def test_save_2D_facet_function(tempdir, encoding, data_type):
if invalid_config(encoding):
pytest.skip("XDMF unsupported in current configuration")
dtype_str, dtype = data_type
mesh = UnitSquareMesh(MPI.comm_world, 32, 32)
mf = MeshFunction(dtype_str, mesh, mesh.topology.dim - 1, 0)
mf.rename("facets")
if (MPI.size(mesh.mpi_comm()) == 1):
for facet in Facets(mesh):
mf[facet] = dtype(facet.index())
else:
for facet in Facets(mesh):
mf[facet] = dtype(facet.global_index())
filename = os.path.join(tempdir, "mf_facet_2D_%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 = 0
for facet in Facets(mesh):
diff += (mf_in[facet] - mf[facet])
assert diff == 0
def test_save_mesh_value_collection(tempdir, encoding, data_type):
dtype_str, dtype = data_type
mesh = UnitCubeMesh(MPI.comm_world, 4, 4, 4)
tdim = mesh.topology.dim
meshfn = MeshFunction(dtype_str, mesh, mesh.topology.dim, False)
meshfn.rename("volume_marker")
for c in Cells(mesh):
if c.midpoint()[1] > 0.1:
meshfn[c] = dtype(1)
if c.midpoint()[1] > 0.9:
meshfn[c] = dtype(2)
for mvc_dim in range(0, tdim + 1):
mvc = MeshValueCollection(dtype_str, mesh, mvc_dim)
tag = "dim_%d_marker" % mvc_dim
mvc.rename(tag)
mesh.init(mvc_dim, tdim)
for e in MeshEntities(mesh, mvc_dim):
if (e.midpoint()[0] > 0.5):
mvc.set_value(e.index(), dtype(1))
filename = os.path.join(tempdir, "mvc_%d.xdmf" % 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_and_checkpoint_vector(tempdir, encoding, fe_degree, fe_family,
mesh_tdim, mesh_n):
if invalid_config(encoding):
pytest.skip("XDMF unsupported in current configuration")
if invalid_fe(fe_family, fe_degree):
pytest.skip("Trivial finite element")
filename = os.path.join(tempdir, "u2_checkpoint.xdmf")
mesh = mesh_factory(mesh_tdim, mesh_n)
FE = VectorElement(fe_family, mesh.ufl_cell(), fe_degree)
V = FunctionSpace(mesh, FE)
u_in = Function(V)
u_out = Function(V)
if mesh.geometry.dim == 1:
u_out.interpolate(Expression(("x[0]", ), degree=1))
elif mesh.geometry.dim == 2:
u_out.interpolate(Expression(("x[0]*x[1]", "x[0]"), degree=2))
elif mesh.geometry.dim == 3:
u_out.interpolate(Expression(("x[0]*x[1]", "x[0]", "x[2]"), degree=2))
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as file:
file.write_checkpoint(u_out, "u_out", 0)
with XDMFFile(mesh.mpi_comm(), filename) as file:
u_in = file.read_checkpoint(V, "u_out", 0)
u_in.vector().axpy(-1.0, u_out.vector())
assert u_in.vector().norm(cpp.la.Norm.l2) < 1.0e-12
def test_save_3D_facet_function(tempdir, encoding, data_type):
dtype_str, dtype = data_type
mesh = UnitCubeMesh(MPI.comm_world, 4, 4, 4)
mf = MeshFunction(dtype_str, mesh, mesh.topology.dim - 1, 0)
mf.rename("facets")
if (MPI.size(mesh.mpi_comm()) == 1):
for facet in Facets(mesh):
mf[facet] = dtype(facet.index())
else:
for facet in Facets(mesh):
mf[facet] = dtype(facet.global_index())
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 = 0
for facet in Facets(mesh):
diff += (mf_in[facet] - mf[facet])
assert diff == 0
def test_save_and_checkpoint_scalar(tempdir, encoding, fe_degree, fe_family,
mesh_tdim, mesh_n):
if invalid_fe(fe_family, fe_degree):
pytest.skip("Trivial finite element")
filename = os.path.join(tempdir, "u1_checkpoint.xdmf")
mesh = mesh_factory(mesh_tdim, mesh_n)
FE = FiniteElement(fe_family, mesh.ufl_cell(), fe_degree)
V = FunctionSpace(mesh, FE)
u_in = Function(V)
u_out = Function(V)
if has_petsc_complex:
u_out.interpolate(Expression("x[0] + j*x[0]", degree=1))
else:
u_out.interpolate(Expression("x[0]", degree=1))
