## 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.


## Documentation

For a brief description see:
  https://colvars.github.io/
  https://github.com/Colvars/colvars/

For the reference manual see:
  http://colvars.github.io/colvars-refman-lammps

A PDF copy is also at:
  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. Hénin,
  Molecular Physics 111, 3345 (2013).
  https://doi.org/10.1080/00268976.2013.813594


## Requirements

The Colvars library can be built for the most part with all major versions of
the C++ language.

A few of the most recent features require C++11 support, which is also required
by LAMMPS, so no additional notes are needed.

## How to build (CMake)

This is the recommended build recipe: no additional settings are normally
needed besides "-D PKG_COLVARS=yes".

Linking to the Lepton library, which is also used by the LEPTON LAMMPS package,
is enabled automatically.  Optionally, support for Lepton within Colvars may
be manually controlled with theCMake setting "-D COLVARS_LEPTON=yes|no".

## How to build (traditional make)

Before building LAMMPS, one must build the Colvars library in lib/colvars
and the Lepton library in lib/lepton.  For building Lepton please see the
README.md file in the lib/lepton folder.

Building the Colvars library can be done manually in the respective
folders by using or adapting one of the provided Makefiles: for example,
Makefile.g++ for the GNU compiler.

In general, it is safer to use build setting consistent with the rest of
LAMMPS.  This is best carried out from the LAMMPS src directory using a
command like these, which simply invoke the lib/colvars/Install.py script
with the specified args:

make lib-colvars                      # print help message
make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled :pre

The "machine" argument of the "-m" flag is used to find a Makefile.machine to
use as build recipe.  If it does not already exist in lib/colvars, it will be
auto-generated by using compiler flags consistent with those parsed from the
core LAMMPS makefiles.

Optional flags may be specified as environment variables:

COLVARS_DEBUG=yes make lib-colvars args="-m machine"  # Build with debug code (much slower)
COLVARS_LEPTON=no make lib-colvars args="-m machine"  # Build without Lepton (included otherwise)

The build should produce two files: the library lib/colvars/libcolvars.a
(which also includes Lepton objects if enabled) and the specification file
lib/colvars/Makefile.lammps.  The latter is auto-generated, and normally does
not need to be edited.