Diffusion lammps (lammm-devel) History

lammps/src
lammm-develb1706060529b82476cab627…

Sep 5 2017

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.

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.
Mods for extra/special/per/atom and add toluene
a5b65c1af48c
·Julien Devemy on Aug 31 2017, 15:03.

Aug 28 2017

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.

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 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 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

Temper_NPT and example
6aa756968d40
·Amulya / GitHub on Aug 18 2017, 21:21.
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

patch 11Aug17
0b3f1b8a156d
·Steve Plimpton on Aug 11 2017, 20:19.
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.
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

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.

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.
avoid division by zero in reaxff bond interaction computations in very rare…
61b1487cbd93
·Axel Kohlmeyer on Jul 21 2017, 00:17.

Jul 20 2017

Merge pull request #585 from akohlmey/make-py-manual-cleanup
3cd597e948fa
·sjplimp / GitHub on Jul 20 2017, 20:05.
Merge pull request #583 from giacomofiorin/colvars-update-2017-07-19
eca61226c267
·sjplimp / GitHub on Jul 20 2017, 20:04.
Merge pull request #581 from libAtoms/idces2quip
fac3e3daa237
·sjplimp / GitHub on Jul 20 2017, 20:04.
Merge pull request #576 from akohlmey/sanitizer-changes
72e5f537c8d0
·sjplimp / GitHub on Jul 20 2017, 20:03.
update manual links that got broken when removing and renumbering a section
a351977c5904
·Axel Kohlmeyer on Jul 20 2017, 18:25.
updates to USER-REAXC code in USER-OMP from Chris Knight. addresses issues with…
8499e72cdc91
·Axel Kohlmeyer on Jul 20 2017, 18:11.

Jul 19 2017

Update Colvars to version 2017-07-15 and support automated builds for it
ee6cac826e65
·Giacomo Fiorin on Jul 19 2017, 20:24.
support QUIP wrapper API version query, relax hybrid restriction to allow…
52a1c54d500e
·Axel Kohlmeyer on Jul 19 2017, 19:17.

Jul 18 2017

fix memory corruption issue in fix reax/c/species
148364949e21
·Axel Kohlmeyer on Jul 18 2017, 22:11.
fix off-by-one bug when copying strings
17aff29fe2e7
·Axel Kohlmeyer on Jul 18 2017, 21:48.
add various checks and improvements to identify incompatible uses and warn or…
f96b9e0dcf55
·Axel Kohlmeyer on Jul 18 2017, 21:48.
add workaround that allows pair style quip to work with -DLAMMPS_BIGBIG…
02572a4099a6
·Axel Kohlmeyer on Jul 18 2017, 20:41.
Prefer DeviceType specification over RangePolicy
1b34bec81a2c
·Stan Moore on Jul 18 2017, 18:59.

lammps/srclammm-develb1706060529b82476cab627…

Sep 5 2017

Sep 1 2017

Aug 31 2017

Aug 28 2017

Aug 26 2017

Aug 24 2017

Aug 23 2017

Aug 21 2017

Aug 20 2017

Aug 19 2017

Aug 18 2017

Aug 17 2017

Aug 16 2017

Aug 12 2017

Aug 11 2017

Aug 10 2017

Aug 9 2017

Aug 8 2017

Aug 4 2017

Jul 31 2017

Jul 28 2017

Jul 27 2017

Jul 26 2017

Jul 25 2017

Jul 24 2017

Jul 23 2017

Jul 22 2017

Jul 21 2017

Jul 20 2017

Jul 19 2017

Jul 18 2017

lammps/src
lammm-develb1706060529b82476cab627…