Merge pull request #692 from ukaea/develop

new double down build and mesh tally arg names
ukaea · Jan 25, 2021 · 8188fb5 · 8188fb5
2 parents 3ce4c71 + d46d687
commit 8188fb5
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Showing 8 changed files with 99 additions and 62 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -90,7 +90,7 @@ RUN if [ "$include_neutronics" = "true" ] ; \
 
 # Clone and install NJOY2016
 RUN if [ "$include_neutronics" = "true" ] ; \
-    then git clone https://github.com/njoy/NJOY2016 /opt/NJOY2016 ; \
+    then git clone --single-branch --branch master https://github.com/njoy/NJOY2016.git /opt/NJOY2016 ; \
     cd /opt/NJOY2016 ; \
     mkdir build ; \
     cd build ; \
@@ -101,7 +101,7 @@ RUN if [ "$include_neutronics" = "true" ] ; \
 
 # Clone and install Embree
 RUN if [ "$include_neutronics" = "true" ] ; \
-    then git clone https://github.com/embree/embree ; \
+    then git clone --single-branch --branch master https://github.com/embree/embree.git ; \
     cd embree ; \
     mkdir build ; \
     cd build ; \
@@ -117,7 +117,7 @@ RUN if [ "$include_neutronics" = "true" ] ; \
     mkdir MOAB ; \
     cd MOAB ; \
     mkdir build ; \
-    git clone  --single-branch --branch develop https://bitbucket.org/fathomteam/moab/ ; \
+    git clone  --single-branch --branch develop https://bitbucket.org/fathomteam/moab.git ; \
     cd build ; \
     cmake ../moab -DENABLE_HDF5=ON \
                   -DENABLE_NETCDF=ON \
@@ -144,13 +144,13 @@ RUN if [ "$include_neutronics" = "true" ] ; \
 
 # Clone and install Double-Down
 RUN if [ "$include_neutronics" = "true" ] ; \
-    then git clone https://github.com/pshriwise/double-down ; \
+    then git clone --single-branch --branch main https://github.com/pshriwise/double-down.git ; \
     cd double-down ; \
     mkdir build ; \
     cd build ; \
     cmake .. -DMOAB_DIR=/MOAB \
              -DCMAKE_INSTALL_PREFIX=.. \
-             -DEMBREE_DIR=/embree/lib/cmake/embree-3.12.1 ; \
+             -DEMBREE_DIR=/embree ; \
     make -j"$compile_cores" ; \
     make -j"$compile_cores" install ; \
     fi
@@ -159,16 +159,16 @@ RUN if [ "$include_neutronics" = "true" ] ; \
 RUN if [ "$include_neutronics" = "true" ] ; \
     then mkdir DAGMC ; \
     cd DAGMC ; \
-    git clone -b develop https://github.com/svalinn/dagmc ; \
+    git clone --single-branch --branch develop https://github.com/svalinn/DAGMC.git ; \
     mkdir build ; \
     cd build ; \
-    cmake ../dagmc -DBUILD_TALLY=ON \
+    cmake ../DAGMC -DBUILD_TALLY=ON \
                    -DMOAB_DIR=/MOAB \
                    -DBUILD_STATIC_EXE=OFF \
                    -DBUILD_STATIC_LIBS=OFF \
-                   -DCMAKE_INSTALL_PREFIX=/dagmc/ ; \
+                   -DCMAKE_INSTALL_PREFIX=/DAGMC/ ; \
     make -j"$compile_cores" install ; \
-    rm -rf /DAGMC/dagmc /DAGMC/build ; \
+    rm -rf /DAGMC/DAGMC /DAGMC/build ; \
     fi
 
 # Clone and install OpenMC with DAGMC

diff --git a/DockerfileDependencies b/DockerfileDependencies
@@ -90,7 +90,7 @@ RUN if [ "$include_neutronics" = "true" ] ; \
 
 # Clone and install NJOY2016
 RUN if [ "$include_neutronics" = "true" ] ; \
-    then git clone https://github.com/njoy/NJOY2016 /opt/NJOY2016 ; \
+    then git clone --single-branch --branch master https://github.com/njoy/NJOY2016.git /opt/NJOY2016 ; \
     cd /opt/NJOY2016 ; \
     mkdir build ; \
     cd build ; \
@@ -101,7 +101,7 @@ RUN if [ "$include_neutronics" = "true" ] ; \
 
