Merge pull request #112 from svalinn/export_cub5

add option to export to cub5

Examples/config.yaml

@@ -63,6 +63,7 @@ invessel_build:
       mat_tag: vac_vessel
   plasma_mat_tag: Vacuum
   sol_mat_tag: Vacuum
+  split_chamber: True
   export_cad_to_dagmc: False
 
 magnet_coils:
@@ -83,3 +84,5 @@ dagmc_export:
   skip_imprint: False
   legacy_faceting: True
   filename: dagmc
+
+cub5_export: False

Examples/parastell_example.py

@@ -93,10 +93,13 @@
     export_dir=export_dir
 )
 
+# Build Cubit model of Parastell Components
+stellarator.build_cubit_model(
+    skip_imprint=False,
+    legacy_faceting=True)
+
 # Export DAGMC neutronics H5M file
 stellarator.export_dagmc(
-    skip_imprint=False,
-    legacy_faceting=True,
     filename='dagmc',
     export_dir=export_dir
 )

parastell/cubit_io.py

@@ -61,6 +61,18 @@ def export_step_cubit(filename, export_dir=''):
     export_path = Path(export_dir) / Path(filename).with_suffix('.step')
     cubit.cmd(f'export step "{export_path}" overwrite')
 
+def export_cub5(filename, export_dir=''):
+    """Export cub5 representation of model (native Cubit format).
+    
+    Arguments:
+        filename (str): name of cub5 output file, excluding '.cub5' extension.
+        export_dir (str): directory to which to export the cub5 output file
+            (defaults to empty string).
+    """
+    init_cubit()
+
+    export_path = Path(export_dir) / Path(filename).with_suffix('.cub5')
+    cubit.cmd(f'save cub5 "{export_path}" overwrite')
 
 def export_mesh_cubit(filename, export_dir=''):
     """Exports Cubit mesh to H5M file format, first exporting to Exodus format

parastell/parastell.py

@@ -14,11 +14,16 @@
 from . import cubit_io
 from .utils import read_yaml_config, filter_kwargs, m2cm
 
+build_cubit_model_allowed_kwargs = ['skip_imprint', 'legacy_faceting']
+export_dagmc_allowed_kwargs = ['faceting_tolerance', 'length_tolerance',
+                               'normal_tolerance', 'anisotropic_ratio',
+                               'deviation_angle']
+
 
 def make_material_block(mat_tag, block_id, vol_id_str):
     """Issue commands to make a material block using Cubit's
     native capabilities.
-    
+
     Arguments:
        mat_tag (str) : name of material block
        block_id (int) : block number
@@ -58,7 +63,7 @@ def __init__(
         vmec_file,
         logger=None
     ):
-        
+
         self.logger = logger
         self.vmec_file = vmec_file
 
@@ -69,7 +74,7 @@ def __init__(
     @property
     def vmec_file(self):
         return self._vmec_file
-    
+
     @vmec_file.setter
     def vmec_file(self, file):
         self._vmec_file = file
@@ -82,7 +87,7 @@ def vmec_file(self, file):
     @property
     def logger(self):
         return self._logger
-    
+
     @logger.setter
     def logger(self, logger_object):
         self._logger = log.check_init(logger_object)
@@ -340,7 +345,7 @@ def _tag_materials_native(self):
             block_id = min(vol_list)
             vol_id_str = " ".join(str(i) for i in vol_list)
             make_material_block(self.magnet_set.mat_tag, block_id, vol_id_str)
-        
+
         if self.invessel_build:
             for data in (
                 self.invessel_build.radial_build.radial_build.values()
@@ -349,19 +354,42 @@ def _tag_materials_native(self):
                 vol_id_str = str(block_id)
                 make_material_block(data['mat_tag'], block_id, vol_id_str)
 
-    def export_dagmc(
-        self, skip_imprint=False, legacy_faceting=True, filename='dagmc',
-        export_dir='', **kwargs
-    ):
-        """Exports DAGMC neutronics H5M file of ParaStell components via
-        Coreform Cubit.
+    def build_cubit_model(self, skip_imprint=False, legacy_faceting=True):
+        """Build model for DAGMC neutronics H5M file of Parastell components via
+        Coreform Cubit
 
