def test_pointsource_vector_fs(mesh, point):
"""Tests point source when given constructor PointSource(V, point,
mag) with a vector for a vector function space that isn't placed
at a node for 1D, 2D and 3D. Global points given to constructor
from rank 0 processor.
"""
rank = MPI.rank(mesh.mpi_comm())
V = VectorFunctionSpace(mesh, "CG", 1)
v = TestFunction(V)
b = assemble(dot(Constant([0.0]*mesh.geometry().dim()), v)*dx)
if rank == 0:
ps = PointSource(V, point, 10.0)
else:
ps = PointSource(V, [])
ps.apply(b)
# Checks array sums to correct value
b_sum = b.sum()
assert round(b_sum - 10.0*V.num_sub_spaces()) == 0
# Checks point source is added to correct part of the array
v2d = vertex_to_dof_map(V)
for v in vertices(mesh):
if near(v.midpoint().distance(point), 0.0):
for spc_idx in range(V.num_sub_spaces()):
ind = v2d[v.index()*V.num_sub_spaces() + spc_idx]
if ind < len(b.get_local()):
assert np.round(b.get_local()[ind] - 10.0) == 0
def test_multi_ps_vector(mesh):
"""Tests point source PointSource(V, source) for mulitple point
sources applied to a vector for 1D, 2D and 3D. Global points given
to constructor from rank 0 processor.
"""
c_ids = [0, 1, 2]
rank = MPI.rank(mesh.mpi_comm())
V = FunctionSpace(mesh, "CG", 1)
v = TestFunction(V)
b = assemble(Constant(0.0) * v * dx)
source = []
if rank == 0:
for c_id in c_ids:
cell = Cell(mesh, c_id)
point = cell.midpoint()
source.append((point, 10.0))
ps = PointSource(V, source)
ps.apply(b)
# Checks b sums to correct value
b_sum = b.sum()
assert round(b_sum - len(c_ids) * 10.0) == 0
def test_multi_ps_vector(mesh):
"""Tests point source PointSource(V, source) for mulitple point
sources applied to a vector for 1D, 2D and 3D. Global points given
to constructor from rank 0 processor.
"""
c_ids = [0, 1, 2]
rank = MPI.rank(mesh.mpi_comm())
V = FunctionSpace(mesh, "CG", 1)
v = TestFunction(V)
b = assemble(Constant(0.0)*v*dx)
source = []
if rank == 0:
for c_id in c_ids:
cell = Cell(mesh, c_id)
point = cell.midpoint()
source.append((point, 10.0))
ps = PointSource(V, source)
ps.apply(b)
# Checks b sums to correct value
b_sum = b.sum()
assert round(b_sum - len(c_ids)*10.0) == 0
def test_pointsource_matrix_second_constructor(mesh, point):
"""Tests point source when given different constructor PointSource(V1,
V2, point, mag) with a matrix and when placed at a node for 1D, 2D
and 3D. Global points given to constructor from rank 0
processor. Currently only implemented if V1=V2.
"""
V1 = FunctionSpace(mesh, "CG", 1)
V2 = FunctionSpace(mesh, "CG", 1)
rank = MPI.rank(mesh.mpi_comm())
u, v = TrialFunction(V1), TestFunction(V2)
w = Function(V1)
A = assemble(Constant(0.0)*u*v*dx)
if rank == 0:
ps = PointSource(V1, V2, point, 10.0)
else:
ps = PointSource(V1, V2, [])
ps.apply(A)
# Checks array sums to correct value
a_sum = MPI.sum(mesh.mpi_comm(), np.sum(A.array()))
assert round(a_sum - 10.0) == 0
# Checks point source is added to correct part of the array
A.get_diagonal(w.vector())
v2d = vertex_to_dof_map(V1)
for v in vertices(mesh):
if near(v.midpoint().distance(point), 0.0):
ind = v2d[v.index()]
if ind < len(A.array()):
assert np.round(w.vector()[ind] - 10.0) == 0
def test_multi_ps_matrix(mesh):
"""Tests point source PointSource(V, source) for mulitple point
sources applied to a matrix for 1D, 2D and 3D. Global points given
to constructor from rank 0 processor.