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as file:
file.write_checkpoint(u_out, "u_out", 0)
with XDMFFile(mesh.mpi_comm(), filename) as file:
u_in = file.read_checkpoint(V, "u_out", 0)
u_in.vector().axpy(-1.0, u_out.vector())
assert u_in.vector().norm(cpp.la.Norm.l2) < 1.0e-12
def test_save_and_checkpoint_timeseries(tempdir, encoding):
mesh = UnitSquareMesh(MPI.comm_world, 16, 16)
filename = os.path.join(tempdir, "u2_checkpoint.xdmf")
FE = FiniteElement("CG", mesh.ufl_cell(), 2)
V = FunctionSpace(mesh, FE)
times = [0.5, 0.2, 0.1]
u_out = [None] * len(times)
u_in = [None] * len(times)
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as file:
for i, p in enumerate(times):
u_out[i] = interpolate(Expression("x[0]*p", p=p, degree=1), V)
file.write_checkpoint(u_out[i], "u_out", p)
with XDMFFile(mesh.mpi_comm(), filename) as file:
for i, p in enumerate(times):
u_in[i] = file.read_checkpoint(V, "u_out", i)
for i, p in enumerate(times):
u_in[i].vector().axpy(-1.0, u_out[i].vector())
assert u_in[i].vector().norm(cpp.la.Norm.l2) < 1.0e-12
# test reading last
with XDMFFile(mesh.mpi_comm(), filename) as file:
u_in_last = file.read_checkpoint(V, "u_out", -1)
u_out[-1].vector().axpy(-1.0, u_in_last.vector())
assert u_out[-1].vector().norm(cpp.la.Norm.l2) < 1.0e-12
def test_distribute_mesh(subset_comm, tempdir, mesh_factory):
func, args = mesh_factory
mesh = func(*args)
if not is_simplex(mesh.cell_type):
return
# Order mesh
cpp.mesh.Ordering.order_simplex(mesh)
encoding = XDMFFile.Encoding.HDF5
ghost_mode = cpp.mesh.GhostMode.none
filename = os.path.join(tempdir, "mesh.xdmf")
comm = mesh.mpi_comm()
parts = comm.size
partitioner = cpp.mesh.Partitioner.scotch
with XDMFFile(mesh.mpi_comm(), filename, encoding) as file:
file.write(mesh)
# Use the subset_comm to read and partition mesh, then distribute to all
# available processes
with XDMFFile(subset_comm, filename) as file:
cell_type, points, cells, indices = file.read_mesh_data(subset_comm)
partition_data = cpp.mesh.partition_cells(subset_comm, parts, cell_type,
cells, partitioner)
dist_mesh = cpp.mesh.build_from_partition(MPI.comm_world, cell_type, points,
cells, indices, ghost_mode,
partition_data)
assert(mesh.cell_type == dist_mesh.cell_type)
assert mesh.num_entities_global(0) == dist_mesh.num_entities_global(0)
dim = dist_mesh.topology.dim
assert mesh.num_entities_global(dim) == dist_mesh.num_entities_global(dim)
def test_custom_partition(tempdir, mesh_factory):
func, args = mesh_factory
mesh = func(*args)
if not is_simplex(mesh.cell_type):
return
comm = mesh.mpi_comm()
filename = os.path.join(tempdir, "mesh.xdmf")
encoding = XDMFFile.Encoding.HDF5
ghost_mode = cpp.mesh.GhostMode.none
with XDMFFile(comm, filename, encoding) as file:
file.write(mesh)
with XDMFFile(comm, filename) as file:
cell_type, points, cells, global_indices = file.read_mesh_data(comm)
# Create a custom partition array
part = numpy.zeros(cells.shape[0], dtype=numpy.int32)
part[:] = comm.rank
ghost_procs = cpp.mesh.ghost_cell_mapping(comm, part, cell_type, cells)
cell_partition = cpp.mesh.PartitionData(part, ghost_procs)
dist_mesh = cpp.mesh.build_from_partition(comm, cell_type, points,
cells, global_indices,
ghost_mode, cell_partition)
assert(mesh.cell_type == dist_mesh.cell_type)
assert mesh.num_entities_global(0) == dist_mesh.num_entities_global(0)
dim = dist_mesh.topology.dim
assert mesh.num_entities_global(dim) == dist_mesh.num_entities_global(dim)
def compute_rates():
"Compute convergence rates for degrees 1 and 2."