 # Clone and install Embree
 RUN if [ "$include_neutronics" = "true" ] ; \
-    then git clone https://github.com/embree/embree ; \
+    then git clone --single-branch --branch master https://github.com/embree/embree.git ; \
     cd embree ; \
     mkdir build ; \
     cd build ; \
@@ -117,7 +117,7 @@ RUN if [ "$include_neutronics" = "true" ] ; \
     mkdir MOAB ; \
     cd MOAB ; \
     mkdir build ; \
-    git clone  --single-branch --branch develop https://bitbucket.org/fathomteam/moab/ ; \
+    git clone  --single-branch --branch develop https://bitbucket.org/fathomteam/moab.git ; \
     cd build ; \
     cmake ../moab -DENABLE_HDF5=ON \
                   -DENABLE_NETCDF=ON \
@@ -144,13 +144,13 @@ RUN if [ "$include_neutronics" = "true" ] ; \
 
 # Clone and install Double-Down
 RUN if [ "$include_neutronics" = "true" ] ; \
-    then git clone https://github.com/pshriwise/double-down ; \
+    then git clone --single-branch --branch main https://github.com/pshriwise/double-down.git ; \
     cd double-down ; \
     mkdir build ; \
     cd build ; \
     cmake .. -DMOAB_DIR=/MOAB \
              -DCMAKE_INSTALL_PREFIX=.. \
-             -DEMBREE_DIR=/embree/lib/cmake/embree-3.12.1 ; \
+             -DEMBREE_DIR=/embree ; \
     make -j"$compile_cores" ; \
     make -j"$compile_cores" install ; \
     fi
@@ -159,16 +159,16 @@ RUN if [ "$include_neutronics" = "true" ] ; \
 RUN if [ "$include_neutronics" = "true" ] ; \
     then mkdir DAGMC ; \
     cd DAGMC ; \
-    git clone -b develop https://github.com/svalinn/dagmc ; \
+    git clone --single-branch --branch develop https://github.com/svalinn/DAGMC.git ; \
     mkdir build ; \
     cd build ; \
-    cmake ../dagmc -DBUILD_TALLY=ON \
+    cmake ../DAGMC -DBUILD_TALLY=ON \
                    -DMOAB_DIR=/MOAB \
                    -DBUILD_STATIC_EXE=OFF \
                    -DBUILD_STATIC_LIBS=OFF \
-                   -DCMAKE_INSTALL_PREFIX=/dagmc/ ; \
+                   -DCMAKE_INSTALL_PREFIX=/DAGMC/ ; \
     make -j"$compile_cores" install ; \
-    rm -rf /DAGMC/dagmc /DAGMC/build ; \
+    rm -rf /DAGMC/DAGMC /DAGMC/build ; \
     fi
 
 # Clone and install OpenMC with DAGMC

diff --git a/README.md b/README.md
@@ -37,6 +37,37 @@ have helped the development in the
 The code has been professionally reviewed by [PullRequest.com](https://www.pullrequest.com/) who
 produced a [report](https://github.com/ukaea/paramak/files/5704872/PULLREQUEST.Paramak.Project.Review.pdf) and inline [suggestions](https://github.com/ukaea/paramak/pull/639).
 
+## Citing
+
+If you use the Paramak in your research, please consider giving proper
+attribution by citing the our [Publication](https://f1000research.com/articles/10-27/v1):
+
+- J. Shimwell, J. Billingsley and R. Delaporte-Mathurin et al. The Paramak: 
+  Automated Parametric Geometry Construction for Fusion Reactor Designs.
+  F1000Research, vol. 10, Jan. 2021, p. 27. DOI.org (Crossref),
+  doi:10.12688/f1000research.28224.1.
+
+    <details>
+        <summary>BibTex</summary>
+        <pre><code class="language-html">
+    @article{paramak,
+        title = {The {Paramak}: automated parametric geometry construction for fusion reactor designs.},
+        volume = {10},
+        issn = {2046-1402},
+        shorttitle = {The {Paramak}},
+        url = {https://f1000research.com/articles/10-27/v1},
+        doi = {10.12688/f1000research.28224.1},
+        language = {en},
+        urldate = {2021-01-22},
+        journal = {F1000Research},
+        author = {Shimwell, Jonathan and Billingsley, John and Delaporte-Mathurin, Rémi and Morbey, Declan and Bluteau, Matthew and Shriwise, Patrick and Davis, Andrew},
+        month = jan,
+        year = {2021},
+        pages = {27},
+    }
+        </code></pre>
+    </details>
+
 
