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17458 Commits

Author SHA1 Message Date
Axel Kohlmeyer b1458ceebf
fix typo 2019-06-17 07:42:18 -04:00
Axel Kohlmeyer 92615bda3a
update kolmogorov/crespi/full example input for recent change in REBO 2019-06-17 07:38:11 -04:00
Axel Kohlmeyer 4c0cd0a019
remove memory leak by freeing custom MPI data types 2019-06-17 07:36:03 -04:00
Axel Kohlmeyer fd93c27dcb
make valgrind happy by fully initializing line buffer for thermo output 2019-06-17 07:35:30 -04:00
Axel Kohlmeyer daa53e3008
Merge pull request #1469 from julient31/pppm_spin 
Adding PPPM and Ewald solvers for electric dipoles and magnetic spins
 2019-06-12 14:50:18 -04:00
Stan Moore 7a33d1e328 Code cleanup 2019-06-12 11:36:42 -06:00
Axel Kohlmeyer 0b25d2feef
Merge pull request #1504 from akohlmey/collected-small-fixes 
Collected small bugfixes and changes
 2019-06-11 20:20:19 -04:00
Axel Kohlmeyer 1c1491eebf
Merge pull request #1506 from sniblett402/patch-1 
Bugfix for bond_style table with MPI
 2019-06-11 19:10:41 -04:00
Axel Kohlmeyer 400751f30f
remove redundant call to broadcast r0 2019-06-11 19:09:23 -04:00
sniblett402 4fbf96a353
Bugfix for bond_style table with MPI 
Summary

Very small bug fix - an incorrect MPI datatype was causing undefined behaviour for tabulated bond potentials (bond_style table).

Author(s)

Sam Niblett, LBNL

Licensing

By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).

