Diffusion lammps (master) History

History
master2f298951cff2c6706cdf178…

Sep 14 2016

resolved conflicts
2f298951cff2
·Steve Plimpton on Sep 14 2016, 18:22.
HTML update
717e719b8300
·Steve Plimpton on Sep 14 2016, 17:35.
Merge branch 'integration' of github.com:akohlmey/lammps into integration
10b4411d5b8f
·Steve Plimpton on Sep 14 2016, 01:22.
doc updates
c744b23c4c04
·Steve Plimpton on Sep 14 2016, 01:15.
Merge pull request #27 from akohlmey/small-bugfixes
a69e059be324
·sjplimp / GitHub on Sep 14 2016, 01:11.
Merge pull request #26 from rbberger/is_available_feature
dbc548dd8810
·sjplimp / GitHub on Sep 14 2016, 01:10.
added options to compute bond/local
25e518a4f40b
·Steve Plimpton on Sep 14 2016, 01:03.

Sep 13 2016

clean-up of example files
fe2fca4e9b3b
·Steve Plimpton on Sep 13 2016, 22:58.
pair vashishta/table
ed52f9ea5e39
·Steve Plimpton on Sep 13 2016, 22:54.
final version of pair vashishta/table
944289b018a7
·Steve Plimpton on Sep 13 2016, 22:45.
flag 'allocated' must be initialized in constructor
80c5b01bfcd6
·Axel Kohlmeyer on Sep 13 2016, 20:33.
Merge branch 'small-bugfixes' of github.com:akohlmey/lammps into small-bugfixes
51e4a568c9b1
·Axel Kohlmeyer on Sep 13 2016, 20:32.
fix qeq Kokkos bug fix by Stan
a8081d450728
·Steve Plimpton on Sep 13 2016, 18:54.
ignore Makefile.lammps in lib tree
14bed44743d6
·Axel Kohlmeyer on Sep 13 2016, 15:36.
ignore *.mod generated by fortran compilers
18cacb8e1dab
·Axel Kohlmeyer on Sep 13 2016, 15:36.

Sep 11 2016

update html file updated boundary.txt file
e53862ca4a23
·Axel Kohlmeyer on Sep 11 2016, 20:55.
document how using shrink-wrap boundaries can cause lost atoms in parallel
a64eb330e3a2
·Axel Kohlmeyer on Sep 11 2016, 20:48.

Sep 9 2016

update docs for lj/sf/dipole/sf
d70e051ecd7f
·Axel Kohlmeyer on Sep 9 2016, 16:00.
restore c++ marker in header comment
37833b537b9b
·Axel Kohlmeyer on Sep 9 2016, 15:43.
simplify phonon code some more
5fcbfa824820
·Axel Kohlmeyer on Sep 9 2016, 15:40.
simplify code
c437195928a0
·Axel Kohlmeyer on Sep 9 2016, 15:40.
import updated pair lj/sf/dipole/sf files from sam genheden
8b1ef1c686cb
·Axel Kohlmeyer on Sep 9 2016, 15:37.
fix typo in comments
c3e8cb2f30c5
·Axel Kohlmeyer on Sep 9 2016, 15:34.
update error message to be consistent with other styles
365707704cf8
·Axel Kohlmeyer on Sep 9 2016, 15:19.
require an atom map for compute voronoi/atom occupation
16323ba391ea
·Axel Kohlmeyer on Sep 9 2016, 13:39.
Add updated HTML documentation about new is_available feature category
e27869daf684
·Richard Berger on Sep 9 2016, 11:56.
Add documentation about new is_available feature category
dc0c0ab214d3
·Richard Berger on Sep 9 2016, 11:55.
Add feature category to is_available function
4b22443b25d2
·Richard Berger on Sep 9 2016, 11:09.

Sep 8 2016

update html file
956af8cebb2c
·Axel Kohlmeyer on Sep 8 2016, 23:41.
Merge remote-tracking branch 'lammps-rw/integration' into vashishta-tabulation
5c927ca8398e
·Axel Kohlmeyer on Sep 8 2016, 23:22.
implement vashishta/table/omp in USER-OMP
4bb42be3cc09
·Axel Kohlmeyer on Sep 8 2016, 23:22.
update vashishta pair style example
7de51430504e
·Axel Kohlmeyer on Sep 8 2016, 23:21.
update documentation for vashishta pair style
71eed1d612ab
·Axel Kohlmeyer on Sep 8 2016, 23:20.
Merge branch 'small' into integration
dd34feb2bdc6
·Steve Plimpton on Sep 8 2016, 22:35.
Merge branch 'small-bugfixes' of https://github.com/akohlmey/lammps into small
2524c5b52654
·Steve Plimpton on Sep 8 2016, 22:31.
Merge remote-tracking branch 'lammps-rw/integration' into vashishta-tabulation
fe581e8ced13
·Axel Kohlmeyer on Sep 8 2016, 22:21.
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.
Update generated HTML docs of info command
1f901c9b2daa
·Richard Berger on Sep 8 2016, 15:53.
Update docs of info command
79b8f6320d62
·Richard Berger on Sep 8 2016, 15:53.
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

