Diffusion lammps (efficient_neuronet) History

lammps/src
efficient_neuronet4629a464f701f919633fd22…

Aug 2 2016

fix elusive uninitialized data bug reported by valgrind
b44492ee05ab
·Axel Kohlmeyer on Aug 2 2016, 22:54.
be a bit more paranoid about initializing data structures
bda51f2bacca
·Axel Kohlmeyer on Aug 2 2016, 22:53.
make it so that dynamic load balancing only uses the timing since the last…
f758a4f4d06f
·Axel Kohlmeyer on Aug 2 2016, 14:09.
minor tweaks and comment fixes
f14e9cee83da
·Axel Kohlmeyer on Aug 2 2016, 13:32.
improve c++-11 compliance. replace variable size stack allocation.
af224028a925
·Axel Kohlmeyer on Aug 2 2016, 12:42.
whitespace cleanup
2e0b9cae2980
·Axel Kohlmeyer on Aug 2 2016, 12:41.
Merge branch 'lammps-icms' into balance-by-time
b635930cfd98
·Axel Kohlmeyer on Aug 2 2016, 12:33.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
cc487af9e494
·Axel Kohlmeyer on Aug 2 2016, 12:20.
disable debug output and include bond cost as well
9ea86965c57a
·Axel Kohlmeyer on Aug 2 2016, 07:24.
implement wall clock based load balancing cost function support
2a57dc6db460
·Axel Kohlmeyer on Aug 2 2016, 07:17.
remove unused function prototype
495ab323d1fd
·Axel Kohlmeyer on Aug 2 2016, 01:03.
implement modified version of balance and fix balance according to steve's…
5a81288329e1
·Axel Kohlmeyer on Aug 2 2016, 00:58.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15422 f3b2605a-c512-4ea7…
7326f8852106
·sjplimp on Aug 2 2016, 00:56.

Aug 1 2016

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15418 f3b2605a-c512-4ea7…
98aee0515239
·sjplimp on Aug 1 2016, 23:30.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15417 f3b2605a-c512-4ea7…
e6c5898e5371
·sjplimp on Aug 1 2016, 23:11.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15416 f3b2605a-c512-4ea7…
a9a8a599d0fd
·sjplimp on Aug 1 2016, 23:01.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15415 f3b2605a-c512-4ea7…
0995ab4b65c3
·sjplimp on Aug 1 2016, 22:55.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15414 f3b2605a-c512-4ea7…
ce5f17428184
·sjplimp on Aug 1 2016, 22:35.
undo changes to Group class
fa856c7657ad
·Axel Kohlmeyer on Aug 1 2016, 21:49.
Merge branch 'weighted_load_balance' of https://github.com/ibethune/lammps into…
aaac40dcb4d8
·Axel Kohlmeyer on Aug 1 2016, 21:46.
more thorough checks on valid numbers when computing box/virial related…
ef2f16a240ae
·Axel Kohlmeyer on Aug 1 2016, 17:52.
remove unused variable
a8f40013b79f
·Axel Kohlmeyer on Aug 1 2016, 13:56.

Jul 31 2016

Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
1d17eed48ca5
·Axel Kohlmeyer on Jul 31 2016, 12:54.

Jul 30 2016

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15413 f3b2605a-c512-4ea7…
6ff87be84925
·sjplimp on Jul 30 2016, 23:24.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15403 f3b2605a-c512-4ea7…
22fe3fd17875
·sjplimp on Jul 30 2016, 16:52.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15401 f3b2605a-c512-4ea7…
b5836fa49170
·sjplimp on Jul 30 2016, 16:47.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
94b4702bb1b3
·Axel Kohlmeyer on Jul 30 2016, 13:55.

Jul 29 2016

correctly initialize natoms_original variable in ewald/disp and call qsum_qsq()…
edd6cb1f3e25
·Axel Kohlmeyer on Jul 29 2016, 17:58.
Comments
638fb5c119e8
·Iain Bethune on Jul 29 2016, 17:39.
remove const qualifier that clashes with many MPI versions
326fde5f9fc7
·Axel Kohlmeyer on Jul 29 2016, 17:37.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15396 f3b2605a-c512-4ea7…
2ac26ab8ac39
·sjplimp on Jul 29 2016, 16:35.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15395 f3b2605a-c512-4ea7…
3297fbeb26e9
·sjplimp on Jul 29 2016, 16:34.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15393 f3b2605a-c512-4ea7…
b936d69f127a
·sjplimp on Jul 29 2016, 16:28.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15392 f3b2605a-c512-4ea7…
f486709150d5
·sjplimp on Jul 29 2016, 16:28.
Merge branch 'lammps-icms' of https://github.com/lammps/lammps into…
48cf74f49ee8
·Iain Bethune on Jul 29 2016, 16:05.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
ba0147f747c2
·Axel Kohlmeyer on Jul 29 2016, 12:39.

