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3837 Commits

Author SHA1 Message Date
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
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
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