[Paraview] Explicit numbering of nodes indexes in Xdmf/h5

[Jason Fleming]

Hello Andy

The XDMF2 library has the ability to assign Attributes and Information data
to Geometry objects. So you wouldn't be changing the node numbers, you'd
just be adding a new Attribute that has different values at each node, and
you'd need to display this new Attribute in Paraview instead of the node
numbers.

Since you mentioned offsets for XDMF arrays: I've been working on an XDMF2
implementation for ADCIRC, a finite element coastal ocean model. Being a
fortran code, ADCIRC uses 1-offset arrays, while the XDMF2 standard is
0-offset.

Its easy enough for us to subtract 1 from the node numbers in the element
table when storing mesh data as XDMF2, reversing the operation upon read
into ADCIRC or leaving them as-is for reading into Paraview. However, when
looking at node and element number labels on ADCIRC data in Paraview, the
analyst has to remember that all the displayed values are actually off by
1.

I emailed the XDMF mailing list and got a reply from the primary developers
that they were previously unaware of the demand for 1-offset arrays, but
they are now researching the possibility of adding this.

Your case is a little different, since it seems you are interested in
arbitrary node numbering. But I thought I would mention the above
background info for completeness. As I said, XDMF2 Attributes may be the
solution for you.

Cheers
Jason






On Mon, Nov 25, 2013 at 10:41 AM, Andrew Parker <
andy.john.parker at googlemail.com> wrote:

> All,
>
> I thought I'd forward this onto the paraview list in case somebody could
> think of a way to do this?  Please see my email below which I originally
> sent to the vtk user list.  Any help would be very much appreciated,
> including the fact that it just cannot be done.  I would in particular
> welcome thoughts from those who have helped develop the xdmf2 lib within
> the paraview source.
>
> Many thanks again,
> Andy
>
> ---------- Forwarded message ----------
> Date: 23 November 2013 17:13
> Subject: [vtkusers] Explicit numbering of nodes for Xdmf/h5
> To: "vtkusers at vtk.org" <vtkusers at vtk.org>
>
>
> All,
>
> In an effort to spark some comments I thought I'd try to provide a small
> example for what I want to do in case my previous post (below) was unclear.
>  Below is a valid xdmf file that paraview understands for a plane.
>
> <?xml version="1.0"?>
> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd">
> <Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
>   <Domain>
>     <Grid GridType="Uniform">
>       <Topology TopologyType="Quadrilateral" Dimensions="1">
>         <DataItem Dimensions="1 4" NumberType="Int" Precision="8"
> Format="XML">
>            0 1 3 2
> </DataItem>
>       </Topology>
>       <Geometry GeometryType="XYZ">
>         <DataItem Dimensions="4 3" NumberType="Float" Precision="4"
> Format="XML">
>   -0.5 -0.5 0
>   0.5 -0.5 0
>   -0.5 0.5 0
>   0.5 0.5 0
> </DataItem>
>       </Geometry>
>     </Grid>
>   </Domain>
> </Xdmf>
>
> ---  Now, what I want to do is to allow for the fact that the nodes
> defining this plane, may happen to be labelled 300, 20, 22, 80 instead of
> 0->3.  The key point being that there is still only 4 nodes, not 300 in the
> file for which I only need 4 to define the geom, but need to write out 300
> to all for the 0-based implicit ordering.  Therefore, I'd like a section in
> the geom part of the xmf file to qualify this numbering.  It doesn't bother
> me if they're subsequently renumbered inside paraview/vtk, only that I
> don't have to, as this is a simplistic version of something more
> complicated.  So to be verbose, it should now look like:
>
> <?xml version="1.0"?>
> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd">
> <Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
>   <Domain>
>     <Grid GridType="Uniform">
>       <Topology TopologyType="Quadrilateral" Dimensions="1">
>         <DataItem Dimensions="1 4" NumberType="Int" Precision="8"
> Format="XML">
>           * 300 20 22 80 *
> </DataItem>
>       </Topology>
>       <Geometry GeometryType="*XYZ_Explicit*">
>         <DataItem Dimensions="4 3" NumberType="Float" Precision="4"
> Format="XML">
> *   20 -0.5 -0.5 0 *
> *   22 0.5 -0.5 0 *
> *   80 -0.5 0.5 0 *
> *   300 0.5 0.5 0 *
>  </DataItem>
>       </Geometry>
>     </Grid>
>   </Domain>
> </Xdmf>
>
> Can this be done, or could this be done in the future?  Am I being daft
> and there is an easy way to do this?
>
> Cheers again,
> Andy
>
>
>
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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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