Merge pull request #268 from svalinn/fix-examples

gonuke · web-flow · commit 19a9aace8906 · 2025-12-22T19:32:48.000-06:00
diff --git a/examples/config.yaml b/examples/config.yaml
@@ -82,7 +82,6 @@ source_mesh:
   filename: source_mesh
 
 dagmc_export:
-  skip_imprint: False
   filename: dagmc
 
 cub5_export: False
diff --git a/examples/custom_first_wall_profile_example.py b/examples/custom_first_wall_profile_example.py
@@ -42,7 +42,7 @@
 # Define desired toroidal and poloidal angles for building the stellarator
 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
+wall_s = 1.0
 
 # Define a matrix of uniform unit thickness
 uniform_unit_thickness = np.ones((len(toroidal_angles), len(poloidal_angles)))
@@ -73,7 +73,7 @@
 }
 # Construct in-vessel components
 stellarator.construct_invessel_build(
-    toroidal_angles, poloidal_angles, wall_s, radial_build_dict, scale=1
+    toroidal_angles, poloidal_angles, wall_s, radial_build_dict
 )
 # Export in-vessel component files
 stellarator.export_invessel_build_step(export_dir=export_dir)
@@ -89,9 +89,6 @@
 )
 # Export magnet files
 stellarator.export_magnets_step(filename="magnets", export_dir=export_dir)
-stellarator.export_magnet_mesh_cubit(
-    filename="magnet_mesh", export_dir=export_dir
-)
 
 # Define source mesh parameters
 cfs_values = np.linspace(0.0, 1.0, num=11)
@@ -102,8 +99,7 @@
 # Export source file
 stellarator.export_source_mesh(filename="source_mesh", export_dir=export_dir)
 
-# Build Cubit model of Parastell Components
-stellarator.build_cubit_model(skip_imprint=True)
-
-# Export DAGMC neutronics H5M file
-stellarator.export_cubit_dagmc(filename="dagmc", export_dir=export_dir)
+# Build DAGMC neutronics model
+stellarator.build_cad_to_dagmc_model()
+# Export DAGMC H5M file
+stellarator.export_cad_to_dagmc(filename="dagmc", export_dir=export_dir)
diff --git a/examples/custom_source_example.py b/examples/custom_source_example.py
@@ -1,6 +1,5 @@
 import parastell.source_mesh as sm
 from parastell.pystell import read_vmec
-import subprocess
 import numpy as np
 
 
@@ -40,6 +39,4 @@ def my_custom_reaction_rate(n_i, T_i):
 source_mesh_obj.create_vertices()
 source_mesh_obj.create_mesh()
 
-# export and convert to vtk for visualization
 source_mesh_obj.export_mesh("source_mesh.h5m")
-subprocess.run("mbconvert source_mesh.h5m source_mesh.vtk", shell=True)
diff --git a/examples/nwl_cubit_example.py b/examples/nwl_cubit_example.py
@@ -44,7 +44,7 @@
 
 # Construct and export DAGMC neutronics model
 dagmc_filename = Path("nwl_geom").with_suffix(".h5m")
-stellarator.build_cubit_model(skip_imprint=True)
+stellarator.build_cubit_model()
 tag_surface(1, "vacuum")
 stellarator.export_cubit_dagmc(filename=dagmc_filename)
 
@@ -67,5 +67,7 @@
         num_threads=6,
     )
 )
-nwl_utils.plot_nwl(nwl_mean, toroidal_bins, poloidal_bins)
-nwl_utils.plot_nwl(nwl_std_dev, toroidal_bins, poloidal_bins)
+nwl_utils.plot_nwl(nwl_mean, toroidal_bins, poloidal_bins, filename="nwl_mean")
+nwl_utils.plot_nwl(
+    nwl_std_dev, toroidal_bins, poloidal_bins, filename="nwl_std_dev"
+)
diff --git a/examples/nwl_pydagmc_example.py b/examples/nwl_pydagmc_example.py
@@ -1,7 +1,6 @@
 from pathlib import Path
 
 import parastell.parastell as ps
-from parastell.cubit_utils import tag_surface
 from parastell import nwl_utils
 import numpy as np
 