         Arguments:
             skip_imprint (bool): choose whether to imprint and merge all in
                 Coreform Cubit or to merge surfaces based on import order and
                 geometry information (optional, defaults to False).
             legacy_faceting (bool): choose legacy or native faceting for DAGMC
                 export (optional, defaults to True).
+        """
+        self.legacy_faceting = legacy_faceting
+
+        self._logger.info(
+            'Building DAGMC neutronics model via Coreform Cubit...'
+        )
+
+        if self.invessel_build:
+            self._import_ivb_step()
+
+        if skip_imprint:
+            self.invessel_build.merge_layer_surfaces()
+        else:
+            cubit.cmd('imprint volume all')
+            cubit.cmd('merge volume all')
+
+        if legacy_faceting:
+            self._tag_materials_legacy()
+        else:
+            self._tag_materials_native()
+
+    def export_dagmc(self, filename='dagmc', export_dir='', **kwargs):
+        """Exports DAGMC neutronics H5M file of ParaStell components via
+        Coreform Cubit.
+
+        Arguments:
             filename (str): name of DAGMC output file, excluding '.h5m'
                 extension (optional, defaults to 'dagmc').
             export_dir (str): directory to which to export DAGMC output file
@@ -387,35 +415,42 @@ def export_dagmc(
                 attribute is used only for the native faceting method.
         """
         cubit_io.init_cubit()
-        
+
         self._logger.info(
             'Exporting DAGMC neutronics model...'
         )
 
-        if self.invessel_build:
-            self._import_ivb_step()
-
-        if skip_imprint:
-            self.invessel_build.merge_layer_surfaces()
-        else:
-            cubit.cmd('imprint volume all')
-            cubit.cmd('merge volume all')
-
-        if legacy_faceting:
-            self._tag_materials_legacy()
+        if self.legacy_faceting:
             cubit_io.export_dagmc_cubit_legacy(
                 filename=filename,
                 export_dir=export_dir,
                 **kwargs
             )
         else:
-            self._tag_materials_native()
             cubit_io.export_dagmc_cubit_native(
                 filename=filename,
                 export_dir=export_dir,
                 **kwargs
             )
 
+    def export_cub5(self, filename='stellarator', export_dir=''):
+        """Export native Coreform Cubit format (cub5) of Parastell model.
+
+        Arguments:
+            filename (str): name of DAGMC output file, excluding '.h5m'
+                extension (optional, defaults to 'dagmc').
+            export_dir (str): directory to which to export DAGMC output file
+                (optional, defaults to empty string).
+        """
+        cubit_io.init_cubit()
+
+        self._logger.info(
+            'Exporting cub5 model...'
+        )
+
+        cubit_io.export_cub5(filename=filename,
+                             export_dir=export_dir)
+
 
 def parse_args():
     """Parser for running as a script.
@@ -445,7 +480,7 @@ def parse_args():
     )
 
     parser.add_argument(
-        '-i', '--ivb', 
+        '-i', '--ivb',
         action='store_true',
         help=(
             'flag to indicate the creation of in-vessel component geometry '
@@ -454,15 +489,15 @@ def parse_args():
     )
 
     parser.add_argument(
-        '-m', '--magnets', 
+        '-m', '--magnets',
         action='store_true',
         help=(
             'flag to indicate the creation of magnet geometry (default: False)'
         )
     )
-    
+
     parser.add_argument(
-        '-s', '--source', 
+        '-s', '--source',
         action='store_true',
         help=(
             'flag to indicate the creation of a tetrahedral source mesh '
@@ -471,7 +506,7 @@ def parse_args():
     )
 
