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13,809 Commits 9 Branches 198 Tags 1.1 GiB
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13809 Commits

Author SHA1 Message Date
Axel Kohlmeyer b7c7492608 handle invalid lookup for bond/angle tabulation 2017-10-13 09:50:56 -04:00
Axel Kohlmeyer cee94da85e bugfix. avoiding operating on uninitialize data. closes #690 2017-10-13 00:15:15 -04:00
Richard Berger 45aa7de171 Limit IPython autocomplete to known commands and properties 2017-10-12 14:43:17 -04:00
Axel Kohlmeyer 53aa92cfaf add support for neighbor list history refactoring in USER-OMP part 2 2017-10-11 10:30:29 -04:00
Axel Kohlmeyer 7e35042c42 add support for neighbor list history refactoring in USER-OMP part 1 2017-10-11 10:29:41 -04:00
Steve Plimpton 01051e4cb1 refactoring of neighbor history 2017-10-10 16:53:51 -06:00
Giacomo Fiorin d90aad887e Add Lepton library within lib/colvars 2017-10-09 15:25:43 -04:00
Ryan S. Elliott 775a15b9da Update lib/kim for kim-api-v1.9.2 2017-10-09 14:06:30 -05:00
Steve Plimpton 93c9a92743 Merge pull request #684 from irisTa56/bugfix-in-domain.cpp 
Bugfix for checking image flags
 2017-10-09 08:30:48 -06:00
Steve Plimpton 14dc1c698c Merge pull request #683 from wmbrownIntel/pppm_intel_fix 
Fixing bug in pppm/intel for AVX-512 with single precision and ik diff.
 2017-10-09 08:29:52 -06:00
Steve Plimpton a1f5693fe0 Merge pull request #681 from lammps/dump-modify 
remove dependence of dump modify 'at' and 'append'
 2017-10-09 08:29:12 -06:00
irisTa56 534b7adde4 Bugfix for checking image flags 2017-10-09 21:29:07 +09:00
Axel Kohlmeyer 02646100e9 correct handling of "at" keyword for netcdf dumps as suggested by @pastewka in PR #681 review 2017-10-09 07:49:29 -04:00
Michael Brown 7e58f084d2 Fixing bug in pppm/intel for AVX-512 with single precision and ik diff. 
This commit simplifies the code by eliminating packing optimizations that were slower
under typical parameters and had some memory bugs.
 2017-10-08 08:33:07 -07:00
Christoph Junghans 0f5d7dcc0f cmake: added USER-UEF 2017-10-07 12:38:41 -06:00
Christoph Junghans b6187173e6 Merge branch 'master' into HEAD 2017-10-07 12:35:51 -06:00
Steve Plimpton 88a33edb50 Merge pull request #680 from lammps/map-yes 
add atom_modify map yes, also timers to create_atoms and replicate
 2017-10-06 17:43:52 -06:00
Axel Kohlmeyer 6820db99e2 avoid merge conflict 2017-10-06 14:41:38 -04:00
Axel Kohlmeyer 58e1969de2 rename misleading "CPU time" into "Time spent" 2017-10-06 14:34:10 -04:00
Steve Plimpton e91e505fb3 remove dependence of dump modify 'at' and 'append' 2017-10-06 09:44:29 -06:00
Steve Plimpton f7cbdcf995 Merge pull request #673 from pastewka/17_dump_nc2 
Multi file support for NetCDF dump style
 2017-10-06 09:14:12 -06:00
Steve Plimpton 4cfa88b70f Merge pull request #674 from wmbrownIntel/user-intel-update 
Mike Brown has added DPD to the USER-INTEL package with speedups over 3X for Xeon Phi and over 1.7X for some Xeon processors.
