def test_save_2D_facet_function(tempdir, encoding, data_type):
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_and_read_function_timeseries(tempdir):
filename = os.path.join(tempdir, "function.h5")
mesh = UnitSquareMesh(MPI.comm_world, 10, 10)
Q = FunctionSpace(mesh, ("CG", 3))
F0 = Function(Q)
F1 = Function(Q)
t = 0.0
@function.expression.numba_eval
def expr_eval(values, x, cell_idx):
values[:, 0] = t * x[:, 0]
E = Expression(expr_eval)
F0.interpolate(E)
# Save to HDF5 File
hdf5_file = HDF5File(mesh.mpi_comm(), filename, "w")
for t in range(10):
F0.interpolate(E)
hdf5_file.write(F0, "/function", t)
hdf5_file.close()
# Read back from file
hdf5_file = HDF5File(mesh.mpi_comm(), filename, "r")
for t in range(10):
F1.interpolate(E)
vec_name = "/function/vector_%d" % t
F0 = hdf5_file.read_function(Q, vec_name)
# timestamp = hdf5_file.attributes(vec_name)["timestamp"]
# assert timestamp == t
F0.vector().axpy(-1.0, F1.vector())
assert F0.vector().norm(cpp.la.Norm.l2) < 1.0e-12
hdf5_file.close()
def test_save_and_read_function(tempdir):
filename = os.path.join(tempdir, "function.h5")
mesh = UnitSquareMesh(MPI.comm_world, 10, 10)
Q = FunctionSpace(mesh, ("CG", 3))
F0 = Function(Q)
F1 = Function(Q)
@function.expression.numba_eval
def expr_eval(values, x, cell_idx):
values[:, 0] = x[:, 0]
E = Expression(expr_eval)
F0.interpolate(E)
# Save to HDF5 File
hdf5_file = HDF5File(mesh.mpi_comm(), filename, "w")
hdf5_file.write(F0, "/function")
hdf5_file.close()
# Read back from file
hdf5_file = HDF5File(mesh.mpi_comm(), filename, "r")
F1 = hdf5_file.read_function(Q, "/function")
F0.vector().axpy(-1.0, F1.vector())
assert F0.vector().norm(dolfin.cpp.la.Norm.l2) < 1.0e-12
hdf5_file.close()
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_and_read_function_timeseries(tempdir):
filename = os.path.join(tempdir, "function.h5")
mesh = UnitSquareMesh(MPI.comm_world, 10, 10)
Q = FunctionSpace(mesh, ("CG", 3))
F0 = Function(Q)
F1 = Function(Q)
t = 0.0
def E(x):
return t * x[:, 0]
F0.interpolate(E)
# Save to HDF5 File
hdf5_file = HDF5File(mesh.mpi_comm(), filename, "w")
for t in range(10):
F0.interpolate(E)
hdf5_file.write(F0, "/function", t)
hdf5_file.close()
# Read back from file
hdf5_file = HDF5File(mesh.mpi_comm(), filename, "r")
for t in range(10):
F1.interpolate(E)
vec_name = "/function/vector_{}".format(t)
F0 = hdf5_file.read_function(Q, vec_name)
# timestamp = hdf5_file.attributes(vec_name)["timestamp"]
# assert timestamp == t
F0.vector.axpy(-1.0, F1.vector)
assert F0.vector.norm() < 1.0e-12
hdf5_file.close()
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_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_save_and_read_function(tempdir):
filename = os.path.join(tempdir, "function.h5")
mesh = UnitSquareMesh(MPI.comm_world, 10, 10)
Q = FunctionSpace(mesh, ("CG", 3))
F0 = Function(Q)
F1 = Function(Q)
def E(values, x):
values[:, 0] = x[:, 0]
F0.interpolate(E)
# Save to HDF5 File
hdf5_file = HDF5File(mesh.mpi_comm(), filename, "w")
hdf5_file.write(F0, "/function")
hdf5_file.close()
# Read back from file
hdf5_file = HDF5File(mesh.mpi_comm(), filename, "r")
