jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
13,895 Commits 9 Branches 198 Tags 1.1 GiB
Commit Graph

83 Commits

Author SHA1 Message Date
Giacomo Fiorin f479f02589 Fix a Colvars error that was hidden by the previous segfault 2017-10-20 13:41:31 -04:00
Giacomo Fiorin 6e7504f153 Import segfault fix in Colvars module 2017-10-19 08:09:44 -04:00
Giacomo Fiorin 3e89b270fd Update Colvars to version 2017-10-11 
Notable features are the umbrella-integration based free energy estimator for
eABF, and the traditional thermodynamic integration estimator now available
for umbrella sampling, SMD, metadynamics.  Also included are several small fixes.

Below is a list of relevant commits in the Colvars repository since the last update.

321d06a 2017-10-10 Add macros to manage colvarscript commands [Giacomo Fiorin]
26c3bec 2017-10-09 Document coming availability of Lepton in LAMMPS [Giacomo Fiorin]
cc8f249 2017-10-04 Clarify that SMP depends on code build [Giacomo Fiorin]
0b2ffac 2017-10-04 Summarize colvar definition options, clarify some details [Giacomo Fiorin]
28002e0 2017-10-01 Separate writing of restart file from other output (e.g. PMFs) [Giacomo Fiorin]
92f7c1d 2017-10-01 Deprecate colvarsTrajAppend [Giacomo Fiorin]
12a707f 2017-09-26 Accurate Jacobian calculation for RMSD variants [Jérôme Hénin]
fe389c9 2017-09-21 Allow subtractAppliedForce with extended-L again [Jérôme Hénin]
c050ce0 2017-09-18 Silence compiler warnings, remove Tabs [Giacomo Fiorin]
cb41905 2017-01-11 Add base class for TI estimator in other biases than ABF [Giacomo Fiorin]
a1bc676 2017-09-14 Avoid writing to unopened traj file [Jérôme Hénin]
b58d8cd 2017-09-08 Function to check for overlapping groups [Jérôme Hénin]
1e5efec 2017-09-07 Check for overlapping groups in coordNum [Jérôme Hénin]
03a61a4 2017-04-06 Add UI-based estimator [fhh2626]
ae43754 2017-08-17 Fix outputCenters parsing [Josh Vermaas]
1619e0e 2017-08-14 Delete static feature arrays in cvm destructor [Jérôme Hénin]
 2017-10-13 13:45:10 -04:00
Giacomo Fiorin d90aad887e Add Lepton library within lib/colvars 2017-10-09 15:25:43 -04:00
Giacomo Fiorin f1fce64ff9 Fix small typo to calculation of accumulated work in Colvars 2017-09-14 12:58:00 -04:00
Steve Plimpton c46d5ff422 Merge pull request #612 from giacomofiorin/colvars-update-2017-08-10 
Minor fixes to Colvars module
 2017-08-17 11:32:38 -06:00
Axel Kohlmeyer 6d24be8bb7 whitespace cleanup 2017-08-10 21:14:40 -04:00
Giacomo Fiorin da01be7c18 More robust change from initial to target restraint centers in Colvars 2017-08-10 09:22:53 -04:00
Axel Kohlmeyer 135b1650f1 revamp of library builds 
- remove cross compiler stuff
- make use of Install.py consistent
- provide options for Makefile.serial and Makefile.mpi that match those in src
 2017-08-07 17:13:01 -04:00
Axel Kohlmeyer 0427f6205e fix typo 2017-07-27 09:25:02 -04:00
Axel Kohlmeyer 1b704bab18 Merge branch 'colvars-safer-makefiles' of https://github.com/giacomofiorin/lammps into colvars-quickfix 2017-07-20 15:59:23 -04:00
Giacomo Fiorin c98f6140e7 Change order of targets in Makefiles for Colvars 2017-07-20 15:49:31 -04:00
Giacomo Fiorin 5031f5b807 Comment out use by Colvars of Makefile.lammps from other packages 2017-07-20 15:48:10 -04:00
Axel Kohlmeyer 9d0d90c038 README clarification from giacomo 2017-07-20 15:25:27 -04:00
Axel Kohlmeyer 66154e8a8b avoid makefile failure, if LAMMPS has not been configured yet 2017-07-20 15:05:58 -04:00
Giacomo Fiorin ef9fb944c7 Detect number of processors for make 2017-07-20 10:53:08 -04:00
Giacomo Fiorin 187a80be77 Add forgotten decode() in Install.py 2017-07-19 22:21:49 -04:00
Giacomo Fiorin ee6cac826e Update Colvars to version 2017-07-15 and support automated builds for it 2017-07-19 14:24:07 -04:00
Steve Plimpton addd87c0f7 new Section package and start doc pages and build scripts 2017-05-04 11:22:20 -06:00
Giacomo Fiorin 5fe6206638 Update Colvars module to version 2017-03-10 2017-03-10 09:16:58 -05:00
Giacomo Fiorin b0263e87bb Fix missing force with extended-Lagrangian mass 2016-12-27 17:16:32 -05:00
Giacomo Fiorin f553e230db Update Colvars library to version 2016-12-22 
Significant code cleanup and several fixes (walls + extended Lagrangian)

