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12579 Commits

Author SHA1 Message Date
Axel Kohlmeyer fa3c7727e1 contributing guidelines, issue and pull request template are now feature complete 
This is still a draft and in need of editing, proofreading and testing for formatting.
 2017-06-27 00:17:37 -04:00
Axel Kohlmeyer 374eef2b17 add first draft of issue template 2017-06-23 01:13:10 -04:00
Axel Kohlmeyer dc7243838b first draft of a contributor's guide file 2017-06-23 00:54:20 -04:00
Axel Kohlmeyer 57d5cfede3 add first draft of a pull request template 2017-06-22 23:07:09 -04:00
sjplimp 7a4a569859 Merge pull request #540 from lammps/neighrespa 
fix issue with rRESPA inner/middle neighbor lists
 2017-06-22 07:54:12 -06:00
sjplimp 4fc3f4f7e5 Merge pull request #538 from akohlmey/collected-small-changes 
Collected small changes and bugfixes
 2017-06-22 07:52:21 -06:00
Axel Kohlmeyer b0ddabbcde update examples for fix filter/corotate to comply with new CHARMM restrictions 2017-06-22 00:19:21 -04:00
Axel Kohlmeyer de3157f720 document new restrictions to CHARMM compatible dihedral styles 2017-06-21 19:31:40 -04:00
Axel Kohlmeyer 0c6a751751 may check for 1-4 scaling factors in CHARMM dihedral styles only when "weightflag" is set, since they may be used with amber 2017-06-21 19:29:31 -04:00
Axel Kohlmeyer 612b44a895 enforce using 'special_bonds charmm' for dihedral styles charmm and charmmfsw 2017-06-21 19:15:52 -04:00
Axel Kohlmeyer 684b7334a5 enforce that CHARMM dihedral styles are run at the same r-RESPA level as pair 2017-06-21 19:08:02 -04:00
Steve Plimpton 1fc2eb1e3e fix issue with rRESPA inner/middle neighbor lists 2017-06-21 15:12:51 -06:00
sjplimp e69ef56f10 Merge pull request #539 from lammps/neighsize 
insure compute pair/property local will use a copy of granular neighbor list
 2017-06-21 15:03:12 -06:00
Steve Plimpton 7dc380b113 insure compute pair/property local will use a copy of granular neigh list 2017-06-21 12:44:35 -06:00
Axel Kohlmeyer 1a77135ed6 whitespace cleanup in docs 2017-06-21 09:38:10 -04:00
Axel Kohlmeyer f45c7e1fb0 update fix ti/spring docs to reflect it is part of USER-MISC 2017-06-21 09:36:30 -04:00
Axel Kohlmeyer 0cfe8980d4 dead code removal 2017-06-20 22:07:40 -04:00
Axel Kohlmeyer 2988508cee correct indexing bug in pair style lj/long/tip4p/long 2017-06-20 17:53:45 -04:00
Axel Kohlmeyer 15c596153a remove dead code 2017-06-20 17:38:28 -04:00
Axel Kohlmeyer e13c94ed4f fix uninitialized variable bug spotted by coverity scan 2017-06-20 17:25:01 -04:00
Axel Kohlmeyer 812f1a8fab remove local variables shadowing global ones in BondsOMP() 2017-06-20 17:20:57 -04:00
Axel Kohlmeyer 218bc92c82 make pre-processor defines for using libc's qsort() consistent 2017-06-20 17:13:42 -04:00
Axel Kohlmeyer ffa906de6f add C++ format identifiers to .h files 2017-06-20 16:18:34 -04:00
Axel Kohlmeyer cccf72a21d make certain class member list is initialized to NULL before assigned to a neighbor list 2017-06-20 16:09:11 -04:00
Steve Plimpton 87c028ed02 patch 20Jun17 2017-06-20 12:06:02 -06:00
sjplimp 84b530cca1 Merge pull request #537 from lammps/neb 
minor changes to NEB doc pages and examples
 2017-06-20 09:38:32 -06:00
Axel Kohlmeyer 50c9167913 small formatting correction in fix neb docs 2017-06-20 10:36:30 -04:00
Steve Plimpton d2610d9e7c minor changes to NEB doc pages and examples 2017-06-20 08:19:23 -06:00
sjplimp 326a8a1289 Merge pull request #536 from akohlmey/fix-nvcc-openmp-conflicts 
Implement workaround for NVCC incompatibilities with OpenMP directives
