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): import firedrake.function as function import firedrake.functionspace as functionspace 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, plex, name, reorder, distribute): """Half-initialise a mesh topology. :arg plex: :class:`DMPlex` representing the mesh topology :arg name: name of the mesh :arg reorder: whether to reorder the mesh (bool) :arg distribute: whether to distribute the mesh to parallel processes """ # Do some validation of the input mesh dmplex.validate_mesh(plex) utils._init() self._plex = plex self.name = name # A cache of function spaces that have been built on this mesh self._cache = {} # 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) dim = plex.getDimension() cStart, cEnd = plex.getHeightStratum(0) # cells cell_nfacets = plex.getConeSize(cStart) self._grown_halos = False self._ufl_cell = ufl.Cell(_cells[dim][cell_nfacets]) def callback(self): """Finish initialisation.""" 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 self._did_reordering = bool(reorder) # 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(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) self._callback = callback
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): import firedrake.function as function import firedrake.functionspace as functionspace 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