def IntervalMesh(comm,
nx: int,
points: list,
ghost_mode=cpp.mesh.GhostMode.shared_facet,
partitioner=cpp.mesh.partition_cells_graph):
"""Create an interval mesh
Parameters
----------
comm
MPI communicator
nx
Number of cells
point
Coordinates of the end points
ghost_mode
"""
domain = ufl.Mesh(ufl.VectorElement("Lagrange", "interval", 1))
cmap = fem.create_coordinate_map(comm, domain)
mesh = cpp.generation.create_interval_mesh(comm, nx, points, cmap,
ghost_mode, partitioner)
domain._ufl_cargo = mesh
mesh._ufl_domain = domain
return mesh
def create_boundary_mesh(mesh, comm, orient=False):
"""
Create a mesh consisting of all exterior facets of a mesh
Input:
mesh - The mesh
comm - The MPI communicator
orient - Boolean flag for reorientation of facets to have
consistent outwards-pointing normal (default: True)
Output:
bmesh - The boundary mesh
bmesh_to_geometry - Map from cells of the boundary mesh
to the geometry of the original mesh
"""
ext_facets = cpp.mesh.exterior_facet_indices(mesh)
boundary_geometry = cpp.mesh.entities_to_geometry(mesh,
mesh.topology.dim - 1,
ext_facets, orient)
facet_type = cpp.mesh.to_string(
cpp.mesh.cell_entity_type(mesh.topology.cell_type,
mesh.topology.dim - 1))
facet_cell = ufl.Cell(facet_type, geometric_dimension=mesh.geometry.dim)
degree = mesh.ufl_domain().ufl_coordinate_element().degree()
ufl_domain = ufl.Mesh(ufl.VectorElement("Lagrange", facet_cell, degree))
bmesh = create_mesh(comm, boundary_geometry, mesh.geometry.x, ufl_domain)
return bmesh, boundary_geometry
def test_volume_quadrilateralR3(coordinates):
x = numpy.array(coordinates, dtype=numpy.float64)
cells = numpy.array([[0, 1, 2, 3]], dtype=numpy.int32)
domain = ufl.Mesh(ufl.VectorElement("Lagrange", "quadrilateral", 1))
mesh = create_mesh(MPI.COMM_SELF, cells, x, domain)
mesh.topology.create_connectivity_all()
assert cpp.mesh.volume_entities(mesh, [0], mesh.topology.dim) == 1.0
def test_cmap_hex(degree, compile_args):
"""Test hexahedron cell"""
# Assuming FIAT Tensor Product layout of cell.
cell = ufl.hexahedron
e = ufl.VectorElement("Lagrange", cell, degree)
mesh = ufl.Mesh(e)
compiled_cmap, module = ffcx.codegeneration.jit.compile_coordinate_maps(
[mesh], cffi_extra_compile_args=compile_args)
assert compiled_cmap[0].is_affine == 0
assert compiled_cmap[0].geometric_dimension == 3
assert compiled_cmap[0].topological_dimension == 3
# Reference coordinates X to basis
phi = np.zeros((degree + 1)**3, dtype=np.float64)
phi_ptr = module.ffi.cast("double *", module.ffi.from_buffer(phi))
X = np.array([[0.5, 0.5, 0.5]], dtype=np.float64)
X_ptr = module.ffi.cast("double *", module.ffi.from_buffer(X))
compiled_cmap[0].evaluate_basis_derivatives(phi_ptr, 0, X.shape[0], X_ptr)
assert np.isclose(sum(phi), 1.0)
num_entity_dofs = compiled_cmap[0].create_scalar_dofmap().num_entity_dofs
assert num_entity_dofs[0] == 1
if degree == 1:
assert num_entity_dofs[1] == 0
assert num_entity_dofs[2] == 0
assert num_entity_dofs[3] == 0
elif degree == 2:
assert num_entity_dofs[1] == 1
assert num_entity_dofs[2] == 1
assert num_entity_dofs[3] == 1
def test_cmap_triangle(degree, compile_args):
"""Test triangle cell."""
cell = ufl.triangle
element = ufl.VectorElement("Lagrange", cell, degree)
mesh = ufl.Mesh(element)
compiled_cmap, module = ffcx.codegeneration.jit.compile_coordinate_maps(
[mesh], cffi_extra_compile_args=compile_args, cache_dir=".")
