Diffusion lammps (master) History

lammps/src
master0af9203fdc991af03cb77a7…

Jul 13 2017

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.
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 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

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

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.

Jun 21 2017

fix issue with rRESPA inner/middle neighbor lists
1fc2eb1e3e4b
·Steve Plimpton on Jun 21 2017, 23:12.
insure compute pair/property local will use a copy of granular neigh list
7dc380b113d8
·Steve Plimpton on Jun 21 2017, 20:44.
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.
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.
Change indexing of all MEAM element arrays
bb47fa8783d8
·Sebastian Hütter on Jun 20 2017, 19:56.
code improvement, less pointer params
c79dc53c6aef
·Sebastian Hütter on Jun 20 2017, 19:36.
Merge branch 'master' into package-meamc
72a1364d854f
·Axel Kohlmeyer / GitHub on Jun 20 2017, 19:21.
fix storing of invalid memory pointer
198fe7ecd7ad
·Sebastian Hütter on Jun 20 2017, 19:00.
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.
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.
fix uninitialized members
a9f3f900255e
·Sebastian Hütter on Jun 19 2017, 12:51.

Jun 17 2017

remove ifdefs for selecting between plain and hybrid merge sort. use hybrid…
9b8de3ba2960
·Axel Kohlmeyer on Jun 17 2017, 15:30.
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

mergesort performance improvements
2a6f026853e6
·Axel Kohlmeyer on Jun 16 2017, 14:05.

lammps/srcmaster0af9203fdc991af03cb77a7…

Jul 13 2017

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Jun 16 2017

lammps/src
master0af9203fdc991af03cb77a7…