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12093 Commits

Author SHA1 Message Date
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 3ec16f3630 fully integrate support for doc_anchor_check into docs makefile 2017-03-22 14:40:30 -04:00
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
sjplimp 145e682ad3 Merge pull request #427 from akohlmey/small-updates-and-corrections 
Various updates and corrections for upcoming stable release
 2017-03-21 08:18:21 -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 82d952ae0e mention NumPy dependency instead of Numeric for python tools 2017-03-20 17:26:19 -04:00
Axel Kohlmeyer 47d6451d03 fix compilation for pymol_asphere tool 2017-03-20 17:18:24 -04:00
Axel Kohlmeyer e110d6961a remove obsolete tools and files 2017-03-20 17:17:35 -04:00
Axel Kohlmeyer a42b0b7dcb update colvars abf integrate tool from git repo 2017-03-20 17:04:16 -04:00
Axel Kohlmeyer 03828b5836 adapt binary2txt.cpp source to current coding conventions 2017-03-20 16:57:32 -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
Axel Kohlmeyer ecf17621aa more permission fixes 2017-03-20 16:25:06 -04:00
Axel Kohlmeyer f0c6ed004d remove xmovie 2017-03-20 16:24:38 -04:00
Axel Kohlmeyer 554531a302 update permissions 2017-03-20 13:51:36 -04:00
sjplimp d496c0fdfa Merge pull request #426 from dstelter92/master 
fix for temper_grem exchange probability
 2017-03-20 08:57:29 -06:00
dstelter92 5c39dfd740 re-ran example with fixed exchanges 2017-03-20 09:22:09 -04:00
dstelter92 5b842f0010 Teff and exchange bugfix, as per Greg Dignon to match python examples 2017-03-20 09:15:48 -04:00
Steve Plimpton 4a90bca7a3 patch 17Mar17 2017-03-17 11:29:23 -06:00
sjplimp 9f35b764f8 Merge pull request #424 from timattox/dpd_restart_fix 
Remove unneeded restart_peratom flags in USER-DPD package
 2017-03-17 11:19:04 -06:00
sjplimp 7ca5dce2f5 Merge pull request #423 from timattox/master_bugfix_irregular 
bugfix for irregular::create_atom and create_data
 2017-03-17 11:18:52 -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
sjplimp a936b7b2ab Merge pull request #419 from rbberger/python_fixes 
Library interface fixes, Python example fixes and better Python 3 compatibility
 2017-03-17 11:16:58 -06:00
sjplimp a91b851f3d Merge pull request #416 from lukin17/filter_corotate 
Added fix filter/corotate.
 2017-03-17 11:14:59 -06:00
Stan Moore d31c591b60 Remove unneeded restart_peratom flags 2017-03-17 09:40:39 -06:00
Axel Kohlmeyer ae5ebf6001 add support for MPI_Request_free() to MPI STUBS library 2017-03-17 11:40:09 -04:00
Axel Kohlmeyer 7fb741d53d Revert "In irregular.cpp use simpler and slightly faster MPI_Reduce_scatter_block()" 
This reverts commit 8e75616c14.
 2017-03-17 11:35:59 -04:00
Tim Mattox 8e75616c14 In irregular.cpp use simpler and slightly faster MPI_Reduce_scatter_block() 2017-03-17 03:02:42 -04:00
Tim Mattox 411c069ba6 BUGFIX: Prevent possible deadlock in Irregular::create_atom and create_data 2017-03-17 03:02:19 -04:00
Axel Kohlmeyer ac82d041cc ignore package pair style 2017-03-16 23:12:49 -04:00
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 bed288339e simplify and shorten examples for fix filter/corotate and combine into a single folder 2017-03-16 15:02:50 -04:00
Axel Kohlmeyer 1995f434f3 fix some more code formatting issues, add newline at EOF 2017-03-16 14:24:28 -04:00
Axel Kohlmeyer db0281b4df Merge branch 'filter_corotate' of https://github.com/lukin17/lammps into pull-416 2017-03-16 12:14:09 -04:00
lukin17 2f5e711acd Merge remote-tracking branch 'upstream/master' into filter_corotate 2017-03-16 10:00:12 +01:00
lukin17 bdb7669e27 Fixed coding style. 2017-03-16 09:44:07 +01:00
Richard Berger cda8213892 Added Python matplotlib plot example 2017-03-16 01:41:28 -04:00
Richard Berger ef940d226c Improve Python 3 compatibility of pizza tools and simplify read_snapshot code 2017-03-16 01:38:05 -04:00
Richard Berger 36da9223ec Fix dump cfg in vizplotgui_atomeye.py example 2017-03-15 22:55:51 -04:00