assert compiled_cmap[0].is_affine == (1 if (degree == 1) else 0)
assert compiled_cmap[0].geometric_dimension == 2
assert compiled_cmap[0].topological_dimension == 2
# Reference coordinates X to basis
phi = np.zeros(((degree + 2) * (degree + 1)) // 2, dtype=np.float64)
phi_ptr = module.ffi.cast("double *", module.ffi.from_buffer(phi))
X = np.array([[1 / 3, 1 / 3]], dtype=np.float64)
X_ptr = module.ffi.cast("double *", module.ffi.from_buffer(X))
compiled_cmap[0].evaluate_basis_derivatives(phi_ptr, 0, X.shape[0], X_ptr)
assert np.isclose(sum(phi), 1.0)
num_entity_dofs = compiled_cmap[0].create_scalar_dofmap().num_entity_dofs
assert num_entity_dofs[0] == 1
assert num_entity_dofs[2] == 0
assert num_entity_dofs[3] == 0
if degree == 1:
assert num_entity_dofs[1] == 0
elif degree == 2:
assert num_entity_dofs[1] == 1
def test_assemble_manifold():
"""Test assembly of poisson problem on a mesh with topological dimension 1
but embedded in 2D (gdim=2).
"""
points = numpy.array([[0.0, 0.0], [0.2, 0.0], [0.4, 0.0], [0.6, 0.0],
[0.8, 0.0], [1.0, 0.0]],
dtype=numpy.float64)
cells = numpy.array([[0, 1], [1, 2], [2, 3], [3, 4], [4, 5]],
dtype=numpy.int32)
cell = ufl.Cell("interval", geometric_dimension=points.shape[1])
domain = ufl.Mesh(ufl.VectorElement("Lagrange", cell, 1))
mesh = create_mesh(MPI.COMM_WORLD, cells, points, domain)
assert mesh.geometry.dim == 2
assert mesh.topology.dim == 1
U = dolfinx.FunctionSpace(mesh, ("P", 1))
u, v = ufl.TrialFunction(U), ufl.TestFunction(U)
w = dolfinx.Function(U)
a = ufl.inner(ufl.grad(u), ufl.grad(v)) * ufl.dx(mesh)
L = ufl.inner(1.0, v) * ufl.dx(mesh)
bcdofs = dolfinx.fem.locate_dofs_geometrical(
U, lambda x: numpy.isclose(x[0], 0.0))
bcs = [dolfinx.DirichletBC(w, bcdofs)]
A = dolfinx.fem.assemble_matrix(a, bcs)
A.assemble()
b = dolfinx.fem.assemble_vector(L)
dolfinx.fem.apply_lifting(b, [a], [bcs])
dolfinx.fem.set_bc(b, bcs)
assert numpy.isclose(b.norm(), 0.41231)
assert numpy.isclose(A.norm(), 25.0199)
def test_collision_2nd_order_triangle():
points = np.array([[0, 0], [1, 0], [0, 1], [0.65, 0.65], [0, 0.5], [0.5, 0]])
cells = np.array([[0, 1, 2, 3, 4, 5]])
cell = ufl.Cell("triangle", geometric_dimension=2)
domain = ufl.Mesh(ufl.VectorElement("Lagrange", cell, 2))
mesh = create_mesh(MPI.COMM_WORLD, cells, points, domain)
# Sample points along an interior line of the domain. The last point
# is outside the simplex made by the vertices.
sample_points = np.array([[0.1, 0.3, 0], [0.2, 0.5, 0], [0.6, 0.6, 0]])
# Create boundingboxtree
tree = geometry.BoundingBoxTree(mesh, mesh.geometry.dim)
for point in sample_points:
colliding_cell = geometry.compute_colliding_cells(tree, mesh, point, 1)
assert(len(colliding_cell) == 1)
# Check if there is a point on the linear approximation of the
# curved facet
def line_through_points(p0, p1):
return lambda x: (p1[1] - p0[1]) / (p1[0] - p0[0]) * (x - p0[0]) + p0[1]
line_func = line_through_points(points[2], points[3])
point = np.array([0.2, line_func(0.2), 0])
# Point inside 2nd order geometry, outside linear approximation
# Usefull for debugging on a later stage
# point = np.array([0.25, 0.89320760, 0])
distance = cpp.geometry.squared_distance(mesh, mesh.topology.dim - 1, 2, point)
assert np.isclose(distance, 0)
def test_triangle_mesh(order):
points = []
points += [[i / order, 0] for i in range(order + 1)]
for j in range(1, order):
points += [[i / order + 0.1, j / order] for i in range(order + 1 - j)]
points += [[0, 1]]
def coord_to_vertex(x, y):
return y * (2 * order + 3 - y) // 2 + x
# Define a cell using dolfin ordering
cell = [coord_to_vertex(i, j) for i, j in [(0, 0), (order, 0), (0, order)]]
if order > 1:
for i in range(1, order):
cell.append(coord_to_vertex(order - i, i))
for i in range(1, order):
cell.append(coord_to_vertex(0, i))
for i in range(1, order):
cell.append(coord_to_vertex(i, 0))
for j in range(1, order):
for i in range(1, order - j):
cell.append(coord_to_vertex(i, j))
domain = ufl.Mesh(
ufl.VectorElement("Lagrange",
ufl.Cell("triangle", geometric_dimension=2), order))
check_cell_volume(points, cell, domain, 0.5)
def xtest_tetrahedron_integral(space_type, space_order):
domain = ufl.Mesh(ufl.VectorElement("Lagrange", "tetrahedron", 1))
temp_points = np.array([[-1., 0., -1.], [0., 0., 0.], [1., 0., 1.],
[0., 1., 0.], [0., 0., 1.]])
