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12556 Commits

Author SHA1 Message Date
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
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
sjplimp 9a7207e34c Merge pull request #511 from akohlmey/add-compute-cnp 
Integrate compute cnp/atom contributed by Paulo Branicio (USC)
 2017-06-15 08:38:05 -06:00
sjplimp d41c617d1d Merge pull request #509 from akohlmey/add-atomonly-npair-for-omp 
add "atomonly" optimized neighbor list build styles to USER-OMP
 2017-06-15 08:24:44 -06:00
sjplimp 1ec9e588ff Merge pull request #504 from andeplane/hexorder_fix 
Using correct ndegree instead of nnn
 2017-06-15 08:24:25 -06:00
sjplimp 3c7417fb59 Merge pull request #497 from lammps/add-user-reaxc-omp 
Add USER-OMP compatible OpenMP support to USER-REAXC
 2017-06-15 08:24:03 -06:00
sjplimp 34cfc7bd51 Merge pull request #490 from EmileMaras/NEB-Change 
added several features to the NEB
 2017-06-15 08:23:04 -06:00
Oliver Henrich c98bb7fa5f Corrected minor bug in utility script 2017-06-15 12:57:44 +01:00
Oliver Henrich 77ca68a2b4 Changed affiliation 2017-06-15 12:52:19 +01:00
Axel Kohlmeyer 06fe703eed add missing mergesort header 2017-06-14 23:22:49 -04:00
Axel Kohlmeyer 8500a197ae whitespace cleanup 2017-06-14 23:13:10 -04:00
Axel Kohlmeyer 1f17e8ebbb remove need for static class member variables in Dump and Irregular 
The dump and irregular classes were using qsort() from the C-library
for sorting lists through custom comparison functions, which required
access to additional data, which was passed via static class variables,
i.e. globals. This collides with having multiple LAMMPS instances in
the same address space.

the calls to qsort() are replaced with a custom merge sort, which passes
a void pointer to the comparison functions, which can contain any kind
of desired information, e.g. a class handle or a list
 2017-06-14 23:10:53 -04:00
Axel Kohlmeyer fcc387f232 change ring communication API to no longer require a static variable pointing to 'this' of the caller 2017-06-14 17:01:06 -04:00
dstelter92 e7634a44f4 updated thermo_modify in example 2017-06-14 13:11:54 -04:00