Diffusion lammps (master) History

History
master2106dce2b3822283d5b0682…

Oct 18 2016

new fix halt command, other sundry small bug fixes
2106dce2b382
·Steve Plimpton on Oct 18 2016, 21:11.
Merge pull request #221 from akohlmey/collected-bugfixes
713b2af067cb
·sjplimp / GitHub on Oct 18 2016, 20:58.
Merge branch 'collected-bugfixes' of github.com:akohlmey/lammps into collected…
a752966eefec
·Axel Kohlmeyer on Oct 18 2016, 20:07.
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.
Merge branch 'halt2'
6eadd45c4567
·Steve Plimpton on Oct 18 2016, 19:16.
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.

Oct 16 2016

fix typo
e4ff8128f1b2
·Axel Kohlmeyer on Oct 16 2016, 18:29.

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 #220 from rbberger/fix-doc-makefile
d11363c7eb76
·sjplimp / GitHub on Oct 14 2016, 01:00.
Merge pull request #219 from akohlmey/python-no-double-load
5aefb2a88232
·sjplimp / GitHub on Oct 14 2016, 00:58.
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 13 2016

Allow building other targets without Python3 and virtualenv
95cca1bd9f63
·Richard Berger on Oct 13 2016, 17:40.
do not require the LAMMPS shared library when loading the python wrapper from…
0b426dadc1d1
·Axel Kohlmeyer on Oct 13 2016, 00:36.

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.
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.
correct broken link
39a22039e918
·Axel Kohlmeyer on Oct 12 2016, 05:57.
updates for recent changes to the manual
b75860048bd7
·Axel Kohlmeyer on Oct 12 2016, 05:50.

Oct 11 2016

tweaks to new USER-DPD docs
0eb7fbf34d23
·Steve Plimpton on Oct 11 2016, 23:43.
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 #203 from rbberger/txt2rst-external-link-fix
e70d530c46ed
·sjplimp / GitHub on Oct 10 2016, 21:59.
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.
Merge pull request #204 from rbberger/fix-user-omp
467bcad0a04e
·sjplimp / GitHub on Oct 10 2016, 21:57.
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.
edited documentation
72ac0734123f
·Steven Strong / Axel Kohlmeyer on Oct 10 2016, 15:38.
edited documentation
49c45ab03b6f
·Steven Strong / Axel Kohlmeyer on Oct 10 2016, 15:38.
first draft of documentation for respa
c2cd43994412
·Steven Strong / Axel Kohlmeyer on Oct 10 2016, 15:38.
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

revert to previous style conventions for size_t constants
683689c80807
·Axel Kohlmeyer on Oct 8 2016, 17:00.
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: update the USER/dpd examples and their reference outputs
9789f047d78e
·Tim Mattox on Oct 7 2016, 21:55.
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.
Fix broken link
7f3a7c5cbe5e
·Richard Berger on Oct 7 2016, 02:33.
Fix issue with external links containing anchors
e78b4267b7c2
·Richard Berger on Oct 7 2016, 02:29.

Oct 6 2016

Merge pull request #202 from akohlmey/doc-formatting-fixes
e9fed8092893
·sjplimp / GitHub on Oct 6 2016, 23:49.
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.
collected documentation updates and corrections from LAMMPS-ICMS
0b5d71537a8b
·Axel Kohlmeyer on Oct 6 2016, 21:48.
Merge pull request #197 from giacomofiorin/colvars_2016-10-05
c2134575508a
·sjplimp / GitHub on Oct 6 2016, 21:02.
Merge pull request #196 from akohlmey/charmm-cmap-updates
0f45cd61a542
·sjplimp / GitHub on Oct 6 2016, 21:02.
clean up doc src
493873fb933d
·Steve Plimpton on Oct 6 2016, 21:00.
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.
update reference data files for updated/corrected clayff parameters
0853cdbe6f69
·Axel Kohlmeyer on Oct 6 2016, 17:47.
bugfix for AngleAngle term in CLASS2 impropers by Ivan A. Strelnikov, ICP RAS
83bcdb6a5053
·Axel Kohlmeyer on Oct 6 2016, 17:27.
improved whitespace handling in msi2lmp for force fields and topologies
22ce6718048b
·Axel Kohlmeyer on Oct 6 2016, 17:16.
bugfix for virial tally for improper style umbrella from Steven Vandenbrande (U…
4921dc18a058
·Axel Kohlmeyer on Oct 6 2016, 16:47.
Merge branch 'master' of https://github.com/albapa/lammps into small-changes
d133167bf676
·Axel Kohlmeyer on Oct 6 2016, 15:32.
add NETCDF libs (as defined in QUIP) to the linking line if QUIP was built with…
8ea063378eac
·A Bartok-Partay on Oct 6 2016, 13:16.
removed dump_modify command
fd16118cbb22
·A Bartok-Partay on Oct 6 2016, 13:02.
update include statement format
f9f955d5b5d0
·Axel Kohlmeyer on Oct 6 2016, 04:34.
some more updates to the README file to reflect the inclusion of the CMAP…
d7d321a51249
·Axel Kohlmeyer on Oct 6 2016, 00:41.
Colvars update: issue a warning that cannot be ignored regarding total forces
8809a603fb2d
·Giacomo Fiorin on Oct 6 2016, 00:26.
Colvars update: make ABF check that the colvar isn't using already…
969d3cf4b0c4
·Giacomo Fiorin on Oct 6 2016, 00:25.
added 1GB1 example from Robert Latour and update 1AC7 example files
326fdf2cf13a
·Axel Kohlmeyer on Oct 6 2016, 00:20.
added tweak to write out the command line used for the conversion to the…
f32819dd1086
·Axel Kohlmeyer on Oct 6 2016, 00:13.
import updated README file for charmm2lammps.pl with CMAP support
c07a01c661d6
·Axel Kohlmeyer on Oct 6 2016, 00:11.

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.

Historymaster2106dce2b3822283d5b0682…

Oct 18 2016

Oct 16 2016

Oct 15 2016

Oct 14 2016

Oct 13 2016

Oct 12 2016

Oct 11 2016

Oct 10 2016

Oct 8 2016

Oct 7 2016

Oct 6 2016

Oct 5 2016

History
master2106dce2b3822283d5b0682…