"""
c_ids = [0, 1, 2]
rank = MPI.rank(mesh.mpi_comm())
V = VectorFunctionSpace(mesh, "CG", 1, dim=2)
u, v = TrialFunction(V), TestFunction(V)
A = assemble(Constant(0.0) * dot(u, v) * dx)
source = []
if rank == 0:
for c_id in c_ids:
cell = Cell(mesh, c_id)
point = cell.midpoint()
source.append((point, 10.0))
ps = PointSource(V, source)
ps.apply(A)
# Checks b sums to correct value
a_sum = MPI.sum(mesh.mpi_comm(), np.sum(A.array()))
assert round(a_sum - 2 * len(c_ids) * 10) == 0
def test_pointsource_mixed_space(mesh, point):
"""Tests point source when given constructor PointSource(V, point,
mag) with a vector for a mixed function space that isn't placed at
a node for 1D, 2D and 3D. Global points given to constructor from
rank 0 processor.
"""
rank = MPI.rank(mesh.mpi_comm())
ele1 = FiniteElement("CG", mesh.ufl_cell(), 1)
ele2 = FiniteElement("DG", mesh.ufl_cell(), 2)
ele3 = VectorElement("CG", mesh.ufl_cell(), 2)
V = FunctionSpace(mesh, MixedElement([ele1, ele2, ele3]))
value_dimension = V.element().value_dimension(0)
v = TestFunction(V)
b = assemble(dot(Constant([0.0]*value_dimension), v)*dx)
if rank == 0:
ps = PointSource(V, point, 10.0)
else:
ps = PointSource(V, [])
ps.apply(b)
# Checks array sums to correct value
b_sum = b.sum()
assert round(b_sum - 10.0*value_dimension) == 0
def _get_forces_as_point_sources(self):
"""
Creates 2 dicts of PointSources that can be applied to the assembled system.
Applies filter_point_source to avoid forces being applied to already existing Dirichlet BC, since this would
lead to an overdetermined system that cannot be solved.
:return: Returns lists of PointSources TODO: get rid of this legacy code, dicts should be used for a PointSource, since they can provide the location of the PointSouce, as well. Even, inside the FEniCS user code.
"""
# PointSources are scalar valued, therefore we need an individual scalar valued PointSource for each dimension in a vector-valued setting
# TODO: a vector valued PointSource would be more straightforward, but does not exist (as far as I know)
x_forces = dict() # dict of PointSources for Forces in x direction
y_forces = dict() # dict of PointSources for Forces in y direction
vertices_x = self._coupling_mesh_vertices[0, :]
vertices_y = self._coupling_mesh_vertices[1, :]
for i in range(self._n_vertices):
px, py = vertices_x[i], vertices_y[i]
key = (px, py)
x_forces[key] = PointSource(self._function_space.sub(0),
Point(px, py),
self._read_data[i, 0])
y_forces[key] = PointSource(self._function_space.sub(1),
Point(px, py),
self._read_data[i, 1])
# Avoid application of PointSource and Dirichlet boundary condition at the same point by filtering
x_forces = filter_point_sources(x_forces, self._Dirichlet_Boundary)
y_forces = filter_point_sources(y_forces, self._Dirichlet_Boundary)
return x_forces.values(), y_forces.values() # don't return dictionary, but list of PointSources
def test_multi_ps_matrix(mesh):
"""Tests point source PointSource(V, source) for mulitple point
sources applied to a matrix for 1D, 2D and 3D. Global points given
to constructor from rank 0 processor.
