cad-to-dagmc 0.8.2__py3-none-any.whl → 0.9.1__py3-none-any.whl

_version.py

@@ -1,8 +1,13 @@
-# file generated by setuptools_scm
+# file generated by setuptools-scm
 # don't change, don't track in version control
+
+__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+
 TYPE_CHECKING = False
 if TYPE_CHECKING:
-    from typing import Tuple, Union
+    from typing import Tuple
+    from typing import Union
+
     VERSION_TUPLE = Tuple[Union[int, str], ...]
 else:
     VERSION_TUPLE = object
@@ -12,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.8.2'
-__version_tuple__ = version_tuple = (0, 8, 2)
+__version__ = version = '0.9.1'
+__version_tuple__ = version_tuple = (0, 9, 1)

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 cad_to_dagmc import __version__
 
 
 def define_moab_core_and_tags() -> tuple[core.Core, dict]:
@@ -229,19 +231,18 @@ def get_volumes(gmsh, assembly, method="file", scale_factor=1.0):
 def init_gmsh():
     gmsh.initialize()
     gmsh.option.setNumber("General.Terminal", 1)
-    gmsh.model.add("made_with_cad_to_dagmc_package")
+    gmsh.model.add(f"made_with_cad_to_dagmc_package_{__version__}")
     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
@@ -251,8 +252,6 @@ 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.
 
@@ -278,25 +277,42 @@ 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
 
@@ -318,7 +334,9 @@ def mesh_to_vertices_and_triangles(
     for dim_and_vol in dims_and_vol_ids:
         # removes all groups so that the following getEntitiesForPhysicalGroup
         # command only finds surfaces for the volume
-        gmsh.model.removePhysicalGroups()
+        face_groups = gmsh.model.getPhysicalGroups(2)
+        if face_groups:  # Only remove if 2D groups exist
+            gmsh.model.removePhysicalGroups(face_groups)
 
         vol_id = dim_and_vol[1]
         entities_in_volume = gmsh.model.getAdjacencies(3, vol_id)
@@ -399,64 +417,122 @@ def order_material_ids_by_brep_order(original_ids, scrambled_id, material_tags):
     return material_tags_in_brep_order
 
 
-class MeshToDagmc:
-    """Convert a GMSH mesh file to a DAGMC h5m file"""
+def export_gmsh_object_to_dagmc_h5m_file(
+    material_tags: list[str] | None = None,
+    implicit_complement_material_tag: str | None = None,
+    filename: str = "dagmc.h5m",
+) -> str:
+    """
+    Exports a GMSH object to a DAGMC-compatible h5m file. Note gmsh should
+    be initialized by the user prior and the gmsh model should be meshed before
+    calling this. Also users should ensure that the gmsh model is finalized.
 
-    def __init__(self, filename: str):
-        self.filename = filename
+    Args:
+        material_tags: A list of material tags corresponding to the volumes in the GMSH object.
+        implicit_complement_material_tag: The material tag for the implicit complement (void space).
+        filename: The name of the output h5m file. Defaults to "dagmc.h5m".
 
-    # TODO add export_unstructured_mesh_file
-    # TODO add add_gmsh_msh_file
-    # TODO test for exports result in files
+    Returns:
+        str: The filename of the generated DAGMC h5m file.
 
-    def export_dagmc_h5m_file(
-        self,
-        material_tags: list[str],
-        implicit_complement_material_tag: str | None = None,
-        filename: str = "dagmc.h5m",
-    ):
-        """Saves a DAGMC h5m file of the geometry
+    Raises:
+        ValueError: If the number of material tags does not match the number of volumes in the GMSH object.
+    """
 
-        Args:
-            material_tags (list[str]): the names of the DAGMC
-                material tags to assign. These will need to be in the same
-                order as the volumes in the GMESH mesh and match the
-                material tags used in the neutronics code (e.g. OpenMC).
-            implicit_complement_material_tag (str | None, optional):
-                the name of the material tag to use for the implicit
-                complement (void space). Defaults to None which is a vacuum.
-            filename (str, optional): _description_. Defaults to "dagmc.h5m".
+    if material_tags is None:
+        material_tags = _get_material_tags_from_gmsh()
 
-        Raises:
-            ValueError: _description_
+    dims_and_vol_ids = gmsh.model.getEntities(3)
 
-        Returns:
-            _type_: _description_
-        """
+    if len(dims_and_vol_ids) != len(material_tags):
+        msg = f"Number of volumes {len(dims_and_vol_ids)} is not equal to number of material tags {len(material_tags)}"
+        raise ValueError(msg)
 
