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adds option to output velocity gradient

Merged Cristian Lalescu requested to merge feat/expand_rfields into master
All threads resolved!

This expands get_rfields with the option to output velocity gradient as well.

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  • Cristian Lalescu requested review from @g-lbent

    requested review from @g-lbent

  • assigned to @chichi

  • @g-lbent : please test this by (1) calling the get_rfields tool with all output options turned on and (2) writing a python code from scratch that reads velocity gradient, vorticity and TrS2, and then compares vorticity and TrS2 from file with (python-side) newly computed vorticity and TrS2.

    • Resolved by Cristian Lalescu

      It's not working, yet, I believe.

      • Iterations > 0 of my test simulation match very well in TrS2. Vorticity matches with some error bars (atol=1e-5, rtol=1e-5) but only up to a sign. I'm computing vorticity as
      vort[..., 0] = grad[..., 2, 1] - grad[..., 1, 2]
      vort[..., 1] = grad[..., 0, 2] - grad[..., 2, 0]
      vort[..., 2] = grad[..., 1, 0] - grad[..., 0, 1]
      • Iteration 0 of the test simulation (Gaussian initial condition) matches in TrS2 but not in vorticity. Could that be related to some incompressibility issue?
      • I am getting this warning on running get_rfields: "file /localdisk/bt307719/simulations/test_rfields/test_checkpoint_0.h5 does not have velocity group" It seems a bit strange to me that for this postprocessing, a test_fields.h5 is created linking to the checkpoint file, and then the output of the postprocessing is written back into the checkpoint file. In this case, the extra fields file does not seem necessary.
  • Cristian Lalescu added 7 commits

    added 7 commits

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  • Cristian Lalescu resolved all threads

    resolved all threads

  • Cristian Lalescu marked this merge request as ready

    marked this merge request as ready

  • Cristian Lalescu mentioned in commit e76cf3b1

    mentioned in commit e76cf3b1

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