"""
c_ids = [0, 1, 2]
rank = MPI.rank(mesh.mpi_comm())
V = VectorFunctionSpace(mesh, "CG", 1, dim=2)
u, v = TrialFunction(V), TestFunction(V)
A = assemble(Constant(0.0)*dot(u, v)*dx)
source = []
if rank == 0:
for c_id in c_ids:
cell = Cell(mesh, c_id)
point = cell.midpoint()
source.append((point, 10.0))
ps = PointSource(V, source)
ps.apply(A)
# Checks b sums to correct value
a_sum = MPI.sum(mesh.mpi_comm(), np.sum(A.array()))
assert round(a_sum - 2*len(c_ids)*10) == 0
def add_points(self, src_loc):
""" Create and add more point sources """
for pts in self.src_loc:
self.src_loc.append(pts)
delta = PointSource(self.V, self.list2point(pts))
bs = self.b.copy()
delta.apply(bs)
self.PtSrc.append(self._PointSourcecorrection(bs))
def _modify_linear_equation(self, x, y, z):
logger.debug(
'Defining point source to compensate boundary flux...')
point = Point(0, 0, 0)
delta = PointSource(self._fm.function_space, point,
-self._boundary_flux())
logger.debug('Done. Applying changes to the vector...')
delta.apply(self._known_terms)
logger.debug('Done.')
def add_points(self, src_loc):
""" Create and add more point sources """
for pts in self.src_loc:
self.src_loc.append(pts)
delta = PointSource(self.V, self.list2point(pts))
bs = self.b.copy()
delta.apply(bs)
bs[:] = self.PointSourcecorrection(bs)
self.PtSrc.append(bs)
def __init__(self, V, src_loc):
""" Inputs:
V = FunctionSpace
src_loc = iterable that returns coordinates of the point """
self.V = V
self.src_loc = src_loc
test = TestFunction(self.V)
f = Constant('0')
L = f * test * dx
self.b = assemble(L)
self.PtSrc = []
for pts in self.src_loc:
delta = PointSource(self.V, self.list2point(pts))
bs = self.b.copy()
delta.apply(bs)
self.PtSrc.append(self._PointSourcecorrection(bs))
def __init__(self, V, src_loc):
""" Inputs:
V = FunctionSpace
src_loc = iterable that returns coordinates of the point """
self.V = V
self.src_loc = src_loc
test = TestFunction(self.V)
f = Constant('0')
L = f*test*dx
self.b = assemble(L)
self.PtSrc = []
for pts in self.src_loc:
delta = PointSource(self.V, self.list2point(pts))
bs = self.b.copy()
delta.apply(bs)
bs[:] = self.PointSourcecorrection(bs)
self.PtSrc.append(bs)
def test_multi_ps_matrix_node_vector_fs(mesh):
"""Tests point source applied to a matrix with given constructor
PointSource(V, source) and a vector function space when points
placed at 3 vertices for 1D, 2D and 3D. Global points given to
constructor from rank 0 processor.
"""
point = [0.0, 0.5, 1.0]
rank = MPI.rank(mesh.mpi_comm())
V = VectorFunctionSpace(mesh, "CG", 1, dim=2)
u, v = TrialFunction(V), TestFunction(V)
w = Function(V)
A = assemble(Constant(0.0) * dot(u, v) * dx)
dim = mesh.geometry().dim()
source = []
point_coords = np.zeros(dim)
for p in point:
for i in range(dim):
point_coords[i - 1] = p
if rank == 0:
source.append((Point(point_coords), 10.0))
ps = PointSource(V, source)
ps.apply(A)
# Checks array sums to correct value
A.get_diagonal(w.vector())
a_sum = MPI.sum(mesh.mpi_comm(), np.sum(A.array()))
assert round(a_sum - 2 * len(point) * 10) == 0
# Check if coordinates are in portion of mesh and if so check that
# diagonal components sum to the correct value.
mesh_coords = V.tabulate_dof_coordinates()
for p in point:
for i in range(dim):
point_coords[i] = p
j = 0
for i in range(len(mesh_coords) // (dim)):
mesh_coords_check = mesh_coords[j:j + dim - 1]
if np.array_equal(point_coords, mesh_coords_check) is True:
assert np.round(w.vector()[j // (dim)] - 10.0) == 0.0
j += dim
def test_multi_ps_matrix_node_vector_fs(mesh):
"""Tests point source applied to a matrix with given constructor
PointSource(V, source) and a vector function space when points
placed at 3 vertices for 1D, 2D and 3D. Global points given to
constructor from rank 0 processor.
