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3822 Commits

Author SHA1 Message Date
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
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
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