 ## System Installation
 

diff --git a/examples/example_neutronics_simulations/component_based_mesh_simulation.py b/examples/example_neutronics_simulations/component_based_mesh_simulation.py
@@ -34,8 +34,8 @@ def make_model_and_simulate():
             source=source,
             materials={'center_column_shield_mat': 'eurofer'},
             cell_tallies=['heating', 'TBR'],
-            mesh_tally_2D=['heating'],
-            mesh_tally_3D=['heating'],
+            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
         )

diff --git a/paramak/parametric_neutronics/neutronics_model.py b/paramak/parametric_neutronics/neutronics_model.py
@@ -56,8 +56,10 @@ class NeutronicsModel():
             neutronics-material-maker.MultiMaterial. All components within the
             geometry object must be accounted for. Material tags required
             for a Reactor or Shape can be obtained with .material_tags.
-        mesh_tally_2D (list of strings): the mesh based tallies to calculate,
-            options include tritium_production, heating and flux
+        mesh_tally_2d (list of str): the 2D mesh based tallies to calculate,
+            options include tritium_production, heating and flux.
+        mesh_tally_3d (list of str): the 3D mesh based tallies to calculate,
+            options include tritium_production, heating and flux.
         fusion_power (float): the power in watts emitted by the fusion
             reaction recalling that each DT fusion reaction emitts 17.6 MeV or
             2.819831e-12 Joules
@@ -69,10 +71,14 @@ class NeutronicsModel():
             Defaults to 1e-4.
         faceting_tolerance (float): the tolerance to use when faceting surfaces.
             Defaults to 1e-1.
-        mesh_2D_resolution (tuple of ints): The mesh resolution in the height
+        mesh_2D_resolution (tuple of ints): The 3D mesh resolution in the height
             and width directions. The larger the resolution the finer the mesh
             and more computational intensity is required to converge each mesh
             element.
+        mesh_3D_resolution (tuple of int): The 3D mesh resolution in the height,
+            width and depth directions. The larger the resolution the finer the
+            mesh and the more computational intensity is required to converge each
+            mesh element.
     """
 
     def __init__(
@@ -81,8 +87,8 @@ def __init__(
         source,
         materials,
         cell_tallies=None,
-        mesh_tally_2D=None,
-        mesh_tally_3D=None,
+        mesh_tally_2d=None,
+        mesh_tally_3d=None,
         simulation_batches: int = 100,
         simulation_particles_per_batch: int = 10000,
         max_lost_particles: int = 10,
@@ -97,8 +103,8 @@ def __init__(
         self.geometry = geometry
         self.source = source
         self.cell_tallies = cell_tallies
-        self.mesh_tally_2D = mesh_tally_2D
-        self.mesh_tally_3D = mesh_tally_3D
+        self.mesh_tally_2d = mesh_tally_2d
+        self.mesh_tally_3d = mesh_tally_3d
         self.simulation_batches = simulation_batches
         self.simulation_particles_per_batch = simulation_particles_per_batch
         self.max_lost_particles = max_lost_particles
@@ -167,48 +173,48 @@ def cell_tallies(self, value):
         self._cell_tallies = value
 
     @property
-    def mesh_tally_2D(self):
-        return self._mesh_tally_2D
+    def mesh_tally_2d(self):
+        return self._mesh_tally_2d
 
-    @mesh_tally_2D.setter
-    def mesh_tally_2D(self, value):
+    @mesh_tally_2d.setter
+    def mesh_tally_2d(self, value):
         if value is not None:
             if not isinstance(value, list):
                 raise TypeError(
-                    "NeutronicsModelFromReactor.mesh_tally_2D should be a\
+                    "NeutronicsModelFromReactor.mesh_tally_2d should be a\
                     list")
             output_options = ['tritium_production', 'heating', 'flux',
                               'fast flux', 'dose']
             for entry in value:
                 if entry not in output_options:
                     raise ValueError(
-                        "NeutronicsModelFromReactor.mesh_tally_2D argument",
+                        "NeutronicsModelFromReactor.mesh_tally_2d argument",
                         entry,
                         "not allowed, the following options are supported",
                         output_options)
-        self._mesh_tally_2D = value
+        self._mesh_tally_2d = value
 
