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12752 Commits

Author SHA1 Message Date
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
dstelter92 3214d639aa removed unneeded .gitignore 2017-06-14 12:26:52 -04:00
dstelter92 0ad66ecb89 Added compute_scalar to fix_grem for easier output managment, updated example to show use 2017-06-14 12:18:22 -04:00
Anders Hafreager e139a7fd45 Updated docs for vashishta/gpu 2017-06-14 13:52:03 +02:00
Anders Hafreager d7646aeeed Fixed opencl error 2017-06-14 12:03:47 +02:00
Anders Hafreager 5f9341813d Removed debug output 2017-06-14 10:57:54 +02:00
Anders Hafreager 8441307185 Removed non-general CUDA-dir in makefile 2017-06-14 10:28:46 +02:00
Anders Hafreager 720af5c360 Added vashishta to OpenCL makefile 2017-06-14 10:27:52 +02:00
Anders Hafreager eeff0b8633 Added vashishta GPU package for NVidia 2017-06-14 10:24:16 +02:00
Axel Kohlmeyer 32b967ed9c add rigid body overlap warnings to change_box and delete_atoms 2017-06-13 16:26:49 -04:00
Sebastian Hütter 3d066283b6 fix compilation, move meam_cleanup to destructor 2017-06-13 19:41:29 +02:00
Sebastian Hütter 29e60fa53a Move rho/gamma arrays to fields of MEAM, remove arguments and arrdim macros 2017-06-13 18:39:40 +02:00
Axel Kohlmeyer 11751521e7 remove dead code 2017-06-12 22:49:31 -04:00
Axel Kohlmeyer 7a05d87f7c update USER-TALLY examples 2017-06-12 22:20:36 -04:00
Axel Kohlmeyer b01143102d refactoring of USER-TALLY computes to handle sparse and hybrid systems 
with sparse and hybrid systems, Pair::ev_tally() may not be called on
every processor and thus the computes in USER-TALLY may hang during
reverse communication because of the error->all() call after checking
whether callback from Pair::ev_tally() has been called at least once.
To address this cleanly, a second callback function needs to be added,
which is run during Pair::ev_setup() and will now handle all memory
re-allocation and clearing of accumulators, just like it is done for
regular tallied data.
 2017-06-12 22:12:12 -04:00
Axel Kohlmeyer e530ba46f4 cleanup and bugfix for compute heat/flux/tally 
- make heatj a pointer instead of a static array
- fix memory leaks for eatom, stress
- simplify and streamline computation
 2017-06-12 21:46:00 -04:00
Axel Kohlmeyer 420db44596 print incompatible pair style warnings in USER-TALLY only on MPI rank 0 2017-06-12 20:05:15 -04:00
Axel Kohlmeyer cfeb9b5ba5 Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes 2017-06-12 14:20:50 -04:00
Axel Kohlmeyer 0c805d0b70 correctly skip over point particles and point dipoles when counting extendend particles in fix rigid/small 2017-06-12 14:20:38 -04:00
Axel Kohlmeyer 6b289b0794 change incorrect EINERTIA constant in rigid body integrators from 4.0 to 2.0 (same as in other integrators) 2017-06-12 14:07:40 -04:00
Sebastian Hütter 078f2a0a47 Convert/Reindex phir* arrays 2017-06-12 17:41:09 +02:00
Axel Kohlmeyer bdd908c303 update documentation for USER-MEAMC package and pair style meam/c 2017-06-11 21:54:18 -04:00
Axel Kohlmeyer b45a95107d remove ambiguous access conflict to fm_exp() in pair style agni/omp after moving fm_exp() to math_special.h 2017-06-11 18:45:40 -04:00
Sebastian Hütter 9f852f5f58 Improve C++-ness, eliminate some macros 
- fm_exp moved to math_special (exp2 was already there)
- use std::min/max template instead of macros
- use memory->create for dynamic arrays (still 1-indexed with macro)
- remove _ from function names, adjust method visibility
 2017-06-11 16:55:41 +02:00
Axel Kohlmeyer fea28d8028 ensure that allocatable_double_2d types are initialized 2017-06-11 07:29:44 -04:00