Diffusion lammps (master) History

History
master8f59c0e188b9dc0d03621a5…

Jul 27 2017

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.
Merge pull request #594 from junghans/license
2eaea2d274e5
·sjplimp / GitHub on Jul 24 2017, 16:56.
Merge pull request #595 from libAtoms/idces2quip
1ddace4dba51
·sjplimp / GitHub on Jul 24 2017, 16:55.
Merge pull request #593 from akohlmey/collected-bug-fixes-and-small-updates
af3d0ca381dd
·sjplimp / GitHub on Jul 24 2017, 16:54.

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.
Clarified some points in in.molecular example
1afab981b022
·Max Veit on Jul 22 2017, 15:40.
Update in.molecular
1af937e99d71
·Axel Kohlmeyer / GitHub on Jul 22 2017, 04:00.
Add a (contrived) molecular example for USER-QUIP
4e0a249e2779
·Max Veit on Jul 22 2017, 02:33.
LICENSE: update address of Free Software Foundation
edc756a65f76
·Christoph Junghans on Jul 22 2017, 01:13.
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.
update readme for examples
b1b399d5c3dd
·Axel Kohlmeyer on Jul 21 2017, 21:06.
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.
Merge pull request #592 from akohlmey/reaxc-bugfix
5c13b087e4a1
·sjplimp / GitHub on Jul 21 2017, 00:26.
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 #590 from lammps/fortran-dftb
e53583d9c652
·sjplimp / GitHub on Jul 20 2017, 23:30.
revert change, that is part of the kim-install branch and changeset
551001f172a3
·Axel Kohlmeyer on Jul 20 2017, 23:08.
revert change that accidentally undoes part of PRs #583 and #588
5dbe2df85455
·Axel Kohlmeyer on Jul 20 2017, 23:07.
Merge pull request #588 from akohlmey/colvars-quickfix
3f83396837ea
·sjplimp / GitHub on Jul 20 2017, 22:45.
update of Fortran-DFTB interface to be compatible with fix msst
59db5f6a1782
·Steve Plimpton on Jul 20 2017, 22:40.
Merge branch 'colvars-safer-makefiles' of https://github.
1b704bab18ba
·Axel Kohlmeyer on Jul 20 2017, 21:59.
Change order of targets in Makefiles for Colvars
c98f6140e755
·Giacomo Fiorin on Jul 20 2017, 21:49.
Comment out use by Colvars of Makefile.lammps from other packages
5031f5b8079c
·Giacomo Fiorin on Jul 20 2017, 21:48.
README clarification from giacomo
9d0d90c03860
·Axel Kohlmeyer on Jul 20 2017, 21:25.
avoid makefile failure, if LAMMPS has not been configured yet
66154e8a8b31
·Axel Kohlmeyer on Jul 20 2017, 21:05.
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.
remove references to Make.py and USER-CUDA
bdd2f3a6b2c7
·Axel Kohlmeyer on Jul 20 2017, 18:25.
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.
Detect number of processors for make
ef9fb944c727
·Giacomo Fiorin on Jul 20 2017, 16:53.
Add forgotten decode() in Install.py
187a80be7738
·Giacomo Fiorin on Jul 20 2017, 04:21.

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.
Update USER_QUIP docs to clarify use of "special_bonds"
fcf9607a6666
·Max Veit on Jul 19 2017, 18:47.

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.
Revert "use neighbor list exclusions instead of a zero cutoff"
d9186c8fde6d
·Axel Kohlmeyer on Jul 18 2017, 07:17.
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.
Merge pull request #577 from v0i0/airebo-kim-difference
cc9b3864bff6
·sjplimp / GitHub on Jul 15 2017, 00:22.

Jul 14 2017

use neighbor list exclusions instead of a zero cutoff
bbb4d63db980
·Axel Kohlmeyer on Jul 14 2017, 20:52.
move updated gauss_flow example to the correct folder
1c92eecea7fc
·Axel Kohlmeyer on Jul 14 2017, 20:01.
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.
provide working examples for all four peridynamics models and reference outputs
14f1d646ad76
·Axel Kohlmeyer on Jul 14 2017, 19:46.
correct formatting error in peridynamics pair style docs
3b1134c1649a
·Axel Kohlmeyer on Jul 14 2017, 19:42.
restore gaussian flow example that was lost. tweak input to make it usable for…
4d4c03a1e4f5
·Axel Kohlmeyer on Jul 14 2017, 18:33.
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 #563 from akohlmey/airebo-example
9988030409f9
·sjplimp / GitHub on Jul 13 2017, 21:12.
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 #572 from junghans/data2xmovie
983eb0e80dab
·sjplimp / GitHub on Jul 13 2017, 19:27.
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 #569 from ellio167/kim-install-py
b64849d5748e
·sjplimp / GitHub on Jul 13 2017, 19:24.
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.

Historymaster8f59c0e188b9dc0d03621a5…

Jul 27 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

Jul 17 2017

Jul 16 2017

Jul 15 2017

Jul 14 2017

Jul 13 2017

History
master8f59c0e188b9dc0d03621a5…