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12193 Commits

Author SHA1 Message Date
Richard Berger 2d8bce78a6 Refactor PYTHON package and wrapper classes 2017-04-11 21:22:30 -04:00
Richard Berger 9a027a01da Add Python 3 compatibility to PYTHON package 2017-04-11 20:24:42 -04:00
Steve Plimpton 4da8c1c4e2 patch 11Apr17 2017-04-11 09:00:37 -06:00
Steve Plimpton 49dd9449b8 fix gcmc updates from Aidan, trimming of output for replica commands 2017-04-11 08:35:09 -06:00
sjplimp 76fd936972 Merge pull request #443 from Pakketeretet2/user-manifold-fix-every-keyword 
User manifold fix every keyword
 2017-04-11 08:27:53 -06:00
sjplimp 06cebb9fb4 Merge pull request #445 from Pakketeretet2/extract_for_bond 
Extract for bond
 2017-04-11 08:27:31 -06:00
sjplimp b9d844ca8d Merge pull request #444 from ohenrich/user-cgdna 
Minor updates to docu of USER-CGDNA package
 2017-04-11 08:25:09 -06:00
sjplimp ccc9367de7 Merge pull request #442 from akohlmey/small-updates-and-bugfixes 
collected small updates and bugfixes
 2017-04-11 08:24:32 -06:00
sjplimp 4c4a3fe5d1 Merge pull request #439 from rbberger/python_mixed_use_support 
Support mixed Python use by honoring Python GIL
 2017-04-11 08:24:06 -06:00
Axel Kohlmeyer 84ea8a79e6 correct link for dispersion parameter how-to and reformat 2017-04-10 20:43:24 -04:00
Stefan Paquay f19f558220 Removed changed bond_harmonic from wrong position. 2017-04-10 10:06:03 -04:00
Stefan Paquay 1ad7d856fe Added forgotten #include string to bond_harmonic.cpp 2017-04-10 09:57:54 -04:00
Axel Kohlmeyer d6357420ae propagate global package installation bugfix to explicit package scripts 2017-04-07 15:29:56 -04:00
Axel Kohlmeyer 62b9fa22b8 when computing only rotational temperature, we must not subtract the default n-dim extra DOFs 2017-04-07 15:11:26 -04:00
Axel Kohlmeyer 1725832b6c address issue where uninstalling an empty package will erase all code in src 2017-04-06 11:08:57 -04:00
Stefan Paquay 874944f2ec Made fix adapt support bond harmonic. 2017-04-04 19:37:17 -04:00
Oliver Henrich 497a5d88af Merge branch 'master' into user-cgdna 2017-04-04 20:03:57 +01:00
Oliver Henrich 8993daaa31 Minor update to docu 2017-04-04 19:54:22 +01:00
Axel Kohlmeyer e190eb15f5 remove debug printf 2017-04-04 17:54:33 +00:00
Stefan Paquay b6bc33bac6 Merge branch 'user_manifold_fix' into user-manifold-fix-every-keyword 2017-04-04 13:31:22 -04:00
Stefan Paquay 03a6f5237f Made every keyword for user-manifold work as advertised. 2017-04-04 13:30:49 -04:00
Stefan Paquay 28e86917a0 Made fix adapt work with bond_harmonic. 2017-04-04 12:35:26 -04:00
Axel Kohlmeyer 6f1bbd3cec protect fix ave/histo from segfaulting on non-existing computes, fixes or variables 2017-04-03 18:08:15 -04:00
Steve Plimpton ae56b9ad89 patch 31Mar17 for stable release 2017-03-30 10:07:27 -06:00
sjplimp 4466d9fb4a Merge pull request #440 from ohenrich/user-cgdna 
Updated lammps.book, USER-CGDNA install script
 2017-03-30 09:34:35 -06:00
Oliver Henrich ac1aa9edea Updated README 2017-03-29 11:18:04 +01:00
Oliver Henrich c733204a70 Updated lammps.book and install script 2017-03-29 08:28:03 +01:00
Richard Berger 1544b51dcb Support mixed Python use by honoring Python GIL 
This enables support to both drive LAMMPS with a Python interpreter and
evaluating Python expressions inside of LAMMPS using that same interpreter.
Previously this has been avoided through an error message because the
binding code did not ensure that the necessary GIL (global interpreter lock)
structures exist (see issue #438).

All code paths which call Python C API functions must first acquire the
GIL through a call PyGILState_Ensure and release it with PyGILState_Release.
 2017-03-29 01:49:15 -04:00
Steve Plimpton 4b9d0a9566 sync with SVN 2017-03-28 13:26:12 -06:00
Steve Plimpton 0637f23875 patch 28Mar17 2017-03-28 13:12:23 -06:00
sjplimp 9f6e126a2f Merge pull request #437 from ohenrich/user-cgdna 
User cgdna
 2017-03-28 12:52:26 -06:00
sjplimp 645f56cf70 Merge pull request #436 from Pakketeretet2/better_incorrect_input_handling_nh 
Changed the check on initial and final temperature to <= 0 for both.
 2017-03-28 12:51:17 -06:00
sjplimp 80e5111dca Merge pull request #434 from akohlmey/imgflags-in-library 
improved image flag handling in library interface
 2017-03-28 12:50:13 -06:00
sjplimp 7e9f05b617 Merge pull request #433 from akohlmey/fixes-for-stable 
More small fixes for stable release
 2017-03-28 12:49:09 -06:00
Axel Kohlmeyer 1d8f0c762d Merge branch 'master' into fixes-for-stable 2017-03-28 14:37:30 -04:00
Axel Kohlmeyer ef6070cbde remove executable permissions for potential files 2017-03-28 14:35:58 -04:00
Steve Plimpton 61f3ff1d2b Merge branch 'master' of github.com:lammps/lammps 2017-03-28 12:35:33 -06:00
Steve Plimpton 111d350a22 fix gcmc units change for chemical potential 2017-03-28 12:34:46 -06:00
sjplimp 1dfd61f532 Merge pull request #432 from Pakketeretet2/user_manifold_fix 
Fixed a bug with equal-style variables as manifold params.
 2017-03-28 12:33:45 -06:00
Oliver Henrich 5c1f5462e7 Removed contribution line from header files 2017-03-28 19:08:24 +01:00
Oliver Henrich 66a6375405 Resolved merge conflict 2017-03-28 18:58:31 +01:00
Oliver Henrich 604afebf6f Update to oxDNA2 2017-03-28 18:22:02 +01:00
Oliver Henrich 8afed61db1 Upgrade to oxDNA2 2017-03-28 18:16:36 +01:00
Stefan Paquay ee55a98103 Changed the check on initial and final temperature to <= 0 for both. 2017-03-28 11:22:10 -04:00
Axel Kohlmeyer f8da9a866a synchronize dump custom/vtk documentation with that of dump custom 2017-03-28 11:00:22 -04:00
Axel Kohlmeyer 28bdebd3c0 avoid segfault when calling PPPM*::memory_usage() before grid communication is initialized 2017-03-28 07:50:48 -04:00
Axel Kohlmeyer fc51c38abb add some docs for the special treatment of image flags 2017-03-28 02:22:45 -04:00
Axel Kohlmeyer 443ea13eff add image flag packing/unpacking to library/python interface 2017-03-28 02:05:05 -04:00
Axel Kohlmeyer 5feeb79c13 one more line of dead code removed 2017-03-27 15:16:28 -04:00
Axel Kohlmeyer a241b2d0f7 fix problems with references 2017-03-27 15:01:32 -04:00