Move files introduced by #56 to src/

src/cubit_utils.py

@@ -0,0 +1,293 @@
+import cubit
+from pathlib import Path
+import os
+import inspect
+import subprocess
+
+
+def init_cubit(cubit_flag):
+    """Initializes Coreform Cubit with the DAGMC plugin.
+
+    Arguments:
+        cubit_flag (bool): flag to indicate whether Coreform Cubit has been
+            initialized.
+
+    Returns:
+        cubit_flag (bool): flag to indicate whether Coreform Cubit has been
+            initialized.
+    """
+    if not cubit_flag:
+        cubit_plugin_dir = (
+            Path(os.path.dirname(inspect.getfile(cubit))) / Path('plugins')
+        )
+        cubit.init([
+            'cubit',
+            '-nojournal',
+            '-nographics',
+            '-information', 'off',
+            '-warning', 'off',
+            '-commandplugindir',
+            str(cubit_plugin_dir)
+        ])
+        cubit_flag = True
+
+    return cubit_flag
+
+
+def import_step_cubit(filename, import_dir):
+    """Imports STEP file into Coreform Cubit.
+
+    Arguments:
+        filename (str): name of STEP input file, excluding '.step' extension.
+        import_dir (str): directory from which to import STEP file.
+
+    Returns:
+        vol_id (int): Cubit volume ID of imported CAD solid.
+    """
+    import_path = Path(import_dir) / Path(filename).with_suffix('.step')
+    cubit.cmd(f'import step "{import_path}" heal')
+    vol_id = cubit.get_last_id("volume")
+
+    return vol_id
+
+
+def export_step_cubit(filename, export_dir=''):
+    """Export CAD solid as a STEP file via Coreform Cubit.
+
+    Arguments:
+        filename (str): name of STEP output file, excluding '.step' extension.
+        export_dir (str): directory to which to export the STEP output file
+            (defaults to empty string).
+    """
+    export_path = Path(export_dir) / Path(filename).with_suffix('.step')
+    cubit.cmd(f'export step "{export_path}" overwrite')
+
+
+def export_tet_mesh_cubit(volume_ids, filename, export_dir=''):
+    """Creates tetrahedral mesh of CAD volumes and exports to Exodus format via
+    Coreform Cubit and converts to H5M via MOAB.
+
+    Arguments:
+        volume_ids (iterable of int): iterable of Cubit volume IDs.
+        filename (str): name of H5M output file, excluding '.h5m' extension.
+        export_dir (str): directory to which to export the H5M output file
+            (defaults to empty string).
+    """
+    for vol in volume_ids:
+        cubit.cmd(f'volume {vol} scheme tetmesh')
+        cubit.cmd(f'mesh volume {vol}')
+
+    exo_path = Path(export_dir) / Path(filename).with_suffix('.exo')
+    h5m_path = Path(export_dir) / Path(filename).with_suffix('.h5m')
+
+    cubit.cmd(f'export mesh "{exo_path}" overwrite')
+    subprocess.run(f'mbconvert {exo_path} {h5m_path}', shell=True)
+    Path.unlink(exo_path)
+
+
+def orient_spline_surfaces(volume_id):
+    """Extracts the inner and outer surface IDs for a given ParaStell in-vessel
+    component volume in Coreform Cubit.
+
+    Arguments:
+        volume_id (int): Cubit volume ID.
+
+    Returns:
+        inner_surface_id (int): Cubit ID of in-vessel component inner surface.
+        outer_surface_id (int): Cubit ID of in-vessel component outer surface.
+    """
+    surfaces = cubit.get_relatives('volume', volume_id, 'surface')
+
+    spline_surfaces = []
+    for surface in surfaces:
+        if cubit.get_surface_type(surface) == 'spline surface':
+            spline_surfaces.append(surface)
+
+    if len(spline_surfaces) == 1:
+        outer_surface_id = spline_surfaces[0]
+        inner_surface_id = None
+    else:
+        # The outer surface bounding box will have the larger maximum XY value
+        if (
+            cubit.get_bounding_box('surface', spline_surfaces[1])[4] >
+            cubit.get_bounding_box('surface', spline_surfaces[0])[4]
+        ):
+            outer_surface_id = spline_surfaces[1]
+            inner_surface_id = spline_surfaces[0]
+        else:
+            outer_surface_id = spline_surfaces[0]
+            inner_surface_id = spline_surfaces[1]
+
+    return inner_surface_id, outer_surface_id
+
+
+def merge_layer_surfaces(components_dict):
+    """Merges ParaStell in-vessel component surfaces in Coreform Cubit based on
+    surface IDs rather than imprinting and merging all. Assumes that the
+    components dictionary is ordered radially outward. Note that overlaps
+    between magnet volumes and in-vessel components will not be merged in this
+    workflow.
