Diffusion lammps (master) History

lammps/src
master5cd1dc93dc5956a89a1ba42…

Jul 31 2017

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

Jul 28 2017

Fix execution space issues in comm_kokkos
7edb294b447c
·Stan Moore on Jul 28 2017, 18:44.

Jul 27 2017

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.

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.
Removing stray file
9df61b642e56
·Stan Moore on Jul 18 2017, 18:44.
Fixing execution space issues in KOKKOS package
3c88b2a9805b
·Stan Moore on Jul 18 2017, 17:53.
protect LAMMPS from calling incompatible QUIP library with -DLAMMPS_BIGBIG
085cbee1163d
·Axel Kohlmeyer on Jul 18 2017, 17:17.
safer handling of memory management for lists in reax/c
4ad952899922
·Axel Kohlmeyer on Jul 18 2017, 13:37.
avoid division by zero in peri pair styles
358915d16ee7
·Axel Kohlmeyer on Jul 18 2017, 13:26.
fix unitialized pointer issue in USER-OMP with pppm/disp
bc5186bc30e1
·Axel Kohlmeyer on Jul 18 2017, 06:44.
fix memory leak in list of neighbor list requests
c083d5d6f3f8
·Axel Kohlmeyer on Jul 18 2017, 06:18.
plug small memory leak in USER-OMP variants of pppm kspace styles
c3a2ed0d1b30
·Axel Kohlmeyer on Jul 18 2017, 05:56.
skip table consistency check for bitmapped tables
23033404b0a4
·Axel Kohlmeyer on Jul 18 2017, 00:18.

Jul 17 2017

Modified the quip/lammps interface to pass lammps atom ids
bda07301693a
·Max Veit on Jul 17 2017, 17:55.

Jul 16 2017

add sanity checks to EAM potential file reader subroutine
992ce797010d
·Axel Kohlmeyer on Jul 16 2017, 20:37.

Jul 15 2017

avoid division by zero when using cutoff 0.0 with pair_modify shift yes
4ec07422f07c
·Axel Kohlmeyer on Jul 15 2017, 05:33.
Revert "do not allow pairwise cutoffs <= 0.0. avoids undefined behavior and…
3f297382ac1f
·Axel Kohlmeyer on Jul 15 2017, 04:41.

Jul 14 2017

do not allow pairwise cutoffs <= 0.0. avoids undefined behavior and division by…
a04711b21f06
·Axel Kohlmeyer on Jul 14 2017, 19:49.
print warnings in Pair::init() only on MPI rank 0
e084d4dad633
·Axel Kohlmeyer on Jul 14 2017, 19:48.
avoid casts to the wrong derived class, which upsets code analysis tools. seems…
522bc13d6786
·Axel Kohlmeyer on Jul 14 2017, 19:47.
AIREBO: Add doc about OpenKIM issue
e5405cdb0477
·Markus Hoehnerbach on Jul 14 2017, 17:57.
silence static code analysis warning
8a1db83b7306
·Axel Kohlmeyer on Jul 14 2017, 16:31.

Jul 13 2017

Merge branch 'compute_rdf_dynamic' into sanitizer-changes
de45a46529f9
·Axel Kohlmeyer on Jul 13 2017, 23:39.
whitespace cleanup
32ca58bdf23c
·Axel Kohlmeyer on Jul 13 2017, 23:34.
avoid trying to free NULL pointers and reallocate storage for OpenMP, when not…
111786e92e0f
·Axel Kohlmeyer on Jul 13 2017, 23:33.
protect warning printf()s to be only printed on rank 0
132cee984051
·Axel Kohlmeyer on Jul 13 2017, 23:33.
add flag to reax/c system struct to signaling, whether OpenMP is active
609c8b1e8774
·Axel Kohlmeyer on Jul 13 2017, 23:32.
Merge pull request #561 from v0i0/fix-airebo-various
fc36754ca22a
·sjplimp / GitHub on Jul 13 2017, 21:10.
Merge pull request #574 from lammps/snap-virial
3a46c34c2fa3
·sjplimp / GitHub on Jul 13 2017, 21:07.
Merge branch 'master' into compute_rdf_dynamic
cb935730c0b6
·Axel Kohlmeyer on Jul 13 2017, 21:02.
Merge pull request #571 from hasanmetin/reaxc-omp-credits-update
fc6c10c9a98a
·sjplimp / GitHub on Jul 13 2017, 19:27.
Merge pull request #570 from akohlmey/collected-small-changes
a3a0c9b144c5
·sjplimp / GitHub on Jul 13 2017, 19:26.
Merge pull request #568 from akohlmey/fix_gcmc_parallel_workaround
e58bcd8b4aa4
·sjplimp / GitHub on Jul 13 2017, 19:23.
Merge pull request #566 from akohlmey/compute_rdf_dynamic
ef2f4980e9dd
·sjplimp / GitHub on Jul 13 2017, 19:23.
Merge pull request #560 from aershadinia/master
d3a45f6d5057
·sjplimp / GitHub on Jul 13 2017, 19:22.
changes to SNAP virial from Aidan
d0cc1dfbb80c
·Steve Plimpton on Jul 13 2017, 19:19.
fix off-by-one memory allocation bug
de8d417aeccd
·Axel Kohlmeyer on Jul 13 2017, 16:55.
remove useless and incorrect neighbor list request in fix qeq/comb/omp
0af9203fdc99
·Axel Kohlmeyer on Jul 13 2017, 00:32.
fix possible uninitialized data access with pppm and pppm/disp
c24fca61f37a
·Axel Kohlmeyer on Jul 13 2017, 00:14.
avoid accessing uninitialized data when exiting LAMMPS early
01e848387ac8
·Axel Kohlmeyer on Jul 13 2017, 00:00.

