Diffusion lammps 8540a9f038dd

Version 11 Oct 2016
8540a9f038dd
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Oct 11 2016, 23:10.

Description

Version 11 Oct 2016

Details

Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Oct 11 2016, 23:10

Pushed

junge

Oct 19 2017, 09:53

Parents

rLAMMPS13b6eb1bae6c: Version 6 Oct 2016
rLAMMPS04f5eadcf14a: added LAST option to dump_modify thresh, more restart info printed out to screen

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Event Timeline

Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPS8540a9f038dd: Version 11 Oct 2016 (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Oct 11 2016, 23:10

Merged Changes

Commit	Author	Details	Committed
04f5eadcf14a	Steve Plimpton	added LAST option to dump_modify thresh, more restart info printed out to screen	Oct 11 2016
e70d530c46ed	sjplimp/GitHub	Merge pull request #203 from rbberger/txt2rst-external-link-fix	Oct 10 2016
ed8cc827137c	sjplimp/GitHub	Merge pull request #211 from akohlmey/add-respa-to-fix-flow-gauss	Oct 10 2016
27dac0246604	sjplimp/GitHub	Merge pull request #209 from akohlmey/static-double-deallocation-workaround	Oct 10 2016
467bcad0a04e	sjplimp/GitHub	Merge pull request #204 from rbberger/fix-user-omp	Oct 10 2016
144e6a809157	Axel Kohlmeyer	whitespace cleanup	Oct 10 2016
72ac0734123f	Steven Strong/Axel Kohlmeyer	edited documentation	Oct 10 2016
49c45ab03b6f	Steven Strong/Axel Kohlmeyer	edited documentation	Oct 10 2016
c2cd43994412	Steven Strong/Axel Kohlmeyer	first draft of documentation for respa	Oct 10 2016
e96ebb29bc59	Steven Strong/Axel Kohlmeyer	adjusted default respa level to be outermost	Oct 10 2016
3ce178d43f9d	Steven Strong/Axel Kohlmeyer	now understand how respa works in lammps	Oct 10 2016
23781d6ec9a6	Steven Strong/Axel Kohlmeyer	added respa to fix_flow_gauss, not fully understood yet	Oct 10 2016
fca6d721c035	Axel Kohlmeyer	completed synchronization with non-threaded version	Oct 10 2016
dd192ca7ea15	Axel Kohlmeyer	whitespace cleanup	Oct 10 2016
683689c80807	Axel Kohlmeyer	revert to previous style conventions for size_t constants	Oct 8 2016
e01e90eb965c	Axel Kohlmeyer	workaround for double free issue when using USER-COLVARS with lammps code…	Oct 8 2016
615a2da044a3	Richard Berger	Migrate changes from GRANULAR to USER-OMP	Oct 7 2016
7f3a7c5cbe5e	Richard Berger	Fix broken link	Oct 7 2016
e78b4267b7c2	Richard Berger	Fix issue with external links containing anchors	Oct 7 2016

