Collective variables module (Colvars)

A software module for molecular simulation and analysis that provides a high-performance implementation of sampling algorithms defined on a reduced space of continuously differentiable functions (aka collective variables).

The module itself implements a variety of functions and algorithms, including free-energy estimators based on thermodynamic forces, non-equilibrium work and probability distributions.

For a brief description see:

http://colvars.github.io/
https://github.com/colvars/colvars/

How to build

This directory has source files to build a library that LAMMPS links against when using the USER-COLVARS package.

This library must be built with a C++ compiler, *before* LAMMPS is built and *after* packages are configured, so that LAMMPS can link against it. You can use the provided Makefile.* files or create your own, specific to your compiler and system. For example:

cd src
make yes-user-colvars
cd ../lib/colvars
make -f Makefile.g++

where Makefile.g++ uses the GNU C++ compiler and is a good template to start.

Optional: if you use the Install.py script provided in this folder, you can give the machine name as the '-m' argument. This can be the suffix of one of the files from either this folder, or from src/MAKE/MACHINES. *This is only supported by the Install.py within the lib/colvars folder*.

When you are done building this library, two files should exist in this directory:

libcolvars.a the library LAMMPS will link against Makefile.lammps settings the LAMMPS Makefile will import

If you want to set a debug flag recognized by the library, the settings in Makefile.common should work.

Note: some Colvars functions use the Lepton mathematical expression parser, which is here included (no additional steps required). For more details, see:

https://simtk.org/projects/lepton

Documentation

For the reference manual see:

http://colvars.github.io/colvars-refman-lammps

A copy of the reference manual is also in:

doc/PDF/colvars-refman-lammps.pdf

Also available is a Doxygen-based developer documentation:

http://colvars.github.io/doxygen/html/

The reference article is:

G. Fiorin, M. L. Klein, and J. Henin,
Molecular Physics 111, 3345 (2013).
http://dx.doi.org/10.1080/00268976.2013.813594

Updating to the latest version

To recompile LAMMPS with the most recent version of this module, the master branch of this repository from GitHub, or clone it via git:

git clone https://github.com/colvars/colvars.git

and run the provided update-colvars-code.sh script against the unpacked LAMMPS source tree:

./update-colvars-code.sh /path/to/lammps/folder

Please report bugs and request new features at: https://github.com/colvars/colvars/issues