Diffusion lammps (master) History

lammps/src
masterd95a5f219e69c4146197191…

Aug 31 2017

Remove all thread fences except one in verlet_kokkos
d95a5f219e69
·Stan Moore on Aug 31 2017, 18:38.

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USER-DPD: remove some out-of-date FIXME comments in fix_shardlow_kokkos.cpp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.

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.
add checks when reading QEQ parameter file to avoid segfaults and memory…
44ccdb86df24
·Axel Kohlmeyer on Aug 19 2017, 01:24.
ignore file recently added to USER-INTEL
2e6a928aa315
·Axel Kohlmeyer on Aug 19 2017, 01:23.
add new compute fragment/atom
6f66e6c45445
·Axel Kohlmeyer on Aug 19 2017, 01:07.

Aug 18 2017

whitespace cleanup
d671a04274f9
·Axel Kohlmeyer on Aug 18 2017, 20:24.
allocate the temporary special array on the heap and not the stack (it may get…
bf7cff73d42a
·Axel Kohlmeyer on Aug 18 2017, 20:23.
molecule maxspecial value corrected when specials autogenerated
9e85b3178a14
·jrgissing on Aug 18 2017, 05:39.
patch 17Aug17
7ddcb6812b44
·Steve Plimpton on Aug 18 2017, 00:02.

Aug 17 2017

Merge pull request #613 from akohlmey/collected-small-changes
76cd61350d4c
·Steve Plimpton / GitHub on Aug 17 2017, 19:34.
Merge pull request #618 from lammps/intel
fa3c0c61d6a8
·Steve Plimpton / GitHub on Aug 17 2017, 19:32.
Merge pull request #612 from giacomofiorin/colvars-update-2017-08-10
c46d5ff422c2
·Steve Plimpton / GitHub on Aug 17 2017, 19:32.
Merge pull request #597 from ndtrung81/three-body-short-nlist
00aafef1a851
·Steve Plimpton / GitHub on Aug 17 2017, 19:31.

Aug 16 2017

USER-INTEL add-ons from Mike
1d4d2155a23b
·Steve Plimpton on Aug 16 2017, 01:12.

Aug 12 2017

fix incorrect preprocessor define for windows
81e7d4a94259
·Axel Kohlmeyer on Aug 12 2017, 06:35.

Aug 11 2017

Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks as of patch 10Aug17
13b804eeeba5
·Tim Mattox on Aug 11 2017, 20:53.
patch 11Aug17
0b3f1b8a156d
·Steve Plimpton on Aug 11 2017, 20:19.
Merge branch 'master' into USER-DPD_kokkos as of patch 10Aug17
4041db8d1a74
·Tim Mattox on Aug 11 2017, 19:25.
fix bug with pair_modify <style> compute not triggering the correct global…
27553283c30e
·Axel Kohlmeyer on Aug 11 2017, 14:28.
trigger relink after package library build through updating the time stamp on…
df56b2d6a43a
·Axel Kohlmeyer on Aug 11 2017, 14:16.
patch 10Aug17
52bec0f380dd
·Steve Plimpton on Aug 11 2017, 00:44.

Aug 10 2017

remove special_bonds extra keyword and refer to read_data and create_box instead
c8741f3a01a2
·Axel Kohlmeyer on Aug 10 2017, 21:12.
add more strict checking of data when parsing molecule files to detect format…
2a7d2dee3652
·Axel Kohlmeyer on Aug 10 2017, 20:49.
More robust change from initial to target restraint centers in Colvars
da01be7c1857
·Giacomo Fiorin on Aug 10 2017, 15:22.
Revert "remove -DLAMMPS_MEMALIGN from "make mpi" and "make serial" for…
0dc3cbaa8acc
·Axel Kohlmeyer on Aug 10 2017, 12:51.
when recomputing special bonds, make certain we do not shrink atom->maxspecial…
ce62c41252f6
·Axel Kohlmeyer on Aug 10 2017, 12:47.
remove -DLAMMPS_MEMALIGN from "make mpi" and "make serial" for increased…
4e97b5750873
·Axel Kohlmeyer on Aug 10 2017, 11:46.
make the deprecation warning nicer looking
77a628e4effe
·Axel Kohlmeyer on Aug 10 2017, 01:13.

Aug 9 2017

add a deprecation warning to pair style meam and make the reax one consistent…
210a77c5a0ea
·Axel Kohlmeyer on Aug 9 2017, 22:36.
Merge pull request #25 from timattox/USER-DPD_GBhacks_cudafix
e86b139817fc
·Tim Mattox / GitHub on Aug 9 2017, 21:32.
Added references to GPU package citations
3e9b41c6b74d
·Trung Nguyen on Aug 9 2017, 17:09.
updated comment for fix neb by steve
be25a7d9a424
·Axel Kohlmeyer on Aug 9 2017, 02:37.

