Diffusion lammps (master) History

lammps/src
master15853a0e38dcefa96274f05…

Oct 6 2017

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.

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.

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.

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.
add support for fix_modify virial yes to fix smd
99e5dc710461
·Axel Kohlmeyer on Sep 15 2017, 07:21.
correct cut-n-paste error, add docs
2cd7cbd96415
·Axel Kohlmeyer on Sep 15 2017, 06:54.
add virial support to fix addforce
8776b8103337
·Axel Kohlmeyer on Sep 15 2017, 06:46.

Sep 14 2017

Bugfix for the limit keyword
da7776f818b8
·Julien Devemy on Sep 14 2017, 11:00.

Sep 12 2017

import changes to various fixes by aidan to include virial contributions
e196a2b9e54a
·Axel Kohlmeyer on Sep 12 2017, 04:24.
update src/.gitignore
cb19ef547e0d
·Axel Kohlmeyer on Sep 12 2017, 04:00.
the original fix qeq went away over 7 years ago, we don't need to purge it
95d849285345
·Axel Kohlmeyer on Sep 12 2017, 03:59.

Sep 11 2017

add infrastructure for enabling fixes to contribute to the virial by aidan
b3547a9eca79
·Axel Kohlmeyer on Sep 11 2017, 17:09.

Sep 8 2017

Merge remote-tracking branch 'origin/master' into exaalt
2f6be88c4a4b
·Christoph Junghans on Sep 8 2017, 15:04.
merging stable and exaalt branches into exaaltstable
7b1542a0ba2b
·Richard Zamora on Sep 8 2017, 00:31.

Sep 6 2017

have only one common MPI makefile for KOKKOS with CUDA
3a5d8362ffdc
·Axel Kohlmeyer on Sep 6 2017, 20:16.
make kokkos_cuda_mpi compatible with both MPICH and OpenMPI
5089b263b23a
·Axel Kohlmeyer on Sep 6 2017, 20:15.
recover ability to compile USER-INTEL without OpenMP enabled
de8297ea194b
·Axel Kohlmeyer on Sep 6 2017, 18:02.
Merge pull request #641 from lammps/doc-tweak
c80203cb0115
·Steve Plimpton / GitHub on Sep 6 2017, 16:52.
Merge pull request #640 from ohenrich/user-cgdna
4161868bcf69
·Steve Plimpton / GitHub on Sep 6 2017, 16:52.
Merge pull request #639 from rbberger/python_interface_improvements
9ca39c89a6a3
·Steve Plimpton / GitHub on Sep 6 2017, 16:51.
Merge pull request #632 from timattox/USER-DPD_kokkos_merge
99791ce01c09
·Steve Plimpton / GitHub on Sep 6 2017, 16:50.
remove duplicate listing of deleted USER-DPD files from Purge.list
0248a7b98e9e
·Tim Mattox on Sep 6 2017, 16:24.

Sep 5 2017

fix stupid typo (too much compiling of fortran codes...)
4c5d901e2b04
·Axel Kohlmeyer on Sep 5 2017, 22:45.
add a couple deleted files from USER-DPD to Purge.list
c8f92c1a617a
·Axel Kohlmeyer on Sep 5 2017, 22:42.
re-indent so that gcc no longer complains about inconsistent indentation
dec1d7b2dc48
·Axel Kohlmeyer on Sep 5 2017, 22:41.
Merge pull request #620 from amilumas/master
b1706060529b
·Steve Plimpton / GitHub on Sep 5 2017, 18:08.
Merge pull request #638 from jdevemy/master
65b295e826aa
·Steve Plimpton / GitHub on Sep 5 2017, 18:05.
Added sequence-dependent stacking and base-pairing strength
12fe614ddf58
·Oliver Henrich on Sep 5 2017, 11:48.
Add missing globals in library interface
6b2d321d1899
·Richard Berger on Sep 5 2017, 01:57.

Sep 1 2017

Merge branch 'master' of github.com:lammps/lammps
2b9646097c86
·Steve Plimpton on Sep 1 2017, 17:16.
patch 1Sep17
f58088ae619d
·Steve Plimpton on Sep 1 2017, 17:15.

Aug 31 2017

add temper/npt to src/USER-MISC/README
397bc225b27c
·Axel Kohlmeyer on Aug 31 2017, 20:56.
update .gitignore
d9d9ba824474
·Axel Kohlmeyer on Aug 31 2017, 20:52.
adapt formatting and naming conventions to fully match LAMMPS style. allow…
eba4be18c29a
·Axel Kohlmeyer on Aug 31 2017, 20:48.
Remove all thread fences except one in verlet_kokkos
d95a5f219e69
·Stan Moore on Aug 31 2017, 18:38.
Mods for extra/special/per/atom and add toluene
a5b65c1af48c
·Julien Devemy on Aug 31 2017, 15:03.

Aug 30 2017

USER-DPD: finish renaming #ifdef DEBUG_PAIR_CT to DEBUG_SSA_PAIR_CT
3e6cdd140011
·Tim Mattox on Aug 30 2017, 21:58.
USER-DPD: Kokkos version of Const Temperature DPD isn't implemented yet
dc7f1281b832
·Tim Mattox on Aug 30 2017, 18:01.
USER-DPD: remove some out-of-date FIXME comments in fix_shardlow_kokkos.cpp
2dd202cc761d
·Tim Mattox on Aug 30 2017, 17:34.
Rename SSA specific debug #ifdef to DEBUG_SSA_PAIR_CT
f2d8c37f27b1
·Tim Mattox on Aug 30 2017, 17:24.
Remove unnecessary check in npair_kokkos
a4a45f1d9cfb
·Stan Moore on Aug 30 2017, 01:25.

Aug 28 2017

Merge branch 'master' (21893539cb Aug 25) into USER-DPD_kokkos_merge
736e063971bc
·Tim Mattox on Aug 28 2017, 21:46.
Add files via upload
d0efd3a422ab
·Amulya / GitHub on Aug 28 2017, 20:48.

Aug 26 2017

Merge pull request #633 from lammps/doc-user-meso
21893539cbca
·Steve Plimpton / GitHub on Aug 26 2017, 01:41.
Merge pull request #582 from stanmoore1/kk_changes
dd101db79ced
·Steve Plimpton / GitHub on Aug 26 2017, 01:06.
tweak an eq in USER-MESO, also allow neigh to be built w/out styles
81ba181349d7
·Steve Plimpton on Aug 26 2017, 01:04.
Merge branch 'master' into USER-DPD_kokkos_merge
01dd0e173e51
·Stan Moore on Aug 26 2017, 00:02.

Aug 25 2017

Remove hardcoded map variables and debug output
1f8c4f2c62df
·Stan Moore on Aug 25 2017, 23:31.
Revert change to read_data.cpp
b73999ef215c
·Stan Moore on Aug 25 2017, 23:25.
Error out if using pair hybrid with Kokkos, but not pair hybrid/overlay
1e16fed9ab94
·Stan Moore on Aug 25 2017, 23:16.

lammps/srcmaster15853a0e38dcefa96274f05…

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lammps/src
master15853a0e38dcefa96274f05…