Diffusion lammps (master) History

History
masterd08e79702603ff134580c00…

Aug 23 2016

Merge branch 'add-fix-gaussFlow' of https://github.com/sstrong99/lammps into…
d08e79702603
·Axel Kohlmeyer on Aug 23 2016, 19:18.
revised fix_flow_gauss
c1a6d2ec30dc
·Steven Strong on Aug 23 2016, 18:23.
revised fix_flow_gauss
6c927a419da4
·Steven Strong on Aug 23 2016, 18:11.
revised fix_flow_gauss
690158939564
·Steven Strong on Aug 23 2016, 18:10.
revised fix_flow_gauss
36bc96ea6112
·Steven Strong on Aug 23 2016, 17:54.
revised fix_flow_gauss
5a5a10c75ff5
·Steven Strong on Aug 23 2016, 17:46.
revised fix_flow_gauss
06996d7782d9
·Steven Strong on Aug 23 2016, 17:38.
revised fix_flow_gauss
2e7404c96c42
·Steven Strong on Aug 23 2016, 17:38.
revised fix_flow_gauss
3309e9d3baf9
·Steven Strong on Aug 23 2016, 17:33.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
c90f3a800fba
·Axel Kohlmeyer on Aug 23 2016, 13:19.
update colvars library to version 2016-08-19
c67326be6d93
·Axel Kohlmeyer on Aug 23 2016, 11:53.
minor cleanup and compiler warning silencing
29ae1bbca86a
·Axel Kohlmeyer on Aug 23 2016, 04:35.
Merge branch 'initialize_pointers' of https://github.com/andeplane/lammps into…
bbf1dcd9db24
·Axel Kohlmeyer on Aug 23 2016, 04:23.
fixed integer division problem in python code snippet
55fe1f6b29cc
·athomps on Aug 23 2016, 00:35.

Aug 22 2016

Added fix_gaussflow
95755ba8b2e9
·Steven Strong on Aug 22 2016, 23:47.
restore accidentally deleted error message.
f83f88d736d7
·Axel Kohlmeyer on Aug 22 2016, 22:28.
Removed if tests in destructor. Also NULLing pointers in destructors
68c4a8c2f1cf
·Anders Hafreager on Aug 22 2016, 12:42.
Initialize pointers to zero before anything else in fix_ave_chunk.cpp
ae2bfec83d97
·Anders Hafreager on Aug 22 2016, 10:13.

Aug 21 2016

correct bug in tracking atom->nlocal vs. atom->nmax when allocating pbc…
45a2dd36d0f0
·Axel Kohlmeyer on Aug 21 2016, 17:18.
fix bug in recent dump changes for -DLAMMPS_BIGBIG
a50793687861
·Axel Kohlmeyer on Aug 21 2016, 17:17.
Merge branch 'valgrind_errors' of https://github.com/rbberger/lammps into merge…
2dd61ffedae2
·Axel Kohlmeyer on Aug 21 2016, 17:02.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
ebbed707c6cf
·Axel Kohlmeyer on Aug 21 2016, 17:00.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15484 f3b2605a-c512-4ea7…
2fff78a78eb2
·sjplimp on Aug 21 2016, 00:43.
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@15482 f3b2605a-c512-4ea7…
ccf8cf20b378
·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 17 2016

fix indexing bugs in accessing compute and fix labels in fix ave/histo
579c52771813
·Axel Kohlmeyer on Aug 17 2016, 05:54.

Aug 16 2016

Remove memory leak and unnecessary allocation
c998f7b81fb7
·Richard Berger on Aug 16 2016, 04:51.
Add missing initialization
054256cf0a85
·Richard Berger on Aug 16 2016, 04:14.

Aug 15 2016

thread timing summare needs to be marked as preformatted
b745636a6760
·Axel Kohlmeyer on Aug 15 2016, 04:01.

Aug 14 2016

Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
27d36f3f145b
·Axel Kohlmeyer on Aug 14 2016, 12:15.

Aug 13 2016

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15479 f3b2605a-c512-4ea7…
b1829c107cd0
·sjplimp on Aug 13 2016, 17:03.
correct small (but harmless) logic error.
ac6f4f8a5672
·Axel Kohlmeyer on Aug 13 2016, 16:53.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15475 f3b2605a-c512-4ea7…
832f6a9f1125
·sjplimp on Aug 13 2016, 16:52.
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.
update colvars to version 2016-08-10
eba3ad9abb37
·Axel Kohlmeyer on Aug 13 2016, 13:24.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
e338a2f38619
·Axel Kohlmeyer on Aug 13 2016, 12:54.
silence warnings about cases, that cannot happen
60bf26bad9c6
·Axel Kohlmeyer on Aug 13 2016, 07:59.
fix bug found by coverity scan
63b41cb1390a
·Axel Kohlmeyer on Aug 13 2016, 07:58.

Aug 12 2016

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15471 f3b2605a-c512-4ea7…
c03252f08da0
·sjplimp on Aug 12 2016, 16:34.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15470 f3b2605a-c512-4ea7…
ff933712b73f
·sjplimp on Aug 12 2016, 16:33.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15469 f3b2605a-c512-4ea7…
112c98159b1c
·sjplimp on Aug 12 2016, 15:49.
adapt input to no longer fail with recent thermo changes
20e0ae364554
·Axel Kohlmeyer on Aug 12 2016, 00:14.

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.

Historymasterd08e79702603ff134580c00…

Aug 23 2016

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Aug 17 2016

Aug 16 2016

Aug 15 2016

Aug 14 2016

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Aug 6 2016

History
masterd08e79702603ff134580c00…