cad-to-dagmc 0.6.1__py3-none-any.whl → 0.7.0__py3-none-any.whl

_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.6.1'
-__version_tuple__ = version_tuple = (0, 6, 1)
+__version__ = version = '0.7.0'
+__version_tuple__ = version_tuple = (0, 7, 0)

cad_to_dagmc/core.py

@@ -189,11 +189,13 @@ def _vertices_to_h5m(
 
     moab_core.write_file(h5m_filename)
 
+    print(f"written DAGMC file {h5m_filename}")
+
     return h5m_filename
 
 
 def _mesh_brep(
-    brep_object: str,
+    occ_shape: str,
     min_mesh_size: float = 1,
     max_mesh_size: float = 10,
     mesh_algorithm: int = 1,
@@ -203,7 +205,7 @@ def _mesh_brep(
     Gmsh.
 
     Args:
-        brep_object: the filename of the Brep file to convert
+        occ_shape: the occ_shape of the Brep file to convert
         min_mesh_size: the minimum mesh element size to use in Gmsh. Passed
             into gmsh.option.setNumber("Mesh.MeshSizeMin", min_mesh_size)
         max_mesh_size: the maximum mesh element size to use in Gmsh. Passed
@@ -220,7 +222,7 @@ def _mesh_brep(
     gmsh.initialize()
     gmsh.option.setNumber("General.Terminal", 1)
     gmsh.model.add("made_with_cad_to_dagmc_package")
-    volumes = gmsh.model.occ.importShapesNativePointer(brep_object)
+    volumes = gmsh.model.occ.importShapesNativePointer(occ_shape)
     gmsh.model.occ.synchronize()
 
     gmsh.option.setNumber("Mesh.Algorithm", mesh_algorithm)
@@ -231,16 +233,13 @@ def _mesh_brep(
     return gmsh, volumes
 
 
-def _mesh_to_h5m_in_memory_method(
-    volumes,
-) -> str:
-    """Converts gmsh volumes into a DAGMC h5m file.
+def mesh_to_vertices_and_triangles(
+    dims_and_vol_ids,
+):
+    """Converts gmsh volumes into vertices and triangles for each face.
 
     Args:
         volumes: the volumes in the gmsh file, found with gmsh.model.occ.importShapes
-        material_tags: A list of material tags to tag the DAGMC volumes with.
-            Should be in the same order as the volumes
-        h5m_filename: the filename of the DAGMC h5m file to write
 
     Returns:
         vertices and triangles (grouped by solid then by face)
@@ -248,7 +247,7 @@ def _mesh_to_h5m_in_memory_method(
 
     n = 3  # number of verts in a triangles
     triangles_by_solid_by_face = {}
-    for dim_and_vol in volumes:
+    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()
@@ -302,6 +301,22 @@ def _get_ids_from_imprinted_assembly(solid_id_dict):
     return ids
 
 
+def _check_material_tags(material_tags, iterable_solids):
+    if material_tags:
+        if len(material_tags) != len(iterable_solids):
+            msg = (
+                "When setting material_tags the number of material_tags \n"
+                "should be equal to the number of volumes in the CAD \n"
+                f"geometry {len(iterable_solids)} volumes found in model \n"
+                f"and {len(material_tags)} material_tags found"
+            )
+            raise ValueError(msg)
+        for material_tag in material_tags:
+            if not isinstance(material_tag, str):
+                msg = f"material_tags should be an iterable of strings."
+                raise ValueError(msg)
+
+
 def order_material_ids_by_brep_order(original_ids, scrambled_id, material_tags):
     material_tags_in_brep_order = []
     for brep_id in scrambled_id:
@@ -310,23 +325,87 @@ 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 __init__(self, filename: str):
+        self.filename = filename
+
+    # TODO add export_unstructured_mesh_file
+    # TODO add add_gmsh_msh_file
+
+    def export_dagmc_h5m_file(
+        self,
+        material_tags: typing.Iterable[str],
+        implicit_complement_material_tag: typing.Optional[str] = None,
+        filename: str = "dagmc.h5m",
+    ):
+        """Saves a DAGMC h5m file of the geometry
+
+        Args:
+            material_tags (typing.Iterable[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 (typing.Optional[str], 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".
+
+        Raises:
+            ValueError: _description_
+
+        Returns:
+            _type_: _description_
+        """
+
+        gmsh.initialize()
+        self.mesh_file = gmsh.open(self.filename)
+        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=filename,
+            implicit_complement_material_tag=implicit_complement_material_tag,
+        )
+
+        return h5m_filename
+
+
 class CadToDagmc:
+    """Converts Step files and CadQuery parts to a DAGMC h5m file"""
+
     def __init__(self):
         self.parts = []
+        self.material_tags = []
 
