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FEM: Fenics mesh: implemented generalized cell writeout function with co-dimension parameter

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joha2
2017-07-23 16:56:05 +02:00
committed by wmayer
parent 785d660dd7
commit 0b98673c7c
1 changed files with 99 additions and 13 deletions
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112
src/Mod/Fem/writeFenicsXDMF.py
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@@ -36,9 +36,19 @@ import numpy as np
ENCODING_ASCII = 'ASCII'
ENCODING_HDF5 = 'HDF5'
FreeCAD_to_Fenics_XDMF_dict = {
("Node", 1): ("polyvertex", 1),
("Edge", 1): ("polyline", 2),
("Edge", 2): ("edge_3", 3),
("Triangle", 1): ("triangle", 3),
("Triangle", 2): ("tri_6", 6),
("Tetra", 1): ("tetrahedron", 4),
("Tetra", 2): ("tet_10", 10)
}
# TODO: export mesh functions (to be defined, cell functions, vertex functions, facet functions)
# TODO: integrate cell function
# TODO: check pyopen for other files
# we need numpy functions to later access and process large data sets in a fast manner
# also the hd5 support better works together with numpy
@@ -96,20 +106,10 @@ def write_fenics_mesh_points_xdmf(fem_mesh_obj, geometrynode, encoding=ENCODING_
return recalc_nodes_ind_dict
def write_fenics_mesh_volumes_xdmf(fem_mesh_obj, topologynode, rd, encoding=ENCODING_ASCII):
def write_fenics_mesh_volumes_xdmf(fem_mesh_obj, topologynode, nodes_dict, encoding=ENCODING_ASCII):
(num_cells, name_cell, dim_cell) = get_MaxDimElementFromList(get_FemMeshObjectElementTypes(fem_mesh_obj))
element_order = get_FemMeshObjectOrder(fem_mesh_obj)
FreeCAD_to_Fenics_XDMF_dict = {
("Node", 1): ("polyvertex", 1),
("Edge", 1): ("polyline", 2),
("Edge", 2): ("edge_3", 3),
("Triangle", 1): ("triangle", 3),
("Triangle", 2): ("tri_6", 6),
("Tetra", 1): ("tetrahedron", 4),
("Tetra", 2): ("tet_10", 10)
}
(topology_type, nodes_per_element) = FreeCAD_to_Fenics_XDMF_dict[(name_cell, element_order)]
topologynode.set("TopologyType", topology_type)
@@ -128,7 +128,7 @@ def write_fenics_mesh_volumes_xdmf(fem_mesh_obj, topologynode, rd, encoding=ENCO
fc_cells = []
print("Dimension of mesh incompatible with export XDMF function: %d" % (dim_cell,))
nodeindices = [(rd[ind] for ind in fem_mesh_obj.FemMesh.getElementNodes(fc_volume_ind)) for (fen_ind, fc_volume_ind) in enumerate(fc_cells)]
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)]
# FC starts after all other entities, fenics start from 0 to size-1
# write nodeindices into dict to access them later
@@ -138,6 +138,53 @@ def write_fenics_mesh_volumes_xdmf(fem_mesh_obj, topologynode, rd, encoding=ENCO
elif encoding == ENCODING_HDF5:
pass
def write_fenics_mesh_codim_xdmf(fem_mesh_obj, topologynode, nodes_dict, codim=0, encoding=ENCODING_ASCII):
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
(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)
print(num_topo)
print(name_topo)
print(dim_topo)
(topology_type, nodes_per_element) = FreeCAD_to_Fenics_XDMF_dict[(name_topo, element_order)]
topologynode.set("TopologyType", topology_type)
topologynode.set("NumberOfElements", str(num_topo))
topologynode.set("NodesPerElement", str(nodes_per_element))
"""
if dim_cell == 3:
fc_cells = fem_mesh_obj.FemMesh.Volumes
elif dim_cell == 2:
fc_cells = fem_mesh_obj.FemMesh.Faces
elif dim_cell == 1:
fc_cells = fem_mesh_obj.FemMesh.Edges
elif dim_cell == 0:
fc_cells = fem_mesh_obj.FemMesh.Nodes
else:
fc_cells = []
print("Dimension of mesh incompatible with export XDMF function: %d" % (dim_cell,))
# FC starts after all other entities, fenics start from 0 to size-1
# write nodeindices into dict to access them later
if encoding == ENCODING_ASCII:
dataitem = ET.SubElement(topologynode, "DataItem", NumberType="UInt", Dimensions="%d %d" % (num_cells, nodes_per_element), Format="XML")
dataitem.text = numpy_array_to_str(tuples_to_numpy(nodeindices))
elif encoding == ENCODING_HDF5:
pass
"""
def write_fenics_mesh_scalar_cellfunctions(name, cell_array, attributenode, encoding=ENCODING_ASCII):
attributenode.set("AttributeType", "Scalar")
@@ -152,6 +199,44 @@ def write_fenics_mesh_scalar_cellfunctions(name, cell_array, attributenode, enco
elif encoding == ENCODING_HDF5:
pass
"""
Example: mesh with two topologies and one mesh function for the facet one
<?xml version="1.0"?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf Version="3.0" xmlns:xi="http://www.w3.org/2001/XInclude">
<Domain>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="162" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="162 4" NumberType="UInt" Format="XML">0 1 5 21
...
</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="64 3" Format="XML">0 0 0
...
</DataItem>
</Geometry>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="378" TopologyType="Triangle" NodesPerElement="3">
<DataItem Dimensions="378 3" NumberType="UInt" Format="XML">0 1 5
...
</DataItem>
</Topology>
<Geometry Reference="XML">/Xdmf/Domain/Grid/Geometry</Geometry>
<Attribute Name="f" AttributeType="Scalar" Center="Cell">
<DataItem Dimensions="378 1" Format="XML">3
...
</DataItem>
</Attribute>
</Grid>
</Domain>
</Xdmf>
"""
def write_fenics_mesh_xdmf(fem_mesh_obj, outputfile, encoding=ENCODING_ASCII):
"""
@@ -189,6 +274,7 @@ def write_fenics_mesh_xdmf(fem_mesh_obj, outputfile, encoding=ENCODING_ASCII):
recalc_dict = write_fenics_mesh_points_xdmf(fem_mesh_obj, geometry, encoding=encoding)
write_fenics_mesh_volumes_xdmf(fem_mesh_obj, topology, recalc_dict, encoding=encoding)
write_fenics_mesh_codim_xdmf(fem_mesh_obj, topology, recalc_dict, codim=0, encoding=encoding)
fem_mesh = fem_mesh_obj.FemMesh
try: