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12290 Commits

Author SHA1 Message Date
Steve Plimpton 7c3b8e014c rename some USER/misc dirs 2017-05-11 10:15:28 -06:00
sjplimp a069d21621 Merge pull request #476 from akohlmey/dump_custom_bugfix 
dump custom memory allocation bugfix
 2017-05-11 09:27:08 -06:00
sjplimp d7f54464c6 Merge pull request #474 from rbberger/dump_vtk_fixes 
Various dump vtk fixes
 2017-05-11 09:25:42 -06:00
sjplimp 998eb44e83 Merge pull request #473 from akohlmey/compress-for-reaxc-fixes 
compressed output via gzip for some ReaxFF fixes
 2017-05-11 09:25:18 -06:00
sjplimp 96d1de8575 Merge pull request #471 from akohlmey/fix-4may2017-issues 
Fix a bunch of remaining issues in the 4 may 2017 release
 2017-05-11 09:24:35 -06:00
sjplimp deff6ffaac Merge pull request #466 from DallasTrinkle/meam-spline-multicomponent 
Meam spline multicomponent
 2017-05-11 09:22:25 -06:00
Axel Kohlmeyer 328ef873d8 fix mixed memory alloc bug in dump custom. this closes #475 2017-05-10 22:41:41 -04:00
Richard Berger 4ecf876a64 Added two examples of using the VTK dump style 2017-05-10 19:52:00 -04:00
Richard Berger c4ac5773cb Fix segmentation fault in dump vtk 2017-05-10 19:51:14 -04:00
Richard Berger cac1bf83ef Work around VTK 7 API change 2017-05-10 19:41:48 -04:00
Axel Kohlmeyer abeb1e096a add support for gzip compressed output to fix reax/bonds, reax/c/bonds and reax/c/species 2017-05-10 11:19:18 -04:00
Axel Kohlmeyer 9f7ce39f9f correct some more omitted updates 2017-05-09 18:14:34 -04:00
Axel Kohlmeyer 29ae8d4ca3 correct broken links and references in documentation 2017-05-09 17:15:07 -04:00
Axel Kohlmeyer 3f4aee1046 implement overlooked changes from 4may2017 patch 2017-05-09 15:57:35 -04:00
Axel Kohlmeyer d0da0639f0 add a couple of simple example single/multi-elment inputs for meam/spline pair styles 2017-05-09 15:51:59 -04:00
Axel Kohlmeyer 390ceb1475 whitespace cleanup 2017-05-09 15:49:37 -04:00
Axel Kohlmeyer 6c5edf6c70 performance improvement through avoiding function call and dereference overhead 
- make i_to_potl() and ij_to_potl() functions inline and const
- don't dereference inside the functions, but cache, if possible in external variables
=> up to 15% speedup.
 2017-05-09 15:38:10 -04:00
Axel Kohlmeyer 9cd994f57c fix issues with potential file parser 
- use Force::open_potential()
- replace ftell()/fseek() with rewind()/fgets() which is safer on windows and other platforms with automatic CR/LF to LF conversion on text files
- make parser use properly NULL terminated strings through using strtok()
 2017-05-09 15:35:48 -04:00
sjplimp a6e2d5b5f7 Merge pull request #470 from lammps/integration 
neighbor list bugfix to prevent cycle in copy lists
 2017-05-09 10:32:25 -06:00
Steve Plimpton 08ec55743e neighbor list bugfix to prevent cycle in copy lists 2017-05-09 08:55:18 -06:00
sjplimp c4f90b3841 Merge pull request #449 from rbberger/python_refactoring 
Add Python 3 compatibility and expand Python interface availability
 2017-05-08 08:29:24 -06:00
Richard Berger f8af7edf92 Merge remote-tracking branch 'upstream/master' into python_refactoring 2017-05-06 16:00:22 -04:00
Steve Plimpton a73402ad93 update src/Purge.list with renamed reaxc src files 2017-05-04 14:53:08 -06:00
Steve Plimpton d7dbff0f54 jive Kokkos/reaxc file names with new user-reaxc file names 2017-05-04 14:46:59 -06:00
DallasTrinkle 42531389df Cleanup of style (removing all tabs, shortened long lines). 2017-05-04 15:28:11 -05:00
DallasTrinkle f7230006fe OpenMP version added. 2017-05-04 15:08:04 -05:00
DallasTrinkle 754b40cb31 Removed unused functions. 2017-05-04 13:16:46 -05:00
DallasTrinkle ffdc8b556d Cleanup. 2017-05-04 13:03:09 -05:00
DallasTrinkle 5accce976a Cleanup. 2017-05-04 13:02:09 -05:00
DallasTrinkle 349c1443a1 Cleanup. 2017-05-04 13:01:45 -05:00
DallasTrinkle 2f71245d82 Removed extra "helper" functions. 2017-05-04 13:00:06 -05:00
Steve Plimpton 51c6d50268 patch 4May17 2017-05-04 11:46:58 -06:00
sjplimp 6499cfcf52 Merge pull request #458 from stanmoore1/kokkos_sync_bugfix 
Fixing auto_sync logic bug in modify_kokkos
 2017-05-04 11:24:11 -06:00
sjplimp f08e206991 Merge pull request #457 from stanmoore1/kokkos_ubuf 
Adding ubuf union to Kokkos atom_vec styles
 2017-05-04 11:23:55 -06:00
sjplimp fbddfe2729 Merge pull request #455 from stanmoore1/kokkos_update 
Updating Kokkos library to version 2.03.00
 2017-05-04 11:23:39 -06:00
sjplimp dcc5472cba Merge pull request #452 from akohlmey/small-fixes-and-updates 
Small fixes and updates
 2017-05-04 11:23:23 -06:00
Steve Plimpton addd87c0f7 new Section package and start doc pages and build scripts 2017-05-04 11:22:20 -06:00
DallasTrinkle 480727815a Starting to refactor in preparation to contruct OMP version. 2017-05-04 11:27:55 -05:00
DallasTrinkle 45187a0fc7 Fix system header #include style. 2017-05-04 11:05:50 -05:00
DallasTrinkle 7409c6d781 Cleaned up atom->x and atom->f deferences. 2017-05-03 16:56:07 -05:00
DallasTrinkle 11cb0212b7 Cleanup: two space indent + no trailing spaces on lines. 2017-05-03 16:49:43 -05:00
Axel Kohlmeyer 7f49ee8fd7 print warning about minimization energy with fix box/relax 2017-05-03 15:33:22 -04:00
sjplimp f5cf1f1314 Merge pull request #464 from akohlmey/rename-cg-cmm-to-cgsdk 
Rename USER-CG-CMM package to USER-CGSDK
 2017-05-03 08:37:20 -06:00
DallasTrinkle 50c7234f26 Fix to communication for mpi. Tested, and now working correctly with MPI. 2017-05-02 09:43:57 -05:00
DallasTrinkle f58fc9488f Fixed neighbor list building that caused error in parallel runs with pair_meam_spline. 2017-05-01 21:56:19 -05:00
DallasTrinkle 408cc19885 Fix for seg fault. 2017-05-01 20:36:09 -05:00
DallasTrinkle c76d27373e Another fix for seg fault in parallel allocation. 2017-05-01 20:33:07 -05:00
DallasTrinkle fb08dc09f3 Small error in elements allocation causing seg. fault for parallel runs; fixed. 2017-05-01 13:38:37 -05:00
DallasTrinkle 8bddf105bf Updated version of equations, documentation. 2017-04-28 20:22:22 -05:00
DallasTrinkle 31446e35b9 Cleanup on equations; JPG to be constructed. 2017-04-28 15:31:49 -05:00