Diffusion lammps (master) History

History
master8820315ff96af5a4d411d17…

Mar 23 2017

Merge branch 'master' into updates-for-stable
8820315ff96a
·Axel Kohlmeyer on Mar 23 2017, 22:57.
fix ave/chunk fixes, 2d disc option, fix_modify dynamic/dof
44841f689127
·Steve Plimpton on Mar 23 2017, 22:31.
remove one more reference to xmovie
2cdcd6d63045
·Axel Kohlmeyer on Mar 23 2017, 21:03.
re-arranged functions to make it easier to compare with non-threaded. port…
47cade2bcff2
·Axel Kohlmeyer on Mar 23 2017, 20:19.
whitespace cleanup
a72efbea3699
·Axel Kohlmeyer on Mar 23 2017, 20:18.

Mar 22 2017

remove reference to removed section on VMD scripts
43a304f56451
·Axel Kohlmeyer on Mar 22 2017, 20:12.
correct inconsistent anchors
a79aef65e84a
·Axel Kohlmeyer on Mar 22 2017, 20:12.
fully integrate support for doc_anchor_check into docs makefile
3ec16f3630c4
·Axel Kohlmeyer on Mar 22 2017, 19:40.

Mar 21 2017

correct typo reported on lammps-users
734e639c5d9d
·Axel Kohlmeyer on Mar 21 2017, 19:12.
changes for next patch, 2d disc options for spheres, fix external upgrade, bug…
dcede304dff9
·Steve Plimpton on Mar 21 2017, 15:56.
Merge pull request #427 from akohlmey/small-updates-and-corrections
145e682ad386
·sjplimp / GitHub on Mar 21 2017, 15:18.

Mar 20 2017

remove references to deleted tools. update/clarify section on restart2data
6482df6c2fbf
·Axel Kohlmeyer on Mar 20 2017, 23:57.
have the relevant LAMMPS version embedded into top part of the html manual
0c9cd11b4e95
·Axel Kohlmeyer on Mar 20 2017, 23:25.
mention NumPy dependency instead of Numeric for python tools
82d952ae0eaf
·Axel Kohlmeyer on Mar 20 2017, 22:26.
fix compilation for pymol_asphere tool
47d6451d033a
·Axel Kohlmeyer on Mar 20 2017, 22:18.
remove obsolete tools and files
e110d6961a48
·Axel Kohlmeyer on Mar 20 2017, 22:17.
update colvars abf integrate tool from git repo
a42b0b7dcb59
·Axel Kohlmeyer on Mar 20 2017, 22:04.
adapt binary2txt.cpp source to current coding conventions
03828b5836f5
·Axel Kohlmeyer on Mar 20 2017, 21:57.
remove non-ASCII characters from doc source files
3b44c3ff1d5f
·Axel Kohlmeyer on Mar 20 2017, 21:55.
correct stan's email address
0d0c2b65f763
·Axel Kohlmeyer on Mar 20 2017, 21:32.
emphasize that the online manual is following the latest development version
2218a9d704dc
·Axel Kohlmeyer on Mar 20 2017, 21:32.
remove duplicate paragraph in nose-hoover fix docs
0a6b33cd78a6
·Axel Kohlmeyer on Mar 20 2017, 21:27.
more permission fixes
ecf17621aa80
·Axel Kohlmeyer on Mar 20 2017, 21:25.
remove xmovie
f0c6ed004dd0
·Axel Kohlmeyer on Mar 20 2017, 21:24.
update permissions
554531a302d7
·Axel Kohlmeyer on Mar 20 2017, 18:51.
Merge pull request #426 from dstelter92/master
d496c0fdfa9f
·sjplimp / GitHub on Mar 20 2017, 15:57.
re-ran example with fixed exchanges
5c39dfd74089
·dstelter92 on Mar 20 2017, 14:22.
Teff and exchange bugfix, as per Greg Dignon to match python examples
5b842f0010a7
·dstelter92 on Mar 20 2017, 14:15.

