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863 Commits

Author SHA1 Message Date
Axel Kohlmeyer 16bf916dd0
Merge pull request #1616 from akohlmey/fixes-for-stable 
Collected small fixes for stable release
 2019-08-05 16:48:50 -04:00
Giacomo Fiorin 97501f0946 Fix typo 2019-08-05 14:59:40 -04:00
Giacomo Fiorin 51ba9bd520 Bugfix for Colvars library (update to version 2019-08-05) 
Bugfix for group2CenterOnly (coordNum option):
https://github.com/Colvars/colvars/pull/278
 2019-08-05 14:14:33 -04:00
Axel Kohlmeyer 0774e92ece
use KIM-API 2.1.2 consistently with CMake and conventional build system 2019-08-03 06:40:31 -04:00
Axel Kohlmeyer 11198e9d29
Merge pull request #1607 from giacomofiorin/colvars-update 
Update Colvars to version 2019-08-01
 2019-08-02 10:43:13 -04:00
Giacomo Fiorin 52e2db44a1 Update Colvars to version 2019-08-01 
One new feature (geometric path variables) and bugfixes.

Minimize occurrence of file-read errors in multiple-walker metadynamics
https://github.com/Colvars/colvars/pull/276

Better error messages for RMSD
https://github.com/Colvars/colvars/pull/272

Ensemble-biased metadynamics documentation
https://github.com/Colvars/colvars/pull/261

Fix bug on multiple walkers metadynamics, pmf included twice
https://github.com/Colvars/colvars/pull/259

Implementation of the geometric path collective variables (C++11-only feature)
https://github.com/Colvars/colvars/pull/249
 2019-08-01 15:15:58 -04:00
Axel Kohlmeyer 2b288bc9e0
add missing mode keyword for substitution 2019-07-30 16:53:27 -04:00
Axel Kohlmeyer 882b2301bb
handle shared library extension on macosx for plumed runtime build 2019-07-30 16:48:50 -04:00
Axel Kohlmeyer 2d93a713e2
Merge branch 'master' into collected-small-changes 2019-07-30 14:14:11 -04:00
Axel Kohlmeyer 3fdadb5875
add configuration for linking VTK 7.1 on Ubuntu 18.04 2019-07-30 06:02:47 -04:00
Axel Kohlmeyer 7ab7691c51
update PLUMED support to version 2.5.2 2019-07-30 05:57:57 -04:00
Axel Kohlmeyer 6833d6def6
Merge branch 'master' into kim-simulator-models 
# Resolved Conflicts:
#	src/KIM/kim_query.cpp
#	src/KIM/pair_kim.cpp
 2019-07-29 20:43:10 -04:00
Axel Kohlmeyer 0f10c55c1c
avoid recursive header inclusion 2019-07-26 17:26:59 -04:00
Axel Kohlmeyer d59737299c
whitespace cleanup 2019-07-24 16:02:49 -04:00
Ryan S. Elliott be86db9dd9 Update /lib/kim stuff 2019-07-23 21:06:02 -05:00
Axel Kohlmeyer 320be3bcef
undo changes to poems library and package as they fail regression testing 2019-07-22 14:22:36 -04:00
Axel Kohlmeyer 68626f577b
Merge branch 'master' into improve-include-consistency 2019-07-12 19:59:56 -04:00
Axel Kohlmeyer e832b5d50b
make clang++ happy when trying to compile the GPU library 2019-07-12 15:42:16 -04:00
Axel Kohlmeyer 06dcc9e283
Merge branch 'master' into improve-include-consistency 
# Conflicts:
#	src/USER-MESO/atom_vec_tdpd.cpp
 2019-07-09 14:50:00 -04:00
Trung Nguyen 46a9772a6d Minor clean-up 2019-07-05 12:12:29 -05:00
Axel Kohlmeyer d07a49aeea
add missing prototypes 2019-07-05 11:37:21 -04:00
Trung Nguyen 49f27573a7 Fixed a bug in lj96 involving missing the special_lj factor 2019-07-03 23:44:33 -05:00
Axel Kohlmeyer e63fe1fe84
please POEMS library in namespace POEMS and remove "using namespace" from headers 2019-07-04 00:09:01 -04:00
Axel Kohlmeyer 42c31227d9
continuing to clean up include file lists 2019-07-01 15:59:16 -04:00
Axel Kohlmeyer 39f5b8c734
transform POEMS library to conform to IWYU conventions 2019-07-01 04:16:00 -04:00
Stan Moore ea2e73119d Update Kokkos library in LAMMPS to v2.9.00 2019-06-28 11:23:24 -06:00
Christoph Junghans 8c3d18520d add missing include needed on ppc64le 2019-06-26 10:45:31 -06:00
Axel Kohlmeyer 2f29bd29f4
Merge pull request #1430 from ndtrung81/gpu-neigh-hybrid 
Enable neighbor build on the device for pair hybrid substyles
 2019-06-17 14:12:40 -04:00
Axel Kohlmeyer b3f4e2055e
Merge pull request #1438 from giacomofiorin/colvars-update 
Update Colvars library to version 2019-04-26
 2019-05-06 12:08:50 -04:00
Giacomo Fiorin 7e00acce53 Update Colvars library to version 2019-04-26 
The following is list of relevant issues fixed and improvements:

