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FEM: Fenics mesh: export and marking, fixed flake8 issues

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This commit is contained in:
joha2
2017-07-24 02:01:14 +02:00
committed by wmayer
parent f95ca7185c
commit b611cfc8ed
1 changed files with 37 additions and 40 deletions
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77
src/Mod/Fem/writeFenicsXDMF.py
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@@ -21,6 +21,11 @@
# ***************************************************************************
from __future__ import print_function
from importToolsFem import get_FemMeshObjectDimension, get_FemMeshObjectElementTypes, get_MaxDimElementFromList, get_FemMeshObjectOrder
from xml.etree import ElementTree as ET # parsing xml files and exporting
import numpy as np
__title__ = "FreeCAD Fenics XDMF mesh writer"
__author__ = "Johannes Hartung"
__url__ = "http://www.freecadweb.org"
@@ -29,18 +34,14 @@ __url__ = "http://www.freecadweb.org"
# \ingroup FEM
# \brief FreeCAD Fenics Mesh XDMF writer for FEM workbench
from importToolsFem import get_FemMeshObjectDimension, get_FemMeshObjectElementTypes, get_MaxDimElementFromList, get_FemMeshObjectOrder
from xml.etree import ElementTree as ET # parsing xml files and exporting
import numpy as np
ENCODING_ASCII = 'ASCII'
ENCODING_HDF5 = 'HDF5'
FreeCAD_Group_Dimensions = {
"Vertex":0,
"Edge":1,
"Face":2,
"Volume":3
"Vertex": 0,
"Edge": 1,
"Face": 2,
"Volume": 3
}
FreeCAD_to_Fenics_XDMF_dict = {
@@ -145,24 +146,25 @@ def write_fenics_mesh_volumes_xdmf(fem_mesh_obj, topologynode, nodes_dict, encod
elif encoding == ENCODING_HDF5:
pass
def write_fenics_mesh_codim_xdmf(fem_mesh_obj,
topologynode,
nodes_dict,
def write_fenics_mesh_codim_xdmf(fem_mesh_obj,
topologynode,
nodes_dict,
codim=0,
encoding=ENCODING_ASCII):
mesh_dimension = get_FemMeshObjectDimension(fem_mesh_obj)
mesh_dimension = get_FemMeshObjectDimension(fem_mesh_obj)
element_types = get_FemMeshObjectElementTypes(fem_mesh_obj, remove_zero_element_entries=True)
element_order = get_FemMeshObjectOrder(fem_mesh_obj)
# we get all elements from mesh to decide which one to write by selection of codim
#nodeindices = [(nodes_dict[ind] for ind in fem_mesh_obj.FemMesh.getElementNodes(fc_volume_ind)) for (fen_ind, fc_volume_ind) in enumerate(fc_cells)]
writeout_element_dimension = mesh_dimension - codim
# nodeindices = [(nodes_dict[ind] for ind in fem_mesh_obj.FemMesh.getElementNodes(fc_volume_ind)) for (fen_ind, fc_volume_ind) in enumerate(fc_cells)]
writeout_element_dimension = mesh_dimension - codim
(num_topo, name_topo, dim_topo) = (0, "", 0)
for (num, name, dim) in element_types:
if writeout_element_dimension == dim:
(num_topo, name_topo, dim_topo) = (num, name, dim)
(topology_type, nodes_per_element) = FreeCAD_to_Fenics_XDMF_dict[(name_topo, element_order)]
topologynode.set("TopologyType", topology_type)
@@ -183,13 +185,12 @@ def write_fenics_mesh_codim_xdmf(fem_mesh_obj,
nodeindices = [(nodes_dict[ind] for ind in fem_mesh_obj.FemMesh.getElementNodes(fc_topo_ind)) for (fen_ind, fc_topo_ind) in enumerate(fc_topo)]
if encoding == ENCODING_ASCII:
dataitem = ET.SubElement(topologynode, "DataItem", NumberType="UInt", Dimensions="%d %d" % (num_topo, nodes_per_element), Format="XML")
dataitem.text = numpy_array_to_str(tuples_to_numpy(nodeindices))
elif encoding == ENCODING_HDF5:
pass
return fc_topo
@@ -287,9 +288,9 @@ def write_fenics_mesh_xdmf(fem_mesh_obj, outputfile, encoding=ENCODING_ASCII):
nodes_dict = write_fenics_mesh_points_xdmf(fem_mesh_obj, base_geometry, encoding=encoding)
write_fenics_mesh_volumes_xdmf(fem_mesh_obj, base_topology, nodes_dict, encoding=encoding)
#####################################
fem_mesh = fem_mesh_obj.FemMesh
try:
try:
gmshgroups = fem_mesh.Groups
except:
gmshgroups = ()
@@ -300,45 +301,41 @@ def write_fenics_mesh_xdmf(fem_mesh_obj, outputfile, encoding=ENCODING_ASCII):
mesh_function_type = fem_mesh.getGroupElementType(g)
mesh_function_codim = dim_cell - FreeCAD_Group_Dimensions[mesh_function_type]
mesh_function_name = fem_mesh.getGroupName(g)
print('group id: %d (label: %s) with element type %s and codim %d' \
% (g, mesh_function_name, mesh_function_type, mesh_function_codim))
print('group id: %d (label: %s) with element type %s and codim %d'
% (g, mesh_function_name, mesh_function_type, mesh_function_codim))
mesh_function_grid = ET.SubElement(domain, "Grid", Name=mesh_function_name+"_mesh", GridType="Uniform")
mesh_function_topology = ET.SubElement(mesh_function_grid, "Topology")
mesh_function_topology_description = write_fenics_mesh_codim_xdmf(fem_mesh_obj,
mesh_function_topology,
nodes_dict,
mesh_function_topology_description = write_fenics_mesh_codim_xdmf(fem_mesh_obj,
mesh_function_topology,
nodes_dict,
codim=mesh_function_codim, encoding=encoding)
mesh_function_geometry = ET.SubElement(mesh_function_grid, "Geometry", Reference="XML")
mesh_function_geometry.text = "/Xdmf/Domain/Grid/Geometry"
mesh_function_attribute = ET.SubElement(mesh_function_grid, "Attribute")
mesh_function_attribute = ET.SubElement(mesh_function_grid, "Attribute")
elem_dict = {}
elem_mark_default = -1
elem_mark_group = g
elem_mark_overlap = g/2
# TODO: is it better to save all groups each at once or collect all codim equal
# groups to put them into one function?
# TODO: nevertheless there has to be a dialog which fixes the default value and the mark value
# TODO: nevertheless there has to be a dialog which fixes the default value and the mark value
for e in fem_mesh.getGroupElements(g):
elem_dict[e] = elem_mark_group
elem_dict[e] = elem_mark_group
val_array = np.array([elem_dict.get(e, elem_mark_default) for e in mesh_function_topology_description])
topo_array = np.vstack((val_array,)).T
write_fenics_mesh_scalar_cellfunctions(mesh_function_name,
topo_array,
write_fenics_mesh_scalar_cellfunctions(mesh_function_name,
topo_array,
mesh_function_attribute, encoding=ENCODING_ASCII)
# TODO: improve cell functions support
# write_fenics_mesh_cellfunctions(fem_mesh_obj, {}, attribute, encoding=encoding)
fp = open(outputfile, "w")
fp.write('''<?xml version="1.0"?>\n<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>\n''')