def get_facet_node_list(mesh, kind, cell_node_list, offsets): """Get the facet->node list for specified dof layout. :arg mesh: The mesh to use. :arg kind: The facet kind (one of ``"interior_facets"`` or ``"exterior_facets"``). :arg cell_node_list: The map from mesh cells to function space nodes, see :func:`get_cell_node_list`. :arg offsets: layer offsets for each entity (maybe ignored). :returns: A numpy array mapping mesh facets to function space nodes. """ assert kind in ["interior_facets", "exterior_facets"] if mesh._plex.getStratumSize(kind, 1) > 0: return dmplex.get_facet_nodes(mesh, cell_node_list, kind, offsets) else: return numpy.array([], dtype=IntType)
def get_facet_node_list(mesh, kind, cell_node_list): """Get the facet->node list for specified dof layout. :arg mesh: The mesh to use. :arg kind: The facet kind (one of ``"interior_facets"`` or ``"exterior_facets"``). :arg cell_node_list: The map from mesh cells to function space nodes, see :func:`get_cell_node_list`. :returns: A numpy array mapping mesh facets to function space nodes. """ assert kind in ["interior_facets", "exterior_facets"] if mesh._plex.getStratumSize(kind, 1) > 0: facet = getattr(mesh, kind) return dm_mod.get_facet_nodes(facet.facet_cell, cell_node_list) else: return numpy.array([], dtype=IntType)
def get_facet_node_list(mesh, kind, cell_node_list): """Get the facet->node list for specified dof layout. :arg mesh: The mesh to use. :arg kind: The facet kind (one of ``"interior_facets"`` or ``"exterior_facets"``). :arg cell_node_list: The map from mesh cells to function space nodes, see :func:`get_cell_node_list`. :returns: A numpy array mapping mesh facets to function space nodes. """ assert kind in ["interior_facets", "exterior_facets"] if mesh._plex.getStratumSize(kind, 1) > 0: facet = getattr(mesh, kind) return dm_mod.get_facet_nodes(facet.facet_cell, cell_node_list) else: return numpy.array([], dtype=numpy.int32)
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 = fiat_utils.FlattenedElement(self.fiat_element) # 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 # # Sorting the keys of the closure entity dofs, the whole cell # comes last [-1], before that the horizontal facet [-2], before # that vertical facets [-3]. We need the horizontal facets here. closure_dofs = self.fiat_element.entity_closure_dofs() b_mask = closure_dofs[sorted(closure_dofs.keys())[-2]][0] t_mask = closure_dofs[sorted(closure_dofs.keys())[-2]][1] self.bt_masks = {} self.bt_masks["topological"] = (b_mask, t_mask) # conversion to tuple # Geometric facet dofs facet_dofs = horiz_facet_support_dofs(self.fiat_element) self.bt_masks["geometric"] = (facet_dofs[0], facet_dofs[1]) 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.name = name self._dim = dim self._mesh = mesh self._index = None dm = PETSc.DMShell().create() dm.setAttr('__fs__', weakref.ref(self)) dm.setPointSF(mesh._plex.getPointSF()) # Create the PetscSection mapping topological entities to DoFs sec = mesh._plex.createSection([1], self._dofs_per_entity, perm=mesh._plex_renumbering) dm.setDefaultSection(sec) self._global_numbering = sec self._dm = dm self._ises = None self._halo = halo.Halo(dm) # Compute entity class offsets self.dof_classes = [0, 0, 0, 0] for d in range(mesh._plex.getDimension()+1): ndofs = self._dofs_per_entity[d] for i in range(4): self.dof_classes[i] += ndofs * mesh._entity_classes[d, i] # Tell the DM about the layout of the global vector from firedrake.function import Function with Function(self).dat.vec_ro as v: self._dm.setGlobalVector(v.duplicate()) self._node_count = self._global_numbering.getStorageSize() self.cell_node_list = mesh.create_cell_node_list(self._global_numbering, self.fiat_element) if mesh._plex.getStratumSize("interior_facets", 1) > 0: self.interior_facet_node_list = \ dmplex.get_facet_nodes(mesh.interior_facets.facet_cell, self.cell_node_list) else: self.interior_facet_node_list = np.array([], dtype=np.int32) if mesh._plex.getStratumSize("exterior_facets", 1) > 0: self.exterior_facet_node_list = \ dmplex.get_facet_nodes(mesh.exterior_facets.facet_cell, self.cell_node_list) else: self.exterior_facet_node_list = np.array([], dtype=np.int32) # 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 = {}
