Diffusion lammps (master) History

lammps/src
master2862c2081501fef58d98010…

Nov 18 2016

Merge branch 'master' into grem-feature
2862c2081501
·Axel Kohlmeyer on Nov 18 2016, 20:51.
new 17Nov16 patch and stable
4b51719e67c2
·Steve Plimpton on Nov 18 2016, 00:51.
compute pressure doc change
25d7be5f3dd5
·Steve Plimpton on Nov 18 2016, 00:11.

Nov 17 2016

Merge pull request #278 from akohlmey/pair-agni
74c0e4dd5c10
·sjplimp / GitHub on Nov 17 2016, 17:04.
Merge pull request #276 from akohlmey/doc-updates
073e8a052485
·sjplimp / GitHub on Nov 17 2016, 17:02.
Merge pull request #275 from andeplane/IP_VORONOI
5320bbf58513
·sjplimp / GitHub on Nov 17 2016, 17:01.
Merge pull request #274 from andeplane/IP_POEMS
44488198240f
·sjplimp / GitHub on Nov 17 2016, 17:01.
Merge pull request #273 from akohlmey/auto-memalign
300ac30332a0
·sjplimp / GitHub on Nov 17 2016, 17:01.
Merge pull request #271 from akohlmey/tersoff-modc
2535e44991a2
·sjplimp / GitHub on Nov 17 2016, 17:00.
Merge pull request #242 from andeplane/vashishta_kokkos
cdae7943833d
·sjplimp / GitHub on Nov 17 2016, 17:00.
Kokkos updates by Stan
8756a1017dc8
·Steve Plimpton on Nov 17 2016, 16:58.
Re-run example with debug off
5ac2d9532ed6
·dstelter92 on Nov 17 2016, 15:43.
turned off dev mode by default in temper_grem
19ac9d295995
·dstelter92 on Nov 17 2016, 15:31.
added internal tempering in grem with example
07e46b797a29
·dstelter92 on Nov 17 2016, 02:27.

Nov 16 2016

Merge branch 'grem-feature' of https://github.com/dstelter92/lammps into grem…
82364d10e335
·Axel Kohlmeyer on Nov 16 2016, 22:11.
add restrict to CCFLAGS for makefiles intended for intel compilers
22d93fe8fbab
·Axel Kohlmeyer on Nov 16 2016, 20:31.
simplify multi-replica run by passing per-replica parameters as variables on…
683f514fac6a
·Axel Kohlmeyer on Nov 16 2016, 20:22.
need to apply fix_modify already in fix grem constructor
f6179939444f
·Axel Kohlmeyer on Nov 16 2016, 19:52.
remove superfluous code
705f66aaee7a
·Axel Kohlmeyer on Nov 16 2016, 19:24.
compute scaled kinetic energy tensor without destroying the original data
e57ae1ce3f7e
·Axel Kohlmeyer on Nov 16 2016, 18:45.
added check for nvt vs npt, enabled nvt simulation with fix_grem
950442b8b151
·dstelter92 on Nov 16 2016, 03:53.

Nov 14 2016

allow to extract properties in NH integrator only when they are active
fdf5d68f9ffb
·Axel Kohlmeyer on Nov 14 2016, 15:27.
whitespace cleanup
0c25f3b1d6d9
·Axel Kohlmeyer on Nov 14 2016, 05:20.
retrieve target temperature and pressure from fix npt. add sanity checks.
14c7cf419733
·Axel Kohlmeyer on Nov 14 2016, 05:18.
bugfix for compute pressure/grem: must make a copy of argument strings
09544d0698a9
·Axel Kohlmeyer on Nov 14 2016, 01:19.
initial import of adapted gREM code by David Stelter and Edyta Malolepsza
20daf82463fd
·Axel Kohlmeyer on Nov 14 2016, 00:44.

Nov 12 2016

add documentation for pair style agni
03b3834fe3b2
·Axel Kohlmeyer on Nov 12 2016, 15:07.
optimized data access and using approximate exponential for USER-OMP version
d0124eac95e1
·Axel Kohlmeyer on Nov 12 2016, 14:36.
add USER-OMP version of pair style agni
5685131fe233
·Axel Kohlmeyer on Nov 12 2016, 01:08.
use special ev_tally() function suitable for this kind of force compute
22fc92f9d87d
·Axel Kohlmeyer on Nov 12 2016, 00:32.
error exit when requested element is not in potential file
9cc0c8badd0a
·Axel Kohlmeyer on Nov 12 2016, 00:10.

Nov 11 2016

first complete implementation of AGNI pair style
9b0987d8c4a7
·Axel Kohlmeyer on Nov 11 2016, 23:32.
implemented parser for 1 element potential files
e453adaf8118
·Axel Kohlmeyer on Nov 11 2016, 21:53.
fix addtorque is compatible with dynamic groups
fdcabd7d1dce
·Axel Kohlmeyer on Nov 11 2016, 15:01.
initialize 'nper'
c5c8c50e97f8
·Axel Kohlmeyer on Nov 11 2016, 13:47.

