def test_compute_entity_collisions_tree_3d():
references = [[
set([18, 19, 20, 21, 22, 23, 42, 43, 44, 45, 46, 47]),
set([0, 1, 2, 3, 4, 5, 24, 25, 26, 27, 28, 29])
], [set([7, 8, 30, 31, 32]),
set([15, 16, 17, 39, 41])]]
points = [Point(0.52, 0.51, 0.3), Point(0.9, -0.9, 0.3)]
for i, point in enumerate(points):
mesh_A = UnitCubeMesh(MPI.comm_world, 2, 2, 2)
mesh_B = UnitCubeMesh(MPI.comm_world, 2, 2, 2)
bgeom = mesh_B.geometry.points
bgeom += point.array()
tree_A = BoundingBoxTree(3)
tree_A.build_mesh(mesh_A, 3)
tree_B = BoundingBoxTree(3)
tree_B.build_mesh(mesh_B, 3)
entities_A, entities_B = tree_A.compute_entity_collisions_bb_mesh(
tree_B, mesh_A, mesh_B)
assert set(entities_A) == references[i][0]
assert set(entities_B) == references[i][1]
def test_compute_entity_collisions_tree_3d():
references = [[set([18, 19, 20, 21, 22, 23, 42, 43, 44, 45, 46, 47]),
set([0, 1, 2, 3, 4, 5, 24, 25, 26, 27, 28, 29])],
[set([7, 8, 30, 31, 32]),
set([15, 16, 17, 39, 41])]]
points = [Point(0.52, 0.51, 0.3), Point(0.9, -0.9, 0.3)]
for i, point in enumerate(points):
mesh_A = UnitCubeMesh(2, 2, 2)
mesh_B = UnitCubeMesh(2, 2, 2)
mesh_B.translate(point)
tree_A = BoundingBoxTree()
tree_A.build(mesh_A)
tree_B = BoundingBoxTree()
tree_B.build(mesh_B)
entities_A, entities_B = tree_A.compute_entity_collisions(tree_B)
assert set(entities_A) == references[i][0]
assert set(entities_B) == references[i][1]
def test_meshpool_base_functionality(dim):
if dim == 2:
mesh1 = UnitSquareMesh(6, 6)
mesh2 = UnitSquareMesh(6, 6)
mesh3 = UnitSquareMesh(6, 6)
mesh4 = UnitSquareMesh(7, 7)
elif dim == 3:
mesh1 = UnitCubeMesh(6, 6, 6)
mesh2 = UnitCubeMesh(6, 6, 6)
mesh3 = UnitCubeMesh(6, 6, 6)
mesh4 = UnitCubeMesh(7, 7, 7)
mp = argmin(norm(mesh3.coordinates() - array([0.5] * dim), axis=1))
mesh3.coordinates()[mp, :] += 0.00001
mesh1 = MeshPool(mesh1)
mesh2 = MeshPool(mesh2)
mesh3 = MeshPool(mesh3)
mesh4 = MeshPool(mesh4)
assert mesh1.id() == mesh2.id(), "1!=2"
assert mesh1.id() != mesh3.id(), "1==3"
assert mesh1.id() != mesh4.id(), "1==4"
assert mesh3.id() != mesh4.id(), "3==4"
# FIXME: While weak referencing meshes don't work, we can not run the following tests
"""
def test_taylor_hood_cube():
pytest.xfail("Problem with Mixed Function Spaces")
meshc = UnitCubeMesh(MPI.comm_world, 2, 2, 2)
meshf = UnitCubeMesh(MPI.comm_world, 3, 4, 5)
Ve = VectorElement("CG", meshc.ufl_cell(), 2)
Qe = FiniteElement("CG", meshc.ufl_cell(), 1)
Ze = MixedElement([Ve, Qe])
Zc = FunctionSpace(meshc, Ze)
Zf = FunctionSpace(meshf, Ze)
def z(values, x):
values[:, 0] = x[:, 0] * x[:, 1]
values[:, 1] = x[:, 1] * x[:, 2]
values[:, 2] = x[:, 2] * x[:, 0]
values[:, 3] = x[:, 0] + 3.0 * x[:, 1] + x[:, 2]
zc = interpolate(z, Zc)
zf = interpolate(z, Zf)
mat = PETScDMCollection.create_transfer_matrix(Zc, Zf)
Zuc = Function(Zf)
mat.mult(zc.vector, Zuc.vector)
Zuc.vector.update_ghost_values()
diff = Function(Zf)
diff.assign(Zuc - zf)
assert diff.vector.norm("l2") < 1.0e-12
def test_vector_p1_3d():
meshc = UnitCubeMesh(MPI.comm_world, 2, 3, 4)
