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Documentation for moment_kinetics.jl

Contents

• Getting started
• • Setup
  • Run a simulation
  • Restarting
  • Post-processing with makie_post_processing
  • Parallel I/O
  • Running parameter scans
  • Tests
  • Manufactured Solutions Tests
• Input Options
• • File I/O
  • Model Options
  • Timestepping Options
  • Special cases
• Post processing
• • How to
  • Interactive use
  • API
• Timestepping
• • Fixed-timestep schemes
  • Adaptive-timestep schemes
  • Input parameters
  • Diagnostics
  • Developing
  • API
• Moment kinetic equations
• • Ion moment equations
  • Ion kinetic equation
  • Neutral equations
  • Reduction to 2D1V
  • Conversion to conventions of 1D1V Excalibur reports
  • Dimensionless equations for code
  • Old 1D1V moment kinetic equations
• Moment kinetic equations for electrons
• • Moment equations
  • Electron collisions
  • 1D2V kinetic equation
  • Reduction to 1D1V
  • Dimensionless equations
  • Old 1D1V kinetic electron equations
• External sources
• • Amplitude
  • API
• Fokker Planck collision operator
• Input parameters
• Magnetic Geometry
• • Supported options
  • Geometric coefficients
• Jacobian matrix calculations
• Debugging
• • Shared-memory parallelism
  • Identifying location of regressions (debug output)
• Developing
• • Dependencies
  • Revise.jl
  • Input options and defaults
  • Array types
  • Timings
  • Parallelization
  • Bounds checking
  • Parallel I/O
  • Package structure
• Manual setup
• • Install Julia
  • Add moment_kinetics packages
  • Set up MPI
  • Using the native Julia MPI
  • Miscellaneous required packages
  • Link HDF5
  • Enable MMS features
  • Enable NetCDF output
  • Set up Plots-based plotting routines
  • An example manual setup script
• machine_setup notes
• • Notes on some prompts from the script
  • Defaults for prompts
  • bin/julia
  • julia.env
  • Setup of post processing packages
  • Use of system images
  • Operations done by machines/machine_setup.sh
  • API documentation
• Parameter scans
• • Running a scan
  • Post processing a scan
  • API
• List of Manufactured Solutions Test TOML inputs
• • 1D1V tests
  • 1D2V tests
  • 1D2V/1D3V test (with neutrals)
  • 2D1V tests
  • 2D2V tests
  • 2D2V/2D3V tests

Modules

• makie_post_processing.makie_post_processing
• moment_kinetics.advection
• moment_kinetics.analysis
• moment_kinetics.array_allocation
• moment_kinetics.bgk
• moment_kinetics.boundary_conditions
• moment_kinetics.calculus
• moment_kinetics.charge_exchange
• moment_kinetics.chebyshev
• moment_kinetics.clenshaw_curtis
• moment_kinetics.command_line_options
• moment_kinetics.communication
• moment_kinetics.constants
• moment_kinetics.continuity
• moment_kinetics.coordinates
• moment_kinetics.debugging
• moment_kinetics.derivatives
• moment_kinetics.electron_vpa_advection
• moment_kinetics.electron_z_advection
• moment_kinetics.em_fields
• moment_kinetics.energy_equation
• moment_kinetics.external_sources
• moment_kinetics.file_io
• moment_kinetics.finite_differences
• moment_kinetics.fokker_planck
• moment_kinetics.fokker_planck_calculus
• moment_kinetics.fokker_planck_test
• moment_kinetics.force_balance
• moment_kinetics.fourier
• moment_kinetics.gauss_legendre
• moment_kinetics.geo
• moment_kinetics.gyroaverages
• moment_kinetics.initial_conditions
• moment_kinetics.input_structs
• moment_kinetics.interpolation
• moment_kinetics.ionization
• moment_kinetics.jacobian_matrices
• moment_kinetics.krook_collisions
• moment_kinetics.lagrange_polynomials
• moment_kinetics.load_data
• moment_kinetics.looping
• moment_kinetics.machine_setup
• moment_kinetics.manufactured_solns
• moment_kinetics.moment_constraints
• moment_kinetics.moment_kinetics
• moment_kinetics.moment_kinetics_input
• moment_kinetics.moment_kinetics_structs
• moment_kinetics.neutral_r_advection
• moment_kinetics.neutral_vz_advection
• moment_kinetics.neutral_z_advection
• moment_kinetics.nonlinear_solvers
• moment_kinetics.numerical_dissipation
• moment_kinetics.quadrature
• moment_kinetics.r_advection
• moment_kinetics.reference_parameters
• moment_kinetics.runge_kutta
• moment_kinetics.source_terms
• moment_kinetics.species_input
• moment_kinetics.time_advance
• moment_kinetics.timer_utils
• moment_kinetics.type_definitions
• moment_kinetics.utils
• moment_kinetics.velocity_grid_transforms
• moment_kinetics.velocity_moments
• moment_kinetics.vpa_advection
• moment_kinetics.z_advection
• plots_post_processing.plot_MMS_sequence
• plots_post_processing.plot_sequence
• plots_post_processing.plots_post_processing
• plots_post_processing.post_processing_input