for repeat in range(10):
order = [i for i, j in enumerate(temp_points)]
shuffle(order)
points = np.zeros(temp_points.shape)
for i, j in enumerate(order):
points[j] = temp_points[i]
cells = []
for cell in [[0, 1, 3, 4], [1, 2, 3, 4]]:
# Randomly number the cell
cell_order = list(range(4))
shuffle(cell_order)
cells.append([order[cell[i]] for i in cell_order])
mesh = create_mesh(MPI.COMM_WORLD, cells, points, domain)
V = FunctionSpace(mesh, (space_type, space_order))
Vvec = VectorFunctionSpace(mesh, ("P", 1))
dofs = [i for i in V.dofmap.cell_dofs(0) if i in V.dofmap.cell_dofs(1)]
for d in dofs:
v = Function(V)
v.vector[:] = [1 if i == d else 0 for i in range(V.dim)]
if space_type in ["RT", "BDM"]:
# Hdiv
def normal(x):
values = np.zeros((3, x.shape[1]))
values[0] = [1 for i in values[0]]
return values
n = Function(Vvec)
n.interpolate(normal)
form = ufl.inner(ufl.jump(v), n) * ufl.dS
elif space_type in ["N1curl", "N2curl"]:
# Hcurl
def tangent1(x):
values = np.zeros((3, x.shape[1]))
values[1] = [1 for i in values[1]]
return values
def tangent2(x):
values = np.zeros((3, x.shape[1]))
values[2] = [1 for i in values[2]]
return values
t1 = Function(Vvec)
t1.interpolate(tangent1)
t2 = Function(Vvec)
t2.interpolate(tangent1)
form = ufl.inner(ufl.jump(v), t1) * ufl.dS
form += ufl.inner(ufl.jump(v), t2) * ufl.dS
else:
form = ufl.jump(v) * ufl.dS
value = fem.assemble_scalar(form)
assert np.isclose(value, 0)
def read_mesh(self,
ghost_mode=cpp.mesh.GhostMode.shared_facet,
name="mesh",
xpath="/Xdmf/Domain"):
# Read mesh data from file
cell_shape, cell_degree = super().read_cell_type(name, xpath)
cells = super().read_topology_data(name, xpath)
x = super().read_geometry_data(name, xpath)
# Construct the geometry map
cell = ufl.Cell(cpp.mesh.to_string(cell_shape),
geometric_dimension=x.shape[1])
domain = ufl.Mesh(ufl.VectorElement("Lagrange", cell, cell_degree))
# Build the mesh
cmap = cpp.fem.CoordinateElement(cell_shape, cell_degree)
mesh = cpp.mesh.create_mesh(self.comm(),
cpp.graph.AdjacencyList_int64(cells), cmap,
x, ghost_mode,
cpp.mesh.partition_cells_graph)
mesh.name = name
domain._ufl_cargo = mesh
mesh._ufl_domain = domain
return mesh
def test_cmap_hex(degree, compile_args):
"""Test hexahedron cell"""
cell = ufl.hexahedron
e = ufl.VectorElement("Lagrange", cell, degree)
mesh = ufl.Mesh(e)
compiled_cmap, module = ffcx.codegeneration.jit.compile_coordinate_maps(
[mesh], cffi_extra_compile_args=compile_args)
assert compiled_cmap[0].is_affine == 0
assert compiled_cmap[0].geometric_dimension == 3
assert compiled_cmap[0].topological_dimension == 3
num_entity_dofs = compiled_cmap[0].create_scalar_dofmap().num_entity_dofs
assert num_entity_dofs[0] == 1
if degree == 1:
assert num_entity_dofs[1] == 0
assert num_entity_dofs[2] == 0
assert num_entity_dofs[3] == 0
elif degree == 2:
assert num_entity_dofs[1] == 1
assert num_entity_dofs[2] == 1
assert num_entity_dofs[3] == 1
def test_quadrilateral_mesh(order):
random.seed(13)
points = []
points += [[i / order, 0] for i in range(order + 1)]
