Codebase overview

The root directory of the GROMACS repository only contains CMakeLists.txt (the root file for the CMake build system), a few files supporting the build system, and a few standard informative files (README etc.). The INSTALL is generated for source packages from docs/install-guide/index.rst.

All other content is in the following top-level directories:

admin/

Contains various scripts for developer use, as well as configuration files and scripts for some of the tools used.

api/

Contains code for the installable C++ API.

cmake/

Contains code fragments and find modules for CMake. Some content here is copied and/or adapted from newer versions of CMake than the minimum currently supported. Default suppression file for valgrind is also included here. See Build system overview for details of the build system.

docs/

Contains the build system logic and source code for all documentation, both user-facing and developer-facing. Some of the documentation is generated from the source code under src/; see Documentation organization. This directory also contains some developer scripts that use the Doxygen documentation for their operation.

scripts/

Contains the templates for GMXRC script, some other installed scripts, as well as installation rules for all these scripts.

share/

Contains data files that will be installed under share/. These include a template for writing C++ analysis tools, and data files used by GROMACS.

src/

Contains all source code. See Source code organization.

tests/

Contains build system logic for some high-level tests. Currently, only the regression test build system logic, while other tests are under src/.

Source code organization

The sample code for the Trajectory Analysis Framework is in share/template/.

Code for the gmxapi Python package and the sample MD extension module is in python_packaging/.

api/ holds code for the installable C++ API, including the legacy gromacs headers and full sources for libgmxapi and NBLIB API.

The rest of the source code is under the src/ directory.

The following figure shows a high-level view of components of what gets built from the source code under src/ and how the code is organized. Arrows indicate the direction of dependencies. The build system is described in detail in Build system overview. With default options, the green and white components are built as part of the default target. The gray parts are for testing, and are by default only built as part of the tests target, but if GMX_DEVELOPER_BUILD is ON, then these are included in the default build target. See Unit testing for details of the testing side.

Only a few files related to the build system are included at the root level. All actual code is in subdirectories:

src/gromacs/

The code under this directory is built into a single library, libgromacs. Installed headers are also located in this hierarchy. This is the main part of the code, and is organized into further subdirectories as modules. See below for details.

src/programs/

The GROMACS executable gmx is built from code under this directory. Also found here is some of the driver code for the mdrun module called by gmx, and numerous end-to-end tests of gmx mdrun.

src/.../tests/

Various subdirectories under src/ contain a subdirectory named tests/. The code from each such directory is built into a test binary. Some such directories also provide shared test code as object libraries that is linked into multiple test binaries from different folders. See Unit testing for details.

src/testutils/

Contains shared utility code for writing Google Test tests. See Unit testing for details.

src/external/

Contains bundled source code for various libraries and components that GROMACS uses internally. All the code from these directories are built using our custom build rules into libgromacs, or in some cases into the test binaries. Some CMake options change which parts of this code are included in the build. See Build system overview for some explanation about how the code in this directory is used.

src/external/build-fftw/

This folder contains the build system code for downloading and building FFTW to be included into libgromacs.

When compiling, the include search path is set to src/ by the legacy_modules CMake target for many of the interfaces that do not have clearer module ownership.

Some directories from under src/external/ may also be included, depending on the compilation options.

Organization under src/gromacs/

The libgromacs library is built from code under src/gromacs/. Again, the top-level directory contains build and installation rules for the library.

The code is organized into subdirectories. These subdirectories are denoted as modules throughout this documentation. Each module consists of a set of routines that do some well-defined task or a collection of tasks. Many modules are represented by distinct CMake targets, and target_link_libraries() should be used to get access to the headers and linkable symbols. Other modules are only expressed by the filesystem hierarchy, and their source files are compiled directly into the monolithic libgromacs CMake target.

Modules under src/gromacs/ are not part of the public installed interface. However, some of the headers that were traditionally installed have been moved api/legacy/include (not duplicated in src/) pending specification of an updated public API. These interfaces are grouped into the legacy_api CMake target (in the build tree), and are available through the IMPORTED Gromacs::libgromacs target for an installation configured with GMX_INSTALL_LEGACY_API=ON. They are installed into a corresponding hierarchy under include/gromacs/ in the installation directory.