New harmonicWalls bias to apply confining boundaries with time-dependent force
constant & integration
 2016-12-27 13:17:34 -05:00
Giacomo Fiorin 6ab716164b Fix seg fault for gyration collective variable 2016-12-27 13:17:02 -05:00
Giacomo Fiorin 7a45c72b97 Allow extended Lagrangian on non-scalar collective variables 2016-12-27 12:35:30 -05:00
Giacomo Fiorin 182141b850 Make SMP parallelism for Colvars optional 2016-10-24 17:13:34 -04:00
Giacomo Fiorin e02505c8cc Add ensemble-biased metadynamics (Fabrizio Marinelli, NIH) 2016-10-24 17:11:09 -04:00
Giacomo Fiorin be2d155cef Minor changes and fixes not relevant to LAMMPS 2016-10-24 17:10:52 -04:00
Giacomo Fiorin c243093980 Fix wall forces and subtractAppliedForce for extended-Lagrangian ABF 2016-10-24 17:05:47 -04:00
Giacomo Fiorin ad57a17f48 Add C-linkage wrapper for colvarscript (useful with ctypes) 2016-10-24 16:48:20 -04:00
Axel Kohlmeyer 683689c808 revert to previous style conventions for size_t constants 2016-10-08 11:00:23 -04:00
Axel Kohlmeyer e01e90eb96 workaround for double free issue when using USER-COLVARS with lammps code loaded as shared library into a standalone executable 2016-10-08 10:45:22 -04:00
Giacomo Fiorin 8809a603fb Colvars update: issue a warning that cannot be ignored regarding total forces 2016-10-05 18:26:21 -04:00
Giacomo Fiorin 969d3cf4b0 Colvars update: make ABF check that the colvar isn't using already subtractAppliedForce 2016-10-05 18:25:40 -04:00
Axel Kohlmeyer 6d200061ca update colvars library to version 2016-09-30 2016-09-30 08:15:44 -04:00
sjplimp 484122b8b6 sync with GH 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15592 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-09-16 19:21:34 +00:00
sjplimp b190abea39 sync with GH 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15561 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-09-08 20:20:32 +00:00
sjplimp efaa84a4ea git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15430 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-03 19:32:03 +00:00
sjplimp ee24be38cb git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15371 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-07-27 14:09:42 +00:00
sjplimp 05398a6863 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15315 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-07-15 22:25:17 +00:00
sjplimp 2fcd26f6c4 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15200 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-06-17 23:07:51 +00:00
sjplimp e653da12a6 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15095 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-06-02 14:03:00 +00:00
sjplimp dfb0f528c0 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15038 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-05-12 13:52:42 +00:00
sjplimp 00f38fdaf0 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14910 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-04-30 18:06:25 +00:00
sjplimp 17fd5898df git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14900 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-04-28 14:48:56 +00:00
sjplimp f50b03fcab git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14830 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-04-15 16:07:28 +00:00
sjplimp 212a955285 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14829 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-04-15 16:07:01 +00:00
sjplimp c46d973c2b git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14823 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-04-13 22:25:46 +00:00
sjplimp 20beaccf0f git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14703 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-03-01 20:40:25 +00:00
sjplimp 08b53bb709 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14657 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-02-18 22:31:59 +00:00
sjplimp 449f373db5 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14165 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-10-22 22:08:30 +00:00