Diffusion lammps (master) History

History
masterdb73eca29f593d3ac1d3076…

Jul 3 2017

correct example inputs for recent changes to create_bonds command
db73eca29f59
·Axel Kohlmeyer on Jul 3 2017, 17:43.
make USER-INTEL compilable again with gcc and without OpenMP active
2d1941ed9b16
·Axel Kohlmeyer on Jul 3 2017, 17:33.
memory allocation bugfix for USER-INTEL pppm from M Brown
e634c5a2dec8
·Steve Plimpton on Jul 3 2017, 16:53.

Jun 30 2017

Merge pull request #557 from lammps/create-bonds
883b7aaa0efc
·sjplimp / GitHub on Jun 30 2017, 22:18.
add backward compatibility item to pull request template
a490e04d2402
·Axel Kohlmeyer on Jun 30 2017, 21:07.
spell-check new additions to create_bonds doc page
b445f8eadf67
·Axel Kohlmeyer on Jun 30 2017, 20:59.
Merge pull request #554 from jewettaij/master
b79044d4f60f
·sjplimp / GitHub on Jun 30 2017, 19:47.
add single options to create_bonds command
711afe5062ff
·Steve Plimpton on Jun 30 2017, 19:30.
Merge pull request #553 from Pakketeretet2/USER-MANIFOLD-gaussian-bump
3bf2c602765f
·sjplimp / GitHub on Jun 30 2017, 19:08.
Merge pull request #550 from stanmoore1/kokkos_leakfix
d5119b2d753a
·sjplimp / GitHub on Jun 30 2017, 19:08.
Merge pull request #547 from akohlmey/collected-bugfixes
b2b621a2e18b
·sjplimp / GitHub on Jun 30 2017, 19:08.
Merge pull request #545 from akohlmey/issue-and-pull-request-templates
b5250d11f63c
·sjplimp / GitHub on Jun 30 2017, 19:06.
update documentation for nb3/harmonic pair style according to e-mail to lammps…
f6faad335cf5
·Axel Kohlmeyer on Jun 30 2017, 17:37.

Jun 29 2017

consolidate and update error message and read_data documentation for the…
d5921e9fb9e8
·Axel Kohlmeyer on Jun 29 2017, 22:30.
change the handling of reading "extra XXX per atom", so that the final choice…
aa3f4b76905b
·Axel Kohlmeyer on Jun 29 2017, 22:09.
new keywords for read_data: extra/X/per/atoms + changes to docs
38075455b674
·Andrew Jewett on Jun 29 2017, 02:55.
Revert "added feature to write_data.cpp to support "extra bonds" (angles…
fa3063546542
·Andrew Jewett on Jun 29 2017, 02:48.

Jun 28 2017

added feature to write_data.cpp to support "extra bonds" (angles,dihedrals…
0c2f7c74be34
·Andrew Jewett on Jun 28 2017, 23:12.
Replaced std::fabs with fabs.
91bce7ccf95e
·Stefan Paquay on Jun 28 2017, 15:48.
consistently check for all per-atom-type masses being set only when per-atom…
d0470799ac8b
·Axel Kohlmeyer on Jun 28 2017, 12:26.

Jun 27 2017

Updated Gaussian bump so that it has a better taper function.
076990c28a67
·Stefan Paquay on Jun 27 2017, 22:48.
remove non-ascii characters and spell check
661e51b6079c
·Axel Kohlmeyer on Jun 27 2017, 06:38.
use itemized list instead of paragraphs for links at the top
d076040471ca
·Axel Kohlmeyer on Jun 27 2017, 06:24.
more formatting issues addressed
2f9c0a3b8efd
·Axel Kohlmeyer on Jun 27 2017, 06:23.
update formatting for contributing ToC
b9d213ee2bfb
·Axel Kohlmeyer on Jun 27 2017, 06:21.
contributing guidelines, issue and pull request template are now feature…
fa3c7727e103
·Axel Kohlmeyer on Jun 27 2017, 06:17.

Jun 26 2017

Remove clean_copy function from pair_vashishta_kokkos
9fec8a0470bd
·Stan Moore on Jun 26 2017, 18:56.
Fixing memory leak in Kokkos neighborlist
b8897765572e
·Stan Moore on Jun 26 2017, 18:51.
Merge branch 'collected-bugfixes' of github.com:akohlmey/lammps into collected…
f7077d96726e
·Axel Kohlmeyer on Jun 26 2017, 17:27.
make USER-INTEL compilable again with gcc and without OpenMP active
f89a7266bfef
·Axel Kohlmeyer on Jun 26 2017, 05:57.

Jun 24 2017

Merge branch 'master' of https://www.github.com/lammps/lammps
125795566234
·Stefan Paquay on Jun 24 2017, 01:31.
patch 23Jun17
1370385c8c9f
·Steve Plimpton on Jun 24 2017, 01:10.
Merge pull request #548 from lammps/doc-update
2240c3d7d3a8
·sjplimp / GitHub on Jun 24 2017, 00:48.