Historically, comments at the top of the header files contain a note about their visibility: public (installed), intra-library (can be used from inside the library), or intra-module/intra-file. Many of these comments remain, but they are no longer maintained.

All headers should compile by themselves, with installed headers doing so without reference to variables defined in config.h or requiring other headers to be included before it. No installed headers are allowed to include config.h. Cyclic include dependencies prevent this, and must be avoided because of this. This is best guaranteed by including every header in some source file as the first header, even before config.h.

Code inside the library should not unnecessarily include headers. In particular, headers should not include other headers if a forward declaration of a type is enough for the header. Within the library source files, include only headers from other modules that are necessary for that file. Check the CMakeLists.txt for the module to see whether you need to target_link_libraries(). Many modules distinguish between a public interface and a private interface intended only for use inside the module implementation. In such cases, the public module headers (for use by other modules in the library) are in src/gromacs/modulename/include/gromacs/modulename subdirectories. Module private headers (located with the source files) may be leaked into the include path, such as through the legacy_modules target, but should not be used by other modules!

See Naming conventions for some common naming patterns for files that can help locating declarations.

Tests, and data required for them, are in a tests/ subdirectory under the module directory. See Unit testing for more details.

Documentation organization

All documentation (including this developer guide) is produced from source files under docs/, except for some command-line help that is generated from the source code (by executing the compiled gmx binary). The build system provides various custom targets that build the documentation; see Build system overview for details.

docs/fragments/

Contains reStructuredText fragments used through .. include:: mechanism from various places in the documentation.

User documentation

docs/install-guide/

Contains reStructuredText source files for building the install guide section of the user documentation, as well as the INSTALL file for the source package. The build rules are in docs/CMakeLists.txt.

docs/reference-manual/

Contains reStructuredText source files to generate the reference manual for html and LaTeX.

docs/manual/

Contains LaTeX helper files to build the reference (PDF) manual.

docs/user-guide/

Contains reStructuredText source files used to build the user guide section of the user documentation. The build rules are in docs/CMakeLists.txt.

docs/how-to/

Contains reStructuredText source files building the how-to section of the user focused documentation.

Unix man pages

Man pages for programs are generated by running the gmx executable after compiling it, and then using Sphinx on the reStructuredText files that gmx writes out.

The build rules for the man pages are in docs/CMakeLists.txt.

Developer guide

docs/dev-manual/

Contains reStructuredText source files used to build the developer guide. The build rules are in docs/CMakeLists.txt.

The organization of the developer guide is explained on the front page of the guide.

Doxygen documentation

docs/doxygen/

Contains the build rules and some overview content for the Doxygen documentation. See Using Doxygen for details of how the Doxygen documentation is built and organized.

The Doxygen documentation is made of a few different parts. Use the list below as a guideline on where to look for a particular kind of content. Since the documentation has been written over a long period of time and the approach has evolved, not all the documentation yet follows these guidelines, but this is where we are aiming at.

documentation pages

These contain mainly overview content, from general-level introduction down into explanation of some particular areas of individual modules. These are generally the place to start familiarizing with the code or a new area of the code. They can be reached by links from the main page, and also through cross-links from places in the documentation where that information is relevant to understand the context.

module documentation

These contain mainly technical content, explaining the general implementation of a particular module and listing the classes, functions etc. in the module. They complement pages that describe the concepts. They can be reached from the Modules tab, and also from all individual classes, functions etc. that make up the module.

class documentation

These document the usage of an individual class, and in some cases that of closely related classes. Where necessary (and time allowing), a broader overview is given on a separate page and/or in the module documentation.

method documentation

These document the individual method. Typically, the class documentation or other overview content is the place to look for how different methods interact.

file and namespace documentation

These are generally only placeholders for links, and do not contain much else. The main content is the list of classes and other entities declared in that file.