Diffusion lammps (master) History

History
masterf7a243a4d9eeca7bc9fdb33…

Jul 26 2017

convert explicit copies back into symbolic links
f7a243a4d9ee
·Axel Kohlmeyer on Jul 26 2017, 20:20.
must not include system headers within 'extern "C"' blocks. breaks with MPICH
f0d286358ea0
·Axel Kohlmeyer on Jul 26 2017, 20:02.
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.
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.

Jul 21 2017

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.
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.

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.
remove absolutely last reference to xmovie
ddc96213255a
·Axel Kohlmeyer on Jul 12 2017, 00:30.
tools/Makefile: remove remains of data2xmovie
f717a70638f9
·Christoph Junghans on Jul 12 2017, 00:16.

Jul 11 2017

whitspace cleanup
f7f4a24930ba
·Axel Kohlmeyer on Jul 11 2017, 21:01.

Historymasterf7a243a4d9eeca7bc9fdb33…

Jul 26 2017

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Jul 11 2017

History
masterf7a243a4d9eeca7bc9fdb33…