Diffusion lammps (master) History

lammps/src
master2fe1d1b904516fe8045fede…

Oct 18 2017

Merge pull request #697 from andeplane/fix_heat_bug
2fe1d1b90451
·Steve Plimpton / GitHub on Oct 18 2017, 21:26.
Merge pull request #695 from timattox/USER-DPD_small_updates
b1b4a52b14e2
·Steve Plimpton / GitHub on Oct 18 2017, 21:25.
Merge pull request #696 from wmbrownIntel/intel-update-oct17
382de5034188
·Steve Plimpton / GitHub on Oct 18 2017, 21:25.
Merge pull request #688 from lammps/history
7dfc6b7eab71
·Steve Plimpton / GitHub on Oct 18 2017, 21:24.
Avoid checking region when not specified
19eb5d389778
·Anders Hafreager on Oct 18 2017, 18:05.
update multi-threaded neighbor list build for neighbor list refactor
17c17ac40996
·Axel Kohlmeyer on Oct 18 2017, 17:25.
update respa/omp integrator style for neighbor list refactor
39ededd46cf7
·Axel Kohlmeyer on Oct 18 2017, 17:24.
update several pair styles to be compliant with refactored respa lists data…
2c7528811d7f
·Axel Kohlmeyer on Oct 18 2017, 17:24.
more changes to rRESPA neighbor lists
0966e14e73a7
·Steve Plimpton on Oct 18 2017, 01:33.

Oct 17 2017

USER-INTEL: Bug fix for case where a bond/angle/dihedral/improper style is…
bb141aaae04f
·Michael Brown on Oct 17 2017, 07:51.

Oct 16 2017

Merge branch 'history' of github.com:lammps/lammps into history
59de1a71c8cd
·Axel Kohlmeyer on Oct 16 2017, 20:37.
USER-DPD Kokkos: propagate the new neigh_modify options from efaa4c67
4c6779cb0d61
·Tim Mattox on Oct 16 2017, 20:37.
update USER-OMP code for shear history neighbor refactoring
5fb5f70ec684
·Axel Kohlmeyer on Oct 16 2017, 20:37.
USER-DPD: remove unused coord2bin() variants, and add ISFINITE checks
b0bba1976b33
·Tim Mattox on Oct 16 2017, 20:36.

Oct 13 2017

Update Colvars to version 2017-10-11
3e89b270fdf8
·Giacomo Fiorin on Oct 13 2017, 19:45.
Fix compile errors from neigh history refactor
f6ddc8c7c9ba
·Stan Moore on Oct 13 2017, 18:49.
drop const qualifier to allow bracketing of lookup index
3df9caf43533
·Axel Kohlmeyer on Oct 13 2017, 16:29.
handle lookup exceptions consistently across energy and energy+force lookup in…
fa2e5ac2d902
·Axel Kohlmeyer on Oct 13 2017, 16:13.
handle invalid lookup for bond/angle tabulation
b7c749260885
·Axel Kohlmeyer on Oct 13 2017, 15:50.
bugfix. avoiding operating on uninitialize data. closes #690
cee94da85e16
·Axel Kohlmeyer on Oct 13 2017, 06:15.

Oct 11 2017

add support for neighbor list history refactoring in USER-OMP part 2
53aa92cfafd1
·Axel Kohlmeyer on Oct 11 2017, 16:30.
add support for neighbor list history refactoring in USER-OMP part 1
7e35042c42e9
·Axel Kohlmeyer on Oct 11 2017, 16:29.
refactoring of neighbor history
01051e4cb13c
·Steve Plimpton on Oct 11 2017, 00:53.