@@ -81,5 +80,7 @@
         num_threads=6,
     )
 )
-nwl_utils.plot_nwl(nwl_mean, toroidal_bins, poloidal_bins)
-nwl_utils.plot_nwl(nwl_std_dev, toroidal_bins, poloidal_bins)
+nwl_utils.plot_nwl(nwl_mean, toroidal_bins, poloidal_bins, filename="nwl_mean")
+nwl_utils.plot_nwl(
+    nwl_std_dev, toroidal_bins, poloidal_bins, filename="nwl_std_dev"
+)
diff --git a/examples/parastell_cad_to_dagmc_example.py b/examples/parastell_cad_to_dagmc_example.py
@@ -49,6 +49,7 @@
 )
 # Export in-vessel component files
 stellarator.export_invessel_build_step(export_dir=export_dir)
+# Export weight window mesh
 stellarator.export_invessel_build_mesh_gmsh(
     [
         "chamber",
@@ -88,8 +89,7 @@
 # Export source file
 stellarator.export_source_mesh(filename="source_mesh", export_dir=export_dir)
 
-# Build Cubit model of Parastell Components
+# Build DAGMC neutronics model
 stellarator.build_cad_to_dagmc_model()
-
-# Export DAGMC neutronics H5M file
+# Export DAGMC H5M file
 stellarator.export_cad_to_dagmc(filename="dagmc", export_dir=export_dir)
diff --git a/examples/parastell_cubit_example.py b/examples/parastell_cubit_example.py
@@ -49,6 +49,7 @@
 )
 # Export in-vessel component files
 stellarator.export_invessel_build_step(export_dir=export_dir)
+# Export weight window mesh
 stellarator.export_invessel_build_mesh_cubit(
     [
         "chamber",
@@ -85,8 +86,7 @@
 # Export source file
 stellarator.export_source_mesh(filename="source_mesh", export_dir=export_dir)
 
-# Build Cubit model of Parastell Components
-stellarator.build_cubit_model(skip_imprint=False)
-
-# Export DAGMC neutronics H5M file
+# Build DAGMC neutronics model
+stellarator.build_cubit_model()
+# Export DAGMC H5M file
 stellarator.export_cubit_dagmc(filename="dagmc", export_dir=export_dir)
diff --git a/examples/parastell_pydagmc_example.py b/examples/parastell_pydagmc_example.py
@@ -58,10 +58,6 @@
     num_ribs=num_ribs,
     num_rib_pts=num_rib_pts,
 )
-# Export in-vessel component files
-stellarator.export_invessel_build_mesh_moab(
-    "vacuum_vessel", "vacuum_vessel_tally_mesh"
-)
 
 # Define build parameters for magnet coils
 coils_file = "coils.example"
@@ -73,7 +69,25 @@
     coils_file, width, thickness, toroidal_extent, sample_mod=6
 )
 
+# PyDAGMC model must be built before any meshing in Gmsh
 stellarator.build_pydagmc_model(
     magnet_exporter="cad_to_dagmc", max_mesh_size=60
 )
 stellarator.export_pydagmc_model(filename="dagmc")
+
+# Export weight window mesh
+# Note that PyDAGMC workflow does not model the vacuum chamber - cannot be meshed
+stellarator.export_invessel_build_mesh_gmsh(
+    [
+        "first_wall",
+        "breeder",
+        "back_wall",
+        "shield",
+        "vacuum_vessel",
+    ],
+    "weight_window_mesh",
+)
+# Export in-vessel component files
+stellarator.export_invessel_build_mesh_moab(
+    ["vacuum_vessel"], "vacuum_vessel_tally_mesh"
+)
diff --git a/examples/radial_distance_example.py b/examples/radial_distance_example.py
@@ -48,7 +48,10 @@
 # symmetric
 available_space = enforce_helical_symmetry(available_space)
 # Modify available space to account for thickness of magnets
-available_space = available_space - max(width, thickness)
+tolerance = 5
+available_space = available_space - (
+    np.sqrt(width * width + thickness * thickness) + tolerance
+)
 
 # Define a matrix of uniform unit thickness
 uniform_unit_thickness = np.ones((len(toroidal_angles), len(poloidal_angles)))
@@ -111,8 +114,7 @@
 # Export source file
 stellarator.export_source_mesh(filename="source_mesh", export_dir=export_dir)
 
