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_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()]
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_mesh_point_3d(self):
"Test mesh-point intersection in 3D"
point = Point(0.1, 0.2, 0.3)
mesh = UnitCubeMesh(8, 8, 8)
intersection = intersect(mesh, point)
if MPI.size(mesh.mpi_comm()) == 1:
self.assertEqual(intersection.intersected_cells(), [816])
def test_compute_entity_collisions_3d(self):
reference = set([876, 877, 878, 879, 880, 881])
p = Point(0.3, 0.3, 0.3)
mesh = UnitCubeMesh(8, 8, 8)
tree = BoundingBoxTree()
tree.build(mesh)
entities = tree.compute_entity_collisions(p)
if MPI.size(mesh.mpi_comm()) == 1:
self.assertEqual(set(entities), reference)
def test_compute_first_entity_collision_3d():
reference = [876, 877, 878, 879, 880, 881]
p = Point(0.3, 0.3, 0.3)
mesh = UnitCubeMesh(8, 8, 8)
tree = BoundingBoxTree()
tree.build(mesh)
first = tree.compute_first_entity_collision(p)
assert first in reference
tree = mesh.bounding_box_tree()
first = tree.compute_first_entity_collision(p)
assert first in reference
def test_compute_collisions_point_3d(self):
reference = {1: set([1364]),
2: set([1967, 1968, 1970, 1972, 1974, 1976]),
3: set([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)
entities = tree.compute_collisions(p)
if MPI.size(mesh.mpi_comm()) == 1:
self.assertEqual(set(entities), reference[dim])
def test_save_3d_vector_series(tempdir, encoding):
if invalid_config(encoding):
pytest.skip("XDMF unsupported in current configuration")
filename = os.path.join(tempdir, "u_3D.xdmf")
mesh = UnitCubeMesh(MPI.comm_world, 2, 2, 2)
u = Function(VectorFunctionSpace(mesh, "Lagrange", 2))
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as file:
u.vector()[:] = 1.0
file.write(u, 0.1)
u.vector()[:] = 2.0
file.write(u, 0.2)
u.vector()[:] = 3.0
file.write(u, 0.3)
def test_compute_first_entity_collision_3d():
reference = [876, 877, 878, 879, 880, 881]
p = Point(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_compute_entity_collisions_3d():
reference = set([876, 877, 878, 879, 880, 881])
p = Point(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_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.create(MPI.comm_world,
[Point(0, 0), Point(1, 1)], [1, 1],
CellType.Type.triangle,
cpp.mesh.GhostMode.none, 'left')
x = mesh2d.geometry.points
x[3] += 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_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_compute_first_entity_collision_3d(self):
reference = [876, 877, 878, 879, 880, 881]
p = Point(0.3, 0.3, 0.3)
mesh = UnitCubeMesh(8, 8, 8)
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_p4_parallel_3d():
mesh = UnitCubeMesh(MPI.comm_world, 3, 5, 8)
Q = FunctionSpace(mesh, ("CG", 5))
F = Function(Q)
@function.expression.numba_eval
def x0(values, x, cell_idx):
values[:, 0] = x[:, 0]
F.interpolate(Expression(x0))
# Generate random points in this mesh partition (one per cell)
x = numpy.zeros(4)
tree = cpp.geometry.BoundingBoxTree(mesh, mesh.geometry.dim)
for c in Cells(mesh):
x[0] = random()
x[1] = random() * (1 - x[0])
x[2] = random() * (1 - x[0] - x[1])
x[3] = 1 - x[0] - x[1] - x[2]
p = Point(0.0, 0.0, 0.0)
for i, v in enumerate(VertexRange(c)):
p += v.point() * x[i]
p = p.array()
assert numpy.isclose(F(p, tree)[0], p[0])
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_save_3D_cell_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, 0)
mf.name = "cells"
mf.values[:] = np.arange(mesh.num_entities(3), dtype=dtype)
filename = os.path.join(tempdir, "mf_3D_%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, "cells")
diff = mf_in.values - mf.values
assert np.all(diff == 0)
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_entity_collision_3d(self):
reference = [876, 877, 878, 879, 880, 881]
p = Point(0.3, 0.3, 0.3)
mesh = UnitCubeMesh(8, 8, 8)
tree = BoundingBoxTree()
