Convert new workflow to one using CAD-to-DAGMC

environment.yml

@@ -9,6 +9,7 @@ dependencies:
   - scikit-learn
   - cadquery
   - moab=5.5.1[build=nompi_tempest_*]
+  - cad_to_dagmc
   - ca-certificates
   - certifi
   - openssl
@@ -18,5 +19,4 @@ dependencies:
       - netcdf4
       - pyyaml
       - pytest
-      - git+https://github.com/aaroncbader/pystell_uw.git
-      - stellarmesh
+      - git+https://github.com/aaroncbader/pystell_uw.git

parastell/invessel_build.py

@@ -14,12 +14,9 @@
     normalize,
     expand_list,
     read_yaml_config,
-    filter_kwargs,
     m2cm,
 )
 
-export_allowed_kwargs = ["export_cad_to_dagmc", "dagmc_filename"]
-
 
 def orient_spline_surfaces(volume_id):
     """Extracts the inner and outer surface IDs for a given ParaStell in-vessel
@@ -839,13 +836,6 @@ def generate_invessel_build():
 
     invessel_build.export_step(export_dir=args.export_dir)
 
-    if invessel_build_dict["export_cad_to_dagmc"]:
-
-        invessel_build.export_cad_to_dagmc(
-            export_dir=args.export_dir,
-            **(filter_kwargs(invessel_build_dict, ["dagmc_filename"])),
-        )
-
 
 if __name__ == "__main__":
     generate_invessel_build()

parastell/parastell.py

@@ -5,7 +5,7 @@
 import cubit
 import numpy as np
 import pystell.read_vmec as read_vmec
-import stellarmesh
+import cad_to_dagmc
 
 from . import log
 from . import invessel_build as ivb
@@ -15,7 +15,7 @@
 from .utils import read_yaml_config, filter_kwargs, m2cm
 
 build_cubit_model_allowed_kwargs = ["skip_imprint", "legacy_faceting"]
-export_dagmc_cubit_allowed_kwargs = [
+export_cf_dagmc_allowed_kwargs = [
     "faceting_tolerance",
     "length_tolerance",
     "normal_tolerance",
@@ -170,28 +170,15 @@ def construct_invessel_build(
         self.invessel_build.calculate_loci()
         self.invessel_build.generate_components()
 
-    def export_invessel_build(
-        self, export_cad_to_dagmc=False, dagmc_filename="dagmc", export_dir=""
-    ):
-        """Exports InVesselBuild component STEP files and, optionally, a DAGMC
-        neutronics H5M file of in-vessel components via CAD-to-DAGMC.
+    def export_invessel_build(self, export_dir=""):
+        """Exports InVesselBuild component STEP files.
 
         Arguments:
-            export_cad_to_dagmc (bool): export DAGMC neutronics H5M file of
-                in-vessel components via CAD-to-DAGMC (optional, defaults to
-                False).
-            dagmc_filename (str): name of DAGMC output file, excluding '.h5m'
-                extension (optional, defaults to 'dagmc').
             export_dir (str): directory to which to export the output files
                 (optional, defaults to empty string).
         """
         self.invessel_build.export_step(export_dir=export_dir)
 
-        if export_cad_to_dagmc:
-            self.invessel_build.export_cad_to_dagmc(
-                dagmc_filename=dagmc_filename, export_dir=export_dir
-            )
-
     def construct_magnets(
         self, coils_file, width, thickness, toroidal_extent, **kwargs
     ):
@@ -391,7 +378,7 @@ def build_cubit_model(self, skip_imprint=False, legacy_faceting=True):
         else:
             self._tag_materials_native()
 
-    def export_dagmc_cubit(self, filename="dagmc", export_dir="", **kwargs):
+    def export_cf_dagmc(self, filename="dagmc", export_dir="", **kwargs):
         """Exports DAGMC neutronics H5M file of ParaStell components via
         Coreform Cubit.
 
@@ -448,24 +435,14 @@ def export_cub5(self, filename="stellarator", export_dir=""):
 
         cubit_io.export_cub5(filename=filename, export_dir=export_dir)
 
-    def build_stellarmesh_model(
-        self, min_mesh_size=20, max_mesh_size=50, **kwargs
-    ):
+    def build_cad_to_dagmc_model(self):
         """Build model for DAGMC neutronics H5M file of Parastell components via
-        Stellarmesh.
-
-        Arguments:
-            min_mesh_size (float): minimum size of mesh elements (defaults to
-                20).
-            max_mesh_size (float): maximum size of mesh elements (defaults to
-                50).
-
-        Optional arguments:
-            num_threads (int): maximum number of threads to use for geometry
-                meshing (defaults to None). Only valid when Gmsh is compiled
-                with OpenMP support. An input value of 0 equates to the system
-                default (i.e. OMP_NUM_THREADS).
+        CAD-to-DAGMC.
         """
+        self._logger.info(
+            "Building DAGMC neutronics model via CAD-to-DAGMC..."
+        )
+
         solids = []
         material_names = []
 