Oct 9 2017

Merge pull request #684 from irisTa56/bugfix-in-domain.cpp
93c9a9274319
·Steve Plimpton / GitHub on Oct 9 2017, 16:30.
Merge pull request #683 from wmbrownIntel/pppm_intel_fix
14dc1c698c60
·Steve Plimpton / GitHub on Oct 9 2017, 16:29.
Merge pull request #681 from lammps/dump-modify
a1f5693fe08e
·Steve Plimpton / GitHub on Oct 9 2017, 16:29.
Bugfix for checking image flags
534b7adde4b3
·irisTa56 on Oct 9 2017, 14:29.
correct handling of "at" keyword for netcdf dumps as suggested by @pastewka in…
02646100e91f
·Axel Kohlmeyer on Oct 9 2017, 13:49.

Oct 8 2017

Fixing bug in pppm/intel for AVX-512 with single precision and ik diff. This…
7e58f084d226
·Michael Brown on Oct 8 2017, 17:33.

Oct 7 2017

Merge pull request #680 from lammps/map-yes
88a33edb5022
·Steve Plimpton / GitHub on Oct 7 2017, 01:43.

Oct 6 2017

rename misleading "CPU time" into "Time spent"
58e1969de241
·Axel Kohlmeyer on Oct 6 2017, 20:34.
remove dependence of dump modify 'at' and 'append'
e91e505fb36e
·Steve Plimpton on Oct 6 2017, 17:44.
Merge pull request #673 from pastewka/17_dump_nc2
f7cbdcf99584
·Steve Plimpton / GitHub on Oct 6 2017, 17:14.
MAINT: Return error when 'at' keyword is used without 'append yes'.
dc0e20947ee7
·Lars Pastewka on Oct 6 2017, 16:37.
Merge branch 'master' into user-intel-update
05847a0e8713
·Axel Kohlmeyer / GitHub on Oct 6 2017, 16:18.
Merge pull request #676 from stanmoore1/kokkos_reverse_comm
15853a0e38dc
·Steve Plimpton / GitHub on Oct 6 2017, 01:08.
Merge pull request #679 from stanmoore1/kk_reax_comm
a9b7ff1154d3
·Steve Plimpton / GitHub on Oct 6 2017, 01:08.
Merge pull request #668 from ovilab/modify_deallocation_fix
7a90eef527ed
·Steve Plimpton / GitHub on Oct 6 2017, 01:00.
Merge pull request #665 from akohlmey/collected-small-fixes
5d0626e50e30
·Steve Plimpton / GitHub on Oct 6 2017, 00:58.
Merge pull request #664 from timattox/kokkos_atom2bin
4b7ca0383aac
·Steve Plimpton / GitHub on Oct 6 2017, 00:58.
add atom_modify map yes, also timers to create_atoms and replicate
214c0cfb2b7e
·Steve Plimpton on Oct 6 2017, 00:44.

Oct 5 2017

Switch to classic comm if ghost_velocity. The check_forward and check_reverse…
e0efdd50fab3
·Stan Moore on Oct 5 2017, 23:47.
Add pre_reverse to verlet_kokkos and comment out timer
44d2e8ff74d5
·Stan Moore on Oct 5 2017, 23:28.
Fix issues in Kokkos comm
6bf2c60c07ed
·Stan Moore on Oct 5 2017, 22:58.
Remove hardcoded value in fix_qeq_reax
eecd2fbaee77
·Stan Moore on Oct 5 2017, 19:23.
Fix memory leak in pair_reaxc_kokkos
2b0bfcb10f90
·Stan Moore on Oct 5 2017, 18:35.

Oct 4 2017

Reduce unnecessary communication in fix_qeq_reax
3653f4012013
·Stan Moore on Oct 4 2017, 20:10.
Destroy unneeded fix in pair_reaxc_kokkos
bda0ee3aa1eb
·Stan Moore on Oct 4 2017, 20:06.
add call to fftw_cleanup() before exiting to avoid bogus leak reports when…
c522b1b7a974
·Axel Kohlmeyer on Oct 4 2017, 06:22.

