Merge pull request #45 from fusion-energy/develop

updating docs and checking cad quality
fusion-energy · Sep 22, 2021 · fb1fbc5 · fb1fbc5
2 parents ff6d4c8 + 90931a8
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diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,15 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Shimwell"
+  given-names: "Jonathan"
+  orcid: "https://orcid.org/0000-0001-6909-0946"
+- family-names: "Labrie-Cleary"
+  given-names: "Luke"
+- family-names: "Gray"
+  given-names: "Ander"
+  orcid: "https://orcid.org/0000-0002-1585-0900"
+title: "cad-to-h5m"
+version: 0.3.0
+date-released: 2021-9-15
+url: "https://github.com/fusion-energy/cad_to_h5m"
diff --git a/README.md b/README.md
@@ -49,6 +49,18 @@ It is also possible to convert .sat files in the following way.
 cad-to-h5m -i part1.sat -o dagmc.h5m -t mat:1 -c /opt/Coreform-Cubit-2021.5/bin/
 ``` -->
 
+# Installation
+
+The package is available via the PyPi package manager and the recommended
+method of installing is via pip.
+```bash
+pip install cad_to_h5m
+```
+
+In addition [Cubit](https://coreform.com/products/coreform-cubit/) and the 
+[Svalinn Plugin](https://github.com/svalinn/Cubit-plugin) needs to be
+installed to make full use of this package.
+
 # Python API usage
 
 Creating a h5m file from a single STP file called ```part1.stp``` and applying
@@ -142,11 +154,22 @@ cad_to_h5m(
     cubit_filename='unstructured_mesh_file.cub'
 )
 ```
-mbconvert is a terminal command that is part of MOAB.
+The ```cub``` file produced contains a tet mesh as well as the faceted geometry.
+The tet mesh can be extracted and converted to another ```h5m``` file for use in
+openmc. MOAB is needed to convert the file and includes the command line tool
+```mbconvert```, MOAB can be installed into a conda environment with:
+
+```
+conda install -c conda-forge moab
+```
+Then ```mbconvert``` can be used to extract and convert the tet mesh from the
+```cub``` file into a ```h5m``` file.
+
 ```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.
@@ -189,13 +212,3 @@ cad_to_h5m(
     implicit_complement_material_tag = 'm2'
 )
 ```
-# Installation
-
-The package is available via the PyPi package manager and the recommended
-method of installing is via pip.
-```bash
-pip install cad_to_h5m
-```
-
-Some Python dependencies (such as Numpy) are installed during the ```pip install cad_to_h5m``` process, however [Cubit](https://coreform.com/products/coreform-cubit/) needs
-to be installed seperatly to make full use of this package.
diff --git a/cad_to_h5m/core.py b/cad_to_h5m/core.py
@@ -45,7 +45,7 @@ def cad_to_h5m(
         use in DAGMC enabled particle transport codes.
     cubit_filename: the file name of the output cubit file. Should end with .cub
         or .cub5. Includes any tet meshes produced and therefore this output
-        can be useful for producing unstructured meshs for use in DAGMC
+        can be useful for producing unstructured meshes 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/"
@@ -101,7 +101,7 @@ def cad_to_h5m(
     except ImportError:
         msg = (
             "import cubit failed, cubit was not importable from the "
-            "provided path {cubit_path}"
+            f"provided path {cubit_path}"
         )
         raise ImportError(msg)
 
@@ -111,7 +111,7 @@ def cad_to_h5m(
         files_with_tags, cubit)
     print(geometry_details)
 
-    scale_geometry(cubit, geometry_details)
+    scale_geometry(geometry_details, cubit)
 
     tag_geometry_with_mats(
         geometry_details, implicit_complement_material_tag, cubit
@@ -140,32 +140,29 @@ def cad_to_h5m(
     return h5m_filename
 
 
-def create_tet_mesh(geometry_details, exo_filename, cubit):
+def create_tet_mesh(geometry_details, cubit):
     cubit.cmd("Trimesher volume gradation 1.3")
 
