def setupMeshes(cls, mesh, N, num_refine=0, randref=(1.0, 1.0)):
"""Create a set of N meshes based on provided mesh. Parameters
num_refine>=0 and randref specify refinement
adjustments. num_refine specifies the number of refinements
per mesh, randref[0] specifies the probability that a given
mesh is refined, and randref[1] specifies the probability that
an element of the mesh is refined (if it is refined at all).
"""
assert num_refine >= 0
assert 0 < randref[0] <= 1.0
assert 0 < randref[1] <= 1.0
# create set of (refined) meshes
meshes = list();
for _ in range(N):
m = Mesh(mesh)
for _ in range(num_refine):
if randref[0] == 1.0 and randref[1] == 1.0:
m = refine(m)
elif random() <= randref[0]:
cell_markers = CellFunction("bool", m)
cell_markers.set_all(False)
cell_ids = range(m.num_cells())
shuffle(cell_ids)
num_ref_cells = int(ceil(m.num_cells() * randref[1]))
for cell_id in cell_ids[0:num_ref_cells]:
cell_markers[cell_id] = True
m = refine(m, cell_markers)
meshes.append(m)
return meshes
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 vtk_ug_to_dolfin_mesh(ug):
"""
Create a DOLFIN Mesh from a vtkUnstructuredGrid object
"""
if not isinstance(ug, vtk.vtkUnstructuredGrid):
raise TypeError("Expected a 'vtkUnstructuredGrid'")
# Get mesh data
num_cells = int(ug.GetNumberOfCells())
num_vertices = int(ug.GetNumberOfPoints())
# Get topological and geometrical dimensions
cell = ug.GetCell(0)
gdim = int(cell.GetCellDimension())
cell_type = cell.GetCellType()
if cell_type not in [vtk.VTK_TETRA, vtk.VTK_TRIANGLE]:
raise TypeError("DOLFIN only support meshes of triangles " + \
"and tetrahedrons.")
tdim = 3 if cell_type == vtk.VTK_TETRA else 2
# Create empty DOLFIN Mesh
mesh = Mesh()
editor = MeshEditor()
editor.open(mesh, tdim, gdim)
editor.init_cells(num_cells)
editor.init_vertices(num_vertices)
editor.close()
# Assign the cell and vertex informations directly from the vtk data
cells_array = array_handler.vtk2array(ug.GetCells().GetData())
# Get the assumed fixed size of indices and create an index array
cell_size = cell.GetPointIds().GetNumberOfIds()
cellinds = np.arange(len(cells_array))
# Each cell_ids_size:th data point need to be deleted from the
# index array
ind_delete = slice(0, len(cells_array), cell_size+1)
# Check that the removed value all have the same value which should
# be the size of the data
if not np.all(cells_array[ind_delete]==cell_size):
raise ValueError("Expected all cells to be of the same size")
cellinds = np.delete(cellinds, ind_delete)
# Get cell data from mesh and make it writeable (cell data is non
# writeable by default) and update the values
mesh_cells = mesh.cells()
mesh_cells.flags.writeable = True
mesh_cells[:] = np.reshape(cells_array[cellinds], \
(num_cells , cell_size))
# Set coordinates from vtk data
vertex_array = array_handler.vtk2array(ug.GetPoints().GetData())
if vertex_array.shape[1] != gdim:
vertex_array = vertex_array[:,:gdim]
mesh.coordinates()[:] = vertex_array
return mesh
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 make_mesh(coordinates, cells, tdim, gdim, mesh=None):
'''Mesh by MeshEditor from vertices and cells'''
if mesh is None:
mesh = Mesh()
assert mesh.mpi_comm().size == 1
module.fill_mesh(coordinates.flatten(), cells.flatten(), tdim, gdim, mesh)
return mesh
def readmesh(mesh_file):
''' read HDF5 or DOLFIN XML mesh '''
# TODO: exceptions, files exist?
from dolfin import Mesh, MeshFunction, CellFunction, HDF5File, \
FacetFunction
tmp = mesh_file.split('/')[-1].split('.')
mesh_type = tmp[-1]
mesh_name = '.'.join(tmp[0:-1])
if mesh_type == 'xml':
mesh = Mesh(mesh_file)
rank = mesh.mpi_comm().Get_rank()
try:
subdomains = MeshFunction("size_t", mesh,
mesh_name+"_physical_region.xml")
except:
if rank == 0:
print('no subdomain file found (%s)' %
(mesh_name+"_physical_region.xml"))
subdomains = CellFunction("size_t", mesh)
try:
boundaries = MeshFunction("size_t", mesh,
mesh_name+"_facet_region.xml")
except:
if rank == 0:
print('no boundary file found (%s)' %
(mesh_name+"_physical_region.xml"))
boundaries = FacetFunction("size_t", mesh)
elif mesh_type == 'h5':
mesh = Mesh()
rank = mesh.mpi_comm().Get_rank()
hdf = HDF5File(mesh.mpi_comm(), mesh_file, "r")
hdf.read(mesh, "/mesh", False)
subdomains = CellFunction("size_t", mesh)
boundaries = FacetFunction("size_t", mesh)
if hdf.has_dataset('subdomains'):
hdf.read(subdomains, "/subdomains")
else:
if rank == 0:
print('no <subdomains> datasets found in file %s' % mesh_file)
if hdf.has_dataset('boundaries'):
hdf.read(boundaries, "/boundaries")
else:
if rank == 0:
print('no <boundaries> datasets found in file %s' % mesh_file)
elif mesh_type in ['xdmf', 'xmf']:
import sys
sys.exit('XDMF not supported yet. Use HDF5 instead!')
else:
import sys
sys.exit('mesh format not recognized. try XML (serial) or HDF5')
# NOTE http://fenicsproject.org/qa/5337/importing-marked-mesh-for-parallel-use
# see file xml2xdmf.py
return mesh, subdomains, boundaries
def cyclic3D(u):
""" Symmetrize with respect to (xyz) cycle. """
try:
nrm = np.linalg.norm(u.vector())
V = u.function_space()
assert V.mesh().topology().dim() == 3
mesh1 = Mesh(V.mesh())
mesh1.coordinates()[:, :] = mesh1.coordinates()[:, [1, 2, 0]]
W1 = FunctionSpace(mesh1, 'CG', 1)
# testing if symmetric
bc = DirichletBC(V, 1, DomainBoundary())
test = Function(V)
bc.apply(test.vector())
test = interpolate(Function(W1, test.vector()), V)
assert max(test.vector()) - min(test.vector()) < 1.1
v1 = interpolate(Function(W1, u.vector()), V)
mesh2 = Mesh(mesh1)
mesh2.coordinates()[:, :] = mesh2.coordinates()[:, [1, 2, 0]]
W2 = FunctionSpace(mesh2, 'CG', 1)
v2 = interpolate(Function(W2, u.vector()), V)
pr = project(u+v1+v2)
assert np.linalg.norm(pr.vector())/nrm > 0.01
return pr
except:
print "Cyclic symmetrization failed!"
return u
def polyhedron_mesh(data):
"""
Build polyhedral mesh. Must be strlike with respect to the origin.
