Diffusion lammps (master) History

History
master5a1e020bf01c8a3454dd915…

Jul 11 2017

updated the credits and citations for pair style reaxc/omp and qeq/reax/omp
5a1e020bf01c
·H. Metin Aktulga on Jul 11 2017, 17:05.

Jul 6 2017

patch 6Jul17
433937994877
·Steve Plimpton on Jul 6 2017, 21:58.
Merge pull request #564 from lammps/fix-external
87af3b1fd982
·sjplimp / GitHub on Jul 6 2017, 16:58.
whitespace cleanup
042397120500
·Axel Kohlmeyer on Jul 6 2017, 06:24.
remove code without effect
4ee7c6f5caa8
·Axel Kohlmeyer on Jul 6 2017, 06:23.
correct comment for Fix::ev_setup()
7f63c09667ff
·Axel Kohlmeyer on Jul 6 2017, 04:35.
fix bug reported by richard berger via https://ci.lammps.
a5234d7aeaf5
·Axel Kohlmeyer on Jul 6 2017, 04:34.

Jul 5 2017

Merge pull request #562 from lammps/fix-external
be8360ac4bd8
·sjplimp / GitHub on Jul 5 2017, 22:46.
make old_velocities allocation safer while retaining the test for nlocal
4de9cec1b63b
·Axel Kohlmeyer on Jul 5 2017, 22:22.
remove dead code
09ad29342555
·Axel Kohlmeyer on Jul 5 2017, 21:04.
safer handling of processors w/o local atoms
e625e7917190
·Axel Kohlmeyer on Jul 5 2017, 21:04.
changes requested by @sjplimp
f1088a5003dd
·Axel Kohlmeyer on Jul 5 2017, 21:03.
additional fix external hooks for calling programs
ea4f16bd79df
·Steve Plimpton on Jul 5 2017, 18:01.

Jul 3 2017

Merge pull request #559 from lammps/fortran3
d0a397d6cb2e
·sjplimp / GitHub on Jul 3 2017, 22:50.
3rd variant of Fortran wrapper for DFTB+ calling LAMMPS
f670dba3d019
·Steve Plimpton on Jul 3 2017, 22:24.
Merge pull request #524 from martok/package-meamc
6fc0a94e8783
·sjplimp / GitHub on Jul 3 2017, 20:30.
Merge pull request #558 from lammps/intel
5c0c8bb4cdbc
·sjplimp / GitHub on Jul 3 2017, 20:25.
Merge pull request #544 from akohlmey/tip4p-triclinic
9eeb97b039f7
·sjplimp / GitHub on Jul 3 2017, 20:24.
add authors tag to pull request template
9ca9b5e2ffbd
·Axel Kohlmeyer on Jul 3 2017, 18:06.
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.

Jul 2 2017

remove some dead code and prune argument lists accordingly
22f3db472321
·Axel Kohlmeyer on Jul 2 2017, 00:16.

Jul 1 2017

remove unused variables
a1574fc03d87
·Axel Kohlmeyer on Jul 1 2017, 23:55.
avoid repeated computation of deltaik and deltajk, calls to pow()
d68fb1cbb82d
·Axel Kohlmeyer on Jul 1 2017, 23:49.
another speedup by folding dsij() into meam_force()
060e32973ef9
·Axel Kohlmeyer on Jul 1 2017, 23:07.
fold screen() function into getscreen() and avoid some repeated operations
a4a15f24bdc1
·Axel Kohlmeyer on Jul 1 2017, 00:44.

Jun 30 2017

Merge pull request #557 from lammps/create-bonds
883b7aaa0efc
·sjplimp / GitHub on Jun 30 2017, 22:18.
update or create example outputs for meam and meam/c
1fff30af90e7
·Axel Kohlmeyer on Jun 30 2017, 21:30.
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.
performance improvement through moving inlinable functions to header file
9dad95d10140
·Axel Kohlmeyer on Jun 30 2017, 19:04.
update documentation for nb3/harmonic pair style according to e-mail to lammps…
f6faad335cf5
·Axel Kohlmeyer on Jun 30 2017, 17:37.
Move stateless functions to separate module, improve style
55487047006f
·Sebastian Hütter on Jun 30 2017, 15:37.
Re-Run clang-format
e0939ac79577
·Sebastian Hütter on Jun 30 2017, 12:28.

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.
Change indexing of remaining variables and locals
8fca667e4b7f
·Sebastian Hütter on Jun 26 2017, 18:09.
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.
pppm must be fully reinitialized after switching to triclinic box to avoid…
73b948dcfc97
·Axel Kohlmeyer on Jun 23 2017, 16:01.
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.
port corrected triclinic handling from pppm/tip4p to pppm/tip4p/omp
f8364342c238
·Axel Kohlmeyer on Jun 23 2017, 00:12.

Jun 22 2017

correct find_M() function in pppm/tip4p to properly account for ghost atoms not…
488d1b7a79fc
·Axel Kohlmeyer on Jun 22 2017, 23:36.
Remove neigh_f2c/c2f, related cleanup
dadd1c8b4d6e
·Sebastian Hütter on Jun 22 2017, 19:02.
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.
Fix some shadowing warnings
f092da80a959
·Sebastian Hütter on Jun 22 2017, 13:28.
update examples for fix filter/corotate to comply with new CHARMM restrictions
b0ddabbcde94
·Axel Kohlmeyer on Jun 22 2017, 06:19.
fix bug in incorrect use of O coordinate instead of M coordinate in pppm/tip4p
b9029ada7785
·Axel Kohlmeyer on Jun 22 2017, 06:07.
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.
fix array bounds issue due to typo. spotted by GCC.
5e165e67822f
·Axel Kohlmeyer on Jun 21 2017, 19:33.
fix typos introduced in original translation: results are correct again
02625b285521
·Sebastian Hütter on Jun 21 2017, 18:54.
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.

Historymaster5a1e020bf01c8a3454dd915…

Jul 11 2017

Jul 6 2017

Jul 5 2017

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Jul 2 2017

Jul 1 2017

Jun 30 2017

Jun 29 2017

Jun 28 2017

Jun 27 2017

Jun 26 2017

Jun 24 2017

Jun 23 2017

Jun 22 2017

Jun 21 2017

Jun 20 2017

History
master5a1e020bf01c8a3454dd915…