+            height=500,
+            inner_radius=50,
+            mid_radius=mid_radius,
+            outer_radius=100,
+            material_tag='center_column_shield_mat'
+        )
+
+        my_shape.export_stp('my_shape' + str(mid_radius) + '.stp')
+
+        # makes the openmc neutron source at x,y,z 0, 0, 0 with isotropic
+        # diections
+        source = openmc.Source()
+        source.space = openmc.stats.Point((0, 0, 0))
+        source.angle = openmc.stats.Isotropic()
+
+        # converts the geometry into a neutronics geometry
+        my_model = paramak.NeutronicsModel(
+            geometry=my_shape,
+            source=source,
+            materials={'center_column_shield_mat': 'eurofer'},
+            cell_tallies=['heating', 'TBR'],
+            mesh_tally_2D=['heating'],
+            mesh_tally_3D=['heating'],
+            simulation_batches=10,  # should be increased for more accurate result
+            simulation_particles_per_batch=10  # settings are low to reduce time required
+        )
+
+        # performs an openmc simulation on the model
+        my_model.simulate(method='pymoab')
+
+        # extracts the heat from the results dictionary
+        heat = my_model.results['center_column_shield_mat_heating']['Watts']['result']
+
+        # adds the heat and the mid radius value to a list
+        simulation_values.append((mid_radius, heat))
+
+    # plots the simualtion results vs the mid_radius used for the simulation
+    plt.plot(
+        [i[0] for i in simulation_values],
+        [i[1] for i in simulation_values],
+        '-p'
+    )
+
+    # adds labels to the graph
+    plt.title("heating vs thickness")
+    plt.xlabel("thickness (cm)")
+    plt.ylabel("heating (watts)")
+
+    plt.savefig('heating_vs_thickness.svg')
+    plt.show()
+
+
+if __name__ == "__main__":
+    make_model_and_simulate()