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Author SHA1 Message Date
DallasTrinkle 8bddf105bf Updated version of equations, documentation. 2017-04-28 20:22:22 -05:00
DallasTrinkle 31446e35b9 Cleanup on equations; JPG to be constructed. 2017-04-28 15:31:49 -05:00
DallasTrinkle 9bdc43bb66 Updates to pair/meam/spline documentation. 2017-04-28 15:15:21 -05:00
DallasTrinkle a0b61d17b5 Updates to documentation: equation. 2017-04-28 15:08:59 -05:00
Axel Kohlmeyer af74874516 rename references to USER-CG-CMM to USER-CGSDK 2017-04-26 19:27:13 -04:00
Axel Kohlmeyer 8f9cb3590a correct units for some improper force constants in docs 2017-04-26 15:34:12 -04:00
Axel Kohlmeyer ddc1e4e86e detect and refuse to run pair style srp together with fix rigid 2017-04-25 13:27:20 -04:00
Axel Kohlmeyer 396e0b5423 correct broken link in html bond doc overview 2017-04-21 14:02:17 -04:00
Axel Kohlmeyer 4e411364ff add support to pair_modify to selectively disable compute/tally callbacks in sub-styles for pair hybrid and hybrid/overlay 2017-04-21 14:01:38 -04:00
Axel Kohlmeyer dfa9815246 update for fix gle docs from michele ceriotti 2017-04-18 17:07:28 -04:00
Axel Kohlmeyer 481927ff16 correct 'thrid' instead of 'third' 2017-04-17 17:49:49 -04:00
Axel Kohlmeyer dd90c860ee refactor msi2lmp documentation to emphasize lack of active development 
- put a note into the manual
- reorder contents of the README file
- request for information should be sent to lammps-users
- add list of known missing features
 2017-04-17 17:40:21 -04:00
Axel Kohlmeyer c9bc141335 remove doc text explaining restrictions that are lifted with the changes in this branch 2017-04-14 12:57:35 -04:00
Steve Plimpton 2f32fb7f8b patch 13Apr17 2017-04-13 11:19:48 -06:00
Steve Plimpton 4da8c1c4e2 patch 11Apr17 2017-04-11 09:00:37 -06:00
Steve Plimpton 49dd9449b8 fix gcmc updates from Aidan, trimming of output for replica commands 2017-04-11 08:35:09 -06:00
sjplimp 06cebb9fb4 Merge pull request #445 from Pakketeretet2/extract_for_bond 
Extract for bond
 2017-04-11 08:27:31 -06:00
sjplimp b9d844ca8d Merge pull request #444 from ohenrich/user-cgdna 
Minor updates to docu of USER-CGDNA package
 2017-04-11 08:25:09 -06:00
Axel Kohlmeyer 84ea8a79e6 correct link for dispersion parameter how-to and reformat 2017-04-10 20:43:24 -04:00
Oliver Henrich 497a5d88af Merge branch 'master' into user-cgdna 2017-04-04 20:03:57 +01:00
Oliver Henrich 8993daaa31 Minor update to docu 2017-04-04 19:54:22 +01:00
Stefan Paquay 28e86917a0 Made fix adapt work with bond_harmonic. 2017-04-04 12:35:26 -04:00
Steve Plimpton ae56b9ad89 patch 31Mar17 for stable release 2017-03-30 10:07:27 -06:00
Oliver Henrich c733204a70 Updated lammps.book and install script 2017-03-29 08:28:03 +01:00
Steve Plimpton 4b9d0a9566 sync with SVN 2017-03-28 13:26:12 -06:00
Steve Plimpton 0637f23875 patch 28Mar17 2017-03-28 13:12:23 -06:00
sjplimp 9f6e126a2f Merge pull request #437 from ohenrich/user-cgdna 
User cgdna
 2017-03-28 12:52:26 -06:00
sjplimp 80e5111dca Merge pull request #434 from akohlmey/imgflags-in-library 
improved image flag handling in library interface
 2017-03-28 12:50:13 -06:00
Axel Kohlmeyer 1d8f0c762d Merge branch 'master' into fixes-for-stable 2017-03-28 14:37:30 -04:00
Steve Plimpton 111d350a22 fix gcmc units change for chemical potential 2017-03-28 12:34:46 -06:00
Oliver Henrich 66a6375405 Resolved merge conflict 2017-03-28 18:58:31 +01:00
Oliver Henrich 604afebf6f Update to oxDNA2 2017-03-28 18:22:02 +01:00
Oliver Henrich 8afed61db1 Upgrade to oxDNA2 2017-03-28 18:16:36 +01:00
Axel Kohlmeyer f8da9a866a synchronize dump custom/vtk documentation with that of dump custom 2017-03-28 11:00:22 -04:00
Axel Kohlmeyer fc51c38abb add some docs for the special treatment of image flags 2017-03-28 02:22:45 -04:00
Axel Kohlmeyer a241b2d0f7 fix problems with references 2017-03-27 15:01:32 -04:00
Axel Kohlmeyer 61e7595a94 remove references to xmovie, streamline dump and viz descriptions 2017-03-27 14:59:58 -04:00
Steve Plimpton 3dfe4505dd 24Mar17 patch sync with SVN 2017-03-24 15:17:51 -06:00
Steve Plimpton 394e9b42b0 new CHARMM pair styles with force swithing/shifting 2017-03-24 13:53:07 -06:00
sjplimp f5a85d68ad Merge pull request #429 from akohlmey/updates-for-stable 
Collected updates for stable release
 2017-03-24 10:01:23 -06:00
sjplimp 277b93cb89 Merge pull request #417 from tonnamb/add-pair-zhou 
add new pair potential for metal-organic interactions - pair style momb
 2017-03-24 09:41:30 -06:00
Axel Kohlmeyer 8820315ff9 Merge branch 'master' into updates-for-stable 2017-03-23 17:57:02 -04:00
Steve Plimpton 44841f6891 fix ave/chunk fixes, 2d disc option, fix_modify dynamic/dof 2017-03-23 15:31:27 -06:00
Axel Kohlmeyer 2cdcd6d630 remove one more reference to xmovie 2017-03-23 16:03:25 -04:00
Axel Kohlmeyer b88a749680 rename a couple more references to pair style zhou into momb 2017-03-23 11:38:33 -04:00
Tonnam Balankura 6d395ec511 change name zhou to momb in docs, fix grammar 2017-03-23 10:08:47 -04:00
Tonnam Balankura bf560e78f3 edit description and add related commands and default 2017-03-22 16:56:40 -04:00
Axel Kohlmeyer 1db5834b99 Revert "Cleanup of a few more references to obsoleted and removed tools like xmovie" 
This reverts commit 127597023d.