Nov 10 2016

dummy framework implementation for AGNI pair style
801111a7abfa
·Axel Kohlmeyer on Nov 10 2016, 21:00.
simpler variant of the segfault workaround, that does not offend Clang c++.
bfc478c32049
·Axel Kohlmeyer on Nov 10 2016, 20:12.
avoid segmentation fault, when creating a LAMMPS instance from the library…
2b75ee761def
·Axel Kohlmeyer on Nov 10 2016, 19:28.
Initializing pointers in VORONOI
c20ee34c7b82
·Anders Hafreager on Nov 10 2016, 09:30.
Initialize pointers in POEMS
95a7f7160e6f
·Anders Hafreager on Nov 10 2016, 09:26.

Nov 9 2016

Stan bug fixes for fix reaxc/bonds/kk
9806da69f3f9
·Steve Plimpton on Nov 9 2016, 23:47.
simplify compiling USER-INTEL package, by defaulting to -DLAMMPS_MEMALIGN=64 in…
fec87c070dd8
·Axel Kohlmeyer on Nov 9 2016, 22:53.
remove unused class member
3e36ec37542c
·Axel Kohlmeyer on Nov 9 2016, 22:17.
Merge branch 'master' into kokkos-vashishta
9ed5c4f0fa98
·Axel Kohlmeyer on Nov 9 2016, 21:15.
integrate pair style tersoff/mod/c contributed by Ganga P Purja Pun (GMU)
71ee2ecaa1e0
·Axel Kohlmeyer on Nov 9 2016, 20:52.
Merge pull request #268 from arielzn/born_dsf
bfea3dce7dab
·sjplimp / GitHub on Nov 9 2016, 19:57.
Merge pull request #267 from akohlmey/pager-help
eef862ee1c47
·sjplimp / GitHub on Nov 9 2016, 19:53.
Merge pull request #266 from andeplane/IP_USER_OMP
0cc2fbf1d6db
·sjplimp / GitHub on Nov 9 2016, 19:52.
Merge pull request #265 from andeplane/IP_DIFF_DPD
ae006669941e
·sjplimp / GitHub on Nov 9 2016, 19:51.
Merge pull request #264 from andeplane/IP_SNAP_SRD
51b3b5fb359c
·sjplimp / GitHub on Nov 9 2016, 19:51.
Merge pull request #263 from andeplane/IP_RIGID_SHOCK
176f2c3aa197
·sjplimp / GitHub on Nov 9 2016, 19:51.
Merge pull request #262 from andeplane/IP_PERI_QEQ_REPLICA
3f71bfb18570
·sjplimp / GitHub on Nov 9 2016, 19:51.
Merge pull request #261 from andeplane/IP_MISC_MOLECULE
cf3ab5167915
·sjplimp / GitHub on Nov 9 2016, 19:51.
Merge pull request #260 from andeplane/IP_MANYBODY_MC
59922f894b18
·sjplimp / GitHub on Nov 9 2016, 19:51.
Merge pull request #259 from andeplane/IP_KSPACE
5e2b9d8bf32d
·sjplimp / GitHub on Nov 9 2016, 19:50.
Merge pull request #258 from andeplane/IP_GRANULAR
2d132cad6b77
·sjplimp / GitHub on Nov 9 2016, 19:50.
Merge pull request #257 from andeplane/IP_CORESHELL
ef6801f8bfa3
·sjplimp / GitHub on Nov 9 2016, 19:50.
Merge pull request #256 from andeplane/IP_BODY
c81a72364268
·sjplimp / GitHub on Nov 9 2016, 19:50.
Merge pull request #255 from andeplane/IP_ASPHERE
f9eb2a99ce8b
·sjplimp / GitHub on Nov 9 2016, 19:50.
Merge pull request #254 from andeplane/IP_root
16a02ef27d4f
·sjplimp / GitHub on Nov 9 2016, 19:47.
fixed links in Section_intro.txt
2c801320c26a
·Steve Plimpton on Nov 9 2016, 19:46.

Nov 8 2016

Building correct shortlists and removed rsq test in force loops
d20b32092ec1
·Anders Hafreager on Nov 8 2016, 18:57.
add FLERR argument to force->bounds() in born/coul/dsf
cdb5d47e9f9d
·arielzn on Nov 8 2016, 18:24.
sync with SVN for creation of stable release
a23b287a7aac
·Steve Plimpton on Nov 8 2016, 17:05.
sync with SVN
31204aab6a1b
·Steve Plimpton on Nov 8 2016, 16:57.
pair style born/coul/dsf added with its coreshell version
667f4dfe28b9
·arielzn on Nov 8 2016, 11:32.