Jun 23 2017

doc page clarifications for CHARMM energy and dipole pre-factors
4fcbd58d5a32
·Steve Plimpton on Jun 23 2017, 23:54.
remove spurious comment line
c2c6dc14588a
·Axel Kohlmeyer on Jun 23 2017, 22:24.
fix qeq/reax/omp bugfix from metin
18983c307e96
·Axel Kohlmeyer on Jun 23 2017, 22:24.
Merge pull request #541 from lammps/charmm
25a5d12af386
·sjplimp / GitHub on Jun 23 2017, 17:10.
skip deleting internal data before setup has been run
05fbf9345518
·Axel Kohlmeyer on Jun 23 2017, 16:37.
add first draft of issue template
374eef2b1752
·Axel Kohlmeyer on Jun 23 2017, 07:13.
first draft of a contributor's guide file
dc7243838b8c
·Axel Kohlmeyer on Jun 23 2017, 06:54.
add first draft of a pull request template
57d5cfede391
·Axel Kohlmeyer on Jun 23 2017, 05:07.
reword the kspace_modify fftbench keyword docs to reflect the current state (i.
feb500b52684
·Axel Kohlmeyer on Jun 23 2017, 01:17.
make neighbor list reset message for minimization more explicit
a714b5774132
·Axel Kohlmeyer on Jun 23 2017, 01:07.
print info messages when changing qqr2e constant in fully CHARMM compatible…
c5430b0a2607
·Axel Kohlmeyer on Jun 23 2017, 00:41.
Merge branch 'master' of https://www.github.com/lammps/lammps
c081d383d1c5
·Stefan Paquay on Jun 23 2017, 00:37.

Jun 22 2017

use CHARMM energy conversion factor with new CHARMM pair styles
60c3f3d64c58
·Steve Plimpton on Jun 22 2017, 17:15.
Merge pull request #540 from lammps/neighrespa
7a4a56985986
·sjplimp / GitHub on Jun 22 2017, 15:54.
Merge pull request #538 from akohlmey/collected-small-changes
4fc3f4f7e563
·sjplimp / GitHub on Jun 22 2017, 15:52.
update examples for fix filter/corotate to comply with new CHARMM restrictions
b0ddabbcde94
·Axel Kohlmeyer on Jun 22 2017, 06:19.
document new restrictions to CHARMM compatible dihedral styles
de3157f720b3
·Axel Kohlmeyer on Jun 22 2017, 01:31.
may check for 1-4 scaling factors in CHARMM dihedral styles only when…
0c6a7517511b
·Axel Kohlmeyer on Jun 22 2017, 01:29.
enforce using 'special_bonds charmm' for dihedral styles charmm and charmmfsw
612b44a8951e
·Axel Kohlmeyer on Jun 22 2017, 01:15.
enforce that CHARMM dihedral styles are run at the same r-RESPA level as pair
684b7334a56c
·Axel Kohlmeyer on Jun 22 2017, 01:08.

Jun 21 2017

fix issue with rRESPA inner/middle neighbor lists
1fc2eb1e3e4b
·Steve Plimpton on Jun 21 2017, 23:12.
Merge pull request #539 from lammps/neighsize
e69ef56f108e
·sjplimp / GitHub on Jun 21 2017, 23:03.
insure compute pair/property local will use a copy of granular neigh list
7dc380b113d8
·Steve Plimpton on Jun 21 2017, 20:44.
Merge branch 'master' of https://www.github.com/lammps/lammps
f47aaa5f3c9b
·Stefan Paquay on Jun 21 2017, 20:11.
whitespace cleanup in docs
1a77135ed65b
·Axel Kohlmeyer on Jun 21 2017, 15:38.
update fix ti/spring docs to reflect it is part of USER-MISC
f45c7e1fb023
·Axel Kohlmeyer on Jun 21 2017, 15:36.
dead code removal
0cfe8980d4ca
·Axel Kohlmeyer on Jun 21 2017, 04:07.

Jun 20 2017

correct indexing bug in pair style lj/long/tip4p/long
2988508cee98
·Axel Kohlmeyer on Jun 20 2017, 23:53.
remove dead code
15c596153aaa
·Axel Kohlmeyer on Jun 20 2017, 23:38.
fix uninitialized variable bug spotted by coverity scan
e13c94ed4f26
·Axel Kohlmeyer on Jun 20 2017, 23:25.
remove local variables shadowing global ones in BondsOMP()
812f1a8fabd7
·Axel Kohlmeyer on Jun 20 2017, 23:20.
make pre-processor defines for using libc's qsort() consistent
218bc92c82d5
·Axel Kohlmeyer on Jun 20 2017, 23:13.
add C++ format identifiers to .h files
ffa906de6ff6
·Axel Kohlmeyer on Jun 20 2017, 22:18.
make certain class member list is initialized to NULL before assigned to a…
cccf72a21d6a
·Axel Kohlmeyer on Jun 20 2017, 22:09.
patch 20Jun17
87c028ed0237
·Steve Plimpton on Jun 20 2017, 20:06.
Merge pull request #537 from lammps/neb
84b530cca189
·sjplimp / GitHub on Jun 20 2017, 17:38.
small formatting correction in fix neb docs
50c9167913d6
·Axel Kohlmeyer on Jun 20 2017, 16:36.
minor changes to NEB doc pages and examples
d2610d9e7c0d
·Steve Plimpton on Jun 20 2017, 16:19.
Merge pull request #536 from akohlmey/fix-nvcc-openmp-conflicts
326a8a1289ef
·sjplimp / GitHub on Jun 20 2017, 15:44.
Merge pull request #533 from lammps/user-intel
b5300724bb8b
·sjplimp / GitHub on Jun 20 2017, 15:44.
Merge pull request #530 from akohlmey/no_static_sort_in_dump
e129f18e6f19
·sjplimp / GitHub on Jun 20 2017, 15:43.