for j in range(1, order):
points += [[i / order + 0.1, j / order] for i in range(order + 1)]
points += [[j / order, 1] for j in range(order + 1)]
def coord_to_vertex(x, y):
return (order + 1) * y + x
# Define a cell using DOLFINx ordering
cell = [coord_to_vertex(i, j)
for i, j in [(0, 0), (order, 0), (0, order), (order, order)]]
if order > 1:
for i in range(1, order):
cell.append(coord_to_vertex(i, 0))
for i in range(1, order):
cell.append(coord_to_vertex(0, i))
for i in range(1, order):
cell.append(coord_to_vertex(order, i))
for i in range(1, order):
cell.append(coord_to_vertex(i, order))
for j in range(1, order):
for i in range(1, order):
cell.append(coord_to_vertex(i, j))
domain = ufl.Mesh(ufl.VectorElement(
"Q", ufl.Cell("quadrilateral", geometric_dimension=2), order))
check_cell_volume(points, cell, domain, 1)
def ufl_domain(self):
"""Returns the ufl domain corresponding to the mesh."""
# Cache object to avoid recreating it a lot
if not hasattr(self, "_ufl_domain"):
self._ufl_domain = ufl.Mesh(
self.ufl_coordinate_element(), ufl_id=self.ufl_id(), cargo=self)
return self._ufl_domain
def BoxMesh(comm,
points: typing.List[numpy.array],
n: list,
cell_type=cpp.mesh.CellType.tetrahedron,
ghost_mode=cpp.mesh.GhostMode.shared_facet,
partitioner=cpp.mesh.partition_cells_graph):
"""Create box mesh
Parameters
----------
comm
MPI communicator
points
List of points representing vertices
n
List of cells in each direction
"""
domain = ufl.Mesh(
ufl.VectorElement("Lagrange", cpp.mesh.to_string(cell_type), 1))
mesh = cpp.generation.create_box_mesh(comm, points, n, cell_type,
ghost_mode, partitioner)
domain._ufl_cargo = mesh
mesh._ufl_domain = domain
return mesh
def create_box(
comm: _MPI.Comm,
points: typing.List[np.array],
n: list,
cell_type=CellType.tetrahedron,
ghost_mode=GhostMode.shared_facet,
partitioner=_cpp.mesh.create_cell_partitioner()
) -> Mesh:
"""Create box mesh
Args:
comm: MPI communicator
points: Coordinates of the 'lower-left' and 'upper-right'
corners of the box
n: List of cells in each direction
cell_type: The cell type
ghost_mode: The ghost mode used in the mesh partitioning
partitioner: Function that computes the parallel distribution of
cells across MPI ranks
Returns:
A mesh of a box domain
"""
domain = ufl.Mesh(ufl.VectorElement("Lagrange", cell_type.name, 1))
mesh = _cpp.mesh.create_box(comm, points, n, cell_type, ghost_mode,
partitioner)
return Mesh.from_cpp(mesh, domain)
def one_cell_mesh(cell_type):
if cell_type == CellType.interval:
points = np.array([[-1.], [2.]])
if cell_type == CellType.triangle:
points = np.array([[-1., -1.], [2., 0.], [0., 0.5]])
elif cell_type == CellType.tetrahedron:
points = np.array([[-1., -1., -1.], [2., 0., 0.], [0., 0.5, 0.], [0., 0., 1.]])
elif cell_type == CellType.quadrilateral:
points = np.array([[-1., 0.], [1., 0.], [-1., 1.5], [1., 1.5]])
elif cell_type == CellType.hexahedron:
points = np.array([[-1., -0.5, 0.], [1., -0.5, 0.], [-1., 1.5, 0.],
[1., 1.5, 0.], [0., -0.5, 1.], [1., -0.5, 1.],
[-1., 1.5, 1.], [1., 1.5, 1.]])