Jul 28 2016

min style hftn doesn't seem to handle extra DOFs correctly
e00d1baf1e31
·Axel Kohlmeyer on Jul 28 2016, 22:48.
initialize box related global data to zero
a051e0807f61
·Axel Kohlmeyer on Jul 28 2016, 22:10.
convert static const variables to in-class enum
111e47a137d3
·Axel Kohlmeyer on Jul 28 2016, 22:09.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15390 f3b2605a-c512-4ea7…
cf2aa231f562
·sjplimp on Jul 28 2016, 20:09.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15387 f3b2605a-c512-4ea7…
c95ec24d1a7b
·sjplimp on Jul 28 2016, 15:51.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15386 f3b2605a-c512-4ea7…
f2f9fe0a6521
·sjplimp on Jul 28 2016, 15:43.
provide better informative messages when OMP_NUM_THREADS is not set or code was…
3080bb534113
·Axel Kohlmeyer on Jul 28 2016, 14:03.
must clear sigma and gamma arrays to avoid valgrind errors when using dpd/tstat…
6a953aec85fd
·Axel Kohlmeyer on Jul 28 2016, 13:30.
we need to do a full force initialization before write_coeff can work due to…
33b26525a8b4
·Axel Kohlmeyer on Jul 28 2016, 13:01.
processor grid is not initialized until the box is defined.
9ec0b15640c4
·Axel Kohlmeyer on Jul 28 2016, 13:01.
silence compiler warning
056ffc90bd08
·Axel Kohlmeyer on Jul 28 2016, 13:00.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
34d5c29bf50b
·Axel Kohlmeyer on Jul 28 2016, 12:40.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15381 f3b2605a-c512-4ea7…
a01058e7d27f
·sjplimp on Jul 28 2016, 01:34.
Added axes keyword
e8c5280ad9d6
·athomps on Jul 28 2016, 01:06.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15375 f3b2605a-c512-4ea7…
ae255c847bf7
·sjplimp on Jul 28 2016, 00:51.

Jul 27 2016

Fixed memory leak from rlist
2479d8031cc8
·athomps on Jul 27 2016, 23:16.
denom_lj is used in some derived classes, so we need to initialize both…
ac74863ab07f
·Axel Kohlmeyer on Jul 27 2016, 22:55.
MPI send buffers should accept pointers to const data
b72f2cbc323f
·Axel Kohlmeyer on Jul 27 2016, 22:28.
fix uninitialized data bug in fix shake
feff85c3551c
·Axel Kohlmeyer on Jul 27 2016, 22:27.
correct use of MPI data types (always those fortran programmers...)
54e4e7a92772
·Axel Kohlmeyer on Jul 27 2016, 21:48.
Fixing Kokkos memory issue
6b79bbfaf39d
·stamoor on Jul 27 2016, 17:48.
Check the correct argument for dipole/dlm
b09c2a0bf4d2
·Iain Bethune on Jul 27 2016, 16:19.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15369 f3b2605a-c512-4ea7…
ddd85f006cc8
·sjplimp on Jul 27 2016, 16:04.
Merge branch 'merge-pull-124' into lammps-icms
f0d1800734ed
·Axel Kohlmeyer on Jul 27 2016, 13:59.
rename dlm option to dipole/dlm and turn on dipole flag with it as well
671ca115f9d0
·Axel Kohlmeyer on Jul 27 2016, 13:56.
port optimizations from pair style lj/sf/dipole/sf to lj/sf/dipole/sf/omp
ef05a24f8773
·Axel Kohlmeyer on Jul 27 2016, 13:27.
Merge branch 'optimised_pair_lj' of https://github.com/ibethune/lammps into…
6fd5b9b3ddf8
·Axel Kohlmeyer on Jul 27 2016, 12:59.
Added back in denom_lj variable, which is used by some subclasses in other…
46f034d1a8a4
·Iain Bethune on Jul 27 2016, 10:58.
Remove the long_14* files, not relevant for this feature branch
9670f5dedf68
·Iain Bethune on Jul 27 2016, 10:09.

Jul 26 2016

some small tweaks and fixes to fix_n*_sphere*.cpp files
c3473f7ca805
·Axel Kohlmeyer on Jul 26 2016, 22:41.
Merge branch 'dlm' of https://github.com/ibethune/lammps into merge-pull-122
4a736370efde
·Axel Kohlmeyer on Jul 26 2016, 20:59.
Set up branch with load balancing code from master
fd8794f52a30
·Iain Bethune on Jul 26 2016, 16:28.
Added optimised pair_lj_* code from master
b928f98006d1
·Iain Bethune on Jul 26 2016, 16:22.
DLM code from master
73db42104816
·Iain Bethune on Jul 26 2016, 15:38.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
0ad5a1775d68
·Axel Kohlmeyer on Jul 26 2016, 12:39.

