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435 Commits

Author SHA1 Message Date
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
Axel Kohlmeyer 3d2e5d0a50 suppress compiler warning 
(cherry picked from commit 6f227e194e)
 2016-09-06 21:27:45 -04:00
Axel Kohlmeyer ec2a6b9f0d update colvars to version 2016-08-10 
(cherry picked from commit f2ddf828e4)
 2016-09-06 21:27:41 -04:00
Axel Kohlmeyer 77620106a4 update colvars library to version 2016-08-05 
(cherry picked from commit 459db2eb6b)

# Conflicts:
#	doc/src/PDF/colvars-refman-lammps.pdf
 2016-09-06 21:26:50 -04:00
stamoor 39be4185c4 Updating Kokkos lib 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15556 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-09-06 23:06:32 +00:00
stamoor 1ad033ec0c Updating Kokkos lib 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15555 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-09-06 23:02:50 +00:00
sjplimp 083ff54c0c small bug fixes 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15527 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-08-31 20:26:15 +00:00
Steve Plimpton 4051aedf2c Merge branch 'small' into integration 
Conflicts:
	src/compute_omega_chunk.cpp
 2016-08-31 13:58:12 -06:00
Steve Plimpton ec8b9e21db sync with SVN 2016-08-31 13:28:26 -06:00
stamoor dbaaf4dbbd Removing aggressive_vectorization flag due to safety issue 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15521 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-08-30 17:52:49 +00:00
Axel Kohlmeyer 493613b495 avoid NaNs in MEAM 2016-08-30 06:54:36 -04:00
Steve Plimpton 2beecd1e73 removal of doc/html/_sources and minor sync with SVN 2016-08-26 11:34:37 -06:00
stamoor cc4b2dd6ed Changing default 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15503 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-08-26 15:50:25 +00:00
Steve Plimpton abc5a32c8a gpu lib sync 2016-08-23 15:30:01 -06:00
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 b8bf3ae5b0 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15391 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-07-29 14:24:21 +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 e6dc896b49 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15327 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-07-15 23:02:09 +00:00