def make_dat(self, val=None, valuetype=None, name=None, uid=None):
"""Return a newly allocated :class:`pyop2.MixedDat` defined on the
:attr:`dof_dset` of this :class:`MixedFunctionSpace`."""
if val is not None:
assert len(val) == len(self)
else:
val = [None for _ in self]
return op2.MixedDat(s.make_dat(v, valuetype, name, utils._new_uid())
for s, v in zip(self._spaces, val))
def __init__(self, function_space, val=None, name=None, dtype=valuetype):
"""
:param function_space: the :class:`.FunctionSpace`, :class:`.VectorFunctionSpace`
or :class:`.MixedFunctionSpace` on which to build this :class:`Function`.
Alternatively, another :class:`Function` may be passed here and its function space
will be used to build this :class:`Function`.
:param val: NumPy array-like (or :class:`op2.Dat`) providing initial values (optional).
:param name: user-defined name for this :class:`Function` (optional).
:param dtype: optional data type for this :class:`Function`
(defaults to :data:`valuetype`).
"""
if isinstance(function_space, Function):
self._function_space = function_space._function_space
elif isinstance(function_space, functionspace.FunctionSpaceBase):
self._function_space = function_space
else:
raise NotImplementedError("Can't make a Function defined on a "
+ str(type(function_space)))
ufl.Coefficient.__init__(self, self._function_space.ufl_element())
self._label = "a function"
self.uid = utils._new_uid()
self._name = name or 'function_%d' % self.uid
if isinstance(val, (op2.Dat, op2.DatView)):
self.dat = val
else:
self.dat = self._function_space.make_dat(val, dtype,
self._name, uid=self.uid)
self._repr = None
self._split = None
if cachetools:
# LRU cache for expressions assembled onto this function
self._expression_cache = cachetools.LRUCache(maxsize=50)
else:
self._expression_cache = None
if isinstance(function_space, Function):
self.assign(function_space)
def __init__(self, meshfile, **kwargs):
"""Construct a mesh object.
Meshes may either be created by reading from a mesh file, or by
providing a PETSc DMPlex object defining the mesh topology.
:param meshfile: Mesh file name (or DMPlex object) defining
mesh topology. See below for details on supported mesh
formats.
:param dim: optional specification of the geometric dimension
of the mesh (ignored if not reading from mesh file).
If not supplied the geometric dimension is deduced from
the topological dimension of entities in the mesh.
:param reorder: optional flag indicating whether to reorder
meshes for better cache locality. If not supplied the
default value in :data:`parameters["reorder_meshes"]`
is used.
:param periodic_coords: optional numpy array of coordinates
used to replace those in the mesh object. These are
only supported in 1D and must have enough entries to be
used as a DG1 field on the mesh. Not supported when
reading from file.
When the mesh is read from a file the following mesh formats
are supported (determined, case insensitively, from the
filename extension):
* GMSH: with extension `.msh`
* Exodus: with extension `.e`, `.exo`
* CGNS: with extension `.cgns`
* Triangle: with extension `.node`
.. note::
When the mesh is created directly from a DMPlex object,
the :data:`dim` parameter is ignored (the DMPlex already
knows its geometric and topological dimensions).
"""
utils._init()
geometric_dim = kwargs.get("dim", None)
reorder = kwargs.get("reorder", parameters["reorder_meshes"])
periodic_coords = kwargs.get("periodic_coords", None)
distribute = kwargs.get("distribute", True)
if isinstance(meshfile, PETSc.DMPlex):
name = "plexmesh"
plex = meshfile
else:
name = meshfile
basename, ext = os.path.splitext(meshfile)
if periodic_coords is not None:
raise RuntimeError("Periodic coordinates are unsupported when reading from file")
if ext.lower() in ['.e', '.exo']:
plex = _from_exodus(meshfile)
elif ext.lower() == '.cgns':
plex = _from_cgns(meshfile)
elif ext.lower() == '.msh':
plex = _from_gmsh(meshfile)
elif ext.lower() == '.node':
plex = _from_triangle(meshfile, geometric_dim)
else:
raise RuntimeError("Mesh file %s has unknown format '%s'."
