cad-to-dagmc 0.9.0__py3-none-any.whl → 0.9.2__py3-none-any.whl

_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.9.0'
-__version_tuple__ = version_tuple = (0, 9, 0)
+__version__ = version = '0.9.2'
+__version_tuple__ = version_tuple = (0, 9, 2)

cad_to_dagmc/core.py

@@ -1,4 +1,5 @@
 from pathlib import Path
+from typing import Iterable
 import cadquery as cq
 import gmsh
 import numpy as np
@@ -6,6 +7,7 @@ from cadquery import importers
 from pymoab import core, types
 import tempfile
 import warnings
+from typing import Iterable
 from cad_to_dagmc import __version__
 
 
@@ -234,15 +236,14 @@ def init_gmsh():
     return gmsh
 
 
-def mesh_brep(
+def set_sizes_for_mesh(
     gmsh,
     min_mesh_size: float | None = None,
     max_mesh_size: float | None = None,
     mesh_algorithm: int = 1,
-    dimensions: int = 2,
     set_size: dict[int, float] | None = None,
 ):
-    """Creates a conformal surface meshes of the volumes in a Brep file using Gmsh.
+    """Sets up the mesh sizes for each volume in the mesh.
 
     Args:
         occ_shape: the occ_shape of the Brep file to convert
@@ -252,8 +253,6 @@ def mesh_brep(
             into gmsh.option.setNumber("Mesh.MeshSizeMax", max_mesh_size)
         mesh_algorithm: The Gmsh mesh algorithm number to use. Passed into
             gmsh.option.setNumber("Mesh.Algorithm", mesh_algorithm)
-        dimensions: The number of dimensions, 2 for a surface mesh 3 for a
-            volume mesh. Passed to gmsh.model.mesh.generate()
         set_size: a dictionary of volume ids (int) and target mesh sizes
             (floats) to set for each volume, passed to gmsh.model.mesh.setSize.
 
@@ -279,25 +278,42 @@ def mesh_brep(
         volumes = gmsh.model.getEntities(3)
         available_volumes = [volume[1] for volume in volumes]
         print("volumes", volumes)
-        for volume_id, size in set_size.items():
-            if volume_id in available_volumes:
-                size = set_size[volume_id]
-                if isinstance(size, dict):
-                    # TODO face specific mesh sizes
-                    pass
-                else:
-                    boundaries = gmsh.model.getBoundary(
-                        [(3, volume_id)], recursive=True
-                    )  # dim must be set to 3
-                    print("boundaries", boundaries)
-                    gmsh.model.mesh.setSize(boundaries, size)
-                    print(f"Set size of {size} for volume {volume_id}")
-            else:
+
+        # Ensure all volume IDs in set_size exist in the available volumes
+        for volume_id in set_size.keys():
+            if volume_id not in available_volumes:
                 raise ValueError(
                     f"volume ID of {volume_id} set in set_sizes but not found in available volumes {volumes}"
                 )
 
-    gmsh.model.mesh.generate(dimensions)
+        # Step 1: Preprocess boundaries to find shared surfaces and decide mesh sizes
+        boundary_sizes = {}  # Dictionary to store the mesh size and count for each boundary
+        for volume_id, size in set_size.items():
+            boundaries = gmsh.model.getBoundary(
+                [(3, volume_id)], recursive=True
+            )  # dim must be set to 3
+            print(f"Boundaries for volume {volume_id}: {boundaries}")
+
+            for boundary in boundaries:
+                boundary_key = (boundary[0], boundary[1])  # (dimension, tag)
+                if boundary_key in boundary_sizes:
+                    # If the boundary is already processed, add the size to the list
+                    boundary_sizes[boundary_key]["total_size"] += size
+                    boundary_sizes[boundary_key]["count"] += 1
+                else:
+                    # Otherwise, initialize the boundary with the current size
+                    boundary_sizes[boundary_key] = {"total_size": size, "count": 1}
+
+        # Step 2: Calculate the average size for each boundary
+        averaged_boundary_sizes = {
+            boundary: data["total_size"] / data["count"]
+            for boundary, data in boundary_sizes.items()
+        }
+
+        # Step 3: Apply mesh sizes to all boundaries
+        for boundary, size in averaged_boundary_sizes.items():
+            gmsh.model.mesh.setSize([boundary], size)
+            print(f"Set mesh size {size} for boundary {boundary}")
 