gdim = 2
tdim = gdim
for coordinate_degree in (1, 2):
for element_degree in (1, 2):
print("\nUsing coordinate degree %d, element degree %d" % (coordinate_degree, element_degree))
ufile = XDMFFile(MPI.comm_world, "poisson-disc-degree-x%d-e%d.xdmf" % (coordinate_degree, element_degree))
encoding = XDMFFile.Encoding.HDF5 if has_hdf5() else XDMFFile.Encoding.ASCII
preverr = None
prevh = None
for i, nsteps in enumerate((1, 8, 64)):
err, h, area, num_cells, u = compute(nsteps, coordinate_degree, element_degree, gdim)
if preverr is None:
conv = 0.0
print("conv = N/A, h = %.3e, err = %.3e, area = %.16f, num_cells = %d" % (h, err, area, num_cells))
else:
conv = math.log(preverr/err, prevh/h)
print("conv = %1.2f, h = %.3e, err = %.3e, area = %.16f, num_cells = %d" % (conv, h, err, area, num_cells))
preverr = err
prevh = h
# Save solution to file
u.rename('u')
if MPI.size(MPI.comm_world) > 1 and encoding == XDMFFile.Encoding.ASCII:
print("XDMF file output not supported in parallel without HDF5")
else:
ufile.write(u, encoding=encoding)
def test_save_and_checkpoint_scalar(tempdir, encoding, fe_degree, fe_family,
mesh_tdim, mesh_n):
if invalid_fe(fe_family, fe_degree):
pytest.skip("Trivial finite element")
filename = os.path.join(tempdir, "u1_checkpoint.xdmf")
mesh = mesh_factory(mesh_tdim, mesh_n)
FE = FiniteElement(fe_family, mesh.ufl_cell(), fe_degree)
V = FunctionSpace(mesh, FE)
u_in = Function(V)
u_out = Function(V)
if has_petsc_complex:
def expr_eval(values, x):
values[:, 0] = x[:, 0] + 1.0j * x[:, 0]
u_out.interpolate(expr_eval)
else:
def expr_eval(values, x):
values[:, 0] = x[:, 0]
u_out.interpolate(expr_eval)
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as file:
file.write_checkpoint(u_out, "u_out", 0)
with XDMFFile(mesh.mpi_comm(), filename) as file:
u_in = file.read_checkpoint(V, "u_out", 0)
u_in.vector.axpy(-1.0, u_out.vector)
assert u_in.vector.norm() < 1.0e-12
def test_read_write_p2_function(tempdir):
mesh = cpp.generation.UnitDiscMesh.create(MPI.comm_world, 3,
cpp.mesh.GhostMode.none)
cmap = fem.create_coordinate_map(mesh.ufl_domain())
mesh.geometry.coord_mapping = cmap
Q = FunctionSpace(mesh, ("Lagrange", 2))
F = Function(Q)
if has_petsc_complex:
F.interpolate(Expression("x[0] + j*x[0]", degree=1))
else:
F.interpolate(Expression("x[0]", degree=1))
filename = os.path.join(tempdir, "tri6_function.xdmf")
with XDMFFile(mesh.mpi_comm(), filename,
encoding=XDMFFile.Encoding.HDF5) as xdmf:
