Merge pull request svalinn#180 from svalinn/os-dagmc-faceting

Examples/nwl_geom_example.py

@@ -25,9 +25,7 @@
     split_chamber=False,
 )
 # Export in-vessel component files
-stellarator.export_invessel_build(
-    export_cad_to_dagmc=False, export_dir=export_dir
-)
+stellarator.export_invessel_build(export_dir=export_dir)
 
 # Define source mesh parameters
 mesh_size = (11, 81, 61)
@@ -48,4 +46,4 @@
 # Export DAGMC neutronics H5M file
 stellarator.build_cubit_model(skip_imprint=True)
 tag_surface(1, "vacuum")
-stellarator.export_dagmc(filename="nwl_geom", export_dir=export_dir)
+stellarator.export_cubit_dagmc(filename="nwl_geom", export_dir=export_dir)

Examples/parastell_cad_to_dagmc_example.py

@@ -0,0 +1,82 @@
+import numpy as np
+
+import parastell.parastell as ps
+
+
+# Define directory to export all output files to
+export_dir = ""
+# Define plasma equilibrium VMEC file
+vmec_file = "wout_vmec.nc"
+
+# Instantiate ParaStell build
+stellarator = ps.Stellarator(vmec_file)
+
+# Define build parameters for in-vessel components
+toroidal_angles = [0.0, 11.25, 22.5, 33.75, 45.0, 56.25, 67.5, 78.75, 90.0]
+poloidal_angles = [0.0, 45.0, 90.0, 135.0, 180.0, 225.0, 270.0, 315.0, 360.0]
+wall_s = 1.08
+
+# Define a matrix of uniform unit thickness
+uniform_unit_thickness = np.ones((len(toroidal_angles), len(poloidal_angles)))
+
+radial_build_dict = {
+    "first_wall": {"thickness_matrix": uniform_unit_thickness * 5},
+    "breeder": {
+        "thickness_matrix": (
+            [
+                [75.0, 75.0, 75.0, 25.0, 25.0, 25.0, 75.0, 75.0, 75.0],
+                [75.0, 75.0, 75.0, 25.0, 25.0, 75.0, 75.0, 75.0, 75.0],
+                [75.0, 75.0, 25.0, 25.0, 75.0, 75.0, 75.0, 75.0, 75.0],
+                [65.0, 25.0, 25.0, 65.0, 75.0, 75.0, 75.0, 75.0, 65.0],
+                [45.0, 45.0, 75.0, 75.0, 75.0, 75.0, 75.0, 45.0, 45.0],
+                [65.0, 75.0, 75.0, 75.0, 75.0, 65.0, 25.0, 25.0, 65.0],
+                [75.0, 75.0, 75.0, 75.0, 75.0, 25.0, 25.0, 75.0, 75.0],
+                [75.0, 75.0, 75.0, 75.0, 25.0, 25.0, 75.0, 75.0, 75.0],
+                [75.0, 75.0, 75.0, 25.0, 25.0, 25.0, 75.0, 75.0, 75.0],
+            ]
+        )
+    },
+    "back_wall": {"thickness_matrix": uniform_unit_thickness * 5},
+    "shield": {"thickness_matrix": uniform_unit_thickness * 50},
+    "vacuum_vessel": {
+        "thickness_matrix": uniform_unit_thickness * 10,
+        "mat_tag": "vac_vessel",
+    },
+}
+# Construct in-vessel components
+stellarator.construct_invessel_build(
+    toroidal_angles, poloidal_angles, wall_s, radial_build_dict
+)
+# Export in-vessel component files
+stellarator.export_invessel_build(export_dir=export_dir)
+
+# Define build parameters for magnet coils
+coils_file = "coils.example"
+width = 40.0
+thickness = 50.0
+toroidal_extent = 90.0
+# Construct magnets
+stellarator.construct_magnets(
+    coils_file, width, thickness, toroidal_extent, sample_mod=6
+)
+# Export magnet files
+stellarator.export_magnets(
+    step_filename="magnets",
+    export_mesh=True,
+    mesh_filename="magnet_mesh",
+    export_dir=export_dir,
+)
+
+# Define source mesh parameters
+mesh_size = (11, 81, 61)
+toroidal_extent = 90.0
+# Construct source
+stellarator.construct_source_mesh(mesh_size, toroidal_extent)
+# Export source file
+stellarator.export_source_mesh(filename="source_mesh", export_dir=export_dir)
+
+# Build Cubit model of Parastell Components
+stellarator.build_cad_to_dagmc_model()
+
+# Export DAGMC neutronics H5M file
+stellarator.export_cad_to_dagmc(filename="dagmc", export_dir=export_dir)

Examples/parastell_example.py → Examples/parastell_cubit_example.py

@@ -48,9 +48,7 @@
     toroidal_angles, poloidal_angles, wall_s, radial_build_dict
 )
 # Export in-vessel component files
-stellarator.export_invessel_build(
-    export_cad_to_dagmc=False, export_dir=export_dir
-)
+stellarator.export_invessel_build(export_dir=export_dir)
 
 # Define build parameters for magnet coils
 coils_file = "coils.example"
@@ -81,4 +79,4 @@
 stellarator.build_cubit_model(skip_imprint=False)
 
 # Export DAGMC neutronics H5M file
-stellarator.export_dagmc(filename="dagmc", export_dir=export_dir)
+stellarator.export_cubit_dagmc(filename="dagmc", export_dir=export_dir)

Examples/radial_distance_example.py

@@ -111,4 +111,4 @@
 stellarator.build_cubit_model(skip_imprint=False)
 
 # Export DAGMC neutronics H5M file
-stellarator.export_dagmc(filename="dagmc", export_dir=export_dir)
+stellarator.export_cubit_dagmc(filename="dagmc", export_dir=export_dir)

INSTALL.md

@@ -12,16 +12,14 @@ conda install -c conda-forge mamba
 
 The subsequent mamba and pip install commands should be run with this environment activated.
 
