def write_fenics_file(ofile, mesh, editor):
dim = mesh.geometry().dim()
for i in range(1, len(cell_map)+1):
if dim == 2:
editor.add_cell(i-1, cell_map[i][0]-1, cell_map[i][1]-1, cell_map[i][2]-1)
else:
editor.add_cell(i-1, cell_map[i][0]-1, cell_map[i][1]-1, cell_map[i][2]-1, cell_map[i][3]-1)
mesh.order()
# Set MeshValueCollections from info in boundary_cell
#mvc = mesh.domains().markers(dim-1)
md = mesh.domains()
for zone, cells in boundary_cells.iteritems():
for cell, nds in cells.iteritems():
dolfin_cell = Cell(mesh, cell-1)
vertices_of_cell = dolfin_cell.entities(0)
vertices_of_face = nds - 1
for jj, ff in enumerate(facets(dolfin_cell)):
facet_vertices = ff.entities(0)
if all(map(lambda x: x in vertices_of_face, facet_vertices)):
local_index = jj
break
#mvc.set_value(cell-1, local_index, zone)
md.set_marker((ff.index(), zone), dim-1)
ofile << mesh
from dolfin import plot
plot(mesh, interactive=True)
print 'Finished writing FEniCS mesh\n'
def write_fenics_file(ofile, mesh, editor):
dim = mesh.geometry().dim()
for i in range(1, len(cell_map) + 1):
if dim == 2:
editor.add_cell(i - 1, cell_map[i][0] - 1, cell_map[i][1] - 1,
cell_map[i][2] - 1)
else:
editor.add_cell(i - 1, cell_map[i][0] - 1, cell_map[i][1] - 1,
cell_map[i][2] - 1, cell_map[i][3] - 1)
mesh.order()
# Set MeshValueCollections from info in boundary_cell
#mvc = mesh.domains().markers(dim-1)
md = mesh.domains()
for zone, cells in boundary_cells.iteritems():
for cell, nds in cells.iteritems():
dolfin_cell = Cell(mesh, cell - 1)
vertices_of_cell = dolfin_cell.entities(0)
vertices_of_face = nds - 1
for jj, ff in enumerate(facets(dolfin_cell)):
facet_vertices = ff.entities(0)
if all(map(lambda x: x in vertices_of_face,
facet_vertices)):
local_index = jj
break
#mvc.set_value(cell-1, local_index, zone)
md.set_marker((ff.index(), zone), dim - 1)
ofile << mesh
from dolfin import plot
plot(mesh, interactive=True)
print 'Finished writing FEniCS mesh\n'
def write_fenics_file(dim, ofilename):
ofile = File(ofilename + '.xml')
mesh = Mesh()
editor = MeshEditor()
editor.open(mesh, dim, dim)
editor.init_vertices(nodes.shape[1])
editor.init_cells(len(cell_map))
for i in range(nodes.shape[1]):
if dim == 2:
editor.add_vertex(i, nodes[0, i], nodes[1, i])
else:
editor.add_vertex(i, nodes[0, i], nodes[1, i], nodes[2, i])
for i in range(1, len(cell_map)+1):
if dim == 2:
editor.add_cell(i-1, cell_map[i][0]-1, cell_map[i][1]-1, cell_map[i][2]-1)
else:
editor.add_cell(i-1, cell_map[i][0]-1, cell_map[i][1]-1, cell_map[i][2]-1, cell_map[i][3]-1)
mesh.order()
mvc = mesh.domains().markers(dim-1)
for zone, cells in boundary_cells.iteritems():
for cell, nds in cells.iteritems():
dolfin_cell = Cell(mesh, cell-1)
nodes_of_cell = dolfin_cell.entities(0)
#print cell
#print nodes_of_cell
nodes_of_face = nds - 1
#print nodes_of_face
for jj, ff in enumerate(facets(dolfin_cell)):
facet_nodes = ff.entities(0)
