VTK output error using unstructured grids (found in regression_tests and shortcourse files)

[James Patterson]

Hey there,

 

I’m an aspiring PFLOTRANer and am just starting out. But I believe found an issue with VTK output of unstructured grids.

 

Issue: output to VTK is successful and text appears plausibly normal, but loading into Paraview gives this error: “Number of cells don’t match!”

 

Conditions: occurs when using the FORMAT VTK option in OUTPUT block after loading in an unstructured file (.h5 or .ugi) via TYPE UNSTRUCTURED <file_name> in GRID. The error does not occur when creating a structured grid directly within PFLOTRAN.

 

To reproduce: take, for example, this regression test: pflotran/regression_tests/default/discretization/mixed_implicit-np4.in and replace “FORMAT HDF5” on line 93 with “FORMAT VTK”. I have reproduced the error on every regression test and shortcourse project which uses unstructured grids (e.g. pflotran/shortcourse/exercises/implicit_grid/mixed_implicit.in). I’ve attached the altered input file and initial VTK output.

 

Possible explanation: I’ve compared these outputs with VTK files which are output from structured grids (e.g. pflotran/shortcourse/exercises/5-spot/pflotran.in), and it seems that the VTK file has no cell vertex/point data at all. It’s missing 3 blocks: POINTS, CELLS, and CELL_TYPES. Instead it just jumped to CELL_DATA and gives the data values but non of the geometry info. Perhaps this is meant as a way of reducing the amount of geometry data that is included in the VTK files, but as .ugi is not a recognized file format for Paraview I don’t see a way to merge the two.

 

System and install info: Ubuntu 22.04, pflotran installed last week following these instructions exactly.

 

 

Thanks for the help and please let me know if there’s anything I can do to make the issue clearer.

 

Cheers,

 

James P.

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[Hammond, Glenn E]

James,

 

This issue was discovered in August and an error message was added to the master branch of the code (development version).

 

https://bitbucket.org/pflotran/pflotran/annotate/master/src/pflotran/output_vtk.F90?at=master#output_vtk.F90-396

 

The output of unstructured grids using VTK is currently not supported as the code does not write the geometries for the cells.

 

I recommend using the .xmf format (FORMAT HDF5) for unstructured grids, and it can be read by Paraview.

 

Glenn

 

From: pflotr...@googlegroups.com <pflotr...@googlegroups.com> On Behalf Of James Patterson
Sent: Monday, October 3, 2022 3:31 PM
To: pflotr...@googlegroups.com
Subject: [pflotran-dev: 6158] VTK output error using unstructured grids (found in regression_tests and shortcourse files)

 

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