Diffusion lammps (master) History

History
master3d3a99c082f723d18bebab0…

Nov 9 2016

added missing potential for tersoff/mod/c
3d3a99c082f7
·Axel Kohlmeyer on Nov 9 2016, 22:50.
correct typo in formula
c55fd502e0b9
·Axel Kohlmeyer on Nov 9 2016, 21:04.
integrate pair style tersoff/mod/c contributed by Ganga P Purja Pun (GMU)
71ee2ecaa1e0
·Axel Kohlmeyer on Nov 9 2016, 20:52.

Nov 8 2016

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.

Nov 4 2016

Merge pull request #252 from akohlmey/preinstalled-vs-scm
77bbf03f0f85
·sjplimp / GitHub on Nov 4 2016, 17:59.
Merge pull request #249 from lammps/unstable
7cff08ca0a88
·sjplimp / GitHub on Nov 4 2016, 17:58.
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.
remove the misleading "(which it is by default)" from several doc files
6cc4eb19af55
·Axel Kohlmeyer on Nov 4 2016, 17:20.
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.
remove work repetitions for 'the'
7fdd6e280771
·Axel Kohlmeyer on Nov 1 2016, 16:40.
remove word repetitions for 'a'
2e0d304c7eeb
·Axel Kohlmeyer on Nov 1 2016, 16:36.

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.
permission cleanup in tools folder
93d393aa691a
·Axel Kohlmeyer on Oct 28 2016, 16:48.
Merge branch 'master' into collected-small-fixes
4216be49f3ce
·Axel Kohlmeyer on Oct 28 2016, 16:46.

Oct 27 2016

Version 27 Oct 2016
c3a1e72183cc
·Axel Kohlmeyer on Oct 27 2016, 17:40.
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.
Merge pull request #238 from giacomofiorin/colvars-2016-10-24
ad5f7c458196
·sjplimp / GitHub on Oct 25 2016, 18:32.
Merge pull request #231 from akohlmey/collected-doc-fixes
6b334991352b
·sjplimp / GitHub on Oct 25 2016, 18:30.
fix issue with docs for orientorder/atom compute reported by @andeplane
63eada242554
·Axel Kohlmeyer on Oct 25 2016, 18:12.
Merge branch 'collected-doc-fixes' of github.com:akohlmey/lammps into collected…
1a436bd7a9bb
·Axel Kohlmeyer on Oct 25 2016, 17:58.
Merge branch 'master' into collected-doc-fixes
52dd9aee5fe6
·Axel Kohlmeyer on Oct 25 2016, 17:55.
Merge branch 'doc'
eca96e21ef25
·Steve Plimpton on Oct 25 2016, 17:46.
doc page changes
9c81ad1ab6e3
·Steve Plimpton on Oct 25 2016, 17:45.

Oct 24 2016

update documentation pdf for updated colvars lib
f8367e3d0fee
·Axel Kohlmeyer on Oct 24 2016, 23:49.
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.
Add ensemble-biased metadynamics (Fabrizio Marinelli, NIH)
e02505c8cc33
·Giacomo Fiorin on Oct 24 2016, 23:11.
Minor changes and fixes not relevant to LAMMPS
be2d155cef25
·Giacomo Fiorin on Oct 24 2016, 23:10.
Fix wall forces and subtractAppliedForce for extended-Lagrangian ABF
c2430939809e
·Giacomo Fiorin on Oct 24 2016, 23:05.
Add C-linkage wrapper for colvarscript (useful with ctypes)
ad57a17f48c8
·Giacomo Fiorin on Oct 24 2016, 22:48.
Merge pull request #232 from akohlmey/small-bugfixes
477ddaf1125b
·sjplimp / GitHub on Oct 24 2016, 16:15.
Merge pull request #230 from akohlmey/manual-in-ebook-format
4f69d91a99dc
·sjplimp / GitHub on Oct 24 2016, 16:12.

