Support UnstructuredMesh for IndependentSource (#2949)

Co-authored-by: Jonathan Shimwell <drshimwell@gmail.com>
Co-authored-by: Paul Romano <paul.k.romano@gmail.com>

openmc/filter.py

@@ -864,10 +864,10 @@ def mesh(self, mesh):
         cv.check_type('filter mesh', mesh, openmc.MeshBase)
         self._mesh = mesh
         if isinstance(mesh, openmc.UnstructuredMesh):
-            if mesh.volumes is None:
-                self.bins = []
-            else:
+            if mesh.has_statepoint_data:
                 self.bins = list(range(len(mesh.volumes)))
+            else:
+                self.bins = []
         else:
             self.bins = list(mesh.indices)
 
@@ -982,7 +982,7 @@ def from_xml_element(cls, elem, **kwargs):
         if translation:
             out.translation = [float(x) for x in translation.split()]
         return out
-    
+
 
 class MeshBornFilter(MeshFilter):
     """Filter events by the mesh cell a particle originated from.

openmc/mesh.py

@@ -3,6 +3,7 @@
 import warnings
 from abc import ABC, abstractmethod
 from collections.abc import Iterable
+from functools import wraps
 from math import pi, sqrt, atan2
 from numbers import Integral, Real
 from pathlib import Path
@@ -39,7 +40,8 @@ class MeshBase(IDManagerMixin, ABC):
     bounding_box : openmc.BoundingBox
         Axis-aligned bounding box of the mesh as defined by the upper-right and
         lower-left coordinates.
-
+    indices : Iterable of tuple
+        An iterable of mesh indices for each mesh element, e.g. [(1, 1, 1), (2, 1, 1), ...]
     """
 
     next_id = 1
@@ -66,6 +68,11 @@ def name(self, name: str):
     def bounding_box(self) -> openmc.BoundingBox:
         return openmc.BoundingBox(self.lower_left, self.upper_right)
 
+    @property
+    @abstractmethod
+    def indices(self):
+        pass
+
     def __repr__(self):
         string = type(self).__name__ + '\n'
         string += '{0: <16}{1}{2}\n'.format('\tID', '=\t', self._id)
@@ -1914,6 +1921,17 @@ def _convert_to_cartesian(arr, origin: Sequence[float]):
         return arr
 
 
+def require_statepoint_data(func):
+    @wraps(func)
+    def wrapper(self: UnstructuredMesh, *args, **kwargs):
+        if not self._has_statepoint_data:
+            raise AttributeError(f'The "{func.__name__}" property requires '
+                                 'information about this mesh to be loaded '
+                                 'from a statepoint file.')
+        return func(self, *args, **kwargs)
+    return wrapper
+
+
 class UnstructuredMesh(MeshBase):
     """A 3D unstructured mesh
 
@@ -1990,6 +2008,7 @@ def __init__(self, filename: PathLike, library: str, mesh_id: Optional[int] = No
         self.library = library
         self._output = False
         self.length_multiplier = length_multiplier
+        self._has_statepoint_data = False
 
     @property
     def filename(self):
@@ -2010,6 +2029,7 @@ def library(self, lib: str):
         self._library = lib
 
     @property
+    @require_statepoint_data
     def size(self):
         return self._size
 
@@ -2028,6 +2048,7 @@ def output(self, val: bool):
         self._output = val
 
     @property
+    @require_statepoint_data
     def volumes(self):
         """Return Volumes for every mesh cell if
         populated by a StatePoint file
@@ -2046,26 +2067,32 @@ def volumes(self, volumes: typing.Iterable[Real]):
         self._volumes = volumes
 
     @property
+    @require_statepoint_data
     def total_volume(self):
         return np.sum(self.volumes)
 
     @property
+    @require_statepoint_data
     def vertices(self):
         return self._vertices
 
     @property
+    @require_statepoint_data
     def connectivity(self):
         return self._connectivity
 
     @property
+    @require_statepoint_data
     def element_types(self):
         return self._element_types
 
     @property
+    @require_statepoint_data
     def centroids(self):
         return np.array([self.centroid(i) for i in range(self.n_elements)])
 
     @property
+    @require_statepoint_data
     def n_elements(self):
         if self._n_elements is None:
             raise RuntimeError("No information about this mesh has "
@@ -2096,6 +2123,15 @@ def dimension(self):
     def n_dimension(self):
         return 3
 
+    @property
+    @require_statepoint_data
+    def indices(self):
+        return [(i,) for i in range(self.n_elements)]
+
+    @property
+    def has_statepoint_data(self) -> bool:
+        return self._has_statepoint_data
+
     def __repr__(self):
         string = super().__repr__()
         string += '{: <16}=\t{}\n'.format('\tFilename', self.filename)
@@ -2106,13 +2142,16 @@ def __repr__(self):
         return string
 
     @property
+    @require_statepoint_data
     def lower_left(self):
         return self.vertices.min(axis=0)
 
     @property
+    @require_statepoint_data
     def upper_right(self):
         return self.vertices.max(axis=0)
 
+    @require_statepoint_data
     def centroid(self, bin: int):
         """Return the vertex averaged centroid of an element
 
@@ -2257,6 +2296,7 @@ def from_hdf5(cls, group: h5py.Group):
         library = group['library'][()].decode()
 
         mesh = cls(filename=filename, library=library, mesh_id=mesh_id)
+        mesh._has_statepoint_data = True
         vol_data = group['volumes'][()]
         mesh.volumes = np.reshape(vol_data, (vol_data.shape[0],))
         mesh.n_elements = mesh.volumes.size

openmc/source.py

@@ -500,9 +500,13 @@ def populate_xml_element(self, elem: ET.Element):
         elem.set("mesh", str(self.mesh.id))
 
