Diffusion lammps (master) History

lammps/src
master546582ea0251245b3396ca8…

Sep 8 2016

Merge branch 'small-bugfixes' of https://github.com/akohlmey/lammps into small
2524c5b52654
·Steve Plimpton on Sep 8 2016, 22:31.
Merge pull request #24 from rbberger/info_command_styles
b866e0663b9f
·sjplimp / GitHub on Sep 8 2016, 22:16.
Merge pull request #23 from akohlmey/doc-corrections-and-updates
5d0da95a0b6d
·sjplimp / GitHub on Sep 8 2016, 22:15.
Merge pull request #22 from akohlmey/colvars-update
07e55ef61e7d
·sjplimp / GitHub on Sep 8 2016, 22:14.
Kokkos lib update
236ebf7fabbb
·Steve Plimpton on Sep 8 2016, 21:56.
ignore all variants of the vashishta pair styles in src/
a6df1e53b43f
·Axel Kohlmeyer on Sep 8 2016, 20:46.
remove executable permissions on non-executables and non-scripts
9b2d5ff3e72d
·Axel Kohlmeyer on Sep 8 2016, 20:45.
delete duplicate fclose() in fix ttm/mod constructor
c33e1049d8dd
·Axel Kohlmeyer on Sep 8 2016, 17:51.
Change info command styles syntax
2dcfb51d1807
·Richard Berger on Sep 8 2016, 15:38.
Use factory for region style creation
ba2b523bf4b7
·Richard Berger on Sep 8 2016, 15:38.
Use factory for dump style creation
fd2b88642278
·Richard Berger on Sep 8 2016, 15:38.
Use factory for minimize style creation
9952d8a210fc
·Richard Berger on Sep 8 2016, 15:38.
Use factory for integrate style creation
85c132943ed5
·Richard Berger on Sep 8 2016, 15:38.
Add missing delete in destructor
55260ad53e5b
·Richard Berger on Sep 8 2016, 15:32.
Use factory for AtomVec style creation
a1e5fc0fca8f
·Richard Berger on Sep 8 2016, 15:32.
Cleanup force.h after refactoring
88e10b401d5e
·Richard Berger on Sep 8 2016, 15:32.
Use factory for kspace style creation
1d03913aa307
·Richard Berger on Sep 8 2016, 15:32.
Use factory for improper style creation
0745a9f33f41
·Richard Berger on Sep 8 2016, 15:32.
Use factory for dihedral style creation
906c50223af6
·Richard Berger on Sep 8 2016, 15:32.
Use factory for angle style creation
35bdeb63e266
·Richard Berger on Sep 8 2016, 15:32.
Use factory for bond style creation
69c58ef0d5df
·Richard Berger on Sep 8 2016, 15:32.
Use pair_map to list pair styles
95ee6440add0
·Richard Berger on Sep 8 2016, 15:32.
Use compute_map and fix_map to list compute and fix styles
00b08bb5e1fe
·Richard Berger on Sep 8 2016, 15:32.
Use command_map to list command styles
e483cb9ef977
·Richard Berger on Sep 8 2016, 15:32.
Add styles output to info command
06e3a11c2dd5
·Richard Berger on Sep 8 2016, 15:32.

Sep 7 2016

replace backquote with regular quote and `` + '' with double quote.
44ce6fac4b91
·Axel Kohlmeyer on Sep 7 2016, 14:29.
update colvars to version 2016-08-10
3b476d914f5e
·Axel Kohlmeyer on Sep 7 2016, 03:27.
update with correct error description. sync with manual.
f56c41eec047
·Axel Kohlmeyer on Sep 7 2016, 03:21.
Merge branch 'integration' into small-bugfixes
91381525638c
·Axel Kohlmeyer on Sep 7 2016, 02:17.
sync with 7Sep16 patch
0252347d43c5
·Steve Plimpton on Sep 7 2016, 01:00.

Sep 6 2016

harden fix shear/history against use-after-delete and from incorrect use of…
4314299be910
·Axel Kohlmeyer on Sep 6 2016, 20:50.
add pppm/kk and fix reax/c issues
3bb3c1a45c81
·Steve Plimpton on Sep 6 2016, 18:46.

Sep 1 2016

Merge branch 'core/cpp_exceptions' of https://github.com/rbberger/lammps into…
639ab0fd3e37
·Steve Plimpton on Sep 1 2016, 00:11.

Aug 31 2016

sync with SVN
7c01ef57eeb0
·Steve Plimpton on Aug 31 2016, 23:17.
Merge pull request #3 from akohlmey/fix-flow-gauss
0316bb579be8
·sjplimp / GitHub on Aug 31 2016, 23:03.
Merge branch 'small' into integration
4051aedf2c78
·Steve Plimpton on Aug 31 2016, 21:58.
sync with SVN
ec8b9e21dbb4
·Steve Plimpton on Aug 31 2016, 21:28.

