xmdf files generated by pyurdme examples faulty

[somathias]

When opening the xmdf files generated by the simple_diffusion example using paraview 4.4.0, the stored data values of the simulation are really small, ~ 10^-16 to 10^-21, ie. basically zero. Only the initial configuration seems to be stored with correct values.

I also ran the coral_reef and cylinder_demo examples, same problem.

[ahellander]

I think the numbers are “correct", but they are in concentration units (molecules/m^m3). If Paraview is not capable of rescaling the output in the visualization, we might have to apply some scaling ourselves.

/Andreas

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Andreas Hellander
Associate Professor, Scientific Computing
Division of Scientific Computing
Department of Information Technology
Uppsala University

On May 13, 2016, at 1:51 PM, somathias <[email protected]mailto:[email protected]> wrote:

When opening the xmdf files generated by the simple_diffusion example using paraview 4.4, the stored data values of the simulation are really small, ~ 10^-16 to 10^-21, ie. basically zero. Only the initial configuration seems to be stored with correct values.

I also ran the coral_reef and cylinder_demo examples, same problem.

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[ahellander]

Verified. The problem is that the data range is too small to render in Paraview. Not sure if this should be treated as a bug in pyurdme or Paraview.