     def add_stp_file(
         self,
         filename: str,
         scale_factor: float = 1.0,
+        material_tags: typing.Optional[typing.Iterable[str]] = None,
     ):
         """Loads the parts from stp file into the model.
 
         Args:
             filename: the filename used to save the html graph.
-            material_tags: the names of the DAGMC material tags to assign.
-                These will need to be in the same order as the volumes in the
-                STP file and match the material tags used in the neutronics
-                code (e.g. OpenMC).
+            material_tags (typing.Iterable[str]): the names of the DAGMC
+                material tags to assign. These will need to be in the
+                same order as the volumes in the geometry added (STP
+                file and CadQuery objects) and match the material tags
+                used in the neutronics code (e.g. OpenMC).
             scale_factor: a scaling factor to apply to the geometry that can be
                 used to increase the size or decrease the size of the geometry.
                 Useful when converting the geometry to cm for use in neutronics
@@ -338,27 +417,38 @@ class CadToDagmc:
             scaled_part = part
         else:
             scaled_part = part.scale(scale_factor)
-        self.add_cadquery_object(object=scaled_part)
+        self.add_cadquery_object(cadquery_object=scaled_part, material_tags=material_tags)
 
     def add_cadquery_object(
         self,
-        object: typing.Union[
+        cadquery_object: typing.Union[
             cq.assembly.Assembly, cq.occ_impl.shapes.Compound, cq.occ_impl.shapes.Solid
         ],
+        material_tags: typing.Optional[typing.Iterable[str]] = None,
     ):
         """Loads the parts from CadQuery object into the model.
 
         Args:
-            object: the cadquery object to convert
+            cadquery_object: the cadquery object to convert, can be a CadQuery assembly
+                cadquery workplane or a cadquery solid
+            material_tags (Optional typing.Iterable[str]): the names of the
+                DAGMC material tags to assign. These will need to be in the
+                same order as the volumes in the geometry added (STP file and
+                CadQuery objects) and match the material tags used in the
+                neutronics code (e.g. OpenMC).
         """
 
-        if isinstance(object, cq.assembly.Assembly):
-            object = object.toCompound()
+        if isinstance(cadquery_object, cq.assembly.Assembly):
+            cadquery_object = cadquery_object.toCompound()
 
-        if isinstance(object, (cq.occ_impl.shapes.Compound, cq.occ_impl.shapes.Solid)):
-            iterable_solids = object.Solids()
+        if isinstance(cadquery_object, (cq.occ_impl.shapes.Compound, cq.occ_impl.shapes.Solid)):
+            iterable_solids = cadquery_object.Solids()
         else:
-            iterable_solids = object.val().Solids()
+            iterable_solids = cadquery_object.val().Solids()
+
+        _check_material_tags(material_tags, iterable_solids)
+        if material_tags:
+            self.material_tags = self.material_tags + material_tags
         self.parts = self.parts + iterable_solids
 
     def export_unstructured_mesh_file(
@@ -375,8 +465,8 @@ class CadToDagmc:
 
         imprinted_assembly, _ = cq.occ_impl.assembly.imprint(assembly)
 
-        gmsh, volumes = _mesh_brep(
-            brep_object=imprinted_assembly.wrapped._address(),
+        gmsh, _ = _mesh_brep(
+            occ_shape=imprinted_assembly.wrapped._address(),
             min_mesh_size=min_mesh_size,
             max_mesh_size=max_mesh_size,
             mesh_algorithm=mesh_algorithm,
@@ -392,6 +482,8 @@ class CadToDagmc:
 
         gmsh.finalize()
 
+        return gmsh
+
     def export_gmsh_mesh_file(
         self,
         filename: str = "mesh.msh",
@@ -418,8 +510,8 @@ class CadToDagmc:
 
         imprinted_assembly, _ = cq.occ_impl.assembly.imprint(assembly)
 
