Diffusion lammps d8bf149edc56

Version 28 Sep 2016
d8bf149edc56
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Sep 29 2016, 16:55.

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Version 28 Sep 2016

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Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Sep 29 2016, 16:55

Pushed

junge

Oct 19 2017, 09:53

Parents

rLAMMPS473b12ded42a: Version 26 Sep 2016
rLAMMPS829d11e88b9b: Merge pull request #44 from rbberger/doc-fixes

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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPSd8bf149edc56: Version 28 Sep 2016 (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Sep 29 2016, 16:55

Merged Changes

This commit merges a very large number of changes. Only the first 50 are shown.

Commit	Author	Details	Committed
829d11e88b9b	sjplimp/GitHub	Merge pull request #44 from rbberger/doc-fixes	Sep 27 2016
96f31d6dade5	sjplimp/GitHub	Merge pull request #43 from akohlmey/doc-fixes	Sep 27 2016
35705217f4bb	Steve Plimpton	enable multi-processor NEB replicas	Sep 27 2016
9a2f7386731e	Steve Plimpton	sync with SVN	Sep 27 2016
a3a3af691c07	Steve Plimpton	Merge branch 'balance' into integration	Sep 27 2016
f9677e6d7b71	Steve Plimpton	released version of weighted balancing	Sep 27 2016
a3277117e250	Richard Berger	Add filter which merges preformatted sections	Sep 27 2016
67d4c07689a3	Richard Berger	Do not escape underscore inside preformat blocks	Sep 27 2016
877a5049332e	Richard Berger	Fix typo in Section_howto.txt	Sep 27 2016
8a951f9d7983	Axel Kohlmeyer	fix typo	Sep 27 2016
69a8842ecb81	Axel Kohlmeyer	update load balance weights documentation for fix balance and balance	Sep 27 2016
2af5c75f4269	Axel Kohlmeyer	correct issue from merge	Sep 27 2016
158599fca211	Axel Kohlmeyer	Merge branch 'balance2' into weighted-balancing	Sep 27 2016
7732548b3c0f	Axel Kohlmeyer	correct issues related to the addition of fix cmap	Sep 27 2016
2c5f6e1a993b	Axel Kohlmeyer	fix a broken link that slipped through the cracks in the previous cleanup	Sep 27 2016
d0aa13b5431c	Richard Berger	Fix broken link in Section_packages.txt	Sep 26 2016
c31b026797cf	Axel Kohlmeyer	Merge branch 'integration' into weighted-balancing	Sep 26 2016
47b52ed2ddf4	Axel Kohlmeyer	Merge branch 'integration' into balance2	Sep 26 2016
c87f9aeb9f4e	Richard Berger	Merge remote-tracking branch 'akohlmey/integration' into ipython-update-and…	Sep 26 2016
08f0bf90253e	Steve Plimpton	new verion of balance weighting	Sep 23 2016
d3406df6a0ca	Richard Berger	Updated instructions in IPython notebooks	Sep 21 2016
a4c8c9b1f973	Richard Berger	Strip IPython notebooks of output	Sep 21 2016
