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452 Commits

Author SHA1 Message Date
Giacomo Fiorin 5fe6206638 Update Colvars module to version 2017-03-10 2017-03-10 09:16:58 -05:00
Richard Berger e261bef7bb Spelling fixes in source files 2017-03-05 18:30:39 -05:00
Stan Moore 90e5ae965d Add missing flags to Kokkos Makefile 2017-02-13 11:19:46 -07:00
Stan Moore 33af7ab248 Remove merge line 2017-02-13 10:59:22 -07:00
Stan Moore 8f9b2aca06 Removing unused files in Kokkos lib 2017-02-13 10:53:51 -07:00
Stan Moore 383da816c2 Updating Kokkos lib 2017-02-13 10:50:34 -07:00
sjplimp d8bc590aaf Merge pull request #327 from stanmoore1/kokkos_lib_update 
Updating Kokkos lib
 2017-01-17 09:04:12 -07:00
Stan Moore 7162cafdf5 Squelching output from Makefile 2017-01-10 14:46:30 -07:00
Stan Moore ee9e7cfbd5 Fixing Kokkos CUDA Makefile issue 2017-01-10 13:22:36 -07:00
Stan Moore 7839c335da Fixing compile error with Kokkos CUDA Makefiles 2017-01-10 13:05:00 -07:00
Steve Plimpton c31f1e9f22 add fix mscg command, example, lib 2017-01-09 13:36:40 -07:00
Stan Moore 9250a55923 Adding enable_lambda to KOKKOS_CUDA_OPTIONS 2017-01-09 12:24:30 -07:00
Stan Moore a9f0b7d523 Updating Kokkos lib 2017-01-09 10:39:46 -07:00
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 019bc0ba0b fix typos in Makefile.lammps for NetCDF support 2016-10-19 07:39:03 -04:00
Axel Kohlmeyer 27796b431e avoid distracting error output 2016-10-18 15:32:20 -04:00
Axel Kohlmeyer 2b47fa6653 update Makefile.lammps and add README according to suggestions by lars pastewka 2016-10-18 15:05:30 -04:00
Axel Kohlmeyer 4502d3276b updated Makefile.lammps for NetCDF support based on suggestions from lars pastewka 2016-10-18 14:45:06 -04:00
Axel Kohlmeyer ecb03dd2df import lammps-netcdf code as USER-NC-DUMP package 2016-10-11 23:03:18 -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
sjplimp 54fc194e5b Merge pull request #199 from akohlmey/small-changes 
Collected small changes and bugfixes
 2016-10-06 15:49:24 -06:00
A Bartok-Partay 8ea063378e add NETCDF libs (as defined in QUIP) to the linking line if QUIP was built with NETCDF support 2016-10-06 12:16:25 +01:00
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 03766dbda7 apply bugfix for MEAM provided by Wolfgang Verestek on lammps-users 
this closes lammps/#188
 2016-10-03 16:28:59 -04:00
Axel Kohlmeyer a3e05a2bac permission cleanup 2016-10-01 06:34:45 -04:00
Axel Kohlmeyer 6d200061ca update colvars library to version 2016-09-30 2016-09-30 08:15:44 -04:00
Axel Kohlmeyer 5b2becd09b Merge branch 'integration' into new-master 2016-09-29 10:37:09 -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
Axel Kohlmeyer 9637a5b530 colvars bugfix. updates colvars library to version 2016-09-14 2016-09-15 19:44:26 -04:00
Axel Kohlmeyer 14bed44743 ignore Makefile.lammps in lib tree 2016-09-13 09:36:48 -04:00
Axel Kohlmeyer 18cacb8e1d ignore *.mod generated by fortran compilers 2016-09-13 09:36:19 -04:00
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 07e55ef61e Merge pull request #22 from akohlmey/colvars-update 
accumulated colvars library update and lib "make clean" improvement
 2016-09-08 14:14:49 -06:00
Steve Plimpton 236ebf7fab Kokkos lib update 2016-09-08 13:56:18 -06:00
Axel Kohlmeyer 3a74ccffa2 update colvars library to version 2016-09-03 
(cherry picked from commit 4181f5ac9d)
 2016-09-06 21:28:59 -04:00
Axel Kohlmeyer c8cfd53c1b adjust makefiles in lib tree, so they don't return an error exit code on "make clean" targets. 
(cherry picked from commit 4117218ca3)
 2016-09-06 21:28:55 -04:00
Axel Kohlmeyer 16607a0132 update colvars library to version 2016-08-19 
(cherry picked from commit c67326be6d)
 2016-09-06 21:27:46 -04:00
Axel Kohlmeyer 3b476d914f update colvars to version 2016-08-10 
(cherry picked from commit eba3ad9abb)
 2016-09-06 21:27:46 -04:00
Axel Kohlmeyer 977b9e542f update colvars to another set of changes from the upstream repo 
(cherry picked from commit cb816f8cba)
 2016-09-06 21:27:45 -04:00
Axel Kohlmeyer 1b33d00785 update colvars makefile dependencies 
(cherry picked from commit df99a85930)
 2016-09-06 21:27:45 -04:00