meshf = UnitCubeMesh(MPI.comm_world, 3, 4, 5)
Vc = VectorFunctionSpace(meshc, ("CG", 1))
Vf = VectorFunctionSpace(meshf, ("CG", 1))
def u(x):
values0 = x[:, 0] + 2.0 * x[:, 1]
values1 = 4.0 * x[:, 0]
values2 = 3.0 * x[:, 2] + x[:, 0]
return np.stack([values0, values1, values2], axis=1)
uc, uf = Function(Vc), Function(Vf)
uc.interpolate(u)
uf.interpolate(u)
mat = PETScDMCollection.create_transfer_matrix(Vc._cpp_object,
Vf._cpp_object)
Vuc = Function(Vf)
mat.mult(uc.vector, Vuc.vector)
diff = Vuc.vector
diff.axpy(-1, uf.vector)
assert diff.norm() < 1.0e-12
def test_compute_collisions_tree_3d():
references = [[
set([18, 19, 20, 21, 22, 23, 42, 43, 44, 45, 46, 47]),
set([0, 1, 2, 3, 4, 5, 24, 25, 26, 27, 28, 29])
],
[
set([6, 7, 8, 9, 10, 11, 30, 31, 32, 33, 34, 35]),
set([12, 13, 14, 15, 16, 17, 36, 37, 38, 39, 40, 41])
]]
points = [numpy.array([0.52, 0.51, 0.3]), numpy.array([0.9, -0.9, 0.3])]
for i, point in enumerate(points):
mesh_A = UnitCubeMesh(MPI.comm_world, 2, 2, 2)
mesh_B = UnitCubeMesh(MPI.comm_world, 2, 2, 2)
bgeom = mesh_B.geometry.points
bgeom += point
tree_A = BoundingBoxTree(mesh_A, mesh_A.topology.dim)
tree_B = BoundingBoxTree(mesh_B, mesh_B.topology.dim)
entities_A, entities_B = tree_A.compute_collisions_bb(tree_B)
assert set(entities_A) == references[i][0]
assert set(entities_B) == references[i][1]
def test_taylor_hood_cube():
pytest.xfail("Problem with Mixed Function Spaces")
meshc = UnitCubeMesh(MPI.comm_world, 2, 2, 2)
meshf = UnitCubeMesh(MPI.comm_world, 3, 4, 5)
Ve = VectorElement("CG", meshc.ufl_cell(), 2)
Qe = FiniteElement("CG", meshc.ufl_cell(), 1)
Ze = MixedElement([Ve, Qe])
Zc = FunctionSpace(meshc, Ze)
Zf = FunctionSpace(meshf, Ze)
z = Expression(
("x[0]*x[1]", "x[1]*x[2]", "x[2]*x[0]", "x[0] + 3*x[1] + x[2]"),
degree=2)
zc = interpolate(z, Zc)
zf = interpolate(z, Zf)
mat = PETScDMCollection.create_transfer_matrix(Zc, Zf)
Zuc = Function(Zf)
mat.mult(zc.vector(), Zuc.vector())
Zuc.vector().update_ghost_values()
diff = Function(Zf)
diff.assign(Zuc - zf)
assert diff.vector().norm("l2") < 1.0e-12
def test_compute_collisions_tree_3d(self):
references = [[set([18, 19, 20, 21, 22, 23, 42, 43, 44, 45, 46, 47]),
set([0, 1, 2, 3, 4, 5, 24, 25, 26, 27, 28, 29])],
[set([6, 7, 8, 9, 10, 11, 30, 31, 32, 33, 34, 35]),
set([12, 13, 14, 15, 16, 17, 36, 37, 38, 39, 40, 41])]]
points = [Point(0.52, 0.51, 0.3), Point(0.9, -0.9, 0.3)]
for i, point in enumerate(points):
mesh_A = UnitCubeMesh(2, 2, 2)
mesh_B = UnitCubeMesh(2, 2, 2)
mesh_B.translate(point)
tree_A = BoundingBoxTree()
tree_A.build(mesh_A)
tree_B = BoundingBoxTree()
tree_B.build(mesh_B)
entities_A, entities_B = tree_A.compute_collisions(tree_B)
if MPI.size(mesh_A.mpi_comm()) == 1:
self.assertEqual(set(entities_A), references[i][0])
self.assertEqual(set(entities_B), references[i][1])
def test_vector_p1_3d():
meshc = UnitCubeMesh(MPI.comm_world, 2, 3, 4)
meshf = UnitCubeMesh(MPI.comm_world, 3, 4, 5)
Vc = VectorFunctionSpace(meshc, ("CG", 1))
Vf = VectorFunctionSpace(meshf, ("CG", 1))
