This library is the portable "colvars" module, originally interfaced with the NAMD MD code, to provide an extensible software framework, that allows enhanced sampling in molecular dynamics simulations. The module is written to maximize performance, portability, flexibility of usage for the user, and extensibility for the developer.

The development of the colvars library is now hosted on github at: http://colvars.github.io/ You can use this site to get access to the latest development sources and the up-to-date documentation.

Copy of the specific documentation is also in doc/PDF/colvars-refman-lammps.pdf

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

The following publications describe the principles of the implementation of this library:

Using collective variables to drive molecular dynamics simulations,
Giacomo Fiorin , Michael L. Klein & Jérôme Hénin (2013):
Molecular Physics DOI:10.1080/00268976.2013.813594

Exploring Multidimensional Free Energy Landscapes Using 
Time-Dependent Biases on Collective Variables, 
 J. Hénin, G. Fiorin, C. Chipot, and M. L. Klein, 
 J. Chem. Theory Comput., 6, 35-47 (2010).

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, so LAMMPS can link against it.

You can type "make lib-colvars" from the src directory to see help on how to build this library via make commands, or you can do the same thing by typing "python Install.py" from within this directory, or you can do it manually by following the instructions below.

Build the library using one of the provided Makefile.* files or create your own, specific to your compiler and system. For example:

make -f Makefile.g++

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

Makefile.lammps is created by the make command, by copying one of the Makefile.lammps.* files. See the EXTRAMAKE setting at the top of the Makefile.* files.

Makefile.lammps has settings for 3 variables:

user-colvars_SYSINC = leave blank for this package unless debugging user-colvars_SYSLIB = leave blank for this package user-colvars_SYSPATH = leave blank for this package

You have several choices for these settings:

Since they do not normally need to be set, the settings in Makefile.lammps.empty should work.

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