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17491 Commits

Author SHA1 Message Date
Axel Kohlmeyer 5d73b0790f
Merge pull request #1510 from evoyiatzis/respa_class_2 
Implementation of inner/middle/outer compute methods for lj/class2
 2019-06-17 14:13:47 -04:00
Axel Kohlmeyer 93fd33aad9
Merge pull request #1507 from athomps/yarray 
Back-porting of Zombie SNAP improvements
 2019-06-17 14:13:28 -04:00
Axel Kohlmeyer 6536399fc3
Merge pull request #1476 from uihsnv/log_spacing 
A function logfreq3(), for logarithmic spacing
 2019-06-17 14:12:59 -04:00
Axel Kohlmeyer 2f29bd29f4
Merge pull request #1430 from ndtrung81/gpu-neigh-hybrid 
Enable neighbor build on the device for pair hybrid substyles
 2019-06-17 14:12:40 -04:00
Axel Kohlmeyer ac57b41b4d
fix line endings and missing EOL at end 2019-06-14 07:13:06 -04:00
Evangelos Voyiatzis 43e3c1520b
cleaning pair_lj_class2.h of windows line endings 
removing DOS/Windows style CR/LF line endings
 2019-06-14 11:50:56 +02:00
Evangelos Voyiatzis e7116c8680
Update pair_class2.txt 
Addition of a few lines in the documentation file
 2019-06-14 09:04:03 +02:00
Aidan Thompson 4d7d3a5d53 Switched algorithm for compute_yi to one based on zlist ordering 2019-06-13 15:56:18 -06:00
Evangelos Voyiatzis c1550ba29b
implementation of inner/middle/outer for lj/class2 
Implementation of inner/middle/outer functions in style lj/class2 to enable integration with respa
 2019-06-13 22:23:01 +02:00
Aidan Thompson 5fb505ca8c Fixed typo 2019-06-13 10:24:18 -06:00
Aidan Thompson 67a1a63f5f Removed old text 2019-06-13 10:10:37 -06:00
Aidan P. Thompson 65b87fa278 Updated SNAP in KOKKOS package so it compiles and runs 2019-06-13 09:54:56 -06:00
athomps c5c03230cb
Not part of this pull request 2019-06-12 17:05:47 -06:00
athomps be5d3d6a19
Not part of this pull request 2019-06-12 17:04:22 -06:00
athomps f8e257d219
Not part of this pull request 2019-06-12 17:04:05 -06:00
athomps 3f523ea906
Not part of this pull request 2019-06-12 17:02:59 -06:00
Aidan Thompson a973700295 Completed back-porting of Zombie SNAP improvements, particularly noteworthy is reduction in memory footprint, elimination of most multidimensional arrays, elimination of diagonal_style, elimination of Z array in force calculation. 2019-06-12 16:42:28 -06:00
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
Aidan Thompson 0559e155f2 Implemented lists instead of multidim arrays 2019-06-11 18:24:02 -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