Diffusion lammps (master) History

History
masterd1ba974fa8ee4e1d66013d6…

Aug 23 2016

correction made
d1ba974fa8ee
·aaramoon on Aug 23 2016, 16:50.

Aug 17 2016

fix_bond_create_updated
180776e4f702
·aaramoon on Aug 17 2016, 16:12.

Aug 11 2016

remove duplicated statement
bc7c97b88231
·Axel Kohlmeyer on Aug 11 2016, 13:30.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
c6ef337b2eb0
·Axel Kohlmeyer on Aug 11 2016, 13:28.
improve the weight assignment algorithm for compute time based balancing
2b052c2a9c8e
·Axel Kohlmeyer on Aug 11 2016, 02:52.
add run 0 to USER-TALLY examples to enforce shake constraints on step 0
433741564d16
·Axel Kohlmeyer on Aug 11 2016, 02:25.

Aug 10 2016

Merge branch 'merge-pull-134' into lammps-icms
ea4655d5e565
·Axel Kohlmeyer on Aug 10 2016, 21:52.
Merge branch 'python_interface_enhancements' of https://github.
7abc52d4cfc2
·Axel Kohlmeyer on Aug 10 2016, 21:50.
Add utility function to IPyLammps for embedding videos
57d7a4a6ad5f
·Richard Berger on Aug 10 2016, 20:35.
Add verbose option in PyLammps methods
054b1cedb06d
·Richard Berger on Aug 10 2016, 20:31.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15468 f3b2605a-c512-4ea7…
639ea6c39647
·sjplimp on Aug 10 2016, 16:59.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15467 f3b2605a-c512-4ea7…
b3364ae94333
·sjplimp on Aug 10 2016, 16:46.
update colvars to another set of changes from the upstream repo
cb816f8cba63
·Axel Kohlmeyer on Aug 10 2016, 15:35.
update colvars makefile dependencies
df99a85930a8
·Axel Kohlmeyer on Aug 10 2016, 15:13.
suppress compiler warning
6f227e194e1f
·Axel Kohlmeyer on Aug 10 2016, 15:12.
update colvars to version 2016-08-10
f2ddf828e485
·Axel Kohlmeyer on Aug 10 2016, 15:03.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
aef16fed2a27
·Axel Kohlmeyer on Aug 10 2016, 13:26.
builtins module doesn't seem to exist in some older python 2.x installations.
3eba86e650f2
·Axel Kohlmeyer on Aug 10 2016, 02:57.
Merge branch 'merge-pull-133' into lammps-icms
791e56039cd7
·Axel Kohlmeyer on Aug 10 2016, 01:40.
Merge branch 'python_interface_enhancements' of https://github.
77ce967888b5
·Axel Kohlmeyer on Aug 10 2016, 01:36.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15466 f3b2605a-c512-4ea7…
3349f7e14366
·sjplimp on Aug 10 2016, 01:25.
python2/3 portability changes suggested by futurize -1
0ab96350f088
·Axel Kohlmeyer on Aug 10 2016, 00:36.

Aug 9 2016

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15465 f3b2605a-c512-4ea7…
de2b6cf6bde1
·sjplimp on Aug 9 2016, 22:45.
apply changes suggested by futurize -1 -2 for improved python 2/3 compatibility
ae3f4173c0b4
·Axel Kohlmeyer on Aug 9 2016, 22:04.
perform stage 2 of python2/3 compatibility conversion with futurize
8d2fc6b14f39
·Axel Kohlmeyer on Aug 9 2016, 22:00.
process with futurize -1 to increase its portability.
2495bee1d8b4
·Axel Kohlmeyer on Aug 9 2016, 21:50.
port changes to lj/sf/dipole/sf to lj/sf/dipole/sf/omp
ad652c9b82b0
·Axel Kohlmeyer on Aug 9 2016, 16:30.
change pair_coeff syntax for lj/sf/dipole/sf to be backward compatible and…
0369d79c398a
·Axel Kohlmeyer on Aug 9 2016, 16:28.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15463 f3b2605a-c512-4ea7…
6c8d3ed4e849
·sjplimp on Aug 9 2016, 16:10.
import updated pair lj/sf/dipole/sf files from sam genheden
ae691ab7865b
·Axel Kohlmeyer on Aug 9 2016, 15:33.
Merge branch 'balance-doc-fix' of https://github.com/ibethune/lammps into merge…
e55875a5a485
·Axel Kohlmeyer on Aug 9 2016, 15:25.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
96e415ad8af4
·Axel Kohlmeyer on Aug 9 2016, 13:01.
Allow setting the position of atoms
39b643a94bf6
·Richard Berger on Aug 9 2016, 10:11.
Return 2D vectors in 2D cases
0a75617f4d9a
·Richard Berger on Aug 9 2016, 10:11.
Fix resource leak
c17e700e866e
·Richard Berger on Aug 9 2016, 10:08.

Aug 8 2016

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15462 f3b2605a-c512-4ea7…
550be1d5129e
·sjplimp on Aug 8 2016, 21:41.
Fix typo
3b8ecd5c0634
·Iain Bethune on Aug 8 2016, 15:55.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15461 f3b2605a-c512-4ea7…
563e06997104
·sjplimp on Aug 8 2016, 15:50.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15460 f3b2605a-c512-4ea7…
17e8e9a9c98d
·sjplimp on Aug 8 2016, 15:48.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15459 f3b2605a-c512-4ea7…
056ff192c619
·sjplimp on Aug 8 2016, 15:47.

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.