Jul 25 2016

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15368 f3b2605a-c512-4ea7…
8c04540e8a48
·sjplimp on Jul 25 2016, 21:55.
no need to use a cast on atom->ntypes
a6eb7d022792
·Axel Kohlmeyer on Jul 25 2016, 15:07.
formatting and comment cleanup in fix_qmmm to be more consistent with LAMMPS
0f9c14485a93
·Axel Kohlmeyer on Jul 25 2016, 12:50.
USER-QMMM enhancement from carlo cavazzoni that moves computation from MM to QM…
7ce10e8a9ebe
·Axel Kohlmeyer on Jul 25 2016, 12:46.

Jul 24 2016

Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
44694867075e
·Axel Kohlmeyer on Jul 24 2016, 23:46.

Jul 23 2016

remove useless and dead code.
960be2dd72d6
·Axel Kohlmeyer on Jul 23 2016, 18:40.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15367 f3b2605a-c512-4ea7…
751786364deb
·sjplimp on Jul 23 2016, 18:11.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
01881e6fcc2d
·Axel Kohlmeyer on Jul 23 2016, 12:28.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15364 f3b2605a-c512-4ea7…
08ac3d54dd94
·sjplimp on Jul 23 2016, 02:24.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15361 f3b2605a-c512-4ea7…
c04c7756318e
·sjplimp on Jul 23 2016, 01:04.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15357 f3b2605a-c512-4ea7…
2f936d5e564b
·sjplimp on Jul 23 2016, 00:57.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15356 f3b2605a-c512-4ea7…
87a6c1368f6f
·sjplimp on Jul 23 2016, 00:56.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15355 f3b2605a-c512-4ea7…
cff65b956adc
·sjplimp on Jul 23 2016, 00:52.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15354 f3b2605a-c512-4ea7…
87bfe1941b6f
·sjplimp on Jul 23 2016, 00:51.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15353 f3b2605a-c512-4ea7…
e519cfb1dccb
·sjplimp on Jul 23 2016, 00:50.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15351 f3b2605a-c512-4ea7…
0659a1fc5a1c
·sjplimp on Jul 23 2016, 00:10.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15350 f3b2605a-c512-4ea7…
ff10357ef205
·sjplimp on Jul 23 2016, 00:10.

Jul 22 2016

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15349 f3b2605a-c512-4ea7…
f9a4b697a49e
·sjplimp on Jul 22 2016, 23:20.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15348 f3b2605a-c512-4ea7…
0f71c66b6fe5
·sjplimp on Jul 22 2016, 23:19.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15347 f3b2605a-c512-4ea7…
f7c2fdf33543
·sjplimp on Jul 22 2016, 21:41.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15346 f3b2605a-c512-4ea7…
137f19ba9fbb
·sjplimp on Jul 22 2016, 21:41.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
2a030dea7509
·Axel Kohlmeyer on Jul 22 2016, 13:21.
give access to (current) simulation time minus offset via lammps_extract_global…
8586d1b92df9
·Axel Kohlmeyer on Jul 22 2016, 01:44.
add new API to library interface lammps_get_thermo(). include support in python…
182425df1593
·Axel Kohlmeyer on Jul 22 2016, 01:43.
give access to nbonds, nangles, ndihedral, nimpropers in Atom via…
ae7af38eacfa
·Axel Kohlmeyer on Jul 22 2016, 01:41.
correct typo
955c7862472b
·Axel Kohlmeyer on Jul 22 2016, 01:39.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15345 f3b2605a-c512-4ea7…
efa508d90521
·sjplimp on Jul 22 2016, 01:18.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15344 f3b2605a-c512-4ea7…
3ceaf974f8e7
·sjplimp on Jul 22 2016, 01:18.

Jul 21 2016

guarantee initialization of local variables
4473577ae00c
·Axel Kohlmeyer on Jul 21 2016, 15:36.

lammps/srcefficient_neuronet4629a464f701f919633fd22…

Aug 2 2016

Aug 1 2016

Jul 31 2016

Jul 30 2016

Jul 29 2016

Jul 28 2016

Jul 27 2016

Jul 26 2016

Jul 25 2016

Jul 24 2016

Jul 23 2016

Jul 22 2016

Jul 21 2016

lammps/src
efficient_neuronet4629a464f701f919633fd22…