Diffusion lammps 5a6dea7a2217

Merge branch 'master' into user-nc-dump
5a6dea7a2217
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Oct 18 2016, 21:36.

Description

Merge branch 'master' into user-nc-dump

Details

Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Oct 18 2016, 21:36

Pushed

junge

Oct 19 2017, 09:53

Parents

rLAMMPS2106dce2b382: new fix halt command, other sundry small bug fixes
rLAMMPS27796b431ee5: avoid distracting error output

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Event Timeline

Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPS5a6dea7a2217: Merge branch 'master' into user-nc-dump (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Oct 18 2016, 21:36

Merged Changes

Commit	Author	Details	Committed
2106dce2b382	Steve Plimpton	new fix halt command, other sundry small bug fixes	Oct 18 2016
713b2af067cb	sjplimp/GitHub	Merge pull request #221 from akohlmey/collected-bugfixes	Oct 18 2016
a752966eefec	Axel Kohlmeyer	Merge branch 'collected-bugfixes' of github.com:akohlmey/lammps into collected…	Oct 18 2016
1f7693faf289	Axel Kohlmeyer	fix typo	Oct 18 2016
2c5ea9fc61e4	Axel Kohlmeyer	reapply changes to the timer class that got lost somehow	Oct 18 2016
3e88fb535547	Axel Kohlmeyer	Merge branch 'master' into collected-bugfixes	Oct 18 2016
6eadd45c4567	Steve Plimpton	Merge branch 'halt2'	Oct 18 2016
003581c6a80c	Steve Plimpton	final changes to fix halt	Oct 18 2016
1f1c87235a07	Axel Kohlmeyer	add support for "error continue" option, which resets the timer timeout setting…	Oct 18 2016
394c3bb50453	Axel Kohlmeyer	add Timer::reset_timeout() API, that allows restoring the previous timeout…	Oct 18 2016
954d536826ee	Steve Plimpton	added bondmax method to fix halt	Oct 18 2016
e4ff8128f1b2	Axel Kohlmeyer	fix typo	Oct 16 2016
e7825ba21a0b	Axel Kohlmeyer	import fix halt prototype code with corrections for soft exit	Oct 15 2016
e77e1f6b8ea6	Axel Kohlmeyer	replace complex solution to implement a soft exit with simpler one	Oct 15 2016
909ec2c09658	Axel Kohlmeyer	remove unused class members	Oct 14 2016
f67975fd8adf	Axel Kohlmeyer	apply proper initialization and remove redundant variable declaration	Oct 14 2016
deceb9d5c6a4	Axel Kohlmeyer	remove assignment without effect	Oct 14 2016
c9c66ca0bd1a	Axel Kohlmeyer	replace unsafe code	Oct 14 2016
d07703efff5c	Axel Kohlmeyer	re-apply bugfix from two years ago	Oct 14 2016
411ecca8df96	Axel Kohlmeyer	plug memory leak	Oct 14 2016
d11363c7eb76	sjplimp/GitHub	Merge pull request #220 from rbberger/fix-doc-makefile	Oct 14 2016
5aefb2a88232	sjplimp/GitHub	Merge pull request #219 from akohlmey/python-no-double-load	Oct 14 2016
40f2310a2ab5	sjplimp/GitHub	Merge pull request #218 from timattox/USER-DPD_fix_rx_init_bugfix	Oct 14 2016
2c8a7a318a4a	Steve Plimpton	bug fix for fix GCMC w/ fix shake, enhance of fix wall/gran/region with…	Oct 14 2016
95cca1bd9f63	Richard Berger	Allow building other targets without Python3 and virtualenv	Oct 13 2016
0b426dadc1d1	Axel Kohlmeyer	do not require the LAMMPS shared library when loading the python wrapper from…	Oct 13 2016
fcb52710267a	Tim Mattox	USER-DPD: Initialize the dpdThetaLocal array consistently in fix_rx	Oct 12 2016
4958e114bac6	Tim Mattox	USER-DPD bugfix: Properly initialize the local temperature averaging array.	Oct 12 2016
63e71cd45b27	Steve Plimpton	patch to add DPD-VV	Oct 12 2016
4a5d9eaae23c	sjplimp/GitHub	Merge pull request #217 from akohlmey/small-fixes	Oct 12 2016
4e3a55047f0e	sjplimp/GitHub	Merge pull request #215 from timattox/USER-DPD_bugfix_for_dtsqrt	Oct 12 2016
f8a26dd158ff	Axel Kohlmeyer	update Timer::force_timeout() to trigger at next loop iteration	Oct 12 2016
c24bf512f31a	Axel Kohlmeyer	update #include statements for system includes	Oct 12 2016
6b4ab0a39044	Axel Kohlmeyer	update .gitignore	Oct 12 2016
adc98e07df5d	Axel Kohlmeyer	whitespace cleanup in USER-DPD	Oct 12 2016
39a22039e918	Axel Kohlmeyer	correct broken link	Oct 12 2016
b75860048bd7	Axel Kohlmeyer	updates for recent changes to the manual	Oct 12 2016
2f07a627a27d	Tim Mattox	Forgot to remove my call to reset_dt()	Oct 11 2016
559637f4bcae	Tim Mattox	USER-DPD Bugfix: reset_dt() is not called when I thought it should be called.	Oct 11 2016

Changes (86)

