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Final transfer version#306

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johnomotani merged 58 commits intomastermabarnes/moment_kinetics:masterfrom final_transfer_versionmabarnes/moment_kinetics:final_transfer_versionCopy head branch name to clipboardJan 18, 2025

+82,082-663

Commits

Commits on Sep 18, 2024

• Update naming of update_qpar for ions to be update_ion_qpar, in line with update_neutral_qz

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• Add ion_physics flag to determine drift_kinetic, gyrokinetic or braginskii ion physics. Gyrokinetic flag replacement of the gyrokinetic_ions case will happen in a later commit, so right now the gyr…

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• Update gyrokinetic flag uses throughout the repo, so that instead of gyrokinetic_ions = true being the test, we see whether ion_physics == gyrokinetic_ions

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Commits on Sep 19, 2024

• Some of the Braginskii functionality (unfinished)

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• Merge branch 'master' into ion_flags

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• Merge branch 'ion_flags' into ion_braginskii_fluid

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• Make initialisation for braginskii ion heat flux be calculated from unnormalised pdf (then subsequent heat flux updates will be with the braginskii closure)

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• Merge branch 'master' into ion_braginskii_fluid

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Commits on Sep 20, 2024

• Add braginskii heat flux formula by adding an ion dT_dz component in the struct, as well as an ion temp

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• add loop to allow n_neutral_species = 0 and CFL plots to still be made for ions

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• Merge branch 'master' into ion_braginskii_fluid

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• Move order of krook_collisions.jl inclusion to allow velocity_moments.jl to use the reference collision frequency to calculate braginskii heat flux

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Commits on Sep 21, 2024

• Add plotting for collisionality (comparing gradient scale lengths to mean free path) and braginskii heat flux boundary condition at walls, following Stangeby (though I haven't checked the subtracte…

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Commits on Sep 23, 2024

• Add comparison plots functionality for collisionality_plots, and add small correction to ion braginskii heat flux boundary condition

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• Add comments to boundary condition of braginskii heat flux, and add docstring for collisionality_plots function in makie_post_processing

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• Fix bug during restarts to allow for multiple sources while external_source_controller_integral is still unused

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• Make collisionality_plots plot the last timestep value (which was originally hard coded)

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• Merge branch 'master' into ion_braginskii_fluid

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Commits on Sep 26, 2024

• Merge branch 'master' into ion_braginskii_fluid

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Commits on Sep 27, 2024

• Add option of overlaying what the Braginskii heat flux would be for that run (for when heat flux in the simulation is calculated using the shape function - having this option for braginskii_ions wo…

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• Add option for super Gaussian with decay of 4th power instead of second power in upstream external source. Might add higher powers later.

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• Merge branch 'master' into ion_braginskii_fluid

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Commits on Sep 28, 2024

• Fix typo when energy source used

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Commits on Sep 30, 2024

• Don't plot braginskii overlay if the original simulation itself was a braginskii one (which just overplots the old one, apart from the boundaries)

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Commits on Oct 1, 2024

• Add string to braginskii_overlay system to tell you its an overlay, which is much clearer than just writing braginskii everywhere. Note that I will soon change the naming system to collisional_krook

  LucasMontoya4

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• Merge branch 'ion_braginskii_fluid' of github.com:mabarnes/moment_kinetics into ion_braginskii_fluid

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Commits on Oct 3, 2024

• Fix PI_controller file io for option

  LucasMontoya4

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• Edit PI_controller for density_midpoint_control option to begin the source with an input guess, which is the source_strength option in the input file. This means when you restart a run from another…

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• remove printing function that was used for debugging

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• Change naming from Braginskii_ions to coll_krook_ions, and change instances of the name braginskii for ion functions to coll_krook. The electron braginskii fluid naming is unchanged for now.

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• Don't evolve shape function if heat flux closure comes from coll_krook coefficient calculation.

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Commits on Oct 4, 2024

• Allow collisionality_plots to animate comparison runs with different numbers of timesteps

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• add neutral controller_integral file_io.jl bug fix (ion version was fixed in previous commit)

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Commits on Oct 6, 2024

• skip chodura condition check in coll_krook fluid ion case, so that ngrid and nelement can both be 1 (to speed up process easily). Also change gamma_i to 4.0 for stability of more dense cases in col…

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• Merge branch 'master' into remove_redundant_shapefn_evolution

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Commits on Oct 7, 2024

• change gamma back to 2, and change the boundary condition for heat flux of coll_krook calculation to reflect the 1D pressure rather than 3D isotropic pressure used. Also comment out line where boun…

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• Create new module for collision_frequency calculations, so that krook collisions module can be defined later in moment_kinetics.jl. This fixes the issue highlighted in the previous commit.

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• Change gamma_i to 2.5, from Stangeby (25.2)

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Commits on Oct 9, 2024

• Add temperature_midpoint_control source option. This will change the amplitude of an energy source so that the temperature midpoint is kept at a desired level. A few notes on this for now: 1. The t…

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• Merge branch 'master' into remove_redundant_shapefn_evolution

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Commits on Oct 15, 2024

• Change gamma_i boundary condition for coll_krook heat flux closure depending on whether we're 1V or 2V

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Commits on Oct 31, 2024

• Correction to heat flux itself, should be 1D instead of 3D calculation

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Commits on Jan 7, 2025

• Include all input files that I made for transfer, and the files that I used to generate input files/ make plots.

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Commits on Jan 8, 2025

• Add tests for multi source functionality and PI controllers

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• small changes

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• Merge remote-tracking branch 'origin/master' into final_transfer_version

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Commits on Jan 13, 2025

• Merge branch 'master' of github.com:mabarnes/moment_kinetics into final_transfer_version

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Commits on Jan 14, 2025

• Merge branch 'master' into final_transfer_version

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• Merge remote-tracking branch 'origin/master' into final_transfer_version

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• move transfer input files from examples to publication inputs folder

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• Add a couple of example multi source files with a collisional closure as well.

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• deleted transfer input files as they were moved

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• Add docs page for collision_frequencies.jl

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Commits on Jan 16, 2025

• remove example files so they are not run by remote server checks

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• Change input file for multi source tests to only include 2 tests, which consist of two ion sources each. Neither uses a PI controller. The latter two tests (that I have now commented out) would hav…

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• Comment out julia-actions/cache in documentation CI job

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Commits on Jan 17, 2025

• Fix MPI in setup_external_sources!() when ignore_MPI = true

  johnomotani

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• Apply suggestions from code review

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