Input:
data[0] - list of vertices
data[1] - list of faces
data[2] - optional other starlike point, instead of the origin
"""
# TODO: Center of mass of the vertices as origin
vertex_data = np.array(data[0], dtype='double')
lowest = np.min(flatten(data[1]))
face_data = [list(np.array(d) - lowest) for d in data[1]]
numv = len(vertex_data) # will be the index of the origin
if len(data) > 2:
origin = np.array(data[2], dtype='double')
else:
origin = [0.0, 0.0, 0.0]
mesh = Mesh()
editor = DynamicMeshEditor()
editor.open(mesh, "tetrahedron", 3, 3, numv + 1, len(face_data))
for i, vert in enumerate(vertex_data):
editor.add_vertex(i, *vert)
editor.add_vertex(numv, *origin)
newv = numv + 1 # next vertex index
newf = 0 # next face index
for face in face_data:
if len(face) == 3:
# triangular face, no splitting
editor.add_cell(newf, numv, *face) # face + origin
newf += 1
else:
# split face into triangles using center of mass
# average face vertices to get the center
vert = list(np.mean(vertex_data[np.array(face)], axis=0))
editor.add_vertex(newv, *vert) # new vertex: face center
face.append(face[0])
for i in zip(face[:-1], face[1:]):
# pairs of vertices
editor.add_cell(newf, numv, newv, *i) # + face center + origin
newf += 1
newv += 1
editor.close()
mesh.order()
return mesh
def convert_and_create_facet_mesh_function ( ifilename, ofilename ):
# First convert the gmsh mesh
meshconvert.convert2xml ( ifilename, ofilename )
# Now load the created mesh and initialise the required connectivity information
mesh = Mesh ( ofilename )
mesh.order()
File ( ofilename ) << mesh
D = mesh.topology().dim()
mesh.init(D-1, 0)
# read the data from the gmsh file once again
dim_count, vertices_used, tags = process_gmsh_elements( ifilename, D-1 )
# Get the facet-node connectivity information (reshape as a row of node indices per facet)
facets_as_nodes = mesh.topology()(D-1,0)().reshape ( mesh.num_facets(), D )
# Create and initialise the mesh function
facet_mark_function = MeshFunction ( 'uint', mesh, D-1 )
facet_mark_function.set_all( 0 )
# set the relevant values of the mesh function
facets_to_check = range( mesh.num_facets() )
for i in range(len(tags)):
nodes = np.sort(np.array(vertices_used[2*i:(2*i+D)]))
value = tags[i][0]
if value != 0:
found = False
for j in range(len(facets_to_check)):
index = facets_to_check[j]
if np.array_equal(facets_as_nodes[index,:], nodes):
found = True;
facets_to_check.pop(j)
# set the value of the mesh function
facet_mark_function[index] = value
break;
if not found:
raise Exception ( "The facet (%d) was not found to mark: %s" % (i, nodes) )
# save the mesh function to file
fname = os.path.splitext(ofilename)[0]
mesh_function_file = File("%s_%s.xml" % (fname, "facet_regions"))
mesh_function_file << facet_mark_function
def write_fenics_file(dim, ofilename):
ofile = File(ofilename + '.xml')
mesh = Mesh()
editor = MeshEditor()
editor.open(mesh, dim, dim)
editor.init_vertices(nodes.shape[1])
editor.init_cells(len(cell_map))
for i in range(nodes.shape[1]):
if dim == 2:
editor.add_vertex(i, nodes[0, i], nodes[1, i])
else:
editor.add_vertex(i, nodes[0, i], nodes[1, i], nodes[2, i])
for i in range(1, len(cell_map)+1):
if dim == 2:
editor.add_cell(i-1, cell_map[i][0]-1, cell_map[i][1]-1, cell_map[i][2]-1)
else:
editor.add_cell(i-1, cell_map[i][0]-1, cell_map[i][1]-1, cell_map[i][2]-1, cell_map[i][3]-1)
mesh.order()
mvc = mesh.domains().markers(dim-1)
for zone, cells in boundary_cells.iteritems():
for cell, nds in cells.iteritems():
dolfin_cell = Cell(mesh, cell-1)
nodes_of_cell = dolfin_cell.entities(0)
#print cell
#print nodes_of_cell
nodes_of_face = nds - 1
#print nodes_of_face
for jj, ff in enumerate(facets(dolfin_cell)):
facet_nodes = ff.entities(0)
#print facet_nodes
if all(map(lambda x: x in nodes_of_face, facet_nodes)):
local_index = jj
break
mvc.set_value(cell-1, local_index, zone)
ofile << mesh
from dolfin import plot
plot(mesh, interactive=True)
print 'Finished writing FEniCS mesh\n'
def rotational(u, n):
""" Symmetrize with respect to n-fold symmetry. """
# TODO: test one rotation only
V = u.function_space()
if V.mesh().topology().dim() > 2 or n < 2:
return u
mesh = V.mesh()
sum = u
nrm = np.linalg.norm(u.vector())
rotation = np.array([[np.cos(2*np.pi/n), np.sin(2*np.pi/n)],
[-np.sin(2*np.pi/n), np.cos(2*np.pi/n)]])
for i in range(1, n):
mesh = Mesh(mesh)
mesh.coordinates()[:, :] = np.dot(mesh.coordinates(), rotation)
W = FunctionSpace(mesh, 'CG', 1)
v = interpolate(Function(W, u.vector()), V)
sum += v
pr = project(sum)
if np.linalg.norm(pr.vector())/nrm > 0.01:
return pr
else:
return u
def get(self):
"""Two cells."""
topx, topy = self.pad(self.values)
mesh = Mesh()
editor = MeshEditor()
editor.open(mesh, 2, 2)
editor.init_vertices(4)
editor.init_cells(2)
editor.add_vertex(0, 0, 0)
editor.add_vertex(1, 1, 0)
editor.add_vertex(2, topx, topy)
editor.add_vertex(3, 1 - topx, -topy)
editor.add_cell(0, 0, 1, 2)
editor.add_cell(1, 0, 1, 3)
editor.close()
return mesh
def test_manifold_point_search():
# Simple two-triangle surface in 3d
vertices = [(0.0, 0.0, 1.0), (1.0, 1.0, 1.0), (1.0, 0.0, 0.0), (0.0, 1.0,
0.0)]
cells = [(0, 1, 2), (0, 1, 3)]
mesh = Mesh(MPI.comm_world, CellType.Type.triangle,
numpy.array(vertices, dtype=numpy.float64),
numpy.array(cells, dtype=numpy.int32), [],
cpp.mesh.GhostMode.none)
bb = BoundingBoxTree(mesh, mesh.topology.dim)
p = Point(0.5, 0.25, 0.75)
assert bb.compute_first_entity_collision(p, mesh) == 0
p = Point(0.25, 0.5, 0.75)
assert bb.compute_first_entity_collision(p, mesh) == 1
def symmetrize(u, d, sym):
""" Symmetrize function u. """
if len(d) == 3:
# three dimensions -> cycle XYZ
return cyclic3D(u)
elif len(d) >= 4:
# four dimensions -> rotations in 2D
return rotational(u, d[-1])
nrm = np.linalg.norm(u.vector())
V = u.function_space()
mesh = Mesh(V.mesh())
# test if domain is symmetric using function equal 0 inside, 1 on boundary
# extrapolation will force large values if not symmetric since the flipped
# domain is different
bc = DirichletBC(V, 1, DomainBoundary())
test = Function(V)
bc.apply(test.vector())
if len(d) == 2:
# two dimensions given: swap dimensions
mesh.coordinates()[:, d] = mesh.coordinates()[:, d[::-1]]
else:
# one dimension given: reflect
mesh.coordinates()[:, d[0]] *= -1
# FIXME functionspace takes a long time to construct, maybe copy?
W = FunctionSpace(mesh, 'CG', 1)
try:
# testing
test = interpolate(Function(W, test.vector()), V)
# max-min should be around 1 if domain was symmetric
# may be slightly above due to boundary approximation
assert max(test.vector()) - min(test.vector()) < 1.1
v = interpolate(Function(W, u.vector()), V)
if sym:
# symmetric
pr = project(u + v)
else:
# antisymmetric
pr = project(u - v)
# small solution norm most likely means that symmetrization gives
# trivial function
assert np.linalg.norm(pr.vector()) / nrm > 0.01
return pr
except:
# symmetrization failed for some reason
print "Symmetrization " + str(d) + " failed!"
return u
def build_mesh_old(cells, vertices):
"""Assemble a mesh object from cells and vertices."""