"""
point = [0.0, 0.5, 1.0]
rank = MPI.rank(mesh.mpi_comm())
V = VectorFunctionSpace(mesh, "CG", 1, dim=2)
u, v = TrialFunction(V), TestFunction(V)
w = Function(V)
A = assemble(Constant(0.0)*dot(u, v)*dx)
dim = mesh.geometry().dim()
source = []
point_coords = np.zeros(dim)
for p in point:
for i in range(dim):
point_coords[i - 1] = p
if rank == 0:
source.append((Point(point_coords), 10.0))
ps = PointSource(V, source)
ps.apply(A)
# Checks array sums to correct value
A.get_diagonal(w.vector())
a_sum = MPI.sum(mesh.mpi_comm(), np.sum(A.array()))
assert round(a_sum - 2*len(point)*10) == 0
# Check if coordinates are in portion of mesh and if so check that
# diagonal components sum to the correct value.
mesh_coords = V.tabulate_dof_coordinates()
for p in point:
for i in range(dim):
point_coords[i] = p
j = 0
for i in range(len(mesh_coords)//(dim)):
mesh_coords_check = mesh_coords[j:j+dim-1]
if np.array_equal(point_coords, mesh_coords_check) is True:
assert np.round(w.vector()[j//(dim)] - 10.0) == 0.0
j += dim
def test_point_outside():
"""Tests point source fails if given a point outside the domain."""
mesh = UnitIntervalMesh(10)
point = Point(1.2)
V = FunctionSpace(mesh, "CG", 1)
v = TestFunction(V)
assemble(Constant(0.0) * v * dx)
# Runtime Error is only produced on one process which causes the
# whole function to fail but makes this test hang in parallel.
with pytest.raises(RuntimeError):
PointSource(V, point, 10.0)
def gaussian_distribution(mb,
mu,
sigma,
function=None,
lumping=True,
nsteps=100):
"Gaussian distribution via heat equation"
tend = 0.5 * sigma**2
dt = Constant(tend / nsteps, name="smooth")
# prepare the problem
P1e = FiniteElement("CG", mb.ufl_cell(), 1)
Ve = FunctionSpace(mb, P1e)
u, v = TrialFunction(Ve), TestFunction(Ve)
uold = Function(Ve)
if lumping:
# diffusion
K = assemble(dt * inner(grad(u), grad(v)) * dx)
# we use mass lumping to avoid negative values
Md = assemble(action(u * v * dx, Constant(1.0)))
# full matrix (divide my mass)
M = Matrix(K)
M.zero()
M.set_diagonal(Md)
A = M + K
else:
a = u * v * dx + dt * inner(grad(u), grad(v)) * dx
L = uold * v * dx
A = assemble(a)
# initial conditions
dist = function or Function(Ve)
dist.vector().zero()
PointSource(Ve, mu, 1.0).apply(dist.vector())
# iterations
for t in range(nsteps):
uold.assign(dist)
if lumping:
solve(A, dist.vector(), M * uold.vector())
else:
b = assemble(L)
solve(A, dist.vector(), b)
# normalize
area = assemble(dist * dx)
dist.vector()[:] /= area
if function is None:
return dist
def test_multi_ps_vector_node_local(mesh):
"""Tests point source when given constructor PointSource(V, V, point,
mag) with a matrix when points placed at 3 node for 1D, 2D and
3D. Local points given to constructor.
"""
V = FunctionSpace(mesh, "CG", 1)
v = TestFunction(V)
b = assemble(Constant(0.0)*v*dx)
source = []
point_coords = mesh.coordinates()[0]
source.append((Point(point_coords), 10.0))
ps = PointSource(V, source)
ps.apply(b)
# Checks b sums to correct value
size = MPI.size(mesh.mpi_comm())
b_sum = b.sum()
assert round(b_sum - size*10.0) == 0
def test_multi_ps_vector_node_local(mesh):
"""Tests point source when given constructor PointSource(V, V, point,
mag) with a matrix when points placed at 3 node for 1D, 2D and
3D. Local points given to constructor.