% (meshfile, ext[1:]))
# Mark exterior and interior facets
# Note. This must come before distribution, because otherwise
# DMPlex will consider facets on the domain boundary to be
# exterior, which is wrong.
with timed_region("Mesh: label facets"):
label_boundary = op2.MPI.comm.size == 1 or distribute
dmplex.label_facets(plex, label_boundary=label_boundary)
# Distribute the dm to all ranks
if op2.MPI.comm.size > 1 and distribute:
# We distribute with overlap zero, in case we're going to
# refine this mesh in parallel. Later, when we actually use
# it, we grow the halo.
plex.distribute(overlap=0)
# A cache of function spaces that have been built on this mesh
self._cache = {}
self.parent = None
self.name = name
self._plex = plex
self.uid = utils._new_uid()
topological_dim = self._plex.getDimension()
if geometric_dim is None:
geometric_dim = topological_dim
cStart, cEnd = self._plex.getHeightStratum(0) # cells
cell_facets = self._plex.getConeSize(cStart)
self._ufl_cell = ufl.Cell(fiat_utils._cells[topological_dim][cell_facets],
geometric_dimension=geometric_dim)
self._ufl_domain = ufl.Domain(self.ufl_cell(), data=self)
self._grown_halos = False
def callback(self):
del self._callback
if op2.MPI.comm.size > 1:
self._plex.distributeOverlap(1)
self._grown_halos = True
if reorder:
with timed_region("Mesh: reorder"):
old_to_new = self._plex.getOrdering(PETSc.Mat.OrderingType.RCM).indices
reordering = np.empty_like(old_to_new)
reordering[old_to_new] = np.arange(old_to_new.size, dtype=old_to_new.dtype)
else:
# No reordering
reordering = None
# Mark OP2 entities and derive the resulting Plex renumbering
with timed_region("Mesh: renumbering"):
dmplex.mark_entity_classes(self._plex)
self._entity_classes = dmplex.get_entity_classes(self._plex)
self._plex_renumbering = dmplex.plex_renumbering(self._plex,
self._entity_classes,
reordering)
with timed_region("Mesh: cell numbering"):
# Derive a cell numbering from the Plex renumbering
entity_dofs = np.zeros(topological_dim+1, dtype=np.int32)
entity_dofs[-1] = 1
self._cell_numbering = self._plex.createSection([1], entity_dofs,
perm=self._plex_renumbering)
entity_dofs[:] = 0
entity_dofs[0] = 1
self._vertex_numbering = self._plex.createSection([1], entity_dofs,
perm=self._plex_renumbering)
# Note that for bendy elements, this needs to change.
with timed_region("Mesh: coordinate field"):
if periodic_coords is not None:
if self.ufl_cell().geometric_dimension() != 1:
raise NotImplementedError("Periodic coordinates in more than 1D are unsupported")
# We've been passed a periodic coordinate field, so use that.
self._coordinate_fs = functionspace.VectorFunctionSpace(self, "DG", 1)
self.coordinates = function.Function(self._coordinate_fs,
val=periodic_coords,
name="Coordinates")
else:
self._coordinate_fs = functionspace.VectorFunctionSpace(self, "Lagrange", 1)
coordinates = dmplex.reordered_coords(self._plex, self._coordinate_fs._global_numbering,
(self.num_vertices(), geometric_dim))
self.coordinates = function.Function(self._coordinate_fs,
val=coordinates,
name="Coordinates")
self._ufl_domain = ufl.Domain(self.coordinates)
# Build a new ufl element for this function space with the
# correct domain. This is necessary since this function space
# is in the cache and will be picked up by later
# VectorFunctionSpace construction.
self._coordinate_fs._ufl_element = self._coordinate_fs.ufl_element().reconstruct(domain=self.ufl_domain())
