Merge pull request #30 from fusion-energy/develop

changed filename tag to cad_filename

.circleci/config.yml

@@ -18,13 +18,7 @@ jobs:
       - run:
           name: run utils tests
           command:
-            pytest tests/test_python_api.py -v --cov=cad_to_h5m --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
-
-      - store_test_results:
-          path: test-reports
-
-      - run: bash <(curl -s https://codecov.io/bash)
-
+            pytest tests/test_python_api.py -v
 
 workflows:
   version: 2

.github/workflows/ci_with_docker_build.yml

@@ -10,19 +10,12 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-
-    # ports:
-    #   # Opens ports needed for Cubit license server communication on the host
-    #   - 5053:5053
-    #   - 5119:5119
-
+
     steps:
       - name: Checkout repository
         uses: actions/checkout@v2
 
       - name: Build and test with Docker
         run: |
-          printf '${{ github.license_file }}' >> license.lic
-          cat license.lic
           docker build -t cad_to_h5m .
           docker run --rm --network host cad_to_h5m  /bin/bash -c "bash run_tests.sh"

.github/workflows/ci_with_install.yml

@@ -26,7 +26,4 @@ jobs:
 
       - name: Run test_utils
         run: |
-          pytest tests/test_python_api.py -v --cov=cad_to_h5m --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
-
-      - name: Upload to codecov
-        uses: codecov/codecov-action@v2
+          pytest tests/test_python_api.py -v 

Dockerfile

@@ -63,9 +63,6 @@ RUN apt-get install -y wget
 RUN wget https://github.com/svalinn/Cubit-plugin/releases/download/0.2.1/svalinn-plugin_debian-10.10_cubit_2021.5.tgz
 RUN tar -xzvf svalinn-plugin_debian-10.10_cubit_2021.5.tgz -C /opt/Coreform-Cubit-2021.5
 
-# makes a python file and trys to import cubit
-RUN printf 'import sys\nsys.path.append("/opt/Coreform-Cubit-2021.5/bin/")\nimport cubit\ncubit.init([])\n' >> test_cubit_import.py
-
 # writes a non commercial license file
 # RUN printf 'Fri May 28 2021' >> /opt/Coreform-Cubit-2021.5/bin/licenses/cubit-learn.lic
 RUN mkdir -p /root/.config/Coreform/licenses

README.md

@@ -58,7 +58,7 @@ a material tag to the volume.
 from cad_to_h5m import cad_to_h5m
 
 cad_to_h5m(
-    files_with_tags=[{'filename':'part1.stp', 'material_tags':'m1'}],
+    files_with_tags=[{'cad_filename':'part1.stp', 'material_tags':'m1'}],
     h5m_filename='dagmc.h5m',
     cubit_path='/opt/Coreform-Cubit-2021.5/bin/'
 )
@@ -73,8 +73,8 @@ from cad_to_h5m import cad_to_h5m
 
 cad_to_h5m(
     files_with_tags=[
-        {'filename':'part1.stp', 'material_tags':'m1'},
-        {'filename':'part2.stp', 'material_tags':'m2'}
+        {'cad_filename':'part1.stp', 'material_tags':'m1'},
+        {'cad_filename':'part2.stp', 'material_tags':'m2'}
     ],
     h5m_filename='dagmc.h5m',
     cubit_path='/opt/Coreform-Cubit-2021.5/bin/'
@@ -88,7 +88,7 @@ extension.
 from cad_to_h5m import cad_to_h5m
 
 cad_to_h5m(
-    files_with_tags=[{'filename':'part1.sat', 'material_tags':'m1'}],
+    files_with_tags=[{'cad_filename':'part1.sat', 'material_tags':'m1'}],
     h5m_filename='dagmc.h5m',
     cubit_path='/opt/Coreform-Cubit-2021.5/bin/'
 )
@@ -106,7 +106,7 @@ for the use of unstructured meshes in OpenMC.
 from cad_to_h5m import cad_to_h5m
 
 cad_to_h5m(
-    files_with_tags=[{'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'

cad_to_h5m/core.py

@@ -30,10 +30,10 @@ def cad_to_h5m(
 
     files_with_tags: The file names of the input CAD files with associated
         materials tags in the form of a list of dictionaries were each
-        dictionary has a "filename" and "material_tag" key. For example
-        [{"material_tag": "mat1", "filename": "part1.stp"}, {"material_tag":
-        "mat2", "filename": "part2.stp"}]. There is also an option to create a
-        tet mesh of entries by including a "tet_mesh" key in the dictionary.
+        dictionary has a "cad_filename" and "material_tag" key. For example
+        [{"material_tag": "mat1", "cad_filename": "part1.stp"}, {"material_tag":
+        "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
@@ -71,14 +71,15 @@ def cad_to_h5m(
 
     cubit.init([])
 