mesh = Mesh()
editor = MeshEditor()
dim = len(vertices[0])
if dim == 2:
editor.open(mesh, 'triangle', 2, 2)
else:
editor.open(mesh, 'tetrahedron', 3, 3)
editor.init_vertices(len(vertices))
editor.init_cells(len(cells))
for i, v in enumerate(vertices):
editor.add_vertex(i, *v)
for i, c in enumerate(cells):
editor.add_cell(i, *c)
editor.close()
return mesh
def create_mesh(lcar):
x0 = 0.0
x1 = 0.1
y0 = 0.0
y1 = 0.2
mesh_eps = 1.0e-12
# pylint: disable=no-self-use
class HotBoundary(SubDomain):
def inside(self, x, on_boundary):
return (on_boundary and x0 + mesh_eps < x[0] < x1 - mesh_eps
and y0 + mesh_eps < x[1] < y1 - mesh_eps)
hot_boundary = HotBoundary()
class CoolBoundary(SubDomain):
def inside(self, x, on_boundary):
return (on_boundary
and (x[0] < x0 + mesh_eps or x[0] > x1 - mesh_eps
or x[1] < y0 + mesh_eps or x[1] > y1 - mesh_eps))
cool_boundary = CoolBoundary()
cache_file = 'boussinesq-{}.msh'.format(lcar)
if os.path.isfile(cache_file):
print('Using mesh from cache \'{}\'.'.format(cache_file))
points, cells, _, _, _ = meshio.read(cache_file)
else:
geom = pygmsh.Geometry()
circle = geom.add_circle([0.05, 0.05, 0.0],
0.02,
lcar,
make_surface=False)
geom.add_rectangle(x0, x1, y0, y1, 0.0, lcar, holes=[circle])
points, cells, _, _, _ = pygmsh.generate_mesh(geom)
meshio.write(cache_file, points, cells)
# https://fenicsproject.org/qa/12891/initialize-mesh-from-vertices-connectivities-at-once
meshio.write('test.xml', points, cells)
return Mesh('test.xml'), hot_boundary, cool_boundary
def get(self):
"""Part of the regular polygon construction."""
sides, angle = self.pad(self.values)
mesh = Mesh()
editor = MeshEditor()
editor.open(mesh, 2, 2) # dimension
editor.init_vertices(angle + 2)
editor.init_cells(angle)
editor.add_vertex(0, 0, 0)
for i in range(0, angle + 1):
editor.add_vertex(i + 1, cos(2 * pi * i / sides),
sin(2 * pi * i / sides))
editor.add_cell(0, 2, 1, 0)
for i in range(1, angle):
editor.add_cell(i, 0, i + 1, i + 2)
editor.close()
return mesh
def get(self):
"""One triangle per side with common vertex at (0,0)."""
sides = self.values[0]
mesh = Mesh()
editor = MeshEditor()
editor.open(mesh, 2, 2)
editor.init_vertices(sides + 1)
editor.init_cells(sides)
editor.add_vertex(0, 0, 0)
for i in range(1, sides + 1):
editor.add_vertex(i, cos(2 * pi * i / sides),
sin(2 * pi * i / sides))
for i in range(sides - 1):
editor.add_cell(i, 0, i + 1, i + 2)
editor.add_cell(sides - 1, 0, sides, 1)
editor.close()
return mesh
def plot(args):
from dolfin import plot, interactive, Mesh, Function, VectorFunctionSpace
# Plot the mesh
mesh = Mesh(args.xml)
plot(mesh, title="Mesh")
interactive()
# Plot velocities
if args.velocity is not None:
G = VectorFunctionSpace(mesh, "DG", 0)
base_file = args.velocity[:-4] + "_{}.xml"
for i, u in enumerate(fvcom_reader.velocity):
g = Function(G, base_file.format(i))
plot(g, title="Velocity time={}".format(i))
interactive()
def import_mesh_from_xdmf(domain="domain.xdmf",
boundaries="boundaries.xdmf",
labels="labels.yaml",
subdomains=False,
dim=2,
directory="."):
"""
Function importing a msh mesh and converting it into a dolfin mesh.
Arguments:
- domain (str): name of the domain XDMF file;
- boundaries (str): name of the boundaries XDMF file;
- dim (int): dimension of the domain;
- subdomains (bool): true if there are subdomains, else false
- directory (str): (optional) directory of the mesh;
Output:
- dolfin Mesh object containing the domain;
- dolfin MeshFunction object containing the physical lines (dim=2) or
surfaces (dim=3) defined in the msh file and the sub-domains;
- a dictionary with labels for boundaries and subdomains
"""
# Import the converted domain
mesh = Mesh()
with XDMFFile("{}/{}".format(directory, domain)) as infile:
infile.read(mesh)
# Import the boundaries
boundaries_mvc = MeshValueCollection("size_t", mesh, dim=dim)
with XDMFFile("{}/{}".format(directory, boundaries)) as infile:
infile.read(boundaries_mvc, 'boundaries')
boundaries_mf = MeshFunctionSizet(mesh, boundaries_mvc)
# Import the subdomains
if subdomains:
subdomains_mvc = MeshValueCollection("size_t", mesh, dim=dim)
with XDMFFile("{}/{}".format(directory, domain)) as infile:
infile.read(subdomains_mvc, 'subdomains')
subdomains_mf = MeshFunctionSizet(mesh, subdomains_mvc)
# Import labels
with open("{}/{}".format(directory, labels), 'r') as infile:
labels = yaml.load(infile, Loader=yaml.FullLoader)
# Return the Mesh and the MeshFunction objects
if not subdomains:
return mesh, boundaries_mf, labels
else:
return mesh, boundaries_mf, subdomains_mf, labels
print(labels)
def get(self):
"""Build cells based on triangulated regular polygon."""
sides, h, x, y = self.pad(self.values)
mesh = Mesh()
editor = MeshEditor()
editor.open(mesh, 3, 3) # dimension
editor.init_vertices(sides + 2)
editor.init_cells(sides)
editor.add_vertex(0, x, y, h)
for i in range(1, sides + 1):
editor.add_vertex(i, cos(2 * pi * i / sides),
sin(2 * pi * i / sides), 0)
editor.add_vertex(sides + 1, 0, 0, 0)
for i in range(sides - 1):
editor.add_cell(i, 0, i + 1, i + 2, sides + 1)
editor.add_cell(sides - 1, 0, sides, 1, sides + 1)
editor.close()
return mesh
def get_reference_element(dim=2):
nodes, cell = get_reference_coordinates(dim)
cells = np.atleast_2d(np.arange(
dim + 1, dtype=np.uintp)) # connection of nodes (defines element)
# this piece of code creates a mesh containing one element only
mesh = Mesh()
editor = MeshEditor()
editor.open(mesh, cell, dim, dim)
editor.init_vertices(dim + 1)
editor.init_cells(1)
for i, n in enumerate(nodes):
p = Point(n)
editor.add_vertex(i, p)
for i, n in enumerate(cells):
editor.add_cell(i, n)
editor.close()
return mesh
def project_gradients(
mesh: df.Mesh,
scalar_solutions: Dict[str, df.Function],
fiber_space: str = "CG_1",
) -> Dict[str, np.ndarray]:
"""
Calculate the gradients using projections
Arguments
---------
mesh : dolfin.Mesh
The mesh
fiber_space : str
A string on the form {familiy}_{degree} which
determines for what space the fibers should be calculated for.
scalar_solutions: dict
A dictionary with the scalar solutions that you
want to compute the gradients of.
"""
Vv = utils.space_from_string(fiber_space, mesh, dim=3)
V = utils.space_from_string(fiber_space, mesh, dim=1)
data = {}
V_cg = df.FunctionSpace(mesh,
df.VectorElement("Lagrange", mesh.ufl_cell(), 1))
for case, scalar_solution in scalar_solutions.items():
scalar_solution_int = df.interpolate(scalar_solution, V)
if case != "lv_rv":
gradient_cg = df.project(df.grad(scalar_solution),
V_cg,
solver_type="cg")
gradient = df.interpolate(gradient_cg, Vv)
# Add gradient data
data[case + "_gradient"] = gradient.vector().get_local()
# Add scalar data
if case != "apex":
data[case + "_scalar"] = scalar_solution_int.vector().get_local()
# Return data
return data
def load_h5_mesh(h5_file, scale_factor=None):
'''Unpack to mesh, volumes and surfaces'''
mesh = Mesh()
h5 = HDF5File(mesh.mpi_comm(), h5_file, 'r')
h5.read(mesh, 'mesh', False)
# Convert units
if scale_factor is not None:
assert scale_factor > 0, "Scale factor must be a positive real number!"
mesh.coordinates()[:] *= scale_factor
surfaces = MeshFunction('size_t', mesh, mesh.topology().dim() - 1)
h5.read(surfaces, 'surfaces')
volumes = MeshFunction('size_t', mesh, mesh.topology().dim())
h5.read(volumes, 'volumes')
return mesh, volumes, surfaces
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 build_interval_mesh(vertices, cells):
'''Mesh of 1d topology in n-dims.'''