     parser.add_argument(
-        '-n', '--nwl', 
+        '-n', '--nwl',
         action='store_true',
         help=(
             'flag to indicate the creation of a geometry for neutron wall '
@@ -503,30 +538,30 @@ def check_inputs(
     ivb_tor_ext = (repeat + 1) * invessel_build['toroidal_angles'][-1]
     mag_tor_ext = magnet_coils['toroidal_extent']
     src_tor_ext = source_mesh['toroidal_extent']
-    
+
     if ivb_tor_ext != mag_tor_ext:
         w = Warning(
             f'The total toroidal extent of the in-vessel build, {ivb_tor_ext} '
             'degrees, does not match the toroidal extent of the magnet coils, '
             f'{mag_tor_ext} degrees.'
         )
         logger.warning(w.args[0])
-    
+
     if ivb_tor_ext != src_tor_ext:
         w = Warning(
             f'The total toroidal extent of the in-vessel build, {ivb_tor_ext} '
             'degrees, does not match the toroidal extent of the source mesh, '
             f'{src_tor_ext} degrees.'
         )
         logger.warning(w.args[0])
-    
+
     if mag_tor_ext != src_tor_ext:
         w = Warning(
             f'The toroidal extent of the magnet coils, {mag_tor_ext} degrees, '
             f'does not match that of the source mesh, {src_tor_ext} degrees.'
         )
         logger.warning(w.args[0])
-    
+
     if 'scale' in invessel_build:
         ivb_scale = invessel_build['scale']
     else:
@@ -544,7 +579,7 @@ def check_inputs(
         )
         logger.error(e.args[0])
         raise e
-    
+
     if (
         'export_cad_to_dagmc' in invessel_build and
         invessel_build['export_cad_to_dagmc']
@@ -553,7 +588,7 @@ def check_inputs(
             ivb_dagmc_filename = invessel_build['dagmc_filename']
         else:
             ivb_dagmc_filename = 'dagmc'
-        
+
         if 'filename' in dagmc_export:
             ps_dagmc_filename = dagmc_export['filename']
         else:
@@ -610,7 +645,7 @@ def parastell():
         stellarator.export_magnets(
             export_dir=args.export_dir,
             **(filter_kwargs(magnet_coils, mc.export_allowed_kwargs))
-    )
+        )
 
     if args.source:
         source_mesh = all_data['source_mesh']
@@ -619,20 +654,26 @@ def parastell():
             export_dir=args.export_dir,
             **(filter_kwargs(source_mesh, sm.export_allowed_kwargs))
         )
-    
+
     if args.ivb or args.magnets:
         dagmc_export = all_data['dagmc_export']
+        stellarator.build_cubit_model(
+            **(filter_kwargs(dagmc_export, build_cubit_model_allowed_kwargs))
+        )
         stellarator.export_dagmc(
             export_dir=args.export_dir,
-            **dagmc_export
+            **(filter_kwargs(dagmc_export, export_dagmc_allowed_kwargs))
         )
 
+        if all_data['cub5_export']:
+            stellarator.export_cub5(export_dir=args.export_dir)
+
     if args.nwl:
         if not args.ivb:
             invessel_build = all_data['invessel_build']
             if not args.magnets:
                 dagmc_export = all_data['dagmc_export']
-        
+
         if cubit_io.initialized:
             cubit.cmd('new')
 
@@ -644,22 +685,22 @@ def parastell():
         nwl_required_keys = [
             'toroidal_angles', 'poloidal_angles', 'wall_s'
         ]
-        
+
         nwl_build = {}
         for key in nwl_keys:
             nwl_build[key] = invessel_build[key]
         nwl_build['radial_build'] = {}
-        
+
         nwl_optional_keys = [
             'num_ribs', 'num_rib_pts', 'repeat', 'scale'
         ]
-        
+
         for key in invessel_build.keys() & nwl_optional_keys:
             nwl_build[key] = invessel_build[key]
 
         nwl_geom.construct_invessel_build(**nwl_build)
         nwl_geom.export_invessel_build(export_dir=args.export_dir)
-        
+
         nwl_geom.export_dagmc(
             skip_imprint=True,
             filename='nwl_geom',

tests/test_parastell.py

@@ -20,6 +20,8 @@ def remove_files():
         Path.unlink('magnet_mesh.h5m')
     if Path('dagmc.h5m').exists():
         Path.unlink('dagmc.h5m')
+    if Path('dagmc.cub5').exists():
+        Path.unlink('dagmc.cub5')
     if Path('source_mesh.h5m').exists():
         Path.unlink('source_mesh.h5m')
     if Path('stellarator.log').exists():
@@ -118,8 +120,11 @@ def test_parastell(stellarator):
 
     filename_exp = 'dagmc'
 
+    stellarator.build_cubit_model()
     stellarator.export_dagmc(filename=filename_exp)
+    stellarator.export_cub5(filename=filename_exp)
 
     assert Path(filename_exp).with_suffix('.h5m').exists()
+    assert Path(filename_exp).with_suffix('.cub5').exists()
 
     remove_files()