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 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()
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
file = open(ifilename, 'r')
csv_file = csv.reader(file, 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 = list(
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 = list(
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 Exception("Inavlid Abaqus parser state..")
# Close CSV object
file.close()
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 = list(iterkeys(nodes))
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 = list(iterkeys(elems))
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_global(len(nodes), len(nodes))
if not vertex_gap:
for v_id, v_coords in list(iteritems(nodes)):
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(iteritems(nodes)):
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_global(len(elems), len(elems))
if not vertex_gap and not cell_gap:
for c_index, c_data in list(iteritems(elems)):
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(iteritems(elems)):
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(iteritems(elems)):
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) > 0:
node_cell_map = {}
for c_dolfin_index, (c_index, c_data) in enumerate(iteritems(elems)):
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(iteritems(node_sets)):
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 list(iteritems(cell_sets)):
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(iteritems(surface_sets)):
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
line = line.rstrip("\n\r")
# 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("$EndElements") == -1:
element = line.split()
elem_type = int(element[1])
num_tags = int(element[2])
if elem_type in supported_gmsh_element_types:
dim = gmsh_dim[elem_type]
if highest_dim < dim:
highest_dim = dim
node_num_list = [int(node) for node in element[3 + num_tags:]]
vertices_used_for_dim[dim].extend(node_num_list)
if num_tags > 0:
tags_for_dim[dim].append(tuple(int(tag) for tag in element[3:3+num_tags]))
dim_count[dim] += 1
else:
#TODO: output a warning here. "gmsh element type %d not supported" % elem_type
pass
line = ifile.readline()
else:
# Read next line
line = ifile.readline()
# Check that we got the cell type and set num_cells_counted
if highest_dim == 0:
_error("Unable to find cells of supported type.")
num_cells_counted = dim_count[highest_dim]
vertex_set = set(vertices_used_for_dim[highest_dim])
vertices_used_for_dim[highest_dim] = None
vertex_dict = {}
for n,v in enumerate(vertex_set):
vertex_dict[v] = n
# Step to beginning of file
ifile.seek(0)
# Set mesh type
handler.set_mesh_type(cell_type_for_dim[highest_dim], highest_dim)
# Initialise node list (gmsh does not export all vertexes in order)
nodelist = {}
# Current state
state = 0
# Write data
num_vertices_read = 0
num_cells_read = 0
# Only import the dolfin objects if facet markings exist
process_facets = False
if len(tags_for_dim[highest_dim-1]) > 0:
# first construct the mesh
try:
from dolfin import MeshEditor, Mesh
except ImportError:
_error("DOLFIN must be installed to handle Gmsh boundary regions")
mesh = Mesh()
mesh_editor = MeshEditor ()
mesh_editor.open( mesh, highest_dim, highest_dim )
process_facets = True
else:
# TODO: Output a warning or an error here
me = None
while state != 10:
# Read next line
line = ifile.readline()
if not line: break
# Skip comments
if line[0] == '#':
continue
# Remove newline
line = line.rstrip("\n\r")
if state == 0:
if line == "$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_global(num_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 node_no in vertex_dict:
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_global(num_cells_counted, 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()
def gmsh_to_dolfin_mesh(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 = {1: 1, 2: 2, 4: 3}
gmsh_cell_type = {1: "interval", 2: "triangle", 3: "tetrahedron"}
# the gmsh element types supported for conversion
supported_gmsh_element_types = [1, 2, 4]
# 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("$Elements") == 0:
line = ifile.readline()
num_elements = int(line)
num_cells_counted = 0
if num_elements == 0:
_error("No elements found in gmsh file.")
line = ifile.readline()
# Now iterate through elements to find largest dimension. Gmsh
# format might include elements of lower dimensions in the element list.
# We also need to count number of elements of correct dimensions.
# Also determine which vertices are not used.
dim_count = {1: 0, 2: 0, 3: 0}
vertices_used = {1: [], 2: [], 3: []}
# Array used to store gmsh tags for 1D (type 1/line), 2D (type 2/triangular) elements and 3D (type 4/tet) elements
tags_for_dim = {1: [], 2: [], 3: []}
while line.find("$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[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[highest_dim])
vertices_used[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(gmsh_cell_type[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
# Now handle the facet markings
if len(tags_for_dim[highest_dim - 1]) > 0:
# first construct the mesh
from dolfin import MeshEditor, Mesh
mesh = Mesh()
me = MeshEditor()
me.open(mesh, highest_dim, highest_dim)
else:
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 == "$Nodes":
state = 4
elif state == 4:
num_vertices = len(vertex_dict)
handler.start_vertices(num_vertices)
if me is not None:
me.init_vertices(num_vertices)
state = 5
elif state == 5:
(node_no, x, y, z) = line.split()
node_no = int(node_no)
x, y, z = [float(xx) for xx in (x, y, z)]
if vertex_dict.has_key(node_no):
node_no = vertex_dict[node_no]
else:
continue
nodelist[int(node_no)] = num_vertices_read
handler.add_vertex(num_vertices_read, [x, y, z])
if me is not None:
if highest_dim == 1:
me.add_vertex(num_vertices_read, x)
elif highest_dim == 2:
me.add_vertex(num_vertices_read, x, y)
elif highest_dim == 3:
me.add_vertex(num_vertices_read, x, y, z)
num_vertices_read += 1
if num_vertices == num_vertices_read:
handler.end_vertices()
state = 6
elif state == 6:
if line == "$EndNodes":
state = 7
elif state == 7:
if line == "$Elements":
state = 8
elif state == 8:
handler.start_cells(num_cells_counted)
if me is not None:
me.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, gmsh_cell_type[dim], num_cells_read))
cell_nodes = [nodelist[n] for n in node_num_list]
handler.add_cell(num_cells_read, cell_nodes)
if me is not None:
me.add_cell(num_cells_read, *cell_nodes)
num_cells_read += 1
if num_cells_counted == num_cells_read:
handler.end_cells()
if me is not None:
me.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:
print tags
print vertices_used[highest_dim - 1]
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)
facets_as_nodes = mesh.topology()(highest_dim - 1, 0)().reshape(
mesh.num_facets(), highest_dim)
# from dolfin import MeshFunction
# # Create and initialise the mesh function
# facet_mark_function = MeshFunction ( 'uint', mesh, highest_dim-1 )
# facet_mark_function.set_all( 0 )
handler.start_meshfunction("facet_region", highest_dim - 1,
mesh.num_facets())
facets_to_check = range(mesh.num_facets())
data = [int(0 * k) for k in range(len(facets_to_check))]
for i, physical_region in enumerate(physical_regions):
nodes = [
n - 1
for n in vertices_used[highest_dim -
1][2 * i:(2 * i + highest_dim)]
]
nodes.sort()
if physical_region != 0:
found = False
for j in range(len(facets_to_check)):
index = facets_to_check[j]
if all(facets_as_nodes[index, k] == nodes[k]
for k in range(len(nodes))):
found = True
facets_to_check.pop(j)
# set the value of the mesh function
# facet_mark_function[index] = physical_region
data[index] = physical_region
break
if not found:
raise Exception(
"The facet (%d) was not found to mark: %s" %
(i, nodes))
# fname = os.path.splitext('tmp.xml')[0]
# mesh_function_file = File("%s_%s.xml" % (fname, "facet_region"))
# mesh_function_file << facet_mark_function
for index, physical_region in enumerate(data):
handler.add_entity_meshfunction(index, physical_region)
handler.end_meshfunction()
mf = MeshFunction('uint', mesh, 'tmp_facet_region.xml')
plot(mf, interactive=True)
# 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()