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 = fiat_utils.FlattenedElement( self.fiat_element) # 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 # # Sorting the keys of the closure entity dofs, the whole cell # comes last [-1], before that the horizontal facet [-2], before # that vertical facets [-3]. We need the horizontal facets here. closure_dofs = self.fiat_element.entity_closure_dofs() b_mask = closure_dofs[sorted(closure_dofs.keys())[-2]][0] t_mask = closure_dofs[sorted(closure_dofs.keys())[-2]][1] self.bt_masks = (b_mask, t_mask) # conversion to tuple 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.name = name self._dim = dim self._mesh = mesh self._index = None dm = PETSc.DMShell().create() dm.setAttr('__fs__', weakref.ref(self)) dm.setPointSF(mesh._plex.getPointSF()) # Create the PetscSection mapping topological entities to DoFs sec = mesh._plex.createSection([1], self._dofs_per_entity, perm=mesh._plex_renumbering) dm.setDefaultSection(sec) self._global_numbering = sec self._dm = dm self._ises = None self._halo = halo.Halo(dm) # Compute entity class offsets self.dof_classes = [0, 0, 0, 0] for d in range(mesh._plex.getDimension() + 1): ndofs = self._dofs_per_entity[d] for i in range(4): self.dof_classes[i] += ndofs * mesh._entity_classes[d, i] # Tell the DM about the layout of the global vector from firedrake.function import Function with Function(self).dat.vec_ro as v: self._dm.setGlobalVector(v.duplicate()) self._node_count = self._global_numbering.getStorageSize() self.cell_node_list = mesh.create_cell_node_list( self._global_numbering, self.fiat_element) if mesh._plex.getStratumSize("interior_facets", 1) > 0: self.interior_facet_node_list = \ dmplex.get_facet_nodes(mesh.interior_facets.facet_cell, self.cell_node_list) else: self.interior_facet_node_list = np.array([], dtype=np.int32) if mesh._plex.getStratumSize("exterior_facets", 1) > 0: self.exterior_facet_node_list = \ dmplex.get_facet_nodes(mesh.exterior_facets.facet_cell, self.cell_node_list) else: self.exterior_facet_node_list = np.array([], dtype=np.int32) # 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 = {}
def __new__(cls, mesh, element, name=None, shape=()): """ :param mesh: :class:`MeshTopology` to build this space on :param element: :class:`ufl.FiniteElementBase` to build this space from :param name: user-defined name for this space :param shape: shape of a :class:`.VectorFunctionSpace` or :class:`.TensorFunctionSpace` """ assert mesh.ufl_cell() == element.cell() self = super(FunctionSpaceBase, cls).__new__(cls, mesh, element, name, shape) if self._initialized: return self self._mesh = mesh self._ufl_element = element self.name = name self._shape = shape # Compute the FIAT version of the UFL element above self.fiat_element = fiat_utils.fiat_from_ufl_element(element) entity_dofs = self.fiat_element.entity_dofs() dofs_per_entity = mesh.make_dofs_per_plex_entity(entity_dofs) self.extruded = bool(mesh.layers) self.offset = mesh.make_offset(entity_dofs, self.fiat_element.space_dimension()) if mesh.layers: # Compute the top and bottom masks to identify boundary dofs # # Sorting the keys of the closure entity dofs, the whole cell # comes last [-1], before that the horizontal facet [-2], before # that vertical facets [-3]. We need the horizontal facets here. closure_dofs = self.fiat_element.entity_closure_dofs() b_mask = closure_dofs[sorted(closure_dofs.keys())[-2]][0] t_mask = closure_dofs[sorted(closure_dofs.keys())[-2]][1] self.bt_masks = {} self.bt_masks["topological"] = (b_mask, t_mask ) # conversion to tuple # Geometric facet dofs facet_dofs = horiz_facet_support_dofs(self.fiat_element) self.bt_masks["geometric"] = (facet_dofs[0], facet_dofs[1]) else: self.bt_masks = None dm = PETSc.DMShell().create() dm.setAttr('__fs__', weakref.ref(self)) dm.setPointSF(mesh._plex.getPointSF()) # Create the PetscSection mapping topological entities to DoFs sec = mesh._plex.createSection([1], dofs_per_entity, perm=mesh._plex_renumbering) dm.setDefaultSection(sec) self._global_numbering = sec self._dm = dm self._ises = None self._halo = halo.Halo(dm) # Compute entity class offsets self.dof_classes = [0, 0, 0, 0] for d in range(mesh._plex.getDimension() + 1): ndofs = dofs_per_entity[d] for i in range(4): self.dof_classes[i] += ndofs * mesh._entity_classes[d, i] # Tell the DM about the layout of the global vector with self.make_dat().vec_ro as v: self._dm.setGlobalVector(v.duplicate()) self._node_count = self._global_numbering.getStorageSize() self.cell_node_list = mesh.make_cell_node_list(self._global_numbering, entity_dofs) if mesh._plex.getStratumSize("interior_facets", 1) > 0: self.interior_facet_node_list = \ dmplex.get_facet_nodes(mesh.interior_facets.facet_cell, self.cell_node_list) else: self.interior_facet_node_list = np.array([], dtype=np.int32) if mesh._plex.getStratumSize("exterior_facets", 1) > 0: self.exterior_facet_node_list = \ dmplex.get_facet_nodes(mesh.exterior_facets.facet_cell, self.cell_node_list) else: self.exterior_facet_node_list = np.array([], dtype=np.int32) # 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 = {} self._initialized = True return self
def __new__(cls, mesh, element, name=None, shape=()): """ :param mesh: :class:`MeshTopology` to build this space on :param element: :class:`ufl.FiniteElementBase` to build this space from :param name: user-defined name for this space :param shape: shape of a :class:`.VectorFunctionSpace` or :class:`.TensorFunctionSpace` """ assert mesh.ufl_cell() == element.cell() self = super(FunctionSpaceBase, cls).__new__(cls, mesh, element, name, shape) if self._initialized: return self self._mesh = mesh self._ufl_element = element self.name = name self._shape = shape # Compute the FIAT version of the UFL element above self.fiat_element = fiat_utils.fiat_from_ufl_element(element) entity_dofs = self.fiat_element.entity_dofs() dofs_per_entity = mesh.make_dofs_per_plex_entity(entity_dofs) self.extruded = bool(mesh.layers) self.offset = mesh.make_offset(entity_dofs, self.fiat_element.space_dimension()) if mesh.layers: # Compute the top and bottom masks to identify boundary dofs # # Sorting the keys of the closure entity dofs, the whole cell # comes last [-1], before that the horizontal facet [-2], before # that vertical facets [-3]. We need the horizontal facets here. closure_dofs = self.fiat_element.entity_closure_dofs() b_mask = closure_dofs[sorted(closure_dofs.keys())[-2]][0] t_mask = closure_dofs[sorted(closure_dofs.keys())[-2]][1] self.bt_masks = {} self.bt_masks["topological"] = (b_mask, t_mask) # conversion to tuple # Geometric facet dofs facet_dofs = horiz_facet_support_dofs(self.fiat_element) self.bt_masks["geometric"] = (facet_dofs[0], facet_dofs[1]) else: self.bt_masks = None dm = PETSc.DMShell().create() dm.setAttr('__fs__', weakref.ref(self)) dm.setPointSF(mesh._plex.getPointSF()) # Create the PetscSection mapping topological entities to DoFs sec = mesh._plex.createSection([1], dofs_per_entity, perm=mesh._plex_renumbering) dm.setDefaultSection(sec) self._global_numbering = sec self._dm = dm self._ises = None self._halo = halo.Halo(dm) # Compute entity class offsets self.dof_classes = [0, 0, 0, 0] for d in range(mesh._plex.getDimension()+1): ndofs = dofs_per_entity[d] for i in range(4): self.dof_classes[i] += ndofs * mesh._entity_classes[d, i] # Tell the DM about the layout of the global vector with self.make_dat().vec_ro as v: self._dm.setGlobalVector(v.duplicate()) self._node_count = self._global_numbering.getStorageSize() self.cell_node_list = mesh.make_cell_node_list(self._global_numbering, entity_dofs) if mesh._plex.getStratumSize("interior_facets", 1) > 0: self.interior_facet_node_list = \ dmplex.get_facet_nodes(mesh.interior_facets.facet_cell, self.cell_node_list) else: self.interior_facet_node_list = np.array([], dtype=np.int32) if mesh._plex.getStratumSize("exterior_facets", 1) > 0: self.exterior_facet_node_list = \ dmplex.get_facet_nodes(mesh.exterior_facets.facet_cell, self.cell_node_list) else: self.exterior_facet_node_list = np.array([], dtype=np.int32) # 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 = {} self._initialized = True return self