@@ -483,28 +460,41 @@ def build_stellarmesh_model(
                 )
             )
 
-        geometry = stellarmesh.Geometry(solids, material_names)
-        self.full_mesh = stellarmesh.Mesh.from_geometry(
-            geometry,
-            min_mesh_size=min_mesh_size,
-            max_mesh_size=max_mesh_size,
-            **kwargs,
-        )
+        self.dagmc_model = cad_to_dagmc.CadToDagmc()
 
-    def export_dagmc_stellarmesh(self, filename="dagmc", export_dir=""):
+        for solid, mat_tag in zip(solids, material_names):
+            self.dagmc_model.add_cadquery_object(
+                solid, material_tags=[mat_tag]
+            )
+
+    def export_cad_to_dagmc(
+        self,
+        filename="dagmc",
+        export_dir="",
+        min_mesh_size=20,
+        max_mesh_size=50,
+    ):
         """Exports DAGMC neutronics H5M file of ParaStell components via
-        Stellarmesh.
+        CAD-to-DAGMC.
 
         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).
+            min_mesh_size (float): minimum size of mesh elements (defaults to
+                20).
+            max_mesh_size (float): maximum size of mesh elements (defaults to
+                50).
         """
-        export_path = Path(export_dir) / Path(filename).with_suffix(".h5m")
+        self._logger.info("Exporting DAGMC neutronics model...")
 
-        self.dagmc_model = stellarmesh.DAGMCModel.from_mesh(self.full_mesh)
-        self.dagmc_model.write(export_path)
+        export_path = Path(export_dir) / Path(filename).with_suffix(".h5m")
+        self.dagmc_model.export_dagmc_h5m_file(
+            filename=str(export_path),
+            min_mesh_size=min_mesh_size,
+            max_mesh_size=max_mesh_size,
+        )
 
 
 def parse_args():
@@ -640,29 +630,6 @@ 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"]
-    ):
-        if "dagmc_filename" in invessel_build:
-            ivb_dagmc_filename = invessel_build["dagmc_filename"]
-        else:
-            ivb_dagmc_filename = "dagmc"
-
-        if "filename" in dagmc_export:
-            ps_dagmc_filename = dagmc_export["filename"]
-        else:
-            ps_dagmc_filename = "dagmc"
-
-        if ivb_dagmc_filename == ps_dagmc_filename:
-            e = ValueError(
-                "The DAGMC H5M filename for the CAD-to-DAGMC export matches "
-                "that of the Coreform Cubit DAGMC export. Please change one to "
-                "prevent overwriting files."
-            )
-            logger.error(e.args[0])
-            raise e
-
 
 def parastell():
     """Main method when run as a command line script."""
@@ -690,10 +657,7 @@ def parastell():
     if args.ivb:
         invessel_build = all_data["invessel_build"]
         stellarator.construct_invessel_build(**invessel_build)
-        stellarator.export_invessel_build(
-            export_dir=args.export_dir,
-            **(filter_kwargs(invessel_build, ivb.export_allowed_kwargs)),
-        )
+        stellarator.export_invessel_build(export_dir=args.export_dir)
 
     if args.magnets:
         magnet_coils = all_data["magnet_coils"]
@@ -718,7 +682,7 @@ def parastell():
         )
         stellarator.export_dagmc_cubit(
             export_dir=args.export_dir,
-            **(filter_kwargs(dagmc_export, export_dagmc_cubit_allowed_kwargs)),
+            **(filter_kwargs(dagmc_export, export_cf_dagmc_allowed_kwargs)),
         )
 
         if all_data["cub5_export"]:
@@ -750,7 +714,7 @@ def parastell():
         nwl_geom.construct_invessel_build(**nwl_build)
         nwl_geom.export_invessel_build(export_dir=args.export_dir)
 
-        nwl_geom.export_dagmc_cubit(
+        nwl_geom.export_cf_dagmc(
             skip_imprint=True, filename="nwl_geom", export_dir=args.export_dir
         )
 

tests/test_parastell.py

@@ -135,18 +135,17 @@ def test_parastell(stellarator):
     )
     assert stellarator.magnet_set.volume_ids == magnet_volume_ids_exp
 
-    stellarator.export_dagmc_cubit(filename=filename_exp)
+    stellarator.export_cf_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()
 
-    stellarator.build_stellarmesh_model(
-        min_mesh_size=50, max_mesh_size=100, num_threads=0
-    )
-    stellarator.export_dagmc_stellarmesh()
-    print([volume.global_id for volume in stellarator.dagmc_model.volumes])
+    stellarator.build_cad_to_dagmc_model()
+    stellarator.export_cad_to_dagmc(min_mesh_size=50, max_mesh_size=100)
+
+    assert Path(filename_exp).with_suffix(".h5m").exists()
 
     remove_files()