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4376 Commits

Author SHA1 Message Date
Axel Kohlmeyer 605b4dca22 fix overlooked merge conflict 2018-06-18 18:09:59 -04:00
Axel Kohlmeyer dade67664d restore bugfix for refrences 2018-06-18 18:07:26 -04:00
Axel Kohlmeyer 93d6510d34 restore deleted file 2018-06-18 18:02:40 -04:00
Axel Kohlmeyer 4f8d1893e9 restore fix for formatting cleanup 2018-06-18 18:01:28 -04:00
Axel Kohlmeyer 7c7a80b31a restore deleted file 2018-06-18 17:59:22 -04:00
julient31 f2a6aa249f Commit2 JT 052918: doc 2018-05-29 17:18:45 -06:00
julient31 1641f78e3e Merge from lammps master 2018-05-21 16:06:53 -06:00
jrgissing 363d8ef775 tweaks1 2018-05-13 15:45:43 -06:00
jrgissing a449488b1d simplify 2018-05-13 12:14:15 -06:00
jrgissing e076d08ee9 correctly render doc page 2018-05-12 14:17:29 -06:00
Steve Plimpton ca6920be72
Merge pull request #907 from akohlmey/dump_maxfile 
Implement 'dump_modify maxfiles' feature
 2018-05-12 12:59:33 -06:00
Steven J. Plimpton 0f32d603b5 tweaks to dump_modify maxfiles doc page 2018-05-11 15:52:18 -06:00
Steve Plimpton 3440b1a2a7
Merge pull request #909 from lammps/tablecut 
new dihedral table/cut command
 2018-05-11 15:41:52 -06:00
Axel Kohlmeyer 4d34e55072 rename jpeg file, recreate tex file and fix typo in docs for dihedral style table/cut 2018-05-11 17:31:14 -04:00
Axel Kohlmeyer 821ef0cf77 update documentation for dihedral style table/cut 2018-05-11 16:08:23 -04:00
Steven J. Plimpton 8d24101df4 patch 11May18 2018-05-11 14:04:49 -06:00
Steven J. Plimpton 9674512997 new dihedral table/cut command 2018-05-11 07:36:40 -06:00
Axel Kohlmeyer 7780d92823 implement 'dump_modify maxfiles' feature as discussed 2018-05-10 23:25:26 -04:00
Axel Kohlmeyer 671876efef
Make the description of global properties more explicit 2018-05-08 15:33:42 -04:00
robeme 53fc9f1f0f updated doc for new fix restrain output 2018-05-08 10:11:00 +02:00
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 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
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 a7c9418629
Merge pull request #890 from jrgissing/bond_react_final_touches 
bond/react final touches
 2018-05-07 10:37:47 -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 5e49976b70 correct typo in fix bond/react docs 2018-05-06 11:17:34 -04:00
jrgissing 916ed71760 fix bond/react final touches 2018-05-06 00:34:03 -06:00
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
Steven J. Plimpton 844858d3a7 2nd set of updates 2018-05-03 17:00:08 -06:00
Steven J. Plimpton 2b8576c7c7 first updates 2018-05-03 16:55:22 -06:00
Steve Plimpton eeee2d3026
Merge pull request #803 from jrgissing/fix_bond_react 
Fix bond react
 2018-05-03 14:16:46 -06:00
Steve Plimpton 749f1ff407
Merge pull request #875 from akohlmey/collected-small-fixes 
Collected small changes and bug fixes for the next patch release
 2018-05-03 11:28:00 -06:00
Steve Plimpton 35294dafbc
Merge pull request #883 from giacomofiorin/colvars-update 
Fixes to Colvars library (version 2018-04-29)
 2018-05-03 11:25:32 -06:00
Steven J. Plimpton 75cffc78c5 updates to quadratic form of SNAP potential 2018-05-03 10:23:50 -06:00
Giacomo Fiorin 0c005f5cb0 Small fixes to Colvars library 
Primarily a list of small fixes, combined with cosmetic changes and cleanups
in several files.

6d0c917 2018-04-29 Fix missing deallocation of output stream object (reported by HanatoK) [Giacomo Fiorin]
c92d369 2018-04-17 Do not test for atom group size [Jérôme Hénin]
431e52a 2018-04-06 Allow scripted/custom colvars to be periodic [Jérôme Hénin]
81d391f 2018-04-05 Split colvarcomp constructor into POD constructor + init() function [Giacomo Fiorin]
9b85d5f 2018-03-13 Fix issue with out-of-order atom selections; clarify format for ref positions [Giacomo Fiorin]
0e0ed37 2018-03-07 Support triclinic unit cells in VMD, clean up PBC functions [Giacomo Fiorin]
eed97c9 2018-02-24 Obtain integer version number from version string [Giacomo Fiorin]
c17f3cd 2018-02-23 Write trajectory labels only when needed [Giacomo Fiorin]
 2018-05-02 15:03:56 -04:00
Michael DeLyser efbee4a292
Delete man_fix_bocs.html 2018-05-02 11:27:31 -04:00
Axel Kohlmeyer 25ac1fd16c mention that fix reax/bonds and reax/c/bonds do not honor the group id 2018-05-01 18:55:00 -04:00
julient31 1b8669c620 Commit JT 042018, new spin/precession and pair/spin (peru virtual) 2018-04-26 15:26:31 -06:00
julient31 ce80d1a3ea Commit JT 041618 
Enabling multiple exchange interactions
 2018-04-26 15:26:31 -06:00
julient31 8709f6044b Commit modifs before release 2 (04/02/18) 2018-04-26 15:26:31 -06:00
julient31 08bc115380 Commit before meeting 032218 2018-04-26 15:26:13 -06:00