				Path
	M			doc/Makefile
	M			doc/README
	M			doc/src/Manual.txt
	M			doc/src/Section_commands.txt
	M			doc/src/compute_pe_atom.txt
	M			doc/src/compute_stress_atom.txt
	M			doc/src/dump_modify.txt
	M			doc/src/fix_dpd_energy.txt
	A			doc/src/fix_halt.txt
	M			doc/src/fix_temp_berendsen.txt
	M			doc/src/fix_temp_rescale.txt
	M			doc/src/fix_wall_gran.txt
	M			doc/src/fix_wall_gran_region.txt
	M			doc/src/fixes.txt
	M			doc/src/minimize.txt
	M			doc/src/pair_dpd_fdt.txt
	M			doc/src/read_restart.txt
	M			doc/src/run.txt
	A			examples/DIFFUSE/log.13Oct16.msd.2d.g++.8
	A			examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8
	D			examples/DIFFUSE/log.1Feb14.msd.2d.g++.8
	D			examples/DIFFUSE/log.1Feb14.vacf.2d.g++.8
	V			examples/KAPPA/{log.13Oct16.ehex.g++.8 ← log.7Jun16.ehex.g++.8}
	V			examples/KAPPA/{log.13Oct16.heat.g++.8 ← log.7Jun16.heat.g++.8}
	A			examples/KAPPA/log.13Oct16.heatflux.g++.8
	A			examples/KAPPA/log.13Oct16.langevin.g++.8
	A			examples/KAPPA/log.13Oct16.mp.g++.8
	D			examples/KAPPA/log.1Feb14.heatflux.g++.8
	D			examples/KAPPA/log.1Feb14.langevin.g++.8
	D			examples/KAPPA/log.1Feb14.mp.g++.8
	V			examples/KAPPA/{log.7Jun16.ehex.g++.8 → log.13Oct16.ehex.g++.8}
	V			examples/KAPPA/{log.7Jun16.heat.g++.8 → log.13Oct16.heat.g++.8}
	V			examples/MC/{log.13Oct16.mc.g++.1 ← log.6Jun14.mc.g++.1}
	V			examples/MC/{log.6Jun14.mc.g++.1 → log.13Oct16.mc.g++.1}
	A			examples/VISCOSITY/log.13Oct16.einstein.2d.g++.1
	A			examples/VISCOSITY/log.13Oct16.gk.2d.g++.1
	A			examples/VISCOSITY/log.13Oct16.mp.2d.g++.1
	A			examples/VISCOSITY/log.13Oct16.nemd.2d.g++.1
	A			examples/VISCOSITY/log.13Oct16.wall.2d.g++.1
	D			examples/VISCOSITY/log.1Feb14.gk.2d.g++.1
	D			examples/VISCOSITY/log.1Feb14.mp.2d.g++.1
	D			examples/VISCOSITY/log.1Feb14.nemd.2d.g++.1
	D			examples/VISCOSITY/log.1Feb14.wall.2d.g++.1
	A			examples/VISCOSITY/profile.13Oct16.einstein.2d.g++.1
	A			examples/VISCOSITY/profile.13Oct16.gk.2d.g++.1
	A			examples/VISCOSITY/profile.13Oct16.mp.2d.g++.1
	A			examples/VISCOSITY/profile.13Oct16.nemd.2d.g++.1
	A			examples/VISCOSITY/profile.13Oct16.wall.2d.g++.1
	D			examples/VISCOSITY/profile.1Feb14.gk.2d.g++.1
	D			examples/VISCOSITY/profile.1Feb14.mp.2d.g++.1
	D			examples/VISCOSITY/profile.1Feb14.nemd.2d.g++.1
	D			examples/VISCOSITY/profile.1Feb14.wall.2d.g++.1
	M			python/lammps.py
	M			src/.gitignore
	M			src/GRANULAR/fix_wall_gran.cpp
	M			src/GRANULAR/fix_wall_gran_region.cpp
	M			src/GRANULAR/fix_wall_gran_region.h
	M			src/MC/fix_bond_create.cpp
	M			src/MC/fix_gcmc.cpp
	M			src/USER-DPD/fix_dpd_energy.cpp
	P			src/USER-DPD/fix_dpd_energy.h Copied to src/fix_halt.h
	M			src/USER-DPD/fix_eos_table_rx.cpp
	M			src/USER-DPD/fix_rx.cpp
	M			src/USER-DPD/fix_shardlow.cpp
	M			src/USER-DPD/fix_shardlow.h
	M			src/USER-DPD/pair_exp6_rx.cpp
	M			src/USER-DPD/pair_multi_lucy_rx.cpp
	M			src/USER-DPD/pair_table_rx.cpp
	M			src/dump_custom.cpp
	M			src/finish.cpp
	A			src/fix_halt.cpp
	P			src/fix_halt.h Copied from src/USER-DPD/fix_dpd_energy.h
	M			src/fix_recenter.cpp
	M			src/fix_temp_rescale.cpp
	M			src/lammps.cpp
	M			src/region.cpp
	M			src/region.h
	M			src/region_cone.cpp
	M			src/region_cylinder.cpp
	M			src/region_intersect.cpp
	M			src/region_intersect.h
	M			src/region_union.cpp
	M			src/region_union.h
	M			src/timer.cpp
	M			src/timer.h
	M			src/version.h