     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")
                 # example entry ' size 0.5'
                 cubit.cmd(f"volume {volume} " + entry["tet_mesh"])
                 cubit.cmd("mesh volume " + str(volume))
-            print('meshed some volumes')
 
 
-def scale_geometry(cubit, geometry_details):
+def scale_geometry(geometry_details: dict, cubit):
     for entry in geometry_details:
         if 'scale' in entry.keys():
             cubit.cmd(
                 f'volume {" ".join(entry["volumes"])}  scale  {entry["scale"]}')
 
-
+# TODO implent a flag to allow tet file info to be saved
 # def save_tet_details_to_json_file(
 #         geometry_details,
 #         filename="mesh_details.json"):
@@ -179,14 +176,15 @@ def scale_geometry(cubit, geometry_details):
 #     with open(filename, "w") as outfile:
 #         json.dump(geometry_details, outfile, indent=4)
 
+
 def save_output_files(
-    make_watertight,
-    geometry_details,
-    h5m_filename,
-    cubit_filename,
-    geometry_details_filename,
-    faceting_tolerance,
-    exo_filename,
+    make_watertight: bool,
+    geometry_details: dict,
+    h5m_filename: str,
+    cubit_filename: str,
+    geometry_details_filename: str,
+    faceting_tolerance: float,
+    exo_filename: str,
     cubit,
 ):
     """This saves the output files"""
@@ -215,7 +213,7 @@ def save_output_files(
             + str(faceting_tolerance)
         )
 
-    create_tet_mesh(geometry_details, exo_filename, cubit)
+    create_tet_mesh(geometry_details, cubit)
 
     if exo_filename is not None:
         Path(exo_filename).parents[0].mkdir(parents=True, exist_ok=True)
@@ -231,11 +229,16 @@ def imprint_geometry(cubit):
     cubit.cmd("imprint body all")
 
 
-def merge_geometry(merge_tolerance, cubit):
-    # optional as there is a default
+def merge_geometry(merge_tolerance: float, cubit):
+    """merges the geometry with te specified tolerance
+
+    Args:
+        merge_tolerance: The allowable distance between surfaces before merging
+            them together. Optional as there is a default built into the DAGMC
+            export command
+    """
     cubit.cmd(f"merge tolerance {merge_tolerance}")
     cubit.cmd("merge vol all group_results")
-    cubit.cmd("graphics tol angle 3")
 
 
 def find_all_surfaces_of_reflecting_wedge(new_vols, cubit):
@@ -256,8 +259,6 @@ 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
@@ -330,15 +331,9 @@ def tag_geometry_with_mats(
 
 def find_number_of_volumes_in_each_step_file(files_with_tags, cubit):
     """ """
-    body_ids = ""
-    volumes_in_each_step_file = []
-    # all_groups=cubit.parse_cubit_list("group","all")
-    # starting_group_id = len(all_groups)
     for entry in files_with_tags:
-        print(entry)
-        # starting_group_id = starting_group_id +1
+        print(f'loading {entry["cad_filename"]}')
         current_vols = cubit.parse_cubit_list("volume", "all")
-        # print(os.path.join(basefolder, entry['cad_filename']))
         if entry["cad_filename"].endswith(
                 ".stp") or entry["cad_filename"].endswith(".step"):
             import_type = "step"
@@ -352,8 +347,6 @@ def find_number_of_volumes_in_each_step_file(files_with_tags, cubit):
             msg = f'File with filename {entry["cad_filename"]} could not be found'
             raise FileNotFoundError(msg)
         short_file_name = os.path.split(entry["cad_filename"])[-1]
-        # print('short_file_name',short_file_name)
-        # cubit.cmd('import '+import_type+' "' + entry['stp_filename'] + '" separate_bodies no_surfaces no_curves no_vertices group "'+str(short_file_name)+'"')
         cubit.cmd(
             "import "
             + import_type
@@ -364,11 +357,6 @@ def find_number_of_volumes_in_each_step_file(files_with_tags, cubit):
         all_vols = cubit.parse_cubit_list("volume", "all")
         new_vols = set(current_vols).symmetric_difference(set(all_vols))
         new_vols = list(map(str, new_vols))
-        print("new_vols", new_vols, type(new_vols))
-        current_bodies = cubit.parse_cubit_list("body", "all")
-        print("current_bodies", current_bodies)
-        # volumes_in_group = cubit.cmd('volume in group '+str(starting_group_id))
-        # print('volumes_in_group',volumes_in_group,type(volumes_in_group))
         if len(new_vols) > 1:
             cubit.cmd(
                 "unite vol " +
@@ -394,4 +382,8 @@ def find_number_of_volumes_in_each_step_file(files_with_tags, cubit):
                 entry["surface_reflectivity"])
     cubit.cmd("separate body all")
 