xdmf.write(F)
Q = VectorFunctionSpace(mesh, ("Lagrange", 1))
F = Function(Q)
if has_petsc_complex:
F.interpolate(Expression(("x[0] + j*x[0]", "x[1] + j*x[1]"), degree=1))
else:
F.interpolate(Expression(("x[0]", "x[1]"), degree=1))
filename = os.path.join(tempdir, "tri6_vector_function.xdmf")
with XDMFFile(mesh.mpi_comm(), filename,
encoding=XDMFFile.Encoding.HDF5) as xdmf:
xdmf.write(F)
def test_save_and_checkpoint_timeseries(tempdir, encoding):
mesh = UnitSquareMesh(MPI.comm_world, 16, 16)
filename = os.path.join(tempdir, "u2_checkpoint.xdmf")
FE = FiniteElement("CG", mesh.ufl_cell(), 2)
V = FunctionSpace(mesh, FE)
times = [0.5, 0.2, 0.1]
u_out = [None] * len(times)
u_in = [None] * len(times)
p = 0.0
def expr_eval(values, x):
values[:, 0] = x[:, 0] * p
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as file:
for i, p in enumerate(times):
u_out[i] = interpolate(expr_eval, V)
file.write_checkpoint(u_out[i], "u_out", p)
with XDMFFile(mesh.mpi_comm(), filename) as file:
for i, p in enumerate(times):
u_in[i] = file.read_checkpoint(V, "u_out", i)
for i, p in enumerate(times):
u_in[i].vector.axpy(-1.0, u_out[i].vector)
assert u_in[i].vector.norm() < 1.0e-12
# test reading last
with XDMFFile(mesh.mpi_comm(), filename) as file:
u_in_last = file.read_checkpoint(V, "u_out", -1)
u_out[-1].vector.axpy(-1.0, u_in_last.vector)
assert u_out[-1].vector.norm() < 1.0e-12
def test_save_mesh_value_collection(tempdir, encoding, data_type):
dtype_str, dtype = data_type
mesh = UnitCubeMesh(MPI.comm_world, 4, 4, 4)
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_cell_function(tempdir, encoding, data_type):
if invalid_config(encoding):
pytest.skip("XDMF unsupported in current configuration")
dtype_str, dtype = data_type
mesh = UnitCubeMesh(MPI.comm_world, 4, 4, 4)
mf = MeshFunction(dtype_str, mesh, mesh.topology.dim, 0)
mf.rename("cells")
for cell in Cells(mesh):
mf[cell] = dtype(cell.index())
filename = os.path.join(tempdir, "mf_3D_%s.xdmf" % dtype_str)
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as file:
file.write(mf)
# mf_in = MeshFunction(dtype_str, mesh, mesh.topology.dim, 0)
with XDMFFile(mesh.mpi_comm(), filename) as xdmf:
read_function = getattr(xdmf, "read_mf_" + dtype_str)
mf_in = read_function(mesh, "cells")
diff = 0
for cell in Cells(mesh):
diff += (mf_in[cell] - mf[cell])
assert diff == 0
def test_Write(f):
"""Construct and save a simple meshfunction."""
