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3658 Commits

Author SHA1 Message Date
sjplimp ad5f7c4581 Merge pull request #238 from giacomofiorin/colvars-2016-10-24 
Colvars fixes and small changes
 2016-10-25 10:32:41 -06:00
Axel Kohlmeyer 63eada2425 fix issue with docs for orientorder/atom compute reported by @andeplane 
this closes #243
 2016-10-25 12:12:48 -04:00
Steve Plimpton 9c81ad1ab6 doc page changes 2016-10-25 09:45:55 -06:00
Axel Kohlmeyer f8367e3d0f update documentation pdf for updated colvars lib 2016-10-24 17:49:53 -04:00
Axel Kohlmeyer 607246f923 ignore mobi file as well 2016-10-21 13:25:53 -04:00
Axel Kohlmeyer 6742fb634a remove mobi file format creation from makefile and explain it in README instead 2016-10-21 12:05:21 -04:00
Axel Kohlmeyer ed3f02f249 ignore generated PDF and ePUB files 2016-10-21 12:04:48 -04:00
Axel Kohlmeyer 2cf77ff778 Add support for ebook generation in ePUB and mobi format 2016-10-20 16:16:17 -04:00
Axel Kohlmeyer 8c3f5cb307 support generation of manual in ePUB format 2016-10-20 09:27:26 -04:00
Steve Plimpton 9954d5d346 forgot pair table change 2016-10-19 10:47:07 -06:00
sjplimp b0cf1ded38 Merge pull request #229 from akohlmey/small-corrections 
collected various small corrections and updates
 2016-10-19 08:57:54 -06:00
sjplimp 393337e7cf Merge pull request #226 from akohlmey/pair-gauss-mixing 
add mixing support for pair styles gauss and gauss/cut
 2016-10-19 08:37:32 -06:00
Axel Kohlmeyer 566effc9c9 account for new fix halt properly in PDF and online docs 2016-10-19 09:08:20 -04:00
Axel Kohlmeyer 7b7cb297e6 add mixing for pair styles gauss and gauss/cut contributed by andrew jewett. also add support for write_data. 2016-10-18 22:26:47 -04:00
Axel Kohlmeyer 5a6dea7a22 Merge branch 'master' into user-nc-dump 2016-10-18 15:36:18 -04:00
Steve Plimpton 2106dce2b3 new fix halt command, other sundry small bug fixes 2016-10-18 13:11:40 -06:00
Axel Kohlmeyer e4ff8128f1 fix typo 
(cherry picked from commit c65fb0e311)
 2016-10-16 12:29:53 -04:00
sjplimp d11363c7eb Merge pull request #220 from rbberger/fix-doc-makefile 
Allow building non-html doc targets without Python3 and virtualenv
 2016-10-13 17:00:23 -06:00
Steve Plimpton 2c8a7a318a bug fix for fix GCMC w/ fix shake, enhance of fix wall/gran/region with restarting 2016-10-13 16:55:53 -06:00
Richard Berger 95cca1bd9f Allow building other targets without Python3 and virtualenv 2016-10-13 11:40:44 -04:00
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 e10ea91c5f add doc file to toctree 2016-10-11 23:51:42 -04:00
Axel Kohlmeyer b75860048b updates for recent changes to the manual 2016-10-11 23:50:45 -04:00
Axel Kohlmeyer 69cb831705 import dump nc and dump nc/mpiio from lammps-netcdf as USER-NC-DUMP package by lars pastewka 2016-10-11 23:44:34 -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