forked from lijiext/lammps
87 lines
2.8 KiB
Plaintext
87 lines
2.8 KiB
Plaintext
## Collective variables module (Colvars)
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A software module for molecular simulation and analysis that provides a
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high-performance implementation of sampling algorithms defined on a reduced
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space of continuously differentiable functions (aka collective variables).
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The module itself implements a variety of functions and algorithms, including
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free-energy estimators based on thermodynamic forces, non-equilibrium work and
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probability distributions.
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For a brief description see:
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http://colvars.github.io/
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https://github.com/colvars/colvars/
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## How to build
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This directory has source files to build a library that LAMMPS
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links against when using the USER-COLVARS package.
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This library must be built with a C++ compiler, *before* LAMMPS is built and
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*after* packages are configured, so that LAMMPS can link against it.
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You can use the provided Makefile.* files or create your own, specific to your
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compiler and system. For example:
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cd src
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make yes-user-colvars
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cd ../lib/colvars
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make -f Makefile.g++
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where Makefile.g++ uses the GNU C++ compiler and is a good template to start.
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**Optional**: if you use the Install.py script provided in this folder, you
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can give the machine name as the '-m' argument. This can be the suffix of one
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of the files from either this folder, or from src/MAKE/MACHINES.
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*This is only supported by the Install.py within the lib/colvars folder*.
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When you are done building this library, two files should
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exist in this directory:
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libcolvars.a the library LAMMPS will link against
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Makefile.lammps settings the LAMMPS Makefile will import
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IMPORTANT: You must examine the final Makefile.lammps to insure it is
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correct for your system, else the LAMMPS build will likely fail.
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If you want to set a debug flag recognized by the library, the
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settings in Makefile.common should work.
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Note: some Colvars functions use the Lepton mathematical expression parser,
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which is here included (no additional steps required). For more details, see:
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https://simtk.org/projects/lepton
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## Documentation
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For the reference manual see:
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http://colvars.github.io/colvars-refman-lammps
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A copy of the reference manual is also in:
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doc/PDF/colvars-refman-lammps.pdf
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Also available is a Doxygen-based developer documentation:
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http://colvars.github.io/doxygen/html/
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The reference article is:
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G. Fiorin, M. L. Klein, and J. Henin,
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Molecular Physics 111, 3345 (2013).
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http://dx.doi.org/10.1080/00268976.2013.813594
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## Updating to the latest version
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To recompile LAMMPS with the most recent version of this module, the `master`
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branch of this repository from GitHub, or clone it via git:
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git clone https://github.com/colvars/colvars.git
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and run the provided `update-colvars-code.sh` script against the unpacked
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LAMMPS source tree:
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./update-colvars-code.sh /path/to/lammps/folder
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Please report bugs and request new features at:
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https://github.com/colvars/colvars/issues
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