def cell_closure(self):
"""2D array of ordered cell closures
Each row contains ordered cell entities for a cell, one row per cell.
"""
plex = self._plex
topological_dim = plex.getDimension()
# Cell numbering and global vertex numbering
cell_numbering = self._cell_numbering
vertex_numbering = self._vertex_numbering.createGlobalSection(plex.getPointSF())
cStart, cEnd = plex.getHeightStratum(0) # cells
cell_facets = plex.getConeSize(cStart)
if topological_dim + 1 == cell_facets:
# Simplex mesh
a_closure = plex.getTransitiveClosure(cStart)[0]
entity_per_cell = np.zeros(topological_dim + 1, dtype=np.int32)
for dim in xrange(topological_dim + 1):
start, end = plex.getDepthStratum(dim)
entity_per_cell[dim] = sum(map(lambda idx: start <= idx < end,
a_closure))
return dmplex.closure_ordering(plex, vertex_numbering,
cell_numbering, entity_per_cell)
elif topological_dim == 2 and cell_facets == 4:
# Quadrilateral mesh
cell_ranks = dmplex.get_cell_remote_ranks(plex)
facet_orientations = dmplex.quadrilateral_facet_orientations(
plex, vertex_numbering, cell_ranks)
cell_orientations = dmplex.orientations_facet2cell(
plex, vertex_numbering, cell_ranks,
facet_orientations, cell_numbering)
dmplex.exchange_cell_orientations(plex,
cell_numbering,
cell_orientations)
return dmplex.quadrilateral_closure_ordering(
plex, vertex_numbering, cell_numbering, cell_orientations)
else:
raise RuntimeError("Unsupported mesh: neither simplex, nor quadrilateral.")
def cell_closure(self):
"""2D array of ordered cell closures
Each row contains ordered cell entities for a cell, one row per cell.
"""
dm = self._plex
a_cell = dm.getHeightStratum(0)[0]
a_closure = dm.getTransitiveClosure(a_cell)[0]
topological_dimension = dm.getDimension()
entity_per_cell = np.zeros(topological_dimension + 1, dtype=np.int32)
for dim in xrange(topological_dimension + 1):
start, end = dm.getDepthStratum(dim)
entity_per_cell[dim] = sum(map(lambda idx: start <= idx < end, a_closure))
return dmplex.closure_ordering(dm, dm.getDefaultGlobalSection(),
self._cell_numbering, entity_per_cell)
def __init__(self, mesh, element, name=None, dim=1, rank=0):
"""
:param mesh: :class:`Mesh` to build this space on
:param element: :class:`ufl.FiniteElementBase` to build this space from
:param name: user-defined name for this space
:param dim: vector space dimension of a :class:`.VectorFunctionSpace`
:param rank: rank of the space, not the value rank
"""
self._ufl_element = element
# Compute the FIAT version of the UFL element above
self.fiat_element = fiat_utils.fiat_from_ufl_element(element)
if isinstance(mesh, mesh_t.ExtrudedMesh):
# Set up some extrusion-specific things
# The bottom layer maps will come from element_dof_list
# dof_count is the total number of dofs in the extruded mesh
# Get the flattened version of the FIAT element
self.flattened_element = self.fiat_element.flattened_element()
entity_dofs = self.flattened_element.entity_dofs()
self._dofs_per_cell = [len(entity)*len(entity[0]) for d, entity in entity_dofs.iteritems()]
# Compute the number of DoFs per dimension on top/bottom and sides
entity_dofs = self.fiat_element.entity_dofs()
top_dim = mesh._plex.getDimension()
self._xtr_hdofs = [len(entity_dofs[(d, 0)][0]) for d in range(top_dim+1)]
self._xtr_vdofs = [len(entity_dofs[(d, 1)][0]) for d in range(top_dim+1)]
# Compute the dofs per column
self.dofs_per_column = eutils.compute_extruded_dofs(self.fiat_element,
self.flattened_element.entity_dofs(),
mesh._layers)
# Compute the offset for the extrusion process
self.offset = eutils.compute_offset(self.fiat_element.entity_dofs(),
self.flattened_element.entity_dofs(),
self.fiat_element.space_dimension())
# Compute the top and bottom masks to identify boundary dofs
b_mask = self.fiat_element.get_lower_mask()
t_mask = self.fiat_element.get_upper_mask()
self.bt_masks = (b_mask, t_mask)
self.extruded = True
self._dofs_per_entity = self.dofs_per_column
else:
