def test_convert_diffpack(self):
from dolfin import Mesh, MPI, MeshFunction
if MPI.num_processes() != 1:
return
fname = os.path.join("data", "diffpack_tet")
dfname = fname+".xml"
# Read triangle file and convert to a dolfin xml mesh file
meshconvert.diffpack2xml(fname+".grid", dfname)
# Read in dolfin mesh and check number of cells and vertices
mesh = Mesh(dfname)
self.assertEqual(mesh.num_vertices(), 27)
self.assertEqual(mesh.num_cells(), 48)
self.assertEqual(mesh.domains().markers(3).size(), 48)
self.assertEqual(mesh.domains().markers(2).size(), 16)
mf_basename = dfname.replace(".xml", "_marker_%d.xml")
for marker, num in [(3, 9), (6, 9), (7, 3), (8, 1)]:
mf_name = mf_basename % marker
mf = MeshFunction("uint", mesh, mf_name)
self.assertEqual(sum(mf.array()==marker), num)
os.unlink(mf_name)
# Clean up
os.unlink(dfname)
def test_convert_diffpack_2d(self):
from dolfin import Mesh, MPI, MeshFunction
fname = os.path.join(os.path.dirname(__file__), "data", "diffpack_tri")
dfname = fname + ".xml"
# Read triangle file and convert to a dolfin xml mesh file
meshconvert.diffpack2xml(fname + ".grid", dfname)
# Read in dolfin mesh and check number of cells and vertices
mesh = Mesh(dfname)
self.assertEqual(mesh.num_vertices(), 41)
self.assertEqual(mesh.num_cells(), 64)
self.assertEqual(len(mesh.domains().markers(2)), 64)
mf_basename = dfname.replace(".xml", "_marker_%d.xml")
for marker, num in [(1, 10), (2, 5), (3, 5)]:
mf_name = mf_basename % marker
mf = MeshFunction("size_t", mesh, mf_name)
self.assertEqual(sum(mf.array() == marker), num)
os.unlink(mf_name)
# Clean up
os.unlink(dfname)
def test_convert_diffpack(self):
from dolfin import Mesh, MPI, MeshFunction, mpi_comm_world
if MPI.size(mpi_comm_world()) != 1:
return
fname = os.path.join("data", "diffpack_tet")
dfname = fname + ".xml"
# Read triangle file and convert to a dolfin xml mesh file
meshconvert.diffpack2xml(fname + ".grid", dfname)
# Read in dolfin mesh and check number of cells and vertices
mesh = Mesh(dfname)
self.assertEqual(mesh.num_vertices(), 27)
self.assertEqual(mesh.num_cells(), 48)
self.assertEqual(len(mesh.domains().markers(3)), 48)
self.assertEqual(len(mesh.domains().markers(2)), 16)
mf_basename = dfname.replace(".xml", "_marker_%d.xml")
for marker, num in [(3, 9), (6, 9), (7, 3), (8, 1)]:
mf_name = mf_basename % marker
mf = MeshFunction("size_t", mesh, mf_name)
self.assertEqual(sum(mf.array() == marker), num)
os.unlink(mf_name)
# Clean up
os.unlink(dfname)
def test_convert_diffpack_2d(self):
from dolfin import Mesh, MPI, MeshFunction, mpi_comm_world
fname = os.path.join(os.path.dirname(__file__), "data", "diffpack_tri")
dfname = fname+".xml"
# Read triangle file and convert to a dolfin xml mesh file
meshconvert.diffpack2xml(fname+".grid", dfname)
# Read in dolfin mesh and check number of cells and vertices
mesh = Mesh(dfname)
self.assertEqual(mesh.num_vertices(), 41)
self.assertEqual(mesh.num_cells(), 64)
self.assertEqual(len(mesh.domains().markers(2)), 64)
mf_basename = dfname.replace(".xml", "_marker_%d.xml")
for marker, num in [(1,10), (2,5), (3,5)]:
mf_name = mf_basename % marker
mf = MeshFunction("size_t", mesh, mf_name)
self.assertEqual(sum(mf.array()==marker), num)
os.unlink(mf_name)
# Clean up
os.unlink(dfname)
def CladdingR_solver(FC_mesh, FC_facets, FC_fs, FC_info, D_post, R_path):