f1183cb97c19	Richard Berger	Remove old copies of IPython notebooks	Sep 21 2016
40b68820d968	Axel Kohlmeyer	update html docs to be used with latest version of converter tools	Sep 14 2016
90e22a79097d	Axel Kohlmeyer	Merge branch 'integration' into weighted-balancing	Sep 14 2016
0f7873c0b8d2	Axel Kohlmeyer	Merge branch 'integration' into weighted-balancing	Sep 1 2016
eac721772089	Axel Kohlmeyer	Merge remote-tracking branch 'lammps-rw/integration' into weighted-balancing	Aug 31 2016
93401a83c6e0	Axel Kohlmeyer	reintroduce pointer nullification for fix balance	Aug 31 2016
82859c4e2573	Axel Kohlmeyer	Merge branch 'integration' into weighted-balancing	Aug 31 2016
10edfa297bbc	Axel Kohlmeyer	Merge branch 'integration' into weighted-balancing	Aug 31 2016
74b1caf2e651	Axel Kohlmeyer	undo changes that belong to a different branch or are redundant	Aug 22 2016
243137d5526c	Axel Kohlmeyer	undo obsoleted changes to group command by iain bethune	Aug 22 2016
40fd97bd4c92	Axel Kohlmeyer	silence warnings about cases, that cannot happen	Aug 22 2016
8492212c4bd5	Axel Kohlmeyer	fix bug found by coverity scan	Aug 22 2016
1976314f4041	Axel Kohlmeyer	improve the weight assignment algorithm for compute time based balancing	Aug 22 2016
17c1d3a9413c	Iain Bethune/Axel Kohlmeyer	Fix typo	Aug 22 2016
fec59ee3b97a	Axel Kohlmeyer	update documentation for refactored load-balancing	Aug 22 2016
33a98d79fe6a	Axel Kohlmeyer	remove upper limit for weigh factor on neighbor list and time weights	Aug 22 2016
0902b600fb1b	Axel Kohlmeyer	add new imbalance module store, which allows to store weights in an atom…	Aug 22 2016
7f20afe122a5	Axel Kohlmeyer	convert from using fix property/atom to using fix store	Aug 22 2016
7e0dc7a74df1	Axel Kohlmeyer	whitespace cleanup	Aug 22 2016
b954283ec221	Axel Kohlmeyer	properly handle the case of neighbor lists never been computed before	Aug 22 2016
ecc136b6dc67	Axel Kohlmeyer	plug small memory leak	Aug 22 2016
4a536d71ebf8	Axel Kohlmeyer	simplify and correct logic to pass weight to balancer algorithms	Aug 22 2016
460bc1482235	Axel Kohlmeyer	correct string hanlding with building custom property label	Aug 22 2016
bb40f63a34b8	Axel Kohlmeyer	we cannot add a fix while creating a fix. move fix addintion to Fix::init()	Aug 22 2016
c6699e19e6a6	Axel Kohlmeyer	rewrote balancing to use per-atom data stored via fix property/atom	Aug 22 2016
257489116064	Axel Kohlmeyer	fix optional argument scanning bug	Aug 22 2016
332d6821ca43	Axel Kohlmeyer	remove unused class member	Aug 22 2016
b20108bddb03	Axel Kohlmeyer	incorporate refactored weighting into fix balance	Aug 22 2016