@function.expression.numba_eval
def expr_eval(values, x, cell_idx):
values[:, 0] = x[:, 0] + 2.0 * x[:, 1]
values[:, 1] = 4.0 * x[:, 0]
values[:, 2] = 3.0 * x[:, 2] + x[:, 0]
u = Expression(expr_eval, shape=(3, ))
uc = interpolate(u, Vc)
uf = interpolate(u, Vf)
mat = PETScDMCollection.create_transfer_matrix(Vc._cpp_object,
Vf._cpp_object)
Vuc = Function(Vf)
mat.mult(uc.vector(), Vuc.vector())
diff = Vuc.vector()
diff.axpy(-1, uf.vector())
assert diff.norm() < 1.0e-12
def test_scalar_p1_scaled_mesh():
# Make coarse mesh smaller than fine mesh
meshc = UnitCubeMesh(MPI.comm_world, 2, 2, 2)
meshc.geometry.points *= 0.9
meshf = UnitCubeMesh(MPI.comm_world, 3, 4, 5)
Vc = FunctionSpace(meshc, "CG", 1)
Vf = FunctionSpace(meshf, "CG", 1)
u = Expression("x[0] + 2*x[1] + 3*x[2]", degree=1)
uc = interpolate(u, Vc)
uf = interpolate(u, Vf)
mat = PETScDMCollection.create_transfer_matrix(Vc, Vf).mat()
Vuc = Function(Vf)
mat.mult(uc.vector().vec(), Vuc.vector().vec())
diff = Vuc.vector()
diff.vec().axpy(-1, uf.vector().vec())
assert diff.norm(Norm.l2) < 1.0e-12
# Now make coarse mesh larger than fine mesh
meshc.geometry.points *= 1.5
uc = interpolate(u, Vc)
mat = PETScDMCollection.create_transfer_matrix(Vc, Vf).mat()
mat.mult(uc.vector().vec(), Vuc.vector().vec())
diff = Vuc.vector()
diff.vec().axpy(-1, uf.vector().vec())
assert diff.norm(Norm.l2) < 1.0e-12
def test_compute_entity_collisions_3d():
reference = set([876, 877, 878, 879, 880, 881])
p = numpy.array([0.3, 0.3, 0.3])
mesh = UnitCubeMesh(MPI.comm_world, 8, 8, 8)
tree = BoundingBoxTree(mesh, mesh.topology.dim)
entities = tree.compute_entity_collisions_mesh(p, mesh)
assert set(entities) == reference
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_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_facet_iterators():
"""Iterate over facets"""
mesh = UnitCubeMesh(MPI.comm_world, 5, 5, 5)
n = 0
for f in Facets(mesh):
n += 1
assert n == mesh.num_entities(mesh.topology.dim - 1)
def test_radius_ratio_tetrahedron():
# Create mesh and compute ratios
mesh = UnitCubeMesh(MPI.comm_world, 14, 14, 14)
ratios = MeshQuality.radius_ratios(mesh)
for c in Cells(mesh):
assert round(ratios[c] - 0.717438935214, 7) == 0
def test_facet_iterators():
"Iterate over facets"
mesh = UnitCubeMesh(MPI.comm_world, 5, 5, 5)
n = 0
for f in Facets(mesh):
n += 1
assert n == mesh.num_facets()
def test_face_iterator():
"Iterate over faces"
mesh = UnitCubeMesh(MPI.comm_world, 5, 5, 5)
for i in range(4):
mesh.init(2, i)
# Test connectivity
cons = [(i, mesh.topology.connectivity(2, i)) for i in range(4)]
# Test writability
for i, con in cons:
def assign(con, i):
con(i)[0] = 1
with pytest.raises(Exception):
assign(con, i)
n = 0
for i, f in enumerate(Faces(mesh)):
n += 1
for j, con in cons:
assert numpy.all(con(i) == f.entities(j))
assert n == mesh.num_entities(2)
def imgseq2funvec(img: np.array) -> np.array:
"""Takes a 3D array and returns an array suited to assign to piecewise
linear approximation on a triangle grid.