#print facet_nodes
if all(map(lambda x: x in nodes_of_face, facet_nodes)):
local_index = jj
break
mvc.set_value(cell-1, local_index, zone)
ofile << mesh
from dolfin import plot
plot(mesh, interactive=True)
print 'Finished writing FEniCS mesh\n'
def mesh_to_boundarymesh_dofmap(boundary, V, Vb, _should_own="cdof"):
"Find the mapping from dofs on full mesh FS to dofs on boundarymesh FS"
from dolfin import dolfin_version, MPI, mpi_comm_world
#if dolfin_version() != '1.4.0' and MPI.size(mpi_comm_world()) > 1:
# raise RuntimeError("mesh_to_boundarymesh_dofmap is currently not supported in parallel in version %s" %(dolfin_version()))
assert V.ufl_element().family() == Vb.ufl_element().family()
assert V.ufl_element().degree() == Vb.ufl_element().degree()
assert _should_own in ["cdof", "bdof"]
# Currently only CG1 and DG0 spaces are supported
assert V.ufl_element().family() in ["Lagrange", "Discontinuous Lagrange"]
if V.ufl_element().family() == "Discontinuous Lagrange":
assert V.ufl_element().degree() == 0
else:
assert V.ufl_element().degree() == 1
D = boundary.topology().dim()
mesh = V.mesh()
V_dm = V.dofmap()
Vb_dm = Vb.dofmap()
dofmap_to_boundary = {}
# Extract maps from boundary to mesh
vertex_map = boundary.entity_map(0)
cell_map = boundary.entity_map(D)
for i in xrange(len(cell_map)):
boundary_cell = Cell(boundary, i)
mesh_facet = Facet(mesh, cell_map[i])
mesh_cell_index = mesh_facet.entities(D + 1)[0]
mesh_cell = Cell(mesh, mesh_cell_index)
cell_dofs = V_dm.cell_dofs(mesh_cell_index)
boundary_dofs = Vb_dm.cell_dofs(i)
if V_dm.num_entity_dofs(0) > 0:
for v_idx in boundary_cell.entities(0):
mesh_v_idx = vertex_map[int(v_idx)]
mesh_list_idx = where(
mesh_cell.entities(0) == mesh_v_idx)[0][0]
boundary_list_idx = where(
boundary_cell.entities(0) == v_idx)[0][0]
bdofs = boundary_dofs[Vb_dm.tabulate_entity_dofs(
0, boundary_list_idx)]
cdofs = cell_dofs[V_dm.tabulate_entity_dofs(0, mesh_list_idx)]
for bdof, cdof in zip(bdofs, cdofs):
#if dolfin_version() in ["1.4.0+", "1.5.0", "1.6.0"]:
if LooseVersion(dolfin_version()) > LooseVersion("1.4.0"):
bdof = Vb_dm.local_to_global_index(bdof)
cdof = V_dm.local_to_global_index(cdof)
if _should_own == "cdof" and not (V_dm.ownership_range(
)[0] <= cdof < V_dm.ownership_range()[1]):
continue
elif _should_own == "bdof" and not (Vb_dm.ownership_range(
)[0] <= bdof < Vb_dm.ownership_range()[1]):
continue
else:
dofmap_to_boundary[bdof] = cdof
if V_dm.num_entity_dofs(D + 1) > 0 and V_dm.num_entity_dofs(0) == 0:
bdofs = boundary_dofs[Vb_dm.tabulate_entity_dofs(D, 0)]
cdofs = cell_dofs[V_dm.tabulate_entity_dofs(D + 1, 0)]
for bdof, cdof in zip(bdofs, cdofs):
#if dolfin_version() in ["1.4.0+", "1.5.0"]:
if LooseVersion(dolfin_version()) > LooseVersion("1.4.0"):
bdof = Vb_dm.local_to_global_index(bdof)
cdof = V_dm.local_to_global_index(cdof)
dofmap_to_boundary[bdof] = cdof
return dofmap_to_boundary
