Welcome to BOUT++’s documentation!

The documentation is divided into the following sections:

• User documentation

  • Getting started

  • BOUT++ models

  • Model inputs

  • Model outputs

  • BOUT++ interfaces

• Developer Documentation

Getting started

• Introduction
  • License and terms of use
• Getting started
  • Pre-built binaries
  • Obtaining BOUT++
  • Installing dependencies
  • Configuring BOUT++
  • CMake
  • Natural Language Support
  • Configuring analysis routines
  • Compiling BOUT++
  • Running the test suite
  • Installing BOUT++ (experimental)
• Advanced installation options
  • Optimisation and run-time checking
  • Manually set compilation flags
  • Machine-specific installation
  • File formats
  • OpenMP
  • SUNDIALS
  • PETSc
  • LAPACK
  • MPI compilers
  • Installing FFTW from source
  • Compiling and running under AIX
  • Issues
• Running BOUT++
  • Quick start
  • Analysing the output using Python
  • Natural language support
  • When things go wrong
  • Startup output
  • Per-timestep output
  • Restarting runs
  • Stopping simulations
  • Manipulating restart files

BOUT++ models

• BOUT++ physics models
  • Heat conduction
  • Magnetohydrodynamics (MHD)
  • Reduced MHD
  • Logging output
  • Updating Physics Models from v3 to v4
  • More examples
• Makefiles and compiling BOUT++
  • Executables example
  • Modules example
  • bout-config script
• Variable initialisation
  • Initialisation of time evolved variables
  • Initalising variables with the FieldFactory class
  • Adding a new function
  • Parser internals
• Boundary conditions
  • Boundary conditions for non-orthogonal grids
  • Relaxing boundaries
  • Shifted boundaries
  • Changing the width of boundaries
  • Examples
  • Boundary regions
  • Boundary regions
  • Boundary operations
  • Boundary modifiers
  • Boundary factory
• Testing
  • Automated tests and code coverage
  • Unit tests
  • Integrated tests
  • Method of Manufactured Solutions
  • Timing

Model inputs

• BOUT++ options
  • BOUT.inp input file
  • Command line options
  • General options
  • Communications
  • Differencing methods
  • Model-specific options
  • Input and Output
  • Implementation
  • Reading options
  • Reading and writing to NetCDF
  • FFT
  • Types for multi-valued options
• Generating input grids
  • BOUT++ Topology
  • 3D variables
  • From EFIT files
  • From ELITE and GATO files
  • Generating equilibria
  • Zoidberg grid generator

Model outputs

• Post-processing
  • Python routines
  • Python analysis routines
  • Reading BOUT++ output into IDL
  • Summary of IDL file routines
  • IDL analysis routines
  • Matlab routines
  • Mathematica routines
  • Octave routines
• Reproducibility and provenance tracking
• The python boutcore module
  • Installing
  • Purpose
  • State
  • Functions
  • Examples
  • Functions - undocumented
  • Functions - special and inherited

BOUT++ interfaces

• Time integration
  • Options
  • CVODE
  • IMEX-BDF2
  • Split-RK
  • Backward Euler - SNES
  • ODE integration
  • Preconditioning
  • Jacobian function
  • DAE constraint equations
  • IMEX-BDF2
  • Monitoring the simulation output
  • Implementation internals
• Parallel Transforms
  • Field-aligned grid
  • Shifted metric
  • FCI method
• Laplacian inversion
  • Usage of the laplacian inversion
  • Numerical implementation
  • Implementation internals
  • LaplaceXY
  • LaplaceXZ
• Differential operators
  • Differencing methods
  • User registered methods
  • Mixed second-derivative operators
  • Non-uniform meshes
  • General operators
  • Clebsch operators
  • The bracket operators
  • Finite volume, conservative finite difference methods
  • Derivatives of the Fourier transform
• Algebraic operators
• Staggered grids
• Eigenvalue solver
  • Configuring with SLEPc
  • SLEPc options
  • Examples
• Nonlocal heat flux models
  • Spitzer-Harm heat flux
  • SNB model
• Invertable operators
• PETSc solvers

Field-aligned coordinate systems

• Field-aligned coordinates
• BOUT++ preconditioning
• Geometry and Differential Operator

Developer Documentation

• Contributing to BOUT++
• Git crash course
• Code layout
• Arrays, scalar and vector field types
• PETSc interface
• Mesh
• File I/O
• Natural Language Support
• Performance profiling
• API reference

Indices and tables

• Index

• Search Page