Merge pull request #703 from akohlmey/custom-rigid-body-generation (aaf5e87c) · Commits · 郑智淋 / lammps

doc/src/fix_rigid.txt

+28 −6

Original line number	Diff line number	Diff line
		@@ -26,6 +26,9 @@ style = {rigid} or {rigid/nve} or {rigid/nvt} or {rigid/npt} or {rigid/nph} or {
		bodystyle = {single} or {molecule} or {group} :l
		{single} args = none
		{molecule} args = none
		{custom} args = {i_propname} or {v_varname}
		i_propname = an integer property defined via fix property/atom
		v_varname = an atom-style or atomfile-style variable
		{group} args = N groupID1 groupID2 ...
		N = # of groups
		groupID1, groupID2, ... = list of N group IDs :pre
		@@ -81,6 +84,16 @@ fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0
		fix 1 water rigid/nph molecule iso 0.5 0.5 1.0
		fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0 :pre

		variable bodyid atom 1.0gmask(clump1)+2.0gmask(clump2)+3.0*gmask(clump3)
		fix 1 clump rigid custom v_bodyid :pre

		variable bodyid atomfile bodies.txt
		fix 1 clump rigid custom v_bodyid :pre

		fix 0 all property/atom i_bodyid
		read_restart data.rigid fix 0 NULL Bodies
		fix 1 clump rigid/small custom i_bodyid :pre

		[Description:]

		Treat one or more sets of atoms as independent rigid bodies. This
		@@ -100,7 +113,7 @@ of a biomolecule such as a protein.

		Example of small rigid bodies are patchy nanoparticles, such as those
		modeled in "this paper"_#Zhang1 by Sharon Glotzer's group, clumps of
		granular particles, lipid molecules consiting of one or more point
		granular particles, lipid molecules consisting of one or more point
		dipoles connected to other spheroids or ellipsoids, irregular
		particles built from line segments (2d) or triangles (3d), and
		coarse-grain models of nano or colloidal particles consisting of a
		@@ -203,11 +216,11 @@ most one rigid body. Which atoms are in which bodies can be defined
		via several options.

		NOTE: With the {rigid/small} styles, which require that {bodystyle} be
		specified as {molecule}, you can define a system that has no rigid
		bodies initially. This is useful when you are using the {mol} keyword
		in conjunction with another fix that is adding rigid bodies on-the-fly
		as molecules, such as "fix deposit"_fix_deposit.html or "fix
		pour"_fix_pour.html.
		specified as {molecule} or {custom}, you can define a system that has
		no rigid bodies initially. This is useful when you are using the {mol}
		keyword in conjunction with another fix that is adding rigid bodies
		on-the-fly as molecules, such as "fix deposit"_fix_deposit.html or
		"fix pour"_fix_pour.html.

		For bodystyle {single} the entire fix group of atoms is treated as one
		rigid body. This option is only allowed for the {rigid} styles.
		@@ -222,6 +235,15 @@ molecule ID = 0) surrounding rigid bodies, this may not be what you
		want. Thus you should be careful to use a fix group that only
		includes atoms you want to be part of rigid bodies.

		Bodystyle {custom} is similar to bodystyle {molecule}, however some
		custom properties are used to group atoms into rigid bodies. The
		special case for molecule/body ID = 0 is not available. Possible
		custom properties are an integer property associated with atoms through
		"fix property/atom"_fix_property_atom.html or an atom style variable
		or an atomfile style variable. For the latter two, the variable value
		will be rounded to an integer and then rigid bodies defined from
		those values.

		For bodystyle {group}, each of the listed groups is treated as a
		separate rigid body. Only atoms that are also in the fix group are
		included in each rigid body. This option is only allowed for the

examples/rigid/bodies.txt

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		2 1
		3 1
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		9 1
		10 2
		11 2
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		81 9

examples/rigid/data.rigid-property

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Original line number	Diff line number	Diff line
		# LAMMPS data file for rigid bodies