-        gmsh, volumes = _mesh_brep(
-            brep_object=imprinted_assembly.wrapped._address(),
+        gmsh, _ = _mesh_brep(
+            occ_shape=imprinted_assembly.wrapped._address(),
             min_mesh_size=min_mesh_size,
             max_mesh_size=max_mesh_size,
             mesh_algorithm=mesh_algorithm,
@@ -428,32 +520,34 @@ class CadToDagmc:
 
         gmsh.write(filename)
 
+        print(f"written GMSH mesh file {filename}")
+
         gmsh.finalize()
 
     def export_dagmc_h5m_file(
         self,
-        material_tags: typing.Iterable[str],
         filename: str = "dagmc.h5m",
         min_mesh_size: float = 1,
         max_mesh_size: float = 5,
         mesh_algorithm: int = 1,
         implicit_complement_material_tag: typing.Optional[str] = None,
-    ):
+    ) -> str:
         """Saves a DAGMC h5m file of the geometry
 
         Args:
-            filename
-            min_mesh_size: the minimum size of mesh elements to use.
-            max_mesh_size: the maximum size of mesh elements to use.
-            mesh_algorithm: the gmsh mesh algorithm to use.
-            material_tags: the names of the DAGMC material tags to assign.
-                These will need to be in the same order as the volumes in the
-                geometry geometry added (STP file and CadQuery objects) and
-                match the material tags used in the neutronics code (e.g. OpenMC).
-            implicit_complement_material_tag: the name of the material tag to
-                use for the implicit complement (void space). Defaults to None
-                which is a vacuum.
+
+            filename (str, optional): the filename to use for the saved DAGMC file. Defaults to "dagmc.h5m".
+            min_mesh_size (float, optional): the minimum size of mesh elements to use. Defaults to 1.
+            max_mesh_size (float, optional): the maximum size of mesh elements to use. Defaults to 5.
+            mesh_algorithm (int, optional): the GMSH mesh algorithm to use.. Defaults to 1.
+            implicit_complement_material_tag (typing.Optional[str], optional):
+                the name of the material tag to use for the implicit complement
+                (void space). Defaults to None which is a vacuum. Defaults to None.
+
+        Returns:
+            str: the DAGMC filename saved
         """
+
         assembly = cq.Assembly()
         for part in self.parts:
             assembly.add(part)
@@ -466,30 +560,28 @@ class CadToDagmc:
         # both id lists should be the same length as each other and the same
         # length as the self.material_tags
 
-        if len(original_ids) != len(material_tags):
-            msg = f"Number of volumes {len(original_ids)} is not equal to number of material tags {len(material_tags)}"
+        if len(original_ids) != len(self.material_tags):
+            msg = f"Number of volumes {len(original_ids)} is not equal to number of material tags {len(self.material_tags)}"
             raise ValueError(msg)
 
         material_tags_in_brep_order = order_material_ids_by_brep_order(
-            original_ids, scrambled_ids, material_tags
+            original_ids, scrambled_ids, self.material_tags
         )
 
+        _check_material_tags(material_tags_in_brep_order, self.parts)
+
         gmsh, volumes = _mesh_brep(
-            brep_object=imprinted_assembly.wrapped._address(),  # in memory address
+            occ_shape=imprinted_assembly.wrapped._address(),  # in memory address
             min_mesh_size=min_mesh_size,
             max_mesh_size=max_mesh_size,
             mesh_algorithm=mesh_algorithm,
         )
 
-        if isinstance(material_tags_in_brep_order, str):
-            msg = f"material_tags should be a list of strings, not a single string."
-            raise ValueError(msg)
-
-        if len(volumes) != len(material_tags_in_brep_order):
-            msg = f"{len(volumes)} volumes found in Brep file is not equal to the number of material_tags {len(material_tags_in_brep_order)} provided."
-            raise ValueError(msg)
+        dims_and_vol_ids = volumes
 
-        vertices, triangles_by_solid_by_face = _mesh_to_h5m_in_memory_method(volumes=volumes)
+        vertices, triangles_by_solid_by_face = mesh_to_vertices_and_triangles(
+            dims_and_vol_ids=dims_and_vol_ids
+        )
 
         gmsh.finalize()
 