FC_fi, FC_fo = FC_fs
h, Tfc_inner, Tb, FC_Tave = FC_info
# Reading mesh data stored in .xdmf files.
mesh = Mesh()
with XDMFFile(FC_mesh) as infile:
infile.read(mesh)
mvc = MeshValueCollection("size_t", mesh, 1)
with XDMFFile(FC_facets) as infile:
infile.read(mvc, "name_to_read")
mf = cpp.mesh.MeshFunctionSizet(mesh, mvc)
#File("Circle_facet.pvd").write(mf)
# Mesh data
print('CladdingRod_mesh data\n', 'Number of cells: ', mesh.num_cells(),
'\n Number of nodes: ', mesh.num_vertices())
# Define variational problem
V = FunctionSpace(mesh, 'P', 1)
u = Function(V)
v = TestFunction(V)
# Define boundary conditions base on pygmsh mesh mark
bc = DirichletBC(V, Constant(Tfc_inner), mf, FC_fi)
ds = Measure("ds", domain=mesh, subdomain_data=mf, subdomain_id=FC_fo)
# Variational formulation
# Klbda_ZrO2 = 18/1000 # W/(m K) --> Nuclear reactor original source
# Klbda_ZrO2 = Constant(K_ZrO2(FC_Tave))
F = K_ZrO2(u) * dot(grad(u), grad(v)) * dx + h * (u - Tb) * v * ds
# Compute solution
du = TrialFunction(V)
Gain = derivative(F, u, du)
solve(F==0, u, bc, J=Gain, \
solver_parameters={"newton_solver": {"linear_solver": "lu",
"relative_tolerance": 1e-9}}, \
form_compiler_parameters={"cpp_optimize": True,
"representation": "uflacs",
"quadrature_degree" : 2}
) # mumps
# Save solution
if D_post:
fU_out = XDMFFile(os.path.join(R_path, 'FuelCladding', 'u.xdmf'))
fU_out.write_checkpoint(u, "T", 0, XDMFFile.Encoding.HDF5, False)
fU_out.close()
def FuelR_solver(FR_mesh, FR_facets, FR_f, FRod_info, D_post, R_path):
Qv, Tfr_outer, FR_Tave = FRod_info
# Reading mesh data stored in .xdmf files.
mesh = Mesh()
with XDMFFile(FR_mesh) as infile:
infile.read(mesh)
mvc = MeshValueCollection("size_t", mesh, 1)
with XDMFFile(FR_facets) as infile:
infile.read(mvc, "name_to_read")
mf = cpp.mesh.MeshFunctionSizet(mesh, mvc)
#File("Circle_facet.pvd").write(mf)
# Mesh data
print('FuelRod_mesh data\n', 'Number of cells: ', mesh.num_cells(),
'\n Number of nodes: ', mesh.num_vertices())
# Define variational problem
V = FunctionSpace(mesh, 'P', 1)
u = Function(V)
v = TestFunction(V)
f = Constant(Qv)
# Define boundary conditions base on pygmsh mesh mark
bc = DirichletBC(V, Constant(Tfr_outer), mf, FR_f)
# Variational formulation
# Klbda_UO2 = Constant(K_UO2(FR_Tave))
F = K_UO2(u) * dot(grad(u), grad(v)) * dx - f * v * dx
# Compute solution
du = TrialFunction(V)
Gain = derivative(F, u, du)
solve(F==0, u, bc, J=Gain, \
solver_parameters={"newton_solver": {"linear_solver": "lu",
"relative_tolerance": 1e-9}}, \
form_compiler_parameters={"cpp_optimize": True,
"representation": "uflacs",
"quadrature_degree" : 2}
) # mumps
# Save solution
if D_post:
fU_out = XDMFFile(os.path.join(R_path, 'FuelRod', 'u.xdmf'))
fU_out.write_checkpoint(u, "T", 0, XDMFFile.Encoding.HDF5, False)
fU_out.close()
class TestIonTag(unittest.TestCase):
def setUp(self, *args, **kwargs):
self.mesh = Mesh()
editor = MeshEditor()
editor.open(self.mesh, 2, 2) # topo_dim = 2, geom dim = 2
editor.init_vertices(6)
editor.init_cells(2)
vertex_0 = Vertex(self.mesh, 0)
vertex_1 = Vertex(self.mesh, 1)
vertex_2 = Vertex(self.mesh, 2)
vertex_3 = Vertex(self.mesh, 3)
vertex_4 = Vertex(self.mesh, 4)
vertex_5 = Vertex(self.mesh, 5)
editor.add_cell(0,1,2,3)
editor.add_cell(1,0,2,3)
editor.close()
def test_init(self):