     return gmsh
 
@@ -615,11 +631,13 @@ class CadToDagmc:
         scale_factor: float = 1.0,
         imprint: bool = True,
         set_size: dict[int, float] | None = None,
+        volumes: Iterable[int] | None = None,
     ):
         """
-        Exports an unstructured mesh file in VTK format for use with openmc.UnstructuredMesh.
-        Compatible with the MOAB unstructured mesh library. Example useage
-        openmc.UnstructuredMesh(filename="umesh.vtk", library="moab")
+        Exports an unstructured mesh file in VTK format for use with
+        openmc.UnstructuredMesh. Compatible with the MOAB unstructured mesh
+        library. Example useage openmc.UnstructuredMesh(filename="umesh.vtk",
+        library="moab").
 
         Parameters:
         -----------
@@ -648,6 +666,8 @@ class CadToDagmc:
                 and this can save time.
             set_size: a dictionary of volume ids (int) and target mesh sizes
                 (floats) to set for each volume, passed to gmsh.model.mesh.setSize.
+            volumes: a list of volume ids (int) to include in the mesh. If left
+                as default (None) then all volumes will be included.
 
 
         Returns:
@@ -672,17 +692,30 @@ class CadToDagmc:
 
         gmsh = init_gmsh()
 
-        gmsh, _ = get_volumes(gmsh, imprinted_assembly, method=method, scale_factor=scale_factor)
+        gmsh, volumes_in_model = get_volumes(
+            gmsh, imprinted_assembly, method=method, scale_factor=scale_factor
+        )
 
-        gmsh = mesh_brep(
+        gmsh = set_sizes_for_mesh(
             gmsh=gmsh,
             min_mesh_size=min_mesh_size,
             max_mesh_size=max_mesh_size,
             mesh_algorithm=mesh_algorithm,
-            dimensions=3,
             set_size=set_size,
         )
 
+        if volumes:
+            for volume_id in volumes_in_model:
+                if volume_id[1] not in volumes:
+                    gmsh.model.occ.remove([volume_id], recursive=True)
+            gmsh.option.setNumber("Mesh.SaveAll", 1)
+            gmsh.model.occ.synchronize()
+            # Clear the mesh
+            gmsh.model.mesh.clear()
+            gmsh.option.setNumber("Mesh.SaveElementTagType", 3)  # Save only volume elements
+
+        gmsh.model.mesh.generate(3)
+
         # makes the folder if it does not exist
         if Path(filename).parent:
             Path(filename).parent.mkdir(parents=True, exist_ok=True)
@@ -695,7 +728,7 @@ class CadToDagmc:
 
         gmsh.finalize()
 
-        return gmsh
+        return filename
 
     def export_gmsh_mesh_file(
         self,
@@ -751,15 +784,16 @@ class CadToDagmc:
 
         gmsh, _ = get_volumes(gmsh, imprinted_assembly, method=method, scale_factor=scale_factor)
 
-        gmsh = mesh_brep(
+        gmsh = set_sizes_for_mesh(
             gmsh=gmsh,
             min_mesh_size=min_mesh_size,
             max_mesh_size=max_mesh_size,
             mesh_algorithm=mesh_algorithm,
-            dimensions=dimensions,
             set_size=set_size,
         )
 