imesh = Mesh()
editor = MeshEditor()
editor.open(imesh, 1, vertices.shape[1])
editor.init_vertices(len(vertices))
editor.init_cells(len(cells))
# Add vertices
for vertex_index, v in enumerate(vertices):
editor.add_vertex(vertex_index, v)
# Add cells
for cell_index, (v0, v1) in enumerate(cells):
editor.add_cell(cell_index, v0, v1)
editor.close()
return imesh
def get(self):
""" Unzip and convert to xml if possible."""
mesh = output = None
import tempfile
import os
if not os.path.isfile(self.params):
return None
params = self.params
try:
split = os.path.splitext(params)
if split[-1] == '.gz':
# unzip the mesh
import gzip
f = gzip.open(params, 'rb')
content = f.read()
f.close()
input = tempfile.NamedTemporaryFile(suffix=os.path.splitext(
split[0])[-1],
delete=False)
input.write(content)
input.close()
params = input.name
split = os.path.splitext(params)
if split[-1] != '.xml':
# convert using dolfin's meshconvert
from dolfin_utils.meshconvert import meshconvert
output = tempfile.NamedTemporaryFile(suffix='.xml',
delete=False)
output.close()
meshconvert.convert2xml(params, output.name)
params = output.name
# use Mesh constructor with filename
mesh = Mesh(params)
try:
os.unlink(output.name)
except OSError:
pass
os.unlink(input.name)
# many things could go wrong here
# just return None as mesh if mesh importing failed
finally:
return mesh
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 symmetrize(u, d, sym):
""" Symmetrize function u. """
if len(d) == 3:
# three dimensions -> cycle XYZ
return cyclic3D(u)
elif len(d) >= 4:
# four dimensions -> rotations in 2D
return rotational(u, d[-1])
nrm = np.linalg.norm(u.vector())
V = u.function_space()
mesh = Mesh(V.mesh())
# test if domain is symmetric using function equal 0 inside, 1 on boundary
# extrapolation will force large values if not symmetric since the flipped
# domain is different
bc = DirichletBC(V, 1, DomainBoundary())
test = Function(V)
bc.apply(test.vector())
if len(d) == 2:
# two dimensions given: swap dimensions
mesh.coordinates()[:, d] = mesh.coordinates()[:, d[::-1]]
else:
# one dimension given: reflect
mesh.coordinates()[:, d[0]] *= -1
# FIXME functionspace takes a long time to construct, maybe copy?
W = FunctionSpace(mesh, 'CG', 1)
try:
# testing
test = interpolate(Function(W, test.vector()), V)
# max-min should be around 1 if domain was symmetric
# may be slightly above due to boundary approximation
assert max(test.vector()) - min(test.vector()) < 1.1
v = interpolate(Function(W, u.vector()), V)
if sym:
# symmetric
pr = project(u+v)
else:
# antisymmetric
pr = project(u-v)
# small solution norm most likely means that symmetrization gives
# trivial function
assert np.linalg.norm(pr.vector())/nrm > 0.01
return pr
except:
# symmetrization failed for some reason
print "Symmetrization " + str(d) + " failed!"
return u
def test_readme_images():
from dolfin import (
MeshEditor, Mesh, FunctionSpace, assemble, EigenMatrix, dot, grad, dx,
TrialFunction, TestFunction
)
import meshzoo
points, cells = meshzoo.rectangle(-1.0, 1.0, -1.0, 1.0, 20, 20)
# Convert points, cells to dolfin mesh
editor = MeshEditor()
mesh = Mesh()
# topological and geometrical dimension 2
editor.open(mesh, 'triangle', 2, 2, 1)
editor.init_vertices(len(points))
editor.init_cells(len(cells))
for k, point in enumerate(points):
editor.add_vertex(k, point[:2])
for k, cell in enumerate(cells.astype(numpy.uintp)):
editor.add_cell(k, cell)
editor.close()
V = FunctionSpace(mesh, 'CG', 1)
u = TrialFunction(V)
v = TestFunction(V)
L = EigenMatrix()
assemble(dot(grad(u), grad(v)) * dx, tensor=L)
A = L.sparray()
# M = A.T.dot(A)
M = A
with tempfile.TemporaryDirectory() as temp_dir:
filepath = os.path.join(temp_dir, 'test.png')
betterspy.write_png(filepath, M, border_width=2)
# betterspy.write_png(
# 'ATA.png', M, border_width=2,
# colormap='viridis'
# )
return
def pons():
base = "../meshes/2d/pons"
mesh = Mesh(base + ".xml")
subdomains = MeshFunction("size_t", mesh, base + "_physical_region.xml")
subdomain_materials = {19: "graphite", 20: "SiC", 21: "air"}
for k in range(1, 19, 2):
subdomain_materials[k] = "air"
for k in range(2, 19, 2):
subdomain_materials[k] = "copper"
coils = [
{
"rings": range(2, 19, 2),
# 'rings': range(10,19,2),
# 'rings': [10],
"c_type": "voltage",
"c_value": 230.0 * numpy.sqrt(2.0),
}
]
wpi = 20
omega = 2 * pi * 10e3
return mesh, subdomains, coils, wpi, subdomain_materials, omega
def prolateGeometry(filename):
from dolfin import XDMFFile, Mesh, MeshValueCollection, MeshTransformation
xdmf_meshfile = "meshes/" + filename + ".xdmf"
xdmf_meshfile_bm = "meshes/" + filename + "_bm.xdmf"
mesh = Mesh()
with XDMFFile(xdmf_meshfile) as infile:
infile.read(mesh)
mvc = MeshValueCollection("size_t", mesh, 2)
with XDMFFile(xdmf_meshfile_bm) as infile:
infile.read(mvc, "name_to_read")
from dolfin import cpp
markers = cpp.mesh.MeshFunctionSizet(mesh, mvc)
ENDOCARD = 20
EPICARD = 10
BASE = 50
NONE = 99
MeshTransformation.scale(mesh, 1e-3)
return mesh, markers, ENDOCARD, EPICARD, BASE, NONE
def currentloop():
base = "../meshes/2d/circle-in-halfcircle"
mesh = Mesh(base + ".xml")
subdomains = MeshFunction("size_t", mesh, base + "_physical_region.xml")
subdomain_materials = {1: "copper", 2: "air"}
coils = [{"rings": [1], "c_type": "voltage", "c_value": 230.0 * numpy.sqrt(2.0)}]
wpi = None
omega = 1.0e3
# According to
# <http://hyperphysics.phy-astr.gsu.edu/hbase/magnetic/curloo.html>,
# the magnitude of the magnetic field is
#
# |B| = mu0*I / (2*r0)
# = mu0*V / (2*r0*R).
#
# at the center of the loop. With a copper wire, this is
#
# |B| = pi * 4e-7 * V / (2*r0*1.535356e-08)
# ~ 40.9 * V/r0.
# = 13.30350e3
#
return mesh, subdomains, coils, wpi, subdomain_materials, omega
def make_mesh(vertices, cells, cell_type):
'''Mesh from data by MeshEditor'''
gdim = cell_type.geometric_dimension()
assert vertices.shape[1] == gdim
tdim = cell_type.topological_dimension()
mesh = Mesh()
editor = MeshEditor()
editor.open(mesh, str(cell_type), tdim, gdim)
editor.init_vertices(len(vertices))
editor.init_cells(len(cells))
for vi, x in enumerate(vertices): editor.add_vertex(vi, x)
for ci, c in enumerate(cells): editor.add_cell(ci, *c)
editor.close()
return mesh
def create_mesh(lcar):
geom = pygmsh.Geometry()
cache_file = 'karman.msh'
if os.path.isfile(cache_file):
print('Using mesh from cache \'{}\'.'.format(cache_file))
points, cells, _, _, _ = meshio.read(cache_file)
else:
# slightly off-center circle
circle = geom.add_circle([0.1, 1.0e-2, 0.0],
0.5 * obstacle_diameter,
lcar,
make_surface=False)
geom.add_rectangle(x0, x1, y0, y1, 0.0, lcar, holes=[circle])
points, cells, _, _, _ = pygmsh.generate_mesh(geom)
meshio.write(cache_file, points, cells)
# https://fenicsproject.org/qa/12891/initialize-mesh-from-vertices-connectivities-at-once
meshio.write('test.xml', points, cells)
return Mesh('test.xml')
def get(self):
"""Build vertices from polar coordinates."""