Mar 17 2017

patch 17Mar17
4a90bca7a3b4
·Steve Plimpton on Mar 17 2017, 18:29.
Merge pull request #424 from timattox/dpd_restart_fix
9f35b764f8cc
·sjplimp / GitHub on Mar 17 2017, 18:19.
Merge pull request #423 from timattox/master_bugfix_irregular
7ca5dce2f56c
·sjplimp / GitHub on Mar 17 2017, 18:18.
Merge pull request #421 from akohlmey/memory-output
fcc3b3bd365d
·sjplimp / GitHub on Mar 17 2017, 18:18.
Merge pull request #420 from rbberger/doc_anchor_check
53a3877c3d3e
·sjplimp / GitHub on Mar 17 2017, 18:17.
Merge pull request #419 from rbberger/python_fixes
a936b7b2ab27
·sjplimp / GitHub on Mar 17 2017, 18:16.
Merge pull request #416 from lukin17/filter_corotate
a91b851f3d40
·sjplimp / GitHub on Mar 17 2017, 18:14.
Remove unneeded restart_peratom flags
d31c591b60f7
·Stan Moore on Mar 17 2017, 16:40.
add support for MPI_Request_free() to MPI STUBS library
ae5ebf600189
·Axel Kohlmeyer on Mar 17 2017, 16:40.
Revert "In irregular.cpp use simpler and slightly faster…
7fb741d53da8
·Axel Kohlmeyer on Mar 17 2017, 16:35.
In irregular.cpp use simpler and slightly faster MPI_Reduce_scatter_block()
8e75616c144d
·Tim Mattox on Mar 17 2017, 08:02.
BUGFIX: Prevent possible deadlock in Irregular::create_atom and create_data
411c069ba66f
·Tim Mattox on Mar 17 2017, 08:02.
ignore package pair style
ac82d041cc44
·Axel Kohlmeyer on Mar 17 2017, 04:12.
Correct off-by-one error in line number reported
621d7d5ce0f2
·Richard Berger on Mar 17 2017, 04:05.
Remove some duplicate anchors in documentation
1bb9c7da42e5
·Richard Berger on Mar 17 2017, 03:36.
Add anchor_check to doc Makefile
f893104b18d1
·Richard Berger on Mar 17 2017, 03:21.
Add utility to detect duplicate anchors in documentation files
efb2a942e046
·Richard Berger on Mar 17 2017, 03:21.

Mar 16 2017

improve memory usage reporting in info and output class
070ce33a13df
·Axel Kohlmeyer on Mar 16 2017, 23:35.
add fix filter/corotate to some administrative files
f604f86cfcd4
·Axel Kohlmeyer on Mar 16 2017, 20:08.
simplify and shorten examples for fix filter/corotate and combine into a single…
bed288339e74
·Axel Kohlmeyer on Mar 16 2017, 20:02.
fix some more code formatting issues, add newline at EOF
1995f434f3d3
·Axel Kohlmeyer on Mar 16 2017, 19:24.
Merge branch 'filter_corotate' of https://github.com/lukin17/lammps into pull…
db0281b4df0b
·Axel Kohlmeyer on Mar 16 2017, 17:14.
Merge remote-tracking branch 'upstream/master' into filter_corotate
2f5e711acd82
·lukin17 on Mar 16 2017, 10:00.
Fixed coding style.
bdb7669e2742
·lukin17 on Mar 16 2017, 09:44.
Added Python matplotlib plot example
cda821389250
·Richard Berger on Mar 16 2017, 06:41.
Improve Python 3 compatibility of pizza tools and simplify read_snapshot code
ef940d226c33
·Richard Berger on Mar 16 2017, 06:38.
Fix dump cfg in vizplotgui_atomeye.py example
36da9223ec43
·Richard Berger on Mar 16 2017, 03:55.
Fix space/tab error in pizza/gl.py
eb29ef32b1b9
·Richard Berger on Mar 16 2017, 03:43.
Fix dump cfg in viz_atomeye.py example
29550d472d23
·Richard Berger on Mar 16 2017, 03:31.
Document property 'uses_exceptions' of Python interface
79cae51156ad
·Richard Berger on Mar 16 2017, 03:20.
Fixes lammps_create_atoms library function and its Python interface variant
a210867025e1
·Richard Berger on Mar 16 2017, 03:13.
Fix Python 3 compatibility by encoding strings passed as c_char_p
0262a54ecfeb
·Richard Berger on Mar 16 2017, 03:00.

Mar 15 2017

Merge branch 'filter_corotate' of https://github.com/lukin17/lammps into pull…
0d8f74f0c52e
·Axel Kohlmeyer on Mar 15 2017, 23:54.
Merge pull request #413 from ohenrich/user-cgdna
3a2da51a8210
·sjplimp / GitHub on Mar 15 2017, 20:12.
Merge pull request #415 from stanmoore1/kk_qeq
b1c59126f750
·sjplimp / GitHub on Mar 15 2017, 20:12.
Merge pull request #414 from sstrong99/flow-gauss-doc-addition
4c77838514d1
·sjplimp / GitHub on Mar 15 2017, 20:11.
Merge pull request #412 from timattox/master_typofix
f9468f46f577
·sjplimp / GitHub on Mar 15 2017, 20:10.
Added fix filter/corotate.
c3ce3747e049
·lukin17 on Mar 15 2017, 11:34.

Mar 14 2017

Tweaking docs for Kokkos package
fdc390ad0548
·Stan Moore on Mar 14 2017, 21:08.
Add neigh/qeq option to Kokkos
580f6b567b12
·Stan Moore on Mar 14 2017, 17:44.
updated the NEMD discussion in the how-to documentation about flow/gauss
27b1c33a1680
·Steven Strong on Mar 14 2017, 17:39.
Minor updates in documentation and setup tool, merge before upgrade to oxDNA2
7a75cd111c3d
·Oliver Henrich on Mar 14 2017, 12:39.
Updated documentation and simple setup tool
23b828793333
·Oliver Henrich on Mar 14 2017, 12:36.

