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19105 Commits

Author SHA1 Message Date
Axel Kohlmeyer e11374d433
print intel package status message only once per run 2020-01-03 01:37:12 -05:00
Vsevak 337b0fd649 Fix 'sametag' transfer 2019-12-22 20:20:12 +03:00
jotelha 3f24144abd
Update cmake/Modules/FindPNetCDF.cmake 
Co-Authored-By: Christoph Junghans <christoph.junghans@gmail.com>
 2019-12-22 13:25:24 +01:00
jotelha 0c7d6a01e8
Update cmake/Modules/FindNetCDF.cmake 
Co-Authored-By: Christoph Junghans <christoph.junghans@gmail.com>
 2019-12-22 13:25:08 +01:00
jotelha 4e7bcee8e3
Update cmake/Modules/FindNetCDF.cmake 
Co-Authored-By: Christoph Junghans <christoph.junghans@gmail.com>
 2019-12-22 13:24:34 +01:00
Axel Kohlmeyer a72f53e367
add stan/steve as code owners for minimizer changes 2019-12-21 16:18:26 -05:00
Axel Kohlmeyer a88a00dbbb
remove trailing whitespace 2019-12-20 15:08:51 -05:00
Axel Kohlmeyer 3b76ab56f0
port gravity changes to rigid fixes to USER-OMP package versions 2019-12-20 12:09:50 -05:00
Johannes Hörmann c8a53d560a Find parallel NetCDF with cmake for USER-NETCDF 
Conflicts:
	cmake/presets/forhlr2-gnu.cmake
 2019-12-20 17:59:05 +01:00
Axel Kohlmeyer 21f454c040
correct truncated AlCu.bop.table potential file from Xiaoweng Zhou 2019-12-20 03:48:08 -05:00
Steve Plimpton a11b886b5c add warning if gravity is used incorrectly with overlapped rigid bodies 2019-12-19 16:17:14 -07:00
Axel Kohlmeyer 402f5585ff
Merge pull request #1795 from jrgissing/bond/react-chiral_centers 
Bond/react chiral centers
 2019-12-19 16:13:32 -05:00
Axel Kohlmeyer 5a2074cc5a
Merge pull request #1816 from stanmoore1/kk_min_fix 
Fix issue in Kokkos minimize
 2019-12-19 16:12:53 -05:00
Axel Kohlmeyer 8283e68cdd
Merge pull request #1807 from ndtrung81/gpu-readme-update 
Updates to README and Makefile's in the GPU package
 2019-12-19 14:59:12 -05:00
Axel Kohlmeyer 27180e0b22
Merge pull request #1812 from ohenrich/user-cgdna 
USER-CGDNA: Added oxRNA2 files to .gitignore
 2019-12-19 14:58:56 -05:00
Axel Kohlmeyer 6192741f79
Merge pull request #1813 from wmbrownIntel/user-intel-tri-fix 
Bug fix for USER-INTEL package with triclinic neighbor builds.
 2019-12-19 14:58:40 -05:00
Jianhua Pan 92b2e4256b
Bug fix for lj/class2/coul/long/gpu 2019-12-19 14:45:19 -05:00
Stan Moore 7d16783366 Fix issue in Kokkos minimize 2019-12-19 09:31:30 -07:00
Vsevak 081839b449 Fix the example according to the convention 2019-12-19 16:44:32 +03:00
Oliver Henrich d05f32d152 Added oxRNA2 files to .gitignore 2019-12-18 11:31:02 +00:00
Michael Brown 3be04e4671 Bug fix for USER-INTEL package with triclinic neighbor builds. 2019-12-18 01:27:39 -08:00
Sebastian Hütter cb20cb9f25 Add range checks for MathSpecial::fm_exp 2019-12-17 22:23:19 +01:00
Sebastian Hütter a231197c10 MEAM/C: remove unused variable alias 2019-12-17 21:55:50 +01:00
Sebastian Hütter 1be9364a89 MEAM/C: document new reference structures 2019-12-17 21:55:38 +01:00
Trung Nguyen 4c3ec145f3 Corrected the wrong use of the stubs path in -rpath 2019-12-17 14:05:39 -06:00
Axel Kohlmeyer 55fde76d59
may only close files on MPI ranks that have a file reader instance 2019-12-16 07:22:41 -05:00
Richard Berger 6c3161cb55
Merge pull request #1796 from athomps/compute-snap-tweak 