tree.build(mesh)
first = tree.compute_first_entity_collision(p)
if MPI.num_processes() == 1:
self.assertIn(first, reference)
tree = mesh.bounding_box_tree()
first = tree.compute_first_entity_collision(p)
if MPI.num_processes() == 1:
self.assertIn(first, reference)
def generate_cube(Nelements, length, refinements=0):
"""
Creates a square mesh of given elements and length with markers on
the sides: left, bottom, right and top
"""
from dolfin import UnitCubeMesh, SubDomain, MeshFunction, Measure, near, refine
mesh = UnitCubeMesh(Nelements, Nelements, Nelements)
for i in range(refinements):
mesh = refine(mesh)
mesh.coordinates()[:] *= length
# Subdomains: Solid
class Xp(SubDomain):
def inside(self, x, on_boundary):
return near(x[0], length) and on_boundary
class Xm(SubDomain):
def inside(self, x, on_boundary):
return near(x[0], 0.0) and on_boundary
class Yp(SubDomain):
def inside(self, x, on_boundary):
return near(x[1], length) and on_boundary
class Ym(SubDomain):
def inside(self, x, on_boundary):
return near(x[1], 0.0) and on_boundary
class Zp(SubDomain):
def inside(self, x, on_boundary):
return near(x[2], length) and on_boundary
class Zm(SubDomain):
def inside(self, x, on_boundary):
return near(x[2], 0.0) and on_boundary
xp, xm, yp, ym, zp, zm = Xp(), Xm(), Yp(), Ym(), Zp(), Zm()
XP, XM, YP, YM, ZP, ZM = 1, 2, 3, 4, 5, 6 # Set numbering
markers = MeshFunction("size_t", mesh, 2)
markers.set_all(0)
boundaries = (xp, xm, yp, ym, zp, zm)
def_names = (XP, XM, YP, YM, ZP, ZM)
for side, num in zip(boundaries, def_names):
side.mark(markers, num)
return mesh, markers, XP, XM, YP, YM, ZP, ZM
def test_advect_periodic(advection_scheme):
xmin, ymin, zmin = 0., 0., 0.
xmax, ymax, zmax = 1., 1., 1.
pres = 10
mesh = UnitCubeMesh(10, 10, 10)
lims = np.array([[xmin, xmin, ymin, ymax, zmin, zmax],
[xmax, xmax, ymin, ymax, zmin, zmax],
[xmin, xmax, ymin, ymin, zmin, zmax],
[xmin, xmax, ymax, ymax, zmin, zmax],
[xmin, xmax, ymin, ymax, zmin, zmin],
[xmin, xmax, ymin, ymax, zmax, zmax]])
vexpr = Constant((1., 1., 1.))
V = VectorFunctionSpace(mesh, "CG", 1)
v = Function(V)
v.assign(vexpr)
x = RandomBox(Point(0., 0., 0.), Point(1., 1.,
1.)).generate([pres, pres, pres])
x = comm.bcast(x, root=0)
dt = 0.05
p = particles(x, [x * 0, x**2], mesh)
if advection_scheme == 'euler':
ap = advect_particles(p, V, v, 'periodic', lims.flatten())
elif advection_scheme == 'rk2':
ap = advect_rk2(p, V, v, 'periodic', lims.flatten())
elif advection_scheme == 'rk3':
ap = advect_rk3(p, V, v, 'periodic', lims.flatten())
else:
assert False
xp0 = p.positions()
t = 0.
while t < 1. - 1e-12:
ap.do_step(dt)
t += dt
xpE = p.positions()
xp0_root = comm.gather(xp0, root=0)
xpE_root = comm.gather(xpE, root=0)
assert len(xp0) == len(xpE)
num_particles = p.number_of_particles()
if comm.Get_rank() == 0:
xp0_root = np.float32(np.vstack(xp0_root))
xpE_root = np.float32(np.vstack(xpE_root))
# Sort on x positions
xp0_root = xp0_root[xp0_root[:, 0].argsort(), :]
xpE_root = xpE_root[xpE_root[:, 0].argsort(), :]
error = np.linalg.norm(xp0_root - xpE_root)
assert error < 1e-10
assert num_particles - pres**3 == 0
def test_compute_first_collision_3d():
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)
assert first in reference[dim]
tree = mesh.bounding_box_tree()
first = tree.compute_first_collision(p)
assert first in reference[mesh.topology().dim()]
def test_save_points_3D(tempdir, encoding):
mesh = UnitCubeMesh(MPI.comm_world, 4, 4, 4)
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_3D.xdmf"),
encoding=encoding) as file:
file.write(points)
with XDMFFile(mesh.mpi_comm(),
os.path.join(tempdir, "points_values_3D.xdmf"),
encoding=encoding) as file:
file.write(points, vals)
def test_save_3d_mesh(tempfile, file_options):
mesh = UnitCubeMesh(MPI.comm_world, 8, 8, 8)
VTKFile(tempfile + "mesh.pvd", "ascii").write(mesh)
f = VTKFile(tempfile + "mesh.pvd", "ascii")
f.write(mesh, 0.)
