Adding export h5m using brep gmsh method

conda/meta.yaml

@@ -18,6 +18,8 @@ requirements:
     - setuptools
   run:
     - cadquery
+    - gmsh
+    - moab  # not available on windows
     - matplotlib
     - mpmath
     - numpy
@@ -30,7 +32,7 @@ requirements:
     - nbformat
     - nbconvert
     - ipywidgets
-    # - jupyter-cadquery not availalbe on conda
+    # - jupyter-cadquery not available on conda
 
 test:
   imports:

conda_build.sh

@@ -22,7 +22,7 @@ rm -rf /tmp/conda-build
 
 
 # VERSION=$(echo $GITHUB_REF | sed 's#.*/v##')
-VERSION=0.6.4
+VERSION=0.7.0
 PLACEHOLDER='version="develop"'
 VERSION_FILE='setup.py'
 # Grep checks that the placeholder is in the file. If grep doesn't find
@@ -37,7 +37,8 @@ conda-build conda/ -c cadquery -c conda-forge --croot /tmp/conda-build
 # conda convert /tmp/conda-build/linux-64/*.tar.bz2 --platform all  -o /tmp/conda-build
 
 # option for converting package to specified platforms
-platforms=( osx-64 linux-64 win-64 )
+# platforms=( osx-64 linux-64 win-64 ) windows does not have moab
+platforms=( osx-64 linux-64 )
 find /tmp/conda-build/linux-64/ -name *.tar.bz2 | while read file
 do
     echo $file

conda_build_config.yaml

@@ -1,6 +1,8 @@
 python:
     - 3.8
-    - 3.7
-    - 3.6
+    # - 3.7
+    # - 3.6
 cadquery:
-    - 2.1
+    - master
+moab:
+    - 5.3.1

docs/source/install.rst

@@ -44,6 +44,7 @@ Then install the Paramak.
 Now you should be ready to import paramak from your new python environment.
 
 
+
 Install (conda + pip)
 ---------------------
 
@@ -65,7 +66,16 @@ Then install the CadQuery.
 
 .. code-block:: bash
 
-   conda install -c cadquery -c conda-forge cadquery=2.1
+   conda install -c cadquery -c conda-forge cadquery=2.2
+
+MOAB and PyMoab are required for the export_dagmc_h5m() feature to work. The
+MOAB Conda install does not currently support Windows and therefore Windows
+users will have to compile MOAB. If the export_dagmc_h5m() feature is not
+needed then this stage can be skipped.
+
+.. code-block:: bash
+
+   conda install -c cadquery -c conda-forge moab=5.3.0
 
 Then pip install the Paramak.
 

paramak/parametric_shapes/extruded_mixed_shape.py

@@ -83,7 +83,10 @@ def create_solid(self):
 
         self.wire = wire
 
-        solid = wire.extrude(distance=extrusion_distance, both=self.extrude_both)
+        try:  # CQ version 2.2
+            solid = wire.extrude(until=extrusion_distance, both=self.extrude_both)
+        except:  # CQ version 2.1
+            solid = wire.extrude(distance=extrusion_distance, both=self.extrude_both)
 
         # filleting rectangular port cutter edges
         # must be done before azimuthal placement

paramak/reactor.py

@@ -1,13 +1,16 @@
-import collections
-import json
-from collections import Counter
+import os
+import tempfile
+
 from collections.abc import Iterable
 from pathlib import Path
 from typing import List, Optional, Tuple, Union
+import warnings
 
+import brep_part_finder as bpf
 import cadquery as cq
 import matplotlib.pyplot as plt
-from cadquery import Compound, exporters
+from brep_to_h5m import brep_to_h5m
+from cadquery import exporters
 
 import paramak
 from paramak.utils import _replace, get_hash
@@ -233,6 +236,86 @@ def show(self, default_edgecolor: Tuple[float, float, float] = (0, 0, 0)):
 
         return show(PartGroup(parts), default_edgecolor=scaled_edge_color)
 