angle, dist = self.values
if len(angle) < 3:
angle = np.array(range(int(angle[0]))) * 360.0 / angle[0]
while len(dist) < len(angle):
dist = dist * 2
dist = np.array(dist)
sides = len(angle)
mesh = Mesh()
editor = MeshEditor()
editor.open(mesh, 2, 2)
editor.init_vertices(sides + 1)
editor.init_cells(sides)
editor.add_vertex(0, 0, 0)
for i in range(1, sides + 1):
editor.add_vertex(i, dist[i - 1] * cos(angle[i - 1] / 180.0 * pi),
dist[i - 1] * sin(angle[i - 1] / 180.0 * pi))
for i in range(sides - 1):
editor.add_cell(i, 0, i + 1, i + 2)
editor.add_cell(sides - 1, 0, sides, 1)
editor.close()
return mesh
def get(self):
"""Eight cells."""
mesh = Mesh()
editor = MeshEditor()
editor.open(mesh, 3, 3)
editor.init_vertices(7)
editor.init_cells(8)
editor.add_vertex(0, 1, 0, 0)
editor.add_vertex(1, 0, 1, 0)
editor.add_vertex(2, 0, 0, 1)
editor.add_vertex(3, -1, 0, 0)
editor.add_vertex(4, 0, -1, 0)
editor.add_vertex(5, 0, 0, -1)
editor.add_vertex(6, 0, 0, 0)
editor.add_cell(0, 6, 0, 1, 2)
editor.add_cell(1, 6, 0, 1, 5)
editor.add_cell(2, 6, 0, 4, 2)
editor.add_cell(3, 6, 0, 4, 5)
editor.add_cell(4, 6, 3, 1, 2)
editor.add_cell(5, 6, 3, 1, 5)
editor.add_cell(6, 6, 3, 4, 2)
editor.add_cell(7, 6, 3, 4, 5)
editor.close()
return mesh
def Lshape(x1, x2, x3, y1, y2, y3, h):
"""
(x1,y3) (x2,y3)
(x2,y2) (x3,y2)
(x1,y1) (x3,y1)
"""
mesh = Mesh()
domain_vertices = [
Point(x1, y1),
Point(x1, y3),
Point(x2, y3),
Point(x2, y2),
Point(x3, y2),
Point(x3, y1),
Point(x1, y1)
]
PolygonalMeshGenerator.generate(mesh, domain_vertices, h)
return mesh
def vedoPlotter(pygmsh_ms):
# Reading mesh data stored in .xdmf files.
mesh = Mesh()
with XDMFFile(pygmsh_ms) as infile:
infile.read(mesh)
# Define variational problem
V = FunctionSpace(mesh, 'P', 1)
u = Function(V)
R_path = "Output_data"
fU_in = XDMFFile(os.path.join(R_path, 'FuelRod_m.xdmf'))
fU_in.read_checkpoint(u, "T", 0)
axes_opts = dict(
xyGrid=True,
axesLineWidth=1,
xTickColor='black',
yTickColor='black',
xMinorTicks=1, # number of minor ticks btw two major ticks
yMinorTicks=1, # number of minor ticks btw two major ticks
xLabelSize=0.02, # size of the numeric labels along axis
yLabelSize=0.02, # offset of numeric labels
)
# nipy_spectral, gnuplot
plot(u,
interactive=True,
cmap='hot',
axes=0,
lw=2,
scalarbar='vertical',
wireframe=True,
alpha=10.,
warpZfactor=0.) # warpZfactor=0.01
plot()
def convert(msh_file, h5_file, save_mvc=False):
'''Temporary version of convertin from msh to h5'''
root, _ = os.path.splitext(msh_file)
assert os.path.splitext(msh_file)[1] == '.msh'
assert os.path.splitext(h5_file)[1] == '.h5'
# Get the xml mesh
xml_file = '.'.join([root, 'xml'])
subprocess.call(['dolfin-convert %s %s' % (msh_file, xml_file)], shell=True)
# Success?
assert os.path.exists(xml_file)
mesh = Mesh(xml_file)
out = HDF5File(mesh.mpi_comm(), h5_file, 'w')
out.write(mesh, 'mesh')
print('Mesh has %d cells' % mesh.num_cells())
print('Mesh size %g %g' % (mesh.hmin(), mesh.hmax()))
# Save ALL data as facet_functions
names = ('surfaces', 'volumes')
if not save_mvc:
for name, region in zip(names, ('facet_region.xml', 'physical_region.xml')):
r_xml_file = '_'.join([root, region])
f = MeshFunction('size_t', mesh, r_xml_file)
print('%d %s with 1' % (sum(1 for _ in SubsetIterator(f, 1)), name))
out.write(f, name)
return True
for name, region in zip(names, ('facet_region.xml', 'physical_region.xml')):
r_xml_file = '_'.join([root, region])
f = MeshFunction('size_t', mesh, r_xml_file)
# With mesh value collection we only store nonzero tags
mvc = MeshValueCollection('size_t', mesh, f.dim())
# Fill
fill_mvc_from_mf(f, mvc)
# And save
out.write(mvc, name)
return True
elif platform.system() == "Darwin":
os.system(
"curl -L https://www.dropbox.com/s/d78g4cyjxl3ylay/cylinder.xml?dl=0 -o cylinder.xml"
)
else:
raise ImportError("Could not determine platform")
# try:
#os.system("gmsh mesh/cylinder.geo -2 -o mesh/cylinder.msh")
#os.system("dolfin-convert mesh/cylinder.msh mesh/cylinder.xml")
#os.system("rm mesh/cylinder.msh")
# except RuntimeError:
#os.system("wget -O cylinder.xml https://www.dropbox.com/s/d78g4cyjxl3ylay/cylinder.xml?dl=0")
##raise "Gmsh is required to run this demo"
mesh = Mesh("cylinder.xml")
H = 0.41
L = 2.2
D = 0.1
center = 0.2
cases = {1: {'Um': 0.3, 'Re': 20.0}, 2: {'Um': 1.5, 'Re': 100.0}}
# Specify boundary conditions
Inlet = AutoSubDomain(lambda x, on_bnd: on_bnd and x[0] < 1e-8)
Wall = AutoSubDomain(lambda x, on_bnd: on_bnd and near(x[1] * (H - x[1]), 0))
Cyl = AutoSubDomain(lambda x, on_bnd: (on_bnd and x[0] > 1e-6 and x[0] < 1 and
x[1] < 3 * H / 4 and x[1] > H / 4))
Outlet = AutoSubDomain(lambda x, on_bnd: on_bnd and x[0] > L - 1e-8)
def coil_in_box():
mesh = Mesh("../meshes/2d/coil-in-box.xml")
f = Constant(0.0)
# Define mesh and boundaries.
class LeftBoundary(SubDomain):
def inside(self, x, on_boundary):
return on_boundary and x[0] < GMSH_EPS
left_boundary = LeftBoundary()
class RightBoundary(SubDomain):
def inside(self, x, on_boundary):
return on_boundary and x[0] > 2.5 - GMSH_EPS
right_boundary = RightBoundary()
class LowerBoundary(SubDomain):
def inside(self, x, on_boundary):
return on_boundary and x[1] < GMSH_EPS
lower_boundary = LowerBoundary()
class UpperBoundary(SubDomain):
def inside(self, x, on_boundary):
return on_boundary and x[1] > 0.4 - GMSH_EPS
upper_boundary = UpperBoundary()
class CoilBoundary(SubDomain):
def inside(self, x, on_boundary):
return (
on_boundary
and x[0] > GMSH_EPS
and x[0] < 2.5 - GMSH_EPS
and x[1] > GMSH_EPS
and x[1] < 0.4 - GMSH_EPS
)
coil_boundary = CoilBoundary()
# heater_temp = 380.0
# room_temp = 293.0
# bcs = [(coil_boundary, heater_temp),
# (left_boundary, room_temp),
# (right_boundary, room_temp),
# (upper_boundary, room_temp),
# (lower_boundary, room_temp)
# ]
boundaries = {}
boundaries["left"] = left_boundary
boundaries["right"] = right_boundary
boundaries["upper"] = upper_boundary
boundaries["lower"] = lower_boundary
boundaries["coil"] = coil_boundary
boundaries = MeshFunction("size_t", mesh, mesh.topology().dim() - 1)
boundaries.set_all(0)
left_boundary.mark(boundaries, 1)
right_boundary.mark(boundaries, 2)
upper_boundary.mark(boundaries, 3)
lower_boundary.mark(boundaries, 4)
coil_boundary.mark(boundaries, 5)
boundary_indices = {"left": 1, "right": 2, "top": 3, "bottom": 4, "coil": 5}
theta0 = Constant(293.0)
return mesh, f, boundaries, boundary_indices, theta0
def convert(ifilename, handler):
""" Convert from Abaqus.