{cad_to_dagmc-0.6.1.dist-info → cad_to_dagmc-0.7.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cad_to_dagmc
-Version: 0.6.1
+Version: 0.7.0
 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
@@ -14,7 +14,6 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: trimesh
 Requires-Dist: networkx
-Requires-Dist: cadquery-ocp >=7.7.2
 Requires-Dist: cadquery >=2.4.0
 Provides-Extra: tests
 Requires-Dist: pytest ; extra == 'tests'
@@ -52,10 +51,59 @@ Also checkout these other software projects that also create DAGMC geometry [CAD
 
 # Installation options
 
+- Install using Mamba
+- Install using Conda
 - Install using Mamba and pip
 - Install using Conda and pip
 - Install using pip and source compilations
 
+## Install using Mamba
+
+In principle, installing any Conda/Mamba distribution will work. A few Conda/Mamba options are:
+- [Miniforge](https://github.com/conda-forge/miniforge) (recommended as it includes mamba)
+- [Anaconda](https://www.anaconda.com/download)
+- [Miniconda](https://docs.conda.io/en/latest/miniconda.html)
+
+This example assumes you have installed the Miniforge option or separately have installed Mamba with ```conda install -c conda-forge mamba -y```
+
+Create a new environment, I've chosen Python 3.10 here but newer versions are
+also supported.
+```bash
+mamba create --name new_env python=3.10 -y
+```
+
+Activate the environment
+```bash
+mamba activate new_env
+```
+
+Then you can install the cad_to_dagmc package
+```bash
+mamba install -y -c conda-forge cad_to_dagmc
+```
+
+## Install using Conda
+
+In principle, installing any Conda/Mamba distribution will work. A few Conda/Mamba options are:
+- [Miniforge](https://github.com/conda-forge/miniforge) (recommended as it includes mamba)
+- [Anaconda](https://www.anaconda.com/download)
+- [Miniconda](https://docs.conda.io/en/latest/miniconda.html)
+
+Create a new environment, I've chosen Python 3.10 here but newer versions are
+also supported.
+```bash
+conda create --name new_env python=3.10 -y
+```
+
+Activate the environment
+```bash
+conda activate new_env
+```
+
+Then you can install the cad_to_dagmc package
+```bash
+conda install -y -c conda-forge cad_to_dagmc
+```
 
 ## Install using Mamba and pip
 
@@ -66,7 +114,7 @@ In principle, installing any Conda/Mamba distribution will work. A few Conda/Mam
 
 This example assumes you have installed the Miniforge option or separately have installed Mamba with ```conda install -c conda-forge mamba -y```
 
-Create a new conda environment, I've chosen Python 3.10 here but newer versions are
+Create a new environment, I've chosen Python 3.10 here but newer versions are
 also supported.
 ```bash
 mamba create --name new_env python=3.10 -y
@@ -82,7 +130,7 @@ Install the dependencies
 mamba install -y -c conda-forge "moab>=5.3.0" gmsh python-gmsh
 ```
 
-Then you can install the cad_to_dagmc package with ```pip```
+Then you can install the cad_to_dagmc package
 ```bash
 pip install cad_to_dagmc
 ```
@@ -97,7 +145,7 @@ In principle, installing any Conda/Mamba distribution will work. A few Conda/Mam
 
 This example uses Conda to install some dependencies that are not available via PyPi.
 
-Create a new conda environment
+Create a new environment
 ```bash
 conda create --name new_env python=3.10 -y
 ```
@@ -112,7 +160,7 @@ Install the dependencies
 conda install -y -c conda-forge "moab>=5.3.0" gmsh python-gmsh
 ```
 
-Then you can install the cad_to_dagmc package with ```pip```
+Then you can install the cad_to_dagmc package
 ```bash
 pip install cad_to_dagmc
 ```
@@ -131,7 +179,7 @@ Then you can install the cad_to_dagmc package with ```pip```
 pip install cad_to_dagmc
 ```
 
-## Install with transport code (e.g OpenMC)
+## Install with OpenMC or other particle transport codes
 
 You may also want to install OpenMC with DAGMC to make use of the h5m geometry files produced in simulations. However you could also use other supported particle transport codes such as MCNP, FLUKA and others [link to DAGMC documentation](https://svalinn.github.io/DAGMC/).
 
