Merge pull request #35 from fusion-energy/develop

Adding tet mesh and scale options

README.md

@@ -94,9 +94,10 @@ cad_to_h5m(
 )
 ```
 
-Creating a EXODUS mesh files compatible with the DAGMC Unstructured  mesh format
-is also possible. Another entry must be added to the ```files_with_tags```
-argument. The following command will produce a ```unstructured_mesh_file.exo```
+Creating a tet mesh files compatible with the OpenMC / DAGMC Unstructured mesh
+format is also possible. Another key called ```tet_mesh``` to the ```files_with_tags``` dictionary will tirgger the meshing of that CAD file.
+The value of the key will be passed to the Cubit mesh command as an instruction.
+The following command will produce a ```unstructured_mesh_file.exo```
 file that can then be used in DAGMC compatable neutronics codes. There are examples
 [1](https://docs.openmc.org/en/latest/examples/unstructured-mesh-part-i.html)
 [2](https://docs.openmc.org/en/latest/examples/unstructured-mesh-part-ii.html) 
@@ -106,13 +107,70 @@ for the use of unstructured meshes in OpenMC.
 from cad_to_h5m import cad_to_h5m
 
 cad_to_h5m(
-    files_with_tags=[{'cad_filename':'part1.sat', 'material_tags':'m1', 'tet_mesh': 'size 0.5'}],
+    files_with_tags=[
+        {
+            'cad_filename':'part1.sat',
+            'material_tags':'m1',
+            'tet_mesh': 'size 0.5'
+        }
+    ],
     h5m_filename='dagmc.h5m',
     cubit_path='/opt/Coreform-Cubit-2021.5/bin/'
     exo_filename='unstructured_mesh_file.exo'
 )
 ```
 
+Use if ```exo``` files requires OpenMC to be compiled with LibMesh. OpenMC also
+accepts DAGMC tet meshes made with MOAB which is another option. The following
+example creates a ```cub``` file that contains a mesh. The MOAB tool 
+```mbconvert``` is then used to extract the tet mesh and save it as a ```h5m```
+file which cna be used in OpenMC as shown in the OpenMC [examples](https://docs.openmc.org/en/stable/examples/unstructured-mesh-part-i.html)
+
+```python
+from cad_to_h5m import cad_to_h5m
+
+cad_to_h5m(
+    files_with_tags=[
+        {
+            'cad_filename':'part1.sat',
+            'material_tags':'m1',
+            'tet_mesh': 'size 0.5'
+        }
+    ],
+    h5m_filename='dagmc.h5m',
+    cubit_path='/opt/Coreform-Cubit-2021.5/bin/'
+    cubit_filename='unstructured_mesh_file.cub'
+)
+```
+mbconvert is a terminal command that is part of MOAB.
+```bash
+mbconvert unstructured_mesh_file.cub unstructured_mesh_file.h5m
+```
+
+Scaling geometry is also possible. This is useful as particle transport codes
+often make use of cm as the default unit. CAD files typically appear in mm as
+the default limit. Some CAD packages ignore units while others make use of them.
+The h5m files are assumed to be in cm by particle transport codes so often it
+is nessecary to scale up or down the geometry. This can be done by adding
+another key called ```scale``` and a value to the ```files_with_tags```
+dictionary. This example multiplies the geometry by 10.
+
+```python
+from cad_to_h5m import cad_to_h5m
+
+cad_to_h5m(
+    files_with_tags=[
+        {
+            'cad_filename':'part1.sat',
+            'material_tags':'m1',
+            'scale': 10
+        }
+    ],
+    h5m_filename='dagmc.h5m',
+)
+```
+
+
 # Installation
 
 The package is available via the PyPi package manager and the recommended

cad_to_h5m/core.py

@@ -9,6 +9,7 @@ class FilesWithTags(TypedDict, total=False):
     filename: str
     material_tag: str
     tet_mesh: str
+    scale: float
 