-        gmsh.initialize()
-        self.mesh_file = gmsh.open(self.filename)
-        dims_and_vol_ids = gmsh.model.getEntities(3)
+    vertices, triangles_by_solid_by_face = mesh_to_vertices_and_triangles(
+        dims_and_vol_ids=dims_and_vol_ids
+    )
 
-        if len(dims_and_vol_ids) != len(material_tags):
-            msg = f"Number of volumes {len(dims_and_vol_ids)} is not equal to number of material tags {len(material_tags)}"
-            raise ValueError(msg)
+    h5m_filename = vertices_to_h5m(
+        vertices=vertices,
+        triangles_by_solid_by_face=triangles_by_solid_by_face,
+        material_tags=material_tags,
+        h5m_filename=filename,
+        implicit_complement_material_tag=implicit_complement_material_tag,
+    )
 
-        vertices, triangles_by_solid_by_face = mesh_to_vertices_and_triangles(
-            dims_and_vol_ids=dims_and_vol_ids
-        )
+    return h5m_filename
 
-        gmsh.finalize()
 
-        h5m_filename = vertices_to_h5m(
-            vertices=vertices,
-            triangles_by_solid_by_face=triangles_by_solid_by_face,
-            material_tags=material_tags,
-            h5m_filename=filename,
-            implicit_complement_material_tag=implicit_complement_material_tag,
-        )
+def _get_material_tags_from_gmsh() -> list[str]:
+    """Gets the Physical groups of 3D groups from the GMSH object and returns
+    their names."""
+
+    # Get all 3D physical groups (volumes)
+    volume_groups = gmsh.model.getPhysicalGroups(3)
+
+    material_tags = []
+    # Get the name for each physical group
+    for dim, tag in volume_groups:
+        name = gmsh.model.getPhysicalName(dim, tag)
+        material_tags.append(name)
+        print(f"Material tag: {name}")
+    print(f"Material tags: {material_tags}")
+    return material_tags
+
+
+def export_gmsh_file_to_dagmc_h5m_file(
+    gmsh_filename: str,
+    material_tags: list[str] | None = None,
+    implicit_complement_material_tag: str | None = None,
+    dagmc_filename: str = "dagmc.h5m",
+) -> str:
+    """Saves a DAGMC h5m file of the geometry GMsh file. This function
+    initializes and finalizes Gmsh.
+
+    Args:
+        material_tags (list[str]): the names of the DAGMC
+            material tags to assign. These will need to be in the same
+            order as the volumes in the GMESH mesh and match the
+            material tags used in the neutronics code (e.g. OpenMC).
+        implicit_complement_material_tag (str | None, optional):
+            the name of the material tag to use for the implicit
+            complement (void space). Defaults to None which is a vacuum.
+        dagmc_filename (str, optional): _description_. Defaults to "dagmc.h5m".
+
+    Returns:
+        str: The filename of the generated DAGMC h5m file.
+
+    Raises:
+        ValueError: If the number of material tags does not match the number of volumes in the GMSH object.
+    """
+
+    gmsh.initialize()
+    gmsh.open(gmsh_filename)
 
-        return h5m_filename
+    if material_tags is None:
+        material_tags = _get_material_tags_from_gmsh()
+
+    dims_and_vol_ids = gmsh.model.getEntities(3)
+
+    if len(dims_and_vol_ids) != len(material_tags):
+        msg = f"Number of volumes {len(dims_and_vol_ids)} is not equal to number of material tags {len(material_tags)}"
+        raise ValueError(msg)
+
+    vertices, triangles_by_solid_by_face = mesh_to_vertices_and_triangles(
+        dims_and_vol_ids=dims_and_vol_ids
+    )
+
+    gmsh.finalize()
+
+    h5m_filename = vertices_to_h5m(
+        vertices=vertices,
+        triangles_by_solid_by_face=triangles_by_solid_by_face,
+        material_tags=material_tags,
+        h5m_filename=dagmc_filename,
+        implicit_complement_material_tag=implicit_complement_material_tag,
+    )
+
+    return h5m_filename
 
 
 class CadToDagmc:
@@ -554,11 +630,13 @@ 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:
         -----------
@@ -587,6 +665,8 @@ 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:
@@ -611,17 +691,30 @@ 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)
@@ -634,7 +727,7 @@ class CadToDagmc:
 
         gmsh.finalize()
 
