def test_save_and_read_meshfunction_3D(tempdir):
filename = os.path.join(tempdir, "meshfn-3d.h5")
# Write to file
mesh = UnitCubeMesh(MPI.comm_world, 2, 2, 2)
mf_file = HDF5File(mesh.mpi_comm(), filename, "w")
# save meshfuns to compare when reading back
meshfunctions = []
for i in range(0, 4):
mf = MeshFunction('double', mesh, i, 0.0)
# NB choose a value to set which will be the same
# on every process for each entity
for cell in MeshEntities(mesh, i):
mf[cell] = cell.midpoint()[0]
meshfunctions.append(mf)
mf_file.write(mf, "/meshfunction/group/%d/meshfun" % i)
mf_file.close()
# Read back from file
mf_file = HDF5File(mesh.mpi_comm(), filename, "r")
for i in range(0, 4):
mf2 = mf_file.read_mf_double(mesh,
"/meshfunction/group/%d/meshfun" % i)
for cell in MeshEntities(mesh, i):
assert meshfunctions[i][cell] == mf2[cell]
mf_file.close()
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_read_mesh_value_collection(tempdir):
ndiv = 2
filename = os.path.join(tempdir, "mesh_value_collection.h5")
mesh = UnitCubeMesh(MPI.comm_world, ndiv, ndiv, ndiv)
def point2list(p):
return [p[0], p[1], p[2]]
# write to file
with HDF5File(mesh.mpi_comm(), filename, 'w') as f:
for dim in range(mesh.topology.dim):
mvc = MeshValueCollection("size_t", mesh, dim)
mesh.create_entities(dim)
for e in MeshEntities(mesh, dim):
# this can be easily computed to the check the value
val = int(ndiv * sum(point2list(e.midpoint()))) + 1
mvc.set_value(e.index(), val)
f.write(mvc, "/mesh_value_collection_{}".format(dim))
# read from file
with HDF5File(mesh.mpi_comm(), filename, 'r') as f:
for dim in range(mesh.topology.dim):
mvc = f.read_mvc_size_t(mesh,
"/mesh_value_collection_{}".format(dim))
# check the values
for (cell, lidx), val in mvc.values().items():
eidx = Cell(mesh, cell).entities(dim)[lidx]
mid = point2list(MeshEntity(mesh, dim, eidx).midpoint())
assert val == int(ndiv * sum(mid)) + 1
def test_shared_entities(mesh_factory):
func, args = mesh_factory
# xfail_ghosted_quads_hexes(func, ghost_mode)
mesh = func(*args)
dim = mesh.topology.dim
# FIXME: Implement a proper test
for shared_dim in range(dim + 1):
# Initialise global indices (if not already)
mesh.init_global(shared_dim)
assert isinstance(mesh.topology.shared_entities(shared_dim), dict)
assert isinstance(mesh.topology.global_indices(shared_dim),
numpy.ndarray)
if mesh.topology.have_shared_entities(shared_dim):
for e in MeshEntities(mesh, shared_dim):
sharing = e.sharing_processes()
assert isinstance(sharing, set)
assert (len(sharing) > 0) == e.is_shared()
shared_entities = mesh.topology.shared_entities(shared_dim)
# Check that sum(local-shared) = global count
rank = MPI.rank(mesh.mpi_comm())
ct = sum(1 for val in shared_entities.values() if list(val)[0] < rank)
num_entities_global = MPI.sum(mesh.mpi_comm(),
mesh.num_entities(shared_dim) - ct)
assert num_entities_global == mesh.num_entities_global(shared_dim)
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)