Diffusion lammps (master) History

lammps/src
master07e46b797a29915672cc423…

Nov 17 2016

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.
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 9 2016

Stan bug fixes for fix reaxc/bonds/kk
9806da69f3f9
·Steve Plimpton on Nov 9 2016, 23:47.
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

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 28 2016

Merge branch 'master' into manybody-short-neighbor-list
c4b86a25a71a
·Axel Kohlmeyer on Oct 28 2016, 17:12.
Merge branch 'master' into bounds-error-with-code-line
218e121b41d7
·Axel Kohlmeyer on Oct 28 2016, 17:11.
Merge branch 'master' into collected-small-fixes
4216be49f3ce
·Axel Kohlmeyer on Oct 28 2016, 16:46.

Oct 27 2016

new library functions
d9891abdf4d5
·Steve Plimpton on Oct 27 2016, 17:34.

Oct 26 2016

add error location propagation to atom->set_mass() and atom->check_mass()
f9a9e27f5a9a
·Axel Kohlmeyer on Oct 26 2016, 22:01.
add error location propagation to force->bounds() and force->boundsbig()
35753b8f089e
·Axel Kohlmeyer on Oct 26 2016, 21:53.
region cylinder is compatible with open_faces[2], so do not disallow it.
f028a9a9678d
·Axel Kohlmeyer on Oct 26 2016, 21:04.
fix off-by-one bug in buffer re-allocator
ef9f7c818e1a
·Axel Kohlmeyer on Oct 26 2016, 16:14.
add USER-OMP variant of manybody short neighbor list
8e61bed2d855
·Axel Kohlmeyer on Oct 26 2016, 15:51.
simplify short neighbor list implementation. remove unneeded class member
3267b345904e
·Axel Kohlmeyer on Oct 26 2016, 15:29.
add short neighbor list support to pair style tersoff
0a417b4016f3
·Axel Kohlmeyer on Oct 26 2016, 13:06.
consistent short neighbor list for vashishta and vashishta/table
399c0af150e3
·Axel Kohlmeyer on Oct 26 2016, 05:46.
fully tested multi-element compatible short neighbor list for Stillinger-Weber
e8b3f79690d5
·Axel Kohlmeyer on Oct 26 2016, 05:18.

Oct 25 2016

Clean whitespace
7f3f5e8c380b
·ketankhare / GitHub on Oct 25 2016, 20:46.
Enable write_data
f350500e69cf
·ketankhare / GitHub on Oct 25 2016, 20:43.
Enable write_data for dihedral_fourier
d7c77a419d1f
·ketankhare / GitHub on Oct 25 2016, 20:36.
Merge pull request #239 from akohlmey/static-analysis-fixes
efaa8feab591
·sjplimp / GitHub on Oct 25 2016, 18:32.

Oct 24 2016

Merge branch 'colvars-2016-10-24' of https://github.com/giacomofiorin/lammps…
ba6d1528bb17
·Axel Kohlmeyer on Oct 24 2016, 23:34.
Make SMP parallelism for Colvars optional
182141b85005
·Giacomo Fiorin on Oct 24 2016, 23:13.
whitespace cleanup
512c413b7ead
·Axel Kohlmeyer on Oct 24 2016, 23:13.
apply corrections to issues reported by static code analysis
7b89e47a38d5
·Axel Kohlmeyer on Oct 24 2016, 23:12.

Oct 21 2016

stop with error, if molecule command requires special bond auto-generation…
db36c8bcc31e
·Axel Kohlmeyer on Oct 21 2016, 20:51.
have bond style table exit when bond length is outside table range
991034b632c7
·Axel Kohlmeyer on Oct 21 2016, 20:01.
make certain, that atom->maxspecial is incremented with extra special space
a2e34aab0a8c
·Axel Kohlmeyer on Oct 21 2016, 17:55.

Oct 19 2016

forgot pair table change
9954d5d34668
·Steve Plimpton on Oct 19 2016, 18:47.
Merge branch 'master' of github.com:lammps/lammps
3d254780de85
·Steve Plimpton on Oct 19 2016, 16:58.
Merge pull request #229 from akohlmey/small-corrections
b0cf1ded38ab
·sjplimp / GitHub on Oct 19 2016, 16:57.
Merge pull request #228 from akohlmey/correct-prd-for-bigbig
0891ed83a52f
·sjplimp / GitHub on Oct 19 2016, 16:56.
Revert "recognize any word starting with FP as FPRIME style table"
ffb8eb36da4b
·Axel Kohlmeyer on Oct 19 2016, 16:44.
make PRD code compatible with -DLAMMPS_BIGBIG
1a108572441d
·Axel Kohlmeyer on Oct 19 2016, 16:43.
dead code removal
263446867664
·Axel Kohlmeyer on Oct 19 2016, 16:42.
text edit
58141e0559cb
·Steve Plimpton on Oct 19 2016, 16:41.
Merge pull request #226 from akohlmey/pair-gauss-mixing
393337e7cfa2
·sjplimp / GitHub on Oct 19 2016, 16:37.
Merge pull request #224 from akohlmey/get-vars
e0ed218cc496
·sjplimp / GitHub on Oct 19 2016, 16:36.
recognize any word starting with FP as FPRIME style table
86f5b5113344
·Axel Kohlmeyer on Oct 19 2016, 15:05.

lammps/srcmaster07e46b797a29915672cc423…

Nov 17 2016

Nov 16 2016

Nov 14 2016

Nov 9 2016

Nov 8 2016

Nov 7 2016

Nov 4 2016

Nov 3 2016

Nov 2 2016

Nov 1 2016

Oct 28 2016

Oct 27 2016

Oct 26 2016

Oct 25 2016

Oct 24 2016

Oct 21 2016

Oct 19 2016

lammps/src
master07e46b797a29915672cc423…