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4029 Commits

Author SHA1 Message Date
Axel Kohlmeyer 070ce33a13 improve memory usage reporting in info and output class 2017-03-16 18:35:04 -04:00
Axel Kohlmeyer f604f86cfc add fix filter/corotate to some administrative files 2017-03-16 15:08:17 -04:00
Axel Kohlmeyer 0d8f74f0c5 Merge branch 'filter_corotate' of https://github.com/lukin17/lammps into pull-416 2017-03-15 18:54:41 -04:00
sjplimp 3a2da51a82 Merge pull request #413 from ohenrich/user-cgdna 
User cgdna
 2017-03-15 13:12:43 -06:00
sjplimp b1c59126f7 Merge pull request #415 from stanmoore1/kk_qeq 
Add neigh/qeq option to Kokkos package
 2017-03-15 13:12:08 -06:00
sjplimp 4c77838514 Merge pull request #414 from sstrong99/flow-gauss-doc-addition 
flow/gauss documentation update
 2017-03-15 13:11:26 -06:00
lukin17 c3ce3747e0 Added fix filter/corotate. 2017-03-15 11:34:01 +01:00
Stan Moore fdc390ad05 Tweaking docs for Kokkos package 2017-03-14 14:08:14 -06:00
Stan Moore 580f6b567b Add neigh/qeq option to Kokkos 2017-03-14 10:44:31 -06:00
Steven Strong 27b1c33a16 updated the NEMD discussion in the how-to documentation about flow/gauss 2017-03-14 10:39:06 -06:00
Oliver Henrich 7a75cd111c Minor updates in documentation and setup tool, merge before upgrade to oxDNA2 2017-03-14 11:39:09 +00:00
Oliver Henrich 23b8287933 Updated documentation and simple setup tool 2017-03-14 11:36:44 +00:00
Abdoreza Ershadinia d17d99b9dd UPLOAD Formulas for EES 2017-03-13 22:54:09 +09:00
Abdoreza Ershadinia 68b2a454b5 UPLOAD fix_wall_ees_image 2017-03-13 22:53:10 +09:00
Abdoreza Ershadinia 23c3f5622a DOC files for USER-EES 
txt doc files for fix_wall_ees and fix_wall_region_ees added.
 2017-03-13 22:51:15 +09:00
Tim Mattox 4cfe623bc1 Correct a typo in the fix_halt.txt documentation. 2017-03-10 21:30:03 -05:00
Steve Plimpton f871ecdc67 change to RCB cuts in load-balancing commands, also a new option for fix halt 2017-03-10 15:55:07 -07:00
Giacomo Fiorin f70752c18f Include PDF of Colvars doc missing in previous commit 2017-03-10 15:58:35 -05:00
Giacomo Fiorin 0b4adaa9e6 Backport typo fixes that were not previously pushed to the Colvars repository 2017-03-10 09:24:46 -05:00
Giacomo Fiorin 5fe6206638 Update Colvars module to version 2017-03-10 2017-03-10 09:16:58 -05:00
Steve Plimpton 79b005dc3d patch 7Mar17 2017-03-07 11:40:07 -07:00
sjplimp 920641bbff Merge pull request #399 from rbberger/docs_spelling_fixes 
Correct spelling errors in documentation
 2017-03-07 09:47:22 -07:00
sjplimp 4af6557568 Merge pull request #394 from jaapkroe/kolmogorov-crespi 
Added Kolmogorov-Crespi potential
 2017-03-07 09:46:08 -07:00
sjplimp 020e75e7ef Merge pull request #386 from akohlmey/doc-consistentcy 
improve consistency of manual
 2017-03-07 09:33:14 -07:00
Steve Plimpton efaa4c6710 new neigh_modify exclude option, other SNAP changes 2017-03-07 09:31:12 -07:00
Richard Berger 21be86c423 Fix typos in txt2html 2017-03-07 00:58:03 -05:00
Richard Berger 007f3c66a0 Third batch of spelling fixes in manual 2017-03-07 00:51:31 -05:00
Richard Berger 32708860a9 Add remaining false positives 2017-03-07 00:27:35 -05:00
Richard Berger fc9eebb936 Added spellcheck utility to documentation build 
Uses the sphinxcontrib-spelling extension and requires PyEnchant and
aspell-en to be installed.