Jun 19 2017

cleanup from aidan for fix reax/c/species and its KOKKOS version
8c54fcd1b6c9
·Axel Kohlmeyer on Jun 19 2017, 23:31.
augment fix shardlow check for ordering fixes to be KOKKOS compatible
f5047ac3c7f9
·Axel Kohlmeyer on Jun 19 2017, 23:23.
protect all OpenMP pragmas with ifdefs and add special conditions for nvcc to…
164cedf3539c
·Axel Kohlmeyer on Jun 19 2017, 21:31.
massive whitespace cleanup in USER-INTEL
3c329d170791
·Axel Kohlmeyer on Jun 19 2017, 19:23.
insert C++ file format indicator comments
b687d16177fe
·Axel Kohlmeyer on Jun 19 2017, 19:03.
add missing reference for lj/smooth/linear
9d3e34e4922c
·Axel Kohlmeyer on Jun 19 2017, 17:23.
modified the documentation, first and last freeend can have different spring…
8988b692a392
·Emile Maras on Jun 19 2017, 16:30.
corrected the initial free end
c97415aefab7
·Emile Maras on Jun 19 2017, 14:57.

Jun 17 2017

remove ifdefs for selecting between plain and hybrid merge sort. use hybrid…
9b8de3ba2960
·Axel Kohlmeyer on Jun 17 2017, 15:30.
same PR, also has cosmetic changes to new fix neb options
cd88b31450c3
·Steve Plimpton on Jun 17 2017, 01:02.
USER-INTEL upgrade from M Brown
9b9f6d6fe2f4
·Steve Plimpton on Jun 17 2017, 00:56.
restore old qsort() based code and add preprocessor directives to switch
c1b0b1b3f9d7
·Axel Kohlmeyer on Jun 17 2017, 00:17.

Jun 16 2017

Merge pull request #532 from akohlmey/restore-heuristics-in-fix-shardlow
bc0241576fa1
·sjplimp / GitHub on Jun 16 2017, 17:46.
mergesort performance improvements
2a6f026853e6
·Axel Kohlmeyer on Jun 16 2017, 14:05.

Jun 15 2017

restore heuristics for checking against integrators that broke after PR #499…
8728a8ddae67
·Axel Kohlmeyer on Jun 15 2017, 21:16.
Merge pull request #528 from akohlmey/no_static_in_ring_comm
9aa450b83240
·sjplimp / GitHub on Jun 15 2017, 19:13.
Merge pull request #513 from v0i0/bugfix-airebo-nconj-kronecker
0588c382f0a6
·sjplimp / GitHub on Jun 15 2017, 19:12.
Merge pull request #510 from akohlmey/collected-small-changes
d3c90f3c14dd
·sjplimp / GitHub on Jun 15 2017, 19:12.
Revert "avoid undesired negative forces for high particle velocities in…
b62d526cc98d
·Axel Kohlmeyer on Jun 15 2017, 17:01.
Merge pull request #531 from ohenrich/user-cgdna
1a29048940e9
·sjplimp / GitHub on Jun 15 2017, 16:54.
Merge pull request #527 from dstelter92/master
0a6b3f87901c
·sjplimp / GitHub on Jun 15 2017, 16:54.
Merge pull request #526 from andeplane/vashishta_gpu
7227bc415d00
·sjplimp / GitHub on Jun 15 2017, 16:52.
Merge pull request #525 from akohlmey/user-tally-refactor
a4bc233d8631
·sjplimp / GitHub on Jun 15 2017, 16:51.
Merge pull request #522 from akohlmey/tip4p-cleanup-refactor
5c5b4ffadba9
·sjplimp / GitHub on Jun 15 2017, 16:48.
Merge pull request #521 from pastewka/17_dump_nc
30177c4eaeb0
·sjplimp / GitHub on Jun 15 2017, 16:47.
Merge pull request #520 from stanmoore1/kokkos_update
178eff237bc3
·sjplimp / GitHub on Jun 15 2017, 16:47.

Historymasterdb73eca29f593d3ac1d3076…

Jul 3 2017

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History
masterdb73eca29f593d3ac1d3076…