/usr/lib/python2.7/dist-packages/dolfin_utils/meshconvert/abaqus.py is in python-dolfin 2016.2.0-2.
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"""Module for converting the Abaqus mesh format."""
# Copyright (C) 2012 Arve Knudsen and Garth N/ Wells
#
# This file is part of DOLFIN.
#
# DOLFIN is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# DOLFIN is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with DOLFIN. If not, see <http://www.gnu.org/licenses/>.
#
# Modified by Simon Funke (surface export)
from __future__ import print_function
# TODO: The change to python 3 compatible iteration may have introduced performance
# regressions here, with unnecessary list() applications in the below code.
from six import iterkeys, iteritems
import re
import csv
import numpy as np
from . import xml_writer
class State:
Init, Unknown, Invalid, ReadHeading, ReadNodes, ReadCells, \
ReadNodeSet, ReadCellSet, ReadSurfaceSet = list(range(9))
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 _nodes_facet_map(mesh):
# Now process the facet markers
dim = 2
mesh.init(dim, 0)
facets_as_nodes = mesh.topology()(dim, 0)().reshape(mesh.num_facets(), 3)
# Build the reverse map
nodes_as_facets = {}
for facet in range(mesh.num_facets()):
nodes_as_facets[tuple(facets_as_nodes[facet,:])] = facet
return nodes_as_facets
def _read_heading(l):
return l[0].strip()
def _read_part_name(l):
if (len(l) < 2): print("Ooops, length problem.")
part_names = l[1].split('=')
if (len(part_names) < 2): print("Ooops, part names length problem.")
return part_names[1].strip()
def _create_node_list_entry(node_sets, l):
# Check for node set name
node_set_name = None
if len(l) == 2:
set_data = l[1].split('=')
assert len(set_data) == 2, "wrong list length"
if set_data[0].lower() == "nset":
node_set_name = set_data[1]
if node_set_name not in node_sets:
node_sets[node_set_name] = set()
return node_set_name
def _read_element_keywords(cell_sets, l):
# Get element type and element set name
element_type = None
element_set_name = None
for key in l[1:]:
key_parts = key.split('=')
key_name = key_parts[0].lower().strip()
if key_name == "type":
element_type = key_parts[1].lower().strip()
elif key_name == "elset":
element_set_name = key_parts[1].strip()
# Test that element is supported
check_element_support(element_type)
# Add empty set to cell_sets dictionary
if element_set_name:
if element_set_name not in cell_sets:
cell_sets[element_set_name] = set()
return element_type, element_set_name
def _read_nset_keywords(node_sets, l):
node_set_name = None
generate = None
# Get set name and add to dict
set_data = l[1].split('=')
assert len(set_data) == 2, "wrong list length, set name missing"
assert set_data[0].lower() == "nset"
node_set_name = set_data[1]
if node_set_name not in node_sets:
node_sets[node_set_name] = set()
# Check for generate flag
if len(l) == 3:
if l[2].lower() == "generate":
generate = True
return node_set_name, generate
def _read_elset_keywords(sets, l):
set_name = None
generate = None
# Get set name and add to dict
set_data = l[1].split('=')
assert len(set_data) == 2, "wrong list length, set name missing"
assert set_data[0].lower() == "elset"
set_name = set_data[1]
if set_name not in sets: sets[set_name] = set()
# Check for generate flag
if len(l) == 3:
if l[2].lower() == "generate":
generate = True
return set_name, generate
def _read_surface_keywords(sets, l):
surface_name = None
generate = None
# Get surface name and add to dict
surface_data = l[1].split('=')
assert len(surface_data) == 2, "wrong list length, surface name missing"
assert surface_data[0].lower() == "name"
surface_name = surface_data[1]
if surface_name not in sets: sets[surface_name] = set()
generate = False
return surface_name, generate
def check_element_support(element_type):
supported_elements = ('c3d4',)
if element_type.lower() not in supported_elements:
raise Exception("Element type not supported.")
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