Diffusion lammps (master) History

lammps/src
master31204aab6a1bd8c4f8e6383…

Aug 26 2016

improved .gitignore files to show only changes in relevant folders and files
9be235d87258
·Axel Kohlmeyer on Aug 26 2016, 20:34.
removal of doc/html/_sources and minor sync with SVN
2beecd1e7351
·Steve Plimpton on Aug 26 2016, 19:34.

Aug 25 2016

port Make.py so it is compatible with python 2.7 *and* python 3.x
74516b571edf
·Axel Kohlmeyer on Aug 25 2016, 12:30.
find functions in atom.cpp checks for id/name being NULL
b06fa5670ab7
·Anders Hafreager / Axel Kohlmeyer on Aug 25 2016, 12:00.
Fixed so we test for compute,fix and variable id's being NULL in find_ functions
a635c70a26b8
·Anders Hafreager / Axel Kohlmeyer on Aug 25 2016, 12:00.
fix memory leak in compute omega/chunk
849cec34007f
·Axel Kohlmeyer on Aug 25 2016, 05:15.
fix bug in reserving sufficient space for special atoms
a692398b6c3b
·Axel Kohlmeyer on Aug 25 2016, 05:08.

Aug 24 2016

Fixed initialization of arrays in computes
7d43f349e6d8
·Anders Hafreager / Axel Kohlmeyer on Aug 24 2016, 23:26.
Fixed initialization of arrays in computes
5e811f16e87d
·Anders Hafreager / Axel Kohlmeyer on Aug 24 2016, 23:26.
Fixed initialization of arrays in computes
fcd54f02e6b7
·Anders Hafreager / Axel Kohlmeyer on Aug 24 2016, 23:26.
Fixed initialization of arrays in computes
1f3ef8e0ee5e
·Anders Hafreager / Axel Kohlmeyer on Aug 24 2016, 23:26.
Fixed initialization of arrays in computes
3e793d6eb748
·Anders Hafreager / Axel Kohlmeyer on Aug 24 2016, 23:26.
Fixed initialization of arrays in computes
95dde5c04128
·Anders Hafreager / Axel Kohlmeyer on Aug 24 2016, 23:26.
Fixed initialization of arrays in computes
d09a85733bce
·Anders Hafreager / Axel Kohlmeyer on Aug 24 2016, 23:26.
Fixed initialization of arrays in computes
0e7ce194eb7a
·Anders Hafreager / Axel Kohlmeyer on Aug 24 2016, 23:26.
Implemented optional C++ exceptions in Error class
e5c37bc7cb8e
·Richard Berger on Aug 24 2016, 21:31.

Aug 23 2016

changed dump.cpp back to the way it was
8750515cc44d
·Steve Plimpton on Aug 23 2016, 23:38.
Merge branch 'integration' into small-bugfixes
270b07b03537
·Steve Plimpton on Aug 23 2016, 23:35.
gpu lib sync
abc5a32c8a4b
·Steve Plimpton on Aug 23 2016, 23:30.
test
0a3464eb30ee
·Steve Plimpton on Aug 23 2016, 23:27.

