def create(mesh, domain_ids, invert=False):
"""
Creates a wrapped mesh from a super mesh for a given collection
of domain IDs.
*Arguments*
mesh (:class:`dolfin.Mesh`)
The mesh.
domain_ids (:class:`[int]`)
List of domain IDs
invert (:class:`bool`)
Invert list of domain IDs
*Returns*
:class:`WrappedMesh`
The wrapped mesh
"""
if invert or isinstance(domain_ids, list) or isinstance(
domain_ids, tuple):
if isinstance(domain_ids, int): domain_ids = (domain_ids, )
subdomains = MeshFunction('size_t', mesh, 3, mesh.domains())
combined_subdomains = CellFunction("size_t", mesh, 0)
for domain_id in domain_ids:
combined_subdomains.array()[subdomains.array() ==
domain_id] = 1
submesh = SubMesh(mesh, combined_subdomains, 0 if invert else 1)
else:
submesh = SubMesh(mesh, domain_ids)
submesh.__class__ = WrappedMesh
submesh._init(mesh)
return submesh
def array_to_meshfunction(x, mesh):
"Convert array x to cell function on Omega"
f = CellFunction("double", mesh)
if not f.size() == x.size:
raise RuntimeError, "Size of vector does not match number of cells."
for i in range(x.size):
f[i] = x[i]
return f
def test_store_mesh(casedir):
pp = PostProcessor(dict(casedir=casedir))
from dolfin import (UnitSquareMesh, CellFunction, FacetFunction,
AutoSubDomain, Mesh, HDF5File, assemble, Expression,
ds, dx)
# Store mesh
mesh = UnitSquareMesh(6, 6)
celldomains = CellFunction("size_t", mesh)
celldomains.set_all(0)
AutoSubDomain(lambda x: x[0] < 0.5).mark(celldomains, 1)
facetdomains = FacetFunction("size_t", mesh)
AutoSubDomain(lambda x, on_boundary: x[0] < 0.5 and on_boundary).mark(
facetdomains, 1)
pp.store_mesh(mesh, celldomains, facetdomains)
# Read mesh back
mesh2 = Mesh()
f = HDF5File(mpi_comm_world(), os.path.join(pp.get_casedir(), "mesh.hdf5"),
'r')
f.read(mesh2, "Mesh", False)
celldomains2 = CellFunction("size_t", mesh2)
f.read(celldomains2, "CellDomains")
facetdomains2 = FacetFunction("size_t", mesh2)
f.read(facetdomains2, "FacetDomains")
e = Expression("1+x[1]", degree=1)
dx1 = dx(1, domain=mesh, subdomain_data=celldomains)
dx2 = dx(1, domain=mesh2, subdomain_data=celldomains2)
C1 = assemble(e * dx1)
C2 = assemble(e * dx2)
assert abs(C1 - C2) < 1e-10
ds1 = ds(1, domain=mesh, subdomain_data=facetdomains)
ds2 = ds(1, domain=mesh2, subdomain_data=facetdomains2)
F1 = assemble(e * ds1)
F2 = assemble(e * ds2)
assert abs(F1 - F2) < 1e-10
def refine_cylinder(mesh):
'Refine mesh by cutting cells around the cylinder.'
h = mesh.hmin()
center = Point(c_x, c_y)
cell_f = CellFunction('bool', mesh, False)
for cell in cells(mesh):
if cell.midpoint().distance(center) < r + h:
cell_f[cell] = True
mesh = refine(mesh, cell_f)
return mesh
def refine_perimeter(mesh):
"""Refine largest boundary triangles."""
