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[BUG/etc.] Bug fixes all over the place!

No issue was ever made for these things. But this PR fixes a number of bugs:

  • Aurora and potential are calculated on the first time-step
  • Electrodynamics code uses bottom of the grid for magnetic coordinates, not the top
  • Remove a few unnecessary calls to calc_[physics/rates/collisions]
  • Finalize was taking a long time
  • Post-processing to NetCDF uses correct time since ... units (Jan 1 1965, not time since run began)
  • DoSeparateHPI flag is correctly handled
  • Logfiles are more concise and do not have overflowing columns
  • Test script is more robust, supports restarts
  • Add restart, separateHPI, Apex&Dynamo tests

Changes to GITM outputs

Some. Test solutions are all updated. IE patterns will be shifted slightly, and restarts may look different. But they should be "more correct" now.

aaronjridley and others added 13 commits October 23, 2025 20:53
Develop was updated, first_time started failing tests. Diagnose why!
- Save logfiles, even if it's a restart
- save all logfiles while running multiple tests in run/data/
- more robust (no hardcoding log000002.dat)
- Logfiles are output with one decimal point now
- get_potential uses iAlt=2, not iAlt=nAlts-1
- potenital & aurora are actually calculated at t=0
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These seem fine!

@aaronjridley aaronjridley merged commit 601cbb8 into develop Nov 7, 2025
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@aaronjridley aaronjridley deleted the first_time branch November 7, 2025 16:53
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3 participants