Mar 11 2017

Correct a typo in the fix_halt.txt documentation.
4cfe623bc17d
·Tim Mattox on Mar 11 2017, 03:30.

Mar 10 2017

change to RCB cuts in load-balancing commands, also a new option for fix halt
f871ecdc67db
·Steve Plimpton on Mar 10 2017, 23:55.
Merge pull request #408 from giacomofiorin/colvars-update-2017-03-10
470353e32080
·sjplimp / GitHub on Mar 10 2017, 22:51.
Merge pull request #406 from stanmoore1/kokkos_bugfix
ffe02d20ca83
·sjplimp / GitHub on Mar 10 2017, 22:51.
Include PDF of Colvars doc missing in previous commit
f70752c18f8d
·Giacomo Fiorin on Mar 10 2017, 21:58.
Merge pull request #405 from stanmoore1/ev_setup_kk
07fcfd6d54a1
·sjplimp / GitHub on Mar 10 2017, 19:01.
Merge pull request #407 from frobnitzem/master
c97feafca6ac
·sjplimp / GitHub on Mar 10 2017, 19:00.
Merge pull request #402 from timattox/USER-DPD_spelling
b20d95d49548
·sjplimp / GitHub on Mar 10 2017, 18:59.
Backport typo fixes that were not previously pushed to the Colvars repository
0b4adaa9e6a1
·Giacomo Fiorin on Mar 10 2017, 15:24.
Update Colvars module to version 2017-03-10
5fe620663813
·Giacomo Fiorin on Mar 10 2017, 15:16.

Mar 9 2017

Add error check to lammps_gather_atoms/lammps_scatter_atoms in library.cpp
65964f3b31ea
·David M. Rogers on Mar 9 2017, 22:49.
Fix half from full nlist issue with Kokkos
b28b84d444a4
·Stan Moore on Mar 9 2017, 22:00.
Fixing memory overflow issue in comm_kokkos
a001a5ceb0c4
·Stan Moore on Mar 9 2017, 20:20.

Mar 8 2017

restore incorrect change due to spell checking in fix imd
2ef713ea1b49
·Axel Kohlmeyer on Mar 8 2017, 22:40.
Disable allocation of per-atom arrays in ev_setup for Kokkos styles
1f6c1942b37e
·Stan Moore on Mar 8 2017, 20:42.
Adding alloc flag to ev_setup
683023d8203f
·Stan Moore on Mar 8 2017, 20:36.

Mar 7 2017

Fix spelling "correction" from 3a054d1a: iterations not interactions. :-)
42d3a8f4982d
·Tim Mattox on Mar 7 2017, 21:41.
patch 7Mar17
79b005dc3d5f
·Steve Plimpton on Mar 7 2017, 19:40.
Merge pull request #393 from akohlmey/small-bugfixes
a2fa6ef4524c
·sjplimp / GitHub on Mar 7 2017, 17:56.
Merge pull request #399 from rbberger/docs_spelling_fixes
920641bbffbc
·sjplimp / GitHub on Mar 7 2017, 17:47.
Merge pull request #398 from stanmoore1/kokkos_changes
c2aabdec229c
·sjplimp / GitHub on Mar 7 2017, 17:46.
Merge pull request #395 from timattox/USER-DPD_bugfix
e4aa735a6809
·sjplimp / GitHub on Mar 7 2017, 17:46.
Merge pull request #394 from jaapkroe/kolmogorov-crespi
4af6557568e7
·sjplimp / GitHub on Mar 7 2017, 17:46.
Merge pull request #389 from akohlmey/update-agni-potential
0798885bdb2a
·sjplimp / GitHub on Mar 7 2017, 17:35.
Merge pull request #386 from akohlmey/doc-consistentcy
020e75e7efff
·sjplimp / GitHub on Mar 7 2017, 17:33.
Merge pull request #376 from v0i0/airebo-bondorderLJ-fixes
d6866f1cfdd7
·sjplimp / GitHub on Mar 7 2017, 17:32.
new neigh_modify exclude option, other SNAP changes
efaa4c67109f
·Steve Plimpton on Mar 7 2017, 17:31.
Fix more typos in tools
08baaa9d8ede
·Richard Berger on Mar 7 2017, 07:00.
Fix typo in python README
359af419a7ab
·Richard Berger on Mar 7 2017, 06:58.

Historymaster8820315ff96af5a4d411d17…

Mar 23 2017

Mar 22 2017

Mar 21 2017

Mar 20 2017

Mar 17 2017

Mar 16 2017

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Mar 14 2017

Mar 11 2017

Mar 10 2017

Mar 9 2017

Mar 8 2017

Mar 7 2017

History
master8820315ff96af5a4d411d17…