mesh.init(1, 2)
perimeter = [
c for c in cells(mesh) if any([f.exterior() for f in facets(c)])
]
marker = CellFunction('bool', mesh, False)
max_size = max([c.diameter() for c in perimeter])
for c in perimeter:
marker[c] = c.diameter() > 0.75 * max_size
return refine(mesh, marker)
def square_with_obstacle():
# Create classes for defining parts of the boundaries and the interior
# of the domain
class Left(SubDomain):
def inside(self, x, on_boundary):
return near(x[0], 0.0)
class Right(SubDomain):
def inside(self, x, on_boundary):
return near(x[0], 1.0)
class Bottom(SubDomain):
def inside(self, x, on_boundary):
return near(x[1], 0.0)
class Top(SubDomain):
def inside(self, x, on_boundary):
return near(x[1], 1.0)
class Obstacle(SubDomain):
def inside(self, x, on_boundary):
return between(x[1], (0.5, 0.7)) and between(x[0], (0.2, 1.0))
# Initialize sub-domain instances
left = Left()
top = Top()
right = Right()
bottom = Bottom()
obstacle = Obstacle()
# Define mesh
mesh = UnitSquareMesh(100, 100, "crossed")
# Initialize mesh function for interior domains
domains = CellFunction("size_t", mesh)
domains.set_all(0)
obstacle.mark(domains, 1)
# Initialize mesh function for boundary domains
boundaries = MeshFunction("size_t", mesh, mesh.topology().dim() - 1)
boundaries.set_all(0)
left.mark(boundaries, 1)
top.mark(boundaries, 2)
right.mark(boundaries, 3)
bottom.mark(boundaries, 4)
boundary_indices = {"left": 1, "top": 2, "right": 3, "bottom": 4}
f = Constant(0.0)
theta0 = Constant(293.0)
return mesh, f, boundaries, boundary_indices, theta0
def refine_mesh(mesh, size, edge=False):
""" Refine mesh to at least given size, using one of two methods. """
dim = mesh.topology().dim()
if not edge:
# FEniCS 1.5 and 1.6 have a bug which prevents uniform refinement
while mesh.size(dim) < size:
mesh = refine(mesh)
else:
# Refine based on MeshFunction
while mesh.size(dim) < size:
print refine(mesh).size(dim)
full = CellFunction("bool", mesh, True)
print refine(mesh, full).size(dim)
mesh = refine(mesh, full)
return mesh
def as_pvd(h5_file):
'''Store facet and cell function for pvd'''
root, ext = os.path.splitext(h5_file)
mesh = Mesh()
hdf = HDF5File(mesh.mpi_comm(), h5_file, 'r')
hdf.read(mesh, '/mesh', False)
facet_markers = FacetFunction('size_t', mesh)
hdf.read(facet_markers, '/facet_markers')
cell_markers = CellFunction('size_t', mesh)
hdf.read(cell_markers, '/cell_markers')
File(root + 'facets' + '.pvd') << facet_markers
File(root + 'volumes' + '.pvd') << cell_markers
return True
def refine_mesh_upto(mesh, size, edge=False):
""" Refine mesh to at most given size, using one of two methods. """
dim = mesh.topology().dim()
if mesh.size(dim) > size:
return mesh
if not edge:
while True:
# FEniCS 1.5 and 1.6 have a bug which prevents uniform refinement
mesh2 = refine(mesh)
if mesh2.size(dim) > size:
return mesh
mesh = mesh2
else:
# Refine based on MeshFunction
while True:
all = CellFunction("bool", mesh, True)
mesh2 = refine(mesh, all)
if mesh2.size(dim) > size:
return mesh
mesh = mesh2
def test_ale(self):
print ""
print "Testing ALE::move(Mesh& mesh0, const Mesh& mesh1)"
# Create some mesh
mesh = UnitSquareMesh(4, 5)
# Make some cell function
# FIXME: Initialization by array indexing is probably
# not a good way for parallel test
cellfunc = CellFunction('size_t', mesh)
cellfunc.array()[0:4] = 0
cellfunc.array()[4:] = 1
# Create submeshes - this does not work in parallel
submesh0 = SubMesh(mesh, cellfunc, 0)
submesh1 = SubMesh(mesh, cellfunc, 1)
# Move submesh0
disp = Constant(("0.1", "-0.1"))
submesh0.move(disp)
# Move and smooth submesh1 accordignly
submesh1.move(submesh0)
# Move mesh accordingly
parent_vertex_indices_0 = \
submesh0.data().array('parent_vertex_indices', 0)
parent_vertex_indices_1 = \
submesh1.data().array('parent_vertex_indices', 0)
mesh.coordinates()[parent_vertex_indices_0[:]] = \
submesh0.coordinates()[:]
mesh.coordinates()[parent_vertex_indices_1[:]] = \
submesh1.coordinates()[:]
# If test passes here then it is probably working
# Check for cell quality for sure
magic_number = 0.28
rmin = MeshQuality.radius_ratio_min_max(mesh)[0]
self.assertTrue(rmin > magic_number)
def adaptive(self, mesh, eigv, eigf):
"""Refine mesh based on residual errors."""
