Diffusion lammps (master) History

lammps/src
master44ccdb86df24ec1d8299ea1…

Aug 19 2017

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.

Aug 18 2017

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 28 2017

remove unused variable
841a92c7fada
·Axel Kohlmeyer on Jul 28 2017, 22:03.

Jul 27 2017

fix bug in power operator in LAMMPS variable expressions
e3973796bacc
·Axel Kohlmeyer on Jul 27 2017, 21:51.
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 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.

Jul 21 2017

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.
update manual links that got broken when removing and renumbering a section
a92d79253734
·Axel Kohlmeyer on Jul 18 2017, 18:55.
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.
better Install.py script for KIM from Ryan Elliott
296e572e6998
·Steve Plimpton on Jul 15 2017, 00:25.

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.

lammps/srcmaster44ccdb86df24ec1d8299ea1…

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 28 2017

Jul 27 2017

Jul 26 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

Jul 12 2017

Jul 11 2017

Jul 10 2017

lammps/src
master44ccdb86df24ec1d8299ea1…