f.write(mesh, 1.)
for file_option in file_options:
VTKFile(tempfile + "mesh.pvd", file_option).write(mesh)
def test_compute_closest_entity_3d():
reference = (0, 0.1)
p = Point(0.1, 0.05, -0.1)
mesh = UnitCubeMesh(MPI.comm_world, 8, 8, 8)
tree = BoundingBoxTree(mesh.geometry.dim)
tree.build(mesh, mesh.topology.dim)
entity, distance = tree.compute_closest_entity(p, mesh)
assert entity == reference[0]
assert round(distance - reference[1], 7) == 0
tree = mesh.bounding_box_tree()
entity, distance = tree.compute_closest_entity(p, mesh)
assert entity == reference[0]
assert round(distance - reference[1], 7) == 0
def test_compute_entity_collisions_3d(self):
reference = [876, 877, 878, 879, 880, 881]
p = Point(0.3, 0.3, 0.3)
mesh = UnitCubeMesh(8, 8, 8)
tree = BoundingBoxTree()
tree.build(mesh)
entities = tree.compute_entity_collisions(p, mesh)
if MPI.num_processes() == 1:
self.assertEqual(sorted(entities), reference)
tree = mesh.bounding_box_tree()
entities = tree.compute_entity_collisions(p, mesh)
if MPI.num_processes() == 1:
self.assertEqual(sorted(entities), reference)
def test_compute_closest_entity_3d():
reference = (0, 0.1)
p = Point(0.1, 0.05, -0.1)
mesh = UnitCubeMesh(8, 8, 8)
tree = BoundingBoxTree()
tree.build(mesh)
entity, distance = tree.compute_closest_entity(p)
assert entity == reference[0]
assert round(distance - reference[1], 7) == 0
tree = mesh.bounding_box_tree()
entity, distance = tree.compute_closest_entity(p)
assert entity == reference[0]
assert round(distance - reference[1], 7) == 0
def test_compute_closest_entity_3d():
reference = (0, 0.1)
p = numpy.array([0.1, 0.05, -0.1])
mesh = UnitCubeMesh(MPI.comm_world, 8, 8, 8)
tree = BoundingBoxTree(mesh, mesh.topology.dim)
entity, distance = tree.compute_closest_entity(p, mesh)
assert entity == reference[0]
assert round(distance - reference[1], 7) == 0
def test_tensor_constant():
mesh = UnitCubeMesh(MPI.comm_world, 2, 2, 2)
data = [[1.0, 2.0, 1.0], [1.0, 2.0, 1.0], [1.0, 2.0, 1.0]]
c0 = Constant(mesh, data)
assert c0.value.shape == (3, 3)
assert c0.value.all() == np.asarray(data).all()
c0.value *= 2.0
assert c0.value.all() == (2.0 * np.asarray(data)).all()
def test_append_and_load_mesh_functions(tempdir, encoding, data_type):
if invalid_config(encoding):
pytest.skip("XDMF unsupported in current configuration")
dtype_str, dtype = data_type
meshes = [
UnitSquareMesh(MPI.comm_world, 12, 12),
UnitCubeMesh(MPI.comm_world, 2, 2, 2)
]
for mesh in meshes:
dim = mesh.topology.dim
vf = MeshFunction(dtype_str, mesh, 0, 0)
vf.rename("vertices")
ff = MeshFunction(dtype_str, mesh, mesh.topology.dim - 1, 0)
ff.rename("facets")
cf = MeshFunction(dtype_str, mesh, mesh.topology.dim, 0)
cf.rename("cells")
if (MPI.size(mesh.mpi_comm()) == 1):
for vertex in Vertices(mesh):
vf[vertex] = dtype(vertex.index())
for facet in Facets(mesh):
ff[facet] = dtype(facet.index())
for cell in Cells(mesh):
cf[cell] = dtype(cell.index())
else:
for vertex in Vertices(mesh):
vf[vertex] = dtype(vertex.global_index())
for facet in Facets(mesh):
ff[facet] = dtype(facet.global_index())
for cell in Cells(mesh):
cf[cell] = dtype(cell.global_index())
filename = os.path.join(tempdir, "appended_mf_%dD.xdmf" % dim)
with XDMFFile(mesh.mpi_comm(), filename, encoding=encoding) as xdmf:
xdmf.write(mesh)
xdmf.write(vf)
xdmf.write(ff)
xdmf.write(cf)
with XDMFFile(mesh.mpi_comm(), filename) as xdmf:
read_function = getattr(xdmf, "read_mf_" + dtype_str)
