def test_append_and_load_mesh_functions(tempdir, encoding, data_type):
dtype_str, dtype = data_type
meshes = [
UnitSquareMesh(MPI.comm_world, 12, 12),
UnitCubeMesh(MPI.comm_world, 2, 2, 2),
UnitSquareMesh(MPI.comm_world, 12, 12, CellType.quadrilateral),
UnitCubeMesh(MPI.comm_world, 2, 2, 2, CellType.hexahedron)
]
for mesh in meshes:
dim = mesh.topology.dim
vf = MeshFunction(dtype_str, mesh, 0, 0)
vf.name = "vertices"
ff = MeshFunction(dtype_str, mesh, mesh.topology.dim - 1, 0)
ff.name = "facets"
cf = MeshFunction(dtype_str, mesh, mesh.topology.dim, 0)
cf.name = "cells"
# vf.values[:] = mesh.topology.global_indices(0)[:]
map = mesh.topology.index_map(0)
vf.values[:] = map.global_indices(True)
map = mesh.topology.index_map(dim - 1)
ff.values[:] = map.global_indices(True)
map = mesh.topology.index_map(dim)
cf.values[:] = map.global_indices(True)
filename = os.path.join(
tempdir, "appended_mf_{0:d}_{1:s}.xdmf".format(
dim, str(mesh.topology.cell_type)))
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as xdmf:
xdmf.write(mesh)
xdmf.write(vf)
xdmf.write(ff)
xdmf.write(cf)
with XDMFFile(mesh.mpi_comm(), filename) as xdmf:
read_function = getattr(xdmf, "read_mf_" + dtype_str)
vf_in = read_function(mesh, "vertices")
ff_in = read_function(mesh, "facets")
cf_in = read_function(mesh, "cells")
diff_vf = vf_in.values - vf.values
diff_ff = ff_in.values - ff.values
diff_cf = cf_in.values - cf.values
assert np.all(diff_vf == 0)
assert np.all(diff_ff == 0)
assert np.all(diff_cf == 0)
def test_multiple_datasets(tempdir, encoding, cell_type):
mesh = UnitSquareMesh(MPI.comm_world, 4, 4, cell_type)
cf0 = MeshFunction('size_t', mesh, 2, 11)
cf0.name = 'cf0'
cf1 = MeshFunction('size_t', mesh, 2, 22)
cf1.name = 'cf1'
filename = os.path.join(tempdir, "multiple_mf.xdmf")
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as xdmf:
xdmf.write(mesh)
xdmf.write(cf0)
xdmf.write(cf1)
with XDMFFile(mesh.mpi_comm(), filename) as xdmf:
mesh = xdmf.read_mesh(cpp.mesh.GhostMode.none)
cf0 = xdmf.read_mf_size_t(mesh, "cf0")
cf1 = xdmf.read_mf_size_t(mesh, "cf1")
assert (cf0.values[0] == 11 and cf1.values[0] == 22)
def test_save_mesh_value_collection(tempdir, encoding, data_type, cell_type):
dtype_str, dtype = data_type
mesh = UnitCubeMesh(MPI.comm_world, 4, 4, 4, cell_type)
tdim = mesh.topology.dim
meshfn = MeshFunction(dtype_str, mesh, mesh.topology.dim, False)
meshfn.name = "volume_marker"
mp = cpp.mesh.midpoints(mesh, tdim, range(mesh.num_entities(tdim)))
for i in range(mesh.num_cells()):
if mp[i, 1] > 0.1:
meshfn.values[i] = 1
if mp[i, 1] > 0.9:
meshfn.values[i] = 2
for mvc_dim in range(0, tdim + 1):
mvc = MeshValueCollection(dtype_str, mesh, mvc_dim)
tag = "dim_{}_marker".format(mvc_dim)
mvc.name = tag
mesh.create_connectivity(mvc_dim, tdim)
mp = cpp.mesh.midpoints(mesh, mvc_dim,
range(mesh.num_entities(mvc_dim)))
for e in range(mesh.num_entities(mvc_dim)):
if (mp[e, 0] > 0.5):
mvc.set_value(e, dtype(1))
filename = os.path.join(tempdir, "mvc_{}.xdmf".format(mvc_dim))
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as xdmf:
xdmf.write(meshfn)
xdmf.write(mvc)
with XDMFFile(mesh.mpi_comm(), filename) as xdmf:
read_function = getattr(xdmf, "read_mvc_" + dtype_str)
mvc = read_function(mesh, tag)
def test_save_3D_edge_function(tempdir, encoding, data_type, cell_type):
dtype_str, dtype = data_type
mesh = UnitCubeMesh(MPI.comm_world, 4, 4, 4, cell_type)
mf = MeshFunction(dtype_str, mesh, 1, 0)
mf.name = "edges"
mf.values[:] = np.arange(mesh.num_entities(1), dtype=dtype)
filename = os.path.join(tempdir, "mf_edge_3D_%s.xdmf" % dtype_str)
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as file:
file.write(mf)
def test_save_3D_cell_function(tempdir, encoding, data_type, cell_type):
dtype_str, dtype = data_type
mesh = UnitCubeMesh(MPI.comm_world, 4, 4, 4, cell_type)
mf = MeshFunction(dtype_str, mesh, mesh.topology.dim, 0)
mf.name = "cells"
mf.values[:] = np.arange(mesh.num_entities(3), dtype=dtype)
filename = os.path.join(tempdir, "mf_3D_%s.xdmf" % dtype_str)
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as file:
file.write(mf)
with XDMFFile(mesh.mpi_comm(), filename) as xdmf:
read_function = getattr(xdmf, "read_mf_" + dtype_str)
mf_in = read_function(mesh, "cells")
diff = mf_in.values - mf.values
assert np.all(diff == 0)
def test_save_2D_vertex_function(tempdir, encoding, data_type, cell_type):
dtype_str, dtype = data_type
mesh = UnitSquareMesh(MPI.comm_world, 32, 32, cell_type)
mf = MeshFunction(dtype_str, mesh, 0, 0)
mf.name = "vertices"
global_indices = mesh.topology.index_map(0).global_indices(False)
mf.values[:] = global_indices[:]
filename = os.path.join(tempdir, "mf_vertex_2D_%s.xdmf" % dtype_str)
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as file:
file.write(mf)
with XDMFFile(mesh.mpi_comm(), filename) as xdmf:
read_function = getattr(xdmf, "read_mf_" + dtype_str)
mf_in = read_function(mesh, "vertices")
diff = mf_in.values - mf.values
assert np.all(diff == 0)
def test_save_3D_facet_function(tempdir, encoding, data_type, cell_type):
dtype_str, dtype = data_type
mesh = UnitCubeMesh(MPI.comm_world, 4, 4, 4, cell_type)
tdim = mesh.topology.dim
mf = MeshFunction(dtype_str, mesh, tdim - 1, 0)
mf.name = "facets"
global_indices = mesh.topology.global_indices(tdim - 1)
mf.values[:] = global_indices[:]
filename = os.path.join(tempdir, "mf_facet_3D_%s.xdmf" % dtype_str)
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as xdmf:
xdmf.write(mf)
with XDMFFile(mesh.mpi_comm(), filename) as xdmf:
read_function = getattr(xdmf, "read_mf_" + dtype_str)
mf_in = read_function(mesh, "facets")
diff = mf_in.values - mf.values
assert np.all(diff == 0)