num_points = len(points)
# Randomly number the points and create the mesh
order = list(range(num_points))
random.shuffle(order)
ordered_points = np.zeros(points.shape)
for i, j in enumerate(order):
ordered_points[j] = points[i]
cells = np.array([order])
domain = ufl.Mesh(ufl.VectorElement("Lagrange", cpp.mesh.to_string(cell_type), 1))
mesh = create_mesh(MPI.COMM_WORLD, cells, ordered_points, domain)
mesh.topology.create_connectivity_all()
return mesh
def create_interval(
comm: _MPI.Comm,
nx: int,
points: list,
ghost_mode=GhostMode.shared_facet,
partitioner=_cpp.mesh.create_cell_partitioner()
) -> Mesh:
"""Create an interval mesh
Args:
comm: MPI communicator
nx: Number of cells
points: Coordinates of the end points
ghost_mode: Ghost mode used in the mesh partitioning. Options
are `GhostMode.none' and `GhostMode.shared_facet`.
partitioner: Partitioning function to use for determining the
parallel distribution of cells across MPI ranks
Returns:
An interval mesh
"""
domain = ufl.Mesh(ufl.VectorElement("Lagrange", "interval", 1))
mesh = _cpp.mesh.create_interval(comm, nx, points, ghost_mode, partitioner)
return Mesh.from_cpp(mesh, domain)
def create_rectangle(comm: _MPI.Comm,
points: typing.List[np.array],
n: list,
cell_type=CellType.triangle,
ghost_mode=GhostMode.shared_facet,
partitioner=_cpp.mesh.create_cell_partitioner(),
diagonal: DiagonalType = DiagonalType.right) -> Mesh:
"""Create rectangle mesh
Args:
comm: MPI communicator
points: Coordinates of the lower-left and upper-right corners of the
rectangle
n: Number of cells in each direction
cell_type: Mesh cell type
ghost_mode: Ghost mode used in the mesh partitioning
partitioner: Function that computes the parallel distribution of
cells across MPI ranks
diagonal: Direction of diagonal of triangular meshes. The
options are ``left``, ``right``, ``crossed``, ``left/right``,
``right/left``.
Returns:
A mesh of a rectangle
"""
domain = ufl.Mesh(ufl.VectorElement("Lagrange", cell_type.name, 1))
mesh = _cpp.mesh.create_rectangle(comm, points, n, cell_type, ghost_mode,
partitioner, diagonal)
return Mesh.from_cpp(mesh, domain)
def test_higher_order_coordinate_map(points, celltype, order):
"""Computes physical coordinates of a cell, based on the coordinate map."""
print(celltype)
cells = np.array([range(len(points))])
domain = ufl.Mesh(ufl.VectorElement("Lagrange", cpp.mesh.to_string(celltype), order))
mesh = create_mesh(MPI.COMM_WORLD, cells, points, domain)
V = FunctionSpace(mesh, ("Lagrange", 2))
X = V.element.interpolation_points()
coord_dofs = mesh.geometry.dofmap
x_g = mesh.geometry.x
cmap = mesh.geometry.cmap
x_coord_new = np.zeros([len(points), mesh.geometry.dim])
i = 0
for node in range(len(points)):
x_coord_new[i] = x_g[coord_dofs.links(0)[node], :mesh.geometry.dim]
i += 1
x = cmap.push_forward(X, x_coord_new)
assert np.allclose(x[:, 0], X[:, 0])
assert np.allclose(x[:, 1], 2 * X[:, 1])
if mesh.geometry.dim == 3:
assert np.allclose(x[:, 2], 3 * X[:, 2])
def test_custom_quadrature(compile_args):
ve = ufl.VectorElement("P", "triangle", 1)
mesh = ufl.Mesh(ve)
e = ufl.FiniteElement("P", mesh.ufl_cell(), 2)
V = ufl.FunctionSpace(mesh, e)
u, v = ufl.TrialFunction(V), ufl.TestFunction(V)
points = [[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [0.5, 0.5], [0.0, 0.5], [0.5, 0.0]]
weights = [1 / 12] * 6
a = u * v * ufl.dx(metadata={"quadrature_rule": "custom",
"quadrature_points": points, "quadrature_weights": weights})
forms = [a]
compiled_forms, module = ffcx.codegeneration.jit.compile_forms(forms, cffi_extra_compile_args=compile_args)
ffi = cffi.FFI()
form = compiled_forms[0][0]
default_integral = form.create_cell_integral(-1)
A = np.zeros((6, 6), dtype=np.float64)
w = np.array([], dtype=np.float64)
c = np.array([], dtype=np.float64)
coords = np.array([0.0, 0.0, 1.0, 0.0, 0.0, 1.0], dtype=np.float64)
default_integral.tabulate_tensor(
ffi.cast("double *", A.ctypes.data),
ffi.cast("double *", w.ctypes.data),
ffi.cast("double *", c.ctypes.data),
ffi.cast("double *", coords.ctypes.data), ffi.NULL, ffi.NULL, 0)
# Check that A is diagonal
assert np.count_nonzero(A - np.diag(np.diagonal(A))) == 0
def RectangleMesh(comm,
points: typing.List[numpy.array],
n: list,
cell_type=cpp.mesh.CellType.triangle,
ghost_mode=cpp.mesh.GhostMode.shared_facet,
diagonal: str = "right"):
"""Create rectangle mesh
Parameters
----------
comm
MPI communicator
points
List of `Points` representing vertices
n
List of number of cells in each direction
diagonal
Direction of diagonal
"""
domain = ufl.Mesh(
ufl.VectorElement("Lagrange", cpp.mesh.to_string(cell_type), 1))
cmap = fem.create_coordinate_map(comm, domain)
mesh = cpp.generation.RectangleMesh.create(comm, points, n, cmap,
ghost_mode, diagonal)
domain._ufl_cargo = mesh
mesh._ufl_domain = domain
return mesh
def create_submesh(mesh, dim, entities):
submesh, vertex_map, geom_map = _cpp.mesh.create_submesh(mesh, dim, entities)
submesh_ufl_cell = ufl.Cell(submesh.topology.cell_name(),
geometric_dimension=submesh.geometry.dim)
