cad-to-dagmc 0.8.1__py3-none-any.whl → 0.9.0__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 = '0.8.1'
-__version_tuple__ = version_tuple = (0, 8, 1)
+__version__ = version = '0.9.0'
+__version_tuple__ = version_tuple = (0, 9, 0)

cad_to_dagmc/core.py

@@ -6,9 +6,10 @@ 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]:
+def define_moab_core_and_tags() -> tuple[core.Core, dict]:
     """Creates a MOAB Core instance which can be built up by adding sets of
     triangles to the instance
 
@@ -62,7 +63,7 @@ def _define_moab_core_and_tags() -> tuple[core.Core, dict]:
     return moab_core, tags
 
 
-def _vertices_to_h5m(
+def vertices_to_h5m(
     vertices: list[tuple[float, float, float]] | list["cadquery.occ_impl.geom.Vector"],
     triangles_by_solid_by_face: list[list[tuple[int, int, int]]],
     material_tags: list[str],
@@ -100,7 +101,7 @@ def _vertices_to_h5m(
             else:
                 face_ids_with_solid_ids[face_id] = [solid_id]
 
-    moab_core, tags = _define_moab_core_and_tags()
+    moab_core, tags = define_moab_core_and_tags()
 
     volume_sets_by_solid_id = {}
     for material_tag, (solid_id, triangles_on_each_face) in zip(
@@ -229,11 +230,11 @@ 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 mesh_brep(
     gmsh,
     min_mesh_size: float | None = None,
     max_mesh_size: float | None = None,
@@ -318,7 +319,9 @@ 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)
@@ -355,21 +358,21 @@ def mesh_to_vertices_and_triangles(
     return vertices, triangles_by_solid_by_face
 
 
-def _get_ids_from_assembly(assembly: cq.assembly.Assembly):
+def get_ids_from_assembly(assembly: cq.assembly.Assembly):
     ids = []
     for obj, name, loc, _ in assembly:
         ids.append(name)
     return ids
 
 
-def _get_ids_from_imprinted_assembly(solid_id_dict):
+def get_ids_from_imprinted_assembly(solid_id_dict):
     ids = []
     for id in list(solid_id_dict.values()):
         ids.append(id[0])
     return ids
 
 
-def _check_material_tags(material_tags, iterable_solids):
+def check_material_tags(material_tags, iterable_solids):
     if material_tags:
         if len(material_tags) != len(iterable_solids):
             msg = (
@@ -399,64 +402,122 @@ 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)
+
+    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)
 
-        return h5m_filename
+    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:
@@ -537,7 +598,7 @@ class CadToDagmc:
         else:
             scaled_iterable_solids = [part.scale(scale_factor) for part in iterable_solids]
 
-        _check_material_tags(material_tags, scaled_iterable_solids)
+        check_material_tags(material_tags, scaled_iterable_solids)
         if material_tags:
             self.material_tags = self.material_tags + material_tags
         self.parts = self.parts + scaled_iterable_solids
@@ -613,7 +674,7 @@ class CadToDagmc:
 
         gmsh, _ = get_volumes(gmsh, imprinted_assembly, method=method, scale_factor=scale_factor)
 
-        gmsh = _mesh_brep(
+        gmsh = mesh_brep(
             gmsh=gmsh,
             min_mesh_size=min_mesh_size,
             max_mesh_size=max_mesh_size,
@@ -690,7 +751,7 @@ class CadToDagmc:
 
         gmsh, _ = get_volumes(gmsh, imprinted_assembly, method=method, scale_factor=scale_factor)
 
-        gmsh = _mesh_brep(
+        gmsh = mesh_brep(
             gmsh=gmsh,
             min_mesh_size=min_mesh_size,
             max_mesh_size=max_mesh_size,
@@ -761,7 +822,7 @@ class CadToDagmc:
         for part in self.parts:
             assembly.add(part)
 
-        original_ids = _get_ids_from_assembly(assembly)
+        original_ids = get_ids_from_assembly(assembly)
 
         # both id lists should be the same length as each other and the same
         # length as the self.material_tags
@@ -774,7 +835,7 @@ class CadToDagmc:
                 assembly
             )
 
-            scrambled_ids = _get_ids_from_imprinted_assembly(imprinted_solids_with_org_id)
+            scrambled_ids = get_ids_from_imprinted_assembly(imprinted_solids_with_org_id)
 
             material_tags_in_brep_order = order_material_ids_by_brep_order(
                 original_ids, scrambled_ids, self.material_tags
@@ -783,7 +844,7 @@ class CadToDagmc:
             material_tags_in_brep_order = self.material_tags
             imprinted_assembly = assembly
 
-        _check_material_tags(material_tags_in_brep_order, self.parts)
+        check_material_tags(material_tags_in_brep_order, self.parts)
 
         gmsh = init_gmsh()
 
@@ -791,7 +852,7 @@ class CadToDagmc:
             gmsh, imprinted_assembly, method=method, scale_factor=scale_factor
         )
 
-        gmsh = _mesh_brep(
+        gmsh = mesh_brep(
             gmsh=gmsh,
             min_mesh_size=min_mesh_size,
             max_mesh_size=max_mesh_size,
@@ -808,7 +869,7 @@ class CadToDagmc:
         gmsh.finalize()
 
         # checks and fixes triangle fix_normals within vertices_to_h5m
-        return _vertices_to_h5m(
+        return vertices_to_h5m(
             vertices=vertices,
             triangles_by_solid_by_face=triangles_by_solid_by_face,
             material_tags=material_tags_in_brep_order,

{cad_to_dagmc-0.8.1.dist-info → cad_to_dagmc-0.9.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: cad_to_dagmc
-Version: 0.8.1
+Version: 0.9.0
 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)
@@ -43,10 +45,13 @@ 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

cad_to_dagmc-0.9.0.dist-info/RECORD

@@ -0,0 +1,8 @@
+_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,,

{cad_to_dagmc-0.8.1.dist-info → cad_to_dagmc-0.9.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (78.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

cad_to_dagmc-0.8.1.dist-info/RECORD

@@ -1,8 +0,0 @@
-_version.py,sha256=Z8fNqmfsoA07nbVEewR90wZCgaN6eyDwPwgtgc2KIak,411
-cad_to_dagmc/__init__.py,sha256=fskHUTyCunSpnpJUvBfAYjx4uwDKXHTTiMP6GqnFRf0,494
-cad_to_dagmc/core.py,sha256=DbxXCaVEIiJxulRJlatoQg-yce37SS9Dx914Gt91qKY,31883
-cad_to_dagmc-0.8.1.dist-info/LICENSE,sha256=B8kznH_777JVNZ3HOKDc4Tj24F7wJ68ledaNYeL9sCw,1070
-cad_to_dagmc-0.8.1.dist-info/METADATA,sha256=AQ41vcWt_gHdZFL_rh7n28O5CheNftqa-FWdaVWvhjI,8700
-cad_to_dagmc-0.8.1.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-cad_to_dagmc-0.8.1.dist-info/top_level.txt,sha256=zTi8C64SEBsE5WOtPovnxhOzt-E6Oc5nC3RW6M_5aEA,22
-cad_to_dagmc-0.8.1.dist-info/RECORD,,