+    def export_dagmc_h5m(
+        self,
+        filename: str = "dagmc.h5m",
+        min_mesh_size: float = 10,
+        max_mesh_size: float = 20,
+        exclude: List[str] = None,
+    ) -> str:
+        """Export a DAGMC compatible h5m file for use in neutronics simulations.
+        This method makes use of Gmsh to create a surface mesh of the geometry.
+        MOAB is used to convert the meshed geometry into a h5m with parts tagged by
+        using the reactor.shape_and_components.name properties. You will need
+        Gmsh installed and MOAB installed to use this function.
+
+        Args:
+            filename: the filename of the DAGMC h5m file to write
+            min_mesh_size: the minimum mesh element size to use in Gmsh. Passed
+                into gmsh.option.setNumber("Mesh.MeshSizeMin", min_mesh_size)
+            max_mesh_size: the maximum mesh element size to use in Gmsh. Passed
+                into gmsh.option.setNumber("Mesh.MeshSizeMax", max_mesh_size)
+            exclude: A list of shape names to not include in the exported
+                geometry. 'plasma' is often excluded as not many neutron
+                interactions occur within a low density plasma.
+        """
+
+        tmp_brep_filename = tempfile.mkstemp(suffix=".brep", prefix="paramak_")[1]
+
+        # saves the reactor as a Brep file with merged surfaces
+        self.export_brep(tmp_brep_filename)
+
+        # brep file is imported
+        brep_file_part_properties = bpf.get_brep_part_properties(tmp_brep_filename)
+
+        shape_properties = {}
+        for shape_or_compound in self.shapes_and_components:
+            sub_solid_descriptions = []
+            for sub_solid in shape_or_compound.solid.val().Solids():
+                part_bb = sub_solid.BoundingBox()
+                part_center = sub_solid.Center()
+                sub_solid_description = {
+                    "volume": sub_solid.Volume(),
+                    "center": (part_center.x, part_center.y, part_center.z),
+                    "bounding_box": (
+                        (part_bb.xmin, part_bb.ymin, part_bb.zmin),
+                        (part_bb.xmax, part_bb.ymax, part_bb.zmax),
+                    ),
+                }
+                sub_solid_descriptions.append(sub_solid_description)
+            shape_properties[shape_or_compound.name] = sub_solid_descriptions
+
+        # request to find part ids that are mixed up in the Brep file
+        # using the volume, center, bounding box that we know about when creating the
+        # CAD geometry in the first place
+        key_and_part_id = bpf.get_dict_of_part_ids(
+            brep_part_properties=brep_file_part_properties,
+            shape_properties=shape_properties,
+        )
+
+        # allows components like the plasma to be removed
+        if isinstance(exclude, Iterable):
+            for name_to_remove in exclude:
+                key_and_part_id = {
+                    key: val
+                    for key, val in key_and_part_id.items()
+                    if val != name_to_remove
+                }
+
+        brep_to_h5m(
+            brep_filename=tmp_brep_filename,
+            volumes_with_tags=key_and_part_id,
+            h5m_filename=filename,
+            min_mesh_size=min_mesh_size,
+            max_mesh_size=max_mesh_size,
+            delete_intermediate_stl_files=True,
+        )
+
+        # temporary brep is deleted
+        os.remove(tmp_brep_filename)
+
+        return filename
+
     def export_stp(
         self,
         filename: Union[List[str], str] = None,
@@ -477,7 +560,6 @@ def make_sector_wedge(
             height=height,
             radius=radius,
             rotation_angle=360 - rotation_angle,
-            surface_reflectivity=True,
             azimuth_placement_angle=rotation_angle,
         )
 

paramak/shape.py

@@ -1,11 +1,13 @@
-import json
 import numbers
-import warnings
+import os
+import tempfile
 from collections.abc import Iterable
 from pathlib import Path
 from typing import List, Optional, Tuple, Union
 
+import brep_part_finder as bpf
 import matplotlib.pyplot as plt
+from brep_to_h5m import brep_to_h5m
 from cadquery import Assembly, Color, Compound, Plane, Workplane, exporters, importers
 from cadquery.occ_impl import shapes
 from matplotlib.collections import PatchCollection
@@ -847,6 +849,44 @@ def export_brep(self, filename):
 
         return str(path_filename)
 
+    def export_dagmc_h5m(
+        self,
+        filename: str = "dagmc.h5m",
+        min_mesh_size: float = 10,
+        max_mesh_size: float = 20,
+    ) -> str:
+        """Export a DAGMC compatible h5m file for use in neutronics simulations.
+        This method makes use of Gmsh to create a surface mesh of the geometry.
+        MOAB is used to convert the meshed geometry into a h5m with parts tagged by
+        using the reactor.shape_and_components.name properties. You will need
+        Gmsh installed and MOAB installed to use this function.
+
+        Args:
+            filename: the filename of the DAGMC h5m file to write
+            min_mesh_size: the minimum mesh element size to use in Gmsh. Passed
+                into gmsh.option.setNumber("Mesh.MeshSizeMin", min_mesh_size)
+            max_mesh_size: the maximum mesh element size to use in Gmsh. Passed
+                into gmsh.option.setNumber("Mesh.MeshSizeMax", max_mesh_size)
+        """
+
+        tmp_brep_filename = tempfile.mkstemp(suffix=".brep", prefix=f"paramak_")[1]
+
+        # saves the reactor as a Brep file with merged surfaces
+        self.export_brep(tmp_brep_filename)
+
+        brep_to_h5m(
+            brep_filename=tmp_brep_filename,
+            volumes_with_tags={1: f"mat_{self.name}"},
+            h5m_filename=filename,
+            min_mesh_size=min_mesh_size,
+            max_mesh_size=max_mesh_size,
+        )
+
+        # temporary brep is deleted
+        os.remove(tmp_brep_filename)
+
+        return filename
+
     def export_stp(
         self,
         filename: str,