# FIXME Don't hard code degree (and maybe Lagrange?)
submesh_domain = ufl.Mesh(ufl.VectorElement("Lagrange", cell=submesh_ufl_cell, degree=1))
return (Mesh.from_cpp(submesh, submesh_domain), vertex_map, geom_map)
def xtest_quadrilateral_integral(space_type, space_order):
domain = ufl.Mesh(ufl.VectorElement("Lagrange", "quadrilateral", 1))
temp_points = np.array([[-1., -1.], [0., 0.], [1., 0.], [-1., 1.],
[0., 1.], [2., 2.]])
for repeat in range(10):
order = [i for i, j in enumerate(temp_points)]
shuffle(order)
points = np.zeros(temp_points.shape)
for i, j in enumerate(order):
points[j] = temp_points[i]
connections = {0: [1, 2], 1: [0, 3], 2: [0, 3], 3: [1, 2]}
cells = []
for cell in [[0, 1, 3, 4], [1, 2, 4, 5]]:
# Randomly number the cell
start = choice(range(4))
cell_order = [start]
for i in range(2):
diff = choice([
i for i in connections[start] if i not in cell_order
]) - cell_order[0]
cell_order += [c + diff for c in cell_order]
cells.append([order[cell[i]] for i in cell_order])
mesh = create_mesh(MPI.COMM_WORLD, cells, points, domain)
V = FunctionSpace(mesh, (space_type, space_order))
Vvec = VectorFunctionSpace(mesh, ("P", 1))
dofs = [i for i in V.dofmap.cell_dofs(0) if i in V.dofmap.cell_dofs(1)]
for d in dofs:
v = Function(V)
v.vector[:] = [1 if i == d else 0 for i in range(V.dim)]
if space_type in ["RTCF"]:
# Hdiv
def normal(x):
values = np.zeros((2, x.shape[1]))
values[0] = [1 for i in values[0]]
return values
n = Function(Vvec)
n.interpolate(normal)
form = ufl.inner(ufl.jump(v), n) * ufl.dS
elif space_type in ["RTCE"]:
# Hcurl
def tangent(x):
values = np.zeros((2, x.shape[1]))
values[1] = [1 for i in values[1]]
return values
t = Function(Vvec)
t.interpolate(tangent)
form = ufl.inner(ufl.jump(v), t) * ufl.dS
else:
form = ufl.jump(v) * ufl.dS
value = fem.assemble_scalar(form)
assert np.isclose(value, 0)
def test_quadrilateral_dof_positions(space_type):
"""Checks that dofs on shared quadrilateral edges match up"""
domain = ufl.Mesh(ufl.VectorElement("Lagrange", "quadrilateral", 1))
if MPI.COMM_WORLD.rank == 0:
# Create a quadrilateral mesh
N = 6
temp_points = np.array([[x / 2, y / 2] for x in range(N)
for y in range(N)])
order = [i for i, j in enumerate(temp_points)]
shuffle(order)
points = np.zeros(temp_points.shape)
for i, j in enumerate(order):
points[j] = temp_points[i]
cells = []
for x in range(N - 1):
for y in range(N - 1):
a = N * y + x
cell = [order[i] for i in [a, a + 1, a + N, a + N + 1]]
cells.append(cell)
# On process 0, input mesh data and distribute to other
# processes
mesh = create_mesh(MPI.COMM_WORLD, cells, points, domain)
else:
mesh = create_mesh(MPI.COMM_WORLD, np.ndarray((0, 4)),