         # write in the order of mesh indices
-        for idx in self.mesh.indices:
-            idx = tuple(i - 1 for i in idx)
-            elem.append(self.sources[idx].to_xml_element())
+        if isinstance(self.mesh, openmc.UnstructuredMesh):
+            for s in self.sources:
+                elem.append(s.to_xml_element())
+        else:
+            for idx in self.mesh.indices:
+                idx = tuple(i - 1 for i in idx)
+                elem.append(self.sources[idx].to_xml_element())
 
     @classmethod
     def from_xml_element(cls, elem: ET.Element, meshes) -> openmc.MeshSource:

tests/unit_tests/test_mesh.py

@@ -298,3 +298,22 @@ def test_CylindricalMesh_get_indices_at_coords():
     assert mesh.get_indices_at_coords([98, 200.1, 299]) == (0, 1, 0)  # second angle quadrant
     assert mesh.get_indices_at_coords([98, 199.9, 299]) == (0, 2, 0)  # third angle quadrant
     assert mesh.get_indices_at_coords([102, 199.1, 299]) == (0, 3, 0)  # forth angle quadrant
+
+def test_umesh_roundtrip(run_in_tmpdir, request):
+    umesh = openmc.UnstructuredMesh(request.path.parent / 'test_mesh_tets.e', 'moab')
+    umesh.output = True
+
+    # create a tally using this mesh
+    mf = openmc.MeshFilter(umesh)
+    tally = openmc.Tally()
+    tally.filters = [mf]
+    tally.scores = ['flux']
+
+    tallies = openmc.Tallies([tally])
+    tallies.export_to_xml()
+
+    xml_tallies = openmc.Tallies.from_xml()
+    xml_tally = xml_tallies[0]
+    xml_mesh = xml_tally.filters[0].mesh
+
+    assert umesh.id == xml_mesh.id

tests/unit_tests/test_source_mesh.py

@@ -208,23 +208,29 @@ def test_roundtrip(run_in_tmpdir, model, request):
 ###################
 # MeshSource tests
 ###################
-@pytest.mark.parametrize('mesh_type', ('rectangular', 'cylindrical'))
-def test_mesh_source_independent(run_in_tmpdir, mesh_type):
+@pytest.fixture
+def void_model():
     """
     A void model containing a single box
     """
-    min, max = -10, 10
-    box = openmc.model.RectangularParallelepiped(
-        min, max, min, max, min, max, boundary_type='vacuum')
+    model = openmc.Model()
 
-    geometry = openmc.Geometry([openmc.Cell(region=-box)])
+    box = openmc.model.RectangularParallelepiped(*[-10, 10]*3, boundary_type='vacuum')
+    model.geometry = openmc.Geometry([openmc.Cell(region=-box)])
 
-    settings = openmc.Settings()
-    settings.particles = 100
-    settings.batches = 10
-    settings.run_mode = 'fixed source'
+    model.settings.particles = 100
+    model.settings.batches = 10
+    model.settings.run_mode = 'fixed source'
+
+    return model
 
-    model = openmc.Model(geometry=geometry, settings=settings)
+
+@pytest.mark.parametrize('mesh_type', ('rectangular', 'cylindrical'))
+def test_mesh_source_independent(run_in_tmpdir, void_model, mesh_type):
+    """
+    A void model containing a single box
+    """
+    model = void_model
 
     # define a 2 x 2 x 2 mesh
     if mesh_type == 'rectangular':
@@ -310,6 +316,41 @@ def test_mesh_source_independent(run_in_tmpdir, mesh_type):
     assert mesh_source.strength == 1.0
 
 
+@pytest.mark.parametrize("library", ('moab', 'libmesh'))
+def test_umesh_source_independent(run_in_tmpdir, request, void_model, library):
+    import openmc.lib
+    # skip the test if the library is not enabled
+    if library == 'moab' and not openmc.lib._dagmc_enabled():
+        pytest.skip("DAGMC (and MOAB) mesh not enabled in this build.")
+
+    if library == 'libmesh' and not openmc.lib._libmesh_enabled():
+        pytest.skip("LibMesh is not enabled in this build.")
+
+    model = void_model
+
+    mesh_filename = Path(request.fspath).parent / "test_mesh_tets.e"
+    uscd_mesh = openmc.UnstructuredMesh(mesh_filename, library)
+    ind_source = openmc.IndependentSource()
+    n_elements = 12_000
+    model.settings.source = openmc.MeshSource(uscd_mesh, n_elements*[ind_source])
+    model.export_to_model_xml()
+    try:
+        openmc.lib.init()
+        openmc.lib.simulation_init()
+        sites = openmc.lib.sample_external_source(10)
+        openmc.lib.statepoint_write('statepoint.h5')
+    finally:
+        openmc.lib.finalize()
+
+    with openmc.StatePoint('statepoint.h5') as sp:
+        uscd_mesh = sp.meshes[uscd_mesh.id]
+
+    # ensure at least that all sites are inside the mesh
+    bounding_box = uscd_mesh.bounding_box
+    for site in sites:
+        assert site.r in bounding_box
+
+
 def test_mesh_source_file(run_in_tmpdir):
     # Creating a source file with a single particle
     source_particle = openmc.SourceParticle(time=10.0)