Aug 30 2016

remove vector/array class members shadowing the base class
a2ea263652c6
·Axel Kohlmeyer on Aug 30 2016, 13:04.
null-ing of pointers and a couple select integers for fix ave/chunk
021ade199a31
·Axel Kohlmeyer on Aug 30 2016, 12:41.
individual computes do not need to set vector/array to NULL. reordering fixes…
b7749ab21285
·Axel Kohlmeyer on Aug 30 2016, 12:41.
Use MPI_Allreduce values instead of each processor's values
554ac7dd12b6
·Efrem Braun / Axel Kohlmeyer on Aug 30 2016, 12:38.
Merge branch 'integration' into small-bugfixes
ef86d1172963
·Axel Kohlmeyer on Aug 30 2016, 12:29.

Aug 29 2016

use correct order when initializing arrays
1c1c9c310146
·Axel Kohlmeyer on Aug 29 2016, 04:23.
Fixed initialization of arrays in computes/fixes in MC package
48ba812f0ada
·Anders Hafreager / Axel Kohlmeyer on Aug 29 2016, 04:23.
Fixed initialization of arrays in computes/fixes in MANYBODY package
f9a21ae65496
·Anders Hafreager / Axel Kohlmeyer on Aug 29 2016, 04:23.
Fixed initialization of arrays in fixes
d6b9d0b9b6cd
·Anders Hafreager / Axel Kohlmeyer on Aug 29 2016, 04:23.
Fixed initialization of arrays in fixes
36e085e393eb
·Anders Hafreager / Axel Kohlmeyer on Aug 29 2016, 04:23.
Fixed initialization of arrays in fixes
425142ba2e73
·Anders Hafreager / Axel Kohlmeyer on Aug 29 2016, 04:23.
Fixed initialization of arrays in fixes
07eb1d443b27
·Anders Hafreager / Axel Kohlmeyer on Aug 29 2016, 04:23.
Fixed initialization of arrays in fixes
265cc14125e4
·Anders Hafreager / Axel Kohlmeyer on Aug 29 2016, 04:23.
Fixed initialization of arrays in fixes
fd05a1325ee1
·Anders Hafreager / Axel Kohlmeyer on Aug 29 2016, 04:23.
Fixed initialization of arrays in fixes
b5a562788bfa
·Anders Hafreager / Axel Kohlmeyer on Aug 29 2016, 04:23.
Fixed initialization of arrays in fixes
2c7241bfe282
·Anders Hafreager / Axel Kohlmeyer on Aug 29 2016, 04:23.
Fixed initialization of arrays in fixes
ee2f6ded2990
·Anders Hafreager / Axel Kohlmeyer on Aug 29 2016, 04:23.
Fixed initialization of arrays in fixes
db077ef186c2
·Anders Hafreager / Axel Kohlmeyer on Aug 29 2016, 04:23.

Aug 28 2016

fix off-by one bug when looking for bonds.
fc5db8a737be
·Axel Kohlmeyer on Aug 28 2016, 20:20.
Merge branch 'integration' into small-bugfixes
f8d6b979ec1a
·Axel Kohlmeyer on Aug 28 2016, 20:16.
Merge branch 'integration' into fix-flow-gauss
4e03df2d197b
·Axel Kohlmeyer on Aug 28 2016, 12:55.
incorporate bugfix and cleanup from lammps-icms and upstream
e1045851c035
·Axel Kohlmeyer on Aug 28 2016, 12:52.
Merge pull request #5 from akohlmey/initialize-pointers
0192d2e35969
·sjplimp / GitHub on Aug 28 2016, 01:14.
sync with SVN
3a1397dc7c36
·Steve Plimpton on Aug 28 2016, 01:11.
Merge pull request #11 from akohlmey/python3-for-make-py
ef69bf8695f3
·sjplimp / GitHub on Aug 28 2016, 01:01.
Merge pull request #12 from akohlmey/shell-script-paranoia
6a4633af0a1e
·sjplimp / GitHub on Aug 28 2016, 00:59.
new fix flow/gauss command
c80dad002883
·Steve Plimpton on Aug 28 2016, 00:25.

Aug 27 2016

enforce C or POSIX locale in all shell scripts and turn of enforced global grep…
c570bf26e0d8
·Axel Kohlmeyer on Aug 27 2016, 07:57.

Aug 26 2016

need to ignore src/Make.py.last as well
742c853775bb
·Axel Kohlmeyer on Aug 26 2016, 23:48.
Merge branch 'integration' into python3-for-make-py
9932b7322702
·Axel Kohlmeyer on Aug 26 2016, 23:48.
some more tweaks needed to improve python2/3 compatibility
90272f6c711d
·Axel Kohlmeyer on Aug 26 2016, 23:46.
correct for futurize not being able to fully convert functionality of the…
8dd42789f8b9
·Axel Kohlmeyer on Aug 26 2016, 23:15.
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.
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.

lammps/srcmaster546582ea0251245b3396ca8…

Sep 8 2016

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Aug 31 2016

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Aug 28 2016

Aug 27 2016

Aug 26 2016

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Aug 22 2016

Aug 21 2016

Aug 13 2016

lammps/src
master546582ea0251245b3396ca8…