vf_in = read_function(mesh, "vertices")
ff_in = read_function(mesh, "facets")
cf_in = read_function(mesh, "cells")
diff = 0
for vertex in Vertices(mesh):
diff += (vf_in[vertex] - vf[vertex])
for facet in Facets(mesh):
diff += (ff_in[facet] - ff[facet])
for cell in Cells(mesh):
diff += (cf_in[cell] - cf[cell])
assert diff == 0
def test_compute_entity_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([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)
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_compute_collisions_point_3d():
reference = {1: set([1364]),
2: set([1967, 1968, 1970, 1972, 1974, 1976]),
3: set([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)
entities = tree.compute_collisions(p)
# FIXME: Face and edges tests are excluded because test
# mistakingly relies on the face and edge indices
tdim = mesh.topology().dim()
if dim != tdim - 1 and dim != tdim - 2:
assert set(entities) == reference[dim]
def testFacetArea():
references = [(UnitIntervalMesh(MPI.comm_world, 1), 2, 2), (UnitSquareMesh(
MPI.comm_world, 1, 1), 4, 4), (UnitCubeMesh(MPI.comm_world, 1, 1, 1),
6, 3)]
for mesh, surface, ref_int in references:
c0 = ufl.FacetArea(mesh)
c1 = dolfin.FacetArea(mesh)
assert (c0)
assert (c1)
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)
u = Expression(("x[0] + 2*x[1]", "4*x[0]", "3*x[2] + x[0]"), 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
def test_vector_constant():
mesh = UnitCubeMesh(MPI.comm_world, 2, 2, 2)
c0 = Constant(mesh, [1.0, 2.0])
c1 = Constant(mesh, np.array([1.0, 2.0]))
assert (c0.value.all() == c1.value.all())
c0.value += 1.0
assert c0.value.all() == np.array([2.0, 3.0]).all()
c0.value -= [1.0, 2.0]
assert c0.value[0] == c0.value[1]
def test_compute_first_entity_collision_3d():
reference = [876, 877, 878, 879, 880, 881]
p = Point(0.3, 0.3, 0.3)
mesh = UnitCubeMesh(MPI.comm_world, 8, 8, 8)
tree = BoundingBoxTree(mesh.geometry.dim)
tree.build_mesh(mesh, mesh.topology.dim)
first = tree.compute_first_entity_collision(p, mesh)
assert first in reference
# 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_entity_collision(p, mesh)
assert first in reference
def test_distance_tetrahedron():
mesh = UnitCubeMesh(MPI.comm_self, 1, 1, 1)
cell = Cell(mesh, 5)
assert round(cell.distance(Point(-1.0, -1.0, -1.0)) - numpy.sqrt(3),
7) == 0
assert round(cell.distance(Point(-1.0, 0.5, 0.5)) - 1, 7) == 0
assert round(cell.distance(Point(0.5, 0.5, 0.5)) - 0.0, 7) == 0
def test_scalar_constant():
mesh = UnitCubeMesh(MPI.comm_world, 2, 2, 2)
c = Constant(mesh, 1.0)
assert c.value.shape == ()
assert c.value == 1.0
c.value += 1.0
assert c.value == 2.0
c.value = 3.0
assert c.value == 3.0
def test_save_3D_facet_function(tempdir, encoding, data_type):
dtype_str, dtype = data_type
mesh = UnitCubeMesh(MPI.comm_world, 4, 4, 4)
tdim = mesh.topology.dim
mf = MeshFunction(dtype_str, mesh, tdim - 1, 0)
mf.name = "facets"
global_indices = mesh.topology.global_indices(tdim - 1)
mf.values[:] = global_indices[:]
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 = mf_in.values - mf.values
assert numpy.all(diff == 0)
def test_computed_norms_against_references():
# Reference values for norm of solution vector
reference = {
("16x16 unit tri square", 1): 9.547454087328376,
("16x16 unit tri square", 2): 18.42366670418269,
("16x16 unit tri square", 3): 27.29583104732836,
("16x16 unit tri square", 4): 36.16867128121694,