Changes (152)
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				Path
	V			bench/{log.15Feb16.chain.fixed.icc.1 → log.6Oct16.chain.fixed.icc.1}
	V			bench/{log.15Feb16.chain.fixed.icc.4 → log.6Oct16.chain.fixed.icc.4}
	V			bench/{log.15Feb16.chain.scaled.icc.4 → log.6Oct16.chain.scaled.icc.4}
	V			bench/{log.15Feb16.chute.fixed.icc.1 → log.6Oct16.chute.fixed.icc.1}
	V			bench/{log.15Feb16.chute.fixed.icc.4 → log.6Oct16.chute.fixed.icc.4}
	V			bench/{log.15Feb16.chute.scaled.icc.4 → log.6Oct16.chute.scaled.icc.4}
	V			bench/{log.15Feb16.eam.fixed.icc.1 → log.6Oct16.eam.fixed.icc.1}
	V			bench/{log.15Feb16.eam.fixed.icc.4 → log.6Oct16.eam.fixed.icc.4}
	V			bench/{log.15Feb16.eam.scaled.icc.4 → log.6Oct16.eam.scaled.icc.4}
	V			bench/{log.15Feb16.lj.fixed.icc.1 → log.6Oct16.lj.fixed.icc.1}
	V			bench/{log.15Feb16.lj.fixed.icc.4 → log.6Oct16.lj.fixed.icc.4}
	V			bench/{log.15Feb16.lj.scaled.icc.4 → log.6Oct16.lj.scaled.icc.4}
	V			bench/{log.15Feb16.rhodo.fixed.icc.1 → log.6Oct16.rhodo.fixed.icc.1}
	V			bench/{log.15Feb16.rhodo.fixed.icc.4 → log.6Oct16.rhodo.fixed.icc.4}
	V			bench/{log.15Feb16.rhodo.scaled.icc.4 → log.6Oct16.rhodo.scaled.icc.4}
	V			bench/{log.6Oct16.chain.fixed.icc.1 ← log.15Feb16.chain.fixed.icc.1}
	V			bench/{log.6Oct16.chain.fixed.icc.4 ← log.15Feb16.chain.fixed.icc.4}
	V			bench/{log.6Oct16.chain.scaled.icc.4 ← log.15Feb16.chain.scaled.icc.4}
	V			bench/{log.6Oct16.chute.fixed.icc.1 ← log.15Feb16.chute.fixed.icc.1}
	V			bench/{log.6Oct16.chute.fixed.icc.4 ← log.15Feb16.chute.fixed.icc.4}
	V			bench/{log.6Oct16.chute.scaled.icc.4 ← log.15Feb16.chute.scaled.icc.4}
	V			bench/{log.6Oct16.eam.fixed.icc.1 ← log.15Feb16.eam.fixed.icc.1}
	V			bench/{log.6Oct16.eam.fixed.icc.4 ← log.15Feb16.eam.fixed.icc.4}
	V			bench/{log.6Oct16.eam.scaled.icc.4 ← log.15Feb16.eam.scaled.icc.4}
	V			bench/{log.6Oct16.lj.fixed.icc.1 ← log.15Feb16.lj.fixed.icc.1}
	V			bench/{log.6Oct16.lj.fixed.icc.4 ← log.15Feb16.lj.fixed.icc.4}
	V			bench/{log.6Oct16.lj.scaled.icc.4 ← log.15Feb16.lj.scaled.icc.4}
	V			bench/{log.6Oct16.rhodo.fixed.icc.1 ← log.15Feb16.rhodo.fixed.icc.1}
	V			bench/{log.6Oct16.rhodo.fixed.icc.4 ← log.15Feb16.rhodo.fixed.icc.4}
	V			bench/{log.6Oct16.rhodo.scaled.icc.4 ← log.15Feb16.rhodo.scaled.icc.4}
	M			doc/src/Manual.txt
	M			doc/src/dump_modify.txt
	M			doc/src/fix_flow_gauss.txt
	M			doc/src/fix_wall_gran_region.txt
	M			doc/src/read_restart.txt