Adds the optional make target 'spelling' which produces the file
spelling/output.txt. It contains all words it detects.

Due to the large number of false positives, words in
utils/sphinx-config/false_positives.txt are ignored.
 2017-03-05 21:23:41 -05:00
Richard Berger 084d831bce Second batch of spelling fixes in manual 2017-03-05 21:02:51 -05:00
Richard Berger fd78486086 First batch of spelling fixes in manual 2017-03-05 18:27:38 -05:00
Jaap Kroes 8a0e44db83 updated documentation and ev_tally 2017-03-01 16:13:44 +01:00
Axel Kohlmeyer 3ac74a1d69 update lammps.book file for latest doc changes 2017-02-28 11:21:18 -05:00
Axel Kohlmeyer 3605208a45 add a few more missing details for integrating pair style kolmogorov/crespi/z 2017-02-28 11:16:27 -05:00
Axel Kohlmeyer 9b01949cac make the introduction of the command-by-category list less confusing 2017-02-28 11:05:40 -05:00
Jaap Kroes 323570c920 added jpg for kolmogorov-crespi-z equations and fixed hybrid/overlay check in source 2017-02-28 15:39:01 +01:00
Jaap Kroes a1b40b902d Added Kolmogorov-Crespi potential 2017-02-28 14:59:13 +01:00
Axel Kohlmeyer 2708c86836 fix typos: moleclue -> molecule 
this closes #386
 2017-02-27 18:03:18 -05:00
Oliver Henrich 458b6749e7 Corrected comment in 3' to 5' directionality check. 2017-02-22 20:03:41 +00:00
Axel Kohlmeyer 20a9ffe69d improve consistency and resolve dead links for USER-CGDNA related doc files 2017-02-21 21:27:34 -05:00
Steve Plimpton 49e83b4348 patch 21Feb17 sync with GHub 2017-02-21 16:07:26 -07:00
sjplimp b70c670aac Merge pull request #383 from stanmoore1/rshan_class2_kk 
Kokkos version of class2 bond, angle, dihedral, and improper from Ray Shan
 2017-02-21 15:52:10 -07:00
sjplimp 429264a12b Merge pull request #380 from hheenen/core_shell_documentation 
updated documentation and examples for coreshell
 2017-02-21 15:50:53 -07:00
Steve Plimpton 1cd4c48ccc new SNAP potential for W 2017-02-21 15:49:21 -07:00
Stan Moore ccaec315db Updating docs for Kokkos class2 2017-02-15 13:00:33 -07:00
Axel Kohlmeyer 0fb8dacc00 one more Finchham to Fincham change 2017-02-14 07:41:05 -05:00
Hendrik Heenen 6b923476b9 updated documentation and examples for coreshell 2017-02-14 13:14:22 +01:00
Steve Plimpton cb982f2f28 sync 13Feb17 patch back to GH 2017-02-13 09:05:03 -07:00
sjplimp 4843296d4e Merge pull request #372 from akohlmey/fft-cleanup 
simplify FFT3d code by removing support for outdated FFT libraries
 2017-02-13 08:53:13 -07:00
Steve Plimpton 2bdda8f6c0 patch 12Feb17 - change int to tagint for compute group/group 2017-02-13 08:40:54 -07:00
Steve Plimpton 0068ef5616 added molecule option to compute group/group command 2017-02-10 09:25:32 -07:00
Oliver Henrich 0efd209480 Merge branch 'master' into user-cgdna 2017-02-09 11:50:03 +00:00
Axel Kohlmeyer 8c074a363a Merge branch 'master' into small-updates-and-fixes 2017-02-08 14:32:44 -05:00
Axel Kohlmeyer 191453e1c7 Merge branch 'master' into fft-cleanup 2017-02-03 16:53:10 -05:00
Axel Kohlmeyer 6595fde0a1 explain in more detail the handling of error checking for numerical inputs 2017-02-02 11:58:12 -05:00
Axel Kohlmeyer 9d1991bf84 remove support for obsolete legacy FFT libraries and point -DFFT_FFTW to FFTW3 2017-02-02 08:10:23 -05:00
Stefan Paquay 0a87b7443a Updated contributing authors and docs 2017-02-02 13:42:47 +01:00