Each pixel corresponds to one vertex of a triangle mesh.
Args:
img (np.array): The input array.
Returns:
np.array: A vector.
"""
# Create mesh.
[m, n, o] = img.shape
mesh = UnitCubeMesh(m-1, n-1, o-1)
mc = mesh.coordinates().reshape((-1, 3))
# Evaluate function at vertices.
hx, hy, hz = 1./(m-1), 1./(n-1), 1./(o-1)
x = np.array(np.round(mc[:, 0]/hx), dtype=int)
y = np.array(np.round(mc[:, 1]/hy), dtype=int)
z = np.array(np.round(mc[:, 2]/hz), dtype=int)
fv = img[x, y, z]
# Create function space.
V = FunctionSpace(mesh, 'CG', 1)
# Map pixel values to vertices.
d2v = dof_to_vertex_map(V)
return fv[d2v]
def test_compute_first_entity_collision_3d():
reference = [876, 877, 878, 879, 880, 881]
p = numpy.array([0.3, 0.3, 0.3])
mesh = UnitCubeMesh(MPI.comm_world, 8, 8, 8)
tree = BoundingBoxTree(mesh, mesh.topology.dim)
first = tree.compute_first_entity_collision(p, mesh)
assert first in reference
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_radius_ratio_min_radius_ratio_max():
mesh1d = UnitIntervalMesh(MPI.comm_self, 4)
x = mesh1d.geometry.points
x[4] = mesh1d.geometry.points[3]
# Create 2D mesh with one equilateral triangle
mesh2d = RectangleMesh(
MPI.comm_world,
[numpy.array([0.0, 0.0, 0.0]),
numpy.array([1.0, 1.0, 0.0])], [1, 1], CellType.Type.triangle,
cpp.mesh.GhostMode.none, 'left')
x = mesh2d.geometry.points
x[3, :2] += 0.5 * (sqrt(3.0) - 1.0)
# Create 3D mesh with regular tetrahedron and degenerate cells
mesh3d = UnitCubeMesh(MPI.comm_self, 1, 1, 1)
x = mesh3d.geometry.points
x[6][0] = 1.0
x[3][1] = 0.0
rmin, rmax = MeshQuality.radius_ratio_min_max(mesh1d)
assert round(rmin - 0.0, 7) == 0
assert round(rmax - 1.0, 7) == 0
rmin, rmax = MeshQuality.radius_ratio_min_max(mesh2d)
assert round(rmin - 2.0 * sqrt(2.0) / (2.0 + sqrt(2.0)), 7) == 0
assert round(rmax - 1.0, 7) == 0
rmin, rmax = MeshQuality.radius_ratio_min_max(mesh3d)
assert round(rmin - 0.0, 7) == 0
assert round(rmax - 1.0, 7) == 0
def test_UnitCubeMeshDistributed():
"""Create mesh of unit cube."""