"""
V = FunctionSpace(mesh, "CG", 1)
v = TestFunction(V)
b = assemble(Constant(0.0) * v * dx)
source = []
point_coords = mesh.coordinates()[0]
source.append((Point(point_coords), 10.0))
ps = PointSource(V, source)
ps.apply(b)
# Checks b sums to correct value
size = MPI.size(mesh.mpi_comm())
b_sum = b.sum()
assert round(b_sum - size * 10.0) == 0
def test_pointsource_mixed_space(mesh, point):
"""Tests point source when given constructor PointSource(V, point,
mag) with a vector for a mixed function space that isn't placed at
a node for 1D, 2D and 3D. Global points given to constructor from
rank 0 processor.
"""
rank = MPI.rank(mesh.mpi_comm())
ele1 = FiniteElement("CG", mesh.ufl_cell(), 1)
ele2 = FiniteElement("DG", mesh.ufl_cell(), 2)
ele3 = VectorElement("CG", mesh.ufl_cell(), 2)
V = FunctionSpace(mesh, MixedElement([ele1, ele2, ele3]))
value_dimension = V.element().value_dimension(0)
v = TestFunction(V)
b = assemble(dot(Constant([0.0] * value_dimension), v) * dx)
if rank == 0:
ps = PointSource(V, point, 10.0)
else:
ps = PointSource(V, [])
ps.apply(b)
# Checks array sums to correct value
b_sum = b.sum()
assert round(b_sum - 10.0 * value_dimension) == 0
def test_pointsource_vector_fs(mesh, point):
"""Tests point source when given constructor PointSource(V, point,
mag) with a vector for a vector function space that isn't placed
at a node for 1D, 2D and 3D. Global points given to constructor
from rank 0 processor.
"""
rank = MPI.rank(mesh.mpi_comm())
V = VectorFunctionSpace(mesh, "CG", 1)
v = TestFunction(V)
b = assemble(dot(Constant([0.0] * mesh.geometry().dim()), v) * dx)
if rank == 0:
ps = PointSource(V, point, 10.0)
else:
ps = PointSource(V, [])
ps.apply(b)
# Checks array sums to correct value
b_sum = b.sum()
assert round(b_sum - 10.0 * V.num_sub_spaces()) == 0
# Checks point source is added to correct part of the array
v2d = vertex_to_dof_map(V)
for v in vertices(mesh):
if near(v.midpoint().distance(point), 0.0):
for spc_idx in range(V.num_sub_spaces()):
ind = v2d[v.index() * V.num_sub_spaces() + spc_idx]
if ind < len(b.get_local()):
assert np.round(b.get_local()[ind] - 10.0) == 0
def test_multi_ps_vector_node(mesh):
"""Tests point source when given constructor PointSource(V, V, point,
mag) with a matrix when points placed at 3 node for 1D, 2D and
3D. Global points given to constructor from rank 0 processor.
"""
point = [0.0, 0.5, 1.0]
dim = mesh.geometry().dim()
rank = MPI.rank(mesh.mpi_comm())
V = FunctionSpace(mesh, "CG", 1)
v = TestFunction(V)
b = assemble(Constant(0.0)*v*dx)
source = []
point_coords = np.zeros(dim)
for p in point:
for i in range(dim):
point_coords[i-1] = p
if rank == 0:
source.append((Point(point_coords), 10.0))
ps = PointSource(V, source)
ps.apply(b)
# Checks b sums to correct value
b_sum = b.sum()
assert round(b_sum - len(point)*10.0) == 0
# Checks values added to correct part of vector
mesh_coords = V.tabulate_dof_coordinates()
for p in point:
for i in range(dim):
point_coords[i] = p
j = 0
for i in range(len(mesh_coords)//(dim)):
mesh_coords_check = mesh_coords[j:j + dim - 1]
if np.array_equal(point_coords, mesh_coords_check) is True:
assert np.round(b.array()[j//(dim)]-10.0) == 0.0
j += dim
def test_pointsource_matrix_second_constructor(mesh, point):
"""Tests point source when given different constructor PointSource(V1,
V2, point, mag) with a matrix and when placed at a node for 1D, 2D
and 3D. Global points given to constructor from rank 0
processor. Currently only implemented if V1=V2.