-Mamba install ParaStell and PyStell-UW Python dependencies available on `conda-forge`:
+Mamba install ParaStell Python dependencies available on `conda-forge`:
 
 ```
-mamba install -c conda-forge numpy scipy scikit-learn cadquery cad_to_dagmc matplotlib
-mamba install -c conda-forge moab=5.5.0=nompi_tempest_*
+mamba install -c conda-forge pip numpy=1.26.4 scipy scikit-learn cadquery moab=5.5.1=nompi_tempest_* cad_to_dagmc ca-certificates certifi openssl openmc=0.15.0=dagmc_nompi_* matplotlib
 ```
 
-Pip install the remaining ParaStell and PyStell-UW Python dependencies:
+Pip install the remaining ParaStell Python dependencies:
 
 ```
-pip install netCDF4
-pip install pyyaml
+pip install netCDF4 pyyaml pytest git+https://github.com/aaroncbader/pystell_uw.git
 ```

parastell/cubit_io.py

@@ -123,10 +123,10 @@ def tag_surface(surface_id, tag):
 
 
 def export_dagmc_cubit(
-    anisotropic_ratio=100.0,
-    deviation_angle=5.0,
     filename="dagmc",
     export_dir="",
+    anisotropic_ratio=100.0,
+    deviation_angle=5.0,
     delete_upon_export=True,
 ):
     """Exports DAGMC neutronics H5M file of ParaStell components via Coreform

parastell/invessel_build.py

@@ -6,7 +6,6 @@
 
 import cubit
 import cadquery as cq
-import cad_to_dagmc
 import pystell.read_vmec as read_vmec
 
 from . import log
@@ -15,12 +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
@@ -316,35 +312,22 @@ def export_step(self, export_dir=""):
             )
             cq.exporters.export(component, str(export_path))
 
-    def export_cad_to_dagmc(self, dagmc_filename="dagmc", export_dir=""):
-        """Exports DAGMC neutronics H5M file of ParaStell in-vessel components
-        via CAD-to-DAGMC.
+    def extract_solids_and_mat_tags(self):
+        """Appends in-vessel component CadQuery solid objects and material
+        tags to corresponding input lists.
 
-        Arguments:
-            dagmc_filename (str): name of DAGMC output file, excluding '.h5m'
-                extension (optional, defaults to 'dagmc').
-            export_dir (str): directory to which to export the DAGMC output file
-                (optional, defaults to empty string).
+        Returns:
+            solids (list): list of in-vessel component CadQuery solid objects.
+            mat_tags (list): list of in-vessel component material tags.
         """
-        self._logger.info(
-            "Exporting DAGMC neutronics model of in-vessel components..."
-        )
-
-        model = cad_to_dagmc.CadToDagmc()
+        solids = []
+        mat_tags = []
 
-        for name, component in self.Components.items():
-            model.add_cadquery_object(
-                component,
-                material_tags=[
-                    self.radial_build.radial_build[name]["mat_tag"]
-                ],
-            )
-
-        export_path = Path(export_dir) / Path(dagmc_filename).with_suffix(
-            ".h5m"
-        )
+        for name, solid in self.Components.items():
+            solids.append(solid)
+            mat_tags.append(self.radial_build.radial_build[name]["mat_tag"])
 
-        model.export_dagmc_h5m_file(filename=str(export_path))
+        return solids, mat_tags
 
     def export_component_mesh(
         self, components, mesh_size=5, import_dir="", export_dir=""
@@ -875,13 +858,6 @@ 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/magnet_coils.py

@@ -238,6 +238,8 @@ def build_magnet_coils(self):
 
         self._cut_magnets()
 
+        self.coil_solids = [coil.solid for coil in self.magnet_coils]
+
     def import_step_cubit(self):
         """Import STEP file for magnet set into Coreform Cubit."""
         first_vol_id = 1
@@ -268,11 +270,22 @@ def export_step(self, step_filename="magnet_set", export_dir=""):
             self.step_filename
         ).with_suffix(".step")
 
-        coil_set = cq.Compound.makeCompound(
-            [coil.solid for coil in self.magnet_coils]
-        )
+        coil_set = cq.Compound.makeCompound(self.coil_solids)
         cq.exporters.export(coil_set, str(export_path))
 
+    def extract_solids_and_mat_tag(self):
+        """Appends magnet set CadQuery solid objects and material tag to
+        corresponding input lists.
+
+        Returns:
+            solids (list): list of magnet set CadQuery solid objects.
+            mat_tags (list): list of magnet set material tags.
+        """
+        solids = self.coil_solids
+        mat_tags = [self.mat_tag] * len(self.coil_solids)
+
+        return solids, mat_tags
+
     def mesh_magnets(self, min_size=20.0, max_size=50.0, max_gradient=1.5):
         """Creates tetrahedral mesh of magnet volumes via Coreform Cubit.