# test possible arguments and failure cases...
#@todo implement the test once we have exception handling in the init method
# pass in a string for values and see what happens
values = 'i am just a string'
t = IonTag('foo',3,'int', self.mesh)
v = MeshEntity(self.mesh,0,1)
try:
t[v] = values
except ValueError:
pass
else:
raise AssertionError('It should have raised a value error!')
def test_get_set_del(self):
#Test the getter, setter and delete method
values = [1,2,3]
t = IonTag('foo',3,'int', self.mesh)
for v in vertices(self.mesh):
# test the setter
t[v] = values
# choose an entity in the mesh
v = MeshEntity(self.mesh,0,1)
# test the getter
self.assertTrue((t[v] == values).all())
#---------------------------------------------------------------------------------------
# Check delete of a tag entry (for an entity)
#---------------------------------------------------------------------------------------
# choose an entity to delete
entity_tuple = (v.dim(),v.index())
# check that tag has the entity, v, in it
self.assertTrue(t._entity_values.has_key(entity_tuple))
# delete a tag entry for an entity
del t[entity_tuple]
# check that the tag no longer has the entity, v, in it
self.assertFalse(t._entity_values.has_key(entity_tuple))
#---------------------------------------------------------------------------------------
# Add less number of values than the size defined in the tag object
#---------------------------------------------------------------------------------------
values = [1]
t = IonTag('foo',3,'int', self.mesh)
v = MeshEntity(self.mesh,0,1)
#@todo check to see why self.assertRaises is not working for unittest:
# with self.assertRaises(ValueError):
# t[v] = values
try:
t[v] = values
except ValueError:
pass
else:
raise AssertionError('A Value Error should have been raised!')
#---------------------------------------------------------------------------------------
# Add more number of values that the size defined in the tag object
#---------------------------------------------------------------------------------------
values = [1,2,3,4]
size = 2
t = IonTag('foo',size,'int', self.mesh)
v = MeshEntity(self.mesh,0,1)
t[v] = values
for key, value in t.iteritems():
self.assertEqual(len(value), size)
def test_len(self):
t = IonTag('foo',3,'int', self.mesh)
# we create a tag entry for every vertex of the mesh
for v in vertices(self.mesh):
# testing setter
t[v] = [1,2,3]
# we check that the number of tag entries is the same as the number we created
self.assertEqual(len(t), self.mesh.num_vertices())
def test_contains(self):
values = [1,2,3]
t = IonTag('foo',3,'int', self.mesh)
for v in vertices(self.mesh):
# testing setter
t[v] = values
v = MeshEntity(self.mesh,0,1)
# testing getter
self.assertTrue((t[v] == values).all())
#---------------------------------------------------------------------------------------
# Delete a tag entry (for an entity)
#---------------------------------------------------------------------------------------
# choose an entity to delete
entity_tuple = (v.dim(),v.index())
# check that tag has the entity, v, in it
self.assertTrue(t.__contains__(entity_tuple))
del t._entity_values[entity_tuple]
# check that the tag no longer has the entity, v, in it
self.assertFalse(t.__contains__(entity_tuple))
def test_len(self):
# Initial step: Feed in values to the vertices in the mesh
t = IonTag('foo',1,'int', self.mesh)
for x,v in enumerate(vertices(self.mesh)):
t[v] = (x,)
# test len
self.assertEqual(len(t), self.mesh.num_vertices())
def test_types(self):
# test with different types:
#@todo for each type check that input is cast to type
#---------------------------------------------------------------------------------------
# Ints
#---------------------------------------------------------------------------------------
t = IonTag('foo',3,'int', self.mesh)