np.ndarray((0, 2)), domain)
V = FunctionSpace(mesh, space_type)
dofmap = V.dofmap
edges = {}
# Get coordinates of dofs and edges and check that they are the same
# for each global dof number
X = V.element.dof_reference_coordinates()
coord_dofs = mesh.geometry.dofmap
x_g = mesh.geometry.x
cmap = fem.create_coordinate_map(mesh.ufl_domain())
for cell_n in range(coord_dofs.num_nodes):
dofs = dofmap.cell_dofs(cell_n)
x_coord_new = np.zeros([4, 2])
for v in range(4):
x_coord_new[v] = x_g[coord_dofs.links(cell_n)[v], :2]
x = X.copy()
cmap.push_forward(x, X, x_coord_new)
edge_dofs_local = []
for i in range(4):
edge_dofs_local += list(dofmap.dof_layout.entity_dofs(1, i))
edge_dofs = [dofs[i] for i in edge_dofs_local]
for i, j in zip(edge_dofs, x[edge_dofs_local]):
if i in edges:
assert np.allclose(j, edges[i])
else:
edges[i] = j
def test_tetrahedron_mesh(order):
points = []
points += [[i / order, j / order, 0] for j in range(order + 1)
for i in range(order + 1 - j)]
for k in range(1, order):
points += [[i / order, j / order + 0.1, k / order]
for j in range(order + 1 - k)
for i in range(order + 1 - k - j)]
points += [[0, 0, 1]]
def coord_to_vertex(x, y, z):
return z * (3 * order**2 - 3 * order * z + 12 * order + z**2 - 6 * z +
11) // 6 + y * (2 * (order - z) + 3 - y) // 2 + x
# Define a cell using dolfin ordering
cell = [
coord_to_vertex(x, y, z)
for x, y, z in [(0, 0, 0), (order, 0, 0), (0, order, 0), (0, 0, order)]
]
if order > 1:
for i in range(1, order):
cell.append(coord_to_vertex(0, order - i, i))
for i in range(1, order):
cell.append(coord_to_vertex(order - i, 0, i))
for i in range(1, order):
cell.append(coord_to_vertex(order - i, i, 0))
for i in range(1, order):
cell.append(coord_to_vertex(0, 0, i))
for i in range(1, order):
cell.append(coord_to_vertex(0, i, 0))
for i in range(1, order):
cell.append(coord_to_vertex(i, 0, 0))
for j in range(1, order):
for i in range(1, order - j):
cell.append(coord_to_vertex(order - i - j, i, j))
for j in range(1, order):
for i in range(1, order - j):
cell.append(coord_to_vertex(0, i, j))
for j in range(1, order):
for i in range(1, order - j):
cell.append(coord_to_vertex(i, 0, j))
for j in range(1, order):
for i in range(1, order - j):
cell.append(coord_to_vertex(i, j, 0))
for k in range(1, order):
for j in range(1, order - k):
for i in range(1, order - j - k):
cell.append(coord_to_vertex(i, j, k))
domain = ufl.Mesh(
ufl.VectorElement("Lagrange",
ufl.Cell("tetrahedron", geometric_dimension=3),
order))
check_cell_volume(points, cell, domain, 1 / 6)
def test_fourth_order_quad(L, H, Z):
"""Test by comparing integration of z+x*y against sympy/scipy integration
of a quad element. Z>0 implies curved element.