	M			doc/utils/converters/lammpsdoc/txt2rst.py
	M			doc/utils/converters/tests/test_txt2rst.py
	V			examples/ASPHERE/box/{log.1Feb14.box.g++.8 ← log.box.1Feb14}
	V			examples/ASPHERE/box/{log.1Feb14.box.mp.g++.8 ← log.box.mp.1Feb14}
	V			examples/ASPHERE/box/{log.box.1Feb14 → log.1Feb14.box.g++.8}
	V			examples/ASPHERE/box/{log.box.mp.1Feb14 → log.1Feb14.box.mp.g++.8}
	V			examples/ASPHERE/dimer/{log.1Feb14.dimer.g++.8 ← log.dimer.1Feb14}
	V			examples/ASPHERE/dimer/{log.1Feb14.dimer.mp.g++.8 ← log.dimer.mp.1Feb14}
	V			examples/ASPHERE/dimer/{log.dimer.1Feb14 → log.1Feb14.dimer.g++.8}
	V			examples/ASPHERE/dimer/{log.dimer.mp.1Feb14 → log.1Feb14.dimer.mp.g++.8}
	V			examples/ASPHERE/ellipsoid/{log.1Feb14.ellipsoid.g++.8 ← log.ellipsoid.1Feb14}
	V			examples/ASPHERE/ellipsoid/{log.1Feb14.ellipsoid.mp.g++.8 ← log.ellipsoid.mp.1Feb14}
	V			examples/ASPHERE/ellipsoid/{log.ellipsoid.1Feb14 → log.1Feb14.ellipsoid.g++.8}
	V			examples/ASPHERE/ellipsoid/{log.ellipsoid.mp.1Feb14 → log.1Feb14.ellipsoid.mp.g++.8}
	V			examples/ASPHERE/line/{log.1Feb14.line.g++.8 ← log.line.1Feb14}
	V			examples/ASPHERE/line/{log.1Feb14.line.srd.g++.8 ← log.line.srd.1Feb14}
	V			examples/ASPHERE/line/{log.line.1Feb14 → log.1Feb14.line.g++.8}
	V			examples/ASPHERE/line/{log.line.srd.1Feb14 → log.1Feb14.line.srd.g++.8}
	V			examples/ASPHERE/poly/{log.1Feb14.poly.g++.8 ← log.poly.1Feb14}
	V			examples/ASPHERE/poly/{log.1Feb14.poly.mp.g++.8 ← log.poly.mp.1Feb14}
	V			examples/ASPHERE/poly/{log.poly.1Feb14 → log.1Feb14.poly.g++.8}
	V			examples/ASPHERE/poly/{log.poly.mp.1Feb14 → log.1Feb14.poly.mp.g++.8}
	V			examples/ASPHERE/star/{log.1Feb14.star.g++.8 ← log.star.1Feb14}
	V			examples/ASPHERE/star/{log.1Feb14.star.mp.g++.8 ← log.star.mp.1Feb14}
	V			examples/ASPHERE/star/{log.star.1Feb14 → log.1Feb14.star.g++.8}
	V			examples/ASPHERE/star/{log.star.mp.1Feb14 → log.1Feb14.star.mp.g++.8}
	V			examples/ASPHERE/tri/{log.1Feb14.tri.srd.g++.8 ← log.tri.srd.1Feb14}
	V			examples/ASPHERE/tri/{log.tri.srd.1Feb14 → log.1Feb14.tri.srd.g++.8}
	V			examples/DIFFUSE/{log.1Feb14.msd.2d.g++.8 ← log.msd.2d.1Feb14}
	V			examples/DIFFUSE/{log.1Feb14.vacf.2d.g++.8 ← log.vacf.2d.1Feb14}
	V			examples/DIFFUSE/{log.msd.2d.1Feb14 → log.1Feb14.msd.2d.g++.8}
	V			examples/DIFFUSE/{log.vacf.2d.1Feb14 → log.1Feb14.vacf.2d.g++.8}
	V			examples/HEAT/{in.lj.ehex ← in.lj_ehex}
	V			examples/HEAT/{in.lj.hex ← in.lj_hex}
	V			examples/HEAT/{in.lj_ehex → in.lj.ehex}