F1 = hdf5_file.read_function(Q, "/function")
F0.vector().axpy(-1.0, F1.vector())
assert F0.vector().norm() < 1.0e-12
hdf5_file.close()
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_save_points_2D(tempdir, encoding):
mesh = UnitSquareMesh(MPI.comm_world, 16, 16)
points = mesh.geometry.points
vals = numpy.linalg.norm(points, axis=1)
with XDMFFile(mesh.mpi_comm(),
os.path.join(tempdir, "points_2D.xdmf"),
encoding=encoding) as file:
file.write(points)
with XDMFFile(mesh.mpi_comm(),
os.path.join(tempdir, "points_values_2D.xdmf"),
encoding=encoding) as file:
file.write(points, vals)
def test_compute_entity_collisions_tree_2d(self):
references = [[set([20, 21, 22, 23, 28, 29, 30, 31]),
set([0, 1, 2, 3, 8, 9, 10, 11])],
[set([6]),
set([25])]]
points = [Point(0.52, 0.51), Point(0.9, -0.9)]
for i, point in enumerate(points):
mesh_A = UnitSquareMesh(4, 4)
mesh_B = UnitSquareMesh(4, 4)
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)
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_krylov_solver_lu():
mesh = UnitSquareMesh(MPI.comm_world, 12, 12)
V = FunctionSpace(mesh, ("Lagrange", 1))
u, v = TrialFunction(V), TestFunction(V)
a = inner(u, v) * dx
L = inner(1.0, v) * dx
A = assemble_matrix(a)
A.assemble()
b = assemble_vector(L)
b.ghostUpdate(addv=PETSc.InsertMode.ADD, mode=PETSc.ScatterMode.REVERSE)
norm = 13.0
solver = PETScKrylovSolver(mesh.mpi_comm())
solver.set_options_prefix("test_lu_")
PETScOptions.set("test_lu_ksp_type", "preonly")
PETScOptions.set("test_lu_pc_type", "lu")
solver.set_from_options()
x = A.createVecRight()
solver.set_operator(A)
solver.solve(x, b)
# *Tight* tolerance for LU solves
assert round(x.norm(PETSc.NormType.N2) - norm, 12) == 0
def test_UnitSquareMeshDistributed():
"""Create mesh of unit square."""
mesh = UnitSquareMesh(MPI.comm_world, 5, 7)
assert mesh.num_entities_global(0) == 48
assert mesh.num_entities_global(2) == 70
assert mesh.geometry.dim == 2
assert MPI.sum(mesh.mpi_comm(), mesh.topology.ghost_offset(0)) == 48
def mesh():
mesh = UnitSquareMesh(3, 3)
assert MPI.size(mesh.mpi_comm()) in (1, 2, 3, 4)
# 1 processor -> test serial case
# 2 and 3 processors -> test case where submesh in contained only on one processor
# 4 processors -> test case where submesh is shared by two processors, resulting in shared facets and vertices
return mesh
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_2d_tensor(tempdir, encoding):
filename = os.path.join(tempdir, "tensor.xdmf")
mesh = UnitSquareMesh(MPI.comm_world, 16, 16)
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_save_2D_cell_function(tempdir, encoding, data_type):
dtype_str, dtype = data_type
filename = os.path.join(tempdir, "mf_2D_%s.xdmf" % dtype_str)
mesh = UnitSquareMesh(MPI.comm_world, 32, 32)
mf = MeshFunction(dtype_str, mesh, mesh.topology.dim, 0)
mf.name = "cells"
mf.values[:] = numpy.arange(mesh.num_entities(2), dtype=dtype)
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_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_krylov_solver_lu():
mesh = UnitSquareMesh(MPI.comm_world, 12, 12)
V = FunctionSpace(mesh, ("Lagrange", 1))
