2013-05-31 03:26:34 +08:00
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This library is the portable "colvars" module, originally interfaced
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with the NAMD MD code, to provide an extensible software framework,
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that allows enhanced sampling in molecular dynamics simulations.
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The module is written to maximize performance, portability,
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flexibility of usage for the user, and extensibility for the developer.
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2012-05-24 00:20:04 +08:00
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2013-06-28 06:48:27 +08:00
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The development of the colvars library is now hosted on github at:
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http://colvars.github.io/
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You can use this site to get access to the latest development sources
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and the up-to-date documentation.
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Copy of the specific documentation is also in
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doc/PDF/colvars-refman-lammps.pdf
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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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The following publications describe the principles of
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2012-05-24 00:20:04 +08:00
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the implementation of this library:
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2013-06-28 06:48:27 +08:00
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Using collective variables to drive molecular dynamics simulations,
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Giacomo Fiorin , Michael L. Klein & Jérôme Hénin (2013):
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Molecular Physics DOI:10.1080/00268976.2013.813594
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2012-05-24 00:20:04 +08:00
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Exploring Multidimensional Free Energy Landscapes Using
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Time-Dependent Biases on Collective Variables,
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J. Hénin, G. Fiorin, C. Chipot, and M. L. Klein,
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J. Chem. Theory Comput., 6, 35-47 (2010).
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2013-05-31 03:26:34 +08:00
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-------------------------------------------------
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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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2012-05-24 00:20:04 +08:00
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This library must be built with a C++ compiler, before LAMMPS is
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built, so LAMMPS can link against it.
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2013-05-31 03:26:34 +08:00
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Build the library using one of the provided Makefile.* files or create
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your own, specific to your compiler and system. For example:
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2012-05-24 00:20:04 +08:00
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make -f Makefile.g++
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2013-05-31 03:26:34 +08:00
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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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Makefile.lammps is created by the make command, by copying one of the
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Makefile.lammps.* files. See the EXTRAMAKE setting at the top of the
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Makefile.* files.
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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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Makefile.lammps has settings for 3 variables:
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user-colvars_SYSINC = leave blank for this package unless debugging
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user-colvars_SYSLIB = leave blank for this package
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user-colvars_SYSPATH = leave blank for this package
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You have several choices for these settings:
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Since they do not normally need to be set, the settings in
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Makefile.lammps.empty should work.
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2012-05-24 00:20:04 +08:00
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2013-05-31 03:26:34 +08:00
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If you want to set a debug flag recognized by the library, the
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settings in Makefile.lammps.debug should work.
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