Diffusion lammps (master) History

History
master29550d472d23343c5d925bf…

Mar 16 2017

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 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.

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.
Fix typos in txt2html
21be86c42393
·Richard Berger on Mar 7 2017, 06:58.
Fix more typos in examples
d6800405a518
·Richard Berger on Mar 7 2017, 06:57.
Fix more typos in src files
3a054d1a82b2
·Richard Berger on Mar 7 2017, 06:55.
Third batch of spelling fixes in manual
007f3c66a033
·Richard Berger on Mar 7 2017, 06:51.
Add remaining false positives
32708860a9fa
·Richard Berger on Mar 7 2017, 06:27.

Mar 6 2017

Added spellcheck utility to documentation build
fc9eebb9367c
·Richard Berger on Mar 6 2017, 03:23.
Fix typos in tools folder
dd76ac5010ae
·Richard Berger on Mar 6 2017, 03:18.
Convert USER/lb/polymer files to UNIX line endings and remove trailing…
17486a9319f8
·Richard Berger on Mar 6 2017, 03:16.
Fix typos in examples folder
778a79b8eef7
·Richard Berger on Mar 6 2017, 03:10.
Fix typos in src files
7dd60f97377a
·Richard Berger on Mar 6 2017, 03:03.
Second batch of spelling fixes in manual
084d831bce01
·Richard Berger on Mar 6 2017, 03:02.
Spelling fixes in source files
e261bef7bba7
·Richard Berger on Mar 6 2017, 00:30.
First batch of spelling fixes in manual
fd78486086d9
·Richard Berger on Mar 6 2017, 00:27.

Mar 3 2017

Improving memory access in comm_kokkos
6382d3c89a2f
·Stan Moore on Mar 3 2017, 17:14.
USER-DPD: pair_multi_lucy_rx bugfix for systems with multiple atom types
763a00e8b02e
·Tim Mattox on Mar 3 2017, 15:29.
Merge branch 'pair_write_fix' of https://github.com/andeplane/lammps into small…
ce1a3f25e193
·Axel Kohlmeyer on Mar 3 2017, 14:11.
Print error if pair_write does not get correct number of arguments
eaf7ed770750
·Anders Hafreager on Mar 3 2017, 06:25.

Mar 1 2017

USER-DPD bugfix: make atom_vec_dpd work properly with atom_vec_hybrid. We were…
9a560b90914c
·Tim Mattox on Mar 1 2017, 21:22.
updated documentation and ev_tally
8a0e44db83de
·Jaap Kroes on Mar 1 2017, 16:13.

Feb 28 2017

USER-DPD: correct off-by-one errors in PairMultiLucyRX::coeff()
1dc78a7e58c8
·Tim Mattox on Feb 28 2017, 23:45.
USER-DPD: correct off-by-one errors in PairTableRX::coeff()
7a593c2fc886
·Tim Mattox on Feb 28 2017, 20:25.
update lammps.book file for latest doc changes
3ac74a1d6995
·Axel Kohlmeyer on Feb 28 2017, 17:21.
add a few more missing details for integrating pair style kolmogorov/crespi/z
3605208a45bb
·Axel Kohlmeyer on Feb 28 2017, 17:16.
make the introduction of the command-by-category list less confusing
9b01949cacfc
·Axel Kohlmeyer on Feb 28 2017, 17:05.
added jpg for kolmogorov-crespi-z equations and fixed hybrid/overlay check in…
323570c92036
·Jaap Kroes on Feb 28 2017, 15:39.
email added
df13a7a00382
·Jaap Kroes on Feb 28 2017, 15:12.
Added Kolmogorov-Crespi potential
a1b40b902d3e
·Jaap Kroes on Feb 28 2017, 14:59.
implement bugfix from issue #388
b921b69f4792
·Axel Kohlmeyer on Feb 28 2017, 00:22.
trigger recomputing ichunk between runs unless requested otherwise
c0cf50bce551
·Axel Kohlmeyer on Feb 28 2017, 00:19.
fix typos: moleclue -> molecule
2708c8683626
·Axel Kohlmeyer on Feb 28 2017, 00:03.

Feb 24 2017

remove outdated log files, too.
9999f363a1f8
·Axel Kohlmeyer on Feb 24 2017, 21:34.
update AGNI potential for Al, reference runs and output and citation
a18b4ef4b0cf
·Axel Kohlmeyer on Feb 24 2017, 21:33.