The Abaqus format first defines a node block, then there should be a number
of elements containing these nodes.
"""
# Dictionary of nodes (maps node id to coordinates)
nodes = {}
# Dictionary of elements (maps cell id to list of cell nodes)
elems = {}
# Lists of nodes for given name (key)
node_sets = {}
# Lists of cells for given name (key)
cell_sets = {}
# Lists of surfaces for given name (key) in the format:
# {'SS1': [set(['SS1_S1', 'S1']), set(['SS1_S4', 'S4'])]},
# where SS1 is the name of the surface, SS1_S1 is the name of the
# cell list whose first face is to be selected, ...
surface_sets = {}
# Open file Abaqus file
csv_file = csv.reader(open(ifilename, 'rb'), delimiter=',', skipinitialspace=True)
node_set_name = None
generate = None
# Set intial state state
state = State.Init
# Read data from input file
for l in csv_file:
# Sanity check
if (len(l) == 0): print "Ooops, zero length."
if l[0].startswith('**'): # Pass over comments
continue
elif l[0].startswith('*'): # Have a keyword
state = State.Unknown
if l[0].lower() == "*heading":
state = State.ReadHeading
elif l[0].lower() == "*part":
part_name = _read_part_name(l)
elif l[0].lower() == "*end part":
state = State.Invalid
elif l[0].lower() == "*node":
node_set_name = _create_node_list_entry(node_sets, l)
state = State.ReadNodes
elif l[0].lower() == "*element":
cell_type, cell_set_name = _read_element_keywords(cell_sets, l)
state = State.ReadCells
elif l[0].lower() == "*nset":
node_set_name, generate = _read_nset_keywords(node_sets, l)
state = State.ReadNodeSet
elif l[0].lower() == "*elset":
cell_set_name, generate = _read_elset_keywords(cell_sets, l)
if generate:
print "WARNING: generation of *elsets not tested."
state = State.ReadCellSet
elif l[0].lower() == "*surface":
surface_set_name, generate = _read_surface_keywords(surface_sets, l)
state = State.ReadSurfaceSet
else:
print "WARNING: unrecognised Abaqus input keyword:", l[0]
state = State.Unknown
else:
if state == State.ReadHeading:
model_name = _read_heading(l)
elif state == State.ReadNodes:
node_id = int(l[0]) - 1
coords = [float(c) for c in l[1:]]
nodes[node_id] = coords
if node_set_name is not None:
node_sets[node_set_name].add(node_id)
elif state == State.ReadCells:
cell_id = int(l[0]) - 1
cell_connectivity = [int(v) - 1 for v in l[1:]]
elems[cell_id] = cell_connectivity
if cell_set_name is not None:
cell_sets[cell_set_name].add(cell_id)
elif state == State.ReadNodeSet:
try:
if generate:
n0, n1, increment = l
node_range = range(int(n0) - 1, int(n1) - 1, int(increment))
node_range.append(int(n1) - 1)
node_sets[node_set_name].update(node_range)
else:
# Strip empty term at end of list, if present
if l[-1] == '': l.pop(-1)
node_range = [int(n) - 1 for n in l]
node_sets[node_set_name].update(node_range)
except:
print "WARNING: Non-integer node sets not yet supported."
elif state == State.ReadCellSet:
try:
if generate:
n0, n1, increment = l
cell_range = range(int(n0) - 1, int(n1) - 1, int(increment))
cell_range.append(int(n1) - 1)
cell_sets[cell_set_name].update(cell_range)
else:
# Strip empty term at end of list, if present
if l[-1] == '': l.pop(-1)
cell_range = [int(n) - 1 for n in l]
cell_sets[cell_set_name].update(cell_range)
except:
print "WARNING: Non-integer element sets not yet supported."
elif state == State.ReadSurfaceSet:
# Strip empty term at end of list, if present
if l[-1] == '': l.pop(-1)
surface_sets[surface_set_name].update([tuple(l)])
elif state == State.Invalid: # part
raise StandardError("Inavlid Abaqus parser state..")
# Close CSV object
del csv_file
# Write data to XML file
# Note that vertices/cells must be consecutively numbered, which
# isn't necessarily the case in Abaqus. Therefore we enumerate and
# translate original IDs to sequence indexes if gaps are present.
# FIXME
handler.set_mesh_type("tetrahedron", 3)
process_facets = len(surface_sets) > 0
if process_facets:
try:
from dolfin import MeshEditor, Mesh
except ImportError:
_error("DOLFIN must be installed to handle Abaqus boundary regions")
mesh = Mesh()
mesh_editor = MeshEditor()
mesh_editor.open(mesh, 3, 3)
node_ids_order = {}
# Check for gaps in vertex numbering
node_ids = nodes.keys()
if len(node_ids) > 0:
vertex_gap = (min(node_ids) != 0 or max(node_ids) != len(node_ids) - 1)
for x, y in enumerate(node_ids):
node_ids_order[y]= x # Maps Abaqus IDs to Dolfin IDs
else:
vertex_gap = True
# Check for gaps in cell numbering
elemids = elems.keys()
if len(elemids) > 0:
cell_gap = (min(elemids) != 0 or max(elemids) != len(elemids) - 1)
else:
cell_gap = True
# Write vertices to XML file
handler.start_vertices(len(nodes))
if process_facets:
mesh_editor.init_vertices (len(nodes))
if not vertex_gap:
for v_id, v_coords in nodes.items():
handler.add_vertex(v_id, v_coords)
if process_facets:
mesh_editor.add_vertex(v_id, np.array(v_coords, dtype=np.float_))
else:
for idx, (v_id, v_coords) in enumerate(nodes.items()):
handler.add_vertex(idx, v_coords)
if process_facets:
mesh_editor.add_vertex(idx, np.array(v_coords, dtype=np.float_))
handler.end_vertices()
# Write cells to XML file
handler.start_cells(len(elems))
if process_facets:
mesh_editor.init_cells(len(elems))
if not vertex_gap and not cell_gap:
for c_index, c_data in elems.items():
for v_id in c_data:
if not (0 <= v_id < len(nodes)):
handler.error("Element %s references non-existent node %s" % (c_index, v_id))
handler.add_cell(c_index, c_data)
if process_facets:
c_data_tmp = np.array(c_data)
c_data_tmp.sort()
mesh_editor.add_cell(c_index, np.array(c_data_tmp, dtype=np.uintp))
elif not vertex_gap and cell_gap:
for idx, (c_index, c_data) in enumerate(elems.items()):
for v_id in c_data:
if not (0 <= v_id < len(nodes)):
handler.error("Element %s references non-existent node %s" % (c_index, v_id))
handler.add_cell(idx, c_data)
if process_facets:
c_data_tmp = np.array(c_data)
c_data_tmp.sort()
mesh_editor.add_cell(idx, np.array(c_data_tmp, dtype=np.uintp))
else:
for idx, (c_id, c_data) in enumerate(elems.items()):
c_nodes = []
for v_id in c_data:
try: c_nodes.append(node_ids_order[v_id])
except ValueError:
handler.error("Element %s references non-existent node %s" % (c_id, v_id))
handler.add_cell(idx, c_nodes)
if process_facets:
c_nodes.sort()
mesh_editor.add_cell(idx, np.array(c_nodes, dtype=np.uintp))
handler.end_cells()
# Write MeshValueCollections to XML file
handler.start_domains()
