def test_save_3d_vector(tempdir, encoding, cell_type):
filename = os.path.join(tempdir, "u_3Dv.xdmf")
mesh = UnitCubeMesh(MPI.COMM_WORLD, 2, 2, 2, cell_type)
u = Function(VectorFunctionSpace(mesh, ("Lagrange", 1)))
u.vector.set(1.0 + (1j if has_petsc_complex else 0))
with XDMFFile(mesh.mpi_comm(), filename, "w", encoding=encoding) as file:
file.write_mesh(mesh)
file.write_function(u)
def test_UnitCubeMeshDistributed():
"""Create mesh of unit cube."""
mesh = UnitCubeMesh(MPI.COMM_WORLD, 5, 7, 9)
assert mesh.topology.index_map(0).size_global == 480
assert mesh.topology.index_map(3).size_global == 1890
assert mesh.geometry.dim == 3
assert mesh.mpi_comm().allreduce(
mesh.topology.index_map(0).size_local, MPI.SUM) == 480
def test_save_3d_scalar(tempdir, encoding, cell_type):
filename = os.path.join(tempdir, "u3.xdmf")
mesh = UnitCubeMesh(MPI.COMM_WORLD, 4, 3, 4, cell_type)
V = FunctionSpace(mesh, ("Lagrange", 2))
u = Function(V)
u.vector.set(1.0)
with XDMFFile(mesh.mpi_comm(), filename, "w", encoding=encoding) as file:
file.write_mesh(mesh)
file.write_function(u)
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)
def test_save_3d_tensor(tempdir):
mesh = UnitCubeMesh(MPI.COMM_WORLD, 8, 8, 8)
u = Function(TensorFunctionSpace(mesh, ("Lagrange", 2)))
with u.vector.localForm() as loc:
loc.set(1.0)
filename = os.path.join(tempdir, "u.pvd")
with VTKFile(mesh.mpi_comm(), filename, "w") as vtk:
vtk.write_function(u, 0.)
def test_save_and_load_3d_mesh(tempdir, encoding, cell_type):
filename = os.path.join(tempdir, "mesh_3D.xdmf")
mesh = UnitCubeMesh(MPI.comm_world, 4, 4, 4, cell_type)
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as file:
file.write(mesh)
with XDMFFile(MPI.comm_world, filename) as file:
mesh2 = file.read_mesh(cpp.mesh.GhostMode.none)
assert mesh.num_entities_global(0) == mesh2.num_entities_global(0)
dim = mesh.topology.dim
assert mesh.num_entities_global(dim) == mesh2.num_entities_global(dim)
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_vector_series(tempdir, encoding, cell_type):
filename = os.path.join(tempdir, "u_3D.xdmf")
mesh = UnitCubeMesh(MPI.comm_world, 2, 2, 2, cell_type)
u = Function(VectorFunctionSpace(mesh, ("Lagrange", 2)))
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as file:
u.vector.set(1.0 + (1j if has_petsc_complex else 0))
file.write(u, 0.1)
u.vector.set(2.0 + (2j if has_petsc_complex else 0))
file.write(u, 0.2)
u.vector.set(3.0 + (3j if has_petsc_complex else 0))
file.write(u, 0.3)
def test_save_and_read_mesh_value_collection_with_only_one_marked_entity(
tempdir):
ndiv = 2
filename = os.path.join(tempdir, "mesh_value_collection.h5")
mesh = UnitCubeMesh(MPI.comm_world, ndiv, ndiv, ndiv)
mvc = MeshValueCollection("size_t", mesh, 3)
mesh.create_entities(3)
if MPI.rank(mesh.mpi_comm()) == 0:
mvc.set_value(0, 1)
# write to file
with HDF5File(mesh.mpi_comm(), filename, 'w') as f:
f.write(mvc, "/mesh_value_collection")
# read from file
with HDF5File(mesh.mpi_comm(), filename, 'r') as f:
mvc = f.read_mvc_size_t(mesh, "/mesh_value_collection")
assert MPI.sum(mesh.mpi_comm(), mvc.size()) == 1
if MPI.rank(mesh.mpi_comm()) == 0:
assert mvc.get_value(0, 0) == 1
def test_save_and_load_3d_mesh(tempdir, encoding, cell_type):
filename = os.path.join(tempdir, "mesh.xdmf")
mesh = UnitCubeMesh(MPI.COMM_WORLD, 12, 12, 8, cell_type)
with XDMFFile(mesh.mpi_comm(), filename, "w", encoding=encoding) as file:
file.write_mesh(mesh)
with XDMFFile(MPI.COMM_WORLD, filename, "r", encoding=encoding) as file:
mesh2 = file.read_mesh()
assert mesh.topology.index_map(0).size_global == mesh2.topology.index_map(0).size_global
assert mesh.topology.index_map(mesh.topology.dim).size_global == mesh2.topology.index_map(
mesh.topology.dim).size_global
def test_xdmf_timeseries_write_to_closed_hdf5_using_with(tempdir, cell_type):
mesh = UnitCubeMesh(MPI.comm_world, 2, 2, 2, cell_type)
V = FunctionSpace(mesh, ("CG", 1))
u = Function(V)
filename = os.path.join(tempdir, "time_series_closed_append.xdmf")
with XDMFFile(mesh.mpi_comm(), filename) as xdmf:
xdmf.write(u, float(0.0))
xdmf.write(u, float(1.0))
xdmf.close()
with xdmf:
xdmf.write(u, float(2.0))
def test_UnitHexMesh_assemble():
mesh = UnitCubeMesh(MPI.COMM_WORLD, 6, 7, 5, CellType.hexahedron)
vol = assemble_scalar(1 * dx(mesh))
vol = mesh.mpi_comm().allreduce(vol, MPI.SUM)
assert (vol == pytest.approx(1, rel=1e-9))
def test_UnitHexMesh():
mesh = UnitCubeMesh(MPI.COMM_WORLD, 5, 7, 9, CellType.hexahedron)
assert mesh.topology.index_map(0).size_global == 480
assert mesh.topology.index_map(3).size_global == 315
assert mesh.geometry.dim == 3
assert mesh.mpi_comm().allreduce(mesh.topology.index_map(0).size_local, MPI.SUM) == 480
def test_UnitHexMesh_assemble():
mesh = UnitCubeMesh(MPI.comm_world, 6, 7, 5, CellType.hexahedron)
vol = assemble_scalar(1 * dx(mesh))
vol = MPI.sum(mesh.mpi_comm(), vol)
assert (vol == pytest.approx(1, rel=1e-9))
def test_UnitHexMesh():
mesh = UnitCubeMesh(MPI.comm_world, 5, 7, 9, CellType.hexahedron)
assert mesh.num_entities_global(0) == 480
assert mesh.num_entities_global(3) == 315
assert mesh.geometry.dim == 3
assert MPI.sum(mesh.mpi_comm(), mesh.topology.index_map(0).size_local) == 480