Diffusion lammps (master) History

lammps/src
master49b4cf9a770cd407ff8c324…

Jul 18 2017

update manual links that got broken when removing and renumbering a section
a92d79253734
·Axel Kohlmeyer on Jul 18 2017, 18:55.

Jul 15 2017

better Install.py script for KIM from Ryan Elliott
296e572e6998
·Steve Plimpton on Jul 15 2017, 00:25.

Jul 14 2017

AIREBO: Add doc about OpenKIM issue
e5405cdb0477
·Markus Hoehnerbach on Jul 14 2017, 17:57.

Jul 13 2017

Merge pull request #561 from v0i0/fix-airebo-various
fc36754ca22a
·sjplimp / GitHub on Jul 13 2017, 21:10.
Merge pull request #574 from lammps/snap-virial
3a46c34c2fa3
·sjplimp / GitHub on Jul 13 2017, 21:07.
Merge pull request #571 from hasanmetin/reaxc-omp-credits-update
fc6c10c9a98a
·sjplimp / GitHub on Jul 13 2017, 19:27.
Merge pull request #570 from akohlmey/collected-small-changes
a3a0c9b144c5
·sjplimp / GitHub on Jul 13 2017, 19:26.
Merge pull request #568 from akohlmey/fix_gcmc_parallel_workaround
e58bcd8b4aa4
·sjplimp / GitHub on Jul 13 2017, 19:23.
Merge pull request #566 from akohlmey/compute_rdf_dynamic
ef2f4980e9dd
·sjplimp / GitHub on Jul 13 2017, 19:23.
Merge pull request #560 from aershadinia/master
d3a45f6d5057
·sjplimp / GitHub on Jul 13 2017, 19:22.
changes to SNAP virial from Aidan
d0cc1dfbb80c
·Steve Plimpton on Jul 13 2017, 19:19.
fix off-by-one memory allocation bug
de8d417aeccd
·Axel Kohlmeyer on Jul 13 2017, 16:55.
remove useless and incorrect neighbor list request in fix qeq/comb/omp
0af9203fdc99
·Axel Kohlmeyer on Jul 13 2017, 00:32.
fix possible uninitialized data access with pppm and pppm/disp
c24fca61f37a
·Axel Kohlmeyer on Jul 13 2017, 00:14.
avoid accessing uninitialized data when exiting LAMMPS early
01e848387ac8
·Axel Kohlmeyer on Jul 13 2017, 00:00.

Jul 12 2017

avoid small memory leak with USER-REAXC + USER-OMP, spotted by GCC's address…
734729b0a4d5
·Axel Kohlmeyer on Jul 12 2017, 23:27.
update src/.gitignore for fix wall*/ees sources
a419c7c57c52
·Axel Kohlmeyer on Jul 12 2017, 17:40.
fix enforce2d has to be defined after fixes with enforce2d_flag set
69d97fa60cf0
·Axel Kohlmeyer on Jul 12 2017, 17:26.
avoid segfault when calling enforce2d before langevin data has been initialized
a9ff593763c7
·Axel Kohlmeyer on Jul 12 2017, 15:48.

Jul 11 2017

whitspace cleanup
f7f4a24930ba
·Axel Kohlmeyer on Jul 11 2017, 21:01.
combine citeme.log entry for pair reax/c/omp and fix qeq/reax/omp
338fc2897073
·Axel Kohlmeyer on Jul 11 2017, 20:59.
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 10 2017

white space cleanup
b5e9e90bb66d
·Axel Kohlmeyer on Jul 10 2017, 23:21.
disallow MC moves with fix rigid and fix shake active. update examples and add…
92395e9bb412
·Axel Kohlmeyer on Jul 10 2017, 23:19.

Jul 7 2017

add support for recomputing normalization factors and finite size correction…
fe888e462219
·Axel Kohlmeyer on Jul 7 2017, 21:39.

Jul 6 2017

patch 6Jul17
433937994877
·Steve Plimpton on Jul 6 2017, 21:58.
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

Fix sigcut class variable actually used
e493b6a648b2
·Markus Hoehnerbach on Jul 5 2017, 22:52.
make old_velocities allocation safer while retaining the test for nlocal
4de9cec1b63b
·Axel Kohlmeyer on Jul 5 2017, 22:22.
remove unused variables to silence compiler warnings
8c3f6947ad48
·Axel Kohlmeyer on Jul 5 2017, 22:19.
simplify parsing of optional arguments
894e0c3cf506
·Axel Kohlmeyer on Jul 5 2017, 22:19.
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.
coding style and whitespace cleanup to match LAMMPS style
6eddc1a2ee77
·Axel Kohlmeyer on Jul 5 2017, 18:33.
Updated credits
1bf1cb150fae
·Markus Hoehnerbach on Jul 5 2017, 18:26.
additional fix external hooks for calling programs
ea4f16bd79df
·Steve Plimpton on Jul 5 2017, 18:01.
fixed a typo
9fa4588eb720
·Abdoreza Ershadinia / GitHub on Jul 5 2017, 16:46.
Examples moved
8e279d4ec84e
·Abdo on Jul 5 2017, 16:16.
Sync AIREBO USER-OMP implementation.
ff761d639a78
·Markus Hoehnerbach on Jul 5 2017, 15:29.
AIREBO Fix Credits
d2f7f4843a7c
·Markus Hoehnerbach on Jul 5 2017, 15:16.
Feature: AIREBO parametrize cutoff switching
7e42af18bc68
·Markus Hoehnerbach on Jul 5 2017, 15:11.
Fix AIREBO missing derivative in bondorderLJ
74d63c24fd34
·Markus Hoehnerbach on Jul 5 2017, 14:51.
Proper spline coefficient calculation for AIREBO
769870cfc957
·Markus Hoehnerbach on Jul 5 2017, 12:55.
Files Added to MISC
d3b8e688c972
·Abdo on Jul 5 2017, 07:57.
deleteing USER-EES
67d474df2a5d
·Abdo on Jul 5 2017, 07:39.

Jul 3 2017

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.
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.
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.
performance improvement through moving inlinable functions to header file
9dad95d10140
·Axel Kohlmeyer on Jun 30 2017, 19:04.
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.

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

patch 23Jun17
1370385c8c9f
·Steve Plimpton on Jun 24 2017, 01:10.

Jun 23 2017

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.
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.
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.
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.
fix bug in incorrect use of O coordinate instead of M coordinate in pppm/tip4p
b9029ada7785
·Axel Kohlmeyer on Jun 22 2017, 06:07.
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.

lammps/srcmaster49b4cf9a770cd407ff8c324…

Jul 18 2017

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lammps/src
master49b4cf9a770cd407ff8c324…