def markBoundarySubdomains(mesh, boundaries, **kwargs):
'''Mark the boundaries of a mesh given a geometry
All interior faces are marked with zero
boundaries is a dictionary {label: definition of boundary}
'''
bndSubdomains = MeshFunction("size_t", mesh, mesh.geometry().dim()-1)
bndSubdomains.set_all(0)
for i in boundaries:
class BndSubDomain(SubDomain):
def inside(self, x, on_boundary):
value = array([0.0])
boundaries[i].eval(value, x)
return (value==1.0) and on_boundary
aux = BndSubDomain()
aux.mark(bndSubdomains, i)
# Save Dolfin XML format of the subdomains
if 'outputXmlGz' in kwargs:
File(kwargs['outputXmlGz']) << bndSubdomains
# Save sub domains to VTK files
if 'outputPvd' in kwargs:
File(kwargs['outputPvd']) << bndSubdomains
return bndSubdomains
## If there exist dirichlet boundary
#if hasDirichlet:
# if os.path.isfile(dirichletPath):
# dirichletSubdomain = MeshFunction("bool", mesh, dirichletPath)
# else:
# # Mark faces
# dirichletSubdomain.set_all(False)
# class Aux(SubDomain):
# def inside(self, x, on_boundary):
# value = array([0.0])
# physics.dirichletBnd.eval(value, x)
# return (value==1.0) and on_boundary
# aux = Aux()
# aux.mark(dirichletSubdomain, True)
# aux.mark(bndSubdomains, 0)
def markBoundariesOfMesh(mesh, geo, **kwargs):
'''Mark the boundaries of a mesh given a geometry
All interior faces are marked with zero
If the geometry has no marks, it will be mared using the convention:
face[0] = 1
face[1] = 2
...
face[N] = N+1
'''
# Reference point indexes in each face
geoBndPoints = [ face[0] for face in geo._faces ]
# Face normals
geoNormals = geo.getNormals()
# Create mesh functions over the cell facets
faceSubdomains = MeshFunction("size_t", mesh, geo._nDim-1)
# Mark all facets of the domain as 0
faceSubdomains.set_all(0)
# Mark boundary faces for face elements
for i in range(geo.getNoFaces()):
class BndSubDomain(SubDomain):
def inside(self, x, on_boundary):
return near( geoNormals[i].dot(Point(x)-geo._points[geoBndPoints[i]]), 0.0 ) and on_boundary
aSubDomain = BndSubDomain()
label = i+1
if hasattr(geo, 'facesMarkers'):
label = geo.facesMarkers[i]
aSubDomain.mark(faceSubdomains, label)
# Save Dolfin XML format of the subdomains
if 'outputXmlGz' in kwargs:
File(kwargs['outputXmlGz']) << faceSubdomains
# Save sub domains to VTK files
if 'outputPvd' in kwargs:
File(kwargs['outputPvd']) << faceSubdomains
return faceSubdomains
# Here we consider 0 as a internal face
bndSubdomains = markBoundariesOfMesh(mesh, geo, outputPvd="localBoundary.pvd")
globalBndSubdomains = MeshFunction("size_t", mesh, geo._nDim - 1)
# If there exist marked boundary
if 'boundaries' in dir(physics):
if (reutilizeBoundaryInfo and isfile(bndPath)):
globalBndSubdomains = MeshFunction("size_t", mesh, bndPath)
else:
globalBndSubdomains = markBoundarySubdomains(mesh,
physics.boundaries,
outputXmlGz=bndPath,
outputPvd=bndPvd)
else:
globalBndSubdomains.set_all(0)
# Boundary measures
ds = Measure('ds', domain=mesh, subdomain_data=bndSubdomains)
dsGlobal = Measure('ds', domain=mesh, subdomain_data=globalBndSubdomains)
###
### Numerical configuration
###
# MHM parameters
psiL = 1
# Psi scalar strings
# psiString = [ "1.0" ]
# psiString = []
else:
print("Mesh bndFile does not exist!")
exit(1)
# Here we consider 0 as a internal face
#dirichletSubdomain = MeshFunction("bool", mesh, geo.nDim-1)
bndSubdomains = MeshFunction("size_t", mesh, geo._nDim-1)
# If there exist marked boundary
if 'boundaries' in dir(physics):
if (reutilizeBoundaryInfo and isfile(bndPath)):
bndSubdomains = MeshFunction("size_t", mesh, bndPath)
else:
bndSubdomains = markBoundarySubdomains(mesh, physics.boundaries, outputXmlGz=bndPath, outputPvd=bndPvd)
else:
bndSubdomains.set_all(0)
## Get the set of subdomains
#setneumannSubdomains = set(neumannSubdomains.array())
#nBoundarySubdomains = len(setneumannSubdomains)-1 #exclude 0 labels
# Define measures
ds = Measure('ds', domain=mesh, subdomain_data=bndSubdomains) # boundary measure
# Plot mesh
#plot(mesh, interactive=True)
#plot(bndSubdomains, interactive=True)
#plot(dirichletSubdomain, interactive=True)
###
### Variational scheme