 2017-10-06 09:12:39 -06:00
Lars Pastewka 352a20fc1c DOC: Updated doc to separate description of 'append' and 'at' keywords. 2017-10-06 16:38:15 +02:00
Lars Pastewka dc0e20947e MAINT: Return error when 'at' keyword is used without 'append yes'. 2017-10-06 16:37:52 +02:00
Axel Kohlmeyer 05847a0e87 Merge branch 'master' into user-intel-update 2017-10-06 10:18:38 -04:00
Steve Plimpton 439c2fd980 Merge pull request #677 from stanmoore1/kk_update 
Update to Kokkos r2.04.04 and add workaround for performance regression
 2017-10-05 17:10:00 -06:00
Steve Plimpton 15853a0e38 Merge pull request #676 from stanmoore1/kokkos_reverse_comm 
Add Kokkos threaded reverse communication
 2017-10-05 17:08:49 -06:00
Steve Plimpton bd17ee5df7 Merge pull request #675 from wesbarnett/master 
cmake: Add -restrict for Intel compilers
 2017-10-05 17:08:35 -06:00
Steve Plimpton a9b7ff1154 Merge pull request #679 from stanmoore1/kk_reax_comm 
ReaxC optimizations
 2017-10-05 17:08:17 -06:00
Steve Plimpton 0dd7ba26c0 Merge pull request #672 from akohlmey/phana-w-tricubic 
Streamline compilation of "phana" tool for fix phonon
 2017-10-05 17:01:37 -06:00
Steve Plimpton 7a90eef527 Merge pull request #668 from ovilab/modify_deallocation_fix 
Fixed proper deletion of fixes if fix is NULL
 2017-10-05 17:00:10 -06:00
Steve Plimpton 5d0626e50e Merge pull request #665 from akohlmey/collected-small-fixes 
Collected small fixes
 2017-10-05 16:58:49 -06:00
Steve Plimpton 4b7ca0383a Merge pull request #664 from timattox/kokkos_atom2bin 
Kokkos atom2bin
 2017-10-05 16:58:16 -06:00
Steve Plimpton 0ed987dc61 Merge pull request #663 from jdevemy/master 
Authorize hybrid/overlay for fix srp
 2017-10-05 16:56:20 -06:00
Steve Plimpton 55a3fdca80 Merge pull request #660 from junghans/latte_fix 
cmake: fix build with system latte
 2017-10-05 16:55:22 -06:00
Steve Plimpton 214c0cfb2b add atom_modify map yes, also timers to create_atoms and replicate 2017-10-05 16:44:24 -06:00
Stan Moore e0efdd50fa Switch to classic comm if ghost_velocity. The check_forward and check_reverse tests aren't necessary because the fix/pair/etc. comm is done in a separate routine. 2017-10-05 15:47:46 -06:00
Stan Moore 44d2e8ff74 Add pre_reverse to verlet_kokkos and comment out timer 2017-10-05 15:28:35 -06:00
Stan Moore 6bf2c60c07 Fix issues in Kokkos comm 2017-10-05 14:58:05 -06:00
Stan Moore eecd2fbaee Remove hardcoded value in fix_qeq_reax 2017-10-05 11:23:31 -06:00
Stan Moore 2b0bfcb10f Fix memory leak in pair_reaxc_kokkos 2017-10-05 10:35:09 -06:00
Stan Moore 3653f40120 Reduce unnecessary communication in fix_qeq_reax 2017-10-04 12:10:13 -06:00
Stan Moore bda0ee3aa1 Destroy unneeded fix in pair_reaxc_kokkos 2017-10-04 12:06:03 -06:00
Ulf R. Pedersen 957263431a Ensure consistency with documentation 2017-10-04 09:38:43 +02:00
Axel Kohlmeyer f12031f84d add support for building rigid bodies from custom atom properties or atom style variables 2017-10-04 01:14:57 -04:00
Axel Kohlmeyer c522b1b7a9 add call to fftw_cleanup() before exiting to avoid bogus leak reports when compiling with FFTW v3.x 2017-10-04 00:22:56 -04:00
Stan Moore a55adf4a68 Update to Kokkos r2.04.04 and add workaround for performance regression 2017-10-03 11:30:00 -06:00
James Barnett 2876baafd0 Use -restrict whenever Intel is used, no matter the package 2017-10-03 13:08:56 -04:00
Stan Moore ca032f21fb Add Kokkos threaded reverse comm option 2017-10-03 10:14:24 -06:00
James Barnett 197f082784 cmake: Add -restrict for Intel compilers for some packages 
Some packages (USER-OMP, OPT, and USER-INTEL) require the -restrict
flag when using the Intel compiler.
 2017-10-03 11:28:33 -04:00