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12201 Commits

Author SHA1 Message Date
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
Richard Berger 0262a54ecf Fix Python 3 compatibility by encoding strings passed as c_char_p 2017-03-15 22:00:43 -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
sjplimp f9468f46f5 Merge pull request #412 from timattox/master_typofix 
Correct a typo in the fix_halt.txt documentation.
 2017-03-15 13:10:58 -06:00
Tonnam Balankura ec1778b586 add pair_zhou 2017-03-15 11:10:04 -04:00
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
sjplimp 470353e320 Merge pull request #408 from giacomofiorin/colvars-update-2017-03-10 
Colvars update 2017-03-10
 2017-03-10 14:51:16 -07:00
sjplimp ffe02d20ca Merge pull request #406 from stanmoore1/kokkos_bugfix 
Fix Kokkos issues
 2017-03-10 14:51:04 -07:00
Giacomo Fiorin f70752c18f Include PDF of Colvars doc missing in previous commit 2017-03-10 15:58:35 -05:00
sjplimp 07fcfd6d54 Merge pull request #405 from stanmoore1/ev_setup_kk 
Add alloc flag to ev_setup
 2017-03-10 11:01:51 -07:00
sjplimp c97feafca6 Merge pull request #407 from frobnitzem/master 
Add error check to lammps_gather_atoms/lammps_scatter_atoms in library.cpp
 2017-03-10 11:00:30 -07:00
sjplimp b20d95d495 Merge pull request #402 from timattox/USER-DPD_spelling 
Fix spelling "correction" from 3a054d1a: iterations not interactions and imd_writen not imd_written
 2017-03-10 10:59:43 -07:00
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
David M. Rogers 65964f3b31 Add error check to lammps_gather_atoms/lammps_scatter_atoms in library.cpp 2017-03-09 16:49:07 -05:00
Stan Moore b28b84d444 Fix half from full nlist issue with Kokkos 2017-03-09 14:00:27 -07:00
Stan Moore a001a5ceb0 Fixing memory overflow issue in comm_kokkos 2017-03-09 12:20:49 -07:00
Axel Kohlmeyer 2ef713ea1b restore incorrect change due to spell checking in fix imd 2017-03-08 16:40:16 -05:00
Stan Moore 1f6c1942b3 Disable allocation of per-atom arrays in ev_setup for Kokkos styles 2017-03-08 12:42:44 -07:00
Stan Moore 683023d820 Adding alloc flag to ev_setup 2017-03-08 12:36:23 -07:00
Tim Mattox 42d3a8f498 Fix spelling "correction" from 3a054d1a: iterations not interactions. :-) 2017-03-07 15:41:06 -05:00
Steve Plimpton 79b005dc3d patch 7Mar17 2017-03-07 11:40:07 -07:00
sjplimp a2fa6ef452 Merge pull request #393 from akohlmey/small-bugfixes 
Small bugfixes
 2017-03-07 09:56:03 -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 c2aabdec22 Merge pull request #398 from stanmoore1/kokkos_changes 
Kokkos changes
 2017-03-07 09:46:54 -07:00
sjplimp e4aa735a68 Merge pull request #395 from timattox/USER-DPD_bugfix 
USER-DPD: a variety of small but important bugfixes
 2017-03-07 09:46:40 -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 0798885bdb Merge pull request #389 from akohlmey/update-agni-potential 
update AGNI potential for Al, reference runs and output and citation
 2017-03-07 09:35:31 -07:00
sjplimp 020e75e7ef Merge pull request #386 from akohlmey/doc-consistentcy 
improve consistency of manual
 2017-03-07 09:33:14 -07:00
sjplimp d6866f1cfd Merge pull request #376 from v0i0/airebo-bondorderLJ-fixes 
Fixes for PairAIREBO::bondorderLJ
 2017-03-07 09:32:30 -07:00