"""
V1 = FunctionSpace(mesh, "CG", 1)
V2 = FunctionSpace(mesh, "CG", 1)
rank = MPI.rank(mesh.mpi_comm())
u, v = TrialFunction(V1), TestFunction(V2)
w = Function(V1)
A = assemble(Constant(0.0) * u * v * dx)
if rank == 0:
ps = PointSource(V1, V2, point, 10.0)
else:
ps = PointSource(V1, V2, [])
ps.apply(A)
# Checks array sums to correct value
a_sum = MPI.sum(mesh.mpi_comm(), np.sum(A.array()))
assert round(a_sum - 10.0) == 0
# Checks point source is added to correct part of the array
A.get_diagonal(w.vector())
v2d = vertex_to_dof_map(V1)
for v in vertices(mesh):
if near(v.midpoint().distance(point), 0.0):
ind = v2d[v.index()]
if ind < len(A.array()):
assert np.round(w.vector()[ind] - 10.0) == 0
def test_multi_ps_vector_node(mesh):
"""Tests point source when given constructor PointSource(V, V, point,
mag) with a matrix when points placed at 3 node for 1D, 2D and
3D. Global points given to constructor from rank 0 processor.
"""
point = [0.0, 0.5, 1.0]
dim = mesh.geometry().dim()
rank = MPI.rank(mesh.mpi_comm())
V = FunctionSpace(mesh, "CG", 1)
v = TestFunction(V)
b = assemble(Constant(0.0) * v * dx)
source = []
point_coords = np.zeros(dim)
for p in point:
for i in range(dim):
point_coords[i - 1] = p
if rank == 0:
source.append((Point(point_coords), 10.0))
ps = PointSource(V, source)
ps.apply(b)
# Checks b sums to correct value
b_sum = b.sum()
assert round(b_sum - len(point) * 10.0) == 0
# Checks values added to correct part of vector
mesh_coords = V.tabulate_dof_coordinates()
for p in point:
for i in range(dim):
point_coords[i] = p
j = 0
for i in range(len(mesh_coords) // (dim)):
mesh_coords_check = mesh_coords[j:j + dim - 1]
if np.array_equal(point_coords, mesh_coords_check) is True:
assert np.round(b.array()[j // (dim)] - 10.0) == 0.0
j += dim
def test_multi_ps_matrix_node_local(mesh):
"""Tests point source when given constructor PointSource(V, V, point,
mag) with a matrix when points placed at 3 node for 1D, 2D and
3D. Local points given to constructor.
"""
V = FunctionSpace(mesh, "CG", 1)
u, v = TrialFunction(V), TestFunction(V)
w = Function(V)
A = assemble(Constant(0.0)*u*v*dx)
source = []
point_coords = mesh.coordinates()[0]
source.append((Point(point_coords), 10.0))
ps = PointSource(V, source)
ps.apply(A)
# Checks matrix sums to correct value.
A.get_diagonal(w.vector())
size = MPI.size(mesh.mpi_comm())
a_sum = MPI.sum(mesh.mpi_comm(), np.sum(A.array()))
assert round(a_sum - size*10.0) == 0
def test_multi_ps_matrix_node_local(mesh):
"""Tests point source when given constructor PointSource(V, V, point,
mag) with a matrix when points placed at 3 node for 1D, 2D and
3D. Local points given to constructor.
"""
V = FunctionSpace(mesh, "CG", 1)
u, v = TrialFunction(V), TestFunction(V)
w = Function(V)
A = assemble(Constant(0.0) * u * v * dx)
source = []
point_coords = mesh.coordinates()[0]
source.append((Point(point_coords), 10.0))
ps = PointSource(V, source)
ps.apply(A)