+        gmsh.model.mesh.generate(dimensions)
+
         # makes the folder if it does not exist
         if Path(filename).parent:
             Path(filename).parent.mkdir(parents=True, exist_ok=True)
@@ -785,6 +819,8 @@ class CadToDagmc:
         scale_factor: float = 1.0,
         imprint: bool = True,
         set_size: dict[int, float] | None = None,
+        unstructured_volumes: Iterable[int] | None = None,
+        umesh_filename: str = "umesh.vtk",
     ) -> str:
         """Saves a DAGMC h5m file of the geometry
 
@@ -813,9 +849,13 @@ class CadToDagmc:
                 and this can save time.
             set_size: a dictionary of volume ids (int) and target mesh sizes
                 (floats) to set for each volume, passed to gmsh.model.mesh.setSize.
+            unstructured_volumes: a list of volume ids to be saved in as an
+                unstructured mesh file.
+            umesh_filename: the filename to use for the optional unstructured
+                mesh file. Only used if unstructured_volumes is not empty.
 
         Returns:
-            str: the DAGMC filename saved
+            str: the filenames(s) for the files created.
         """
 
         assembly = cq.Assembly()
@@ -852,7 +892,7 @@ class CadToDagmc:
             gmsh, imprinted_assembly, method=method, scale_factor=scale_factor
         )
 
-        gmsh = mesh_brep(
+        gmsh = set_sizes_for_mesh(
             gmsh=gmsh,
             min_mesh_size=min_mesh_size,
             max_mesh_size=max_mesh_size,
@@ -860,19 +900,39 @@ class CadToDagmc:
             set_size=set_size,
         )
 
-        dims_and_vol_ids = volumes
+        gmsh.model.mesh.generate(2)
 
         vertices, triangles_by_solid_by_face = mesh_to_vertices_and_triangles(
-            dims_and_vol_ids=dims_and_vol_ids
+            dims_and_vol_ids=volumes
         )
 
-        gmsh.finalize()
-
-        # checks and fixes triangle fix_normals within vertices_to_h5m
-        return vertices_to_h5m(
+        dagmc_filename = vertices_to_h5m(
             vertices=vertices,
             triangles_by_solid_by_face=triangles_by_solid_by_face,
             material_tags=material_tags_in_brep_order,
             h5m_filename=filename,
             implicit_complement_material_tag=implicit_complement_material_tag,
         )
+
+        if unstructured_volumes:
+            # remove all the unused occ volumes, this prevents them being meshed
+            for volume_dim, volume_id in volumes:
+                if volume_id not in unstructured_volumes:
+                    gmsh.model.occ.remove([(volume_dim, volume_id)], recursive=True)
+            gmsh.option.setNumber("Mesh.SaveAll", 1)
+            gmsh.model.occ.synchronize()
+
+            # removes all the 2D groups so that 2D faces are not included in the vtk file
+            all_2d_groups = gmsh.model.getPhysicalGroups(2)
+            for entry in all_2d_groups:
+                gmsh.model.removePhysicalGroups([entry])
+
+            gmsh.model.mesh.generate(3)
+            gmsh.option.setNumber("Mesh.SaveElementTagType", 3)  # Save only volume elements
+            gmsh.write(umesh_filename)
+
+            gmsh.finalize()
+
+            return dagmc_filename, umesh_filename
+        else:
+            return dagmc_filename

{cad_to_dagmc-0.9.0.dist-info → cad_to_dagmc-0.9.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cad_to_dagmc
-Version: 0.9.0
+Version: 0.9.2
 Summary: Converts CAD files to a DAGMC h5m file
 Author-email: Jonathan Shimwell <mail@jshimwell.com>
 Project-URL: Homepage, https://github.com/fusion-energy/cad_to_dagmc
@@ -55,6 +55,8 @@ Cad-to-dagmc offers a wide range of features including.
 - Geometry scaling with ```scale_factor``` argument
 - Model wide mesh size parameters with ```min_mesh_size``` and ```max_mesh_size``` arguments
 - Volume specific mesh sizing parameters with the ```set_size``` argument
+- Unstructured mesh that share the same coordinates as the surface mesh.
+- Volume mesh allows selecting individual volumes in the geometry.
 - Parallel meshing to quickly mesh the geometry using multiple CPU cores
 - Imprint and merging of CAD geometry, or disable with the ```imprint``` argument
 - Add geometry from multiple sources ([STEP](http://www.steptools.com/stds/step/) files, [CadQuery](https://cadquery.readthedocs.io) objects and [Gmsh](https://gmsh.info/) meshes)
@@ -130,21 +132,10 @@ First ensure hdf5 is installed as this is needed by MOAB pip install command
 sudo apt-get install libhdf5-dev
 ```
 
-Then clone the latest version of MOAB and cd into the moab directory.
+Then install MOAB, currently available from the repo.
 