 2017-03-22 15:12:49 -04:00
Axel Kohlmeyer 3070b043be Revert "correct inconsistent anchors" 
This reverts commit a14d58259c.
 2017-03-22 15:12:47 -04:00
Axel Kohlmeyer ef3f323fc4 Revert "remove reference to removed section on VMD scripts" 
This reverts commit 66eb9c2486.
 2017-03-22 15:12:43 -04:00
Axel Kohlmeyer 43a304f564 remove reference to removed section on VMD scripts 2017-03-22 15:12:09 -04:00
Axel Kohlmeyer a79aef65e8 correct inconsistent anchors 2017-03-22 15:12:09 -04:00
Axel Kohlmeyer 66eb9c2486 remove reference to removed section on VMD scripts 2017-03-22 15:01:11 -04:00
Axel Kohlmeyer a14d58259c correct inconsistent anchors 2017-03-22 15:00:57 -04:00
Axel Kohlmeyer 127597023d Cleanup of a few more references to obsoleted and removed tools like xmovie 2017-03-22 14:57:37 -04:00
Axel Kohlmeyer 3ec16f3630 fully integrate support for doc_anchor_check into docs makefile 2017-03-22 14:40:30 -04:00
Axel Kohlmeyer cb9059652d a few more small changes to integrate pair style zhou properly 2017-03-22 14:39:46 -04:00
Axel Kohlmeyer 43f27250b5 Merge branch 'add-pair-zhou' of https://github.com/tonnamb/lammps into pull-417 2017-03-22 14:05:16 -04:00
Tonnam Balankura c5d561a312 pair_zhou docs: add equation, add link in section_commands and pairs 2017-03-22 12:00:32 -04:00
Oliver Henrich 7435084375 Verified oxDNA with modified nucleotide layout 2017-03-22 15:59:10 +00:00
Axel Kohlmeyer 734e639c5d correct typo reported on lammps-users 2017-03-21 14:12:00 -04:00
Steve Plimpton dcede304df changes for next patch, 2d disc options for spheres, fix external upgrade, bug fixes for fix ave/chunk for density calcs, Aidan doc page citation deconvolution 2017-03-21 08:56:37 -06:00
Axel Kohlmeyer 6482df6c2f remove references to deleted tools. update/clarify section on restart2data 2017-03-20 18:57:30 -04:00
Axel Kohlmeyer 0c9cd11b4e have the relevant LAMMPS version embedded into top part of the html manual 2017-03-20 18:25:11 -04:00
Axel Kohlmeyer 3b44c3ff1d remove non-ASCII characters from doc source files 2017-03-20 16:55:14 -04:00
Axel Kohlmeyer 0d0c2b65f7 correct stan's email address 2017-03-20 16:32:16 -04:00
Axel Kohlmeyer 2218a9d704 emphasize that the online manual is following the latest development version 2017-03-20 16:32:04 -04:00
Axel Kohlmeyer 0a6b33cd78 remove duplicate paragraph in nose-hoover fix docs 2017-03-20 16:27:00 -04:00
Tonnam Balankura 52987a3615 Started writing pair_zhou.txt 2017-03-18 22:32:39 -04:00
Steve Plimpton 4a90bca7a3 patch 17Mar17 2017-03-17 11:29:23 -06:00
sjplimp fcc3b3bd36 Merge pull request #421 from akohlmey/memory-output 
improve memory usage reporting in info and output class
 2017-03-17 11:18:08 -06:00
sjplimp 53a3877c3d Merge pull request #420 from rbberger/doc_anchor_check 
Add utility to detect duplicate anchors in docs
 2017-03-17 11:17:28 -06:00
Richard Berger 621d7d5ce0 Correct off-by-one error in line number reported 2017-03-16 23:05:03 -04:00
Richard Berger 1bb9c7da42 Remove some duplicate anchors in documentation 2017-03-16 22:36:13 -04:00
Richard Berger f893104b18 Add anchor_check to doc Makefile 2017-03-16 22:21:55 -04:00
Richard Berger efb2a942e0 Add utility to detect duplicate anchors in documentation files 2017-03-16 22:21:12 -04:00
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