("4x4x4 unit tet cube", 1): 12.23389289626038,
("4x4x4 unit tet cube", 2): 28.96491629163837,
("4x4x4 unit tet cube", 3): 49.97350551329799,
("4x4x4 unit tet cube", 4): 74.49938266409099,
("16x16 unit quad square", 1): 9.550848071820747,
("16x16 unit quad square", 2): 18.423668706176354,
("16x16 unit quad square", 3): 27.295831017251672,
("16x16 unit quad square", 4): 36.168671281610855,
("4x4x4 unit hex cube", 1): 12.151954087339782,
("4x4x4 unit hex cube", 2): 28.965646690046885,
("4x4x4 unit hex cube", 3): 49.97349423895635,
("4x4x4 unit hex cube", 4): 74.49938136593539
}
# Mesh files and degrees to check
meshes = [(UnitSquareMesh(MPI.comm_world, 16,
16), "16x16 unit tri square"),
(UnitCubeMesh(MPI.comm_world, 4, 4, 4), "4x4x4 unit tet cube")]
# (UnitSquareMesh(MPI.comm_world, 16, 16, CellType.Type.quadrilateral), "16x16 unit quad square"),
# (UnitCubeMesh(MPI.comm_world, 4, 4, 4, CellType.Type.hexahedron), "4x4x4 unit hex cube")]
degrees = [1, 2]
# For MUMPS, increase estimated require memory increase. Typically
# required for high order elements on small meshes in 3D
PETScOptions.set("mat_mumps_icntl_14", 40)
# Iterate over test cases and collect results
results = []
for mesh in meshes:
for degree in degrees:
gc_barrier()
norm = compute_norm(mesh[0], degree)
results.append((mesh[1], degree, norm))
# Change option back to default
PETScOptions.set("mat_mumps_icntl_14", 20)
# Check results
errors = check_results(results, reference, tol)
# Print errors for debugging if they fail
if errors:
print_errors(errors)
# Print results for use as reference
if any(e[-1] is None for e in errors): # e[-1] is diff
print_reference(results)
# A passing test should have no errors
assert len(errors) == 0 # See stdout for detailed norms and diffs.
def test_mesh_point_3d():
"Test mesh-point intersection in 3D"
point = Point(0.1, 0.2, 0.3)
mesh = UnitCubeMesh(8, 8, 8)
intersection = intersect(mesh, point)
assert intersection.intersected_cells() == [816]
def test_compute_closest_entity_3d(self):
reference = (2, numpy.sqrt(3.0))
p = Point(-1.0, -1.0, -1.0)
mesh = UnitCubeMesh(8, 8, 8)
tree = BoundingBoxTree()
tree.build(mesh)
entity, distance = tree.compute_closest_entity(p, mesh)
if MPI.num_processes() == 1:
self.assertEqual(entity, reference[0])
self.assertAlmostEqual(distance, reference[1])
tree = mesh.bounding_box_tree()
entity, distance = tree.compute_closest_entity(p, mesh)
if MPI.num_processes() == 1:
self.assertEqual(entity, reference[0])
self.assertAlmostEqual(distance, reference[1])
def test_compute_collisions_3d(self):
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)
entities = tree.compute_collisions(p)
if MPI.num_processes() == 1:
self.assertEqual(sorted(entities), reference[dim])
tree = mesh.bounding_box_tree()
entities = tree.compute_collisions(p)
if MPI.num_processes() == 1:
self.assertEqual(sorted(entities), reference[mesh.topology().dim()])
def test_mesh_point_3d_hexahedron():
"Test mesh-point intersection in 3D for hexahedral mesh"
point = Point(0.1, 0.2, 0.3)
mesh = UnitCubeMesh.create(8, 8, 8, CellType.Type.hexahedron)
intersection = intersect(mesh, point)
# Returns [] now, but [136] is the correct cell.
assert intersection.intersected_cells() == [136]
def test_compute_closest_entity_3d(self):
reference = (0, 0.1)
p = Point(0.1, 0.05, -0.1)
mesh = UnitCubeMesh(8, 8, 8)
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])