f = f
f[0] = 1
f[1] = 2
file = XDMFFile(f.mesh().mpi_comm(), "saved_mesh_function.xdmf")
file.write(f)
def test_append_and_load_mesh_functions(tempdir, encoding, data_type):
if invalid_config(encoding):
pytest.skip("XDMF unsupported in current configuration")
dtype_str, dtype = data_type
meshes = [
UnitSquareMesh(MPI.comm_world, 12, 12),
UnitCubeMesh(MPI.comm_world, 2, 2, 2)
]
for mesh in meshes:
dim = mesh.topology.dim
vf = MeshFunction(dtype_str, mesh, 0, 0)
vf.rename("vertices")
ff = MeshFunction(dtype_str, mesh, mesh.topology.dim - 1, 0)
ff.rename("facets")
cf = MeshFunction(dtype_str, mesh, mesh.topology.dim, 0)
cf.rename("cells")
if (MPI.size(mesh.mpi_comm()) == 1):
for vertex in Vertices(mesh):
vf[vertex] = dtype(vertex.index())
for facet in Facets(mesh):
ff[facet] = dtype(facet.index())
for cell in Cells(mesh):
cf[cell] = dtype(cell.index())
else:
for vertex in Vertices(mesh):
vf[vertex] = dtype(vertex.global_index())
for facet in Facets(mesh):
ff[facet] = dtype(facet.global_index())
for cell in Cells(mesh):
cf[cell] = dtype(cell.global_index())
filename = os.path.join(tempdir, "appended_mf_%dD.xdmf" % dim)
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 = 0
for vertex in Vertices(mesh):
diff += (vf_in[vertex] - vf[vertex])
for facet in Facets(mesh):
diff += (ff_in[facet] - ff[facet])
for cell in Cells(mesh):
diff += (cf_in[cell] - cf[cell])
assert diff == 0
def test_save_and_load_2d_mesh(tempdir, encoding):
filename = os.path.join(tempdir, "mesh_2D.xdmf")
mesh = UnitSquareMesh(MPI.comm_world, 32, 32)
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_points_3D(tempdir, encoding):
mesh = UnitCubeMesh(MPI.comm_world, 4, 4, 4)
points = mesh.geometry.points
vals = numpy.linalg.norm(points, axis=1)
with XDMFFile(mesh.mpi_comm(),
os.path.join(tempdir, "points_3D.xdmf"),
encoding=encoding) as file:
file.write(points)
with XDMFFile(mesh.mpi_comm(),
os.path.join(tempdir, "points_values_3D.xdmf"),
encoding=encoding) as file:
file.write(points, vals)
def test_append_and_load_mesh_value_collections(tempdir, encoding, data_type):
if invalid_config(encoding):
pytest.skip("XDMF unsupported in current configuration")
dtype_str, dtype = data_type
mesh = UnitCubeMesh(MPI.comm_world, 2, 2, 2)
mesh.init()
for d in range(mesh.geometry.dim + 1):
mesh.init_global(d)
mvc_v = MeshValueCollection(dtype_str, mesh, 0)
mvc_v.rename("vertices")
mvc_e = MeshValueCollection(dtype_str, mesh, 1)
mvc_e.rename("edges")
mvc_f = MeshValueCollection(dtype_str, mesh, 2)
mvc_f.rename("facets")
mvc_c = MeshValueCollection(dtype_str, mesh, 3)
mvc_c.rename("cells")
mvcs = [mvc_v, mvc_e, mvc_f, mvc_c]
filename = os.path.join(tempdir, "appended_mvcs.xdmf")
with XDMFFile(mesh.mpi_comm(), filename) as xdmf:
for mvc in mvcs:
for ent in MeshEntities(mesh, mvc.dim):
assert (mvc.set_value(ent.index(), dtype(ent.global_index())))
xdmf.write(mvc)
mvc_v_in = MeshValueCollection(dtype_str, mesh, 0)
mvc_e_in = MeshValueCollection(dtype_str, mesh, 1)
mvc_f_in = MeshValueCollection(dtype_str, mesh, 2)
mvc_c_in = MeshValueCollection(dtype_str, mesh, 3)
with XDMFFile(mesh.mpi_comm(), filename) as xdmf:
read_function = getattr(xdmf, "read_mvc_" + dtype_str)