# HACK alert!
# Replace coordinate Function by one that has a real domain on it (but don't copy values)
self.coordinates = function.Function(self._coordinate_fs, val=self.coordinates.dat)
# Add subdomain_data to the measure objects we store with
# the mesh. These are weakrefs for consistency with the
# "global" measure objects
self._dx = ufl.Measure('cell', subdomain_data=weakref.ref(self.coordinates))
self._ds = ufl.Measure('exterior_facet', subdomain_data=weakref.ref(self.coordinates))
self._dS = ufl.Measure('interior_facet', subdomain_data=weakref.ref(self.coordinates))
# Set the subdomain_data on all the default measures to this
# coordinate field.
# We don't set the domain on the measure since this causes
# an uncollectable reference in the global space (dx is
# global). Furthermore, it's never used anyway.
for measure in [ufl.dx, ufl.ds, ufl.dS]:
measure._subdomain_data = weakref.ref(self.coordinates)
self._callback = callback
def __init__(self, petscsf, global_numbering, universal_numbering):
self._tag = utils._new_uid()
self._comm = op2.MPI.comm
self._nprocs = self.comm.size
self._sends = defaultdict(list)
self._receives = defaultdict(list)
self._gnn2unn = None
remote_sends = defaultdict(list)
if op2.MPI.comm.size <= 1:
return
# Sort the SF by local indices
nroots, nleaves, local, remote = petscsf.getGraph()
local_new, remote_new = (list(x) for x in zip(*sorted(zip(local, remote), key=lambda x: x[0])))
petscsf.setGraph(nroots, nleaves, local_new, remote_new)
# Derive local receives and according remote sends
nroots, nleaves, local, remote = petscsf.getGraph()
for local, (rank, index) in zip(local, remote):
if rank != self.comm.rank:
self._receives[rank].append(local)
remote_sends[rank].append(index)
# Propagate remote send lists to the actual sender
send_reqs = []
for p in range(self._nprocs):
# send sizes
if p != self._comm.rank:
s = np.array(len(remote_sends[p]), dtype=np.int32)
send_reqs.append(self.comm.Isend(s, dest=p, tag=self.tag))
recv_reqs = []
sizes = [np.zeros(1, dtype=np.int32) for _ in range(self._nprocs)]
for p in range(self._nprocs):
# receive sizes
if p != self._comm.rank:
recv_reqs.append(self.comm.Irecv(sizes[p], source=p, tag=self.tag))
MPI.Request.Waitall(recv_reqs)
MPI.Request.Waitall(send_reqs)
for p in range(self._nprocs):
# allocate buffers
if p != self._comm.rank:
if sizes[p][0] > 0:
self._sends[p] = np.empty(sizes[p][0], dtype=np.int32)
send_reqs = []
for p in range(self._nprocs):
if p != self._comm.rank:
if len(remote_sends[p]) > 0:
send_buf = np.array(remote_sends[p], dtype=np.int32)
send_reqs.append(self.comm.Isend(send_buf, dest=p, tag=self.tag))
recv_reqs = []
for p in range(self._nprocs):
if p != self._comm.rank:
if sizes[p][0] > 0:
recv_reqs.append(self.comm.Irecv(self._sends[p], source=p, tag=self.tag))
MPI.Request.Waitall(send_reqs)
MPI.Request.Waitall(recv_reqs)
# Build Global-To-Universal mapping
pStart, pEnd = global_numbering.getChart()
self._gnn2unn = np.zeros(global_numbering.getStorageSize(), dtype=np.int32)
for p in range(pStart, pEnd):
dof = global_numbering.getDof(p)
goff = global_numbering.getOffset(p)
uoff = universal_numbering.getOffset(p)
if uoff < 0:
uoff = (-1*uoff)-1
for c in range(dof):
self._gnn2unn[goff+c] = uoff+c
def _from_dmplex(self, plex, geometric_dim=0,
periodic_coords=None, reorder=None):
""" Create mesh from DMPlex object """
self._plex = plex
self.uid = utils._new_uid()