# If not extruded specific, set things to None/False, etc.
self.offset = None
self.bt_masks = None
self.dofs_per_column = np.zeros(1, np.int32)
self.extruded = False
entity_dofs = self.fiat_element.entity_dofs()
self._dofs_per_entity = [len(entity[0]) for d, entity in entity_dofs.iteritems()]
self._dofs_per_cell = [len(entity)*len(entity[0]) for d, entity in entity_dofs.iteritems()]
self.name = name
self._dim = dim
self._mesh = mesh
self._index = None
# Create the PetscSection mapping topological entities to DoFs
self._global_numbering = mesh._plex.createSection(1, [1], self._dofs_per_entity,
perm=mesh._plex_renumbering)
mesh._plex.setDefaultSection(self._global_numbering)
self._universal_numbering = mesh._plex.getDefaultGlobalSection()
# Re-initialise the DefaultSF with the numbering for this FS
mesh._plex.createDefaultSF(self._global_numbering,
self._universal_numbering)
# Derive the Halo from the DefaultSF
self._halo = halo.Halo(mesh._plex.getDefaultSF(),
self._global_numbering,
self._universal_numbering)
# Compute entity class offsets
self.dof_classes = [0, 0, 0, 0]
for d in range(mesh._plex.getDimension()+1):
ncore = mesh._plex.getStratumSize("op2_core", d)
nowned = mesh._plex.getStratumSize("op2_non_core", d)
nhalo = mesh._plex.getStratumSize("op2_exec_halo", d)
ndofs = self._dofs_per_entity[d]
self.dof_classes[0] += ndofs * ncore
self.dof_classes[1] += ndofs * (ncore + nowned)
self.dof_classes[2] += ndofs * (ncore + nowned + nhalo)
self.dof_classes[3] += ndofs * (ncore + nowned + nhalo)
self._node_count = self._global_numbering.getStorageSize()
# Re-order cell closures from the Plex
if mesh._cell_closure is None:
entity_dofs = self.fiat_element.entity_dofs()
entity_per_cell = [len(entity) for d, entity in entity_dofs.iteritems()]
entity_per_cell = np.array(entity_per_cell, dtype=np.int32)
mesh._cell_closure = dmplex.closure_ordering(mesh._plex,
self._universal_numbering,
mesh._cell_numbering,
entity_per_cell)
if isinstance(self._mesh, mesh_t.ExtrudedMesh):
self.cell_node_list = dmplex.get_extruded_cell_nodes(mesh._plex,
self._global_numbering,
mesh._cell_closure,
self.fiat_element,
sum(self._dofs_per_cell))
else:
self.cell_node_list = dmplex.get_cell_nodes(self._global_numbering,
mesh._cell_closure,
sum(self._dofs_per_cell))
if mesh._plex.getStratumSize("interior_facets", 1) > 0:
# Compute the facet_numbering and store with the parent mesh
if mesh.interior_facets is None:
# Order interior facets by OP2 entity class
interior_facets, interior_facet_classes = \
dmplex.get_facets_by_class(mesh._plex, "interior_facets")
interior_local_facet_number, interior_facet_cell = \
dmplex.facet_numbering(mesh._plex, "interior",
interior_facets,
mesh._cell_numbering,
mesh._cell_closure)
mesh.interior_facets = mesh_t._Facets(mesh, interior_facet_classes,
"interior",
interior_facet_cell,
interior_local_facet_number)
interior_facet_cells = mesh.interior_facets.facet_cell
self.interior_facet_node_list = \
dmplex.get_facet_nodes(interior_facet_cells,
self.cell_node_list)
else:
self.interior_facet_node_list = None
if mesh.interior_facets is None:
mesh.interior_facets = mesh_t._Facets(self, 0, "exterior", None, None)
if mesh._plex.getStratumSize("exterior_facets", 1) > 0:
# Compute the facet_numbering and store with the parent mesh
if mesh.exterior_facets is None:
# Order exterior facets by OP2 entity class
exterior_facets, exterior_facet_classes = \
dmplex.get_facets_by_class(mesh._plex, "exterior_facets")
# Derive attached boundary IDs
if mesh._plex.hasLabel("boundary_ids"):
boundary_ids = np.zeros(exterior_facets.size, dtype=np.int32)
for i, facet in enumerate(exterior_facets):
boundary_ids[i] = mesh._plex.getLabelValue("boundary_ids", facet)
unique_ids = np.sort(mesh._plex.getLabelIdIS("boundary_ids").indices)
else:
boundary_ids = None
unique_ids = None
exterior_local_facet_number, exterior_facet_cell = \
dmplex.facet_numbering(mesh._plex, "exterior",
exterior_facets,
mesh._cell_numbering,
mesh._cell_closure)
mesh.exterior_facets = mesh_t._Facets(mesh, exterior_facet_classes,
"exterior",
exterior_facet_cell,
exterior_local_facet_number,
boundary_ids,
unique_markers=unique_ids)
exterior_facet_cells = mesh.exterior_facets.facet_cell
self.exterior_facet_node_list = \
dmplex.get_facet_nodes(exterior_facet_cells,
self.cell_node_list)
else:
self.exterior_facet_node_list = None
if mesh.exterior_facets is None:
if mesh._plex.hasLabel("boundary_ids"):
unique_ids = np.sort(mesh._plex.getLabelIdIS("boundary_ids").indices)
else:
unique_ids = None
mesh.exterior_facets = mesh_t._Facets(self, 0, "exterior", None, None,
unique_markers=unique_ids)
# Note: this is the function space rank. The value rank may be different.
self.rank = rank
# Empty map caches. This is a sui generis cache
# implementation because of the need to support boundary
# conditions.
self._cell_node_map_cache = {}
self._exterior_facet_map_cache = {}
self._interior_facet_map_cache = {}