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14051 Commits

Author SHA1 Message Date
smoore 7a78875911 Fix issues in Kokkos pair snap and zbl 2018-01-13 21:31:11 -07:00
Richard Berger 1cfc3118cc CMake: remove BUILD_SHARED_LIBS requirement from PYTHON package 2018-01-13 22:17:23 +01:00
Richard Berger 23e8fb0542 Update CMake build for USER-COLVARS 2018-01-13 21:57:24 +01:00
Richard Berger 72eb2dab52 Add missing math.h header 2018-01-13 20:41:05 +01:00
Stan Moore f6075c9d2c One last tweak to npair_halffull_newtoff.cpp 2018-01-12 16:12:57 -07:00
Stan Moore 24f1889b02 Only include ghosts for newton off, since this style exists as a standalone build, but the newton on method doesn't 2018-01-12 16:10:42 -07:00
Stan Moore dea8d592da Optimize npair_halffull styles; the number of i atoms, whether owned or ghost, must match between the child half list and parent full list 2018-01-12 15:51:54 -07:00
Stan Moore 52d3e98f3b Fix issue in npair_skip_kokkos 2018-01-12 15:45:24 -07:00
Stan Moore 6e3acce3be Relax restriction in neighbor.cpp 2018-01-12 15:44:11 -07:00
Stan Moore 1ec54827d6 Add Kokkos halffull neighbor list capability 2018-01-12 15:41:59 -07:00
Axel Kohlmeyer 61ebf6265a address some formatting/markup issues reported by Nandor Tamaskovics 2018-01-12 12:50:02 -05:00
Axel Kohlmeyer 190cc78034 add dummy doc files for not-yet-implemented features 2018-01-12 12:29:03 -05:00
Axel Kohlmeyer 5863f115dd correctly escape 'a_ ' text, which is not a reference unlike 'a_b ' 2018-01-12 12:26:50 -05:00
Axel Kohlmeyer 75d259f5ee improve PDF reader compatibility for the created PDF file. 2018-01-12 12:00:53 -05:00
Axel Kohlmeyer 3b1b9a2cbf replace non-ASCII quotation marks with ASCII equivalent 2018-01-12 11:30:27 -05:00
mkanski 17b6a4c3cd Added more permanent citation 2018-01-12 11:47:35 +01:00
Stan Moore 1c10c78684 Add ghost option to npair_halffull 2018-01-11 15:15:04 -07:00
Axel Kohlmeyer 26917280be state name of the affected variable in error messages where possible 2018-01-11 15:01:08 -05:00
Stan Moore 45674e6cd3 Add Kokkos skip list capability 2018-01-11 10:07:44 -07:00
Stan Moore 22d2d1cdf3 Fix issue in pair_snap_kokkos memory_usage 2018-01-11 10:01:34 -07:00
Stan Moore 0d7bee40ae Add newline at end of pair_snap_kokkos_impl.h 2018-01-11 09:41:37 -07:00
Stan Moore db1ed32a51 Fix minor issues in pair_snap_kokkos 2018-01-11 09:39:53 -07:00
Stan Moore d7d087ae67 Fix issue with peratom energy/virial in pair_snap_kokkos 2018-01-10 10:20:40 -07:00
Stan Moore 92e2df74c1 Fix bug in Kokkos peratom energy/virial with newton on 2018-01-10 10:20:12 -07:00
mkanski 92742c5373 Introduced the change in reax/c/omp 2018-01-10 18:00:22 +01:00
Stan Moore 2047ae76e3 Move compute_bi outside of j-loop 2018-01-09 17:05:57 -07:00
Stan Moore 4adbb882b3 Temper SNAP output 2018-01-09 17:05:34 -07:00
Stan Moore 275c08453f Add Kokkos versions of pair_style snap and zbl 2018-01-09 17:03:49 -07:00
Axel Kohlmeyer 91107cc1f3 add a "coeffs" keyword to the info command for debugging "All XXX coeffs are not set" errors. 2018-01-09 12:47:33 -05:00
mkanski e26c170679 Added example and tabulated close-range correction 2018-01-09 15:08:08 +01:00
