The root directory of the GROMACS repository only contains
(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
All other content is in the following top-level directories:
Contains various scripts for developer use, as well as configuration files and scripts for some of the tools used.
Contains code for the installable C++ API.
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.
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.
Contains the templates for
GMXRCscript, some other installed scripts, as well as installation rules for all these scripts.
Contains data files that will be installed under
share/. These include a template for writing C++ analysis tools, and data files used by GROMACS.
Contains all source code. See Source code organization.
Contains build system logic for some high-level tests. Currently, only the regression test build system logic, while other tests are under
Source code organization#
The sample code for the Trajectory Analysis Framework is in
Code for the gmxapi Python package and the sample MD extension module is in
api/ holds code for the installable C++ API,
including the legacy
and full sources for
libgmxapi and NBLIB API.
The rest of the source code is under the
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
The gray parts are for testing, and are by default only built as part of the
tests target, but if
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:
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.
The GROMACS executable
gmxis built from code under this directory. Also found here is some of the driver code for the
mdrunmodule called by
gmx, and numerous end-to-end tests of
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.
Contains shared utility code for writing Google Test tests. See Unit testing for details.
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.
This folder contains the build system code for downloading and building FFTW to be included into
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.
libgromacs library is built from code under
Again, the top-level directory contains build and installation rules for the
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
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.
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
CMake target (in the build tree), and are available through the IMPORTED
Gromacs::libgromacs target for an installation configured with
They are installed into a corresponding hierarchy under
include/gromacs/ in the installation directory.
All headers should compile by themselves,
with installed headers doing so without reference to variables
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,
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
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
Module private headers (located with the source files) may be leaked
into the include path, such as through the
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.
All documentation (including this developer guide) is produced from source
docs/, except for some command-line help that is generated
from the source code (by executing the compiled
The build system provides various custom targets that build the documentation;
see Build system overview for details.
Contains reStructuredText fragments used through
.. include::mechanism from various places in the documentation.
Contains reStructuredText source files for building the install guide section of the user documentation, as well as the
INSTALLfile for the source package. The build rules are in
Contains reStructuredText source files to generate the reference manual for html and LaTeX.
Contains LaTeX helper files to build the reference (PDF) manual.
Contains reStructuredText source files used to build the user guide section of the user documentation. The build rules are in
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
after compiling it, and then using Sphinx on the reStructuredText files that
gmx writes out.
The build rules for the man pages are in
Contains reStructuredText source files used to build the developer guide. The build rules are in
The organization of the developer guide is explained on the front page of the guide.
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.