Inputs and scripts for @johnomotani's poster at EFTC 2023 #147
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This boundary condition is correct, and better behaved, for simulations with no numerical diffusion, or numerical diffusion that is very small compared to vpa advection.
…volumerecycle.toml
Mostly for debugging - without neutrals these cases do not develop steep gradients near the sheaths, so are easier to run.
This turned out to increase the gradients near the sheath (the hope had been it might do the opposite), so just including as a record.
Gives more reasonable-looking profiles. Also tweak the timestep settings.
As the grid in the split3 case is normalised by thermal speed, a larger vpa_L is needed to get roughly the same physical grid width as the other cases, and capture the source far enough out.
Make extreme points 1.0e-5/1.99999 to avoid zeros. Make range of charge exchange rate match limits needed for normalised plot axis. Remove unnecessary `[output]` section.
Should make it easier to tweak each case to get runs to converge to decent results.
Effectively makes fonts bigger, as this figure is included at a smaller size on the poster.
Write so that units are not needed, e.g. "z/L" instead of "z", etc.
By mistake had committed versions with z_nelement=4 instead of z_nelement=2.
This commit should reproduce the versions of plots used on JTO's EFTC poster.
These input files were (failed?) experiments that are not known to run well.
Remove some commented out lines and ensure `force_minimum_pdf_value = 0.0` is set for the 'split3' cases.
Does not include `moment_kinetics` or `PlasmaDispersionFunctions` - these have to be added specially as described in the README.md, and may cause errors if they already exist in the Project.toml as each would complain that the other cannot be found.
Makes more sense to have a single README.md for the publication_inputs/2023_EFTC_jto-poster directory that includes both sound-wave and wall-bc, especially as the scripts should be run from that directory, not the sound-wave/ and wall-bc/ subdirectories.
Need to set `krook_collisions_option`, not `krook_collisions`.
Adding this to have a working Manifest.toml recorded in the git history, as there are some issues with the latest versions of dependencies at the moment.
Don't want to keep Manifest.toml files in the repository generally, because they interfere with locally-installed dependencies and versions.
...otherwise numerical issues in the first/last elements in z prevent the 'split3' simulations from converging to a state with residuals below 1e-3 (but all input files are changed, not just the 'split3' ones, as the 'split3' simulations need to restart from a case with a sqrt-spaced grid to avoid numerical instability). Adds a note in the README.md that this grid was not used for the plots on the EFTC poster, these were just made accepting slightly higher residuals for the 'split3' case (the difference was in any case not visible on the plots).
If there is no `post_processing_input.toml` file, and a real file name is not passed, then an error is thrown (this will be fixed in makie_post_processing in future). For now, skip the unneeded setup call in get_run_info() to avoid the error.
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Question @mabarnes @mrhardman - is this something that we want to keep in the main repo? It could also make sense to create a repo just for these inputs/plots, which would pull in a fixed version of |
The CI test of the examples runs in serial, so fails if `z_nelement_local` is set in a way that requires distributed MPI parallelism.
johnomotani
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Dec 19, 2023
Fix examples introduced in #147
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Add a subdirectory
publication_inputs/2023_EFTC_jto-posterwhich contains the inputs and scripts needed to create the figures for @johnomotani's poster at EFTC 2023. Includes a README.md with instructions how to recreate the runs and figures.