Steve Plimpton 1bd9e175e9
Merge pull request #749 from akohlmey/collected-bugfixes-and-updates 
Collected bugfixes and updates for the next patch release
 2018-01-08 09:20:18 -07:00
Steve Plimpton 9e9cfe5869
Merge pull request #754 from rbberger/cmake_kokkos_bugfix 
CMake bugfixes for KOKKOS builds
 2018-01-08 09:16:43 -07:00
Steve Plimpton 85ff0c1e46
Merge pull request #750 from stanmoore1/kk_fences 
Add Kokkos thread fences to comm pack/unpack routines
 2018-01-08 09:16:16 -07:00
Steve Plimpton cc9b6118b8
Merge pull request #748 from stanmoore1/kk_docs 
Update Kokkos docs
 2018-01-08 09:15:36 -07:00
Steve Plimpton 09bed0c09a
Merge pull request #747 from stanmoore1/kk_reax_hist 
Fix broken charge history in fix qeq/reax/kk
 2018-01-08 09:15:21 -07:00
Steve Plimpton 1b51efd6b8
Merge pull request #744 from akohlmey/doc-update 
Documentation build updates
 2018-01-08 09:15:02 -07:00
Steve Plimpton 8888b05b18
Merge pull request #742 from rbberger/fix_python_move 
Fix python/move
 2018-01-08 09:14:36 -07:00
Steve Plimpton 3bb8294f31
Merge pull request #718 from timattox/USER-DPD_es_RNG 
USER-DPD: External State RNG
 2018-01-08 09:13:11 -07:00
Steve Plimpton 450c689ae9
Merge pull request #725 from stanmoore1/kk_update 
Update the Kokkos library in LAMMPS to v2.5.00
 2018-01-08 09:12:51 -07:00
mkanski a5d401e164 Fixed header for the force field file 2018-01-08 14:46:32 +01:00
mkanski b96100c0b7 Fixed header for the force field file 2018-01-08 14:42:43 +01:00
mkanski 2690075405 Performance increase for charge-implicit ReaxFF/changed cutoff selection 2018-01-08 14:38:24 +01:00
Axel Kohlmeyer 09ca7b32fc Revert "no need to include library.o in the LAMMPS executable" 
This reverts commit 4a3a6b4455.
As it turns out, when using the LAMMPS python wrapper from inside
code using the PYTHON package, the library symbols *are* needed.
Thanks for Richard Berger (@rbberger) for pointing this out.
 2018-01-06 19:47:33 +01:00
Axel Kohlmeyer 3af389e6cf Revert "no need to include library.o in the LAMMPS executable" 
This reverts commit 4a3a6b4455.
As it turns out, when using the LAMMPS python wrapper from inside
code using the PYTHON package, the library symbols *are* needed.
Thanks for Richard Berger (@rbberger) for pointing this out.
 2018-01-06 12:58:17 -05:00
Axel Kohlmeyer 46217db8a5 make python functions examples more complete by adding exception handling and initializing variables 2018-01-06 12:56:42 -05:00
Richard Berger d6d7dde653 Add error output if python evaluation failed 2018-01-06 18:54:55 +01:00
Axel Kohlmeyer 6070182f06 correctly account for individually added bonds, angles, and dihedrals 2018-01-06 11:03:48 -05:00
Axel Kohlmeyer 6c058fb56c avoid division by zero in ewald for empty and uncharged systems. require kspace_modify gewald 2018-01-05 20:14:25 -05:00
Axel Kohlmeyer 91993b236d avoid division by zero in PPPM for empty and uncharged systems. require kspace_modify gewald 2018-01-05 19:52:51 -05:00
Axel Kohlmeyer 5ecc3ce366 avoid division by zero when trying to run PPPM on a system without atoms 2018-01-04 20:44:40 -05:00