 
 def cad_to_h5m(
@@ -22,7 +23,7 @@ def cad_to_h5m(
     imprint: bool = True,
     geometry_details_filename: Optional[str] = None,
     surface_reflectivity_name: str = "reflective",
-    exo_filename: str = "tet_mesh.exo",
+    exo_filename: Optional[str] = None,
 ):
     """Converts a CAD files in STP or SAT format into a h5m file for use in
     DAGMC simulations. The h5m file contains material tags associated with the
@@ -35,10 +36,16 @@ def cad_to_h5m(
         "mat2", "cad_filename": "part2.stp"}]. There is also an option to create
         a tet mesh of entries by including a "tet_mesh" key in the dictionary.
         The value is passed to the Cubit mesh command. An example entry would be
-        "tet_mesh": "size 0.5"
-    h5m_filename: the file name of the output h5m file
+        "tet_mesh": "size 0.5". The scale key can also be included to scale up
+        or down the geometry so that it is in cm units as required by most
+        particle transport codes. And example entry would be "scale": 10 which
+        would make the geometry 10 times bigger.
+    h5m_filename: the file name of the output h5m file which is suitable for
+        use in DAGMC enabled particle transport codes.
     cubit_filename: the file name of the output cubit file. Should end with .cub
-        or .cub5
+        or .cub5. Includes any tet meshes produced and therefore this output
+        can be useful for producing unstructured meshs for use in DAGMC
+        simulations.
     cubit_path: the path to the Cubit directory used to import Cubit from. On
         Ubuntu with Cubit 2021.5 this would be "/opt/Coreform-Cubit-2021.5/bin/"
     merge_tolerance: The merge tolerance to apply when merging surfaces into
@@ -100,25 +107,29 @@ def cad_to_h5m(
     geometry_details, total_number_of_volumes = find_number_of_volumes_in_each_step_file(
         files_with_tags, cubit)
     print(geometry_details)
+
+    scale_geometry(cubit, geometry_details)
+
     tag_geometry_with_mats(geometry_details, cubit)
 
     if imprint and total_number_of_volumes > 1:
         imprint_geometry(cubit)
     if total_number_of_volumes > 1:
         merge_geometry(merge_tolerance, cubit)
+
+    # TODO method requires further testing
     find_reflecting_surfaces_of_reflecting_wedge(
         geometry_details, surface_reflectivity_name, cubit
     )
 
-    create_tet_mesh(geometry_details, exo_filename, cubit)
-
     save_output_files(
         make_watertight,
         geometry_details,
         h5m_filename,
         cubit_filename,
         geometry_details_filename,
         faceting_tolerance,
+        exo_filename,
         cubit,
     )
     return h5m_filename
@@ -129,19 +140,25 @@ def create_tet_mesh(geometry_details, exo_filename, cubit):
 
     cubit.cmd("volume all size auto factor 5")
     for entry in geometry_details:
+        print('entry=', entry)
         if "tet_mesh" in entry.keys():
             for volume in entry["volumes"]:
+                print('volume=', volume)
                 cubit.cmd(
                     "volume " + str(volume) + " size auto factor 6"
                 )  # this number is the size of the mesh 1 is small 10 is large
-                cubit.cmd(
-                    "volume all scheme tetmesh proximity layers off geometric sizing on")
+                cubit.cmd("volume all scheme tetmesh proximity layers off")
                 # example entry ' size 0.5'
-                cubit.cmd(f"volume {str(volume)} " + entry["tet_mesh"])
+                cubit.cmd(f"volume {volume} " + entry["tet_mesh"])
                 cubit.cmd("mesh volume " + str(volume))
             print('meshed some volumes')
 
-    cubit.cmd(f'export mesh "{exo_filename}" overwrite')
+
+def scale_geometry(cubit, geometry_details):
+    for entry in geometry_details:
+        if 'scale' in entry.keys():
+            cubit.cmd(
+                f'volume {" ".join(entry["volumes"])}  scale  {entry["scale"]}')
 
 
 # def save_tet_details_to_json_file(
@@ -164,6 +181,7 @@ def save_output_files(
     cubit_filename,
     geometry_details_filename,
     faceting_tolerance,
+    exo_filename,
     cubit,
 ):
     """This saves the output files"""
@@ -173,9 +191,6 @@ def save_output_files(
         with open(geometry_details_filename, "w") as outfile:
             json.dump(geometry_details, outfile, indent=4)
 