u, v = TrialFunction(V), TestFunction(V)
a = inner(u, v) * dx
L = inner(1.0, v) * dx
A = assemble_matrix(a)
A.assemble()
b = assemble_vector(L)
b.ghostUpdate(addv=PETSc.InsertMode.ADD, mode=PETSc.ScatterMode.REVERSE)
norm = 13.0
solver = PETSc.KSP().create(mesh.mpi_comm())
solver.setOptionsPrefix("test_lu_")
opts = PETSc.Options("test_lu_")
opts["ksp_type"] = "preonly"
opts["pc_type"] = "lu"
solver.setFromOptions()
x = A.createVecRight()
solver.setOperators(A)
solver.solve(b, x)
# *Tight* tolerance for LU solves
assert x.norm(PETSc.NormType.N2) == pytest.approx(norm, abs=1.0e-12)
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_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_points_2D(tempdir, encoding):
mesh = UnitSquareMesh(MPI.comm_world, 16, 16)
points, values = [], []
for v in Vertices(mesh):
points.append(v.point())
values.append(v.point().norm())
vals = numpy.array(values)
with XDMFFile(mesh.mpi_comm(),
os.path.join(tempdir, "points_2D.xdmf"),
encoding=encoding) as file:
file.write(points)
with XDMFFile(mesh.mpi_comm(),
os.path.join(tempdir, "points_values_2D.xdmf"),
encoding=encoding) as file:
file.write(points, vals)
def test_compute_first_entity_collision_2d(self):
reference = [136, 137]
p = Point(0.3, 0.3)
mesh = UnitSquareMesh(16, 16)
tree = BoundingBoxTree()
tree.build(mesh)
first = tree.compute_first_entity_collision(p)
if MPI.size(mesh.mpi_comm()) == 1:
self.assertIn(first, reference)
tree = mesh.bounding_box_tree()
first = tree.compute_first_entity_collision(p)
if MPI.size(mesh.mpi_comm()) == 1:
self.assertIn(first, reference)
def test_save_2d_scalar(tempdir, encoding):
filename = os.path.join(tempdir, "u2.xdmf")
mesh = UnitSquareMesh(MPI.comm_world, 16, 16)
# FIXME: This randomly hangs in parallel
V = FunctionSpace(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)
def test_compute_entity_collisions_2d(self):
reference = set([136, 137])
p = Point(0.3, 0.3)
mesh = UnitSquareMesh(16, 16)
tree = BoundingBoxTree()
tree.build(mesh)
entities = tree.compute_entity_collisions(p)
if MPI.size(mesh.mpi_comm()) == 1:
self.assertEqual(set(entities), reference)
tree = mesh.bounding_box_tree()
entities = tree.compute_entity_collisions(p)
if MPI.size(mesh.mpi_comm()) == 1:
self.assertEqual(set(entities), reference)
def test_compute_first_collision_2d(self):
reference = {1: [226],
2: [136, 137]}
p = Point(0.3, 0.3)
mesh = UnitSquareMesh(16, 16)
for dim in range(1, 3):
tree = BoundingBoxTree()
tree.build(mesh, dim)
first = tree.compute_first_collision(p)
if MPI.size(mesh.mpi_comm()) == 1:
self.assertIn(first, reference[dim])
tree = mesh.bounding_box_tree()
first = tree.compute_first_collision(p)
if MPI.size(mesh.mpi_comm()) == 1:
self.assertIn(first, reference[mesh.topology().dim()])
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)
c = Constant((1.0 + (1j if has_petsc_complex else 0), 2.0))
u.interpolate(c)
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as file:
file.write(u)
def test_krylov_reuse_pc_lu():
"""Test that LU re-factorisation is only performed after
set_operator(A) is called"""