# Build a abaqus node ID -> dolfin cell ID map (which is not unique but that is irrelevant here)
# and its local entity.
if len(node_sets.items()) > 0:
node_cell_map = {}
for c_dolfin_index, (c_index, c_data) in enumerate(elems.items()):
c_data_tmp = np.array(c_data)
c_data_tmp.sort()
for local_entity, n_index in enumerate(c_data_tmp):
node_cell_map[n_index] = (c_dolfin_index, local_entity)
# Write vertex/node sets
dim = 0
for value, (name, node_set) in enumerate(node_sets.items()):
handler.start_mesh_value_collection(name, dim, len(node_set), "uint")
for node in node_set:
try:
cell, local_entity = node_cell_map[node]
handler.add_entity_mesh_value_collection(dim, cell, value, local_entity=local_entity)
except KeyError:
print "Warning: Boundary references non-existent node %s" % node
handler.end_mesh_value_collection()
# Write cell/element sets
dim = 3
for name, s in cell_sets.items():
handler.start_mesh_value_collection(name, dim, len(s), "uint")
for cell in s:
handler.add_entity_mesh_value_collection(dim, cell, 0)
handler.end_mesh_value_collection()
# Write surface sets
if process_facets:
dim = 2
nodes_facet_map = _nodes_facet_map(mesh)
data = [int(0)] * mesh.num_facets()
S1 = [0, 1, 2]
S2 = [0, 3, 1]
S3 = [1, 3, 2]
S4 = [2, 3, 0]
node_selector = {'S1': S1,
'S2': S2,
'S3': S3,
'S4': S4,
}
for index, (name, s) in enumerate(surface_sets.items()):
cell_face_list = []
for cell_set_name, face_index in s:
cell_face_list += [(cell, face_index) for cell in cell_sets[cell_set_name]]
for cell, face in cell_face_list:
cell_nodes = elems[cell]
# Extract the face nodes
face_nodes = [cell_nodes[i] for i in node_selector[face]]
dolfin_face_nodes = [node_ids_order[n] for n in face_nodes]
dolfin_face_nodes.sort()
# Convert the face_nodes to dolfin IDs
face_id = nodes_facet_map[tuple(dolfin_face_nodes)]
data[face_id] = index + 1
# Create and initialise the mesh function
handler.start_meshfunction("facet_region", dim, mesh.num_facets() )
for index, physical_region in enumerate (data):
handler.add_entity_meshfunction(index, physical_region)
handler.end_meshfunction()
handler.end_domains()
def gmsh2xml(ifilename, handler):
"""Convert between .gmsh v2.0 format (http://www.geuz.org/gmsh/) and .xml,
parser implemented as a state machine:
0 = read 'MeshFormat'
1 = read mesh format data
2 = read 'EndMeshFormat'
3 = read 'Nodes'
4 = read number of vertices
5 = read vertices
6 = read 'EndNodes'
7 = read 'Elements'
8 = read number of cells
9 = read cells
10 = done
Afterwards, extract physical region numbers if they are defined in
the mesh file as a mesh function.
"""
print "Converting from Gmsh format (.msh, .gmsh) to DOLFIN XML format"
# The dimension of the gmsh element types supported here as well as the dolfin cell types for each dimension
gmsh_dim = {15: 0, 1: 1, 2: 2, 4: 3}
cell_type_for_dim = {1: "interval", 2: "triangle", 3: "tetrahedron" }
# the gmsh element types supported for conversion
supported_gmsh_element_types = [1, 2, 4, 15]
# Open files
ifile = open(ifilename, "r")
# Scan file for cell type
cell_type = None
highest_dim = 0
line = ifile.readline()
while line:
# Remove newline
if line[-1] == "\n":
line = line[:-1]
# Read dimension
if line.find("$Elements") == 0:
line = ifile.readline()
num_elements = int(line)
if num_elements == 0:
_error("No elements found in gmsh file.")
line = ifile.readline()
# Now iterate through elements to find largest dimension. Gmsh
# format might include elements of lower dimensions in the element list.
# We also need to count number of elements of correct dimensions.
# Also determine which vertices are not used.
dim_count = {0: 0, 1: 0, 2: 0, 3: 0}
vertices_used_for_dim = {0: [], 1: [], 2: [], 3: []}
# Array used to store gmsh tags for 1D (type 1/line), 2D (type 2/triangular) elements and 3D (type 4/tet) elements
tags_for_dim = {0: [], 1: [], 2: [], 3: []}
while line.find("$EndElements") == -1:
element = line.split()
elem_type = int(element[1])
num_tags = int(element[2])
if elem_type in supported_gmsh_element_types:
dim = gmsh_dim[elem_type]
if highest_dim < dim:
highest_dim = dim
node_num_list = [int(node) for node in element[3 + num_tags:]]
vertices_used_for_dim[dim].extend(node_num_list)
if num_tags > 0:
tags_for_dim[dim].append(tuple(int(tag) for tag in element[3:3+num_tags]))
dim_count[dim] += 1
else:
#TODO: output a warning here. "gmsh element type %d not supported" % elem_type
pass
line = ifile.readline()
else:
# Read next line
line = ifile.readline()
# Check that we got the cell type and set num_cells_counted
if highest_dim == 0:
_error("Unable to find cells of supported type.")
num_cells_counted = dim_count[highest_dim]
vertex_set = set(vertices_used_for_dim[highest_dim])
vertices_used_for_dim[highest_dim] = None
vertex_dict = {}
for n,v in enumerate(vertex_set):
vertex_dict[v] = n
# Step to beginning of file
ifile.seek(0)
# Set mesh type
handler.set_mesh_type(cell_type_for_dim[highest_dim], highest_dim)
# Initialise node list (gmsh does not export all vertexes in order)
nodelist = {}
# Current state
state = 0
# Write data
num_vertices_read = 0
num_cells_read = 0
# Only import the dolfin objects if facet markings exist
process_facets = False
if len(tags_for_dim[highest_dim-1]) > 0:
# first construct the mesh
try:
from dolfin import MeshEditor, Mesh
except ImportError:
_error("DOLFIN must be installed to handle Gmsh boundary regions")
mesh = Mesh()
mesh_editor = MeshEditor ()
mesh_editor.open( mesh, highest_dim, highest_dim )
process_facets = True
else:
# TODO: Output a warning or an error here
me = None
while state != 10:
# Read next line
line = ifile.readline()
if not line: break
# Skip comments
if line[0] == '#':
continue
# Remove newline
if line[-1] == "\n":
line = line[:-1]
if state == 0:
if line == "$MeshFormat":
state = 1
elif state == 1:
(version, file_type, data_size) = line.split()
state = 2
elif state == 2:
if line == "$EndMeshFormat":
state = 3
elif state == 3:
if line == "$Nodes":
state = 4
elif state == 4:
num_vertices = len(vertex_dict)
handler.start_vertices(num_vertices)
if process_facets:
mesh_editor.init_vertices ( num_vertices )
state = 5
elif state == 5:
(node_no, x, y, z) = line.split()
node_no = int(node_no)
x,y,z = [float(xx) for xx in (x,y,z)]
if vertex_dict.has_key(node_no):
node_no = vertex_dict[node_no]
else:
continue
nodelist[int(node_no)] = num_vertices_read
handler.add_vertex(num_vertices_read, [x, y, z])
if process_facets:
if highest_dim == 1:
coords = numpy.array([x])
elif highest_dim == 2:
coords = numpy.array([x, y])
elif highest_dim == 3:
coords = numpy.array([x, y, z])
mesh_editor.add_vertex(num_vertices_read, coords)
num_vertices_read +=1
if num_vertices == num_vertices_read:
handler.end_vertices()
state = 6
elif state == 6:
if line == "$EndNodes":
state = 7
elif state == 7:
if line == "$Elements":
state = 8
elif state == 8:
handler.start_cells(num_cells_counted)
if process_facets:
mesh_editor.init_cells( num_cells_counted )
state = 9
elif state == 9:
element = line.split()
elem_type = int(element[1])
num_tags = int(element[2])
if elem_type in supported_gmsh_element_types:
dim = gmsh_dim[elem_type]
else:
dim = 0
if dim == highest_dim:
node_num_list = [vertex_dict[int(node)] for node in element[3 + num_tags:]]
for node in node_num_list:
if not node in nodelist:
_error("Vertex %d of %s %d not previously defined." %
(node, cell_type_for_dim[dim], num_cells_read))
cell_nodes = [nodelist[n] for n in node_num_list]
handler.add_cell(num_cells_read, cell_nodes)
if process_facets:
cell_nodes = numpy.array([nodelist[n] for n in node_num_list], dtype=numpy.uintp)
mesh_editor.add_cell(num_cells_read, cell_nodes)
num_cells_read +=1
if num_cells_counted == num_cells_read:
handler.end_cells()
if process_facets:
mesh_editor.close()
state = 10
elif state == 10:
