Diffusion lammps (master) History

lammps/src
masterd898afaafb7ac183a8458e9…

Sep 29 2017

use <> for system includes not ""
d898afaafb7a
·Axel Kohlmeyer on Sep 29 2017, 15:19.

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.

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.
Fix execution space issues
a062944de95e
·Stan Moore on Aug 25 2017, 22:45.
Must use atomics for GPUs in pair_exp6_rx_kokkos
a641289d5ba3
·Stan Moore on Aug 25 2017, 20:36.

Aug 24 2017

print write dump systen init warning only on MPI rank 0
dea92fbf5221
·Axel Kohlmeyer on Aug 24 2017, 03:01.

Aug 23 2017

Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks
e55fa9d320d3
·Stan Moore on Aug 23 2017, 23:21.
Merge branch 'master' into USER-DPD_kokkos
cbf3646806f9
·Stan Moore on Aug 23 2017, 23:20.
Remove unnecessary thread fences
f5a99dece766
·Stan Moore on Aug 23 2017, 23:08.
Remove unused function in rand_pool_wrap_kokkos
4784506ba907
·Stan Moore on Aug 23 2017, 23:02.
Fix compile error for CUDA in pair_exp6_rx_kokkos
270abff2a2a1
·Stan Moore on Aug 23 2017, 22:59.
Merge pull request #624 from akohlmey/compute-fragment
7b7a5076d00a
·Steve Plimpton / GitHub on Aug 23 2017, 22:14.
Merge pull request #622 from akohlmey/collected-small-fixes
f7a0a6eb7069
·Steve Plimpton / GitHub on Aug 23 2017, 22:12.
Merge pull request #621 from lammps/user-meso
d80a6cbd317a
·Steve Plimpton / GitHub on Aug 23 2017, 22:12.
add compatibility to NetCDF 4.3.3 as bundled with RHEL 7.x
b52efa28507f
·Axel Kohlmeyer on Aug 23 2017, 21:28.
fix issues indicated by compiler warnings
79d5ca669dcb
·Axel Kohlmeyer on Aug 23 2017, 05:46.
add USER-MESO files to .gitignore
26c15140be20
·Axel Kohlmeyer on Aug 23 2017, 05:46.

Aug 22 2017

Merge branch 'master' into USER-DPD_kokkos
5c985946d58f
·Stan Moore on Aug 22 2017, 21:50.

Aug 21 2017

fix typo
24c00b1f7a20
·Axel Kohlmeyer on Aug 21 2017, 19:12.
add a compute aggregate/atom, that combines the rules for compute cluster/atom…
5a0c3aea8ac1
·Axel Kohlmeyer on Aug 21 2017, 19:12.
add initializers for nmatch/nwant variables in molecule file parser
d1a0c040c9f8
·Axel Kohlmeyer on Aug 21 2017, 05:28.

Aug 20 2017

skip over disabled bonds
c895df73d624
·Axel Kohlmeyer on Aug 20 2017, 15:49.
trim unneeded includes
35fd82b60282
·Axel Kohlmeyer on Aug 20 2017, 15:19.
use list of bonds per atom instead of bondlist, as that will work with shake as…
c5ce3ffe60e4
·Axel Kohlmeyer on Aug 20 2017, 15:18.

Aug 19 2017

more cleanup, checks and generalization of QEQ parameter file parsing
aa1ce09b1264
·Axel Kohlmeyer on Aug 19 2017, 02:03.
new USER-MESO package
f945d4567d4f
·Steve Plimpton on Aug 19 2017, 01:33.

lammps/srcmasterd898afaafb7ac183a8458e9…

Sep 29 2017

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lammps/src
masterd898afaafb7ac183a8458e9…