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18958 Commits

Author SHA1 Message Date
jotelha 4e7bcee8e3
Update cmake/Modules/FindNetCDF.cmake 
Co-Authored-By: Christoph Junghans <christoph.junghans@gmail.com>
 2019-12-22 13:24:34 +01:00
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 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
Stan Moore 7d16783366 Fix issue in Kokkos minimize 2019-12-19 09:31:30 -07:00
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
Trung Nguyen 4c3ec145f3 Corrected the wrong use of the stubs path in -rpath 2019-12-17 14:05:39 -06:00
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
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
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
Richard Berger b1668f28dd
Merge pull request #1674 from rbberger/library_interface_update 
Expose neighbor lists via library interface - Second iteration
 2019-12-04 11:11:50 -07:00
Richard Berger e08ba3f11e Merge branch 'master' into library_interface_update 2019-12-03 12:51:17 -05:00
Aidan Thompson 7233c3fedf Fixed error in compute snap for quadratic and add log files for regression testing 2019-12-02 18:30:38 -07:00
jrgissing e69e96ffbe Update Errors_messages.rst 2019-12-02 15:20:01 -05:00
jrgissing 28fda04526 chiral centers docs 2019-12-02 15:11:59 -05:00
jrgissing 4cb797e63d correct image atom mistake 2019-12-02 14:25:58 -05:00
jrgissing 819fe9ec56 add option to enforce atom chirality 2019-12-02 12:27:57 -05:00
Richard Berger 1d92840918
Merge pull request #1792 from akohlmey/library-define-fix 
Improve handling of LAMMPS integer size defines in library.h
 2019-12-02 08:48:34 -07:00
jrgissing 36e102516f angle constraint bugfix 
ghost atom fix
 2019-12-02 10:34:03 -05:00
Richard Berger 2f4adfc0c8
Merge pull request #1786 from rbberger/doc_command_tables 
Add Sphinx extension to generate tables from lists
 2019-12-02 08:07:22 -07:00
Richard Berger dfcb4edca7 Fix trailing whitespace 2019-12-01 15:42:46 -05:00
Richard Berger 73a4c58ba1 Merge branch 'master' into doc_command_tables 2019-12-01 15:40:52 -05:00
Richard Berger 3ce020eab2
Merge pull request #1779 from athomps/compute-snap 
Compute snap
 2019-12-01 12:52:22 -07:00
Richard Berger acf02bb1a3 Revert split of Commands_bond.rst as requested by @sjplimp 2019-12-01 14:50:29 -05:00
Richard Berger 3611a75ce0
Merge pull request #1771 from julient31/zeeman-rework 
Adding test examples for the SPIN package and correcting some bugs
 2019-12-01 09:10:25 -07:00
Richard Berger 99a6678955
Merge pull request #1787 from akohlmey/collected-small-changes 
Collected small changes
 2019-12-01 08:14:41 -07:00
Richard Berger c5fc920881
Merge pull request #1784 from LucienPan0903/master 
Patch of class2 dihedral in OMP and Kokkos
 2019-12-01 08:11:58 -07:00
Axel Kohlmeyer 9140700701
rather than abort with an error, assume -DLAMMPS_SMALLBIG if no define is set 2019-11-29 10:37:30 -05:00
Axel Kohlmeyer 0c29c2827a
check if one of the required defines is set and correct dependent API check 2019-11-29 10:16:22 -05:00