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[WIP] Adding thermal conduction and viscosity #331

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@jzuhone jzuhone commented Jun 28, 2024

The goal of this PR is to add viscosity and thermal conduction to GAMER.

Here is a checklist--note that a checked item does not mean bugs are fixed.

  • Anisotropic conduction in MHD
  • Isotropic conduction in HD/MHD
  • Anisotropic/Braginskii viscosity in MHD
  • Isotropic viscosity in HD/MHD
  • Cowie & McKee conduction saturation for conduction
  • Crude implementation of Whistler mode suppression of conduction
  • "hard-wall" limiters on Braginskii viscosity based on firehose and mirror instability considerations
  • Conduction test problems
    • 2D Step Function
    • 2D Ring
    • Blast Wave
    • Magnetothermal Instability
  • Viscosity test problems
    • Velocity Damping
    • Linear MHD Waves
    • Circularly Polarized Alfvén Wave
  • Freezing hydro fluxes for test problems (while leaving diffusive fluxes on)
  • Output pressure anisotropy
  • Output conductivity

* main:
  Minor
  Bug fix
  Update to support Plummer.
  Rename the title of the column
  Update the comment.
  Update comment
  Use the test problem Zeldovich as the example
  Remove test line
  Fix typo, rename function and parameters.
  Update by the PR comment
  Add an example of the script.
  Update the comments.
  Bug fix.
  Add a new tool.
* main: (56 commits)
  [Bugfix] Correct the pointer assignement when FLU_GPU_NPGROUP < OMP_NTHREAD in CPU_FluidSolver_MHM.cpp
  [Bugfix] Correct the pointer assignement when FLU_GPU_NPGROUP < OMP_NTHREAD in CPU_FluidSolver_CTU.cpp
  Update by review comment
  Fix warning message.
  chore(docs): Sync wiki to doc/wiki [skip-cd]
  chore(docs): Sync wiki to doc/wiki [skip-cd]
  Update and rename sync-wiki-to-doc.yml to copy-wiki-to-doc.yml
  Update and rename sync-doc-to-wiki.yml to copy-doc-to-wiki.yml
  chore(docs): Sync wiki to doc/wiki [skip-cd]
  chore(docs): Sync wiki to doc/wiki [skip-cd]
  chore(docs): Sync wiki to doc/wiki [skip-cd]
  Create sync-wiki-to-doc.yml
  Create sync-doc-to-wiki.yml
  Add doc/wiki
  Minor
  Remove equal sign
  Fix the wrong size check
  Add check
  Bug fix
  Synchronize Aux_Check_Conservation.cpp from psidm to main
  ...
* main: (21 commits)
  Correct NGrid
  Minor
  Review comments
  Remove redundant codes
  Update description of OPT__OUTPUT_PART
  Remove zip file after decompress
  [Workflow] Update all parameters wiki page
  Support OUTPUT_BOX L1 error
  First try at letting Output_L1Error do slices
  Update description of OPT__OUTPUT_PART
  Add remove Box*
  Update wiki
  Add OUTPUT_BOX mode
  Update z information
  Minor
  Add sha256 check
  Bugfix
  Add sha256sum check
  Update link of LSS
  Uncomment the curl
  ...

# Conflicts:
#	src/Output/Output_L1Error.cpp
* main: (90 commits)
  Minor
  chore(docs): Sync wiki to doc/wiki [skip-cd]
  Minor
  Update wiki
  Update wiki
  Move the script
  Update generate_make.sh
  Update wiki
  Remove prefix and suffix
  Apply suggestions from code review
  Correct indices in Bondi/plot_diagonal.gpt
  Set soliton parameters in Input__TestProb
  Minor
  Simplify the expression of soliton external potential
  Minor
  Style
  Disable Bondi_dynBH by default; convert units
  Add new parameters to Input__TestProb
  Remove Bondi_Soliton_PresProf and GSL since they are only used for Bondi_Init
  Remove Bondi_Init since it's only for testing purposes
  ...
@jzuhone
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jzuhone commented Feb 5, 2025

@hyschive @ChunYen-Chen just a note here:

I have written pretty much all the code that is needed and have written a number of test problems. My very cursory look at all of these test problems is that everything seems to work. I need to do a proper analysis before we should merge this, but I don't anticipate major changes after this analysis is finished. I will try to do it gradually over the next few weeks and put it into a form that is eventually publishable.

I obviously will also need to check formatting, fix parameter files, etc. But this is a major milestone.

@hyschive
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hyschive commented Feb 6, 2025

@jzuhone Excellent! I'm super happy to notice that all the items in the checkbox have been completed! We still start reviewing it as soon as you feel it's ready.

It would be great if you could also update the Wiki in gamer/doc/wiki. Please refer to the instructions here.

(@ChunYen-Chen)

* main:
  Add string restriction description
  [Bugfix] Fix gamer-project#425
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3 participants