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3636 Commits

Author SHA1 Message Date
Steve Plimpton 63e71cd45b patch to add DPD-VV 2016-10-12 07:35:47 -06:00
Axel Kohlmeyer 39a22039e9 correct broken link 2016-10-11 23:57:40 -04:00
Axel Kohlmeyer b75860048b updates for recent changes to the manual 2016-10-11 23:50:45 -04:00
Steve Plimpton 0eb7fbf34d tweaks to new USER-DPD docs 2016-10-11 15:43:59 -06:00
sjplimp 6f1162927a Merge pull request #207 from timattox/USER-DPD_new_VV_for_DPD 
USER-DPD: add support for using VV with DPD
 2016-10-11 13:39:25 -06:00
Steve Plimpton 04f5eadcf1 added LAST option to dump_modify thresh, more restart info printed out to screen 2016-10-11 12:39:52 -06:00
sjplimp e70d530c46 Merge pull request #203 from rbberger/txt2rst-external-link-fix 
txt2rst external link fix
 2016-10-10 13:59:27 -06:00
Axel Kohlmeyer 144e6a8091 whitespace cleanup 2016-10-10 09:40:09 -04:00
Steven Strong 72ac073412 edited documentation 
(cherry picked from commit eff14c74b0)
 2016-10-10 09:38:54 -04:00
Steven Strong 49c45ab03b edited documentation 
(cherry picked from commit fd560889c3)
 2016-10-10 09:38:53 -04:00
Steven Strong c2cd439944 first draft of documentation for respa 
(cherry picked from commit d7dcbcfbd9)
 2016-10-10 09:38:53 -04:00
Tim Mattox e27ed6c94a USER-DPD: Added support to use VV integrator with USER-DPD if desired. 
Includes documentation and examples.
NOTE: VV requires very small timesteps under isoenergetic conditions.
Consider using fix_shardlow instead, since this VV support is
primarily for comparison purposes.
 2016-10-07 15:03:30 -04:00
Richard Berger 7f3a7c5cbe Fix broken link 2016-10-06 20:33:24 -04:00
Richard Berger e78b4267b7 Fix issue with external links containing anchors 2016-10-06 20:29:07 -04:00
sjplimp e9fed80928 Merge pull request #202 from akohlmey/doc-formatting-fixes 
collected documentation updates and corrections from LAMMPS-ICMS
 2016-10-06 15:49:44 -06:00
Steve Plimpton b3d2fb91bb new fix wall/gran/region command, REBO bug fix, new example log files 2016-10-06 15:47:41 -06:00
Axel Kohlmeyer 0b5d71537a collected documentation updates and corrections from LAMMPS-ICMS 
fixes formatting issues due to tabs, permission issues and
a few typos and badly worded text.
 2016-10-06 15:48:18 -04:00
Steve Plimpton 493873fb93 clean up doc src 2016-10-06 13:00:46 -06:00
Steve Plimpton c46be7db62 changes to imbalance weight factors 2016-10-05 10:33:39 -06:00
Steve Plimpton 11c2892e54 Merge branch 'restrict-weights-and-weight-factors' of https://github.com/akohlmey/lammps 2016-10-04 09:49:09 -06:00
sjplimp e079362776 Merge pull request #190 from akohlmey/small-bufixes-and-enhancements 
Small bufixes and enhancements
 2016-10-03 17:58:36 -06:00
Steve Plimpton c3ff8812b3 added XOR operator to variable command 2016-10-03 17:57:33 -06:00
Axel Kohlmeyer 1985db4fb1 correct designation of meam supporting USER-OMP and meam/spline not 2016-10-01 23:05:05 -04:00
Axel Kohlmeyer d45e333f7c restrict choice of weight factors and guarantee that weights are >= 0.001 2016-09-30 11:11:32 -04:00
Axel Kohlmeyer 6d200061ca update colvars library to version 2016-09-30 2016-09-30 08:15:44 -04:00
Steve Plimpton 446e7e7369 patch for allowing prd command to work with sorted atoms 2016-09-28 16:33:30 -06:00
sjplimp 829d11e88b Merge pull request #44 from rbberger/doc-fixes 
Some documentation fixes and IPython updates
 2016-09-27 15:36:10 -06:00
sjplimp 96f31d6dad Merge pull request #43 from akohlmey/doc-fixes 
Documentation fixes
 2016-09-27 15:35:41 -06:00
Steve Plimpton 35705217f4 enable multi-processor NEB replicas 2016-09-27 15:34:08 -06:00
Steve Plimpton 9a2f738673 sync with SVN 2016-09-27 15:32:57 -06:00
Steve Plimpton f9677e6d7b released version of weighted balancing 2016-09-27 10:52:27 -06:00
Richard Berger a3277117e2 Add filter which merges preformatted sections 2016-09-26 18:52:43 -04:00
Richard Berger 67d4c07689 Do not escape underscore inside preformat blocks 2016-09-26 18:52:31 -04:00
Richard Berger 877a504933 Fix typo in Section_howto.txt 2016-09-26 18:44:25 -04:00
Axel Kohlmeyer 8a951f9d79 fix typo 2016-09-26 18:43:03 -04:00
Axel Kohlmeyer 69a8842ecb update load balance weights documentation for fix balance and balance 2016-09-26 18:33:50 -04:00
Axel Kohlmeyer 7732548b3c correct issues related to the addition of fix cmap 2016-09-26 18:14:32 -04:00
Axel Kohlmeyer 2c5f6e1a99 fix a broken link that slipped through the cracks in the previous cleanup 2016-09-26 18:13:18 -04:00
Richard Berger d0aa13b543 Fix broken link in Section_packages.txt 2016-09-26 16:53:18 -04:00
Axel Kohlmeyer 47b52ed2dd Merge branch 'integration' into balance2 2016-09-26 15:19:48 -04:00
Steve Plimpton b97b9dd661 new fix cmap command 2016-09-26 08:40:53 -06:00
sjplimp c00cd6192d Merge pull request #41 from akohlmey/doc-fixes 
Documentation updates and corrections
 2016-09-23 14:57:23 -06:00
Steve Plimpton 6f4b7268de sync with SVN 2016-09-23 14:52:45 -06:00
Steve Plimpton 08f0bf9025 new verion of balance weighting 2016-09-23 14:37:53 -06:00
Axel Kohlmeyer 3d5f5bf40e a few more consolidations of link anchors 2016-09-23 10:25:10 -04:00
Axel Kohlmeyer 065d35eefa update kokkos compilation instructions to use provided preset makefiles 2016-09-22 23:53:19 -04:00
Axel Kohlmeyer 3785249033 use "make mpi" instead of "make g++" in examples 2016-09-22 23:52:52 -04:00
Axel Kohlmeyer e18941e865 delete bogus line (how did this get into the docs?) 2016-09-22 23:41:53 -04:00
Axel Kohlmeyer c6cebe66c7 making more links and anchors consistent and correct errors 2016-09-22 22:26:17 -04:00
Axel Kohlmeyer 08d9792ec8 add an additional explanation to compute XXX/tally docs and fix a typo 2016-09-22 21:46:45 -04:00