Diffusion lammps (master) History

lammps/src
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.
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 21 2017

changes for next patch, 2d disc options for spheres, fix external upgrade, bug…
dcede304dff9
·Steve Plimpton on Mar 21 2017, 15:56.

Mar 20 2017

update permissions
554531a302d7
·Axel Kohlmeyer on Mar 20 2017, 18:51.
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 #419 from rbberger/python_fixes
a936b7b2ab27
·sjplimp / GitHub on Mar 17 2017, 18:16.
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.

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.
fix some more code formatting issues, add newline at EOF
1995f434f3d3
·Axel Kohlmeyer on Mar 16 2017, 19:24.
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.
Fixes lammps_create_atoms library function and its Python interface variant
a210867025e1
·Richard Berger on Mar 16 2017, 03:13.

Mar 15 2017

Merge pull request #413 from ohenrich/user-cgdna
3a2da51a8210
·sjplimp / GitHub on Mar 15 2017, 20:12.
Added fix filter/corotate.
c3ce3747e049
·lukin17 on Mar 15 2017, 11:34.

Mar 14 2017

Add neigh/qeq option to Kokkos
580f6b567b12
·Stan Moore on Mar 14 2017, 17:44.
Minor updates in documentation and setup tool, merge before upgrade to oxDNA2
7a75cd111c3d
·Oliver Henrich on Mar 14 2017, 12:39.

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.
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.
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 #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 src files
3a054d1a82b2
·Richard Berger on Mar 7 2017, 06:55.

Mar 6 2017

Fix typos in src files
7dd60f97377a
·Richard Berger on Mar 6 2017, 03:03.
Spelling fixes in source files
e261bef7bba7
·Richard Berger on Mar 6 2017, 00:30.

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.
add a few more missing details for integrating pair style kolmogorov/crespi/z
3605208a45bb
·Axel Kohlmeyer on Feb 28 2017, 17:16.
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.

Feb 24 2017

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.
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.
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 #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.
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.

Feb 15 2017

Add copymode protection to class2 styles
5f93fad012d8
·Stan Moore on Feb 15 2017, 21:56.
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

Fixed bugs with pppm/gpu when used with compute group/group
20806dd86acf
·Trung Nguyen on Feb 14 2017, 07:26.

Feb 13 2017

USER-DPD: performance optimizations to ssa_update() in fix_shardlow Overall…
15008c9d1889
·Tim Mattox on Feb 13 2017, 19:11.
Moved variable declarations to front for consistency
a323ca1edd79
·Markus Hoehnerbach on Feb 13 2017, 18:11.
In PairAIREBO::bondorderLJ correct omega sum d/drij.
de4af6f15d6a
·Markus Hoehnerbach on Feb 13 2017, 18:11.
In PairAIREBO::bondorderLJ: p^sigma pi account for d/drij derivatives.
0e16dc3ead0b
·Markus Hoehnerbach on Feb 13 2017, 18:11.
In PairAIREBO::bondorderLJ only compute torsion term once.
1b3f6e257a88
·Markus Hoehnerbach on Feb 13 2017, 17:14.
sync 13Feb17 patch back to GH
cb982f2f28ab
·Steve Plimpton on Feb 13 2017, 17:05.
Merge pull request #372 from akohlmey/fft-cleanup
4843296d4e57
·sjplimp / GitHub on Feb 13 2017, 16:53.
patch 12Feb17 - change int to tagint for compute group/group
2bdda8f6c013
·Steve Plimpton on Feb 13 2017, 16:40.

Feb 10 2017

added molecule option to compute group/group command
0068ef56168f
·Steve Plimpton on Feb 10 2017, 17:25.

Feb 8 2017

fix typo
a5f830c40c6e
·Axel Kohlmeyer on Feb 8 2017, 20:33.

Feb 3 2017

Merge branch 'master' into fft-cleanup
191453e1c73d
·Axel Kohlmeyer on Feb 3 2017, 22:53.
Merge pull request #373 from stanmoore1/kk_more_bugfixes
207adc3968ff
·sjplimp / GitHub on Feb 3 2017, 22:45.
Merge pull request #368 from Pakketeretet2/kokkos_morse
84c517159d07
·sjplimp / GitHub on Feb 3 2017, 22:45.
Merge pull request #366 from rbberger/kokkos_lammps_bigbig_fix
6ca377436f8b
·sjplimp / GitHub on Feb 3 2017, 22:43.
Merge pull request #362 from ibaned/warnings2
dc34a32602ef
·sjplimp / GitHub on Feb 3 2017, 22:43.

lammps/srcmaster8820315ff96af5a4d411d17…

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lammps/src
master8820315ff96af5a4d411d17…