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6990 Commits

Author SHA1 Message Date
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 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 77ca68a2b4 Changed affiliation 2017-06-15 12:52:19 +01:00
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 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 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
Axel Kohlmeyer 11751521e7 remove dead code 2017-06-12 22:49:31 -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
Axel Kohlmeyer daa77176ad add restart support to fix deform. only "initial" data is restored and some consistency check performed 2017-06-10 17:28:17 -04:00
Axel Kohlmeyer 8f18c284d3 add crude check to print warning when using compute cnp/atom on multi-type system 2017-06-10 17:08:07 -04:00
Axel Kohlmeyer 06915162b0 whitespace cleanup 2017-06-10 16:56:54 -04:00
Axel Kohlmeyer a849f35dcd adjust compute cnp/atom to match the documentation. need to skip atoms not in compute group. 2017-06-10 16:55:42 -04:00
Axel Kohlmeyer 4c69bbcf5c apply rigid body check to displace_atoms command 2017-06-10 11:37:54 -04:00
Axel Kohlmeyer dd44189d1f fix bug in compute orientorder/atom argument parsing 2017-06-10 04:35:11 -04:00
Axel Kohlmeyer 2f6bbcfbbc output detailed multi-thread performance data only with "timer full" 2017-06-09 15:11:40 -04:00
Axel Kohlmeyer 2686b7f830 simplify compatibility check for fix reax/c/bonds with pair styles 2017-06-09 14:39:52 -04:00
Axel Kohlmeyer d3a863e7af when identifying molecules/clusters fall back to unfiltered coordinates for ghost atoms 2017-06-09 14:35:12 -04:00
Axel Kohlmeyer 64e8000720 expand error message requiring a reax/c derived pair style 2017-06-09 11:42:35 -04:00
Axel Kohlmeyer c160d0cd5e fix reax/c/species/omp doesn't is not needed anymore 2017-06-09 11:04:11 -04:00
Axel Kohlmeyer 9222278fb5 match reax/c pair style variants against prefix and not full name 2017-06-09 11:00:16 -04:00
Lars Pastewka bdf03757e6 MAINT: Simplified GPL headers. 2017-06-08 23:20:21 +02:00
Lars Pastewka 10d2e7c380 MAINT: DumpNetCDF and DumpNetCDFMPIIO need access to thermo output. 2017-06-08 23:18:54 +02:00
Lars Pastewka bd83c7c7f9 MAINT: Updated contact data and fixed typos. 2017-06-08 23:02:22 +02:00
Lars Pastewka d51cee1b82 MAINT: Turned 'global' options into a 'thermo yes'/'thermo no' option that enables dumping of thermo data to the netcdf file (for parallel NetCDF/MPIIO variant). 2017-06-08 22:58:27 +02:00
Lars Pastewka be476c9e1d MAINT: Turned 'global' options into a 'thermo yes'/'thermo no' option that enables dumping of thermo data to the netcdf file. 2017-06-08 22:43:10 +02:00
Axel Kohlmeyer afd4f5b0a6 Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes 2017-06-07 17:37:13 -04:00