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 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 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 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 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'
# 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()
# Rossby radius.
LR = c / params["f"]
class InitialConditions(Expression):
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()