lammps/lib/colvars

## 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

IMPORTANT: You must examine the final Makefile.lammps to insure it is
correct for your system, else the LAMMPS build will likely fail.

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