mesh = UnitCubeMesh(MPI.comm_world, 5, 7, 9)
assert mesh.num_entities_global(0) == 480
assert mesh.num_entities_global(3) == 1890
assert mesh.geometry.dim == 3
assert MPI.sum(mesh.mpi_comm(), mesh.topology.ghost_offset(0)) == 480
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 mesh_factory(tdim, n):
if tdim == 1:
return UnitIntervalMesh(MPI.comm_world, n)
elif tdim == 2:
return UnitSquareMesh(MPI.comm_world, n, n)
elif tdim == 3:
return UnitCubeMesh(MPI.comm_world, n, n, n)
def test_edge_iterators():
"""Iterate over edges"""
mesh = UnitCubeMesh(MPI.comm_world, 5, 5, 5)
for i in range(4):
mesh.create_connectivity(1, i)
connectivities = [(i, mesh.topology.connectivity(1, i)) for i in range(4)]
# Test writability
for i, connectivity in connectivities:
def assign(con, i):
connectivity.connections(i)[0] = 1
with pytest.raises(Exception):
assign(connectivity, i)
n = 0
for i, e in enumerate(Edges(mesh)):
n += 1
for j, connectivity in connectivities:
assert numpy.all(connectivity.connections(i) == e.entities(j))
assert n == mesh.num_entities(1)
def mk_scheme(N, Vname, Vorder, cpp_expr, expr_args, convection_inp, dim=2, comm=None):
if comm is None:
comm = MPI.comm_world
parameters['ghost_mode'] = 'shared_vertex'
if dim == 2:
mesh = UnitSquareMesh(comm, N, N)
else:
mesh = UnitCubeMesh(comm, N, N, N)
V = FunctionSpace(mesh, Vname, Vorder)
C = Function(V)
e = Expression(cpp_expr, element=V.ufl_element(), **expr_args)
C.interpolate(e)
D = Function(V)
D.assign(C)
sim = Simulation()
sim.set_mesh(mesh)
sim.data['constrained_domain'] = None
sim.data['C'] = C
for key, value in convection_inp.items():
sim.input.set_value('convection/C/%s' % key, value)
scheme_name = convection_inp['convection_scheme']
return get_convection_scheme(scheme_name)(sim, 'C')
def test_compute_first_collision_3d():
# FIXME: This test should not use facet indices as there are no guarantees
# on how DOLFIN numbers facets
reference = {
1: [1364],
2: [1967, 1968, 1970, 1972, 1974, 1976],
3: [876, 877, 878, 879, 880, 881]
}
p = Point(0.3, 0.3, 0.3)
mesh = UnitCubeMesh(MPI.comm_world, 8, 8, 8)
for dim in range(1, 4):
tree = BoundingBoxTree(mesh.geometry.dim)
tree.build_mesh(mesh, dim)
first = tree.compute_first_collision(p)
# FIXME: Face and test is excluded because it mistakingly
# relies in the facet indices
tdim = mesh.topology.dim
if dim != tdim - 1 and dim != tdim - 2:
assert first in reference[dim]
# FIXME: remove after Mesh is wrapped in Python
tree_cpp = mesh.bounding_box_tree()
tree = BoundingBoxTree()
tree._cpp_object = tree_cpp
first = tree.compute_first_collision(p)
assert first in reference[mesh.topology.dim]
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_compute_first_collision_3d():
# FIXME: This test should not use facet indices as there are no guarantees
# on how DOLFIN numbers facets
reference = {
1: [1364],
2: [1967, 1968, 1970, 1972, 1974, 1976],
3: [876, 877, 878, 879, 880, 881]
}
p = Point(0.3, 0.3, 0.3)
mesh = UnitCubeMesh(8, 8, 8)
for dim in range(1, 4):
tree = BoundingBoxTree()
tree.build(mesh, dim)
first = tree.compute_first_collision(p)
# FIXME: Face and test is excluded because it mistakingly
# relies in the facet indices
tdim = mesh.topology().dim()
if dim != tdim - 1 and dim != tdim - 2:
assert first in reference[dim]
tree = mesh.bounding_box_tree()
first = tree.compute_first_collision(p)
assert first in reference[mesh.topology().dim()]