-    if cubit_filename is not None:
-        cubit.cmd('save as "' + cubit_filename + '" overwrite')
-
     Path(h5m_filename).parents[0].mkdir(parents=True, exist_ok=True)
 
     print("using faceting_tolerance of ", faceting_tolerance)
@@ -194,6 +209,16 @@ def save_output_files(
             + '" faceting_tolerance '
             + str(faceting_tolerance)
         )
+
+    create_tet_mesh(geometry_details, exo_filename, cubit)
+
+    if exo_filename is not None:
+        Path(exo_filename).parents[0].mkdir(parents=True, exist_ok=True)
+        cubit.cmd(f'export mesh "{exo_filename}" overwrite')
+
+    if cubit_filename is not None:
+        cubit.cmd('save as "' + cubit_filename + '" overwrite')
+
     return h5m_filename
 
 
@@ -226,6 +251,8 @@ def find_all_surfaces_of_reflecting_wedge(new_vols, cubit):
     print("surface_info_dict", surface_info_dict)
     return surface_info_dict
 
+# todo additional testing required
+
 
 def find_reflecting_surfaces_of_reflecting_wedge(
     geometry_details, surface_reflectivity_name, cubit

tests/test_python_api.py

@@ -19,6 +19,9 @@ def setUp(self):
         tar.extractall("tests")
         tar.close()
 
+        url = "https://raw.githubusercontent.com/fusion-energy/neutronics_workflow/2f65bdeb802f2b1b25da683d13dcd2b29ffc9ed3/example_05_3D_unstructured_mesh_tally/stage_1_output/steel.stp"
+        urllib.request.urlretrieve(url, "tests/steel.stp")
+
     def test_h5m_file_creation(self):
         """Checks that a h5m file is created from stp files when make_watertight
         is set to false"""
@@ -140,34 +143,36 @@ def test_faceting_tolerance_increases_file_size(self):
     def test_exo_file_creation_with_different_sizes(self):
         """Checks that a h5m file is created from stp files"""
 
-        os.system("rm umesh_3.exo")
+        os.system("rm umesh_2.exo")
 
         cad_to_h5m(
             files_with_tags=[
                 {
-                    "cad_filename": "tests/fusion_example_for_openmc_using_paramak-0.0.1/stp_files/pf_coils.stp",
+                    "cad_filename": "tests/steel.stp",
                     "material_tag": "mat1",
-                    "tet_mesh": "size 3"}],
-            exo_filename="umesh_3.exo",
+                    "tet_mesh": "size 2"
+                }],
+            exo_filename="umesh_2.exo",
         )
 
-        assert Path("umesh_3.exo").is_file()
+        assert Path("umesh_2.exo").is_file()
 
-        os.system("rm umesh_10.exo")
+        os.system("rm umesh_3.exo")
 
         cad_to_h5m(
             files_with_tags=[
                 {
-                    "cad_filename": "tests/fusion_example_for_openmc_using_paramak-0.0.1/stp_files/pf_coils.stp",
+                    "cad_filename": "tests/steel.stp",
                     "material_tag": "mat1",
-                    "tet_mesh": "size 10"}],
-            exo_filename="umesh_10.exo",
+                    "tet_mesh": "size 3"
+                }],
+            exo_filename="umesh_3.exo",
         )
 
-        assert Path("umesh_10.exo").is_file()
+        assert Path("umesh_3.exo").is_file()
 
-        assert (Path("umesh_10.exo").stat().st_size >
-                Path("umesh_3.exo").stat().st_size)
+        assert (Path("umesh_3.exo").stat().st_size >
+                Path("umesh_2.exo").stat().st_size)
 
     def test_exo_file_creation_with_default_size(self):
         """Checks that a h5m file is created from stp files"""
@@ -226,3 +231,25 @@ def incorrect_suffix():
                 cubit_filename="output_file_with.not_correct_suffix",
             )
         self.assertRaises(ValueError, incorrect_suffix)
+
+    def test_h5m_file_creation_with_scaling(self):
+        """Checks that a h5m file is created from stp files when make_watertight
+        is set to false"""
+
+        os.system("rm test_dagmc.h5m")
+
+        test_h5m_filename = "test_dagmc.h5m"
+
+        returned_filename = cad_to_h5m(
+            files_with_tags=[
+                {
+                    "cad_filename": "tests/fusion_example_for_openmc_using_paramak-0.0.1/stp_files/blanket.stp",
+                    "material_tag": "mat1",
+                    "scale": 0.1,
+                }],
+            h5m_filename=test_h5m_filename,
+        )
+
+        assert Path(test_h5m_filename).is_file()
+        assert Path(returned_filename).is_file()
+        assert test_h5m_filename == returned_filename