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Inputs refactor and extra checking#247

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johnomotani merged 58 commits intomastermabarnes/moment_kinetics:masterfrom coordinates-input-refactormabarnes/moment_kinetics:coordinates-input-refactorCopy head branch name to clipboardSep 18, 2024

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Commits on Sep 8, 2024

• Get coordinate input from separate sections in input file

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• Add recursive_merge() function to merge nested Dicts

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• Replace merge_dict_of_dicts() with recursive_merge()

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Commits on Sep 9, 2024

• Update inputs with new coordinate inputs structure

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• Fix handling of periodic bc in gauss_legendre

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• Comment out nelement_local in some recyclefraction examples

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• Remove spline_derivatives_test.jl script

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• Add Github workflow that checks the 'test_scripts' run without errors

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• [em_fields] section in input

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• [evolve_moments] section in input

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• Remove modified default for neutral vz_dissipation in 1V case

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• Use set_defaults_and_check_section!() for numerical dissipation inputs

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• [reactions] and [electron_fluid_collisions] sections in input

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• Update performance-tests and publication_inputs with new input sections

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• Move "run_name" and "base_directory" into [output] section

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• Check that no unexpected section names were used in an input file

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• Fix override of "write_error_diagnostics" setting

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• Remove/update unused options from inputs

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• Rename scan_input variable to input_dict in mk_input()

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• Fix ASCII I/O option

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• Fix edge case for electron I/O counter

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• Fix Dict type to OptionsDict in gyroaverage_tests.jl

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• Reduce allowed filename length for HDF5 files

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• Remove unused mutable structs from input_structs

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• fix grid_input

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• Add new modules to docs

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Commits on Sep 10, 2024

• Alternative form of set_defaults_and_check_section!() for @kwdef struct

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• Move initial condition defaults to the @kwdef struct definition

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Commits on Sep 11, 2024

• Remove unused external modules from test.

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• Refactor 1D matrix assembly, make it clear that boundary conditions should only be imposed if the matrices are being used for solving ODEs, not for differentiation. Periodic and Dirichlet BC option…

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• Fix default value for "vperp" coordinate

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• Add define_test_coordinate() function

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• Test and correct boundary conditions for solving 1D ODE with Laplacian operator with periodic and Dirichlet (zero) boundaries.

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• Avoid LU decomposition of singular matrix when no valid boundary conditions are supplied for a 1D ODE solve.

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• Fix periodic boundary conditions for weak-form second derivative

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• Include a phase in periodic test functions in calculus_tests.jl

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• Ensure second derivatives give exactly periodic results

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• Set L_matrix_with_bc to nothing when not implemented

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Commits on Sep 12, 2024

• Try to rescue periodic ODE solver in latest changes by distinguishing between periodic BC modifications required for matrices on LHS or RHS in LHS.x = RHS. The ODE solver in the script sets RHS[end…

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• Note that L_matrix_with_bc requires two boundary conditions. In the periodic case, this is one to make the system periodic, and one to fix the constant offset. This should remove the problems with …

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• Remove distinction between periodic_bc_lhs and periodic_bc_rhs

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Commits on Sep 15, 2024

• Merge pull request #249 from mabarnes/correct-1D-matrix-assembly

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Commits on Sep 16, 2024

• Merge branch 'master' into coordinates-input-refactor

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• Use explicitly defined structs for numerical dissipation parameters

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• Improve docstring for define_coordinate()

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• Change default for charge exchange and ionization frequencies to 0

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• Use explicitly defined structs for reactions, electron_fluid_collisions

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• Move manufactured solutions input to setup_manufactured_solutions()

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• Explicitly defined struct for em_fields_input

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• Hard-code the name for the 'stop file'

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• Explicitly defined struct for I/O input

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• Remove outdated comment

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Commits on Sep 17, 2024

• Use Julia-provided OpenMPI for CI test

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• Remove NetCDF from parallel CI tests

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• Save defaults from @kwdef structs in options

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• Fix formatting in setup_global_weak_form_matrix() docstring

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• Make documentation builds strict on CI

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• Merge branch 'master' into coordinates-input-refactor

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