 2017-06-20 07:44:40 -06:00
sjplimp b5300724bb Merge pull request #533 from lammps/user-intel 
Updates for USER-INTEL package and NEB command flags/docs updates and issues
 2017-06-20 07:44:17 -06:00
sjplimp e129f18e6f Merge pull request #530 from akohlmey/no_static_sort_in_dump 
Refactor Dump and Irregular classes to remove static class members
 2017-06-20 07:43:49 -06:00
Axel Kohlmeyer 8c54fcd1b6 cleanup from aidan for fix reax/c/species and its KOKKOS version 
this version eliminates the need for the PBCconnected list and avoids having to access the spec_atom array for ghost atoms
 2017-06-19 17:31:54 -04:00
Axel Kohlmeyer f5047ac3c7 augment fix shardlow check for ordering fixes to be KOKKOS compatible 2017-06-19 17:23:23 -04:00
Axel Kohlmeyer 164cedf353 protect all OpenMP pragmas with ifdefs and add special conditions for nvcc to ignore unsupported directives 2017-06-19 15:31:20 -04:00
Axel Kohlmeyer 3c329d1707 massive whitespace cleanup in USER-INTEL 
removed are:
- DOS/Windows text format carriage return characters (^M)
- tabs replaced with spaces (tabs are evil!!)
- trailing whitespace
 2017-06-19 13:23:01 -04:00
Axel Kohlmeyer b687d16177 insert C++ file format indicator comments 2017-06-19 13:03:23 -04:00
Axel Kohlmeyer 9d3e34e492 add missing reference for lj/smooth/linear 2017-06-19 11:23:30 -04:00
Emile Maras 8988b692a3 modified the documentation, first and last freeend can have different spring constants 2017-06-19 16:30:42 +02:00
Emile Maras c97415aefa corrected the initial free end 2017-06-19 14:57:39 +02:00
Axel Kohlmeyer 9b8de3ba29 remove ifdefs for selecting between plain and hybrid merge sort. use hybrid only. 2017-06-17 09:30:41 -04:00
Steve Plimpton cd88b31450 same PR, also has cosmetic changes to new fix neb options 2017-06-16 17:02:05 -06:00
Steve Plimpton 9b9f6d6fe2 USER-INTEL upgrade from M Brown 2017-06-16 16:56:28 -06:00
Axel Kohlmeyer c1b0b1b3f9 restore old qsort() based code and add preprocessor directives to switch 
-DLMP_USE_LIBC_QSORT will use qsort() from libc to sort (requires static/global variables).
-DLMP_USE_MERGE_SORT will use a plain merge sort. slightly slower for expensive comparisons.
-DLMP_USE_HYBRID_SORT will use hybrid merge sort. faster than merge sort (no static/global variables)
 2017-06-16 18:17:48 -04:00
sjplimp bc0241576f Merge pull request #532 from akohlmey/restore-heuristics-in-fix-shardlow 
recover running USER-DPD with USER-OMP and suffixes
 2017-06-16 09:46:58 -06:00
Axel Kohlmeyer 2a6f026853 mergesort performance improvements 
- use insertion sort to pre-sort data in 32-element chunks
- swap pointers between merge runs instead of copying the data
 2017-06-16 08:05:55 -04:00
Axel Kohlmeyer 8728a8ddae restore heuristics for checking against integrators that broke after PR #499 was merged 2017-06-15 15:16:50 -04:00
sjplimp 9aa450b832 Merge pull request #528 from akohlmey/no_static_in_ring_comm 
Refactor ring communication to no longer require static class variables
 2017-06-15 11:13:07 -06:00
sjplimp 0588c382f0 Merge pull request #513 from v0i0/bugfix-airebo-nconj-kronecker 
Bugfix in AIREBO as reported in #59 by @KammIma
 2017-06-15 11:12:29 -06:00
sjplimp d3c90f3c14 Merge pull request #510 from akohlmey/collected-small-changes 
Collected small changes
 2017-06-15 11:12:14 -06:00
Axel Kohlmeyer b62d526cc9 Revert "avoid undesired negative forces for high particle velocities in granular models" 
This reverts commit 066123007c.
 2017-06-15 11:01:36 -04:00