Oct 3 2017

Add Kokkos threaded reverse comm option
ca032f21fbfa
·Stan Moore on Oct 3 2017, 18:14.
intel_simd.h is currently also needed by dihedral/charmm, not just sw.
9dc42fd4db71
·Michael Brown on Oct 3 2017, 08:53.
Minor adjustments to intel makefiles and documentation based on the reversed…
5e8926963126
·Michael Brown on Oct 3 2017, 08:41.
update README in USER-INTEL for recent LRT logic reversal
d2aa05cb3661
·Axel Kohlmeyer on Oct 3 2017, 03:24.
reverse logic for using MKL pRNG: this way, make serial and make mpi will…
2a24cbfe0c2f
·Axel Kohlmeyer on Oct 3 2017, 03:13.

Oct 2 2017

whitespace cleanup
8d384b9149c7
·Axel Kohlmeyer on Oct 2 2017, 21:03.
Reduce GPU data transfer
529eeb603923
·Stan Moore on Oct 2 2017, 17:31.
Adding pair style dpd/intel and dihedral style fourier/intel Adding raw…
cf24dd026520
·Michael Brown on Oct 2 2017, 13:53.

Oct 1 2017

MAINT: Only set append flag when not in multifile mode.
fbe42cda2d24
·Lars Pastewka on Oct 1 2017, 14:31.
MAINT: Removed obsolete prmtop writer.
56d21bfb057b
·Lars Pastewka on Oct 1 2017, 14:22.
ENH: Enable multi file writes.
100231bba8f1
·Lars Pastewka on Oct 1 2017, 14:21.
MAINT: Renamed _put_var1_x to _put_var1_bigint
84378f8ae27f
·Lars Pastewka on Oct 1 2017, 14:05.
MAINT: bigint (int64) maps onto either long or long long, depending on platform.
6e342d2e45dc
·Lars Pastewka on Oct 1 2017, 14:03.

Sep 30 2017

Reduce memory churn in Kokkos package
a86572f4fcb4
·Stan Moore on Sep 30 2017, 00:20.

Sep 29 2017

Partially revert 01d0a5c, avoid atomics, safe because of the while loop. Worst…
9f2740b7f18f
·Stan Moore on Sep 29 2017, 21:41.
Add sync/modify to nbin_kokkos
d7aac2fed53c
·Stan Moore on Sep 29 2017, 21:26.
use <> for system includes not ""
d898afaafb7a
·Axel Kohlmeyer on Sep 29 2017, 15:19.

Sep 27 2017

Fixed proper deletion of fixes if fix is NULL
23e283f13551
·Anders Hafreager on Sep 27 2017, 16:20.

Sep 26 2017

need to re-init timers after initial setup
53e4ee4f2dc9
·Axel Kohlmeyer on Sep 26 2017, 05:20.
USER-OMP package depends on USER-DRUDE
b60cff7e7773
·Axel Kohlmeyer on Sep 26 2017, 05:15.
-ltbbmalloc is required
38530415c8f0
·Axel Kohlmeyer on Sep 26 2017, 02:03.
update src/.gitignore for LATTE package
0573aaa6da3a
·Axel Kohlmeyer on Sep 26 2017, 01:37.

Sep 25 2017

whitespace fixes, silence compiler warning about too few format specifiers
836a6d292c10
·Axel Kohlmeyer on Sep 25 2017, 22:31.
first pass at implementing atom2bin for KOKKOS neighbor lists
32e0de7a67a1
·Tim Mattox on Sep 25 2017, 21:06.
KOKKOS: minor typo fix
789812ec3dce
·Tim Mattox on Sep 25 2017, 21:06.
Authorize hybrid/overlay for fix srp
78a486c0fdfe
·Julien Devemy on Sep 25 2017, 16:18.

Sep 22 2017

patch 22Sep17
f2c1172741b5
·Steve Plimpton on Sep 22 2017, 23:46.
Make Kokkos comm give warning and switch to classic comm instead of erroring out
3ed39ca844ba
·Stan Moore on Sep 22 2017, 21:03.
Merge pull request #652 from junghans/latte
ee487ef4aa4f
·Steve Plimpton / GitHub on Sep 22 2017, 18:32.