undo changes to vashishita/omp
7e8440cbab58
·Steve Plimpton on Sep 7 2016, 20:02.
created vashishta/table variant
43b05a60c70e
·Steve Plimpton on Sep 7 2016, 19:56.
correct internal links for Modify LAMMPS section
0fe7d1d3612c
·Axel Kohlmeyer on Sep 7 2016, 16:13.
correct reference in modify section
346ff4249833
·Axel Kohlmeyer on Sep 7 2016, 16:10.
regenerate html pages with new txt2rst tool
5feedbd8291d
·Axel Kohlmeyer on Sep 7 2016, 16:09.
replace backquote with regular quote and `` + '' with double quote.
44ce6fac4b91
·Axel Kohlmeyer on Sep 7 2016, 14:29.
Update discussion on parallel python packages. There seem to be only two left.
70d6718aa312
·Axel Kohlmeyer on Sep 7 2016, 13:42.
Make formatting and links more consistent and unique
348b677148ce
·Axel Kohlmeyer on Sep 7 2016, 13:41.
Enforce l,ule or l,ole command order for RST
4c783ea3b726
·Richard Berger / Axel Kohlmeyer on Sep 7 2016, 08:16.
Refactored code and escape RST special character '_'
9e8256aeb0b7
·Richard Berger / Axel Kohlmeyer on Sep 7 2016, 08:16.
Escape RST special character '^' and take care of special math cases
925f1bfb6fc9
·Richard Berger / Axel Kohlmeyer on Sep 7 2016, 08:16.
Escape RST special character '*' in final output
3f312244a01d
·Richard Berger / Axel Kohlmeyer on Sep 7 2016, 08:16.
replace :l,ule and :l,ole with :l :ule or :l :ole
55022d126306
·Axel Kohlmeyer on Sep 7 2016, 08:11.
avoid Inline substitution_reference start-string without end-string
0d491d483c23
·Axel Kohlmeyer on Sep 7 2016, 08:10.
correct error message text, sync with source
a31c5073706c
·Axel Kohlmeyer on Sep 7 2016, 04:15.
update colvars library to version 2016-09-03
3a74ccffa2ed
·Axel Kohlmeyer on Sep 7 2016, 03:28.
adjust makefiles in lib tree, so they don't return an error exit code on "make…
c8cfd53c1b86
·Axel Kohlmeyer on Sep 7 2016, 03:28.
update colvars library to version 2016-08-19
16607a0132d5
·Axel Kohlmeyer on Sep 7 2016, 03:27.
update colvars to version 2016-08-10
3b476d914f5e
·Axel Kohlmeyer on Sep 7 2016, 03:27.
update colvars to another set of changes from the upstream repo
977b9e542f5d
·Axel Kohlmeyer on Sep 7 2016, 03:27.
update colvars makefile dependencies
1b33d00785b9
·Axel Kohlmeyer on Sep 7 2016, 03:27.
suppress compiler warning
3d2e5d0a5031
·Axel Kohlmeyer on Sep 7 2016, 03:27.
update colvars to version 2016-08-10
ec2a6b9f0de3
·Axel Kohlmeyer on Sep 7 2016, 03:27.
update colvars library to version 2016-08-05
77620106a43e
·Axel Kohlmeyer on Sep 7 2016, 03:26.
update with correct error description. sync with manual.
f56c41eec047
·Axel Kohlmeyer on Sep 7 2016, 03:21.
update manual introduction to represent current status. correct some markup to…
fc2d87830538
·Axel Kohlmeyer on Sep 7 2016, 03:20.
Merge branch 'integration' into doc-corrections-and-updates
1c17b9850056
·Axel Kohlmeyer on Sep 7 2016, 02:19.
Merge branch 'integration' into small-bugfixes
91381525638c
·Axel Kohlmeyer on Sep 7 2016, 02:17.
Merge remote-tracking branch 'lammps-rw/clean-up-docs-for-sphinx' into clean-up…
ace5dc3c7c9a
·Axel Kohlmeyer on Sep 7 2016, 01:54.
sync with 7Sep16 patch
0252347d43c5
·Steve Plimpton on Sep 7 2016, 01:00.
Merge pull request #20 from akohlmey/lammps-contribute
c9455c90dee3
·sjplimp / GitHub on Sep 7 2016, 00:55.
Merge pull request #19 from akohlmey/clean-up-docs-for-sphinx
1e4d6fee93cf
·sjplimp / GitHub on Sep 7 2016, 00:54.

Sep 6 2016

one more small correction to document recent fix ave/time changes
42db93e1980b
·Axel Kohlmeyer on Sep 6 2016, 22:10.
fix typos
906bd2454318
·Axel Kohlmeyer on Sep 6 2016, 22:03.
update the discussion on how to submit modifications
4f88c7540152
·Axel Kohlmeyer on Sep 6 2016, 22:02.
harden fix shear/history against use-after-delete and from incorrect use of…
4314299be910
·Axel Kohlmeyer on Sep 6 2016, 20:50.
generate updated html files for corrected .txt files
1a7b04e8a613
·Axel Kohlmeyer on Sep 6 2016, 19:40.
correct link targets
fbc955e5492c
·Axel Kohlmeyer on Sep 6 2016, 19:40.

Historymaster2f298951cff2c6706cdf178…

Sep 14 2016

Sep 13 2016

Sep 11 2016

Sep 9 2016

Sep 8 2016

Sep 7 2016

Sep 6 2016

History
master2f298951cff2c6706cdf178…