 ```
-git clone  master https://bitbucket.org/fathomteam/moab/
-cd moab
-```
-
-Ensure pip is up to date as a new version is needed
-```
-python -m pip install --upgrade pip
-```
-
-Run the pip install command with cmake arguments.
-```
-pip install . --config-settings=cmake.args=-DENABLE_HDF5=ON
+pip install git+https://bitbucket.org/fathomteam/moab/
 ```
 
 Then you can install the cad_to_dagmc package with ```pip```

cad_to_dagmc-0.9.2.dist-info/RECORD

@@ -0,0 +1,8 @@
+_version.py,sha256=eeYYTSIkrgfRwSQ7LKo_py3xs3DvzgfWiAtK4K1JM4A,511
+cad_to_dagmc/__init__.py,sha256=fskHUTyCunSpnpJUvBfAYjx4uwDKXHTTiMP6GqnFRf0,494
+cad_to_dagmc/core.py,sha256=dGj5LRRzboQ8CL8VS5dkvIkGLyj5MJWcbkTPtrFk0QQ,36947
+cad_to_dagmc-0.9.2.dist-info/licenses/LICENSE,sha256=B8kznH_777JVNZ3HOKDc4Tj24F7wJ68ledaNYeL9sCw,1070
+cad_to_dagmc-0.9.2.dist-info/METADATA,sha256=8vLnV93ycmV216LiNj38YI4z445pWtdpBKpcESFLLH0,8990
+cad_to_dagmc-0.9.2.dist-info/WHEEL,sha256=0CuiUZ_p9E4cD6NyLD6UG80LBXYyiSYZOKDm5lp32xk,91
+cad_to_dagmc-0.9.2.dist-info/top_level.txt,sha256=zTi8C64SEBsE5WOtPovnxhOzt-E6Oc5nC3RW6M_5aEA,22
+cad_to_dagmc-0.9.2.dist-info/RECORD,,

{cad_to_dagmc-0.9.0.dist-info → cad_to_dagmc-0.9.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.0)
+Generator: setuptools (80.3.1)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

cad_to_dagmc-0.9.0.dist-info/RECORD

@@ -1,8 +0,0 @@
-_version.py,sha256=fqtOm8q4HIqAgc-mXbjsKoz34kMK1y3t9LDhc4497WE,511
-cad_to_dagmc/__init__.py,sha256=fskHUTyCunSpnpJUvBfAYjx4uwDKXHTTiMP6GqnFRf0,494
-cad_to_dagmc/core.py,sha256=C3NEy5z4bjbg0SQjodGcZSOVqMAc8g5e0zLoF2gs0Og,34140
-cad_to_dagmc-0.9.0.dist-info/licenses/LICENSE,sha256=B8kznH_777JVNZ3HOKDc4Tj24F7wJ68ledaNYeL9sCw,1070
-cad_to_dagmc-0.9.0.dist-info/METADATA,sha256=J3Q4BXSU_ApF86K8sjDXA_hYT_k5GRRAKXaYc-ksbuw,9092
-cad_to_dagmc-0.9.0.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-cad_to_dagmc-0.9.0.dist-info/top_level.txt,sha256=zTi8C64SEBsE5WOtPovnxhOzt-E6Oc5nC3RW6M_5aEA,22
-cad_to_dagmc-0.9.0.dist-info/RECORD,,