-        return gmsh
+        return filename
 
     def export_gmsh_mesh_file(
         self,
@@ -690,15 +783,16 @@ 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)
@@ -791,7 +885,7 @@ 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,
@@ -799,6 +893,8 @@ class CadToDagmc:
             set_size=set_size,
         )
 
+        gmsh.model.mesh.generate(2)
+
         dims_and_vol_ids = volumes
 
         vertices, triangles_by_solid_by_face = mesh_to_vertices_and_triangles(

{cad_to_dagmc-0.8.2.dist-info → cad_to_dagmc-0.9.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: cad_to_dagmc
-Version: 0.8.2
+Version: 0.9.1
 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
@@ -20,6 +20,8 @@ Requires-Dist: gmsh
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: vtk; extra == "tests"
+Requires-Dist: assembly-mesh-plugin; extra == "tests"
+Dynamic: license-file
 
 
 [![N|Python](https://www.python.org/static/community_logos/python-powered-w-100x40.png)](https://www.python.org)
@@ -43,13 +45,17 @@ cad-to-dagmc can create DAGMC compatible:
 
 cad-to-dagmc can convert the following in to DAGMC compatible meshes:
 - STEP files
-- CadQuery objects (in memory)
-- Gmsh meshes
+- CadQuery objects (optionally use names as material tags)
+- Gmsh meshes (optionally use physical groups as material tags)
 
 Cad-to-dagmc offers a wide range of features including.
+- Compatibly with [assembly-mesh-plugin](https://github.com/CadQuery/assembly-mesh-plugin) (see examples)
+- Access to the Gmsh mesh to allow user to define full set of mesh parameters
+- Option to use Gmsh physical groups as material tags
 - 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
+- Volume mesh selected volumes in the geometry (helps ensure conformal volume and surface mesh).
 - 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)
@@ -125,21 +131,10 @@ 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-0.9.1.dist-info/RECORD

@@ -0,0 +1,8 @@
+_version.py,sha256=QG_t-w_CzDn2UjPaW-Svt-wTU1NXK2QkudawUihJfHA,511
+cad_to_dagmc/__init__.py,sha256=fskHUTyCunSpnpJUvBfAYjx4uwDKXHTTiMP6GqnFRf0,494
+cad_to_dagmc/core.py,sha256=ej1wk_-q-eXJ5F7jfjBwPII4qWHnMQWeMT_XZG_A0xI,35713
+cad_to_dagmc-0.9.1.dist-info/licenses/LICENSE,sha256=B8kznH_777JVNZ3HOKDc4Tj24F7wJ68ledaNYeL9sCw,1070
+cad_to_dagmc-0.9.1.dist-info/METADATA,sha256=S15I2B5N_eEUC7XqFB6sNyiuFwSLrHj8--1CraXkaMo,8947
+cad_to_dagmc-0.9.1.dist-info/WHEEL,sha256=0CuiUZ_p9E4cD6NyLD6UG80LBXYyiSYZOKDm5lp32xk,91
+cad_to_dagmc-0.9.1.dist-info/top_level.txt,sha256=zTi8C64SEBsE5WOtPovnxhOzt-E6Oc5nC3RW6M_5aEA,22
+cad_to_dagmc-0.9.1.dist-info/RECORD,,

{cad_to_dagmc-0.8.2.dist-info → cad_to_dagmc-0.9.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (80.3.1)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

cad_to_dagmc-0.8.2.dist-info/RECORD

@@ -1,8 +0,0 @@
-_version.py,sha256=t6tJJG56wlBKsg_0M1Q4l1ir09jgXRw1tolMbDalW9g,411
-cad_to_dagmc/__init__.py,sha256=fskHUTyCunSpnpJUvBfAYjx4uwDKXHTTiMP6GqnFRf0,494
-cad_to_dagmc/core.py,sha256=dW8p0TuQKJHPR6dqOulc7mTkB9zB2q_odkNSg8mU-Ew,31867
-cad_to_dagmc-0.8.2.dist-info/LICENSE,sha256=B8kznH_777JVNZ3HOKDc4Tj24F7wJ68ledaNYeL9sCw,1070
-cad_to_dagmc-0.8.2.dist-info/METADATA,sha256=aRZgmsBIcMbAB80vBJmuCWUkN6Ejab7X0IPBXsc52lU,8700
-cad_to_dagmc-0.8.2.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-cad_to_dagmc-0.8.2.dist-info/top_level.txt,sha256=zTi8C64SEBsE5WOtPovnxhOzt-E6Oc5nC3RW6M_5aEA,22
-cad_to_dagmc-0.8.2.dist-info/RECORD,,