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18044 Commits

Author SHA1 Message Date
Christoph Junghans 379fa22147 FindKIM-API.cmake: address Ryan's comments 2019-08-16 10:30:09 -06:00
Christoph Junghans cd77f71e99 cmake: add version check for kim-api 2019-08-15 12:56:15 -06:00
Axel Kohlmeyer a12b959f39
Merge pull request #1625 from ellio167/kim-logs 
Added logs for examples/kim
 2019-08-09 13:47:41 -04:00
Ryan S. Elliott 8619462b3b Added logs for examples/kim 2019-08-07 16:14:22 -05:00
Axel Kohlmeyer d08d6b5fb0
Merge pull request #1623 from akohlmey/next-version 
Step version string for stable release
 2019-08-06 11:17:40 -04:00
Axel Kohlmeyer db621fc897
Merge pull request #1622 from akohlmey/fix-ave-histo-bugfix 
fix inconsistent enumerator bug in fix ave/histo vs fix ave/histo/weight
 2019-08-06 10:54:49 -04:00
Axel Kohlmeyer c820c92225
Merge pull request #1620 from lammps/replicate 
fix formatting and augment explanation for bbox option
 2019-08-06 10:12:19 -04:00
Axel Kohlmeyer 59046e7444
step version number for stable release 2019-08-06 08:52:54 -04:00
Axel Kohlmeyer 4a55e9dd0c
fix inconsistent enumerator bug in fix ave/histo vs fix ave/histo/weight 2019-08-06 07:28:00 -04:00
Steve Plimpton 2d64323354 fix formatting and augment explanation for bbox option 2019-08-05 17:21:11 -06:00
Axel Kohlmeyer 25b504d4fd
Merge pull request #1615 from akohlmey/next_version 
Step version string for stable release
 2019-08-05 19:13:17 -04:00
Axel Kohlmeyer 34cc7ed5b1
Merge pull request #1619 from ellio167/kim-doc-update 
Update kim query url in docs
 2019-08-05 17:39:40 -04:00
Axel Kohlmeyer 3ef93d6e1b
cannot forced enable FFMpeg and gzip on windows yet. 2019-08-05 16:59:18 -04:00
Axel Kohlmeyer 2092b2c010
Step version string for stable release 2019-08-05 16:58:26 -04:00
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
Axel Kohlmeyer 3a4bce1e52
Merge pull request #1617 from rbberger/cmake_docs_additions 
Mention LAMMPS_LIB_SUFFIX in docs
 2019-08-05 16:36:48 -04:00
Axel Kohlmeyer 0bd5704107
Merge pull request #1618 from giacomofiorin/colvars-update 
Bugfix for Colvars library (update to version 2019-08-05)
 2019-08-05 16:36:16 -04:00
Ryan S. Elliott e39b85b62f Update kim query url in docs 2019-08-05 15:23:57 -05:00
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
Richard Berger f2757eaf41 Mention LAMMPS_LIB_SUFFIX in docs 2019-08-05 14:00:56 -04:00
Axel Kohlmeyer 096c225594
Merge pull request #1613 from rbberger/cmake_docs_update 
Update CMake documentation
 2019-08-04 18:32:11 -04:00
Axel Kohlmeyer 58d27403f1
CMake tweaks to improve building LAMMPS for windows with mingw on Linux 2019-08-04 18:28:26 -04:00
Richard Berger b65ae605e5 Added one-liner for HTML-only docs in Build.txt 2019-08-03 15:17:18 -04:00
Axel Kohlmeyer d82ae64d16
minor tweak for consistency 2019-08-03 11:16:55 -04:00
Axel Kohlmeyer 5b3423c60e
tweaks for Linux to Windows cross-compilation 2019-08-03 11:16:14 -04:00
Axel Kohlmeyer faefcc776a
sched_getaffinity() is a Linux specific system call. add preprocessor guards 2019-08-03 10:38:41 -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 91fdd98fbc
restore accidentally deleted text 2019-08-02 18:44:40 -04:00
Richard Berger bd87b67232
Update false_positives.txt 2019-08-02 17:35:26 -04:00
Richard Berger eb7fa1b6cb Update CMake documentation 2019-08-02 17:04:59 -04:00
Axel Kohlmeyer aff5f06e8f
Merge pull request #1612 from akohlmey/new_version 
Step version string for next patch release
 2019-08-02 14:27:13 -04:00
Axel Kohlmeyer bd3ffe1321
Merge pull request #1603 from eagunn/iss1572clean 
Iss1572clean: Clean fix for error handling, clarify data requirements for fix bocs input
 2019-08-02 10:43:30 -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
Axel Kohlmeyer a857e7f790
Merge pull request #1608 from wmbrownIntel/intel-eam-eatom-fix 
Bug fix for eam/intel per-atom energy calculation.
 2019-08-02 10:42:54 -04:00
Axel Kohlmeyer 9c691ddd0f
Merge pull request #1610 from wmbrownIntel/intel-ncache-alias-fix 
Bug fixes for use of uninitialized variable and strict-aliasing in USER-INTEL
 2019-08-02 10:42:37 -04:00
Axel Kohlmeyer 828ddfd957
Merge pull request #1611 from evoyiatzis/patch-1 
small clean-up of fix.txt
 2019-08-02 10:42:20 -04:00
Axel Kohlmeyer 7ba6b8a06a
Merge pull request #1604 from akohlmey/timeout-for-replica 
Add support for timeouts to temper commands and a few small fixes
 2019-08-02 10:41:44 -04:00
Anne Gunn d750cc02c0
Changed the code in the read_F_table function to conform to the "expected behavior" description in #1572. Adopted a best-of-both-worlds approach, though, and processed the whole input file all the way through, emitting a message for each problem found, before issuing a final error message to stop processing. Updated doc to clarify requirement for uniform spacing of pressure correction points. 2019-08-02 08:46:04 -04:00
Axel Kohlmeyer 9ed43e55f0
add some more descriptions for fixes to list of style in fix command docs 2019-08-02 08:41:34 -04:00
Axel Kohlmeyer 8fd28cd78d
fix typo 2019-08-02 08:40:59 -04:00
Axel Kohlmeyer b5f19b93c2
Step version string for next patch release 2019-08-02 05:15:29 -04:00
Evangelos Voyiatzis 5076f1a36c
small clean-up of fix.txt 2019-08-02 10:55:18 +02:00
Axel Kohlmeyer f61cd68ca4
add missing parenthesis 2019-08-01 20:43:33 -04:00
Axel Kohlmeyer 5b4b418289
use check_language() instead of enable_language() to get fortran compiler name 2019-08-01 18:24:14 -04:00
Axel Kohlmeyer 8df7f51470
Merge branch 'master' into timeout-for-replica 2019-08-01 16:56:49 -04:00
Axel Kohlmeyer f9e34825f0
workaround for xcode oddity with compiling voro++ 2019-08-01 16:42:52 -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 de366c27e2
Merge pull request #1606 from oywg11/fix-ILP-bug 
Fix a communication bug of potential #839
 2019-08-01 15:01:13 -04:00
Axel Kohlmeyer 5fd323fe32
simplify example folder for ilp/graphene/hbn potential 
- flatten directory structure
- remove CPU time and reduce excess precision from output
- delete redundant and unused files
- regenerate reference outputs
 2019-08-01 14:24:47 -04:00