Oct 23 2016

correct typo in write_dump docs
bc4498800319
·Axel Kohlmeyer on Oct 23 2016, 21:18.

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.
ignore mobi file as well
607246f92310
·Axel Kohlmeyer on Oct 21 2016, 19:25.
remove mobi file format creation from makefile and explain it in README instead
6742fb634aa9
·Axel Kohlmeyer on Oct 21 2016, 18:05.
ignore generated PDF and ePUB files
ed3f02f24944
·Axel Kohlmeyer on Oct 21 2016, 18:04.
make certain, that atom->maxspecial is incremented with extra special space
a2e34aab0a8c
·Axel Kohlmeyer on Oct 21 2016, 17:55.
Merge branch 'collected-small-changes' into collected-doc-fixes
6cd6c106efeb
·Axel Kohlmeyer on Oct 21 2016, 01:27.

Oct 20 2016

Revert "support generation of manual in ePUB format"
a9572275eeb0
·Axel Kohlmeyer on Oct 20 2016, 22:27.
Add support for ebook generation in ePUB and mobi format
2cf77ff778ef
·Axel Kohlmeyer on Oct 20 2016, 22:16.
fix various formatting and broken link issues identified by ebook-convert
f022f6d88ad2
·Axel Kohlmeyer on Oct 20 2016, 20:40.
support generation of manual in ePUB format
8c3f5cb30700
·Axel Kohlmeyer on Oct 20 2016, 15:27.

Oct 19 2016

update packages section in manual with information about USER-NC-DUMP
e8359923f1e4
·Axel Kohlmeyer on Oct 19 2016, 21:58.
Version 20 Oct 2016
d2da0fabb43c
·Axel Kohlmeyer on Oct 19 2016, 21:29.
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.
Merge pull request #216 from akohlmey/user-nc-dump
efc7b23bd863
·sjplimp / GitHub on Oct 19 2016, 16:33.
account for new fix halt properly in PDF and online docs
566effc9c961
·Axel Kohlmeyer on Oct 19 2016, 15:08.
recognize any word starting with FP as FPRIME style table
86f5b5113344
·Axel Kohlmeyer on Oct 19 2016, 15:05.
fix typo
ccca642b3ae6
·Axel Kohlmeyer on Oct 19 2016, 14:08.
fix typos in Makefile.lammps for NetCDF support
019bc0ba0be2
·Axel Kohlmeyer on Oct 19 2016, 13:39.
add mixing for pair styles gauss and gauss/cut contributed by andrew jewett.
7b7cb297e6be
·Axel Kohlmeyer on Oct 19 2016, 04:26.

Oct 18 2016

Version 18 Oct 2016
13ce1037f23d
·Axel Kohlmeyer on Oct 18 2016, 21:46.
Merge branch 'master' into user-nc-dump
5a6dea7a2217
·Axel Kohlmeyer on Oct 18 2016, 21:36.
avoid distracting error output
27796b431ee5
·Axel Kohlmeyer on Oct 18 2016, 21:32.
new fix halt command, other sundry small bug fixes
2106dce2b382
·Steve Plimpton on Oct 18 2016, 21:11.
make plain nc dump style a compile time option as well
6e54443d8c19
·Axel Kohlmeyer on Oct 18 2016, 21:11.
update Makefile.lammps and add README according to suggestions by lars pastewka
2b47fa66533e
·Axel Kohlmeyer on Oct 18 2016, 21:05.
Merge pull request #221 from akohlmey/collected-bugfixes
713b2af067cb
·sjplimp / GitHub on Oct 18 2016, 20:58.
forgot to include USER-NC-DUMP in PACKUSER variable
ae77664bddd5
·Axel Kohlmeyer on Oct 18 2016, 20:45.

Historymaster3d3a99c082f723d18bebab0…

Nov 9 2016

Nov 8 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 23 2016

Oct 21 2016

Oct 20 2016

Oct 19 2016

Oct 18 2016

History
master3d3a99c082f723d18bebab0…