-    geometry_details = find_number_of_volumes_in_each_step_file(
+    geometry_details, total_number_of_volumes = find_number_of_volumes_in_each_step_file(
         files_with_tags, cubit)
     print(geometry_details)
     tag_geometry_with_mats(geometry_details, cubit)
 
-    if imprint:
+    if imprint and total_number_of_volumes > 1:
         imprint_geometry(cubit)
-    merge_geometry(merge_tolerance, cubit)
+    if total_number_of_volumes > 1:
+        merge_geometry(merge_tolerance, cubit)
     find_reflecting_surfaces_of_reflecting_wedge(
         geometry_details, surface_reflectivity_name, cubit
     )
@@ -269,27 +270,27 @@ def find_number_of_volumes_in_each_step_file(files_with_tags, cubit):
         print(entry)
         # starting_group_id = starting_group_id +1
         current_vols = cubit.parse_cubit_list("volume", "all")
-        # print(os.path.join(basefolder, entry['filename']))
-        if entry["filename"].endswith(
-                ".stp") or entry["filename"].endswith(".step"):
+        # print(os.path.join(basefolder, entry['cad_filename']))
+        if entry["cad_filename"].endswith(
+                ".stp") or entry["cad_filename"].endswith(".step"):
             import_type = "step"
-        elif entry["filename"].endswith(".sat"):
+        elif entry["cad_filename"].endswith(".sat"):
             import_type = "acis"
         else:
-            msg = (f'File format for {entry["filename"]} is not supported.'
+            msg = (f'File format for {entry["cad_filename"]} is not supported.'
                    'Try step files or sat files')
             raise ValueError(msg)
-        if not Path(entry["filename"]).is_file():
-            msg = f'File with filename {entry["filename"]} could not be found'
+        if not Path(entry["cad_filename"]).is_file():
+            msg = f'File with filename {entry["cad_filename"]} could not be found'
             raise FileNotFoundError(msg)
-        short_file_name = os.path.split(entry["filename"])[-1]
+        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
             + ' "'
-            + entry["filename"]
+            + entry["cad_filename"]
             + '" separate_bodies no_surfaces no_curves no_vertices '
         )
         all_vols = cubit.parse_cubit_list("volume", "all")
@@ -324,4 +325,5 @@ def find_number_of_volumes_in_each_step_file(files_with_tags, cubit):
                 "entry['surface_reflectivity']",
                 entry["surface_reflectivity"])
     cubit.cmd("separate body all")
-    return files_with_tags
+
+    return files_with_tags, sum(all_vols)

examples/create_h5m_from_download_stp_files.py

@@ -14,37 +14,37 @@
 cad_to_h5m(h5m_filename='dagmc.h5m',
            cubit_path="/opt/Coreform-Cubit-2021.5/bin/",
            files_with_tags=[{"material_tag": "pf_coil_mat",
-                             "filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/pf_coils.stp",
+                             "cad_filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/pf_coils.stp",
                              },
                             {"material_tag": "pf_coil_case_mat",
-                             "filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/pf_coil_cases.stp",
+                             "cad_filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/pf_coil_cases.stp",
                              },
                             {"material_tag": "center_column_shield_mat",
-                             "filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/center_column_shield.stp",
+                             "cad_filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/center_column_shield.stp",
                              },
                             {"material_tag": "firstwall_mat",
-                             "filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/outboard_firstwall.stp",
+                             "cad_filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/outboard_firstwall.stp",
                              },
                             {"material_tag": "blanket_mat",
-                             "filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/blanket.stp",
+                             "cad_filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/blanket.stp",
                              },
                             {"material_tag": "divertor_mat",
-                             "filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/divertor.stp",
+                             "cad_filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/divertor.stp",
                              },
                             {"material_tag": "supports_mat",
-                             "filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/supports.stp",
+                             "cad_filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/supports.stp",
                              },
                             {"material_tag": "blanket_rear_wall_mat",
-                             "filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/outboard_rear_blanket_wall.stp",
+                             "cad_filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/outboard_rear_blanket_wall.stp",
                              },
                             {"material_tag": "inboard_tf_coils_mat",
-                             "filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/inboard_tf_coils.stp",
+                             "cad_filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/inboard_tf_coils.stp",
                              },
                             {"material_tag": "outer_tf_coil_mat",
-                             "filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/outboard_tf_coil.stp",
+                             "cad_filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/outboard_tf_coil.stp",
                              },
                             {"material_tag": "graveyard",
-                             "filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/graveyard.stp",
+                             "cad_filename": "fusion_example_for_openmc_using_paramak-0.0.1/stp_files/graveyard.stp",
                              },
                             ],
            )