Nov 7 2016

improve help and it through a pager, when screen == stdout
21694ca3a843
·Axel Kohlmeyer on Nov 7 2016, 23:10.
make name of the actual executable (i.e. arg[0]) accessible
9b910d5511b1
·Axel Kohlmeyer on Nov 7 2016, 23:07.
Initializing pointers in USER-OMP
054ab6bff32f
·Anders Hafreager on Nov 7 2016, 21:07.
Initializing pointers in USER-DIFFRACTION and USER-DPD
616420cda841
·Anders Hafreager on Nov 7 2016, 20:51.
Initialize pointers in SNAP and SRD
fb3ac9afba39
·Anders Hafreager on Nov 7 2016, 20:30.
Initialize pointers in RIGID and SHOCK
7cd7cda2d4b7
·Anders Hafreager on Nov 7 2016, 20:22.
Initializing pointers in PERI, QEQ and REPLICA
db0524278a69
·Anders Hafreager on Nov 7 2016, 19:58.
Initialized pointers in MISC and MOLECULE
1ff75eaba2bf
·Anders Hafreager on Nov 7 2016, 17:15.
Initialize pointers in MANYBODY and MC
30dede867af9
·Anders Hafreager on Nov 7 2016, 17:02.
Initialize pointers in KSPACE
a5c6104d6403
·Anders Hafreager on Nov 7 2016, 16:54.
Initialize pointers in GRANULAR
c5869bdee209
·Anders Hafreager on Nov 7 2016, 16:33.
Initialize pointers in CORESHELL
e7a2c6b5d1f3
·Anders Hafreager on Nov 7 2016, 16:26.
Initialized pointers in BODY
06959a9c597c
·Anders Hafreager on Nov 7 2016, 16:21.
Initialize pointers in ASPHERE
cd65d44d9507
·Anders Hafreager on Nov 7 2016, 16:15.
NULLed ptrs in files
45f2e86dd63e
·Anders Hafreager on Nov 7 2016, 16:07.
NULL ptrs in dump_custom and dump_image
f8226e8ae5c8
·Anders Hafreager on Nov 7 2016, 15:56.
NULLing ptrs in comm_brick and dump*.cpp
b221b15d24ec
·Anders Hafreager on Nov 7 2016, 15:50.

Nov 4 2016

Merge pull request #248 from akohlmey/collected-small-fixes
f0131393e00a
·sjplimp / GitHub on Nov 4 2016, 17:58.
Merge pull request #247 from akohlmey/bounds-error-with-code-line
32e0a5834319
·sjplimp / GitHub on Nov 4 2016, 17:58.
Merge pull request #246 from akohlmey/manybody-short-neighbor-list
60908eeab424
·sjplimp / GitHub on Nov 4 2016, 17:57.
Merge pull request #244 from ketankhare/patch-2
8214555b2977
·sjplimp / GitHub on Nov 4 2016, 17:57.
added examples/threebody, fix reaxc/speceies/kk
f48b71f46ba6
·Steve Plimpton on Nov 4 2016, 17:56.
add thorough checking for valid arguments to -partition or -p
7d23a0737ef5
·Axel Kohlmeyer on Nov 4 2016, 05:42.

Nov 3 2016

add temporary force accumulation to local variables for vashishta styles
02510ec3217c
·Axel Kohlmeyer on Nov 3 2016, 03:32.
accumulate forces in temporary local variables for tersoff
33140e500493
·Axel Kohlmeyer on Nov 3 2016, 03:16.

Nov 2 2016

use local variables for more efficient force accumulation
639fb6f444a0
·Axel Kohlmeyer on Nov 2 2016, 22:20.
build short neighbor list for sw on based on ij parameters only
b156771721ee
·Axel Kohlmeyer on Nov 2 2016, 22:09.
avoid tiny memory leak, when the restart command is specified multiple times
5d787f7f16c9
·Axel Kohlmeyer on Nov 2 2016, 02:39.

Nov 1 2016

avoid uninitialized data for using ewald/disp with lj only
c8f4b55588ac
·Axel Kohlmeyer on Nov 1 2016, 21:48.
avoid memory leak in pppm/disp/omp
e13e4031cfd4
·Axel Kohlmeyer on Nov 1 2016, 21:48.
avoid memory leaks when using kspace solvers for lennard-jones
782a3280807e
·Axel Kohlmeyer on Nov 1 2016, 19:55.
do not access uninitialized data for ewald/disp and pppm/disp
e81ae21dbd3a
·Axel Kohlmeyer on Nov 1 2016, 19:54.

Oct 29 2016

Using short neighborlists in neigh full
f333d659c229
·Anders Hafreager on Oct 29 2016, 22:54.
Using short neighbor lists
51e2313fac2c
·Anders Hafreager on Oct 29 2016, 22:35.

lammps/srcmaster2862c2081501fef58d98010…

Nov 18 2016

Nov 17 2016

Nov 16 2016

Nov 14 2016

Nov 12 2016

Nov 11 2016

Nov 10 2016

Nov 9 2016

Nov 8 2016

Nov 7 2016

Nov 4 2016

Nov 3 2016

Nov 2 2016

Nov 1 2016

Oct 29 2016

lammps/src
master2862c2081501fef58d98010…