Code

Preparation for adding electrons#207

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johnomotani merged 42 commits intomastermabarnes/moment_kinetics:masterfrom pre-electron-updatesmabarnes/moment_kinetics:pre-electron-updatesCopy head branch name to clipboardApr 29, 2024

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Commits on Apr 26, 2024

• Filter out size-1 dimensions from combinations to check in debug tests

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Commits on Apr 27, 2024

• Rename 'charged' to 'ion'

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• Separate dissipation parameters for ions, electrons, neutrals (#192)

  

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• Fix duplicated calculations in steady state residual check

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• Try-catch in calculate_steady_state_residual() post-proc function

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• Throw error when assign_endpoint!() fails

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• Move boundary conditions out of initial_conditions to separate module

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• Include begin_*_region() calls in derivative functions

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• Set debug flags in ldiv!() method for MPIDebugSharedArray

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• Let value in setindex!() method for DebugMPISharedArray be any Number

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• Save run_id in io_input

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• Split I/O for ions and neutrals into separate functions

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• Write out most recent version of constraints coefficients as diagnostic

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• Refactor krook_collisions, ready for adding collisions for electrons

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• Setup fields, advection_structs, scratch_dummy outside setup_time_advance!()

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• Function for setup of time_info struct

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• Add shared-memory scratch arrays to coordinate structs

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• Restore writing of ion distribution function to ascii output files

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• Allow saving/loading when some coordinates are not present

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• Refactor reloading functions

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• Refactor restart - move functionality to functions in utils module

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• Fix typo in external_sources docs

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• Fix source moments to be compatible with source_type="energy_source"

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• Fix typo in docs for source term in neutral moment-kinetic equation

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• Add 'git' module in setup for Marconi

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• Support selection by it for the time variable in title of animations

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• Fix formatting of docstrings for plot_vs_* and animate_vs_* functions

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• Allow passing a label kwarg to 1d animation functions

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• Make plots of coefficients for moment constraints

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• Fix lookup of dfn vars from makie_post_processing input

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• Support it argument for CFL animations in timestep_diagnostics()

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• Simplify arguments to define_dynamic_dfn_variables!()

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• Move moments and pdf structs to moment_kinetics_structs

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• Reload *_constraints_*_coefficient, to avoid using uninitialized values

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• Type check on coords argument of write_single_value!()

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• Simplify imports in load_data

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• Add missing 'return' for extended_moments in load_ion_moments_data()

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• Simplify getting 'per step' values from 'cumulative'

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• deepcopy() inputs in tests to ensure they are not accidentally modified

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• Add comments about using ignore_MPI=true argument in tests

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• Allow nstep = 0

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Commits on Apr 28, 2024

• Fix ascii I/O for the ion distribution function

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