Backward Compatibility

No impact

Implementation Notes

The equilibrium bond length of the tabulated potential (tb->r0) was incorrectly specified as an MPI_INT during a broadcast. Therefore, all non-root processes received a truncated value of this parameter. This simple fix produced the expected behaviour for me.
 2019-06-11 13:48:01 -07:00
Axel Kohlmeyer 1dc8bb163d
Merge pull request #1485 from Adrian-Diaz/memcpy2memmove 
replace some calls to `memcpy()` with calls to `memmove()`
 2019-06-11 14:07:46 -04:00
Axel Kohlmeyer bb0240d8eb
Merge pull request #1501 from uihsnv/vim_files 
Simplify and update vim syntax highlighting files
 2019-06-11 14:06:58 -04:00
Axel Kohlmeyer fd592d510f
Merge branch 'collected-small-fixes' of github.com:akohlmey/lammps into collected-small-fixes 
# Conflicts:
#	cmake/CMakeLists.txt
 2019-06-11 14:03:27 -04:00
Axel Kohlmeyer dbafb92dd5
cmake minor cleanup and removal of redundant code and empty lines 2019-06-11 14:02:41 -04:00
Axel Kohlmeyer 83060f0902
Merge branch 'master' into collected-small-fixes 2019-06-11 13:35:42 -04:00
Axel Kohlmeyer fd55d7d367
update list of known LAMMPS keywords 2019-06-11 11:15:04 -04:00
Axel Kohlmeyer 3d5db63381
minor cleanup 2019-06-11 10:36:04 -04:00
Axel Kohlmeyer 42b0cb5e3e
Merge pull request #1502 from rbberger/cmake_cleanup 
Refactor CMake configuration
 2019-06-11 10:19:07 -04:00
Axel Kohlmeyer 4cee333c07
need to use C++ compiler when checking for includes 
this is the same bugfix as in PR #1504
 2019-06-11 07:12:39 -04:00
Axel Kohlmeyer 7f4c611e21
must use C++ compiler to check for include files 2019-06-11 06:51:03 -04:00
Axel Kohlmeyer fe29572737
Merge pull request #1496 from akkamesh/enh-ext-reaxc 
reaxc/qeq optimization - using kokkos hierarchical parallelism
 2019-06-10 21:37:12 -04:00
Axel Kohlmeyer 9421466f57
Merge branch 'master' into enh-ext-reaxc 
Resolved Merge Conflict in src/KOKKOS/kokkos.cpp
 2019-06-10 20:14:40 -04:00
Axel Kohlmeyer 8d985e53f4
Merge pull request #1494 from mkanski/extep_hybrid 
Fix for extep when NULL or only some elements from potential file are used.
 2019-06-10 20:04:24 -04:00
Axel Kohlmeyer e72ac92a7f
Merge pull request #1422 from stanmoore1/team_opt 
Optimize KOKKOS package for small systems
 2019-06-10 20:03:53 -04:00
Axel Kohlmeyer 3e2f3a8058
avoid a case of mixing malloc()/free() with new/delete 2019-06-10 18:22:04 -04:00
Axel Kohlmeyer 72b295d7f4
add support for internal style variables to info command 2019-06-10 18:21:17 -04:00
Stan Moore fa76472135 Add Kamesh as contributing author to fix_qeq_reax_kokkos 2019-06-10 15:48:53 -06:00
Richard Berger b368b11d60 Move ShowHelp test into Testing.cmake 2019-06-09 22:31:56 -04:00
Richard Berger 591e6836fd Move CMake configuration for USER-H5MD into its own file 2019-06-09 22:24:59 -04:00
Richard Berger 4ac100fe69 Define additional LAMMPS_*_DIRS to remove relative paths later 2019-06-09 22:05:53 -04:00
Richard Berger 4ecd81f81b Move CMake configuration of PYTHON package into its own file 2019-06-09 21:48:05 -04:00
Richard Berger 203c6d122b Move KSPACE CMake configuration into its own file 2019-06-09 21:37:34 -04:00
Richard Berger e788d32678 Move autogen check into utility function 2019-06-09 04:02:08 -04:00
Richard Berger ae59ffe83e Move more CMake configurations to own files 2019-06-09 03:54:52 -04:00
Richard Berger 99a8d3c2ed Create CMake files for several packages 
This remove the CMake configuration of several larger packages and places
it into their own files in the Modules/Packages folder.
 - COMPRESS
 - KIM
 - LATTE
 - MESSAGE
 - MSCG
 - USER-MOLFILE
 - USER-NETCDF
 - USER-PLUMED
 - USER-QMMM
 - USER-QUIP
 - USER-SCAFACOS
 - USER-SMD
 - USER-VTK
 2019-06-09 03:35:25 -04:00
Richard Berger ca1445788e Move CMake configuration of VORONOI package into its own file 2019-06-09 03:23:23 -04:00
Richard Berger 0908bd7aaf Move code coverage and testing into their own files 2019-06-09 03:18:20 -04:00
Vishnu V. Krishnan 239dfe163c
Simplify vim-files 
Resolves #1500
 2019-06-08 17:11:20 +05:30
Stan Moore 31dc5dbb51 Fix variable type 2019-06-07 17:00:43 -06:00
Stan Moore 9e3dc26599 Fix name in pair_exp6_rx_kokkos 2019-06-07 16:41:41 -06:00
Stan Moore 8da75c2040 Merge branch 'master' of github.com:lammps/lammps into enh-ext-reaxc 2019-06-07 16:33:44 -06:00
Stan Moore 85999fc4a7 Restore original compute_h in fix_qeq_reax_kokkos 2019-06-07 16:31:31 -06:00
Stan Moore 73fa8d4055 Rename Kokkos variables 2019-06-07 16:30:02 -06:00
Stan Moore bd237a05b8 Tweak scalar view allocation 2019-06-07 15:46:04 -06:00
Stan Moore 4941f11ad4 Remove unused tag 2019-06-07 15:37:49 -06:00
Richard Berger afab5ef303 Move CMake part on coverage into its own file 2019-06-07 12:24:35 -04:00
Richard Berger a7c02e699e Move CMake utilities into LAMMPSUtils.cmake 2019-06-07 12:18:49 -04:00
Richard Berger 8fed39d726 Move CMake documentation build section into its own file 2019-06-07 12:16:01 -04:00
Axel Kohlmeyer b9e10d55e2
Merge pull request #1492 from akohlmey/collected-small-changes 
Collected small changes for the next patch
 2019-06-07 11:07:10 -04:00
Axel Kohlmeyer 1f1a0f95b2
Merge pull request #1497 from junghans/check_for_immintrin 
cmake: check for immintrin.h
 2019-06-07 10:57:56 -04:00