# Introduction¶

BOUT++ is a C++ framework for writing plasma fluid simulations with an arbitrary number of equations in 3D curvilinear coordinates. More specifically, it is a multiblock structured finite difference (/volume) code in curvilinear coordinates, with some features to support unusual coordinate systems used in fusion plasma physics. It has been developed from the original BOUndary Turbulence 3D 2-fluid edge simulation code written by X.Xu and M.Umansky at LLNL.

The aim of BOUT++ is to automate the common tasks needed for simulation codes, and to separate the complicated (and error-prone) details such as differential geometry, parallel communication, and file input/output from the user-specified equations to be solved. Thus the equations being solved are made clear, and can be easily changed with only minimal knowledge of the inner workings of the code. As far as possible, this allows the user to concentrate on the physics, rather than worrying about the numerics. This doesn’t mean that users don’t have to think about numerical methods, and so selecting differencing schemes and boundary conditions is discussed in this manual. The generality of BOUT++ of course also comes with a limitation: although there is a large class of problems which can be tackled by this code, there are many more problems which require a more specialised solver and which BOUT++ will not be able to handle. Hopefully this manual will enable you to test whether BOUT++ is suitable for your problem as quickly and painlessly as possible.

BOUT++ treats time integration and spatial operators separately, an approach called the Method of Lines (MOL). This means that BOUT++ consists of two main parts:

1. A set of Ordinary Differential Equation (ODE) integrators, including implicit, explicit and IMEX schemes, such as Runge-Kutta and the CVODE solver from SUNDIALS. These don’t “know” anything about the equations being solved, only requiring the time derivative of the system state. For example they make no distinction between the different evolving fields, or the number of dimensions in the simulation. This kind of problem-specific information can be used to improve efficiency, and is usually supplied in the form of user-supplied preconditioners. See section Options for more details.
2. A set of operators and data types for calculating time derivatives, given the system state. These calculate things like algebraic operations (+,-,*,/ etc), spatial derivatives, and some integral operators.

Each of these two parts treats the other as a black box (mostly), and they communicate by exchanging arrays of data: The ODE integrator finds the system state at a given time and passes it to the problem-dependent code, which uses a combination of operators to calculate the time derivative. This time derivative is passed back to the ODE integrator, which updates the state and the cycle continues. This scheme has some advantages in terms of flexibility: Each part of the code doesn’t depend on thedetails of the other, so can be changed without requiring modifications to the other. Unfortunately for many problems the details can make a big difference, so ways to provide problem-specific information to time integrators, such as preconditioners, are also provided.

Though designed to simulate tokamak edge plasmas, the methods used are very general and almost any metric tensor can be specified, allowing the code to be used to perform simulations in (for example) slab, sheared slab, and cylindrical coordinates. The restrictions on the simulation domain are that the equilibrium must be axisymmetric (in the z coordinate), and that the parallelisation is done in the $$x$$ and $$y$$ (parallel to $$\mathbf{B}$$) directions.

After describing how to install BOUT++ (section Getting started), run the test suite (section Running the test suite) and a few examples (section Running BOUT++, more detail in section More examples), increasingly sophisticated ways to modify the problem being solved are introduced. The simplest way to modify a simulation case is by altering the input options, described in section BOUT++ options. Checking that the options are doing what you think they should be by looking at the output logs is described in section Running BOUT++, and an overview of the IDL analysis routines for data post-processing and visualisation is given in section Post-processing. Generating new grid files, particularly for tokamak equilibria, is described in section Generating input grids.

Up to this point, little programming experience has been assumed, but performing more drastic alterations to the physics model requires modifying C++ code. Section BOUT++ physics models describes how to write a new physics model specifying the equations to be solved, using ideal MHD as an example. The remaining sections describe in more detail aspects of using BOUT++: section Differential operators describes the differential operators and methods available; section Staggered grids covers the experimental staggered grid system.

Various sources of documentation are:

• This manual
• Most directories in the BOUT++ distribution contain a README file. This should describe briefly what the contents of the directory are and how to use them.
• Most of the code contains Doxygen comment tags (which are slowly getting better). Running doxygen on these files should therefore generate an HTML reference. This is probably going to be the most up-to-date documentation.

Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu

BOUT++ is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

BOUT++ is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with BOUT++. If not, see <https://www.gnu.org/licenses/>.

A copy of the LGPL license is in COPYING.LESSER. Since this is based on (and refers to) the GPL, this is included in COPYING.

BOUT++ is free software, but since it is a scientific code we also ask that you show professional courtesy when using this code:

1. Since you are benefiting from work on BOUT++, we ask that you submit any improvements you make to the code to us by emailing Ben Dudson at bd512@york.ac.uk
2. If you use BOUT++ results in a paper or professional publication, we ask that you send your results to one of the BOUT++ authors first so that we can check them. It is understood that in most cases if one or more of the BOUT++ team are involved in preparing results then they should appear as co-authors.
3. Publications or figures made with the BOUT++ code should acknowledge the BOUT++ code by citing B.Dudson et. al. Comp.Phys.Comm 2009 and/or other BOUT++ papers. See the file CITATION for details.