self.assertEqual(t._type, 'int')
# Add some float values to the tag, and check if they are converted to
# int tag values
values = [1.23,2.232,3.323] # a list of int values
v = MeshEntity(self.mesh,0,1)
t[v] = values
for key, item in t.iteritems():
for num in item:
self.assertTrue(isinstance(num, int))
#---------------------------------------------------------------------------------------
# Floats
#---------------------------------------------------------------------------------------
t = IonTag('foo',3,'float', self.mesh)
self.assertEqual(t._type, 'float')
# Add some int values to the tag, and check if they are converted to
# float tag values
values = [1,2,3] # a list of int values
v = MeshEntity(self.mesh,0,1)
t[v] = values
for key, item in t.iteritems():
for num in item:
self.assertTrue(isinstance(num, float))
# now pass in complex values
values = [complex(1,2), complex(3,4), complex(5,6), complex(7,8)]
try:
t[v] = values
except TypeError:
pass
else:
raise AssertionError('Did not raise type error. Python should complain when converting from complex to float')
for key, item in t.iteritems():
for num in item:
self.assertTrue(isinstance(num, float))
#---------------------------------------------------------------------------------------
# Complex
#---------------------------------------------------------------------------------------
t = IonTag('foo',3,'complex', self.mesh)
self.assertEqual(t._type, 'complex')
values = [1,2,3,4,5]
v = MeshEntity(self.mesh,0,1)
t[v] = values
for key, item in t.iteritems():
for num in item:
self.assertTrue(isinstance(num, complex))
#---------------------------------------------------------------------------------------
# String
#---------------------------------------------------------------------------------------
#@todo: Strings cannot be passed in. This is because it is a variable sized data type, and numpy cannot handle it
# t = IonTag('foo',3,'string', self.mesh)
# self.assertEqual(t._type, 'string')
#
# v = MeshEntity(self.mesh,0,1)
#
# # passing in a string
# values = ['string1', ' string2']
# t[v] = values
#
# # passing in a number
# values = [3,4]
# try:
# t[v] = values
# except ValueError:
# pass
# else:
# raise AssertionError('Numpy should complain')
#
#
# for key, item in t.iteritems():
# for num in item:
# self.assertTrue(isinstance(num, str))
#---------------------------------------------------------------------------------------
# User defined
#---------------------------------------------------------------------------------------
# t = IonTag('foo',3,'user_defined', self.mesh)
# self.assertEqual(t._type, 'user_defined')
#---------------------------------------------------------------------------------------
# Object
#---------------------------------------------------------------------------------------
#@todo: numpy cannot create object arrays from iterator. so objects cannot be passed in as values
# t = IonTag('foo',3,'object', self.mesh)
# self.assertEqual(t._type, 'object')
#
# values = [1,2,3,4]
#
# v = MeshEntity(self.mesh,0,1)
# t[v] = values
#
# for key, item in t.iteritems():
# for num in item:
# self.assertTrue(isinstance(num, object))
def test_iter(self):
# test the iterator and verify that the correct type is passed back
#------------------------------------------------------------
# Initial step: Feed in values to the vertices in the mesh
#------------------------------------------------------------
t = IonTag('foo',1,'int', self.mesh)
for x,v in enumerate(vertices(self.mesh)):
t[v] = (x,)
#------------------------------------------------------------
# Test the iteration over the tags
#------------------------------------------------------------
for key, item in t.iteritems():
self.assertEqual(t[ key ], item )
self.assertTrue(isinstance(key, MeshEntity))
self.assertTrue(isinstance(item[0], int ))
def test_properties(self):