     @property
-    def mesh_tally_3D(self):
-        return self._mesh_tally_3D
+    def mesh_tally_3d(self):
+        return self._mesh_tally_3d
 
-    @mesh_tally_3D.setter
-    def mesh_tally_3D(self, value):
+    @mesh_tally_3d.setter
+    def mesh_tally_3d(self, value):
         if value is not None:
             if not isinstance(value, list):
                 raise TypeError(
-                    "NeutronicsModelFromReactor.mesh_tally_3D should be a\
+                    "NeutronicsModelFromReactor.mesh_tally_3d should be a\
                     list")
             output_options = ['tritium_production', 'heating', 'flux',
                               'fast flux', 'dose']
             for entry in value:
                 if entry not in output_options:
                     raise ValueError(
-                        "NeutronicsModelFromReactor.mesh_tally_3D argument",
+                        "NeutronicsModelFromReactor.mesh_tally_3d argument",
                         entry,
                         "not allowed, the following options are supported",
                         output_options)
-        self._mesh_tally_3D = value
+        self._mesh_tally_3d = value
 
     @property
     def materials(self):
@@ -390,7 +396,7 @@ def _make_watertight(self):
 
     def create_neutronics_model(self, method: str = None):
         """Uses OpenMC python API to make a neutronics model, including tallies
-        (cell_tallies and mesh_tally_2D), simulation settings (batches,
+        (cell_tallies and mesh_tally_2d), simulation settings (batches,
         particles per batch).
 
         Arguments:
@@ -422,7 +428,7 @@ def create_neutronics_model(self, method: str = None):
         # details about what neutrons interactions to keep track of (tally)
         self.tallies = openmc.Tallies()
 
-        if self.mesh_tally_3D is not None:
+        if self.mesh_tally_3d is not None:
             mesh_xyz = openmc.RegularMesh(mesh_id=1, name='3d_mesh')
             mesh_xyz.dimension = self.mesh_3D_resolution
             mesh_xyz.lower_left = [
@@ -437,7 +443,7 @@ def create_neutronics_model(self, method: str = None):
                 self.geometry.largest_dimension
             ]
 
-            for standard_tally in self.mesh_tally_3D:
+            for standard_tally in self.mesh_tally_3d:
                 if standard_tally == 'tritium_production':
                     score = '(n,Xt)'  # where X is a wild card
                     prefix = 'tritium_production'
@@ -451,7 +457,7 @@ def create_neutronics_model(self, method: str = None):
                 tally.scores = [score]
                 self.tallies.append(tally)
 
-        if self.mesh_tally_2D is not None:
+        if self.mesh_tally_2d is not None:
 
             # Create mesh which will be used for tally
             mesh_xz = openmc.RegularMesh(mesh_id=2, name='2d_mesh_xz')
@@ -512,7 +518,7 @@ def create_neutronics_model(self, method: str = None):
                 self.geometry.largest_dimension
             ]
 
-            for standard_tally in self.mesh_tally_2D:
+            for standard_tally in self.mesh_tally_2d:
                 if standard_tally == 'tritium_production':
                     score = '(n,Xt)'  # where X is a wild card
                     prefix = 'tritium_production'

diff --git a/paramak/utils.py b/paramak/utils.py
@@ -122,8 +122,8 @@ def find_center_point_of_circle(point_a: Tuple[float, float],
         point_b (float, float): point 2 coordinates
         point3 (float, float): point 3 coordinates
     Returns:
-        float, float: center of the circle coordinates or
-        None if 3 points on a line are input.
+        (float, float), float: center of the circle coordinates or
+        None if 3 points on a line are input and the radius
     """
 
     temp = point_b[0] * point_b[0] + point_b[1] * point_b[1]

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="paramak",
-    version="0.2.1",
+    version="0.2.2",
     author="The Paramak Development Team",
     author_email="[email protected]",
     description="Create 3D fusion reactor CAD models based on input parameters",