[Paraview] xdmf + hdf5 error in Paraview

[Jason Fleming]

Are the connectivity indices numbered starting from zero or staring from
one? Paraview numbers your mesh vertices starting from zero, and if your
element connectivity refers to vertices numbered from 1:n, it will totally
scramble your connectivity when Paraview displays the mesh.

Cheers
Jason

On Wed, Mar 2, 2016 at 8:56 AM, John Jomo <john.jomo at tum.de> wrote:

> Hallo guys,
>
> have a bug using xdmf + hdf5 in Paraview that I cant seem to solve:
>
> I am trying to visualize my results from a finite element computation
> using xdmf and hdf5.
>
> The results consist of the geometry and topology of the mesh and different
> point and cell data.
> I store coordinates of 2 million points in one hdf5 dataset (X,Y,Z
> components) and the connectivity of the resulting 19 million cells (
> hexagonals and lines ) in a one dimensional hdf5 dataset.
>
> I use the following xdmf file to view the data in paraview
>
> <?xml version="1.0"?>
> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
> <Xdmf>
>         <Domain>
>                 <Grid GridType="Collection" CollectionType="Temporal">
>                         <Grid Name="element0" Type="Uniform">
>                                 <Time Type="Single" Value="0" />
>                                 <Geometry GeometryType="XYZ">
>                                         <DataStructure Dimensions="3
> 22078224" NumberType="Float" Presicion="8" Format="HDF" >
>
> SegmentedVertebra.h5:/points_0_0.000000
>                                         </DataStructure>
>                                 </Geometry>
>                                 <Topology Type="Mixed"
> NumberOfElements="19948716">
>                                         <DataStructure
> Dimensions="177553764 1" NumberType="Int64" Presicion="8" Format="HDF" >
>
> SegmentedVertebra.h5:/CellAndConnectivity_0_0.000000
>                                         </DataStructure>
>                                 </Topology>
>                                 <Attribute Name="Displacement"
> Center="Node" AttributeType="Vector">
>                                         <DataStructure Format="HDF"
> DataType="Float" Precision="8" Dimensions="3 22078224">
>
> SegmentedVertebra.h5:/Displacement_0_0.000000
>                                         </DataStructure>
>                                 </Attribute>
>                       </Grid>
>                 </Grid>
>         </Domain>
> </Xdmf>
>
>
> *Question:* For some strange reason the cell connectivity gets completely
> messed up, and I get a totaly wrong output in Paraview.
> I verified the content of the hdf5 file and all the points and cells are
> correct.
>
> The hdf5 is about 5 GB large.
>
> Does anyone know how the cause of this strange behaviour? I tried
> visualizing the content in visIT but got the same error.
>
> thanks in advance
>
> John.
>
> --
> John Jomo M.Sc.
> Technische Universität München
> Computation in Engineering
> Simulation in Applied Mechanics - SAM
> Arcisstraße 21
> 80333 München
> Tel.:     0049 / 89 / 289 25064
> Fax:      0049 / 89 / 289 25051
> E-Mail:   john.jomo at tum.de<mailto:john.jomo at tum.de> <john.jomo at tum.de>
> Internet: www.cie.bgu.tum.de<http://www.cie.bgu.tum.de/> <http://www.cie.bgu.tum.de/>
>
>
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-- 
Dr. Jason G. Fleming
Chief Engineer, Seahorse Coastal Consulting
3103 Mandy Ln
Morehead City, NC 28557
Tel: (252) 726-6323
Mobile: (252) 269-0962
Web: http://www.seahorsecoastal.com
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