*---------* 20-21-22-23-24-41--42--43--44
| | | | |
| | 15 16 17 18 19 37 38 39 40
| | | | |
| | 10 11 12 13 14 33 34 35 36
| | | | |
| | 5 6 7 8 9 29 30 31 32
| | | | |
*---------* 0--1--2--3--4--25--26--27--28
"""
points = np.array([[0, 0, 0], [L / 4, 0, 0], [L / 2, 0, 0], # 0 1 2
[3 * L / 4, 0, 0], [L, 0, 0], # 3 4
[0, H / 4, -Z / 3], [L / 4, H / 4, -Z / 3], [L / 2, H / 4, -Z / 3], # 5 6 7
[3 * L / 4, H / 4, -Z / 3], [L, H / 4, -Z / 3], # 8 9
[0, H / 2, 0], [L / 4, H / 2, 0], [L / 2, H / 2, 0], # 10 11 12
[3 * L / 4, H / 2, 0], [L, H / 2, 0], # 13 14
[0, (3 / 4) * H, 0], [L / 4, (3 / 4) * H, 0], # 15 16
[L / 2, (3 / 4) * H, 0], [3 * L / 4, (3 / 4) * H, 0], # 17 18
[L, (3 / 4) * H, 0], [0, H, Z], [L / 4, H, Z], # 19 20 21
[L / 2, H, Z], [3 * L / 4, H, Z], [L, H, Z], # 22 23 24
[(5 / 4) * L, 0, 0], [(6 / 4) * L, 0, 0], # 25 26
[(7 / 4) * L, 0, 0], [2 * L, 0, 0], # 27 28
[(5 / 4) * L, H / 4, -Z / 3], [(6 / 4) * L, H / 4, -Z / 3], # 29 30
[(7 / 4) * L, H / 4, -Z / 3], [2 * L, H / 4, -Z / 3], # 31 32
[(5 / 4) * L, H / 2, 0], [(6 / 4) * L, H / 2, 0], # 33 34
[(7 / 4) * L, H / 2, 0], [2 * L, H / 2, 0], # 35 36
[(5 / 4) * L, 3 / 4 * H, 0], # 37
[(6 / 4) * L, 3 / 4 * H, 0], # 38
[(7 / 4) * L, 3 / 4 * H, 0], [2 * L, 3 / 4 * H, 0], # 39 40
[(5 / 4) * L, H, Z], [(6 / 4) * L, H, Z], # 41 42
[(7 / 4) * L, H, Z], [2 * L, H, Z]]) # 43 44
# VTK ordering
cells = np.array([[0, 4, 24, 20, 1, 2, 3, 9, 14, 19, 21, 22, 23, 5, 10, 15, 6, 7, 8, 11, 12, 13, 16, 17, 18],
[4, 28, 44, 24, 25, 26, 27, 32, 36, 40, 41, 42, 43, 9, 14, 19,
29, 30, 31, 33, 34, 35, 37, 38, 39]])
cells = cells[:, perm_vtk(CellType.quadrilateral, cells.shape[1])]
cell = ufl.Cell("quadrilateral", geometric_dimension=points.shape[1])
domain = ufl.Mesh(ufl.VectorElement("Lagrange", cell, 4))
mesh = create_mesh(MPI.COMM_WORLD, cells, points, domain)
def e2(x):
return x[2] + x[0] * x[1]
V = FunctionSpace(mesh, ("CG", 4))
u = Function(V)
u.interpolate(e2)
intu = assemble_scalar(u * dx(mesh))
intu = mesh.mpi_comm().allreduce(intu, op=MPI.SUM)
nodes = [0, 5, 10, 15, 20]
ref = sympy_scipy(points, nodes, 2 * L, H)
assert ref == pytest.approx(intu, rel=1e-5)
def ufl_mesh_from_gmsh(gmsh_cell: int, gdim: int):
"""
Create a UFL mesh from a Gmsh cell identifier and the geometric dimension.
See: # http://gmsh.info//doc/texinfo/gmsh.html#MSH-file-format
"""
shape, degree = _gmsh_to_cells[gmsh_cell]
cell = ufl.Cell(shape, geometric_dimension=gdim)
return ufl.Mesh(ufl.VectorElement("Lagrange", cell, degree))
def ufl_domain(mesh):
"""Returns the ufl domain corresponding to the mesh."""
# Cache object to avoid recreating it a lot
if not hasattr(mesh, "_ufl_domain"):
mesh._ufl_domain = ufl.Mesh(mesh.ufl_coordinate_element(),
ufl_id=mesh.ufl_id(),
cargo=mesh)
return mesh._ufl_domain
def create_quad_mesh(offset):
"""Creates a mesh of a single square element if offset = 0, or a
trapezium element if |offset| > 0."""
x = np.array([[0, 0], [1, 0], [0, 0.5 + offset], [1, 0.5 - offset]])
cells = np.array([[0, 1, 2, 3]])
ufl_mesh = ufl.Mesh(ufl.VectorElement("Lagrange", "quadrilateral", 1))
mesh = create_mesh(MPI.COMM_WORLD, cells, x, ufl_mesh)
return mesh
def test_second_order_vtx(tempdir):
filename = os.path.join(tempdir, "mesh_fides.bp")
points = np.array([[0, 0, 0], [1, 0, 0], [0.5, 0, 0]], dtype=np.float64)
cells = np.array([[0, 1, 2]], dtype=np.int32)
cell = ufl.Cell("interval", geometric_dimension=points.shape[1])
domain = ufl.Mesh(ufl.VectorElement("Lagrange", cell, 2))
mesh = create_mesh(MPI.COMM_WORLD, cells, points, domain)
with VTXWriter(mesh.comm, filename, mesh) as f:
f.write(0.0)
