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12089 Commits

Author SHA1 Message Date
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
Richard Berger eb29ef32b1 Fix space/tab error in pizza/gl.py 2017-03-15 22:43:00 -04:00
Richard Berger 29550d472d Fix dump cfg in viz_atomeye.py example 2017-03-15 22:31:14 -04:00
Richard Berger 79cae51156 Document property 'uses_exceptions' of Python interface 2017-03-15 22:20:30 -04:00
Richard Berger a210867025 Fixes lammps_create_atoms library function and its Python interface variant 
The interface of that function has changed and includes two additional
parameters, which haven't been added to the Python interface either.
This showed up by trying to run the simple.py example.
 2017-03-15 22:13:06 -04:00