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_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_mesh_function_assign_2D_cells():
mesh = UnitSquareMesh(MPI.comm_world, 3, 3)
ncells = mesh.num_cells()
f = MeshFunction("int", mesh, mesh.topology.dim, 0)
for c in range(ncells):
f.values[c] = ncells - c
g = MeshValueCollection("int", mesh, 2)
g.assign(f)
assert ncells == len(f.values)
assert ncells == g.size()
f2 = MeshFunction("int", mesh, g, 0)
for c in range(mesh.num_cells()):
value = ncells - c
assert value == g.get_value(c, 0)
assert f2.values[c] == g.get_value(c, 0)
h = MeshValueCollection("int", mesh, 2)
global_indices = mesh.topology.global_indices(2)
ncells_global = mesh.num_entities_global(2)
for c in range(mesh.num_cells()):
if global_indices[c] in [5, 8, 10]:
continue
value = ncells_global - global_indices[c]
h.set_value(c, int(value))
f3 = MeshFunction("int", mesh, h, 0)
values = f3.values
values[values > ncells_global] = 0.
assert MPI.sum(mesh.mpi_comm(), values.sum() * 1.0) == 140.
def test_mesh_function_assign_2D_cells():
mesh = UnitSquareMesh(MPI.comm_world, 3, 3)
ncells = mesh.num_cells()
f = MeshFunction("int", mesh, mesh.topology.dim, 0)
for cell in Cells(mesh):
f[cell] = ncells - cell.index()
g = MeshValueCollection("int", mesh, 2)
g.assign(f)
assert ncells == f.size()
assert ncells == g.size()
f2 = MeshFunction("int", mesh, g, 0)
for cell in Cells(mesh):
value = ncells - cell.index()
assert value == g.get_value(cell.index(), 0)
assert f2[cell] == g.get_value(cell.index(), 0)
h = MeshValueCollection("int", mesh, 2)
global_indices = mesh.topology.global_indices(2)
ncells_global = mesh.num_entities_global(2)
for cell in Cells(mesh):
if global_indices[cell.index()] in [5, 8, 10]:
continue
value = ncells_global - global_indices[cell.index()]
h.set_value(cell.index(), int(value))
f3 = MeshFunction("int", mesh, h, 0)
values = f3.array()
values[values > ncells_global] = 0.
assert MPI.sum(mesh.mpi_comm(), values.sum() * 1.0) == 140.
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_read_mesh_value_collection(tempdir):
ndiv = 2
filename = os.path.join(tempdir, "mesh_value_collection.h5")
mesh = UnitCubeMesh(MPI.comm_world, ndiv, ndiv, ndiv)
# 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)
mp = cpp.mesh.midpoints(mesh, dim, range(mesh.num_entities(dim)))
for e in range(mesh.num_entities(dim)):
# this can be easily computed to the check the value
val = int(ndiv * mp[e].sum()) + 1
mvc.set_value(e, 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))
mp = cpp.mesh.midpoints(mesh, dim, range(mesh.num_entities(dim)))
# check the values
for (cell, lidx), val in mvc.values().items():
eidx = MeshEntity(mesh, mesh.topology.dim,
cell).entities(dim)[lidx]
mid = mp[eidx]
assert val == int(ndiv * mid.sum()) + 1
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_assign_2D_cells():
mesh = UnitSquareMesh(MPI.comm_world, 3, 3)
ncells = mesh.num_cells()
f = MeshValueCollection("int", mesh, 2)
all_new = True
for c in range(ncells):
value = ncells - c
all_new = all_new and f.set_value(c, value)
g = MeshValueCollection("int", mesh, 2)
g.assign(f)
assert ncells == f.size()
assert ncells == g.size()
assert all_new
for c in range(ncells):
value = ncells - c
assert value, g.get_value(c == 0)
old_value = g.get_value(0, 0)
g.set_value(0, 0, old_value + 1)
assert old_value + 1 == g.get_value(0, 0)
def test_assign_2D_vertices():
mesh = UnitSquareMesh(MPI.comm_world, 3, 3)
mesh.create_connectivity(2, 0)
ncells = mesh.num_cells()
f = MeshValueCollection("int", mesh, 0)
all_new = True
for cell in Cells(mesh):
value = ncells - cell.index()
for i, vert in enumerate(VertexRange(cell)):
all_new = all_new and f.set_value(cell.index(), i, value + i)
g = MeshValueCollection("int", mesh, 0)
g.assign(f)
assert ncells * 3 == f.size()
assert ncells * 3 == g.size()
assert all_new
for cell in Cells(mesh):
value = ncells - cell.index()
for i, vert in enumerate(VertexRange(cell)):
assert value + i == g.get_value(cell.index(), i)
def test_assign_2D_facets():
mesh = UnitSquareMesh(MPI.comm_world, 3, 3)
mesh.init(2, 1)
ncells = mesh.num_cells()
f = MeshValueCollection("int", mesh, 1)
all_new = True
for cell in Cells(mesh):
value = ncells - cell.index()
for i, facet in enumerate(FacetRange(cell)):
all_new = all_new and f.set_value(cell.index(), i, value + i)
g = MeshValueCollection("int", mesh, 1)
g.assign(f)
assert ncells * 3 == f.size()
assert ncells * 3 == g.size()
assert all_new
for cell in Cells(mesh):
value = ncells - cell.index()
for i, facet in enumerate(FacetRange(cell)):
assert value + i == g.get_value(cell.index(), i)
def test_assign_2D_vertices():
mesh = UnitSquareMesh(MPI.comm_world, 3, 3)
mesh.create_connectivity(2, 0)
ncells = mesh.num_cells()
num_cell_vertices = cpp.mesh.cell_num_vertices(mesh.cell_type)
f = MeshValueCollection("int", mesh, 0)
all_new = True
for c in range(ncells):
value = ncells - c
for i in range(num_cell_vertices):
all_new = all_new and f.set_value(c, i, value + i)
g = MeshValueCollection("int", mesh, 0)
g.assign(f)
assert ncells * 3 == f.size()
assert ncells * 3 == g.size()
assert all_new
for c in range(ncells):
value = ncells - c
for i in range(num_cell_vertices):
assert value + i == g.get_value(c, i)
def test_assign_2D_facets():
mesh = UnitSquareMesh(MPI.comm_world, 3, 3)
mesh.create_connectivity(2, 1)
tdim = mesh.topology.dim
num_cell_facets = cpp.mesh.cell_num_entities(mesh.cell_type, tdim - 1)
ncells = mesh.num_cells()
f = MeshValueCollection("int", mesh, 1)
all_new = True
for c in range(ncells):
value = ncells - c
for i in range(num_cell_facets):
all_new = all_new and f.set_value(c, i, value + i)
g = MeshValueCollection("int", mesh, 1)
g.assign(f)
assert ncells * 3 == f.size()
assert ncells * 3 == g.size()
assert all_new
for c in range(ncells):
value = ncells - c
for i in range(num_cell_facets):
assert value + i == g.get_value(c, i)