Directory tree

Directory tree#

FARGO3D was developed as a general code. It solves a set of coupled differential equations on a mesh. Because it was developed as a general solver, it is necessary to keep certain general features isolated from other, more specific ones (that correspond to a specific problem).

A simple example of that is the initial condition (IC) of a problem. Obviously, the IC is a problem-dependent feature, and a mechanism is needed to keep it isolated from another problem. Touching the main structure of the code only to change the IC is not a good idea (yes, you can, but this is ugly, error-prone and wreaks havoc with versioning systems). This kind of problem is solved using the concept of SETUPS, and with the help of the VPATH Makefile variable. If you know the RAMSES code (https://bitbucket.org/rteyssie/ramses), you will see that we use the same patch concept.

Warning

In practice, when using FARGO3D you do not need to know about the VPATH variable, but if you want to develop some new features, it is a good idea to keep in mind that it is used under the hood.

Another problem is related to the different modules of the code. For example, in some situations, we need to use the MHD module, but for another set of problems, the MHD is irrelevant. In order to avoid a lot of logical runtime tests inside the code (if’s), we prefer to use MACROCOMMAND variables. These variables are interpreted prior to compilation time, by the so-called preprocessor, and activate/deactivate certain features (lines) of the code, allowing a tailor-made executable, built for a specific problem. All these variables are activated from the Makefile (they are defined actually in the .opt files that we shall see below).

The most important file to ultimately build a FARGO3D executable is obviously the Makefile. For this reason, there is a section devoted to this particular file. But, because FARGO3D uses a lot of scripting at compilation time, the process of building the code does not simply reduce to the Makefile. We refer to the FARGO3D building process as “the make process”.

A given instance of FARGO3D has many different properties, and storing each one in an organized manner is achieved through a number of different subdirectories. In this section, we give a brief explanation of each one.

Directories#

src/#

The directory where the main sources are stored is the src/ directory. Inside it, you will find all the files related to the initialization, evolution, and visualization of the data. All the sources are pure C files, plus some headers and a very few CUDA files. Also, in this folder, you can find the main makefile (src/makefile). This makefile should never be called directly. All the fundamental changes to the code must be done here.

scripts/#

In the scripts/ directory you will find the fundamental python-scripts used at compilation time. There are scripts for:

  • Defining the variables.

  • Analyzing the boundary conditions.

  • Analyzing and defining the units.

  • Generating the CUDA files automatically.

  • Improving the CUDA blocks.

  • Accelerating the make process (executing the makefile in parallel).

  • Making general tests (mandatory for new improvements).

bin/#

This directory is empty by default, but during compilation, this is where all the object files and script-residual data are stored. In practice, this directory is useful for avoiding a mixing between sources and objects, a very useful behavior when you are developing new routines.

outputs/#

The outputs/ directory is the default output directory for all the FARGO3D standard setups. As you could see in the first run, the data were stored in outputs/fargo. By default all the data is stored in outputs/setup_name, where setup_name is one of the setups in the setups/ directory.

setups/#

This directory is where all the different setups are. By default, the make process looks here if the setup is defined, eg:

$: make SETUP=otvortex

After that, the makefile will search inside setups/ whether there is a directory called setups/otvortex. Inside the otvortex/ directory we find all the files necessary to set up the problem and build the code.

planets/#

Inside this directory are the default planetary system files to run a simulation with one or several planets, considered as point-like masses that interact between them and with the disk (onto which they act as an external potential). The syntax of planetary files is for the former FARGO code. It is not mandatory to store your planetary data here, but it is recommended.

std/#

the name std comes from “standard”. This directory stores all the standard configuration files. In this version, these are:

  • boundaries.txt: where the boundary conditions are defined.

  • boundary_template.c: A build helper for the boundaries scripting.

  • centering.txt: A file describing the centering of the different fields with respect to the mesh (helper for boundary conditions scripting).

  • defaultflags: A file with all the default flags for the make process.

  • std.par: Default parameters. It is used when you have not defined the value of a certain parameter in your parameter file. It is used for compatibility with some specific problems related to disks simulations and some plot-related parameters.

  • standard.units: The scaling rules for all standard real variables of the code.

  • func_arch.cfg: The standard architecture file. This file selects where each function will run (CPU or GPU). It only makes sense if the compilation was done with GPU-Compatibility (GPU=1). By default, all the function run on the GPU, but this file is a great tool for debugging the code (one of the best tools to develop a kernel!).

test_suite/#

This directory was developed to ensure a stable development of the code. Here there is a set of test files written in python. All of them use the script test.py. They are easy to understand. The main idea is: if your recent developments pass all the tests, at least, your new improvements do not interfere with the main code and do not alter its behavior.

utils/#

Here is a set of routines to analyze the data. The content inside are self-documented. Feel free to explore it.

doc/#

The doc/ directory is where these documentation files reside. Also, here are some files related to the license of the code.

setups/SETUP directory#

The directory setups/SETUP is one of the most complex directories in FARGO3D. The complexity arises because inside are stored all the information required for a given, specific problem. The extensive list of the files stored for each setup is:

  • condinit.c: this is the file where the initial conditions are written. Thanks to the use of the VPATH variable in the makefile, this file supersedes the file src/condinit.c of the main source.

  • SETUP.par: the parameters required for this setup.

  • SETUP.opt: all the directives for the makefile (this is where you decide the number of dimensions, the equation of state, the geometry, whether you use orbital advection -aka FARGO algorithm-, MHD, etc.)

  • SETUP.bound: set the boundary conditions used in the setup (taken from boundaries.txt).

  • SETUP.mandatories: A list of parameters that must be always explicit in your .par files.

  • SETUP.units: The scale rules for the parameters not explicit in std/standard_units.

  • SETUP.objects: Additional objects you want to include. (Your own developments).

Warning

Any file here has priority over the file with the same name in the src/ directory. So, in theory, inside a SETUP directory, you could have a complete copy of the src/ directory, and the make process will be done with this sources, but in practice, only a few files are needed, for example, depending on your needs: resistivity.c, potential.c, etc.