On 14/05/2015 02:08, Lucas Clemente Vella wrote:
Hi,
I need to write the output of a CFD code, attributes are cell centered
and my mesh looks like the picture attached: orthogonal edges, cells
are rectangular, but unstructured (leafs of a tree, not necessarily
octree).
I know how to work with HDF5, thus I prefer to write it in XDMF +
HDF5, but I could settle with any format that provides compression,
and I am able to write the tree once, and reuse it with different
attribute fields per time step (I know how to do it both from XDMF and
directly from HDF5).
So, is XDMF recommended, or should I use something else?
Also, in the picture, the bigger cell, can it be written as a
hexahedron, ignoring that one face actually interfaces with 4 other
cells, or should I describe it as a 9 face polyhedron, where there are
4 coplanar faces? The former is much easier, is there any difference
from visualization standpoint? Is it more "correct" to use a 9 face
polyhedron?
I have an idea on how to make a XDMF using only hexahedron, but not a
clue with polyhedra of variable number of faces. Could you please
assemble a sample XDMF depicting that mesh for me to use as base?
I think if you are using cell-centered data, it will be OK to use
hexahedra.
If you had vertex-centered data, then the approach you describe above
might make sense, as the values could be interpolated from the hanging
node.
You may notice some artefacts in the rendering, though, due to "internal
surfaces"
between the non-conforming cells. But only if you turn 'opacity' on, for
example.
Here is a simple (XML) example to see what I mean (e.g. try in paraview
with opacity=0.5)
<?xml version="1.0"?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf Version="2.0" xmlns:xi="http://www.w3.org/2001/XInclude";>
<Domain>
<Grid Name="grid_1" GridType="Uniform">
<Topology NumberOfElements="3" TopologyType="Hexahedron">
<DataItem Format="XML" Dimensions="3 8">
0 1 2 3 4 5 6 7
4 8 9 10 11 12 13 14
7 15 17 16 8 12 13 9
</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Format="XML" Dimensions="18 3">
0.0 0.0 0.0
0.0 0.0 1.0
0.0 1.0 1.0
0.0 1.0 0.0
1.0 0.0 0.0
1.0 0.0 1.0
1.0 1.0 1.0
1.0 1.0 0.0
1.0 0.5 0.0
1.0 0.5 0.5
1.0 0.0 0.5
1.5 0.0 0.0
1.5 0.5 0.0
1.5 0.5 0.5
1.5 0.0 0.5
1.5 1.0 0.0
1.0 1.0 0.5
1.5 1.0 0.5
</DataItem>
</Geometry>
<Attribute Name="field" AttributeType="Scalar" Center="Cell">
<DataItem Format="XML" Dimensions="3 1">
1
2
3
</DataItem>
</Attribute>
</Grid>
</Domain>
</Xdmf>
XDMF/HDF5 works really well (especially in parallel).
--
Chris Richardson
BP Institute
Madingley Road
Cambridge CB3 0EZ
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