Feb 22 2017

Corrected comment in 3' to 5' directionality check
3626496c7c6a
·Oliver Henrich on Feb 22 2017, 21:06.
Corrected comment in 3' to 5' directionality check.
458b6749e7b6
·Oliver Henrich on Feb 22 2017, 21:03.
improve consistency and resolve dead links for USER-CGDNA related doc files
20a9ffe69dfd
·Axel Kohlmeyer on Feb 22 2017, 03:27.
patch 21Feb17 sync with GHub
49e83b434800
·Steve Plimpton on Feb 22 2017, 00:07.

Feb 21 2017

Merge pull request #385 from akohlmey/collected-small-bugfixes
6e89ccd522f5
·sjplimp / GitHub on Feb 21 2017, 23:59.
Merge pull request #384 from lammps/another_neigh_refactor
53f3df5bfc94
·sjplimp / GitHub on Feb 21 2017, 23:57.
remove a debug print line
3dbbea342a3b
·Steve Plimpton on Feb 21 2017, 23:57.
Merge pull request #383 from stanmoore1/rshan_class2_kk
b70c670aac56
·sjplimp / GitHub on Feb 21 2017, 23:52.
Merge pull request #382 from timattox/master_kokkos_neigh_bugfix
1d17cae407ff
·sjplimp / GitHub on Feb 21 2017, 23:51.
Merge pull request #380 from hheenen/core_shell_documentation
429264a12bac
·sjplimp / GitHub on Feb 21 2017, 23:50.
Merge pull request #379 from ndtrung81/pppm-gpu-compute-group-group
d001a093455b
·sjplimp / GitHub on Feb 21 2017, 23:50.
Merge pull request #378 from timattox/USER-DPD_ssa_update
cb9d42da0896
·sjplimp / GitHub on Feb 21 2017, 23:50.
Merge pull request #377 from stanmoore1/kokkos_update
7185ec92b3f0
·sjplimp / GitHub on Feb 21 2017, 23:49.
new SNAP potential for W
1cd4c48cccdb
·Steve Plimpton on Feb 21 2017, 23:49.

Feb 17 2017

correct a logic bug in fix wall/gran/region
a88136c3f50d
·Axel Kohlmeyer on Feb 17 2017, 23:58.
remove debug code
ce20c7ffe911
·Axel Kohlmeyer on Feb 17 2017, 18:42.

Feb 16 2017

more neighbor list changes, some new options
4a80df3a99b8
·Steve Plimpton on Feb 16 2017, 00:45.

Feb 15 2017

Add copymode protection to class2 styles
5f93fad012d8
·Stan Moore on Feb 15 2017, 21:56.
Updating docs for Kokkos class2
ccaec315db31
·Stan Moore on Feb 15 2017, 21:00.
Fix a few issues with Kokkos class2 files
c6c1852b3b1a
·Stan Moore on Feb 15 2017, 20:44.
Add files from Ray Shan for Kokkos version of class2 angle, bond, etc.
69a8e19dc5eb
·Stan Moore on Feb 15 2017, 20:29.
neighbor_kokkos.cpp: Don't call grow() on neighbor lists that are copies. This…
928947dcea24
·Tim Mattox on Feb 15 2017, 17:49.
Fixed issue with switching function derivative in PairAIREBO::FLJ
904609a7a3a5
·Markus Hoehnerbach on Feb 15 2017, 16:38.
Fixed a number of issues after verifying against the KIM version
fc3505fac47d
·Markus Hoehnerbach on Feb 15 2017, 16:37.

Feb 14 2017

update names in example, too
48070011d9b7
·Axel Kohlmeyer / GitHub on Feb 14 2017, 13:42.
one more Finchham to Fincham change
0fb8dacc00f8
·Axel Kohlmeyer / GitHub on Feb 14 2017, 13:41.

Historymaster29550d472d23343c5d925bf…

Mar 16 2017

Mar 15 2017

Mar 14 2017

Mar 11 2017

Mar 10 2017

Mar 9 2017

Mar 8 2017

Mar 7 2017

Mar 6 2017

Mar 3 2017

Mar 1 2017

Feb 28 2017

Feb 24 2017

Feb 22 2017

Feb 21 2017

Feb 17 2017

Feb 16 2017

Feb 15 2017

Feb 14 2017

History
master29550d472d23343c5d925bf…