Jul 12 2017

avoid small memory leak with USER-REAXC + USER-OMP, spotted by GCC's address…
734729b0a4d5
·Axel Kohlmeyer on Jul 12 2017, 23:27.
update src/.gitignore for fix wall*/ees sources
a419c7c57c52
·Axel Kohlmeyer on Jul 12 2017, 17:40.
fix enforce2d has to be defined after fixes with enforce2d_flag set
69d97fa60cf0
·Axel Kohlmeyer on Jul 12 2017, 17:26.
avoid segfault when calling enforce2d before langevin data has been initialized
a9ff593763c7
·Axel Kohlmeyer on Jul 12 2017, 15:48.

Jul 11 2017

whitspace cleanup
f7f4a24930ba
·Axel Kohlmeyer on Jul 11 2017, 21:01.
combine citeme.log entry for pair reax/c/omp and fix qeq/reax/omp
338fc2897073
·Axel Kohlmeyer on Jul 11 2017, 20:59.
updated the credits and citations for pair style reaxc/omp and qeq/reax/omp
5a1e020bf01c
·H. Metin Aktulga on Jul 11 2017, 17:05.

Jul 10 2017

white space cleanup
b5e9e90bb66d
·Axel Kohlmeyer on Jul 10 2017, 23:21.
disallow MC moves with fix rigid and fix shake active. update examples and add…
92395e9bb412
·Axel Kohlmeyer on Jul 10 2017, 23:19.

Jul 7 2017

whitespace cleanup
71ddcaf0b607
·Axel Kohlmeyer on Jul 7 2017, 21:50.
add support for recomputing normalization factors and finite size correction…
fe888e462219
·Axel Kohlmeyer on Jul 7 2017, 21:39.

Jul 6 2017

patch 6Jul17
433937994877
·Steve Plimpton on Jul 6 2017, 21:58.
whitespace cleanup
042397120500
·Axel Kohlmeyer on Jul 6 2017, 06:24.
remove code without effect
4ee7c6f5caa8
·Axel Kohlmeyer on Jul 6 2017, 06:23.
correct comment for Fix::ev_setup()
7f63c09667ff
·Axel Kohlmeyer on Jul 6 2017, 04:35.
fix bug reported by richard berger via https://ci.lammps.
a5234d7aeaf5
·Axel Kohlmeyer on Jul 6 2017, 04:34.

Jul 5 2017

Fix sigcut class variable actually used
e493b6a648b2
·Markus Hoehnerbach on Jul 5 2017, 22:52.
make old_velocities allocation safer while retaining the test for nlocal
4de9cec1b63b
·Axel Kohlmeyer on Jul 5 2017, 22:22.
remove unused variables to silence compiler warnings
8c3f6947ad48
·Axel Kohlmeyer on Jul 5 2017, 22:19.
simplify parsing of optional arguments
894e0c3cf506
·Axel Kohlmeyer on Jul 5 2017, 22:19.
remove dead code
09ad29342555
·Axel Kohlmeyer on Jul 5 2017, 21:04.
safer handling of processors w/o local atoms
e625e7917190
·Axel Kohlmeyer on Jul 5 2017, 21:04.
changes requested by @sjplimp
f1088a5003dd
·Axel Kohlmeyer on Jul 5 2017, 21:03.
coding style and whitespace cleanup to match LAMMPS style
6eddc1a2ee77
·Axel Kohlmeyer on Jul 5 2017, 18:33.
Updated credits
1bf1cb150fae
·Markus Hoehnerbach on Jul 5 2017, 18:26.
additional fix external hooks for calling programs
ea4f16bd79df
·Steve Plimpton on Jul 5 2017, 18:01.
fixed a typo
9fa4588eb720
·Abdoreza Ershadinia / GitHub on Jul 5 2017, 16:46.
Examples moved
8e279d4ec84e
·Abdo on Jul 5 2017, 16:16.
Sync AIREBO USER-OMP implementation.
ff761d639a78
·Markus Hoehnerbach on Jul 5 2017, 15:29.
AIREBO Fix Credits
d2f7f4843a7c
·Markus Hoehnerbach on Jul 5 2017, 15:16.

lammps/srcmaster5cd1dc93dc5956a89a1ba42…

Jul 31 2017

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Jul 5 2017

lammps/src
master5cd1dc93dc5956a89a1ba42…