+
+    Arguments:
+        components_dict (dict): dictionary of ParaStell components. This
+            dictionary must have the form
+            {
+                'component_name': {
+                    'vol_id': Coreform Cubit volume ID(s) for component (int or
+                        iterable of int)
+                    (additional keys are allowed)
+                }
+            }
+    """
+    # Tracks the surface id of the outer surface of the previous layer
+    prev_outer_surface_id = None
+
+    for component in components_dict.keys():
+        vol_id = component['vol_id']
+        # Skip merging for magnets
+        if len(vol_id) > 1:
+            continue
+
+        inner_surface_id, outer_surface_id = orient_spline_surfaces(vol_id)
+
+        # Conditionally skip merging (first iteration only)
+        if prev_outer_surface_id is None:
+            prev_outer_surface_id = outer_surface_id
+        else:
+            cubit.cmd(
+                f'merge surface {inner_surface_id} {prev_outer_surface_id}'
+            )
+            prev_outer_surface_id = outer_surface_id
+
+
+def export_h5m_cubit_legacy(
+    components_dict, filename='dagmc', export_dir='', skip_imprint=False,
+    faceting_tolerance=None, length_tolerance=None, normal_tolerance=None
+):
+    """Exports DAGMC neutronics H5M file of ParaStell components via legacy
+    plug-in faceting method for Coreform Cubit.
+
+    Arguments:
+        components_dict (dict): dictionary of ParaStell components. This
+            dictionary must have the form
+            {
+                'component_name': {
+                    'vol_id': Coreform Cubit volume ID(s) for component (int or
+                        iterable of int)
+                    'h5m_tag': material tag for component (str)
+                    (additional keys are allowed)
+                }
+            }
+        filename (str): name of H5M output file, excluding '.step' extension
+            (defaults to 'dagmc').
+        export_dir (str): directory to which to export the H5M output file
+            (defaults to empty string).
+        skip_imprint (bool): flag for whether the export routine should skip
+            the imprint procedure (defaults to False).
+        faceting_tolerance (double): maximum distance a facet may be from
+            surface of CAD representation for H5M export (defaults to None).
+        length_tolerance (double): maximum length of facet edge for H5M export
+            (double, defaults to None).
+        normal_tolerance (double): maximum change in angle between normal
+            vector of adjacent facets (defaults to None).
+    """
+    if skip_imprint:
+        merge_layer_surfaces()
+
+    else:
+        cubit.cmd('imprint volume all')
+        cubit.cmd('merge volume all')
+
+    for component in components_dict.keys():
+        if len(component['vol_id']) > 1:
+            vol_id_str = " ".join(str(i) for i in component["vol_id"])
+        else:
+            vol_id_str = str(component['vol_id'])
+
+        cubit.cmd(
+            f'group "mat:{component["h5m_tag"]}" add volume {vol_id_str}'
+        )
+
+    facet_tol_str = ''
+    len_tol_str = ''
+    norm_tol_str = ''
+
+    if faceting_tolerance is not None:
+        facet_tol_str = f'faceting_tolerance {faceting_tolerance}'
+    if length_tolerance is not None:
+        len_tol_str = f'length_tolerance {length_tolerance}'
+    if normal_tolerance is not None:
+        norm_tol_str = f'normal_tolerance {normal_tolerance}'
+
+    export_path = Path(export_dir) / Path(filename).with_suffix('.h5m')
+    cubit.cmd(
+        f'export dagmc "{export_path}" {facet_tol_str} {len_tol_str} '
+        f'{norm_tol_str} make_watertight'
+    )
+
+
+def export_h5m_cubit_native(
+    components_dict, filename='dagmc', export_dir='', skip_imprint=False,
+    anisotropic_ratio=100.0, deviation_angle=5.0
+):
+    """Exports DAGMC neutronics H5M file of ParaStell components via native faceting method for Coreform Cubit.
+
+    Arguments:
+        components_dict (dict): dictionary of ParaStell components. This
+            dictionary must have the form
+            {
+                'component_name': {
+                    'vol_id': Coreform Cubit volume ID(s) for component (int or
+                        iterable of int)
+                    'h5m_tag': material tag for component (str)
+                    (additional keys are allowed)
+                }
+            }
+        filename (str): name of H5M output file, excluding '.step' extension
+            (defaults to 'dagmc').
+        export_dir (str): directory to which to export the H5M output file
+            (defaults to empty string).
+        skip_imprint (bool): flag for whether the export routine should skip
+            the imprint procedure (defaults to False).
+        anisotropic_ratio (double): controls edge length ratio of elements
+            (defaults to 100.0).
+        deviation_angle (double): controls deviation angle of facet from
+            surface (i.e., lesser deviation angle results in more elements in
+            areas with higher curvature) (defaults to 5.0).
+    """
+    if skip_imprint:
+        merge_layer_surfaces()
+    else:
+        cubit.cmd('imprint volume all')
+        cubit.cmd('merge volume all')
+
+    cubit.cmd('set duplicate block elements off')
+
+    for component in components_dict.keys():
+        if len(component['vol_id']) > 1:
+            block_id = min(component['vol_id'])
+            vol_id_str = " ".join(str(i) for i in component["vol_id"])
+        else:
+            block_id = component['vol_id']
+            vol_id_str = str(component['vol_id'])
+
+        cubit.cmd(
+            f'create material "{component["h5m_tag"]}" property_group '
+            '"CUBIT-ABAQUS"'
+        )
+        cubit.cmd(
+            f'block {block_id} add volume {vol_id_str}'
+        )
+        cubit.cmd(
+            f'block {block_id} material \'{component['h5m_tag']}\''
+        )
+
+    cubit.cmd(
+        f'set trimesher coarse on ratio {anisotropic_ratio} '
+        f'angle {deviation_angle}'
+    )
+    cubit.cmd("surface all scheme trimesh")
+    cubit.cmd("mesh surface all")
+
+    export_path = Path(export_dir) / Path(filename).with_suffix('.h5m')
+    cubit.cmd(f'export cf_dagmc "{export_path}" overwrite')