break
# Write mesh function based on the Physical Regions defined by
# gmsh, but only if they are not all zero. All zero physical
# regions indicate that no physical regions were defined.
if highest_dim not in [1,2,3]:
_error("Gmsh tags not supported for dimension %i. Probably a bug" % dim)
tags = tags_for_dim[highest_dim]
physical_regions = tuple(tag[0] for tag in tags)
if not all(tag == 0 for tag in physical_regions):
handler.start_meshfunction("physical_region", dim, num_cells_counted)
for i, physical_region in enumerate(physical_regions):
handler.add_entity_meshfunction(i, physical_region)
handler.end_meshfunction()
# Now process the facet markers
tags = tags_for_dim[highest_dim-1]
if (len(tags) > 0) and (mesh is not None):
physical_regions = tuple(tag[0] for tag in tags)
if not all(tag == 0 for tag in physical_regions):
mesh.init(highest_dim-1,0)
# Get the facet-node connectivity information (reshape as a row of node indices per facet)
if highest_dim==1:
# for 1d meshes the mesh topology returns the vertex to vertex map, which isn't what we want
# as facets are vertices
facets_as_nodes = numpy.array([[i] for i in range(mesh.num_facets())])
else:
facets_as_nodes = mesh.topology()(highest_dim-1,0)().reshape ( mesh.num_facets(), highest_dim )
# Build the reverse map
nodes_as_facets = {}
for facet in range(mesh.num_facets()):
nodes_as_facets[tuple(facets_as_nodes[facet,:])] = facet
data = [int(0*k) for k in range(mesh.num_facets()) ]
for i, physical_region in enumerate(physical_regions):
nodes = [n-1 for n in vertices_used_for_dim[highest_dim-1][highest_dim*i:(highest_dim*i+highest_dim)]]
nodes.sort()
if physical_region != 0:
try:
index = nodes_as_facets[tuple(nodes)]
data[index] = physical_region
except IndexError:
raise Exception ( "The facet (%d) was not found to mark: %s" % (i, nodes) )
# # Create and initialise the mesh function
handler.start_meshfunction("facet_region", highest_dim-1, mesh.num_facets() )
for index, physical_region in enumerate ( data ):
handler.add_entity_meshfunction(index, physical_region)
handler.end_meshfunction()
# Check that we got all data
if state == 10:
print "Conversion done"
else:
_error("Missing data, unable to convert \n\ Did you use version 2.0 of the gmsh file format?")
# Close files
ifile.close()
# Rossby radius.
LR=c/params["f"]
class InitialConditions(Expression):
def __init__(self):
pass
def eval(self, values, X):
r=(X[0]**2+X[1]**2)**0.5
if r>0.0001:
values[0]=-0.05*c*exp((r-r0)/LR)*X[0]/r*X[1]/r
values[1]= 0.05*c*exp((r-r0)/LR)*X[0]/r*X[0]/r
values[2]= 0.05*exp((r-r0)/LR)*X[0]/r
else:
values[0]=0.
values[1]=0.
values[2]=0.
def value_shape(self):
return (3,)
try:
mesh=Mesh("basin.xml")
except RuntimeError:
import sys
import os.path
mesh=Mesh(os.path.dirname(sys.argv[0]) + os.path.sep + "basin.xml")
mesh.order()
mesh.init()
def get_antarctica_coarse(): filename = inspect.getframeinfo(inspect.currentframe()).filename home = os.path.dirname(os.path.abspath(filename)) mesh = Mesh(home + '/antarctica/antarctica_50H_5l.xml') mesh.coordinates()[:,2] /= 1000.0 return mesh
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 _load_mesh(self):
with XDMFFile(self._mesh_filename) as fh:
self._mesh = Mesh()
fh.read(self._mesh)
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()
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
def get_greenland_detailed(): filename = inspect.getframeinfo(inspect.currentframe()).filename home = os.path.dirname(os.path.abspath(filename)) mesh = Mesh(home + '/greenland/greenland_detailed_mesh.xml') mesh.coordinates()[:,2] /= 100000.0 return mesh
def get_circle(): filename = inspect.getframeinfo(inspect.currentframe()).filename home = os.path.dirname(os.path.abspath(filename)) mesh = Mesh(home + '/test/circle.xml') mesh.coordinates()[:,2] /= 1000.0 return mesh
import numpy as np
import pylab as p
from dolfin import Mesh
from finmag.sim.llg import LLG
from finmag.drivers.llg_integrator import llg_integrator
# Create mesh
mu = 1e-9
mesh = Mesh("coarse_bar.xml.gz")
#mesh = Mesh("bar.xml.gz")
# Setup LLG
llg = LLG(mesh, unit_length=mu)
llg.Ms = 0.86e6
llg.A = 13.0e-12
llg.alpha = 0.5
llg.set_m((1, 0, 1))
llg.setup(use_exchange=True, use_dmi=False, use_demag=True, demag_method="FK")
# Set up time integrator
integrator = llg_integrator(llg, llg.m)
dt = 5e-12
######
# After ten time steps, plot the energy density
# from z=0 to z=100 through the center of the body.
######
# Integrate
integrator.run_until(dt * 10)
exch = llg.exchange.energy_density_function()
def __init__(self):
# https://fenicsproject.org/qa/12891/initialize-mesh-from-vertices-connectivities-at-once
points, cells, _, cell_data, _ = meshes.ball_in_tube_cyl.generate()
# 2018.1
# self.mesh = Mesh(
# dolfin.mpi_comm_world(), dolfin.cpp.mesh.CellType.Type_triangle,
# points[:, :2], cells['triangle']
# )
with TemporaryDirectory() as temp_dir:
tmp_filename = os.path.join(temp_dir, "test.xml")
meshio.write_points_cells(
tmp_filename,
points,
cells,
cell_data=cell_data,
file_format="dolfin-xml",
)
self.mesh = Mesh(tmp_filename)
V0_element = FiniteElement("CG", self.mesh.ufl_cell(), 2)
V1_element = FiniteElement("B", self.mesh.ufl_cell(), 3)
self.W = FunctionSpace(self.mesh, V0_element * V1_element)
self.P = FunctionSpace(self.mesh, "CG", 1)
# Define mesh and boundaries.
class LeftBoundary(SubDomain):
# pylint: disable=no-self-use
def inside(self, x, on_boundary):
return on_boundary and x[0] < GMSH_EPS
left_boundary = LeftBoundary()
class RightBoundary(SubDomain):
# pylint: disable=no-self-use
def inside(self, x, on_boundary):
return on_boundary and x[0] > 1.0 - GMSH_EPS
right_boundary = RightBoundary()
class LowerBoundary(SubDomain):
# pylint: disable=no-self-use
def inside(self, x, on_boundary):
return on_boundary and x[1] < GMSH_EPS
lower_boundary = LowerBoundary()
# class UpperBoundary(SubDomain):
# # pylint: disable=no-self-use
# def inside(self, x, on_boundary):
# return on_boundary and x[1] > 5.0-GMSH_EPS
class CoilBoundary(SubDomain):
# pylint: disable=no-self-use
def inside(self, x, on_boundary):
# One has to pay a little bit of attention when defining the
# coil boundary; it's easy to miss the edges closest to x[0]=0.
return (
on_boundary
and x[1] > 1.0 - GMSH_EPS
and x[1] < 2.0 + GMSH_EPS
and x[0] < 1.0 - GMSH_EPS
)
coil_boundary = CoilBoundary()
self.u_bcs = [
DirichletBC(self.W, (0.0, 0.0), right_boundary),
DirichletBC(self.W.sub(0), 0.0, left_boundary),
DirichletBC(self.W, (0.0, 0.0), lower_boundary),
DirichletBC(self.W, (0.0, 0.0), coil_boundary),
]
self.p_bcs = []
# self.p_bcs = [DirichletBC(Q, 0.0, upper_boundary)]
return