@@ -145,7 +193,6 @@ It might not be possible to install OpenMC and cad-to-dagmc in the same conda/ma
 Another option would be to [install OpenMC from source](https://docs.openmc.org/en/stable/quickinstall.html) which would also need compiling with MOAB and DAGMC options.
 
 
-
 # Known incompatibilities
 
 The package requires newer versions of Linux. For example the package does not work on Ubuntu 18.04 or older.
@@ -154,20 +201,6 @@ The package requires newer versions of pip. It is recommended to ensure that you
 
 Installing one of the package dependancies (gmsh) with pip appears to result in occational errors when passing cad objects between cadquery / ocp and gmsh. The conda install gmsh appears to work fine.
 
-# Usage - with OpenMC
-
-You may also want to install OpenMC with DAGMC to make use of the h5m geometry files produced in simulations. However you could also use other supported particle transport codes such as MCNP, FLUKA and others supported by [DAGMC](https://svalinn.github.io/DAGMC/).
-
-You can run ```mamba install -c conda-forge openmc``` however this may choose to install OpenMC without DAGMC included.
-
-You can be more specific with conda/mamba commands to make sure the latest version of OpenMC which contains DAGMC is chosen by conda / mamba
-```bash
-mamba install -c conda-forge -y "openmc=0.14.0=dagmc*nompi*"
-```
-
-You could also [install OpenMC from source](https://docs.openmc.org/en/stable/quickinstall.html) which might be prefered as it can be tricky for the conda enviroment to get resolved.
-
-
 
 # Usage - creation of DAGMC h5m files
 

cad_to_dagmc-0.7.0.dist-info/RECORD

@@ -0,0 +1,8 @@
+_version.py,sha256=akvr8ObxvMF-aaLBzW41juT4_KL3BjQUrjbwkIuQXMk,411
+cad_to_dagmc/__init__.py,sha256=fskHUTyCunSpnpJUvBfAYjx4uwDKXHTTiMP6GqnFRf0,494
+cad_to_dagmc/core.py,sha256=WJXKGK9yOtary66qPRB7cmdLlSdhSTkv1b4TxHtIvxw,21495
+cad_to_dagmc-0.7.0.dist-info/LICENSE,sha256=B8kznH_777JVNZ3HOKDc4Tj24F7wJ68ledaNYeL9sCw,1070
+cad_to_dagmc-0.7.0.dist-info/METADATA,sha256=40zC0CAVvVveGQ7wRpLvTE0gEhCtt5a-3ZvJQYCZc80,8770
+cad_to_dagmc-0.7.0.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+cad_to_dagmc-0.7.0.dist-info/top_level.txt,sha256=zTi8C64SEBsE5WOtPovnxhOzt-E6Oc5nC3RW6M_5aEA,22
+cad_to_dagmc-0.7.0.dist-info/RECORD,,

cad_to_dagmc-0.6.1.dist-info/RECORD

@@ -1,8 +0,0 @@
-_version.py,sha256=lgiCYGSijhLK71WmuudWf_AyhNAutwQWx2V8bV6a5VQ,411
-cad_to_dagmc/__init__.py,sha256=fskHUTyCunSpnpJUvBfAYjx4uwDKXHTTiMP6GqnFRf0,494
-cad_to_dagmc/core.py,sha256=eMwKgKOjje3gBZEqjNzy9O6NF8a02WxD-VhXB5AJg58,18108
-cad_to_dagmc-0.6.1.dist-info/LICENSE,sha256=B8kznH_777JVNZ3HOKDc4Tj24F7wJ68ledaNYeL9sCw,1070
-cad_to_dagmc-0.6.1.dist-info/METADATA,sha256=Fw_uOmqvNJCm1-XPMr1vy4fWgxWW4ZPmqSgCJouGmr4,8183
-cad_to_dagmc-0.6.1.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-cad_to_dagmc-0.6.1.dist-info/top_level.txt,sha256=zTi8C64SEBsE5WOtPovnxhOzt-E6Oc5nC3RW6M_5aEA,22
-cad_to_dagmc-0.6.1.dist-info/RECORD,,