mvc_v_in = read_function(mesh, "vertices")
mvc_e_in = read_function(mesh, "edges")
mvc_f_in = read_function(mesh, "facets")
mvc_c_in = read_function(mesh, "cells")
mvcs_in = [mvc_v_in, mvc_e_in, mvc_f_in, mvc_c_in]
for (mvc, mvc_in) in zip(mvcs, mvcs_in):
mf = MeshFunction(dtype_str, mesh, mvc, 0)
mf_in = MeshFunction(dtype_str, mesh, mvc_in, 0)
diff = 0
for ent in MeshEntities(mesh, mf.dim):
diff += (mf_in[ent] - mf[ent])
assert (diff == 0)
def test_save_and_load_1d_mesh(tempdir, encoding):
if invalid_config(encoding):
pytest.skip("XDMF unsupported in current configuration")
filename = os.path.join(tempdir, "mesh.xdmf")
mesh = UnitIntervalMesh(MPI.comm_world, 32)
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(MPI.comm_world, 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_read_write_p2_function(tempdir):
mesh = cpp.generation.UnitDiscMesh.create(MPI.comm_world, 3,
cpp.mesh.GhostMode.none)
cmap = fem.create_coordinate_map(mesh.ufl_domain())
mesh.geometry.coord_mapping = cmap
Q = FunctionSpace(mesh, ("Lagrange", 2))
F = Function(Q)
if has_petsc_complex:
@function.expression.numba_eval
def expr_eval(values, x, cell_idx):
values[:, 0] = x[:, 0] + 1.0j * x[:, 0]
F.interpolate(Expression(expr_eval))
else:
@function.expression.numba_eval
def expr_eval(values, x, cell_idx):
values[:, 0] = x[:, 0]
F.interpolate(Expression(expr_eval))
filename = os.path.join(tempdir, "tri6_function.xdmf")
with XDMFFile(mesh.mpi_comm(), filename,
encoding=XDMFFile.Encoding.HDF5) as xdmf:
xdmf.write(F)
Q = VectorFunctionSpace(mesh, ("Lagrange", 1))
F = Function(Q)
if has_petsc_complex:
@function.expression.numba_eval
def expr_eval(values, x, cell_idx):
values[:, 0] = x[:, 0] + 1.0j * x[:, 0]
values[:, 1] = x[:, 1] + 1.0j * x[:, 1]
F.interpolate(Expression(expr_eval, shape=(2, )))
else:
@function.expression.numba_eval
def expr_eval(values, x, cell_idx):
values[:, 0] = x[:, 0]
values[:, 1] = x[:, 1]
F.interpolate(Expression(expr_eval, shape=(2, )))
filename = os.path.join(tempdir, "tri6_vector_function.xdmf")
with XDMFFile(mesh.mpi_comm(), filename,
encoding=XDMFFile.Encoding.HDF5) as xdmf:
xdmf.write(F)
def test_read_write_p2_mesh(tempdir):
mesh = cpp.generation.UnitDiscMesh.create(MPI.comm_world, 3,
cpp.mesh.GhostMode.none)
filename = os.path.join(tempdir, "tri6_mesh.xdmf")
with XDMFFile(mesh.mpi_comm(), filename,
encoding=XDMFFile.Encoding.HDF5) as xdmf:
xdmf.write(mesh)
with XDMFFile(mesh.mpi_comm(), filename) as xdmf:
mesh2 = xdmf.read_mesh(mesh.mpi_comm(), cpp.mesh.GhostMode.none)
assert mesh2.num_entities_global(
mesh.topology.dim) == mesh.num_entities_global(mesh.topology.dim)
assert mesh2.num_entities_global(0) == mesh.num_entities_global(0)
def test_multiple_datasets(tempdir, encoding):
mesh = UnitSquareMesh(MPI.comm_world, 2, 2)
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_3D_cell_function(tempdir, encoding, data_type):
dtype_str, dtype = data_type
mesh = UnitCubeMesh(MPI.comm_world, 4, 4, 4)
mf = MeshFunction(dtype_str, mesh, mesh.topology.dim, 0)
mf.name = "cells"
mf.values[:] = numpy.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 numpy.all(diff == 0)
def test_save_1d_mesh(tempdir, encoding):
filename = os.path.join(tempdir, "mf_1D.xdmf")
