## 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