-# Build Cubit model of Parastell Components
-stellarator.build_cubit_model(skip_imprint=False)
-
-# Export DAGMC neutronics H5M file
-stellarator.export_cubit_dagmc(filename="dagmc", export_dir=export_dir)
+# Build DAGMC neutronics model
+stellarator.build_cad_to_dagmc_model()
+# Export DAGMC H5M file
+stellarator.export_cad_to_dagmc(filename="dagmc", export_dir=export_dir)
diff --git a/parastell/nwl_utils.py b/parastell/nwl_utils.py
@@ -330,8 +330,6 @@ def compute_nwl(
         poloidal_extent + poloidal_extent / num_poloidal_bins / 2
     )
 
-    toroidal_angles = []
-    poloidal_angles = []
     nwl_all_batches = []
 
     batch_size = math.ceil(num_particles / num_batches)
@@ -343,20 +341,20 @@ def compute_nwl(
 
         crossings = coords[batch_start : batch_start + batch_size]
 
-        toroidal_angle_batch, poloidal_angle_batch = compute_flux_coordinates(
-            ref_surf,
-            wall_s,
-            crossings,
-            num_threads,
-            conv_tol,
+        toroidal_angles_batch, poloidal_angles_batch = (
+            compute_flux_coordinates(
+                ref_surf,
+                wall_s,
+                crossings,
+                num_threads,
+                conv_tol,
+            )
         )
-        toroidal_angles += toroidal_angle_batch
-        poloidal_angles += poloidal_angle_batch
 
         # Bin particle crossings
         counts, toroidal_bin_edges, poloidal_bin_edges = np.histogram2d(
-            toroidal_angles,
-            poloidal_angles,
+            toroidal_angles_batch,
+            poloidal_angles_batch,
             bins=[num_toroidal_bins, num_poloidal_bins],
             range=[
                 [toroidal_bin_min, toroidal_bin_max],
diff --git a/parastell/parastell.py b/parastell/parastell.py
@@ -18,7 +18,6 @@
 from .utils import read_yaml_config, filter_kwargs, m2cm, combine_dagmc_models
 from .pystell import read_vmec
 
-build_cubit_model_allowed_kwargs = ["skip_imprint"]
 export_cubit_dagmc_allowed_kwargs = [
     "filename",
     "export_dir",
@@ -506,12 +505,12 @@ def _tag_materials(self):
             if isinstance(self.magnet_set.mat_tag, (list, tuple)):
                 for idx, _ in enumerate(["outer", "inner"]):
                     mat_tag = self.magnet_set.mat_tag[idx]
-                    volume_ids = list(self.magnet_set.volume_ids[:, idx])
+                    volume_ids = list(self.magnet_set.cubit_volume_ids[:, idx])
                     volume_id_str = " ".join(str(i) for i in volume_ids)
                     block_id = min(volume_ids)
                     make_material_block(mat_tag, block_id, volume_id_str)
             else:
-                volume_ids = self.magnet_set.volume_ids.flatten()
+                volume_ids = self.magnet_set.cubit_volume_ids.flatten()
                 volume_id_str = " ".join(str(i) for i in volume_ids)
                 block_id = min(volume_ids)
                 make_material_block(
@@ -713,9 +712,6 @@ def build_pydagmc_model(self, magnet_exporter, **kwargs):
             being used.
 
             For magnet_exporter = 'cubit'
-            skip_imprint (bool): choose whether to imprint and merge all in
-                Coreform Cubit or to merge surfaces based on import order and
-                geometry information (Defaults to False).
             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
@@ -739,9 +735,7 @@ def build_pydagmc_model(self, magnet_exporter, **kwargs):
 
         if self.magnet_set:
             if magnet_exporter == "cubit":
-                self.build_cubit_model(
-                    **(filter_kwargs(kwargs, build_cubit_model_allowed_kwargs))
-                )
+                self.build_cubit_model()
                 self.export_cubit_dagmc(
                     **(
                         filter_kwargs(
@@ -963,9 +957,7 @@ def parastell():
 
     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.build_cubit_model()
         stellarator.export_cubit_dagmc(
             export_dir=args.export_dir,
             **(filter_kwargs(dagmc_export, export_cubit_dagmc_allowed_kwargs)),
@@ -997,7 +989,7 @@ def parastell():
         nwl_geom.construct_invessel_build(**nwl_build)
         nwl_geom.export_invessel_build(export_dir=args.export_dir)
 
-        nwl_geom.build_cubit_model(skip_imprint=True)
+        nwl_geom.build_cubit_model()
         nwl_geom.export_cubit_dagmc(
             filename="nwl_geom", export_dir=args.export_dir
         )