fraction = 0.1
C = FunctionSpace(mesh, "DG", 0) # constants on triangles
w = TestFunction(C)
h = CellSize(mesh)
n = FacetNormal(mesh)
marker = CellFunction("bool", mesh)
print len(marker)
indicators = np.zeros(len(marker))
for e, u in zip(eigv, eigf):
errform = avg(h) * jump(grad(u), n) ** 2 * avg(w) * dS \
+ h * (inner(grad(u), n) - Constant(e) * u) ** 2 * w * ds
if self.degree > 1:
errform += h**2 * div(grad(u))**2 * w * dx
indicators[:] += assemble(errform).array() # errors for each cell
print "Residual error: ", sqrt(sum(indicators) / len(eigv))
cutoff = sorted(indicators,
reverse=True)[int(len(indicators) * fraction) - 1]
marker.array()[:] = indicators > cutoff # mark worst errors
mesh = refine(mesh, marker)
return mesh
#for mesh in [UnitSquareMesh(8,8)]:
for mesh in [UnitSquareMesh(8, 8), UnitCubeMesh(6, 6, 6)]:
#print mesh.num_cells()
#exit()
# from dolfin import BoundaryMesh
#mesh = BoundaryMesh(mesh, "exterior")
#mf = MeshFunction("size_t", mesh, mesh.ufl_cell().topological_dimension())
#mf.set_all(0)
#class Left(SubDomain):
# def inside(self, x, on_boundary):
# return x[0] < 0.4
#Left().mark(mf, 1)
cell_domains = CellFunction("size_t", mesh)
cell_domains.set_all(0)
subdomains = AutoSubDomain(lambda x: x[0] < 0.5)
subdomains.mark(cell_domains, 1)
if MPI.size(mpi_comm_world()) == 1:
submesh = SubMesh(mesh, cell_domains, 1)
else:
submesh = create_submesh(mesh, cell_domains, 1)
#MPI.barrier(mpi_comm_world())
#continue
V = FunctionSpace(submesh, "CG", 2)
expr = Expression("x[0]*x[1]*x[1]+4*x[2]", degree=2)
u = project(expr, V)
def test_convert_triangle(
self): # Disabled because it fails, see FIXME below
# test no. 1
from dolfin import Mesh, MPI, mpi_comm_world
# MPI_COMM_WORLD wrapper
if MPI.size(mpi_comm_world()) != 1:
return
fname = os.path.join("data", "triangle")
dfname = fname + ".xml"
# Read triangle file and convert to a dolfin xml mesh file
meshconvert.triangle2xml(fname, dfname)
# Read in dolfin mesh and check number of cells and vertices
mesh = Mesh(dfname)
self.assertEqual(mesh.num_vertices(), 96)
self.assertEqual(mesh.num_cells(), 159)
# Clean up
os.unlink(dfname)
# test no. 2
from dolfin import MPI, Mesh, MeshFunction, \
edges, Edge, faces, Face, \
SubsetIterator, facets, CellFunction, mpi_comm_world
if MPI.size(mpi_comm_world()) != 1:
return
fname = os.path.join("data", "test_Triangle_3")
dfname = fname + ".xml"
dfname0 = fname + ".attr0.xml"
# Read triangle file and convert to a dolfin xml mesh file
meshconvert.triangle2xml(fname, dfname)
# Read in dolfin mesh and check number of cells and vertices
mesh = Mesh(dfname)
mesh.init()
mfun = MeshFunction('double', mesh, dfname0)
self.assertEqual(mesh.num_vertices(), 58)
self.assertEqual(mesh.num_cells(), 58)
# Create a size_t CellFunction and assign the values based on the
# converted Meshfunction
cf = CellFunction("size_t", mesh)
cf.array()[mfun.array() == 10.0] = 0
cf.array()[mfun.array() == -10.0] = 1
# Meassure total area of cells with 1 and 2 marker
add = lambda x, y: x + y
area0 = reduce(add, (Face(mesh, cell.index()).area() \
for cell in SubsetIterator(cf, 0)), 0.0)
area1 = reduce(add, (Face(mesh, cell.index()).area() \
for cell in SubsetIterator(cf, 1)), 0.0)
total_area = reduce(add, (face.area() for face in faces(mesh)), 0.0)
# Check that all cells in the two domains are either above or below y=0
self.assertTrue(
all(cell.midpoint().y() < 0 for cell in SubsetIterator(cf, 0)))