Oliver Henrich ed0a347fbf Merge branch 'master' into user-cgdna 2017-01-30 10:31:50 +00:00
Steve Plimpton f8506fee23 sync GHub with SVN 2017-01-26 14:06:43 -07:00
Oliver Henrich 149f37e764 Corrected reference to Fig.1 2017-01-26 19:08:59 +00:00
Steve Plimpton caea8973a3 add neighbor list kind output to screen 2017-01-20 13:24:09 -07:00
Steve Plimpton 9a299875da simplified neighbor list copying to avoid possible same-timestep re-build issues 2017-01-19 17:01:15 -07:00
sjplimp 3af4b3c28c Merge pull request #337 from ohenrich/user-cgdna 
Added source code and documentation for USER-CGDNA
 2017-01-18 11:31:35 -07:00
Steve Plimpton d2fc88a626 patch 17Jan17 2017-01-17 10:14:53 -07:00
sjplimp c19d2011bb Merge pull request #334 from sstrong99/flow_gauss_changeRef 
Updated the reference for the flow/gauss method
 2017-01-17 09:12:22 -07:00
sjplimp 973bef4d45 Merge pull request #332 from akohlmey/coord-atom-orientorder-atom-enhancements 
Coord atom orientorder atom enhancements
 2017-01-17 09:11:45 -07:00
sjplimp 252e07e083 Merge pull request #330 from akohlmey/collected-small-bugfixes 
Collected small bugfixes
 2017-01-17 09:08:00 -07:00
sjplimp d8bc590aaf Merge pull request #327 from stanmoore1/kokkos_lib_update 
Updating Kokkos lib
 2017-01-17 09:04:12 -07:00
sjplimp c9bea60710 Merge pull request #326 from Pakketeretet2/github-tutorial-update 
Updated images of succesful merge.
 2017-01-17 09:03:46 -07:00
Steve Plimpton 5cd856c97f fix spring doc page update 2017-01-17 09:02:56 -07:00
Axel Kohlmeyer 98ceb6feb1 add missing html files to lammps.book 2017-01-13 18:11:23 -05:00
Axel Kohlmeyer 374abea0f0 some minor documentation integration tweaks for USER-CGDNA package 2017-01-13 18:09:45 -05:00
Oliver Henrich 96259ea2d2 Added source code and documentation for USER-CGDNA 2017-01-13 13:36:54 +00:00
Steven Strong 1229f6f60b Updated the reference for the flow/gauss method, the new reference is much more comprehensive 2017-01-12 10:15:18 -07:00
Axel Kohlmeyer 6950a99162 Revert "remove obsolete warning about fix rigid image flag restrictions" 
This reverts commit 51e52b477a.
 2017-01-11 19:49:58 -05:00
Axel Kohlmeyer 1d0e600ab7 formatting improvements and small corrections for timer settings and output discussions 2017-01-10 23:47:14 -05:00
Axel Kohlmeyer 95706ac846 import contributed code for computes coord/atom and orientorder/atom 2017-01-10 12:29:22 -05:00
Axel Kohlmeyer 0db2a07993 another workaround for duplicate labels (which sphinx does not like) 2017-01-09 17:51:19 -05:00
Axel Kohlmeyer 33412c76ed correct some formatting issues with USER-NC-DUMP 2017-01-09 17:50:49 -05:00
Axel Kohlmeyer e5ac49d1de Merge branch 'master' into collected-small-bugfixes 2017-01-09 17:13:46 -05:00
Steve Plimpton c31f1e9f22 add fix mscg command, example, lib 2017-01-09 13:36:40 -07:00
Stan Moore ebd25cc078 Updating docs for Kokkos package 2017-01-09 12:40:33 -07:00
Stefan Paquay 20f8a8c219 Merge branch 'master' into github-tutorial-update 2017-01-09 14:38:09 +01:00
Axel Kohlmeyer 51e52b477a remove obsolete warning about fix rigid image flag restrictions 2017-01-06 21:30:33 -05:00
Axel Kohlmeyer 20a4e365b7 reduce warning when processing manual with sphinx 2017-01-06 21:30:13 -05:00
Steve Plimpton 51fa33a407 patch 6Jan17 2017-01-06 11:14:48 -07:00
Stefan Paquay ccd09e3967 Updated images of succesful merge. 2017-01-06 19:04:26 +01:00