# Mark exterior and interior facets
# Note. This must come before distribution, because otherwise
# DMPlex will consider facets on the domain boundary to be
# exterior, which is wrong.
dmplex.label_facets(self._plex)
if geometric_dim == 0:
geometric_dim = plex.getDimension()
# Distribute the dm to all ranks
if op2.MPI.comm.size > 1:
self.parallel_sf = plex.distribute(overlap=1)
self._plex = plex
if reorder:
old_to_new = self._plex.getOrdering(PETSc.Mat.OrderingType.RCM).indices
reordering = np.empty_like(old_to_new)
reordering[old_to_new] = np.arange(old_to_new.size, dtype=old_to_new.dtype)
else:
# No reordering
reordering = None
# Mark OP2 entities and derive the resulting Plex renumbering
dmplex.mark_entity_classes(self._plex)
self._plex_renumbering = dmplex.plex_renumbering(self._plex, reordering)
cStart, cEnd = self._plex.getHeightStratum(0) # cells
cell_vertices = self._plex.getConeSize(cStart)
self._ufl_cell = ufl.Cell(fiat_utils._cells[geometric_dim][cell_vertices],
geometric_dimension=geometric_dim)
self._ufl_domain = ufl.Domain(self.ufl_cell(), data=self)
dim = self._plex.getDimension()
self._cells, self.cell_classes = dmplex.get_cells_by_class(self._plex)
# Derive a cell numbering from the Plex renumbering
cell_entity_dofs = np.zeros(dim+1, dtype=np.int32)
cell_entity_dofs[-1] = 1
self._cell_numbering = self._plex.createSection(1, [1],
cell_entity_dofs,
perm=self._plex_renumbering)
self._cell_closure = None
self.interior_facets = None
self.exterior_facets = None
# Note that for bendy elements, this needs to change.
if periodic_coords is not None:
if self.ufl_cell().geometric_dimension() != 1:
raise NotImplementedError("Periodic coordinates in more than 1D are unsupported")
# We've been passed a periodic coordinate field, so use that.
self._coordinate_fs = functionspace.VectorFunctionSpace(self, "DG", 1)
self.coordinates = function.Function(self._coordinate_fs,
val=periodic_coords,
name="Coordinates")
else:
self._coordinate_fs = functionspace.VectorFunctionSpace(self, "Lagrange", 1)
coordinates = dmplex.reordered_coords(self._plex, self._coordinate_fs._global_numbering,
(self.num_vertices(), geometric_dim))
self.coordinates = function.Function(self._coordinate_fs,
val=coordinates,
name="Coordinates")
self._ufl_domain = ufl.Domain(self.coordinates)
# Build a new ufl element for this function space with the
# correct domain. This is necessary since this function space
# is in the cache and will be picked up by later
# VectorFunctionSpace construction.
self._coordinate_fs._ufl_element = self._coordinate_fs.ufl_element().reconstruct(domain=self.ufl_domain())
# HACK alert!
# Replace coordinate Function by one that has a real domain on it (but don't copy values)
self.coordinates = function.Function(self._coordinate_fs, val=self.coordinates.dat)
# Add domain and subdomain_data to the measure objects we store with the mesh.
self._dx = ufl.Measure('cell', domain=self, subdomain_data=self.coordinates)
self._ds = ufl.Measure('exterior_facet', domain=self, subdomain_data=self.coordinates)
self._dS = ufl.Measure('interior_facet', domain=self, subdomain_data=self.coordinates)
# Set the subdomain_data on all the default measures to this
# coordinate field. Also set the domain on the measure.
for measure in [ufl.dx, ufl.ds, ufl.dS]:
measure._subdomain_data = self.coordinates
measure._domain = self.ufl_domain()
