def get_node_set(mesh, nodes_per_entity):
"""Get the :class:`node set <pyop2.Set>`.
:arg mesh: The mesh to use.
:arg nodes_per_entity: The number of function space nodes per
topological entity.
:returns: A :class:`pyop2.Set` for the function space nodes.
"""
global_numbering = get_global_numbering(mesh, nodes_per_entity)
# Use a DM to create the halo SFs
dm = PETSc.DMShell().create(mesh.comm)
dm.setPointSF(mesh._plex.getPointSF())
dm.setDefaultSection(global_numbering)
node_classes = tuple(numpy.dot(nodes_per_entity, mesh._entity_classes))
node_set = op2.Set(node_classes, halo=halo_mod.Halo(dm), comm=mesh.comm)
# Don't need it any more, explicitly destroy.
dm.destroy()
extruded = bool(mesh.layers)
if extruded:
node_set = op2.ExtrudedSet(node_set, layers=mesh.layers)
assert global_numbering.getStorageSize() == node_set.total_size
if not extruded and node_set.total_size >= (1 <<
(IntType.itemsize * 8 - 4)):
raise RuntimeError(
"Problems with more than %d nodes per process unsupported",
(1 << (IntType.itemsize * 8 - 4)))
return node_set
def get_node_set(mesh, key):
"""Get the :class:`node set <pyop2.Set>`.
:arg mesh: The mesh to use.
:arg key: a (nodes_per_entity, real_tensorproduct) tuple where
nodes_per_entity is a tuple of the number of nodes per topological
entity; real_tensorproduct is True if the function space is a
degenerate fs x Real tensorproduct.
:returns: A :class:`pyop2.Set` for the function space nodes.
"""
nodes_per_entity, real_tensorproduct = key
global_numbering = get_global_numbering(
mesh, (nodes_per_entity, real_tensorproduct))
node_classes = mesh.node_classes(nodes_per_entity,
real_tensorproduct=real_tensorproduct)
halo = halo_mod.Halo(mesh._topology_dm, global_numbering)
node_set = op2.Set(node_classes, halo=halo, comm=mesh.comm)
extruded = mesh.cell_set._extruded
assert global_numbering.getStorageSize() == node_set.total_size
if not extruded and node_set.total_size >= (1 <<
(IntType.itemsize * 8 - 4)):
raise RuntimeError(
"Problems with more than %d nodes per process unsupported",
(1 << (IntType.itemsize * 8 - 4)))
return node_set
def get_node_set(mesh, nodes_per_entity):
"""Get the :class:`node set <pyop2.Set>`.
:arg mesh: The mesh to use.
:arg nodes_per_entity: The number of function space nodes per
topological entity.
:returns: A :class:`pyop2.Set` for the function space nodes.
"""
global_numbering = get_global_numbering(mesh, nodes_per_entity)
node_classes = mesh.node_classes(nodes_per_entity)
halo = halo_mod.Halo(mesh._plex, global_numbering)
node_set = op2.Set(node_classes, halo=halo, comm=mesh.comm)
extruded = mesh.cell_set._extruded
if extruded:
# FIXME! This is a LIE! But these sets should not be extruded
# anyway, only the code gen in PyOP2 is busted.
node_set = op2.ExtrudedSet(node_set, layers=2)
assert global_numbering.getStorageSize() == node_set.total_size
if not extruded and node_set.total_size >= (1 <<
(IntType.itemsize * 8 - 4)):
raise RuntimeError(
"Problems with more than %d nodes per process unsupported",
(1 << (IntType.itemsize * 8 - 4)))
return node_set
def get_node_set(mesh, nodes_per_entity):
"""Get the :class:`node set <pyop2.Set>`.
:arg mesh: The mesh to use.
:arg nodes_per_entity: The number of function space nodes per
topological entity.
:returns: A :class:`pyop2.Set` for the function space nodes.
"""
global_numbering = get_global_numbering(mesh, nodes_per_entity)
# Use a DM to create the halo SFs
dm = PETSc.DMShell().create()
dm.setPointSF(mesh._plex.getPointSF())
dm.setDefaultSection(global_numbering)
node_classes = tuple(numpy.dot(nodes_per_entity, mesh._entity_classes))
node_set = op2.Set(node_classes, halo=halo_mod.Halo(dm))
# Don't need it any more, explicitly destroy.
dm.destroy()
extruded = bool(mesh.layers)
if extruded:
node_set = op2.ExtrudedSet(node_set, layers=mesh.layers)
assert global_numbering.getStorageSize() == node_set.total_size
return node_set
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