Fix forces and missing output of runtime histogram for histogramRestraint
https://github.com/Colvars/colvars/pull/246

Use fix_modify to add configuration to Colvars:
https://github.com/Colvars/colvars/pull/216

Fix componentCoeff and name not working with orientationAngle components:
https://github.com/Colvars/colvars/issues/213

Fix 1-timestep offset with extendedLagrangian:
https://github.com/Colvars/colvars/pull/210

Changes to improve compiler support:
https://github.com/Colvars/colvars/pull/203

Fix ignored anisotropic cutoff3 for groupCoordNum:
https://github.com/Colvars/colvars/pull/202

New dipoleMagnitude variable:
https://github.com/Colvars/colvars/pull/198

Parser improvements:
https://github.com/Colvars/colvars/pull/196
 2019-04-30 13:46:37 -04:00
Richard Berger 8145c5028d Fix OpenCL compilation errors due to bad comments in macros 2019-04-30 00:44:12 -04:00
Trung Nguyen 4a4297591e Did some more cleanups 2019-04-17 12:04:31 -05:00
Trung Nguyen 1f43efc111 Cleaned up the changes in Device and the base class of the pair styles 2019-04-17 00:09:49 -05:00
Trung Nguyen c55009a0ac Enabled neighbor list build on the device with pair_style hybrid and hybrid/overlay 2019-04-16 23:30:25 -05:00
Axel Kohlmeyer c52a330a79
update USER-PLUMED support for version 2.5.1 and fix bug in Install.py script 2019-04-04 14:19:53 -04:00
Axel Kohlmeyer 265ad4512d
add sanity check on plumed pre-installed path location 2019-04-04 13:18:27 -04:00
Axel Kohlmeyer 1696432e82
resolve conflict between src/STUBS/mpi.h and lib/message/cslib/src/STUBS_MPI/mpi.h 2019-04-03 01:00:53 -04:00
Ryan S. Elliott 9d0e518cc5 Updates for kim-api-2.0.2 release 2019-03-28 15:35:22 -05:00
Axel Kohlmeyer 2f20581b29
Merge pull request #1374 from akohlmey/collected-small-fixes 
Collected small changes for the next patch release
 2019-03-25 13:15:45 -04:00
Axel Kohlmeyer cd6b23d104
explicitly request OpenCL version 1.2 compatibility when compiling GPU package kernels for OpenCL 2019-03-22 09:50:31 -04:00
Axel Kohlmeyer 741a7fe630
final touches to support compiling with libcurl transparently 2019-03-19 15:40:49 -04:00
Ryan S. Elliott b628e3b1b6 Update openkim.org urls in various places 2019-03-06 10:26:03 -06:00
Ryan S. Elliott 54e5c76333 Bump KIM API version to 2.0.1 2019-02-27 15:50:08 -06:00
Ryan S. Elliott e95cf4e917 Some various doc updates for kim-api support 2019-02-14 13:38:28 -06:00
Ryan S. Elliott 333154633b Merge branch 'master' into kim-v2-update 2019-02-14 13:29:50 -06:00
Axel Kohlmeyer 9ac908f05f
switch download server for voro++ from LBL to download.lammps.org, which seems much more reliable 2019-02-13 09:53:20 -05:00
Stan Moore 773476634b Update Kokkos library in LAMMPS to v2.8.00 2019-02-08 08:50:26 -07:00
Ryan S. Elliott 927dc262b2 Update CMake & Install.py for KIM API v2 2019-02-06 23:41:45 -06:00
Ryan S. Elliott d677335b23 Merge remote-tracking branch 'lammps/master' into kim-v2-update 2019-02-03 12:45:44 -06:00
Ryan S. Elliott a9b0fb9e9d Some adjustments to kim Install.py 2019-02-03 12:43:48 -06:00