Diffusion lammps (efficient_neuronet) History

History
efficient_neuronete3eb61765260966c952d8a5…

Aug 1 2016

update several old input files to current syntax
e3eb61765260
·Axel Kohlmeyer on Aug 1 2016, 00:32.

Jul 31 2016

correct typo
11f772969f88
·Axel Kohlmeyer on Jul 31 2016, 12:55.
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@15412 f3b2605a-c512-4ea7…
26622f2826fa
·sjplimp on Jul 30 2016, 20:40.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15411 f3b2605a-c512-4ea7…
7ec3c90b86b0
·sjplimp on Jul 30 2016, 18:09.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15410 f3b2605a-c512-4ea7…
fd05571ee03e
·sjplimp on Jul 30 2016, 18:09.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15409 f3b2605a-c512-4ea7…
5b5f839265b4
·sjplimp on Jul 30 2016, 18:08.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15407 f3b2605a-c512-4ea7…
d3e47eef1cc1
·sjplimp on Jul 30 2016, 17:17.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15406 f3b2605a-c512-4ea7…
f9c6ec768b49
·sjplimp on Jul 30 2016, 17:11.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15404 f3b2605a-c512-4ea7…
fb13763ef91d
·sjplimp on Jul 30 2016, 16:52.
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@15402 f3b2605a-c512-4ea7…
58be921a0932
·sjplimp on Jul 30 2016, 16:51.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15401 f3b2605a-c512-4ea7…
b5836fa49170
·sjplimp on Jul 30 2016, 16:47.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15400 f3b2605a-c512-4ea7…
4eb6664ba8a2
·sjplimp on Jul 30 2016, 16:45.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15399 f3b2605a-c512-4ea7…
ee86bd2463f0
·sjplimp on Jul 30 2016, 16:45.
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.
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@15397 f3b2605a-c512-4ea7…
f609827de85b
·sjplimp on Jul 29 2016, 16:35.
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@15394 f3b2605a-c512-4ea7…
642c01a15088
·sjplimp on Jul 29 2016, 16:32.
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.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15391 f3b2605a-c512-4ea7…
b8bf3ae5b0d7
·sjplimp on Jul 29 2016, 16:24.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
ba0147f747c2
·Axel Kohlmeyer on Jul 29 2016, 12:39.

Jul 28 2016

update min_style docs about the limitations in hftn minimizer
f13ff2e1351f
·Axel Kohlmeyer on Jul 28 2016, 23:15.
min style hftn doesn't seem to handle extra DOFs correctly
e00d1baf1e31
·Axel Kohlmeyer on Jul 28 2016, 22:48.
add tests for anisotropic and triclinic box relaxation
55a138cdca6a
·Axel Kohlmeyer on Jul 28 2016, 22:47.
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@15389 f3b2605a-c512-4ea7…
87b66263580f
·sjplimp on Jul 28 2016, 15:53.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15388 f3b2605a-c512-4ea7…
70bfc1c0979a
·sjplimp on Jul 28 2016, 15:52.
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@15382 f3b2605a-c512-4ea7…
e561aa052909
·sjplimp on Jul 28 2016, 01:34.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15381 f3b2605a-c512-4ea7…
a01058e7d27f
·sjplimp on Jul 28 2016, 01:34.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15379 f3b2605a-c512-4ea7…
308461125e72
·sjplimp on Jul 28 2016, 01:27.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15378 f3b2605a-c512-4ea7…
a91dae3f2b81
·sjplimp on Jul 28 2016, 01:26.
Added axes keyword
e8c5280ad9d6
·athomps on Jul 28 2016, 01:06.
Added axes keyword
5241c0326e4b
·athomps on Jul 28 2016, 01:03.
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@15372 f3b2605a-c512-4ea7…
ef6ff80366a7
·sjplimp on Jul 27 2016, 16:13.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15371 f3b2605a-c512-4ea7…
ee24be38cbc3
·sjplimp on Jul 27 2016, 16:09.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15370 f3b2605a-c512-4ea7…
c1fc5aef12fa
·sjplimp on Jul 27 2016, 16:08.
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.
Merge branch 'merge-pull-122' into lammps-icms
80ef98f8ffa0
·Axel Kohlmeyer on Jul 27 2016, 13:57.
rename dlm option to dipole/dlm and turn on dipole flag with it as well
671ca115f9d0
·Axel Kohlmeyer on Jul 27 2016, 13:56.
Merge branch 'dlm' of https://github.com/ibethune/lammps into merge-pull-122
01e12e23c289
·Axel Kohlmeyer on Jul 27 2016, 13:33.
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.
Doc updates for fix_nh (alongside existing update dipole keyword)
9b9c3416c6a8
·Iain Bethune on Jul 27 2016, 10:54.
Add reference
6e050e243d39
·Iain Bethune on Jul 27 2016, 10:50.
Update doc for nve/sphere
b99f255eed4f
·Iain Bethune on Jul 27 2016, 10:40.
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.
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.
stupid debian bourne shell...
c28a1eb4e028
·Axel Kohlmeyer on Jul 23 2016, 12:44.
correct unwanted error exit on false branch in test case
ab439608bbe6
·Axel Kohlmeyer on Jul 23 2016, 12:37.
remove erroneously added backup files
c76672ab86e3
·Axel Kohlmeyer on Jul 23 2016, 12:30.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
01881e6fcc2d
·Axel Kohlmeyer on Jul 23 2016, 12:28.
re-enable forcing using ccache with a workaround for clang
06761ff09bee
·Axel Kohlmeyer on Jul 23 2016, 05:37.
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@15362 f3b2605a-c512-4ea7…
caf9483a0a7c
·sjplimp on Jul 23 2016, 01:05.
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@15360 f3b2605a-c512-4ea7…
7dc6873c513c
·sjplimp on Jul 23 2016, 00:59.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15359 f3b2605a-c512-4ea7…
952a0d1fb776
·sjplimp on Jul 23 2016, 00:58.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15358 f3b2605a-c512-4ea7…
778f4d338c78
·sjplimp on Jul 23 2016, 00:57.
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.