Diffusion lammps (master) History

lammps/src
master399c0af150e39accdf79dd9…

Oct 26 2016

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

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.
USER-DPD: Add atom_style compatibility checks in fix_eos_*.cpp files.
a2b084006467
·Tim Mattox on Oct 10 2016, 19:40.
whitespace cleanup
144e6a809157
·Axel Kohlmeyer on Oct 10 2016, 15:40.
adjusted default respa level to be outermost
e96ebb29bc59
·Steven Strong / Axel Kohlmeyer on Oct 10 2016, 15:38.
now understand how respa works in lammps
3ce178d43f9d
·Steven Strong / Axel Kohlmeyer on Oct 10 2016, 15:38.
added respa to fix_flow_gauss, not fully understood yet
23781d6ec9a6
·Steven Strong / Axel Kohlmeyer on Oct 10 2016, 15:38.
completed synchronization with non-threaded version
fca6d721c035
·Axel Kohlmeyer on Oct 10 2016, 15:16.
whitespace cleanup
dd192ca7ea15
·Axel Kohlmeyer on Oct 10 2016, 15:15.

Oct 8 2016

workaround for double free issue when using USER-COLVARS with lammps code…
e01e90eb965c
·Axel Kohlmeyer on Oct 8 2016, 16:45.

Oct 7 2016

USER-DPD: whitespace and indentation fixes
9507a786f013
·Tim Mattox on Oct 7 2016, 21:59.
USER-DPD: Added support to use VV integrator with USER-DPD if desired. Includes…
e27ed6c94a2e
·Tim Mattox on Oct 7 2016, 21:03.
Migrate changes from GRANULAR to USER-OMP
615a2da044a3
·Richard Berger on Oct 7 2016, 03:48.

Oct 6 2016

Merge pull request #199 from akohlmey/small-changes
54fc194e5b33
·sjplimp / GitHub on Oct 6 2016, 23:49.
new fix wall/gran/region command, REBO bug fix, new example log files
b3d2fb91bb6c
·Steve Plimpton on Oct 6 2016, 23:47.
Revert "bugfix for AngleAngle term in CLASS2 impropers by Ivan A. Strelnikov…
19984c9bd17c
·Axel Kohlmeyer on Oct 6 2016, 23:23.
Revert "bugfix for virial tally for improper style umbrella from Steven…
f92618a33b74
·Axel Kohlmeyer on Oct 6 2016, 23:21.
bugfix for virial tally for improper style umbrella from Steven Vandenbrande (U…
887981cfaa29
·Axel Kohlmeyer on Oct 6 2016, 23:20.
Merge pull request #197 from giacomofiorin/colvars_2016-10-05
c2134575508a
·sjplimp / GitHub on Oct 6 2016, 21:02.
Merge branch 'USER-DPD_pair_exp6_rx_mathfix' of https://github.
60a031ebacef
·Axel Kohlmeyer on Oct 6 2016, 20:28.
Merge branch 'USER-DPD_hybrid_atom_bugfix' of https://github.
27e76a70b9d7
·Axel Kohlmeyer on Oct 6 2016, 20:27.
USER-DPD: math corrections in pair_exp6_rx.cpp (by Jim Larentzos)
e1e9a5c12604
·Tim Mattox on Oct 6 2016, 19:49.
USER-DPD: bugfix in unpack_comm_hybrid(); now works with hybrid atom style
d31121b18cde
·Tim Mattox on Oct 6 2016, 19:21.
bugfix for AngleAngle term in CLASS2 impropers by Ivan A. Strelnikov, ICP RAS
83bcdb6a5053
·Axel Kohlmeyer on Oct 6 2016, 17:27.
bugfix for virial tally for improper style umbrella from Steven Vandenbrande (U…
4921dc18a058
·Axel Kohlmeyer on Oct 6 2016, 16:47.
update include statement format
f9f955d5b5d0
·Axel Kohlmeyer on Oct 6 2016, 04:34.
Colvars update: make ABF check that the colvar isn't using already…
969d3cf4b0c4
·Giacomo Fiorin on Oct 6 2016, 00:25.

Oct 5 2016

adjustments to balancing weights and factors, also XOR op for formulas, if…
02bfa898eeb1
·Steve Plimpton on Oct 5 2016, 23:46.
Merge pull request #193 from akohlmey/eam-bugfix
030df745bc57
·sjplimp / GitHub on Oct 5 2016, 18:54.
changes to imbalance weight factors
c46be7db625e
·Steve Plimpton on Oct 5 2016, 18:33.

Oct 4 2016

correct the bug discovered by stan due to uninitialized scale factors for…
4381db846bcb
·Axel Kohlmeyer on Oct 4 2016, 20:33.
Merge branch 'restrict-weights-and-weight-factors' of https://github.
11c2892e54cf
·Steve Plimpton on Oct 4 2016, 17:49.

lammps/srcmaster399c0af150e39accdf79dd9…

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

Oct 8 2016

Oct 7 2016

Oct 6 2016

Oct 5 2016

Oct 4 2016

lammps/src
master399c0af150e39accdf79dd9…