39ededd46c
update respa/omp integrator style for neighbor list refactor
2017-10-18 11:24:44 -04:00
2c7528811d
update several pair styles to be compliant with refactored respa lists data structures
2017-10-18 11:24:12 -04:00
0966e14e73
more changes to rRESPA neighbor lists
2017-10-17 17:33:01 -06:00
59de1a71c8
Merge branch 'history' of github.com:lammps/lammps into history
2017-10-16 14:37:30 -04:00
5fb5f70ec6
update USER-OMP code for shear history neighbor refactoring
2017-10-16 14:37:20 -04:00
f6ddc8c7c9
Fix compile errors from neigh history refactor
2017-10-13 10:49:31 -06:00
53aa92cfaf
add support for neighbor list history refactoring in USER-OMP part 2
2017-10-11 10:30:29 -04:00
7e35042c42
add support for neighbor list history refactoring in USER-OMP part 1
2017-10-11 10:29:41 -04:00
01051e4cb1
refactoring of neighbor history
2017-10-10 16:53:51 -06:00
93c9a92743
Merge pull request #684 from irisTa56/bugfix-in-domain.cpp
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Bugfix for checking image flags
2017-10-09 08:30:48 -06:00
14dc1c698c
Merge pull request #683 from wmbrownIntel/pppm_intel_fix
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Fixing bug in pppm/intel for AVX-512 with single precision and ik diff.
2017-10-09 08:29:52 -06:00
a1f5693fe0
Merge pull request #681 from lammps/dump-modify
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remove dependence of dump modify 'at' and 'append'
2017-10-09 08:29:12 -06:00
534b7adde4
Bugfix for checking image flags
2017-10-09 21:29:07 +09:00
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
7e58f084d2
Fixing bug in pppm/intel for AVX-512 with single precision and ik diff.
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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
88a33edb50
Merge pull request #680 from lammps/map-yes
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add atom_modify map yes, also timers to create_atoms and replicate
2017-10-06 17:43:52 -06:00
58e1969de2
rename misleading "CPU time" into "Time spent"
2017-10-06 14:34:10 -04:00
e91e505fb3
remove dependence of dump modify 'at' and 'append'
2017-10-06 09:44:29 -06:00
f7cbdcf995
Merge pull request #673 from pastewka/17_dump_nc2
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Multi file support for NetCDF dump style
2017-10-06 09:14:12 -06:00
dc0e20947e
MAINT: Return error when 'at' keyword is used without 'append yes'.
2017-10-06 16:37:52 +02:00
05847a0e87
Merge branch 'master' into user-intel-update
2017-10-06 10:18:38 -04:00
15853a0e38
Merge pull request #676 from stanmoore1/kokkos_reverse_comm
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Add Kokkos threaded reverse communication
2017-10-05 17:08:49 -06:00
a9b7ff1154
Merge pull request #679 from stanmoore1/kk_reax_comm
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ReaxC optimizations
2017-10-05 17:08:17 -06:00
7a90eef527
Merge pull request #668 from ovilab/modify_deallocation_fix
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Fixed proper deletion of fixes if fix is NULL
2017-10-05 17:00:10 -06:00
5d0626e50e
Merge pull request #665 from akohlmey/collected-small-fixes
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Collected small fixes
2017-10-05 16:58:49 -06:00
4b7ca0383a
Merge pull request #664 from timattox/kokkos_atom2bin
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Kokkos atom2bin
2017-10-05 16:58:16 -06:00
214c0cfb2b
add atom_modify map yes, also timers to create_atoms and replicate
2017-10-05 16:44:24 -06:00
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
44d2e8ff74
Add pre_reverse to verlet_kokkos and comment out timer
2017-10-05 15:28:35 -06:00
6bf2c60c07
Fix issues in Kokkos comm
2017-10-05 14:58:05 -06:00
eecd2fbaee
Remove hardcoded value in fix_qeq_reax
2017-10-05 11:23:31 -06:00
2b0bfcb10f
Fix memory leak in pair_reaxc_kokkos
2017-10-05 10:35:09 -06:00
3653f40120
Reduce unnecessary communication in fix_qeq_reax
2017-10-04 12:10:13 -06:00
bda0ee3aa1
Destroy unneeded fix in pair_reaxc_kokkos
2017-10-04 12:06:03 -06:00
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
ca032f21fb
Add Kokkos threaded reverse comm option
2017-10-03 10:14:24 -06:00
9dc42fd4db
intel_simd.h is currently also needed by dihedral/charmm, not just sw.
2017-10-02 23:53:05 -07:00
5e89269631
Minor adjustments to intel makefiles and documentation based on the reversed
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preprocessor logic and default memory align. Removing knl_coprocessor makefile.
2017-10-02 23:41:14 -07:00
d2aa05cb36
update README in USER-INTEL for recent LRT logic reversal
2017-10-02 21:24:51 -04:00
2a24cbfe0c
reverse logic for using MKL pRNG: this way, make serial and make mpi will compile LAMMPS with USER-INTEL installed
2017-10-02 21:13:51 -04:00
8d384b9149
whitespace cleanup
2017-10-02 15:03:48 -04:00
529eeb6039
Reduce GPU data transfer
2017-10-02 09:31:39 -06:00
cf24dd0265
Adding pair style dpd/intel and dihedral style fourier/intel
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Adding raw performance numbers for Skylake xeon server.
Fixes for using older Intel compilers and compiling without OpenMP.
Fix adding in hooks for using USER-INTEL w/ minimization.
2017-10-02 04:53:17 -07:00
fbe42cda2d
MAINT: Only set append flag when not in multifile mode.
2017-10-01 14:31:33 +02:00
56d21bfb05
MAINT: Removed obsolete prmtop writer.
2017-10-01 14:22:04 +02:00
100231bba8
ENH: Enable multi file writes.
2017-10-01 14:21:09 +02:00
84378f8ae2
MAINT: Renamed _put_var1_x to _put_var1_bigint
2017-10-01 14:05:12 +02:00
6e342d2e45
MAINT: bigint (int64) maps onto either long or long long, depending on platform. Automatically choose the correct one.
2017-10-01 14:03:52 +02:00
a86572f4fc
Reduce memory churn in Kokkos package
2017-09-29 16:20:19 -06:00
9f2740b7f1
Partially revert 01d0a5c, avoid atomics, safe because of the while loop. Worst case is the resize will happen again because max wasn't accurate
2017-09-29 13:41:35 -06:00
