Diffusion lammps (lammps-icms) History

History
lammps-icms3b8ecd5c0634816337fc948…

Aug 8 2016

Fix typo
3b8ecd5c0634
·Iain Bethune on Aug 8 2016, 15:55.

Aug 7 2016

update colvars library to version 2016-08-05
459db2eb6b7b
·Axel Kohlmeyer on Aug 7 2016, 15:54.
plug small memory leak
93554fac5e3e
·Axel Kohlmeyer on Aug 7 2016, 05:43.
update documentation for refactored load-balancing
7abc061bf7b4
·Axel Kohlmeyer on Aug 7 2016, 05:31.
remove upper limit for weigh factor on neighbor list and time weights
797c6dc2dd27
·Axel Kohlmeyer on Aug 7 2016, 04:49.
add new imbalance module store, which allows to store weights in an atom…
5405622f3bda
·Axel Kohlmeyer on Aug 7 2016, 04:48.
convert from using fix property/atom to using fix store
280aef55d2b7
·Axel Kohlmeyer on Aug 7 2016, 01:31.
whitespace cleanup
b3bd35c7beef
·Axel Kohlmeyer on Aug 7 2016, 01:30.

Aug 6 2016

properly handle the case of neighbor lists never been computed before
fcba14a0aa97
·Axel Kohlmeyer on Aug 6 2016, 21:47.
plug small memory leak
c00aa3c600c0
·Axel Kohlmeyer on Aug 6 2016, 21:11.
simplify and correct logic to pass weight to balancer algorithms
529417f86c4d
·Axel Kohlmeyer on Aug 6 2016, 20:40.
correct string hanlding with building custom property label
6a519e5eefb5
·Axel Kohlmeyer on Aug 6 2016, 20:40.
we cannot add a fix while creating a fix. move fix addintion to Fix::init()
4c26534245e2
·Axel Kohlmeyer on Aug 6 2016, 20:39.
rewrote balancing to use per-atom data stored via fix property/atom
1da862b44077
·Axel Kohlmeyer on Aug 6 2016, 19:21.
custom property names should be compatible with string literals
4b3783d18c3d
·Axel Kohlmeyer on Aug 6 2016, 19:20.
Merge branch 'lammps-icms' into balance-refactor
62443e27bc14
·Axel Kohlmeyer on Aug 6 2016, 13:24.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
78b47137ba70
·Axel Kohlmeyer on Aug 6 2016, 13:22.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15456 f3b2605a-c512-4ea7…
0029040f1152
·sjplimp on Aug 6 2016, 00:12.

Aug 5 2016

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15455 f3b2605a-c512-4ea7…
decd072117f3
·sjplimp on Aug 5 2016, 22:58.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15454 f3b2605a-c512-4ea7…
30d60075655c
·sjplimp on Aug 5 2016, 22:45.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15453 f3b2605a-c512-4ea7…
390b492d081c
·sjplimp on Aug 5 2016, 20:28.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15452 f3b2605a-c512-4ea7…
9a3b988b2b8e
·sjplimp on Aug 5 2016, 20:28.
Attempted to straighten out italics
36a0c644a906
·athomps on Aug 5 2016, 20:21.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15450 f3b2605a-c512-4ea7…
96a73d51cd98
·sjplimp on Aug 5 2016, 20:16.
Fixed error in ave/time version
1780c86b8601
·athomps on Aug 5 2016, 19:53.
clarified energy contribution to minimization energy
32c8c9d63e4e
·athomps on Aug 5 2016, 18:27.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15445 f3b2605a-c512-4ea7…
754103324663
·sjplimp on Aug 5 2016, 17:50.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15444 f3b2605a-c512-4ea7…
2d694f934e36
·sjplimp on Aug 5 2016, 17:50.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15442 f3b2605a-c512-4ea7…
ce7581b86932
·sjplimp on Aug 5 2016, 17:38.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15441 f3b2605a-c512-4ea7…
42cc69b843b1
·sjplimp on Aug 5 2016, 17:17.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15440 f3b2605a-c512-4ea7…
e09caf843d4b
·sjplimp on Aug 5 2016, 17:17.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15439 f3b2605a-c512-4ea7…
82a29a8adbfe
·sjplimp on Aug 5 2016, 17:14.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15438 f3b2605a-c512-4ea7…
091fb71a9312
·sjplimp on Aug 5 2016, 17:14.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15437 f3b2605a-c512-4ea7…
3fe162a42d13
·sjplimp on Aug 5 2016, 17:11.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15436 f3b2605a-c512-4ea7…
9a9897cd447f
·sjplimp on Aug 5 2016, 17:07.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
290cbb9b9126
·Axel Kohlmeyer on Aug 5 2016, 12:42.
Merge branch 'lammps-icms' into balance-refactor
cd01e5855d2c
·Axel Kohlmeyer on Aug 5 2016, 04:34.

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.