Diffusion lammps (efficient_neuronet) History

History
efficient_neuronetb0940dec80b55afb1f3c00e…

Aug 4 2016

create/use a ke compute instead of converting from temperature
0f2e7241900b
·Axel Kohlmeyer on Aug 4 2016, 22:36.
remove unused variable
a19ea3ee5e16
·Axel Kohlmeyer on Aug 4 2016, 22:34.
port changes to dump file formatting from upstream to COMPRESS package
f4f8ce57a53e
·Axel Kohlmeyer on Aug 4 2016, 20:16.
fix bug introduced by steve.
73368211c536
·Axel Kohlmeyer on Aug 4 2016, 20:02.
Merge branch 'lammps-icms' of bitbucket.org:akohlmey/lammps-icms into lammps…
88062030752a
·Axel Kohlmeyer on Aug 4 2016, 19:43.
delete redundant code and add comment to avoid doing this in the future
ca1050f5875b
·Axel Kohlmeyer on Aug 4 2016, 19:24.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15435 f3b2605a-c512-4ea7…
0bffc1711e3e
·sjplimp on Aug 4 2016, 18:39.
fix optional argument scanning bug
2a90afe7e9a1
·Axel Kohlmeyer on Aug 4 2016, 14:28.
remove unused class member
f884bb2c92ec
·Axel Kohlmeyer on Aug 4 2016, 14:18.
incorporate refactored weighting into fix balance
71ef6fb4d95a
·Axel Kohlmeyer on Aug 4 2016, 14:04.
convert weight array from class member to local pointer to temporary storage
ecbbdc2e7ff0
·Axel Kohlmeyer on Aug 4 2016, 14:03.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
ad0633f7c142
·Axel Kohlmeyer on Aug 4 2016, 12:56.
proof-of-concept implementation for neighbor list based balancing with yet…
d40de42af861
·Axel Kohlmeyer on Aug 4 2016, 08:02.
re-factored balance command now works with group and time weights
3f674e5062aa
·Axel Kohlmeyer on Aug 4 2016, 00:34.

Aug 3 2016

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15432 f3b2605a-c512-4ea7…
677da2ea52d9
·sjplimp on Aug 3 2016, 21:40.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15431 f3b2605a-c512-4ea7…
a93e6e83ed58
·sjplimp on Aug 3 2016, 21:39.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15430 f3b2605a-c512-4ea7…
efaa84a4eab8
·sjplimp on Aug 3 2016, 21:32.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15429 f3b2605a-c512-4ea7…
1f6518400e83
·sjplimp on Aug 3 2016, 21:31.
complete implementation for group based imbalance class
8ff0085cba09
·Axel Kohlmeyer on Aug 3 2016, 19:43.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15428 f3b2605a-c512-4ea7…
be6c086cb4c1
·sjplimp on Aug 3 2016, 18:29.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15427 f3b2605a-c512-4ea7…
a6ade15e60bb
·sjplimp on Aug 3 2016, 18:29.
port code from serial implementation to /omp version
b3664c217b1e
·Axel Kohlmeyer on Aug 3 2016, 18:28.
apply NEIGHMASK in inner loops
c8072e95bb53
·Axel Kohlmeyer on Aug 3 2016, 18:27.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15426 f3b2605a-c512-4ea7…
38226b808685
·sjplimp on Aug 3 2016, 18:09.
prototype implementation for extensible imbalance scheme
362a26a3def0
·Axel Kohlmeyer on Aug 3 2016, 05:19.
fix subtle 64-bit integer bug in fix print and fix store/state
7faba0408985
·Axel Kohlmeyer on Aug 3 2016, 03:42.

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.
update to colvars library version 2016-08-01
81b83331090b
·Axel Kohlmeyer on Aug 2 2016, 21:17.
Merge branch 'balance-by-time' into lammps-icms
58e77eacc721
·Axel Kohlmeyer on Aug 2 2016, 14:24.
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.
undo changes to the group command related to load balancing
047f313356ba
·Axel Kohlmeyer on Aug 2 2016, 01:06.
remove unused function prototype
495ab323d1fd
·Axel Kohlmeyer on Aug 2 2016, 01:03.
Merge branch 'balance-weight-by-group' into lammps-icms
fdbce41887b0
·Axel Kohlmeyer on Aug 2 2016, 01:00.
update documentation according to the modified implementation based on iain…
76b8bbca8ea8
·Axel Kohlmeyer on Aug 2 2016, 00:59.
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@15423 f3b2605a-c512-4ea7…
56502c7c0943
·sjplimp on Aug 2 2016, 00:57.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15422 f3b2605a-c512-4ea7…
7326f8852106
·sjplimp on Aug 2 2016, 00:56.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15420 f3b2605a-c512-4ea7…
1cdd1fd4f809
·sjplimp on Aug 2 2016, 00:43.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15419 f3b2605a-c512-4ea7…
69513a29ab6a
·sjplimp on Aug 2 2016, 00:40.

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.
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.
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.
Docs for load balance changes
fc7afc2242f2
·Iain Bethune on Jul 29 2016, 17:35.
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 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

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.

Historyefficient_neuronetb0940dec80b55afb1f3c00e…

Aug 4 2016

Aug 3 2016

Aug 2 2016

Aug 1 2016

Jul 31 2016

Jul 30 2016

Jul 29 2016

Jul 28 2016

History
efficient_neuronetb0940dec80b55afb1f3c00e…