# contains, len etc...
#@todo may be we can remove this test method as the contains() and len() methods have their own separate test methods
pass
import numpy
from dolfin import Mesh
mesh = Mesh("mesh.xml.gz")
E = mesh.cells()
M = numpy.fromfile('materials.np')
I = -numpy.ones(mesh.num_vertices())
for i in range(6):
edx = numpy.nonzero((M > 10 * (i + 1)) * (M < 10 * (i + 2)))[0]
idx = (numpy.unique(E[edx, 0:3])).astype(int)
I[idx] = i * 0.2
edx = numpy.nonzero(M == 7)[0]
idx = (numpy.unique(E[edx, 0:3])).astype(int)
I[idx] = -2
from viper import Viper
pv = Viper(mesh, I)
pv.interactive()
def test_convert_triangle(self): # Disabled because it fails, see FIXME below
# test no. 1
from dolfin import Mesh, MPI
if MPI.num_processes() != 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
if MPI.num_processes() != 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()
self.assertTrue(edge_markers is not None)
length0 = reduce(add, (Edge(mesh, e.index()).length() \
for e in SubsetIterator(edge_markers, 0)), 0.0)
length1 = reduce(add, (Edge(mesh, e.index()).length() \
for e in SubsetIterator(edge_markers, 1)), 0.0)
# 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 test_convert_triangle(
self): # Disabled because it fails, see FIXME below
# test no. 1
from dolfin import Mesh, MPI
fname = os.path.join(os.path.dirname(__file__), "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
fname = os.path.join(os.path.dirname(__file__), "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 MeshFunction and assign the values based on the
# converted Meshfunction
cf = MeshFunction("size_t", mesh, mesh.topology().dim())
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 list(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)
if __name__ == "__main__":
xlim = 0.0, 3.0
ylim = 0.0, 0.0127
WAid = 12
INid = 13
BND_ids = WAid, INid
meszf = 0.001 # mesh element size factor
Domain, Facets = Generate_PBRpygmsh(xlim,
ylim,
BND_ids,
meszf,
folder='pygmeshio_test')
mesh_D = Mesh()
with XDMFFile(Domain) as infile:
infile.read(mesh_D)
mesh_F = Mesh()
with XDMFFile(Facets) as infile:
infile.read(mesh_F)
print('num_cells :', mesh_D.num_cells())
print('num_vertices:', mesh_D.num_vertices())
print('cell_type :', mesh_D.ufl_cell())
#print('num_facets:', mesh_F.num_facets())
#print('num_edges:', mesh_F.num_edges())
def scalar_laplacians(
mesh: df.Mesh,
markers: Optional[Dict[str, int]] = None,
ffun: Optional[MeshFunction] = None,
use_krylov_solver: bool = False,
krylov_solver_atol: Optional[float] = None,
krylov_solver_rtol: Optional[float] = None,
krylov_solver_max_its: Optional[int] = None,
verbose: bool = False,
strict: bool = False,
) -> Dict[str, df.Function]:
"""
Calculate the laplacians
Arguments
---------
mesh : dolfin.Mesh
A dolfin mesh
markers : dict (optional)
A dictionary with the markers for the
different bondaries defined in the facet function
or within the mesh itself.
The follwing markers must be provided:
'base', 'lv', 'epi, 'rv' (optional).