Aug 22 2016

address uninitialized variable issues pointed out by valgrind/coverity
50a82bb345d3
·Axel Kohlmeyer on Aug 22 2016, 21:49.
undo changes that belong to a different branch or are redundant
74b1caf2e651
·Axel Kohlmeyer on Aug 22 2016, 21:46.
undo obsoleted changes to group command by iain bethune
243137d5526c
·Axel Kohlmeyer on Aug 22 2016, 21:23.
silence warnings about cases, that cannot happen
40fd97bd4c92
·Axel Kohlmeyer on Aug 22 2016, 21:12.
fix bug found by coverity scan
8492212c4bd5
·Axel Kohlmeyer on Aug 22 2016, 21:12.
improve the weight assignment algorithm for compute time based balancing
1976314f4041
·Axel Kohlmeyer on Aug 22 2016, 21:12.
remove upper limit for weigh factor on neighbor list and time weights
33a98d79fe6a
·Axel Kohlmeyer on Aug 22 2016, 21:12.
add new imbalance module store, which allows to store weights in an atom…
0902b600fb1b
·Axel Kohlmeyer on Aug 22 2016, 21:12.
convert from using fix property/atom to using fix store
7f20afe122a5
·Axel Kohlmeyer on Aug 22 2016, 21:12.
whitespace cleanup
7e0dc7a74df1
·Axel Kohlmeyer on Aug 22 2016, 21:12.
properly handle the case of neighbor lists never been computed before
b954283ec221
·Axel Kohlmeyer on Aug 22 2016, 21:12.
plug small memory leak
ecc136b6dc67
·Axel Kohlmeyer on Aug 22 2016, 21:12.
simplify and correct logic to pass weight to balancer algorithms
4a536d71ebf8
·Axel Kohlmeyer on Aug 22 2016, 21:12.
correct string hanlding with building custom property label
460bc1482235
·Axel Kohlmeyer on Aug 22 2016, 21:12.
we cannot add a fix while creating a fix. move fix addintion to Fix::init()
bb40f63a34b8
·Axel Kohlmeyer on Aug 22 2016, 21:12.
rewrote balancing to use per-atom data stored via fix property/atom
c6699e19e6a6
·Axel Kohlmeyer on Aug 22 2016, 21:12.
fix optional argument scanning bug
257489116064
·Axel Kohlmeyer on Aug 22 2016, 21:12.
remove unused class member
332d6821ca43
·Axel Kohlmeyer on Aug 22 2016, 21:12.
incorporate refactored weighting into fix balance
b20108bddb03
·Axel Kohlmeyer on Aug 22 2016, 21:12.
convert weight array from class member to local pointer to temporary storage
8d38db07c7d2
·Axel Kohlmeyer on Aug 22 2016, 21:12.
proof-of-concept implementation for neighbor list based balancing with yet…
4114bafc28aa
·Axel Kohlmeyer on Aug 22 2016, 21:12.
re-factored balance command now works with group and time weights
23a48916d796
·Axel Kohlmeyer on Aug 22 2016, 21:12.
complete implementation for group based imbalance class
34b34d8410f7
·Axel Kohlmeyer on Aug 22 2016, 21:12.
prototype implementation for extensible imbalance scheme
a5d38c0875db
·Axel Kohlmeyer on Aug 22 2016, 21:12.
fix elusive uninitialized data bug reported by valgrind
eb273ab9ea3c
·Axel Kohlmeyer on Aug 22 2016, 21:12.
be a bit more paranoid about initializing data structures
3cf6715d40fb
·Axel Kohlmeyer on Aug 22 2016, 21:12.
make it so that dynamic load balancing only uses the timing since the last…
0b0db201d1c5
·Axel Kohlmeyer on Aug 22 2016, 21:12.
minor tweaks and comment fixes
f76f2c881bd8
·Axel Kohlmeyer on Aug 22 2016, 21:12.
improve c++-11 compliance. replace variable size stack allocation.
7d08d9991eb5
·Axel Kohlmeyer on Aug 22 2016, 21:12.
whitespace cleanup
85cafde77c28
·Axel Kohlmeyer on Aug 22 2016, 21:12.
disable debug output and include bond cost as well
db734c3003cd
·Axel Kohlmeyer on Aug 22 2016, 21:12.
implement wall clock based load balancing cost function support
cc77679851d7
·Axel Kohlmeyer on Aug 22 2016, 21:12.
implement modified version of balance and fix balance according to steve's…
66b4c9b8475d
·Axel Kohlmeyer on Aug 22 2016, 21:12.
Comments
85f58624a72a
·Iain Bethune / Axel Kohlmeyer on Aug 22 2016, 21:12.
Set up branch with load balancing code from master
f784f07b8743
·Iain Bethune / Axel Kohlmeyer on Aug 22 2016, 21:12.
correct bug in tracking atom->nlocal vs. atom->nmax when allocating pbc…
5909bd54298e
·Axel Kohlmeyer on Aug 22 2016, 20:36.
fix bug in recent dump changes for -DLAMMPS_BIGBIG
138368404844
·Axel Kohlmeyer on Aug 22 2016, 20:36.
Remove memory leak and unnecessary allocation
587bafdf2de5
·Richard Berger / Axel Kohlmeyer on Aug 22 2016, 20:36.
Add missing initialization
c8fe3799ed33
·Richard Berger / Axel Kohlmeyer on Aug 22 2016, 20:36.
fix indexing bugs in accessing compute and fix labels in fix ave/histo
9babb7a4c2ae
·Axel Kohlmeyer on Aug 22 2016, 20:35.
correct small (but harmless) logic error.
730e3cb4ac9d
·Axel Kohlmeyer on Aug 22 2016, 20:34.

Aug 21 2016

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15483 f3b2605a-c512-4ea7…
d4891754c862
·sjplimp on Aug 21 2016, 00:42.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15481 f3b2605a-c512-4ea7…
6ccf4b452592
·sjplimp on Aug 21 2016, 00:41.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15480 f3b2605a-c512-4ea7…
bfba361f65f2
·sjplimp on Aug 21 2016, 00:22.

Aug 13 2016

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15474 f3b2605a-c512-4ea7…
650359087584
·sjplimp on Aug 13 2016, 16:51.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15473 f3b2605a-c512-4ea7…
2c9eef57d06a
·sjplimp on Aug 13 2016, 16:49.

Aug 12 2016

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15470 f3b2605a-c512-4ea7…
ff933712b73f
·sjplimp on Aug 12 2016, 16:33.

Aug 10 2016

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15468 f3b2605a-c512-4ea7…
639ea6c39647
·sjplimp on Aug 10 2016, 16:59.

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.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15463 f3b2605a-c512-4ea7…
6c8d3ed4e849
·sjplimp on Aug 9 2016, 16:10.

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.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15459 f3b2605a-c512-4ea7…
056ff192c619
·sjplimp on Aug 8 2016, 15:47.

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@15444 f3b2605a-c512-4ea7…
2d694f934e36
·sjplimp on Aug 5 2016, 17:50.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15436 f3b2605a-c512-4ea7…
9a9897cd447f
·sjplimp on Aug 5 2016, 17:07.

Aug 4 2016

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15435 f3b2605a-c512-4ea7…
0bffc1711e3e
·sjplimp on Aug 4 2016, 18:39.

Aug 3 2016

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@15429 f3b2605a-c512-4ea7…
1f6518400e83
·sjplimp on Aug 3 2016, 21:31.
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@15426 f3b2605a-c512-4ea7…
38226b808685
·sjplimp on Aug 3 2016, 18:09.

Aug 2 2016

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.

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.

Jul 29 2016

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.

Jul 28 2016

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.
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.