# Checks matrix sums to correct value.
A.get_diagonal(w.vector())
size = MPI.size(mesh.mpi_comm())
a_sum = MPI.sum(mesh.mpi_comm(), np.sum(A.array()))
assert round(a_sum - size * 10.0) == 0
def test_pointsource_vector(mesh):
"""Tests point source when given constructor PointSource(V, point,
mag) with a vector that isn't placed at a node for 1D, 2D and
3D. Global points given to constructor from rank 0 processor
"""
cell = Cell(mesh, 0)
point = cell.midpoint()
rank = MPI.rank(mesh.mpi_comm())
V = FunctionSpace(mesh, "CG", 1)
v = TestFunction(V)
b = assemble(Constant(0.0)*v*dx)
if rank == 0:
ps = PointSource(V, point, 10.0)
else:
ps = PointSource(V, [])
ps.apply(b)
# Checks array sums to correct value
b_sum = b.sum()
assert round(b_sum - 10.0) == 0
def main_slice_fem(mesh, subdomains, boundaries, src_pos, snk_pos):
sigma_ROI = Constant(params.sigma_roi)
sigma_SLICE = Constant(params.sigma_slice)
sigma_SALINE = Constant(params.sigma_saline)
sigma_AIR = Constant(0.)
V = FunctionSpace(mesh, "CG", 2)
v = TestFunction(V)
u = TrialFunction(V)
phi = Function(V)
dx = Measure("dx")(subdomain_data=subdomains)
ds = Measure("ds")(subdomain_data=boundaries)
a = inner(sigma_ROI * grad(u), grad(v))*dx(params.roivol) + \
inner(sigma_SLICE * grad(u), grad(v))*dx(params.slicevol) + \
inner(sigma_SALINE * grad(u), grad(v))*dx(params.salinevol)
L = Constant(0) * v * dx
A = assemble(a)
b = assemble(L)
x_pos, y_pos, z_pos = src_pos
point = Point(x_pos, y_pos, z_pos)
delta = PointSource(V, point, 1.)
delta.apply(b)
x_pos, y_pos, z_pos = snk_pos
point1 = Point(x_pos, y_pos, z_pos)
delta1 = PointSource(V, point1, -1.)
delta1.apply(b)
solver = KrylovSolver("cg", "ilu")
solver.parameters["maximum_iterations"] = 1000
solver.parameters["absolute_tolerance"] = 1E-8
solver.parameters["monitor_convergence"] = True
info(solver.parameters, True)
# set_log_level(PROGRESS) does not work in fenics 2018.1.0
solver.solve(A, phi.vector(), b)
ele_pos_list = params.ele_coords
vals = extract_pots(phi, ele_pos_list)
# np.save(os.path.join('results', save_as), vals)
return vals
def test_pointsource_vector(mesh):
"""Tests point source when given constructor PointSource(V, point,
mag) with a vector that isn't placed at a node for 1D, 2D and
3D. Global points given to constructor from rank 0 processor
"""
cell = Cell(mesh, 0)
point = cell.midpoint()
rank = MPI.rank(mesh.mpi_comm())
V = FunctionSpace(mesh, "CG", 1)
v = TestFunction(V)
b = assemble(Constant(0.0) * v * dx)
if rank == 0:
ps = PointSource(V, point, 10.0)
else:
ps = PointSource(V, [])
ps.apply(b)
# Checks array sums to correct value
b_sum = b.sum()
assert round(b_sum - 10.0) == 0
from dolfin import UnitSquareMesh, FunctionSpace, TestFunction, TrialFunction,\
Constant, Expression, assemble, dx, Point, PointSource, plot, interactive,\
inner, nabla_grad, Function, solve, MPI, mpi_comm_world
import numpy as np
from fenicstools.sourceterms import PointSources
mycomm = mpi_comm_world()
myrank = MPI.rank(mycomm)
mesh = UnitSquareMesh(2, 2)
V = FunctionSpace(mesh, 'Lagrange', 1)
trial = TrialFunction(V)
test = TestFunction(V)
f0 = Constant('0')
L0 = f0 * test * dx
b = assemble(L0)
P = Point(0.1, 0.5)
delta = PointSource(V, P, 1.0)
delta.apply(b)
myown = PointSources(V, [[0.1, 0.5], [0.9, 0.5]])
print 'p{}: max(PointSource)={}, max(PointSources[0])={}, max(PointSources[1])={}'.format(\
myrank, max(abs(b.array())), max(abs(myown[0].array())), max(abs(myown[1].array())))