	V			examples/HEAT/{in.lj_hex → in.lj.hex}
	V			examples/HEAT/{in.spce.ehex ← in.spce_ehex}
	V			examples/HEAT/{in.spce.hex ← in.spce_hex}
	V			examples/HEAT/{in.spce_ehex → in.spce.ehex}
	V			examples/HEAT/{in.spce_hex → in.spce.hex}
	V			examples/HEAT/{log.10May16.lj.ehex.g++.32 ← log.lj_ehex}
	V			examples/HEAT/{log.10May16.lj.hex.g++.32 ← log.lj_hex}
	V			examples/HEAT/{log.10May16.spce.ehex.g++.32 ← log.spce_ehex}
	V			examples/HEAT/{log.10May16.spce.hex.g++.32 ← log.spce_hex}
	V			examples/HEAT/{log.lj_ehex → log.10May16.lj.ehex.g++.32}
	V			examples/HEAT/{log.lj_hex → log.10May16.lj.hex.g++.32}
	V			examples/HEAT/{log.spce_ehex → log.10May16.spce.ehex.g++.32}
	V			examples/HEAT/{log.spce_hex → log.10May16.spce.hex.g++.32}
	V			examples/HEAT/{out.10May16.Elj.ehex.g++.32 ← out.Elj_ehex}
	V			examples/HEAT/{out.10May16.Elj.hex.g++.32 ← out.Elj_hex}
	V			examples/HEAT/{out.10May16.Espce.ehex.g++.32 ← out.Espce_ehex}
	V			examples/HEAT/{out.10May16.Espce.hex.g++.32 ← out.Espce_hex}
	V			examples/HEAT/{out.10May16.Tlj.ehex.g++.32 ← out.Tlj_ehex}
	V			examples/HEAT/{out.10May16.Tlj.hex.g++.32 ← out.Tlj_hex}
	V			examples/HEAT/{out.10May16.Tspce.ehex.g++.32 ← out.Tspce_ehex}
	V			examples/HEAT/{out.10May16.Tspce.hex.g++.32 ← out.Tspce_hex}
	V			examples/HEAT/{out.Elj_ehex → out.10May16.Elj.ehex.g++.32}
	V			examples/HEAT/{out.Elj_hex → out.10May16.Elj.hex.g++.32}
	V			examples/HEAT/{out.Espce_ehex → out.10May16.Espce.ehex.g++.32}
	V			examples/HEAT/{out.Espce_hex → out.10May16.Espce.hex.g++.32}
	V			examples/HEAT/{out.Tlj_ehex → out.10May16.Tlj.ehex.g++.32}
	V			examples/HEAT/{out.Tlj_hex → out.10May16.Tlj.hex.g++.32}
	V			examples/HEAT/{out.Tspce_ehex → out.10May16.Tspce.ehex.g++.32}
	V			examples/HEAT/{out.Tspce_hex → out.10May16.Tspce.hex.g++.32}
	V			examples/KAPPA/{log.1Feb14.heatflux.g++.8 ← log.heatflux.1Feb14}
	V			examples/KAPPA/{log.1Feb14.langevin.g++.8 ← log.langevin.1Feb14}
	V			examples/KAPPA/{log.1Feb14.mp.g++.8 ← log.mp.1Feb14}
	V			examples/KAPPA/{log.7Jun16.ehex.g++.8 ← log.ehex.7Jun16}
	V			examples/KAPPA/{log.7Jun16.heat.g++.8 ← log.heat.7Jun16}
	V			examples/KAPPA/{log.ehex.7Jun16 → log.7Jun16.ehex.g++.8}
	V			examples/KAPPA/{log.heat.7Jun16 → log.7Jun16.heat.g++.8}
	V			examples/KAPPA/{log.heatflux.1Feb14 → log.1Feb14.heatflux.g++.8}
	V			examples/KAPPA/{log.langevin.1Feb14 → log.1Feb14.langevin.g++.8}
	V			examples/KAPPA/{log.mp.1Feb14 → log.1Feb14.mp.g++.8}
