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| .. | | 04-Mar-2020 | - |
| Makefile.fermi | H A D | 04-Mar-2020 | 3.6 KiB | 102 | 71 |
| Makefile.g++ | H A D | 04-Mar-2020 | 3.6 KiB | 103 | 71 |
| Makefile.lammps.debug | H A D | 04-Mar-2020 | 150 | 6 | 4 |
| Makefile.lammps.empty | H A D | 04-Mar-2020 | 150 | 6 | 4 |
| Makefile.mingw32-cross | H A D | 04-Mar-2020 | 4 KiB | 112 | 79 |
| Makefile.mingw32-cross-mpi | H A D | 04-Mar-2020 | 232 | 14 | 8 |
| Makefile.mingw64-cross | H A D | 04-Mar-2020 | 4 KiB | 110 | 78 |
| Makefile.mingw64-cross-mpi | H A D | 04-Mar-2020 | 232 | 14 | 8 |
| README | H A D | 04-Mar-2020 | 2.5 KiB | 69 | 48 |
| colvar.cpp | H A D | 04-Mar-2020 | 51.2 KiB | 1,692 | 1,249 |
| colvar.h | H A D | 04-Mar-2020 | 17.7 KiB | 582 | 221 |
| colvaratoms.cpp | H A D | 04-Mar-2020 | 25 KiB | 857 | 655 |
| colvaratoms.h | H A D | 04-Mar-2020 | 11.6 KiB | 333 | 88 |
| colvarbias.cpp | H A D | 04-Mar-2020 | 18.3 KiB | 591 | 457 |
| colvarbias.h | H A D | 04-Mar-2020 | 5.3 KiB | 194 | 61 |
| colvarbias_abf.cpp | H A D | 04-Mar-2020 | 16 KiB | 519 | 378 |
| colvarbias_abf.h | H A D | 04-Mar-2020 | 2.4 KiB | 100 | 52 |
| colvarbias_meta.cpp | H A D | 04-Mar-2020 | 59.2 KiB | 1,718 | 1,312 |
| colvarbias_meta.h | H A D | 04-Mar-2020 | 12.4 KiB | 426 | 200 |
| colvarcomp.cpp | H A D | 04-Mar-2020 | 4.6 KiB | 148 | 108 |
| colvarcomp.h | H A D | 04-Mar-2020 | 49.9 KiB | 1,446 | 862 |
| colvarcomp_angles.cpp | H A D | 04-Mar-2020 | 10.4 KiB | 378 | 284 |
| colvarcomp_coordnums.cpp | H A D | 04-Mar-2020 | 10.1 KiB | 360 | 251 |
| colvarcomp_distances.cpp | H A D | 04-Mar-2020 | 32.6 KiB | 1,151 | 883 |
| colvarcomp_protein.cpp | H A D | 04-Mar-2020 | 10.5 KiB | 386 | 271 |
| colvarcomp_rotations.cpp | H A D | 04-Mar-2020 | 7 KiB | 312 | 216 |
| colvargrid.cpp | H A D | 04-Mar-2020 | 5.7 KiB | 218 | 156 |
| colvargrid.h | H A D | 04-Mar-2020 | 35.2 KiB | 1,189 | 812 |
| colvarmodule.cpp | H A D | 04-Mar-2020 | 43.4 KiB | 1,503 | 1,163 |
| colvarmodule.h | H A D | 04-Mar-2020 | 16 KiB | 532 | 269 |
| colvarparse.cpp | H A D | 04-Mar-2020 | 26.2 KiB | 644 | 482 |
| colvarparse.h | H A D | 04-Mar-2020 | 7.8 KiB | 202 | 83 |
| colvarproxy.h | H A D | 04-Mar-2020 | 5 KiB | 154 | 54 |
| colvartypes.h | H A D | 04-Mar-2020 | 30.4 KiB | 1,099 | 711 |
| colvarvalue.cpp | H A D | 04-Mar-2020 | 7.3 KiB | 262 | 222 |
| colvarvalue.h | H A D | 04-Mar-2020 | 22.1 KiB | 728 | 487 |
README
1This library is the portable "colvars" module, originally interfaced
2with the NAMD MD code, to provide an extensible software framework,
3that allows enhanced sampling in molecular dynamics simulations.
4The module is written to maximize performance, portability,
5flexibility of usage for the user, and extensibility for the developer.
6
7The development of the colvars library is now hosted on github at:
8http://colvars.github.io/
9You can use this site to get access to the latest development sources
10and the up-to-date documentation.
11
12Copy of the specific documentation is also in
13 doc/PDF/colvars-refman-lammps.pdf
14
15Please report bugs and request new features at:
16https://github.com/colvars/colvars/issues
17
18The following publications describe the principles of
19the implementation of this library:
20
21 Using collective variables to drive molecular dynamics simulations,
22 Giacomo Fiorin , Michael L. Klein & Jérôme Hénin (2013):
23 Molecular Physics DOI:10.1080/00268976.2013.813594
24
25 Exploring Multidimensional Free Energy Landscapes Using
26 Time-Dependent Biases on Collective Variables,
27 J. Hénin, G. Fiorin, C. Chipot, and M. L. Klein,
28 J. Chem. Theory Comput., 6, 35-47 (2010).
29
30-------------------------------------------------
31
32This directory has source files to build a library that LAMMPS
33links against when using the USER-COLVARS package.
34
35This library must be built with a C++ compiler, before LAMMPS is
36built, so LAMMPS can link against it.
37
38Build the library using one of the provided Makefile.* files or create
39your own, specific to your compiler and system. For example:
40
41make -f Makefile.g++
42
43When you are done building this library, two files should
44exist in this directory:
45
46libcolvars.a the library LAMMPS will link against
47Makefile.lammps settings the LAMMPS Makefile will import
48
49Makefile.lammps is created by the make command, by copying one of the
50Makefile.lammps.* files. See the EXTRAMAKE setting at the top of the
51Makefile.* files.
52
53IMPORTANT: You must examine the final Makefile.lammps to insure it is
54correct for your system, else the LAMMPS build will likely fail.
55
56Makefile.lammps has settings for 3 variables:
57
58user-colvars_SYSINC = leave blank for this package unless debugging
59user-colvars_SYSLIB = leave blank for this package
60user-colvars_SYSPATH = leave blank for this package
61
62You have several choices for these settings:
63
64Since they do not normally need to be set, the settings in
65Makefile.lammps.empty should work.
66
67If you want to set a debug flag recognized by the library, the
68settings in Makefile.lammps.debug should work.
69