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13969 Commits

Author SHA1 Message Date
Axel Kohlmeyer fa6fc947f2 fix issues in FixNeighHistory and FixNeighHistoryOMP reported in https://sourceforge.net/p/lammps/mailman/message/36138319/ 
This supersedes and closes PR #734
 2017-11-28 11:28:15 -05:00
Axel Kohlmeyer e1189381e0 correct documentation for create_atoms rotate 
This closes #736
 2017-11-28 11:19:19 -05:00
Jaap Kroes 39d24ab7eb ExTeP potential file header update 2017-11-27 21:25:23 +01:00
Jaap Kroes 5770a20e2c added ExTeP to USER-MISC 2017-11-27 21:16:51 +01:00
Steve Plimpton 83ec9815fe
Merge pull request #733 from pastewka/17_dump_nc3 
BUG: Proper handling of bigint data in NetCDF dump style. Affects LAMMPS version compiled with LAMMPS_BIGBIG.
 2017-11-27 11:07:58 -07:00
Axel Kohlmeyer 90ee52296b Merge remote-tracking branch 'andeplane/fix_ave_chunk_bug' into collected-bugfixes 
this closes PR #732
 2017-11-27 11:45:09 -05:00
Lars Pastewka f02eb225c6 Merge branch '17_dump_nc3' of github.com:pastewka/lammps into 17_dump_nc3 2017-11-26 22:39:03 +01:00
Lars Pastewka a111cf640a BUG: Proper handling of bigint data. Corrects behavior when compiled with LAMMPS_BIGBIG. 2017-11-26 22:35:56 +01:00
Lars Pastewka e755a8339d BUG: openfile is called multiple times, second call stopped code with 'at keyword requires use of append yes' 2017-11-26 22:31:47 +01:00
Lars Pastewka f7f6a15ac0 MAINT: Removed superfluous code. 2017-11-26 22:31:47 +01:00
Lars Pastewka 36b7aa73aa MAINT: Use proper data type for bigint when defining NetCDF file. 2017-11-26 22:31:47 +01:00
Anders Hafreager 9a5723123f Set peratom_freq in fix ave/chunk 2017-11-21 23:43:52 -08:00
Stan Moore 7d07f062b6 Remove const from variable 2017-11-20 10:21:19 -07:00
Stan Moore f3ed148828 Fix for big endian machines 2017-11-20 10:18:53 -07:00
Stefan Paquay 5ba80662c3 Undid the removal of rad in pair_yukawa. 2017-11-17 15:07:59 -05:00
Stefan Paquay 53c1558271 Updated docs for pair_yukawa 2017-11-17 14:21:54 -05:00
Stefan Paquay 8e5d4fa891 Added a KOKKOS-enabled Yukawa pair style. 2017-11-17 14:12:16 -05:00
Axel Kohlmeyer ec067bde36 fix cut-n-paste error in create_bond docs 2017-11-13 17:59:16 -05:00
Axel Kohlmeyer adbc75cae6 add alternate log files with the latest version of LAMMPS 2017-11-13 11:52:01 -05:00
Steve Plimpton dde94c28a7 new example scripts for fix gcmc 2017-11-13 09:07:25 -07:00
Steve Plimpton f2dc764d1d
Merge pull request #723 from lammps/replicate_bbox 
Add bounding box to Replicate command
 2017-11-13 09:01:38 -07:00
Steve Plimpton c4c59b909e
Merge pull request #716 from akohlmey/collected-small-changes 
Collected small changes and bugfixes for next patch
 2017-11-13 09:00:26 -07:00
Steve Plimpton e2e21f0661
Merge pull request #714 from Pakketeretet2/user-manifold-plane-wiggle-fix 
User manifold plane wiggle fix
 2017-11-13 08:59:40 -07:00
Steve Plimpton 6abf68f614
Merge pull request #712 from akohlmey/linalg-for-latte 
Update lib/linalg for use with lib/latte
 2017-11-13 08:59:18 -07:00
Steve Plimpton a97553a92e
Merge pull request #709 from abbatux/patch-1 
Update pair_smd_tlsph.cpp
 2017-11-13 08:58:29 -07:00
Steve Plimpton dbd4acc4d6
Merge pull request #708 from abbatux/patch-2 
Update smd_material_models.cpp
 2017-11-13 08:58:07 -07:00
Stan Moore 40e776ebc6 Remove OpenMP from KOKKOS_DEVICES in Kokkos CUDA Makefiles since normally this doesn't improve performance 2017-11-10 09:55:11 -07:00
Tim Mattox f043212511 USER-DPD: fix a segfault when using constant temperature (DPD vs. DPDE) 2017-11-07 13:57:29 -06:00
Stan Moore 4342bcdafc Fix CUDA issue in USER-DPD/random_external_state.h 2017-11-07 09:17:58 -07:00
Axel Kohlmeyer 2e40c00995 add option to the print command to also print to the global universe screen and logfile 2017-11-07 10:00:57 -05:00
Stan Moore f39c6213e1 Change path to nvcc_wrapper 2017-11-06 13:50:16 -07:00
Stan Moore 88474fc5c2 Remove Kokkos tpls directory 2017-11-06 13:48:26 -07:00
Stan Moore 16b5315845 Update Kokkos to v2.04.11 2017-11-06 13:47:33 -07:00
Stan Moore e337db4059 Replicate bbox from Chris Knight 2017-11-06 11:31:43 -07:00
Axel Kohlmeyer ba43465268 Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes 2017-11-06 13:30:08 -05:00
Axel Kohlmeyer 09c61ca598 correct listing of USER-OMP variants of fix rigid styles 2017-11-06 13:29:59 -05:00
Axel Kohlmeyer 0f971bf07c print name of unknown or incorrect variable in error message 2017-11-06 10:41:32 -05:00
Axel Kohlmeyer 5a8c5eb479 provide last input command line with error->one() output 2017-11-06 10:41:01 -05:00
Axel Kohlmeyer aa0d6cd75b Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes 2017-11-04 02:49:28 -04:00
Axel Kohlmeyer b34000a5e1 make *_gpu_reinit() functions consistent in returning void. correct prototypes in src/GPU, too. 
this supersedes and closes #719
 2017-11-04 02:49:22 -04:00
Tim Mattox 279339ebd0 Remove the now unused AIRct_ssa[] array from the NeighList class. 2017-11-03 13:42:36 -05:00
Tim Mattox 605fe53c07 USER-DPD: make the kokkos and non-kokkos fix_shardlow match more closely 
This was accomplished with several key changes:
1) Modified fix_shardlow's control flow to match fix_shardlow_kokkos so
that random numbers are pulled fromn the RNGs in exactly the same order.

2) Created random_external_state.h, a simplified version of the Kokkos
random number generator that keeps its state variables external to itself.
Thus it can be used both with and without Kokkos enabled, as long as the
caller stores and passes in the required state variable.

3) Replaced all references to random_mars.h and Kokkos_Random.hpp code in
the fix_shardlow* files with calls to the random_external_state.h code,
guaranteeing that fix_shardlow* is using an identical RNG in all cases.

Result: most (56 of 61) of our internal tests now generate the same results
with kokkos turned on or off.  Four cases still differ due to what appear
to be vectorization caused rounding differences, and the fifth case
appears to be something triggered by the kokkos "atom_style hybrid" code.
 2017-11-03 12:51:37 -05:00
Axel Kohlmeyer 65b77230fd added missing "dihedral" in compute dihedral/local docs 2017-11-02 15:04:04 -04:00
Lars Pastewka 91e4bcca33 BUG: openfile is called multiple times, second call stopped code with 'at keyword requires use of append yes' 2017-11-01 21:28:14 +01:00
Lars Pastewka 7ef17efe2e MAINT: Removed superfluous code. 2017-11-01 21:20:19 +01:00
Lars Pastewka 8a804460f9 MAINT: Use proper data type for bigint when defining NetCDF file. 2017-11-01 21:19:55 +01:00
Axel Kohlmeyer f6658d10b7 fix incorrect create_atoms example for selecting created atoms with a variable 2017-10-30 23:33:26 -04:00
Axel Kohlmeyer f4d0aa3393 correct cut-n-paste bug reported by Massimo Pica Ciamarra on lammps-users 2017-10-27 11:25:57 -04:00
Stefan Paquay 99a6c6edb4 Fixed a typo in manifold plane wiggle. 2017-10-26 12:33:16 -04:00
Stefan Paquay a26ffc7ff7 Reset plane wiggle in master. 2017-10-26 12:32:30 -04:00