Diffusion lammps (master) History

lammps/src
master31204aab6a1bd8c4f8e6383…

Nov 8 2016

sync with SVN
31204aab6a1b
·Steve Plimpton on Nov 8 2016, 16:57.

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.
fix typo
ccca642b3ae6
·Axel Kohlmeyer on Oct 19 2016, 14:08.
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

Merge branch 'master' into user-nc-dump
5a6dea7a2217
·Axel Kohlmeyer on Oct 18 2016, 21:36.
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.
forgot to include USER-NC-DUMP in PACKUSER variable
ae77664bddd5
·Axel Kohlmeyer on Oct 18 2016, 20:45.
fix typo
1f7693faf289
·Axel Kohlmeyer on Oct 18 2016, 20:06.
reapply changes to the timer class that got lost somehow
2c5ea9fc61e4
·Axel Kohlmeyer on Oct 18 2016, 20:05.
Merge branch 'master' into collected-bugfixes
3e88fb535547
·Axel Kohlmeyer on Oct 18 2016, 19:54.
final changes to fix halt
003581c6a80c
·Steve Plimpton on Oct 18 2016, 19:16.
add support for "error continue" option, which resets the timer timeout setting…
1f1c87235a07
·Axel Kohlmeyer on Oct 18 2016, 18:21.
add Timer::reset_timeout() API, that allows restoring the previous timeout…
394c3bb50453
·Axel Kohlmeyer on Oct 18 2016, 18:20.
added bondmax method to fix halt
954d536826ee
·Steve Plimpton on Oct 18 2016, 17:27.
provide an accessor for names of LAMMPS variables
c5513c4f7503
·Axel Kohlmeyer on Oct 18 2016, 01:56.

Oct 15 2016

import fix halt prototype code with corrections for soft exit
e7825ba21a0b
·Axel Kohlmeyer on Oct 15 2016, 13:30.
replace complex solution to implement a soft exit with simpler one
e77e1f6b8ea6
·Axel Kohlmeyer on Oct 15 2016, 01:40.

Oct 14 2016

remove unused class members
909ec2c09658
·Axel Kohlmeyer on Oct 14 2016, 18:04.
apply proper initialization and remove redundant variable declaration
f67975fd8adf
·Axel Kohlmeyer on Oct 14 2016, 13:37.
remove assignment without effect
deceb9d5c6a4
·Axel Kohlmeyer on Oct 14 2016, 13:31.
replace unsafe code
c9c66ca0bd1a
·Axel Kohlmeyer on Oct 14 2016, 13:28.
re-apply bugfix from two years ago
d07703efff5c
·Axel Kohlmeyer on Oct 14 2016, 13:27.
plug memory leak
411ecca8df96
·Axel Kohlmeyer on Oct 14 2016, 13:27.
Merge pull request #218 from timattox/USER-DPD_fix_rx_init_bugfix
40f2310a2ab5
·sjplimp / GitHub on Oct 14 2016, 00:56.
bug fix for fix GCMC w/ fix shake, enhance of fix wall/gran/region with…
2c8a7a318a4a
·Steve Plimpton on Oct 14 2016, 00:55.

Oct 12 2016

USER-DPD: Initialize the dpdThetaLocal array consistently in fix_rx
fcb52710267a
·Tim Mattox on Oct 12 2016, 21:56.
USER-DPD bugfix: Properly initialize the local temperature averaging array.
4958e114bac6
·Tim Mattox on Oct 12 2016, 21:46.
patch to add DPD-VV
63e71cd45b27
·Steve Plimpton on Oct 12 2016, 15:35.
Merge pull request #217 from akohlmey/small-fixes
4a5d9eaae23c
·sjplimp / GitHub on Oct 12 2016, 15:32.
Merge pull request #215 from timattox/USER-DPD_bugfix_for_dtsqrt
4e3a55047f0e
·sjplimp / GitHub on Oct 12 2016, 15:30.
update Timer::force_timeout() to trigger at next loop iteration
f8a26dd158ff
·Axel Kohlmeyer on Oct 12 2016, 13:26.
USER-SMD was missing from PACKLIB variable
2e8edbd2b973
·Axel Kohlmeyer on Oct 12 2016, 12:53.
update #include directives to match current LAMMPS coding conventions
da66c1e649bb
·Axel Kohlmeyer on Oct 12 2016, 06:07.
update #include statements for system includes
c24bf512f31a
·Axel Kohlmeyer on Oct 12 2016, 06:00.
update .gitignore
6b4ab0a39044
·Axel Kohlmeyer on Oct 12 2016, 06:00.
whitespace cleanup in USER-DPD
adc98e07df5d
·Axel Kohlmeyer on Oct 12 2016, 05:58.
import dump nc and dump nc/mpiio from lammps-netcdf as USER-NC-DUMP package by…
69cb83170599
·Axel Kohlmeyer on Oct 12 2016, 05:44.
import lammps-netcdf code as USER-NC-DUMP package
ecb03dd2dfda
·Axel Kohlmeyer on Oct 12 2016, 05:03.

Oct 11 2016

Forgot to remove my call to reset_dt()
2f07a627a27d
·Tim Mattox on Oct 11 2016, 22:30.
USER-DPD Bugfix: reset_dt() is not called when I thought it should be called.
559637f4bcae
·Tim Mattox on Oct 11 2016, 22:11.
Merge pull request #212 from timattox/USER-DPD_fix_eos_atom_style_checks
fbf7df14b55f
·sjplimp / GitHub on Oct 11 2016, 21:40.
Merge pull request #207 from timattox/USER-DPD_new_VV_for_DPD
6f1162927a78
·sjplimp / GitHub on Oct 11 2016, 21:39.
Merge pull request #214 from akohlmey/make-no-lib-no-mpiio
803dc57bfa23
·sjplimp / GitHub on Oct 11 2016, 20:42.
Merge pull request #213 from akohlmey/improper-virial-bugfixes
3e8e2911cc15
·sjplimp / GitHub on Oct 11 2016, 20:42.
added LAST option to dump_modify thresh, more restart info printed out to screen
04f5eadcf14a
·Steve Plimpton on Oct 11 2016, 20:39.
make no-lib should also remove MPIIO and USER-LB packages
b00b40bccdfd
·Axel Kohlmeyer on Oct 11 2016, 14:03.
bugfix for AngleAngle term in CLASS2 impropers by Ivan A. Strelnikov, ICP RAS
ef079ae4eb87
·Axel Kohlmeyer on Oct 11 2016, 05:56.
Merge branch 'master' into improper-virial-bugfixes
bb0bfd508b2f
·Axel Kohlmeyer on Oct 11 2016, 05:55.

Oct 10 2016

Merge pull request #211 from akohlmey/add-respa-to-fix-flow-gauss
ed8cc827137c
·sjplimp / GitHub on Oct 10 2016, 21:59.
Merge pull request #209 from akohlmey/static-double-deallocation-workaround
27dac0246604
·sjplimp / GitHub on Oct 10 2016, 21:58.

lammps/srcmaster31204aab6a1bd8c4f8e6383…

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 21 2016

Oct 19 2016

Oct 18 2016

Oct 15 2016

Oct 14 2016

Oct 12 2016

Oct 11 2016

Oct 10 2016

lammps/src
master31204aab6a1bd8c4f8e6383…