Steve Plimpton 142770cb2a enable pppm/tip4p to work with triclinic 2017-01-06 10:38:32 -07:00
sjplimp 3ac58452de Merge pull request #310 from EfremBraun/master 
Fix nvk implemented
 2017-01-06 10:02:22 -07:00
sjplimp 9b348d567b Merge pull request #315 from Pakketeretet2/github-tutorial-update 
GitHub tutorial update
 2017-01-06 10:01:57 -07:00
sjplimp 41a6a3076e Merge pull request #309 from giacomofiorin/colvars-2016-12-22 
Update Colvars library to version 2016-12-22
 2017-01-06 09:58:20 -07:00
Axel Kohlmeyer 6af56e686d polish the introduction, some more clarifications, corrections and formatting improvements 2017-01-06 08:31:02 -05:00
Stefan Paquay eb1c6a225c typo fixed 2017-01-06 11:54:30 +01:00
Stefan Paquay 4d0a6d83bd Merged Axel's suggestions and updated text 2017-01-06 11:51:42 +01:00
Stefan Paquay 958722573f Merge branch 'github-tutorial-update' of https://github.com/Pakketeretet2/lammps into github-tutorial-update 2017-01-06 11:44:16 +01:00
Stefan Paquay 9d46670972 Updated text and images on reverse pull requests 2017-01-06 11:44:14 +01:00
Stefan Paquay 1a9f2df3d0 Updated text and images on reverse pull requests 2017-01-06 11:44:00 +01:00
Axel Kohlmeyer fe14158c10 some formatting updates and text rewrites in the "do not use git add -a" section 2017-01-04 13:13:56 -05:00
Stefan Paquay 0bcbcca140 Highlighted the assignee, maintainer changes, and mentioned LAMMPS collaborator 2017-01-04 17:28:22 +01:00
Stefan Paquay 933b288ce9 Added explaination for assignee, changes pushed by others and collaborator. 2017-01-04 14:31:23 +01:00
Richard Berger 4f45d39ac7 Add warning formatting 
Any paragraph starting with IMPORTANT NOTE: is transformed into a warning.
 2017-01-03 02:34:11 +01:00
Axel Kohlmeyer 7d057d4c83 make it more explicit, that master needs to be updated and feature branches should be created from master 2017-01-02 13:02:48 -05:00
Stefan Paquay 4f096dbad5 Updated some inconsistent text. 2017-01-02 18:53:28 +01:00
Stefan Paquay 18b12efc9f Small changes to tutorial text. 2017-01-02 18:25:36 +01:00
Stefan Paquay 2c7fea1e0d Second update round to text and images, a third will follow after succesful merge. 2017-01-02 18:15:08 +01:00
Stefan Paquay 4d98bbdfa5 Almost done with the tutorial now 2017-01-02 18:08:14 +01:00
Stefan Paquay 391ab761a4 Finally updated the github tutorial. 2017-01-02 17:55:02 +01:00
Efrem Braun aa146e9b38 Moved fix_nvk to USER-MISC, updated documentation to reflect move 2016-12-28 19:06:35 +01:00
Efrem Braun 68814d4fc8 Made documentation changes to fix nvk 2016-12-28 16:26:05 +01:00
Efrem Braun 616ca1de03 Fix nvk implemented. 2016-12-28 16:17:07 +01:00
Giacomo Fiorin 925f42727f Fix typo 2016-12-27 14:26:43 -05:00
Giacomo Fiorin f553e230db Update Colvars library to version 2016-12-22 
Significant code cleanup and several fixes (walls + extended Lagrangian)

New harmonicWalls bias to apply confining boundaries with time-dependent force
constant & integration
 2016-12-27 13:17:34 -05:00
Tim Mattox 781daad2a0 USER-DPD: update documentation for changes in commit 3faa57 2016-12-22 17:31:17 -05:00
Steve Plimpton 62dea1bb63 21Dec16 patch 2016-12-21 09:53:32 -07:00
Steve Plimpton 81a2db8a0c 17Dec16 patch 2016-12-16 11:36:54 -07:00
Steve Plimpton 3027ac9250 patch 16Dec16 2016-12-16 10:30:57 -07:00
Steve Plimpton e364b80724 added length keyword to python command 2016-12-16 10:24:25 -07:00