Aug 8 2017

consistently use $(PYTHON) in the master makefile (which defaults to "python")
95ece8a6c01c
·Axel Kohlmeyer on Aug 8 2017, 23:03.
do not pollute global namespace by including mscg header in fix header
b7b62f6893c2
·Axel Kohlmeyer on Aug 8 2017, 19:20.

Aug 4 2017

update .gitignore
163ed276181a
·Axel Kohlmeyer on Aug 4 2017, 22:10.

Jul 31 2017

Revert 7edb294b447c62d3d2dbd4f9df984fb8d14f9a7c temporarily
5cd1dc93dc59
·Stan Moore on Jul 31 2017, 23:32.

Jul 28 2017

remove unused variable
841a92c7fada
·Axel Kohlmeyer on Jul 28 2017, 22:03.
Fix execution space issues in comm_kokkos
7edb294b447c
·Stan Moore on Jul 28 2017, 18:44.

Jul 27 2017

Merge branch 'master' into USER-DPD_kokkos_testing
9695aa60925d
·Stan Moore on Jul 27 2017, 23:51.
fix bug in power operator in LAMMPS variable expressions
e3973796bacc
·Axel Kohlmeyer on Jul 27 2017, 21:51.
Add missing sync to neigh_bond_kokkos
8e834d8be149
·Stan Moore on Jul 27 2017, 17:37.
Fix modify/sync issue in neigh_bond_kokkos
8f59c0e188b9
·Stan Moore on Jul 27 2017, 16:51.
Merge remote-tracking branch 'github/kim-doc' into install-and-docs-reviewed
72419b631313
·Axel Kohlmeyer on Jul 27 2017, 01:35.
Merge branch 'kim-install' into install-and-docs-reviewed
da7a5f55d3e4
·Axel Kohlmeyer on Jul 27 2017, 01:32.
restore lost KIM doc section in Section packages
934cbbbecaff
·Steve Plimpton on Jul 27 2017, 00:07.

Jul 26 2017

avoid invalid calls to memcpy(): when ndot == 0, pointers may be NULL
51a06334ad84
·Axel Kohlmeyer on Jul 26 2017, 18:08.
avoid integer overflow and remove unused function argument causing it
aa5ea95a0f34
·Axel Kohlmeyer on Jul 26 2017, 17:55.
import updated fix msst file with some additional cleanup and simplification
60c67b07dc37
·Axel Kohlmeyer on Jul 26 2017, 16:45.

Jul 25 2017

Fix concurrent modification issue in comm_kokkos
c3c9f357fdfa
·Stan Moore on Jul 25 2017, 22:37.
Merge branch 'master' into kk_changes
76fb4e08152f
·Stan Moore on Jul 25 2017, 22:16.
Fix execution space issues in Kokkos EAM pairstyles
d3fa882280a9
·Stan Moore on Jul 25 2017, 21:49.
Fixing Kokkos execution space issue with regions
557e5b964ad8
·Stan Moore on Jul 25 2017, 21:37.
Fix issue in Kokkos neighborlist
633ca33f2f91
·Stan Moore on Jul 25 2017, 21:08.
Merge branch 'master' into USER-DPD_kokkos_testing
bc446bb8b01b
·Stan Moore on Jul 25 2017, 20:12.

Jul 24 2017

patch 24Jul17
a59b7e4d5647
·Steve Plimpton on Jul 24 2017, 17:09.

Jul 23 2017

avoid floating point overflows in iterative solvers of fix shake
c24e316baaa6
·Axel Kohlmeyer on Jul 23 2017, 05:15.
avoid reporting negative memory allocation when memory_usage() is called before…
2c6e177d5c55
·Axel Kohlmeyer on Jul 23 2017, 05:14.

Jul 22 2017

disallow binary output with dump style local. fixes #596
7b2182833fea
·Axel Kohlmeyer on Jul 22 2017, 16:35.
Remove hardcoded execution spaces
8d485ea128d9
·Stan Moore on Jul 22 2017, 00:04.

Jul 21 2017

Fixing more execution space issues in KOKKOS package
f4b6b67f6ee6
·Stan Moore on Jul 21 2017, 23:04.
Fix execution space in manybody potentials
8ed881947ff9
·Stan Moore on Jul 21 2017, 22:28.
add support for trapping floating point exception as an optional compile time…
a477f26477fa
·Axel Kohlmeyer on Jul 21 2017, 21:37.
handle one more case where allowing shifted potential with cutoff 0.0 would…
00474ab09dcd
·Axel Kohlmeyer on Jul 21 2017, 16:30.
correct typo in USER-REAXC code
733ea61bf107
·Axel Kohlmeyer on Jul 21 2017, 07:15.
fix reaxc division by zero bug also for USER-OMP variant
ec23aef20b22
·Axel Kohlmeyer on Jul 21 2017, 00:19.

lammps/srcmasterd95a5f219e69c4146197191…

Aug 31 2017

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lammps/src
masterd95a5f219e69c4146197191…