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12681 Commits

Author SHA1 Message Date
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
Sebastian Hütter bb47fa8783 Change indexing of all MEAM element arrays 
- arrays in MEAM class
- eltind setting
- remove fmap translation
 2017-06-20 19:56:14 +02:00
Sebastian Hütter c79dc53c6a code improvement, less pointer params 2017-06-20 19:36:07 +02:00
Axel Kohlmeyer 72a1364d85 Merge branch 'master' into package-meamc 2017-06-20 13:21:46 -04:00
Sebastian Hütter 198fe7ecd7 fix storing of invalid memory pointer 2017-06-20 19:00:57 +02:00
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
Sebastian Hütter a9f3f90025 fix uninitialized members 2017-06-19 12:51:18 +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
sjplimp 1a29048940 Merge pull request #531 from ohenrich/user-cgdna 
Affiliation Update for USER-CGDNA
 2017-06-15 08:54:52 -06:00
sjplimp 0a6b3f8790 Merge pull request #527 from dstelter92/master 
Added compute_scalar to fix_grem
 2017-06-15 08:54:22 -06:00
sjplimp 7227bc415d Merge pull request #526 from andeplane/vashishta_gpu 
Implemented pair style vashishta in GPU package
 2017-06-15 08:52:13 -06:00
sjplimp a4bc233d86 Merge pull request #525 from akohlmey/user-tally-refactor 
Refactoring of USER-TALLY computes to handle sparse/hybrid system for many processors plus bugfixes
 2017-06-15 08:51:24 -06:00
sjplimp 5c5b4ffadb Merge pull request #522 from akohlmey/tip4p-cleanup-refactor 
Refactor and bugfix for some TIP4P pair styles
 2017-06-15 08:48:52 -06:00
sjplimp 30177c4eae Merge pull request #521 from pastewka/17_dump_nc 
Updated NetCDF dump style (dump netcdf)
 2017-06-15 08:47:29 -06:00
sjplimp 178eff237b Merge pull request #520 from stanmoore1/kokkos_update 
Kokkos library update to v2.03.05
 2017-06-15 08:47:09 -06:00
sjplimp 576b7f1d97 Merge pull request #519 from Pakketeretet2/USER-MANIFOLD-gaussian-bump 
Some extensions/cleanup in USER-MANIFOLD
 2017-06-15 08:46:55 -06:00
sjplimp 86369fec6b Merge pull request #517 from akohlmey/select-rigid-reinit-option 
Add `reinit` keyword to rigid body fixes
 2017-06-15 08:46:29 -06:00
sjplimp 79341ac5d1 Merge pull request #516 from akohlmey/check-rigid-overlap 
Implement check whether commands or styles try to change cached properties in rigid body integrators
 2017-06-15 08:44:05 -06:00
sjplimp 66945294a9 Merge pull request #515 from stanmoore1/remove_fences 
Remove unnecessary thread fences in Kokkos package
 2017-06-15 08:40:43 -06:00