+    # checks the cad is clean and catches some errors with the geometry early
+    cubit.cmd("validate vol all")
+    cubit.cmd("autoheal analyze vol all")
+
     return files_with_tags, sum(all_vols)
diff --git a/setup.py b/setup.py
@@ -24,8 +24,5 @@
         'License :: OSI Approved :: MIT License',
         'Operating System :: OS Independent',
     ],
-    tests_require=[
-        "pytest",
-    ],
     python_requires='>=3.6',
 )
diff --git a/tests/test_python_api.py b/tests/test_python_api.py
@@ -4,23 +4,27 @@
 import urllib.request
 from pathlib import Path
 
-import pytest
 from cad_to_h5m import cad_to_h5m
 
 
 class TestApiUsage(unittest.TestCase):
     def setUp(self):
 
-        if not Path("tests/v0.0.1.tar.gz").is_file():
+        if not Path("tests/v0.0.2.tar.gz").is_file():
             url = "https://github.com/Shimwell/fusion_example_for_openmc_using_paramak/archive/refs/tags/v0.0.1.tar.gz"
             urllib.request.urlretrieve(url, "tests/v0.0.1.tar.gz")
 
-        tar = tarfile.open("tests/v0.0.1.tar.gz", "r:gz")
-        tar.extractall("tests")
-        tar.close()
+            tar = tarfile.open("tests/v0.0.1.tar.gz", "r:gz")
+            tar.extractall("tests")
+            tar.close()
 
-        url = "https://raw.githubusercontent.com/fusion-energy/neutronics_workflow/main/example_01_single_volume_cell_tally/stage_1_output/steel.stp"
-        urllib.request.urlretrieve(url, "tests/steel.stp")
+        if not Path("tests/v0.0.2.tar.gz").is_file():
+            url = "https://github.com/fusion-energy/neutronics_workflow/archive/refs/tags/v0.0.2.tar.gz"
+            urllib.request.urlretrieve(url, "tests/v0.0.2.tar.gz")
+
+            tar = tarfile.open("tests/v0.0.2.tar.gz", "r:gz")
+            tar.extractall("tests")
+            tar.close()
 
     def test_h5m_file_creation(self):
         """Checks that a h5m file is created from stp files when make_watertight
@@ -148,10 +152,9 @@ def test_exo_file_creation_with_different_sizes(self):
         cad_to_h5m(
             files_with_tags=[
                 {
-                    "cad_filename": "tests/steel.stp",
+                    "cad_filename": "tests/neutronics_workflow-0.0.2/example_01_single_volume_cell_tally/stage_1_output/steel.stp",
                     "material_tag": "mat1",
-                    "tet_mesh": "size 2"
-                }],
+                    "tet_mesh": "size 2"}],
             exo_filename="umesh_2.exo",
         )
 
@@ -162,10 +165,9 @@ def test_exo_file_creation_with_different_sizes(self):
         cad_to_h5m(
             files_with_tags=[
                 {
-                    "cad_filename": "tests/steel.stp",
+                    "cad_filename": "tests/neutronics_workflow-0.0.2/example_01_single_volume_cell_tally/stage_1_output/steel.stp",
                     "material_tag": "mat1",
-                    "tet_mesh": "size 3"
-                }],
+                    "tet_mesh": "size 3"}],
             exo_filename="umesh_3.exo",
         )