	V			examples/KAPPA/{profile.1Feb14.heatflux.g++.8 ← profile.heatflux.1Feb14}
	V			examples/KAPPA/{profile.1Feb14.langevin.g++.8 ← profile.langevin.1Feb14}
	V			examples/KAPPA/{profile.1Feb14.mp.g++.8 ← profile.mp.1Feb14}
	V			examples/KAPPA/{profile.7Jun16.ehex.g++.8 ← profile.ehex.7Jun16}
	V			examples/KAPPA/{profile.7Jun16.heat.g++.8 ← profile.heat.7Jun16}
	V			examples/KAPPA/{profile.ehex.7Jun16 → profile.7Jun16.ehex.g++.8}
	V			examples/KAPPA/{profile.heat.7Jun16 → profile.7Jun16.heat.g++.8}
	V			examples/KAPPA/{profile.heatflux.1Feb14 → profile.1Feb14.heatflux.g++.8}
	V			examples/KAPPA/{profile.langevin.1Feb14 → profile.1Feb14.langevin.g++.8}
	V			examples/KAPPA/{profile.mp.1Feb14 → profile.1Feb14.mp.g++.8}
	V			examples/MC/{log.6Jun14.mc.g++.1 ← log.mc.6Jun14}
	V			examples/MC/{log.mc.6Jun14 → log.6Jun14.mc.g++.1}
	V			examples/VISCOSITY/{log.1Feb14.gk.2d.g++.1 ← log.gk.2d.1Feb14}
	V			examples/VISCOSITY/{log.1Feb14.mp.2d.g++.1 ← log.mp.2d.1Feb14}
	V			examples/VISCOSITY/{log.1Feb14.nemd.2d.g++.1 ← log.nemd.2d.1Feb14}
	V			examples/VISCOSITY/{log.1Feb14.wall.2d.g++.1 ← log.wall.2d.1Feb14}
	V			examples/VISCOSITY/{log.gk.2d.1Feb14 → log.1Feb14.gk.2d.g++.1}
	V			examples/VISCOSITY/{log.mp.2d.1Feb14 → log.1Feb14.mp.2d.g++.1}
	V			examples/VISCOSITY/{log.nemd.2d.1Feb14 → log.1Feb14.nemd.2d.g++.1}
	V			examples/VISCOSITY/{log.wall.2d.1Feb14 → log.1Feb14.wall.2d.g++.1}
	V			examples/VISCOSITY/{profile.1Feb14.gk.2d.g++.1 ← profile.gk.2d.1Feb14}
	V			examples/VISCOSITY/{profile.1Feb14.mp.2d.g++.1 ← profile.mp.2d.1Feb14}
	V			examples/VISCOSITY/{profile.1Feb14.nemd.2d.g++.1 ← profile.nemd.2d.1Feb14}
	V			examples/VISCOSITY/{profile.1Feb14.wall.2d.g++.1 ← profile.wall.2d.1Feb14}
	V			examples/VISCOSITY/{profile.gk.2d.1Feb14 → profile.1Feb14.gk.2d.g++.1}
	V			examples/VISCOSITY/{profile.mp.2d.1Feb14 → profile.1Feb14.mp.2d.g++.1}
	V			examples/VISCOSITY/{profile.nemd.2d.1Feb14 → profile.1Feb14.nemd.2d.g++.1}
	V			examples/VISCOSITY/{profile.wall.2d.1Feb14 → profile.1Feb14.wall.2d.g++.1}
	M			lib/colvars/colvarmodule.cpp
	M			lib/colvars/colvarmodule.h
	M			src/GRANULAR/fix_wall_gran.cpp
	M			src/USER-COLVARS/colvarproxy_lammps.cpp
	M			src/USER-MISC/fix_flow_gauss.cpp
	M			src/USER-MISC/fix_flow_gauss.h
	M			src/USER-OMP/fix_wall_gran_omp.cpp
	M			src/dump_custom.cpp
	M			src/dump_custom.h
	M			src/fix_store.cpp
	M			src/modify.cpp
	M			src/modify.h
	M			src/region.h
	M			src/version.h
	M			src/write_dump.cpp