examples/create_h5m_from_paramak_reactor.py

@@ -1,29 +1,40 @@
 import paramak
+from cad_to_h5m import cad_to_h5m
 
-my_reactor = paramak.BallReactor(
-    inner_bore_radial_thickness=10,
+
+my_reactor = paramak.SubmersionTokamak(
+    inner_bore_radial_thickness=30,
     inboard_tf_leg_radial_thickness=30,
-    center_column_shield_radial_thickness=60,
-    divertor_radial_thickness=150,
-    inner_plasma_gap_radial_thickness=30,
-    plasma_radial_thickness=300,
-    outer_plasma_gap_radial_thickness=30,
+    center_column_shield_radial_thickness=30,
+    divertor_radial_thickness=80,
+    inner_plasma_gap_radial_thickness=50,
+    plasma_radial_thickness=200,
+    outer_plasma_gap_radial_thickness=50,
     firstwall_radial_thickness=30,
-    blanket_radial_thickness=50,
     blanket_rear_wall_radial_thickness=30,
-    elongation=2,
-    triangularity=0.55,
     number_of_tf_coils=16,
-    rotation_angle=90,
+    rotation_angle=360,
+    support_radial_thickness=90,
+    inboard_blanket_radial_thickness=30,
+    outboard_blanket_radial_thickness=30,
+    elongation=2.00,
+    triangularity=0.50,
     pf_coil_case_thicknesses=[10, 10, 10, 10],
     pf_coil_radial_thicknesses=[20, 50, 50, 20],
     pf_coil_vertical_thicknesses=[20, 50, 50, 20],
-    pf_coil_radial_position=[500, 575, 575, 500],
-    pf_coil_vertical_position=[300, 100, -100, -300],
+    pf_coil_radial_position=[500, 550, 550, 500],
+    pf_coil_vertical_position=[270, 100, -100, -270],
     rear_blanket_to_tf_gap=50,
-    outboard_tf_coil_radial_thickness=100,
-    outboard_tf_coil_poloidal_thickness=50,
+    outboard_tf_coil_radial_thickness=30,
+    outboard_tf_coil_poloidal_thickness=30,
 )
 
-# this function makes up of cad_to_h5m within the paramak
-my_reactor.export_h5m_with_cubit()
+my_reactor.export_stp()
+
+files_with_tags = my_reactor.neutronics_description()
+
+cad_to_h5m(
+    h5m_filename=' "dagmc.h5m',
+    cubit_path="/opt/Coreform-Cubit-2021.5/bin/",
+    files_with_tags=files_with_tags
+)

examples/create_h5m_from_paramak_shape.py

@@ -1,4 +1,5 @@
 import paramak
+from cad_to_h5m import cad_to_h5m
 
 my_shape = paramak.Plasma(
     major_radius=620,
@@ -8,5 +9,12 @@
     rotation_angle=90,
 )
 
-# this function makes up of cad_to_h5m within the paramak
-my_shape.export_h5m_with_cubit()
+my_shape.export_stp()
+
+files_with_tags = my_shape.neutronics_description()
+
+cad_to_h5m(
+    h5m_filename=' "dagmc.h5m',
+    cubit_path="/opt/Coreform-Cubit-2021.5/bin/",
+    files_with_tags=files_with_tags
+)

run_tests.sh

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-pytest tests -v --cov=cad_to_h5m --cov-append --cov-report term --cov-report xml
+pytest tests -v

setup.py

@@ -25,8 +25,8 @@
         'Operating System :: OS Independent',
     ],
     tests_require=[
-        "pytest-cov",
+        "pytest",
     ],
     python_requires='>=3.6',
-    install_requires=["pytest-cov"],
+    install_requires=["pytest"],
 )