self.assertTrue(
all(cell.midpoint().y() > 0 for cell in SubsetIterator(cf, 1)))
# Check that the areas add up
self.assertAlmostEqual(area0 + area1, total_area)
# Measure the edge length of the two edge domains
#edge_markers = mesh.domains().facet_domains()
edge_markers = mesh.domains().markers(mesh.topology().dim() - 1)
self.assertTrue(edge_markers is not None)
#length0 = reduce(add, (Edge(mesh, e.index()).length() \
# for e in SubsetIterator(edge_markers, 0)), 0.0)
length0, length1 = 0.0, 0.0
for item in edge_markers.items():
if item[1] == 0:
e = Edge(mesh, int(item[0]))
length0 += Edge(mesh, int(item[0])).length()
elif item[1] == 1:
length1 += Edge(mesh, int(item[0])).length()
# Total length of all edges and total length of boundary edges
total_length = reduce(add, (e.length() for e in edges(mesh)), 0.0)
boundary_length = reduce(add, (Edge(mesh, f.index()).length() \
for f in facets(mesh) if f.exterior()), 0.0)
# Check that the edges add up
self.assertAlmostEqual(length0 + length1, total_length)
self.assertAlmostEqual(length1, boundary_length)
# Clean up
os.unlink(dfname)
os.unlink(dfname0)
def construct_sleeve_geometry(
t_wall=None,
t_gap=None,
t_sleeve=None,
L_wall=None,
L_sleeve=None,
refinement_parameter=16,
):
#
# Define the domain as a polygon
mesh = Mesh()
domain = Polygon([
dolfin.Point(0.0, 0.0),
dolfin.Point(L_wall, 0.0),
dolfin.Point(L_wall, t_wall),
dolfin.Point((L_wall - L_sleeve), t_wall),
dolfin.Point((L_wall - L_sleeve), (t_wall + t_gap)),
dolfin.Point(L_wall, (t_wall + t_gap)),
dolfin.Point(L_wall, (t_sleeve + t_wall + t_gap)),
dolfin.Point((L_wall - L_sleeve), (t_sleeve + t_wall + t_gap)),
dolfin.Point((L_wall - L_sleeve - t_sleeve - t_gap), t_wall),
dolfin.Point(0.0, t_wall),
], )
#
# Define weld region
weld_subdomain = Polygon([
dolfin.Point((L_wall - L_sleeve - t_sleeve - t_gap), t_wall),
dolfin.Point((L_wall - L_sleeve), t_wall),
dolfin.Point((L_wall - L_sleeve), (t_wall + t_sleeve + t_gap)),
])
domain.set_subdomain(1, weld_subdomain)
#
# Mesh
mesh = generate_mesh(domain, refinement_parameter)
#
# Refine in the weld
cell_markers = CellFunction("bool", mesh)
cell_markers.set_all(False)
c = is_in_weld_region(
t_wall=t_wall,
t_gap=t_gap,
t_sleeve=t_sleeve,
L_wall=L_wall,
L_sleeve=L_sleeve,
)
class MyDomain(SubDomain):
def inside(self, x, on_boundary):
return c(x)
my_domain = MyDomain()
my_domain.mark(cell_markers, True)
mesh = refine(mesh, cell_markers)
#
# Define the upper and lower boundaries
class Upper(SubDomain):
def inside(self, x, on_boundary):
#
# Define relevant points
xb1 = (L_wall - L_sleeve - t_sleeve - t_gap)
xb2 = (L_wall - L_sleeve)
yb1 = t_wall
yb2 = (t_wall + t_sleeve + t_gap)
#
# Define params for assessing if on a line between points
dx_line = xb2 - xb1
dy_line = yb2 - yb1
dx = x[0] - xb1
dy = x[1] - yb1
zero = dx * dy_line - dx_line * dy
#
is_upper_region_one = x[0] <= xb1 and near(x[1], yb1)
is_upper_region_two = x[0] >= xb1 and x[0] <= xb2 and near(zero, 0)
is_upper_region_three = x[0] >= xb2 and near(x[1], yb2)
#
return is_upper_region_one or is_upper_region_two or is_upper_region_three
class Lower(SubDomain):
def inside(self, x, on_boundary):
return near(x[1], 0)
#
# Set boundaries
upper = Upper()
lower = Lower()
boundaries = FacetFunction("size_t", mesh)
boundaries.set_all(0)
upper.mark(boundaries, 1)
lower.mark(boundaries, 2)
#
return (mesh, boundaries)