Steve Plimpton f509f133af patch 13Dec16: neighbor refactor, Stan pppm/disp bug fix, M Brown INTEL package updates 2016-12-13 17:14:28 -07:00
sjplimp f3b355bcbe Merge pull request #298 from akohlmey/collected-small-fixes 
Collected small fixes
 2016-12-13 16:23:23 -07:00
Steve Plimpton ae5764beac added functionity to lib interface 2016-12-13 16:22:17 -07:00
Axel Kohlmeyer ddf678da51 make fix gcmc command overview consistent 
this closes #296
 2016-12-09 14:30:27 -05:00
Efrem Braun d3d5ac17bf Fixed small typos in doc 2016-12-07 19:37:51 -08:00
Steve Plimpton fb3f597f41 30Nov16 patch 2016-11-30 14:04:41 -07:00
sjplimp d14814ae2e Merge pull request #289 from akohlmey/collected-updates-and-bugfixes 
Collected updates and bugfixes
 2016-11-30 14:02:41 -07:00
Steve Plimpton beb5a30f67 new compute global/atom command, also bug fix for descending dump sorts 2016-11-30 14:01:27 -07:00
Axel Kohlmeyer 42d430168b fix typo in compute cluster/atom docs 
this closes #292
 2016-11-29 07:24:09 -05:00
Axel Kohlmeyer 02ae2d218a correct broken link to USER-SMD docs PDF 2016-11-28 11:34:22 -05:00
Axel Kohlmeyer 87781771ba fix typo and USER-OMP support omission 2016-11-23 09:02:32 -05:00
Steve Plimpton 59d100ab57 final prep for 22Nov patch 2016-11-22 09:23:02 -07:00
sjplimp b6f2f0e6e9 Merge pull request #287 from rbberger/pylammps/docs 
Created PyLammps documentation
 2016-11-22 08:50:29 -07:00
sjplimp ff0441ac16 Merge pull request #286 from akohlmey/small-fixes-and-updates 
Collected small fixes and updates
 2016-11-22 08:49:46 -07:00
sjplimp 41907d3110 Merge pull request #285 from akohlmey/fix-ipi-update 
update for fix ipi from michele ceriotti
 2016-11-22 08:48:27 -07:00
Steve Plimpton b95f255af4 small changes to temper/grem commands 2016-11-22 08:47:44 -07:00
Michele Ceriotti 87a5a35bad A tiny bugfix for the reset flag, and a brief explanation of the changes 2016-11-20 00:44:23 +01:00
Axel Kohlmeyer 230b29eae6 correct accelerator flags for dpd styles in pair style overview 2016-11-19 11:47:12 -05:00
Richard Berger 2383c31f15 Created PyLammps documentation 
Based on material presented during MD Workshop at Temple University in
August 2016.
 2016-11-18 23:58:57 -07:00
Axel Kohlmeyer d787afcca9 also remove generated html files with 'make clean' in docs folder 2016-11-18 15:37:49 -05:00
Axel Kohlmeyer 176cde8ed3 minor cleanups 2016-11-18 15:36:38 -05:00
Axel Kohlmeyer 2862c20815 Merge branch 'master' into grem-feature 2016-11-18 14:51:46 -05:00
Axel Kohlmeyer 78e018829f Merge branch 'grem-feature' of https://github.com/dstelter92/lammps into grem-feature 2016-11-18 14:48:47 -05:00
Steve Plimpton 4b51719e67 new 17Nov16 patch and stable 2016-11-17 16:51:35 -07:00
Steve Plimpton 25d7be5f3d compute pressure doc change 2016-11-17 16:11:30 -07:00
sjplimp 74c0e4dd5c Merge pull request #278 from akohlmey/pair-agni 
Implementation of the AGNI manybody potential
 2016-11-17 09:04:31 -07:00
sjplimp 073e8a0524 Merge pull request #276 from akohlmey/doc-updates 
Small bugfixes and updates
 2016-11-17 09:02:27 -07:00
sjplimp 2535e44991 Merge pull request #271 from akohlmey/tersoff-modc 
pair style tersoff/mod/c
 2016-11-17 09:00:52 -07:00
dstelter92 747c95c525 revised documentation, added temper_grem ref to fix_grem 2016-11-17 11:00:49 -05:00