Sep 21 2017

update fix latte examples and virial
a8ae8866676e
·Steve Plimpton on Sep 21 2017, 18:40.

Sep 20 2017

whitespace cleanup
ad25a9529758
·Axel Kohlmeyer on Sep 20 2017, 17:13.
new SNAP potentials and examples
dd49d54889a2
·Steve Plimpton on Sep 20 2017, 16:54.
Merge pull request #655 from akohlmey/fixes-for-patch
fbaa7ab8fa55
·Steve Plimpton / GitHub on Sep 20 2017, 16:51.
Merge pull request #645 from akohlmey/kokkos-makefile-updates
2e9803efb31d
·Steve Plimpton / GitHub on Sep 20 2017, 16:40.
LATTE package doc update and some small code changes
ac897ea6457c
·Steve Plimpton on Sep 20 2017, 00:27.

Sep 19 2017

correct USER-INTEL installer script for verlet_lrt_intel files
19f1f3a3e063
·Axel Kohlmeyer on Sep 19 2017, 17:48.
reverse the pre-processor logic of the LRT mode define
cdb6ec7419d0
·Axel Kohlmeyer on Sep 19 2017, 17:24.
allow fix viscous to be used with dynamic groups
aad8cd10ffa2
·Axel Kohlmeyer on Sep 19 2017, 00:08.

Sep 18 2017

fix external only needs to collect virial in case it is requested
1ac90815f342
·Axel Kohlmeyer on Sep 18 2017, 05:59.
activate virial contribution in `fix lb/rigid/pc/sphere` by default and protect…
5f1842829e48
·Axel Kohlmeyer on Sep 18 2017, 03:10.
whether virial contributions from fixes are included depend on thermo_virial…
66130f555700
·Axel Kohlmeyer on Sep 18 2017, 02:50.
correctly initialize `thermo_virial` in fix poems and protect access to…
388eab5eebe5
·Axel Kohlmeyer on Sep 18 2017, 02:49.
remove bogus version of temper/npt command
a500048c9c4a
·Axel Kohlmeyer on Sep 18 2017, 01:25.
remove another couple of purge items from long ago
b4ecad7fbf5b
·Axel Kohlmeyer on Sep 18 2017, 01:22.
automatically call 'make purge' before calling 'make package-update' or 'make…
b5894e2190ca
·Axel Kohlmeyer on Sep 18 2017, 01:19.

Sep 16 2017

correct embarrassing typo
6f1935ea4058
·Axel Kohlmeyer on Sep 16 2017, 03:58.
Merge branch 'exaalt' of gitlab.com:exaalt/lammps into latte
cc2a53a8daef
·Christoph Junghans on Sep 16 2017, 01:43.
Merge branch 'exaalt' of gitlab.com:exaalt/lammps into exaalt
d614d56c34c4
·Christian Negre on Sep 16 2017, 01:41.
added fix_latte.txt
39daf3c6f68f
·Christian Negre on Sep 16 2017, 01:40.
Merge remote-tracking branch 'origin/master' into latte
17aeccf19f3f
·Christoph Junghans on Sep 16 2017, 00:18.

Sep 15 2017

Merge pull request #649 from akohlmey/fix-virial-aidan
d101fe3e79fd
·Steve Plimpton / GitHub on Sep 15 2017, 23:25.

lammps/srcmaster2fe1d1b904516fe8045fede…

Oct 18 2017

Oct 17 2017

Oct 16 2017

Oct 13 2017

Oct 11 2017

Oct 9 2017

Oct 8 2017

Oct 7 2017

Oct 6 2017

Oct 5 2017

Oct 4 2017

Oct 3 2017

Oct 2 2017

Oct 1 2017

Sep 30 2017

Sep 29 2017

Sep 27 2017

Sep 26 2017

Sep 25 2017

Sep 22 2017

Sep 21 2017

Sep 20 2017

Sep 19 2017

Sep 18 2017

Sep 16 2017

Sep 15 2017

lammps/src
master2fe1d1b904516fe8045fede…