made plasma optional for export h5m with pymoab

paramak/reactor.py

@@ -362,6 +362,10 @@ def neutronics_description(
         interaction with neutrons. However, it can be added if the
         include_plasma argument is set to True.
 
+        Args:
+            include_plasma: Should the plasma material be included in the JSON
+                returned.
+
         Returns:
             dictionary: a dictionary of materials and filenames for the reactor
         """
@@ -692,6 +696,7 @@ def export_h5m(
             self,
             filename: Optional[str] = 'dagmc.h5m',
             include_graveyard: Optional[bool] = True,
+            include_plasma: Optional[bool] = False,
             method: Optional[str] = None,
             merge_tolerance: Optional[float] = None,
             faceting_tolerance: Optional[float] = None,
@@ -740,12 +745,14 @@ def export_h5m(
                 filename=filename,
                 merge_tolerance=merge_tolerance,
                 faceting_tolerance=faceting_tolerance,
+                include_plasma=include_plasma,
             )
         elif method == 'pymoab':
             output_filename = self.export_h5m_with_pymoab(
                 filename=filename,
                 include_graveyard=include_graveyard,
-                faceting_tolerance=faceting_tolerance
+                faceting_tolerance=faceting_tolerance,
+                include_plasma=include_plasma,
             )
 
         else:
@@ -823,6 +830,7 @@ def export_h5m_with_trelis(
             filename: Optional[str] = 'dagmc.h5m',
             merge_tolerance: Optional[float] = None,
             faceting_tolerance: Optional[float] = None,
+            include_plasma: Optional[bool] = False,
     ) -> str:
         """Produces a dagmc.h5m neutronics file compatable with DAGMC
         simulations using Coreform Trelis.
@@ -853,7 +861,7 @@ def export_h5m_with_trelis(
             self.export_neutronics_description(
                 include_graveyard=True,
                 include_sector_wedge=True,
-                include_plasma=False,
+                include_plasma=include_plasma,
             )
             self.export_stp(
                 include_graveyard=True,
@@ -887,7 +895,8 @@ def export_h5m_with_pymoab(
             self,
             filename: Optional[str] = 'dagmc.h5m',
             include_graveyard: Optional[bool] = True,
-            faceting_tolerance: Optional[float] = None
+            faceting_tolerance: Optional[float] = None,
+            include_plasma: Optional[bool] = False,
     ) -> str:
         """Converts stl files into DAGMC compatible h5m file using PyMOAB. The
         DAGMC file produced has not been imprinted and merged unlike the other
@@ -902,10 +911,13 @@ def export_h5m_with_pymoab(
                 using Reactor.graveyard_size and Reactor.graveyard_offset
                 attribute values.
             faceting_tolerance: the precision of the faceting.
+            include_plasma: Should the plasma material be included in the h5m
+                file.
 
         Returns:
             The filename of the DAGMC file created
         """
+
         if faceting_tolerance is None:
             faceting_tolerance = self.faceting_tolerance
 
@@ -922,18 +934,26 @@ def export_h5m_with_pymoab(
         volume_id = 1
 
         if isinstance(self.shapes_and_components, list):
-            for item in self.shapes_and_components:
+            for entry in self.shapes_and_components:
+
+                if include_plasma is False and (
+                    isinstance(
+                        entry,
+                        (paramak.Plasma,
+                         paramak.PlasmaFromPoints,
+                         paramak.PlasmaBoundaries)) is True or entry.name == 'plasma'):
+                    continue
 
-                item.export_stl(
-                    item.stl_filename,
+                entry.export_stl(
+                    entry.stl_filename,
                     tolerance=faceting_tolerance)
                 moab_core = add_stl_to_moab_core(
                     moab_core,
                     surface_id,
                     volume_id,
-                    item.material_tag,
+                    entry.material_tag,
                     moab_tags,
-                    item.stl_filename)
+                    entry.stl_filename)
                 volume_id += 1
                 surface_id += 1
         else:

tests/test_Reactor.py

@@ -1210,6 +1210,30 @@ def test_export_h5m_with_pymoab_without_faceting_tolerance(self):
         my_reactor.faceting_tolerance = 1e-2
         my_reactor.export_h5m_with_pymoab(faceting_tolerance=None)
 
+    def test_export_h5m_with_pymoab_without_plasma(self):
+        """exports a h5m file with pymoab without the plasma"""
+
+        os.system('rm *.stl')
+
+        test_shape1 = paramak.RotateStraightShape(
+            points=[(0, 0), (0, 20), (20, 20)],
+            stl_filename='RotateStraightShape.stl'
+        )
+        test_shape2 = paramak.Plasma(
+            stl_filename='plasma.stl'
+        )
+
+        my_reactor = paramak.Reactor([test_shape1, test_shape2])
+        my_reactor.export_h5m_with_pymoab(include_plasma=False, filename='no_plasma.h5m')
+
+        assert Path('RotateStraightShape.stl').is_file()
+        assert Path('plasma.stl').is_file() is False
+        my_reactor.export_h5m_with_pymoab(include_plasma=True, filename='with_plasma.h5m')
+        assert Path('plasma.stl').is_file()
+
+        assert Path('with_plasma.h5m').stat().st_size > Path('no_plasma.h5m').stat().st_size
+
+
     def test_export_h5m_with_pymoab_from_manifest_file(self):
         """exports a h5m file when shapes_and_components is set to a string"""
 
@@ -1221,7 +1245,7 @@ def check_correct_error_is_rasied():
             test_shape.export_neutronics_description('manifest.json')
             my_reactor = paramak.Reactor('manifest.json')
             my_reactor.export_h5m_with_pymoab()
-            assert Path('dagmc.h5m').is_file
+            assert Path('dagmc.h5m').is_file()
 
         self.assertRaises(NotImplementedError, check_correct_error_is_rasied)
 
@@ -1233,16 +1257,17 @@ def test_export_vtk(self):
         assert self.test_reactor.h5m_filename is None
         self.test_reactor.export_h5m_with_pymoab()
         self.test_reactor.export_vtk()
-        assert Path('dagmc.h5m').is_file
-        assert Path('dagmc.vtk').is_file
-        assert Path('dagmc_no_graveyard.vtk').is_file
+        assert Path('dagmc.h5m').is_file()
+        assert Path('dagmc.vtk').is_file()
+        self.test_reactor.export_vtk(include_graveyard=False, filename='dagmc_no_graveyard.vtk')
+        assert Path('dagmc_no_graveyard.vtk').is_file()
         assert self.test_reactor.h5m_filename == 'dagmc.h5m'
 
         self.test_reactor.export_vtk(filename='custom_filename.vtk')
-        assert Path('custom_filename.vtk').is_file
+        assert Path('custom_filename.vtk').is_file()
 
         self.test_reactor.export_vtk(filename='suffixless_filename')
-        assert Path('suffixless_filename.vtk').is_file
+        assert Path('suffixless_filename.vtk').is_file()
 
     def test_export_vtk_without_h5m_raises_error(self):
         """exports a h5m file when shapes_and_components is set to a string"""