Steve Plimpton 8756a1017d Kokkos updates by Stan 2016-11-17 08:58:22 -07:00
dstelter92 5c64934bc8 added documention, re-ran temper_grem example 2016-11-17 10:40:10 -05:00
Axel Kohlmeyer b45d1e37ef integrate fix grem docs and update to match current conventions 2016-11-16 16:46:00 -05:00
dstelter92 16c8a307e5 removed leftover tex files 2016-11-16 15:39:02 -05:00
dstelter92 94f14ab051 spell check, minor typos 2016-11-16 15:34:32 -05:00
dstelter92 4641c9e568 Added basic documentation for grem fix 2016-11-16 13:36:13 -05:00
Axel Kohlmeyer 57124b9b25 update documentation metadata files for recent changes 2016-11-12 09:18:21 -05:00
Axel Kohlmeyer 03b3834fe3 add documentation for pair style agni 2016-11-12 09:07:42 -05:00
Axel Kohlmeyer 1f38e1a771 Merge branch 'master' into doc-updates 2016-11-09 18:18:05 -05:00
Steve Plimpton 9806da69f3 Stan bug fixes for fix reaxc/bonds/kk 2016-11-09 15:47:50 -07:00
Axel Kohlmeyer c55fd502e0 correct typo in formula 2016-11-09 15:04:24 -05:00
Axel Kohlmeyer 71ee2ecaa1 integrate pair style tersoff/mod/c contributed by Ganga P Purja Pun (GMU) 
This includes docs, added testing and inclusion of USER-OMP support.
 2016-11-09 14:52:39 -05:00
sjplimp bfea3dce7d Merge pull request #268 from arielzn/born_dsf 
pair styles born/coul/dsf and born/coul/dsf/cs added
 2016-11-09 11:57:09 -07:00
Steve Plimpton 2c801320c2 fixed links in Section_intro.txt 2016-11-09 11:46:10 -07:00
Steve Plimpton a23b287a7a sync with SVN for creation of stable release 2016-11-08 09:05:50 -07:00
Steve Plimpton 31204aab6a sync with SVN 2016-11-08 08:57:51 -07:00
arielzn 25e7d074cf documentation added for born/coul/dsf and born/coul/dsf/cs styles 2016-11-08 16:51:54 +01:00
Axel Kohlmeyer 3a3d96b877 info styles also prints out pair styles 2016-11-04 18:18:40 -04:00
sjplimp 77bbf03f0f Merge pull request #252 from akohlmey/preinstalled-vs-scm 
remove the misleading "(which it is by default)" from several doc files
 2016-11-04 10:59:06 -06:00
sjplimp f0131393e0 Merge pull request #248 from akohlmey/collected-small-fixes 
collected small bugfixes and updates
 2016-11-04 10:58:42 -06:00
Steve Plimpton f48b71f46b added examples/threebody, fix reaxc/speceies/kk 2016-11-04 10:56:04 -06:00
Axel Kohlmeyer 6cc4eb19af remove the misleading "(which it is by default)" from several doc files 2016-11-04 12:20:17 -04:00
Axel Kohlmeyer 7fdd6e2807 remove work repetitions for 'the' 2016-11-01 11:40:07 -04:00
Axel Kohlmeyer 2e0d304c7e remove word repetitions for 'a' 2016-11-01 11:36:11 -04:00
Steve Plimpton d9891abdf4 new library functions 2016-10-27 09:34:04 -06:00
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
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
Axel Kohlmeyer c10aa55fc1 Merge branch 'integration' into doc-fixes 2016-09-22 09:19:45 -04:00
Steve Plimpton b3217218d6 doc page sync with SVN 2016-09-21 20:54:20 -06:00
Axel Kohlmeyer 2943dd5c12 correct another broken link in fix ti/spring 2016-09-20 19:02:13 -04:00
Axel Kohlmeyer 33d9a55d35 remove references to docs for fix ti/rs 2016-09-20 19:01:58 -04:00
Axel Kohlmeyer 5345efb5b8 correct broken link in updated fix ti/spring docs 2016-09-20 18:57:01 -04:00
Axel Kohlmeyer 9bedb8a1c9 ignore generated files in html folder 2016-09-20 18:54:51 -04:00
Axel Kohlmeyer 0d7e4f1e88 update docs for pair style gauss/cut to document optional per pair cutoff 2016-09-20 18:51:50 -04:00