A tiny package to modify the node order of quadratic triangles and tets in a xdmf-hdf mesh to work with FEniCS/DOLFIN.
There is an xdmf import issue in FEniCS/DOLFIN. Quadratic triangles and tetrahedrons
are imported incorrectly. The CLI tool
xdmf-dolfin-fix fixes this issue by reordering element numbers.
xdmf-dolfin-fix old.xdmf # fix old.xdmf xdmf-dolfin-fix old.xdmf new.xdmf # create fixed new.xdmf xdmf-dolfin-fix old.geo -d3 # create fixed old.xdmf from gmsh xdmf-dolfin-fix old.msh new.xdmf # create fixed new.xdmf from gmsh
At some point of the simulation FEniCS/DOLFIN orders the vertices of all elements in numerically accending order. Nodes on the edges of elements -- as present in quadratic triangles and quadratic tetrahedrons -- are not swapped.
So internally, the node numbers of an arbitrary quadratic tetrahedron
[ vertices | edges ] [ 51 74 12 | 14 72 1003 ]
would be reordered to
[ 12 51 74 | 14 72 1003 ]
Now, the vertex nodes
[12 51 74] are sorted, but the edge nodes
[14 72 1003]
are left unchanged. This results in a twisted geometry.
xdmf-dolfin-fix sorts the vertex nodes and reorders the edge nodes accordingly. This
will result in
[ 12 51 74 | 1003 14 74 ]
A further sorting within DOLFIN has no effect and, thus, will not mess up this ordering.
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