Fixed error in compute snap for quadratic and add log files for regre…
 2019-12-13 11:55:20 -07:00
Richard Berger 8030ff255d
Merge pull request #1794 from yafshar/master 
Certificate Verification
 2019-12-12 13:24:21 -07:00
Richard Berger 1f9f85e798 Mark LMP_NO_SSL_CHECK and LMP_DEBUG_CURL as advanced options 2019-12-12 14:17:32 -05:00
Yaser Afshar b0d0037f50 Certificate Verification 
if SSL report an error ("certificate verify failed") during the
handshake and thus refuses further communication with that server,
you can specify your own CA cert path by setting the environment
variable CURL_CA_BUNDLE to the path of your choice.
 2019-12-12 12:57:34 -06:00
Richard Berger a1e49eced7
Merge pull request #1806 from akohlmey/mpi-info-in-help 
Include MPI version and vendor info in LAMMPS help message
 2019-12-12 09:37:28 -07:00
Richard Berger 96f75c7b67
Merge pull request #1802 from rbberger/small-fixes 
Collection of small fixes
 2019-12-12 09:36:53 -07:00
Trung Nguyen 7e8a04d985 More minor update to README 2019-12-12 09:57:49 -06:00
jrgissing bde8b57f0b Update fix_bond_react.rst 2019-12-11 23:10:11 -07:00
Trung Nguyen 99ba15bf6a Updated README and added -L$(CUDA_HOME)/lib64/stubs to the Makefile's 2019-12-11 16:29:42 -06:00
Richard Berger 5e4e6b2853
Merge pull request #1803 from stanmoore1/kk_mpi 
Fix performance issues with CUDA-aware MPI
 2019-12-11 13:34:33 -07:00
Axel Kohlmeyer 5e983b899a
remove unused variable 2019-12-11 08:34:56 -05:00
Axel Kohlmeyer 876032b762
refactor MPI library info query so it can be added to -help flag output 2019-12-11 05:33:16 -05:00
Dan S. Bolintineanu af4e49a517 Merge branch 'rigid-gravity' of github.com:lammps/lammps into rigid-gravity 2019-12-10 14:14:21 -07:00
Richard Berger e0a771d5cb Remove outdated package.txt 2019-12-10 13:46:30 -05:00
Stan Moore fba97b94cb Don't change comm flags when there is only 1 MPI rank 2019-12-10 10:10:12 -07:00
Richard Berger a6a354279c
Merge pull request #1804 from ohenrich/user-cgdna 
USER-CGDNA update for Install.sh script
 2019-12-10 09:31:20 -07:00
Oliver Henrich bf1ee20403 Added oxRNA2 files to Install.sh script 2019-12-10 14:46:24 +00:00
Stan Moore 1b9214c3e9 Fix issues with CUDA-aware MPI 2019-12-09 15:21:47 -07:00
Vsevak a3fca53e97 Separate the computation of newsite into another kernel 
This eliminates the need for thread fence and makes the calculation stable on GTX1070 (CUDA and OpenCL) and TitanV
 2019-12-07 15:54:20 +03:00
Vsevak 4a51e1660f Add thread fence in kernel to fix Volta indeterminacy 2019-12-07 01:16:39 +03:00
Richard Berger 00547d906b Fix whitespace 2019-12-06 14:43:45 -05:00
Richard Berger 2d4d07521d Add false positives to spell check 2019-12-06 14:43:19 -05:00
Richard Berger e68824a392
Merge pull request #1772 from ohenrich/user-cgdna 
USER-CGDNA oxRNA2 Implementation
 2019-12-06 12:23:47 -07:00
Vsevak a2f9fa8e78 Separate the computation of hneigh into another kernel 
Simplify the main GPU kernel and add another kernel 'k_pair_reneigh'. It works good on GTX1070 (Pascal), but still there is a problem with non-deterministic results on Volta.

I reimplement BaseCharge::compute methods in the child class LJ_TIP4PLong to correctly embed a new kernel in the code.

Also commit includes some codestyle fixes.
 2019-12-06 21:41:02 +03:00