If the markers are not provided the following default
vales will be used: base = 10, rv = 20, lv = 30, epi = 40.
fiber_space : str
A string on the form {familiy}_{degree} which
determines for what space the fibers should be calculated for.
use_krylov_solver: bool
If True use Krylov solver, by default False
krylov_solver_atol: float (optional)
If a Krylov solver is used, this option specifies a
convergence criterion in terms of the absolute
residual. Default: 1e-15.
krylov_solver_rtol: float (optional)
If a Krylov solver is used, this option specifies a
convergence criterion in terms of the relative
residual. Default: 1e-10.
krylov_solver_max_its: int (optional)
If a Krylov solver is used, this option specifies the
maximum number of iterations to perform. Default: 10000.
verbose: bool
If true, print more info, by default False
strict: bool
If true raise RuntimeError if solutions does not sum to 1.0
"""
if not isinstance(mesh, df.Mesh):
raise TypeError("Expected a dolfin.Mesh as the mesh argument.")
# Init connectivities
mesh.init(2)
if ffun is None:
ffun = df.MeshFunction("size_t", mesh, 2, mesh.domains())
# Boundary markers, solutions and cases
cases, boundaries, markers = find_cases_and_boundaries(ffun, markers)
markers_str = "\n".join(
["{}: {}".format(k, v) for k, v in markers.items()])
df.info(("Compute scalar laplacian solutions with the markers: \n"
"{}").format(markers_str, ), )
check_boundaries_are_marked(
mesh=mesh,
ffun=ffun,
markers=markers,
boundaries=boundaries,
)
# Compte the apex to base solutons
num_vertices = mesh.num_vertices()
num_cells = mesh.num_cells()
if mesh.mpi_comm().size > 1:
num_vertices = mesh.mpi_comm().allreduce(num_vertices)
num_cells = mesh.mpi_comm().allreduce(num_cells)
df.info(" Num vertices: {0}".format(num_vertices))
df.info(" Num cells: {0}".format(num_cells))
if "mv" in cases and "av" in cases:
# Use Doste approach
pass
# Else use the Bayer approach
return bayer(
cases=cases,
mesh=mesh,
markers=markers,
ffun=ffun,
verbose=verbose,
use_krylov_solver=use_krylov_solver,
strict=strict,
krylov_solver_atol=krylov_solver_atol,
krylov_solver_rtol=krylov_solver_rtol,
krylov_solver_max_its=krylov_solver_max_its,
)
import numpy
from dolfin import Mesh
mesh = Mesh("mesh.xml.gz")
E = mesh.cells()
M = numpy.fromfile('materials.np');
I = -numpy.ones(mesh.num_vertices())
for i in range(6):
edx = numpy.nonzero((M>10*(i+1))*(M<10*(i+2)))[0]
idx = (numpy.unique(E[edx,0:3])).astype(int)
I[idx] = i*0.2
edx = numpy.nonzero(M==7)[0]
idx = (numpy.unique(E[edx,0:3])).astype(int)
I[idx] = -2;
from viper import Viper
pv = Viper(mesh, I)
pv.interactive()
dest='mesh_size',
action='store_false')
parser.set_defaults(mesh_size=False)
args = parser.parse_args()
h5_file = convert(args.input)
# VTK visualize tags
if args.save_pvd or args.mesh_size:
h5 = HDF5File(mpi_comm_world(), h5_file, 'r')
mesh = Mesh()
h5.read(mesh, 'mesh', False)
info('Mesh has %d cells' % mesh.num_cells())
info('Mesh has %d vertices' % mesh.num_vertices())
info('Box size %s' %
(mesh.coordinates().max(axis=0) - mesh.coordinates().min(axis=0)))
hmin, hmax = mesh.hmin(), mesh.hmax()
info('Mesh has sizes %g %g' % (hmin, hmax))
root = os.path.splitext(args.input)[0]
tdim = mesh.topology().dim()
data_sets = ('curves', 'surfaces', 'volumes')
dims = (1, tdim - 1, tdim)
for ds, dim in zip(data_sets, dims):
if h5.has_dataset(ds):
f = MeshFunction('size_t', mesh, dim, 0)
h5.read(f, ds)
