def test_mesh_function_assign_2D_facets():
mesh = UnitSquareMesh(MPI.comm_world, 3, 3)
mesh.create_entities(1)
tdim = mesh.topology.dim
num_cell_facets = cpp.mesh.cell_num_entities(mesh.cell_type, tdim - 1)
f = MeshFunction("int", mesh, tdim - 1, 25)
connectivity = mesh.topology.connectivity(tdim, tdim - 1)
for c in range(mesh.num_cells()):
facets = connectivity.connections(c)
for i in range(num_cell_facets):
assert 25 == f.values[facets[i]]
g = MeshValueCollection("int", mesh, 1)
g.assign(f)
assert mesh.num_entities(tdim - 1) == len(f.values)
assert mesh.num_cells() * 3 == g.size()
for c in range(mesh.num_cells()):
for i in range(num_cell_facets):
assert 25 == g.get_value(c, i)
f2 = MeshFunction("int", mesh, g, 0)
connectivity = mesh.topology.connectivity(tdim, tdim - 1)
for c in range(mesh.num_cells()):
facets = connectivity.connections(c)
for i in range(num_cell_facets):
assert f2.values[facets[i]] == g.get_value(c, i)
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_failsafe_sweep():
interpolate_expression = Expression('x[0]', degree=1)
mesh = UnitSquareMesh(5, 5)
V = FunctionSpace(mesh, "DG", 1)
v = Function(V)
v.assign(interpolate_expression)
np_min, np_max = 1, 2
np_failsafe = 4
# Initialize particles
x = RandomRectangle(Point(0.0, 0.0), Point(1., 1.)).generate([100, 100])
s = assign_particle_values(x, interpolate_expression)
# Broadcast to other procs
x = comm.bcast(x, root=0)
s = comm.bcast(s, root=0)
property_idx = 1
p = particles(x, [s], mesh)
AD = AddDelete(p, np_min, np_max, [v])
AD.do_sweep_failsafe(np_failsafe)
# Must recover linear
lstsq_rho = l2projection(p, V, property_idx)
lstsq_rho.project(v.cpp_object())
error = sqrt(
assemble(
(v - interpolate_expression) * (v - interpolate_expression) * dx))
assert len(p.positions() == mesh.num_cells() * np_failsafe)
assert error < 1e-12
def test_ghost_connectivities(mode):
# Ghosted mesh
meshG = UnitSquareMesh(MPI.comm_world, 4, 4, ghost_mode=mode)
meshG.create_connectivity(1, 2)
# Reference mesh, not ghosted, not parallel
meshR = UnitSquareMesh(MPI.comm_self, 4, 4, ghost_mode=cpp.mesh.GhostMode.none)
meshR.create_connectivity(1, 2)
tdim = meshR.topology.dim
# Create reference mapping from facet midpoint to cell midpoint
reference = {}
facet_mp = cpp.mesh.midpoints(meshR, tdim - 1, range(meshR.num_entities(tdim - 1)))
cell_mp = cpp.mesh.midpoints(meshR, tdim, range(meshR.num_entities(tdim)))
reference = dict.fromkeys([tuple(row) for row in facet_mp], [])
for i in range(meshR.num_entities(tdim - 1)):
for cidx in meshR.topology.connectivity(1, 2).connections(i):
reference[tuple(facet_mp[i])].append(cell_mp[cidx].tolist())
# Loop through ghosted mesh and check connectivities
tdim = meshG.topology.dim
num_facets = meshG.num_entities(tdim - 1) - meshG.topology.ghost_offset(tdim - 1)
allowable_cell_indices = range(meshG.num_cells())
facet_mp = cpp.mesh.midpoints(meshG, tdim - 1, range(meshG.num_entities(tdim - 1)))
cell_mp = cpp.mesh.midpoints(meshG, tdim, range(meshG.num_entities(tdim)))
for i in range(num_facets):
assert tuple(facet_mp[i]) in reference
for cidx in meshG.topology.connectivity(1, 2).connections(i):
assert cidx in allowable_cell_indices
assert cell_mp[cidx].tolist() in reference[tuple(facet_mp[i])]
def test_save_and_read_mesh_2D(tempdir):
filename = os.path.join(tempdir, "mesh2d.h5")
# Write to file
mesh0 = UnitSquareMesh(MPI.comm_world, 20, 20)
mesh_file = HDF5File(mesh0.mpi_comm(), filename, "w")
mesh_file.write(mesh0, "/my_mesh")
mesh_file.close()
# Read from file
mesh_file = HDF5File(mesh0.mpi_comm(), filename, "r")
mesh1 = mesh_file.read_mesh("/my_mesh", False, cpp.mesh.GhostMode.none)
mesh_file.close()
assert mesh0.num_entities_global(0) == mesh1.num_entities_global(0)
