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

Mon Nov 25 11:48:18 EST 2013

Hi Jason,

Many thanks for your reply.  In my case I'm not quite sure how attributes
would help me, but I may not fully understand how they work.  As I posted
in the second xmf example file in my last email, given 4 nodes with 4
unique positions, I can completely define the plane topologically by
writing the node numbers out in the correct order, their actual
label/value/number doesn't matter (as long as it consistently refers to the
correct position).

In my example I used [300 20 22 80] as the node labels to define a 2D
plane.  However, my current understanding of xdmf(2) is that I would need
to supply in the geometry section (regardless of GeometryType) 301 x, y and
z node positions (even if 297 are just zeros), just so that I could conform
to the zero-based implicit numbering of that section.  That allows paraview
to index that data and pick out (the only) 4 positions it requires to
define the plane.

I'm asking whether there is a way round this so that, as I gave as an
example in my second xmf file, one could additionally provide an explicit
node number next to each x,y,z position so that the implicit zero-based
numbering could be skipped and only 4 x,y,z positions needed to be added to
the file in addition to their label/value/number.

Can attributes do this?  If so could you provide a quick example, ideally
just with reference to the second example file I included in my email?  Do
you have a link to the xdmf(2) mail list?

Many thanks again,
Andy

On 25 November 2013 16:13, Jason Fleming
<jason.fleming at seahorsecoastal.com>wrote:

> 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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