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14476 Commits

Author SHA1 Message Date
Axel Kohlmeyer 1888b616c4 remove some extra semicolons 2018-05-07 18:04:25 -04:00
Axel Kohlmeyer 104dde27ed eliminate variable length arrays from AtC lib for C++ standard compliance 2018-05-07 17:36:34 -04:00
Steve Plimpton bfdfd36c1c
Merge pull request #894 from akohlmey/cplusplus-clang-fixes 
More fixes to conform with C++ standards as indicated by Clang
 2018-05-07 14:53:43 -06:00
Steve Plimpton a4759210a8
Merge pull request #893 from ohenrich/user-cgdna 
Docs update and journal reference for USER-CGDNA package
 2018-05-07 14:39:32 -06:00
Steve Plimpton 7fed6c7e4c
Merge pull request #634 from craabreu/master 
Computation of forces/torques on rigid bodies moved to post_force
 2018-05-07 14:39:10 -06:00
Axel Kohlmeyer 82217001c8 must use fabs() on doubles, not abs(), to avoid ambiguity 2018-05-07 15:56:35 -04:00
Axel Kohlmeyer b2370b6986 use correct namespace when instantiating IntelBuffers; 2018-05-07 15:49:51 -04:00
Axel Kohlmeyer 7cf42e42eb
make links to citations unique across files 2/2 2018-05-07 14:25:18 -04:00
Axel Kohlmeyer d80b375e26
make links to citations unique across files 1/2 2018-05-07 14:24:00 -04:00
Axel Kohlmeyer d203118286 update rigid body reference outputs. add bodyforces early examples 2018-05-07 14:19:50 -04:00
Steve Plimpton 74fbb84b8c
Merge pull request #878 from jrgissing/group_extract 
Group extract
 2018-05-07 11:45:37 -06:00
Oliver Henrich 5076b6d161 Removed old documentation 2018-05-07 18:25:55 +01:00
Oliver Henrich fcdcdb3286 Merge branch 'master' into user-cgdna 2018-05-07 18:19:24 +01:00
Oliver Henrich 722549965e Added reference to implementation paper 2018-05-07 18:13:18 +01:00
Steve Plimpton ca96a7ab05
Merge pull request #891 from akohlmey/collected-small-changes 
Collected small changes, fixes and updates
 2018-05-07 10:43:19 -06:00
Steve Plimpton 8ec033e823
Merge pull request #889 from akohlmey/cplusplus-compliance 
Collected changes to restore C++ standard compliance
 2018-05-07 10:42:22 -06:00
Steve Plimpton a7c9418629
Merge pull request #890 from jrgissing/bond_react_final_touches 
bond/react final touches
 2018-05-07 10:37:47 -06:00
Steve Plimpton bc0c405bfa
Merge pull request #887 from akohlmey/create-bonds-single-bugfix 
Fix bug in create_bonds single/bond
 2018-05-07 10:37:00 -06:00
Steve Plimpton 1ea5b9eabb
Merge pull request #879 from mdelyser/USER-BOCS 
USER-BOCS
 2018-05-07 10:34:51 -06:00
Axel Kohlmeyer d9d33ac766 add ability to set multiplicity for dihedrals with fix restrain 
this introduces an optional keyword, so backward compatibility is preserved.
this closes #884
 2018-05-07 07:23:29 -04:00
Axel Kohlmeyer d51745fd27 whitespace cleanup 2018-05-07 07:23:29 -04:00
Axel Kohlmeyer c3588f08b7 provide keyword/value option to compute ackland/atom for selecting legacy or current variant of implementation 2018-05-07 07:23:29 -04:00
Axel Kohlmeyer ecfe5c8373 use american spelling of neighbor consistently in docs and code comments 2018-05-07 07:23:29 -04:00
Axel Kohlmeyer 009666d9a5 need to ignore pair style kim in src/ 2018-05-07 07:23:29 -04:00
Axel Kohlmeyer 551ea9694d add VTK config for recent fedora versions 2018-05-07 07:23:29 -04:00
Axel Kohlmeyer d7339bbd9e significantly expand .github/CODEOWNERS file to automatically notify more contributors of changes to files/packages they maintain 2018-05-07 07:23:29 -04:00
Axel Kohlmeyer 934f825388 update USER-INTEL Install.sh script and dependency handling 2018-05-07 07:23:29 -04:00
Axel Kohlmeyer f4fbdea0b3 update .gitignore for lib/latte 2018-05-07 07:23:29 -04:00
Axel Kohlmeyer 14588f6242 remove dead code and fix compilation for fix mscg 2018-05-07 07:23:29 -04:00
Axel Kohlmeyer 5e49976b70 correct typo in fix bond/react docs 2018-05-06 11:17:34 -04:00
Axel Kohlmeyer 9d9d7cb9ed update example log files 2018-05-06 11:10:40 -04:00
Axel Kohlmeyer 941d289a69 cosmetic changes to avoid compiler warnings 2018-05-06 10:54:34 -04:00
jrgissing e1f9ee1347 fix1 2018-05-06 01:04:23 -06:00
jrgissing 916ed71760 fix bond/react final touches 2018-05-06 00:34:03 -06:00
Axel Kohlmeyer 9d6891823a some more cosmetic changes 2018-05-05 20:38:22 -04:00
Axel Kohlmeyer e14b61e4a4 replace variable length array with constant length through making maxLine constant 2018-05-05 19:51:30 -04:00
Jacob Gissinger 2d321a602c
Merge pull request #10 from lammps/master 
rebase
 2018-05-05 14:22:23 -06:00
Steven J. Plimpton 9acd35abe2 another change to fix poems 2018-05-05 10:52:39 -06:00
Steven J. Plimpton 0c53afbfcf more changes to fix rigid and fix poems 2018-05-05 10:39:01 -06:00
Axel Kohlmeyer 2616dd91f9 include USER-BOCS package in cmake 2018-05-05 12:05:32 -04:00
Axel Kohlmeyer f7c37a7a98 adapt isfinite() handling to upstream 2018-05-05 11:46:35 -04:00
Axel Kohlmeyer 095ca76b5b plug memory leaks in USER-BOCS 2018-05-05 11:44:21 -04:00
Axel Kohlmeyer f9f8e2bdbe update USER-BOCS example to match LAMMPS style and include reference logs 2018-05-05 11:43:05 -04:00
Axel Kohlmeyer 735bceb468 Merge branch 'master' into USER-BOCS 2018-05-05 10:21:21 -04:00
Axel Kohlmeyer 81293b0fda changes to integrate USER-BOCS into LAMMPS and to closer follow the LAMMPS programming/documentation style 2018-05-05 10:21:11 -04:00
Axel Kohlmeyer 88dca11b3c update colvars dependencies 2018-05-05 02:36:02 -04:00
Axel Kohlmeyer 460e8bd298 add return value to non-void function 2018-05-05 02:35:42 -04:00
Axel Kohlmeyer ce86ff6cd1 add missing USER-MOFFF to Makefile and fix typo 2018-05-05 02:15:36 -04:00
Axel Kohlmeyer 36126ccb7d be more verbose in USER-PHONON install script when KSPACE is not installed 2018-05-05 02:14:17 -04:00
Axel Kohlmeyer b7210e931c more cosmetic changes to silence pedantic warnings 2018-05-04 22:34:20 -04:00