mesh = UnitIntervalMesh(MPI.comm_world, 32)
mf = MeshFunction("size_t", mesh, mesh.topology.dim, 0)
mf.values[:] = numpy.arange(mesh.num_entities(1))
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as file:
file.write(mf)
def test_save_3d_tensor(tempdir, encoding):
filename = os.path.join(tempdir, "u3t.xdmf")
mesh = UnitCubeMesh(MPI.comm_world, 4, 4, 4)
u = Function(TensorFunctionSpace(mesh, ("Lagrange", 2)))
u.vector.set(1.0 + (1j if has_petsc_complex else 0))
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as file:
file.write(u)
def test_append_and_load_mesh_value_collections(tempdir, encoding, data_type):
dtype_str, dtype = data_type
mesh = UnitCubeMesh(MPI.comm_world, 2, 2, 2)
mesh.create_connectivity_all()
for d in range(mesh.geometry.dim + 1):
mesh.create_global_indices(d)
mvc_v = MeshValueCollection(dtype_str, mesh, 0)
mvc_v.name = "vertices"
mvc_e = MeshValueCollection(dtype_str, mesh, 1)
mvc_e.name = "edges"
mvc_f = MeshValueCollection(dtype_str, mesh, 2)
mvc_f.name = "facets"
mvc_c = MeshValueCollection(dtype_str, mesh, 3)
mvc_c.name = "cells"
mvcs = [mvc_v, mvc_e, mvc_f, mvc_c]
filename = os.path.join(tempdir, "appended_mvcs.xdmf")
with XDMFFile(mesh.mpi_comm(), filename) as xdmf:
for mvc in mvcs:
global_indices = mesh.topology.global_indices(mvc.dim)
for ent in range(mesh.num_entities(mvc.dim)):
assert (mvc.set_value(ent, global_indices[ent]))
xdmf.write(mvc)
mvc_v_in = MeshValueCollection(dtype_str, mesh, 0)
mvc_e_in = MeshValueCollection(dtype_str, mesh, 1)
mvc_f_in = MeshValueCollection(dtype_str, mesh, 2)
mvc_c_in = MeshValueCollection(dtype_str, mesh, 3)
with XDMFFile(mesh.mpi_comm(), filename) as xdmf:
read_function = getattr(xdmf, "read_mvc_" + dtype_str)
mvc_v_in = read_function(mesh, "vertices")
mvc_e_in = read_function(mesh, "edges")
mvc_f_in = read_function(mesh, "facets")
mvc_c_in = read_function(mesh, "cells")
mvcs_in = [mvc_v_in, mvc_e_in, mvc_f_in, mvc_c_in]
for (mvc, mvc_in) in zip(mvcs, mvcs_in):
mf = MeshFunction(dtype_str, mesh, mvc, 0)
mf_in = MeshFunction(dtype_str, mesh, mvc_in, 0)
diff = mf_in.values - mf.values
assert numpy.all(diff == 0)
def test_save_3D_vertex_function(tempdir, encoding, data_type):
dtype_str, dtype = data_type
filename = os.path.join(tempdir, "mf_vertex_3D_%s.xdmf" % dtype_str)
mesh = UnitCubeMesh(MPI.comm_world, 4, 4, 4)
mf = MeshFunction(dtype_str, mesh, 0, 0)
mf.values[:] = numpy.arange(mesh.num_entities(0), dtype=dtype)
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as file:
file.write(mf)
def test_save_2D_vertex_function(tempdir, encoding, data_type):
dtype_str, dtype = data_type
mesh = UnitSquareMesh(MPI.comm_world, 32, 32)
mf = MeshFunction(dtype_str, mesh, 0, 0)
mf.name = "vertices"
global_indices = mesh.topology.global_indices(0)
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 numpy.all(diff == 0)
def test_save_2d_vector(tempdir, encoding):
filename = os.path.join(tempdir, "u_2dv.xdmf")
mesh = UnitSquareMesh(MPI.comm_world, 16, 16)
V = VectorFunctionSpace(mesh, ("Lagrange", 2))
u = Function(V)
u.vector.set(1.0 + (1j if has_petsc_complex else 0))
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as file:
file.write(u)