# Test requires PETSc version 3.5 or later. Use petsc4py to check
# version number.
try:
from petsc4py import PETSc
except ImportError:
pytest.skip("petsc4py required to check PETSc version")
else:
if not PETSc.Sys.getVersion() >= (3, 5, 0):
pytest.skip("PETSc version must be 3.5 of higher")
mesh = UnitSquareMesh(MPI.comm_world, 12, 12)
V = FunctionSpace(mesh, ("Lagrange", 1))
u, v = TrialFunction(V), TestFunction(V)
a = Constant(1.0) * u * v * dx
L = Constant(1.0) * v * dx
assembler = fem.Assembler(a, L)
A = assembler.assemble_matrix()
b = assembler.assemble_vector()
norm = 13.0
solver = PETScKrylovSolver(mesh.mpi_comm())
solver.set_options_prefix("test_lu_")
PETScOptions.set("test_lu_ksp_type", "preonly")
PETScOptions.set("test_lu_pc_type", "lu")
solver.set_from_options()
solver.set_operator(A)
x = PETScVector(mesh.mpi_comm())
solver.solve(x, b)
assert round(x.norm(cpp.la.Norm.l2) - norm, 10) == 0
assembler = fem.assemble.Assembler(Constant(0.5) * u * v * dx, L)
assembler.assemble(A)
x = PETScVector(mesh.mpi_comm())
solver.solve(x, b)
assert round(x.norm(cpp.la.Norm.l2) - 2.0 * norm, 10) == 0
solver.set_operator(A)
solver.solve(x, b)
assert round(x.norm(cpp.la.Norm.l2) - 2.0 * norm, 10) == 0
def test_compute_closest_entity_2d(self):
reference = (1, 1.0)
p = Point(-1.0, 0.01)
mesh = UnitSquareMesh(16, 16)
tree = BoundingBoxTree()
tree.build(mesh)
entity, distance = tree.compute_closest_entity(p)
if MPI.size(mesh.mpi_comm()) == 1:
self.assertEqual(entity, reference[0])
self.assertAlmostEqual(distance, reference[1])
tree = mesh.bounding_box_tree()
entity, distance = tree.compute_closest_entity(p)
if MPI.size(mesh.mpi_comm()) == 1:
self.assertEqual(entity, reference[0])
self.assertAlmostEqual(distance, reference[1])
def test_mesh_point_2d(self):
"Test mesh-point intersection in 2D"
point = Point(0.1, 0.2)
mesh = UnitSquareMesh(16, 16)
intersection = intersect(mesh, point)
if MPI.size(mesh.mpi_comm()) == 1:
self.assertEqual(intersection.intersected_cells(), [98])
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_compute_collisions_point_2d(self):
reference = {1: set([226]),
2: set([136, 137])}
p = Point(0.3, 0.3)
mesh = UnitSquareMesh(16, 16)
for dim in range(1, 3):
tree = BoundingBoxTree()
tree.build(mesh, dim)
entities = tree.compute_collisions(p)
if MPI.size(mesh.mpi_comm()) == 1:
self.assertEqual(set(entities), reference[dim])
def test_lu_cholesky():
"""Test that PETScLUSolver selects LU or Cholesky solver based on
symmetry of matrix operator.
"""
from petsc4py import PETSc
mesh = UnitSquareMesh(MPI.comm_world, 12, 12)
V = FunctionSpace(mesh, "Lagrange", 1)
u, v = TrialFunction(V), TestFunction(V)
A = PETScMatrix(mesh.mpi_comm())
assemble(Constant(1.0)*u*v*dx, tensor=A)
# Check that solver type is LU
solver = PETScLUSolver(mesh.mpi_comm(), A, "petsc")
pc_type = solver.ksp().getPC().getType()
assert pc_type == "lu"
# Set symmetry flag
A.mat().setOption(PETSc.Mat.Option.SYMMETRIC, True)
# Check symmetry flags
symm = A.mat().isSymmetricKnown()
assert symm[0] == True
assert symm[1] == True
# Check that solver type is Cholesky since matrix has now been
# marked as symmetric
solver = PETScLUSolver(mesh.mpi_comm(), A, "petsc")
pc_type = solver.ksp().getPC().getType()
assert pc_type == "cholesky"
# Re-assemble, which resets symmetry flag
assemble(Constant(1.0)*u*v*dx, tensor=A)
solver = PETScLUSolver(mesh.mpi_comm(), A, "petsc")
pc_type = solver.ksp().getPC().getType()
assert pc_type == "lu"