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).

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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.

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

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.
