Exodus II output and YT visualization


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3 months ago by
The stretch goal of this is to export the Fenics results to the python YT library for volumetric rendering. YT currently has an example from the MOOSE FEM solver which exports its data in Exodus II format (see here: http://yt-project.org/doc/examining/loading_data.html#exodus-ii-data) I have done some digging and I have seen both on the old Q&A (https://fenicsproject.org/qa/9318/dolfin-convert-of-exodus-ii-file/) and in dolfin/site-packages/dolfin_utils/meshconvert/meshconvert.py (https://github.com/FEniCS/dolfin/blob/master/site-packages/dolfin_utils/meshconvert/meshconvert.py) function `exodus2xml` at line 1276 that there is a conversion from the Exodus 2 but is there a way to export the results to Exodus 2 as there are currently with export to the VTK paraview file format.  A good test case would be the elasticity example from the Fenics tutorial (https://github.com/hplgit/fenics-tutorial/blob/6b103f609865eef71eb53cdb91f98473bfecb709/src/vol1/python/elasticity.py)
Community: FEniCS Project

2 Answers


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3 months ago by
We are minimising the number of formats that DOLFIN can read and write, and recommend using other tools for the conversion, e.g. meshio (https://github.com/nschloe/meshio).
I did a bit of digging on the YT side of things where they say here (http://yt-project.org/doc/examining/loading_data.html#unstructured-grid-data) that their inputs are cell average and after doing my own work (see here: https://github.com/GProtoZeroW/IssueNotebooks/blob/master/FENICS%20YT.ipynb) It appears that FENICS is node-centric. will meshio deal with that or is there a setting in FENICS to make it cell centric
written 3 months ago by Steven Armour  
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12 weeks ago by
So after consulting with the yt folks (Re: [yt-project/yt] loading fenics data into yt instead of relying on vtk "Re: [yt-project/yt] load fenics data into yt instead of relying on vtk (#1780)" an answerer was found here: https://github.com/PyLCARS/YT_BeyondAstro/blob/master/FEniCS_and_yt.ipynb
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