dim = mesh0.topology.dim
assert mesh0.num_entities_global(dim) == mesh1.num_entities_global(dim)
# Read from file, and use partition from file
mesh_file = HDF5File(mesh0.mpi_comm(), filename, "r")
mesh2 = mesh_file.read_mesh("/my_mesh", True, cpp.mesh.GhostMode.none)
mesh_file.close()
assert mesh0.num_cells() == mesh2.num_cells()
dim = mesh0.topology.dim
assert mesh0.num_entities_global(dim) == mesh1.num_entities_global(dim)
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_ghost_2d(mode):
N = 8
num_cells = N * N * 2
mesh = UnitSquareMesh(MPI.comm_world, N, N, ghost_mode=mode)
if MPI.size(mesh.mpi_comm()) > 1:
assert MPI.sum(mesh.mpi_comm(), mesh.num_cells()) > num_cells
assert mesh.num_entities_global(0) == 81
assert mesh.num_entities_global(2) == num_cells
def test_mesh_function_assign_2D_vertices():
mesh = UnitSquareMesh(MPI.comm_world, 3, 3)
mesh.create_entities(0)
f = MeshFunction("int", mesh, 0, 25)
g = MeshValueCollection("int", mesh, 0)
g.assign(f)
assert mesh.num_entities(0) == len(f.values)
assert mesh.num_cells() * 3 == g.size()
f2 = MeshFunction("int", mesh, g, 0)
num_cell_vertices = cpp.mesh.cell_num_vertices(mesh.cell_type)
tdim = mesh.topology.dim
connectivity = mesh.topology.connectivity(tdim, 0)
for c in range(mesh.num_cells()):
vertices = connectivity.connections(c)
for i in range(num_cell_vertices):
assert 25 == g.get_value(c, i)
assert f2.values[vertices[i]] == g.get_value(c, i)
def test_mesh_function_assign_2D_vertices():
mesh = UnitSquareMesh(MPI.comm_world, 3, 3)
mesh.create_entities(0)
f = MeshFunction("int", mesh, 0, 25)
g = MeshValueCollection("int", mesh, 0)
g.assign(f)
assert mesh.num_entities(0) == f.size()
assert mesh.num_cells() * 3 == g.size()
f2 = MeshFunction("int", mesh, g, 0)
for cell in Cells(mesh):
for i, vert in enumerate(VertexRange(cell)):
assert 25 == g.get_value(cell.index(), i)
assert f2[vert] == 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()
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_mesh_function_assign_2D_facets():
mesh = UnitSquareMesh(MPI.comm_world, 3, 3)
mesh.init(1)
f = MeshFunction("int", mesh, mesh.topology.dim - 1, 25)
for cell in Cells(mesh):
for i, facet in enumerate(FacetRange(cell)):
assert 25 == f[facet]
g = MeshValueCollection("int", mesh, 1)
g.assign(f)
assert mesh.num_facets() == f.size()
assert mesh.num_cells() * 3 == g.size()
for cell in Cells(mesh):
for i, facet in enumerate(FacetRange(cell)):
assert 25 == g.get_value(cell.index(), i)
f2 = MeshFunction("int", mesh, g, 0)
for cell in Cells(mesh):
for i, facet in enumerate(FacetRange(cell)):
assert f2[facet] == g.get_value(cell.index(), i)
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()
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)
B0 = get_Bhat(dim=dim, pol_order=p, problem=problem)
A = AG.sparray()
if calculate == 1:
print('saving the matrices...')
savemat(filen_data,
dict(A=A, B0=B0, A_T=A_T),
do_compression=True)
else:
data = loadmat(filen_data)
A = data['A']
A_T = data['A_T']
B0 = data['B0']
mem_eff = mesh.num_cells() * A_T[0].size / mem_sparse(A)
com_eff = (2 * (nnz(B0) - ones(B0)) * mesh.num_cells() +
mesh.num_cells() * A_T[0].size) / nnz(A)
mem_Aloc = V.element().space_dimension()**2
print(
'[Ne, p, mem_sparse(A), mem_Aloc, nnz(A_T[0]), nnz(B0), mem_eff, com_eff]'
)
for val in [
Ne, p,
mem_sparse(A), mem_Aloc,
mesh.num_cells() * A_T[0].size, A_T[0].size,
nnz(B0), mem_eff, com_eff
]:
if isinstance(val, int):
ss += ' {:,} &'.format(val)
def test_UnitSquareMeshLocal():
"""Create mesh of unit square."""
mesh = UnitSquareMesh(MPI.comm_self, 5, 7)
assert mesh.num_vertices() == 48
assert mesh.num_cells() == 70
assert mesh.geometry.dim == 2