Changes (87)

				Path
	M			doc/README
	M			doc/src/Manual.txt
	M			doc/src/Section_howto.txt
	M			doc/src/Section_packages.txt
	M			doc/src/balance.txt
	M			doc/src/fix_balance.txt
	M			doc/src/fix_cmap.txt
	M			doc/src/fixes.txt
	M			doc/src/lammps.book
	M			doc/src/neb.txt
	M			doc/src/prd.txt
	M			doc/utils/converters/lammpsdoc/lammps_filters.py
	M			doc/utils/converters/lammpsdoc/txt2rst.py
	M			doc/utils/converters/tests/test_txt2rst.py
	A			examples/balance/in.balance.clock.dynamic
	A			examples/balance/in.balance.clock.static
	A			examples/balance/in.balance.group.dynamic
	A			examples/balance/in.balance.group.static
	A			examples/balance/in.balance.kspace
	A			examples/balance/in.balance.neigh.dynamic
	A			examples/balance/in.balance.neigh.rcb
	A			examples/balance/in.balance.neigh.static
	A			examples/balance/in.balance.var.dynamic
	D			examples/balance/log.15Feb16.balance.bond.fast.g++.1
	D			examples/balance/log.15Feb16.balance.bond.fast.g++.4
	D			examples/balance/log.15Feb16.balance.bond.slow.g++.1
	V			examples/balance/{log.15Feb16.balance.bond.slow.g++.4 → log.27Sep16.balance.bond.slow.g++.4}
	D			examples/balance/log.15Feb16.balance.g++.1
	D			examples/balance/log.15Feb16.balance.g++.4
	A			examples/balance/log.27Sep16.balance.bond.fast.g++.4
	V			examples/balance/{log.27Sep16.balance.bond.slow.g++.4 ← log.15Feb16.balance.bond.slow.g++.4}
	A			examples/balance/log.27Sep16.balance.clock.dynamic.g++.4
	A			examples/balance/log.27Sep16.balance.clock.static.g++.4
	A			examples/balance/log.27Sep16.balance.g++.4
	A			examples/balance/log.27Sep16.balance.group.dynamic.g++.4
	A			examples/balance/log.27Sep16.balance.group.static.g++.4
	A			examples/balance/log.27Sep16.balance.kspace.g++.4
	A			examples/balance/log.27Sep16.balance.neigh.dynamic.g++.4
	A			examples/balance/log.27Sep16.balance.neigh.rcb.g++.4
	A			examples/balance/log.27Sep16.balance.neigh.static.g++.4
	A			examples/balance/log.27Sep16.balance.var.dynamic.g++.2
	M			examples/neb/README
	M			examples/neb/in.neb.hop1
	M			examples/neb/in.neb.hop2
	M			examples/neb/in.neb.sivac
	A			examples/neb/initial.hop1
	A			examples/neb/initial.hop2
	A			examples/neb/initial.sivac
	V			examples/neb/{log.15Feb16.neb.hop1.g++.4 → log.28Sep16.neb.hop1.g++.4}
	P			examples/neb/log.15Feb16.neb.hop2.g++.4 Deleted after being copied to multiple locations: examples/neb/log.28Sep16.neb.hop2.g++.4 examples/neb/log.28Sep16.neb.hop2.g++.8
	P			examples/neb/log.15Feb16.neb.sivac.g++.3 Deleted after being copied to multiple locations: examples/neb/log.28Sep16.neb.sivac.g++.3 examples/neb/log.28Sep16.neb.sivac.g++.6 examples/neb/log.28Sep16.neb.sivac.g++.9
	V			examples/neb/{log.28Sep16.neb.hop1.g++.4 ← log.15Feb16.neb.hop1.g++.4}
	A			examples/neb/log.28Sep16.neb.hop1.g++.8
	P			examples/neb/log.28Sep16.neb.hop2.g++.4 Copied from examples/neb/log.15Feb16.neb.hop2.g++.4
	V			examples/neb/{log.28Sep16.neb.hop2.g++.8 ← log.15Feb16.neb.hop2.g++.4}
	P			examples/neb/log.28Sep16.neb.sivac.g++.3 Copied from examples/neb/log.15Feb16.neb.sivac.g++.3
	P			examples/neb/log.28Sep16.neb.sivac.g++.6 Copied from examples/neb/log.15Feb16.neb.sivac.g++.3
	V			examples/neb/{log.28Sep16.neb.sivac.g++.9 ← log.15Feb16.neb.sivac.g++.3}
	M			examples/snap/Ta06A_pot.snap
	A			python/examples/ipython/.gitignore
	M			python/examples/ipython/interface_usage.ipynb
	D			python/examples/ipython/interface_usage.ipynb.orig
	M			python/examples/ipython/interface_usage_bonds.ipynb
	D			python/examples/ipython/interface_usage_bonds.ipynb.orig
	M			python/examples/ipython/simple.ipynb
	D			python/examples/ipython/simple.ipynb.orig
	M			src/REPLICA/fix_neb.cpp
	M			src/REPLICA/fix_neb.h
	M			src/REPLICA/neb.cpp
	M			src/REPLICA/prd.cpp
	M			src/balance.cpp
	M			src/balance.h
	M			src/fix_balance.cpp
	M			src/fix_balance.h
	A			src/imbalance.cpp
	A			src/imbalance.h
	A			src/imbalance_group.cpp
	A			src/imbalance_group.h
	A			src/imbalance_neigh.cpp
	A			src/imbalance_neigh.h
	A			src/imbalance_store.cpp
	A			src/imbalance_store.h
	A			src/imbalance_time.cpp
	A			src/imbalance_time.h
	A			src/imbalance_var.cpp
	A			src/imbalance_var.h
	M			src/version.h