		81 atoms
		1 atom types

		-12 12 xlo xhi
		-12 12 ylo yhi
		-12 12 zlo zhi

		Masses

		1 1

		Pair Coeffs

		1 1 1

		Atoms

		1 1 0 0 0
		2 1 0 1 0
		3 1 0 0.5 0
		4 1 0.5 0 0
		5 1 0.5 0.5 1
		6 1 1 0.5 0
		7 1 0.5 1 0
		8 1 1 0 0
		9 1 1 1 0
		10 1 2 1 0
		11 1 1 2 0
		12 1 1.5 2 0
		13 1 1.5 1 0
		14 1 1 1.5 0
		15 1 1.5 1.5 1
		16 1 2 1.5 0
		17 1 2 2 0
		18 1 2 3 0
		19 1 2 2.5 0
		20 1 2.5 2 0
		21 1 2.5 2.5 1
		22 1 3 2.5 0
		23 1 2.5 3 0
		24 1 3 2 0
		25 1 3 3 0
		26 1 4 3 0
		27 1 3 4 0
		28 1 3.5 4 0
		29 1 3.5 3 0
		30 1 3 3.5 0
		31 1 3.5 3.5 1
		32 1 4 3.5 0
		33 1 4 4 0
		34 1 4 5 0
		35 1 4 4.5 0
		36 1 4.5 4 0
		37 1 4.5 4.5 1
		38 1 5 4.5 0
		39 1 4.5 5 0
		40 1 5 4 0
		41 1 5 5 0
		42 1 6 5 0
		43 1 5 6 0
		44 1 5.5 6 0
		45 1 5.5 5 0
		46 1 5 5.5 0
		47 1 5.5 5.5 1
		48 1 6 5.5 0
		49 1 6 6 0
		50 1 6 7 0
		51 1 6 6.5 0
		52 1 6.5 6 0
		53 1 6.5 6.5 1
		54 1 7 6.5 0
		55 1 6.5 7 0
		56 1 7 6 0
		57 1 7 7 0
		58 1 8 7 0
		59 1 7 8 0
		60 1 7.5 8 0
		61 1 7.5 7 0
		62 1 7 7.5 0
		63 1 7.5 7.5 1
		64 1 8 7.5 0
		65 1 8 8 0
		66 1 8 9 0
		67 1 8 8.5 0
		68 1 8.5 8 0
		69 1 8.5 8.5 1
		70 1 9 8.5 0
		71 1 8.5 9 0
		72 1 9 8 0
		73 1 9 9 0
		74 1 10 9 0
		75 1 9 10 0
		76 1 9.5 10 0
		77 1 9.5 9 0
		78 1 9 9.5 0
		79 1 9.5 9.5 1
		80 1 10 9.5 0
		81 1 10 10 0

		Bodies

		1 1
		2 1
		3 1
		4 1
		5 1
		6 1
		7 1
		8 1
		9 1
		10 2
		11 2
		12 2
		13 2
		14 2
		15 2
		16 2
		17 2
		18 2
		19 3
		20 3
		21 3
		22 3
		23 3
		24 3
		25 3
		26 3
		27 3
		28 4
		29 4
		30 4
		31 4
		32 4
		33 4
		34 4
		35 4
		36 4
		37 5
		38 5
		39 5
		40 5
		41 5
		42 5
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		45 5
		46 6
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		50 6
		51 6
		52 6
		53 6
		54 6
		55 7
		56 7
		57 7
		58 7
		59 7
		60 7
		61 7
		62 7
		63 7
		64 8
		65 8
		66 8
		67 8
		68 8
		69 8
		70 8
		71 8
		72 8
		73 9
		74 9
		75 9
		76 9
		77 9
		78 9
		79 9
		80 9
		81 9

examples/rigid/in.rigid-atomfile

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Original line number	Diff line number	Diff line
		# Simple rigid body system

		units lj
		atom_style atomic
		atom_modify map array

		pair_style lj/cut 2.5

		read_data data.rigid

		velocity all create 100.0 4928459


		# unconnected bodies

		group clump1 id <> 1 9
		group clump2 id <> 10 18
		group clump3 id <> 19 27
		group clump4 id <> 28 36
		group clump5 id <> 37 45
		group clump6 id <> 46 54
		group clump7 id <> 55 63
		group clump8 id <> 64 72
		group clump9 id <> 73 81

		variable bodies atomfile bodies.txt
		fix 1 all rigid custom v_bodies

		# 1 chain of connected bodies

		#group clump1 id <> 1 9
		#group clump2 id <> 9 18
		#group clump3 id <> 18 27
		#group clump4 id <> 27 36
		#group clump5 id <> 36 45
		#group clump6 id <> 45 54
		#group clump7 id <> 54 63
		#group clump8 id <> 63 72
		#group clump9 id <> 72 81

		#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
		# clump6 clump7 clump8 clump9

		# 2 chains of connected bodies

		#group clump1 id <> 1 9
		#group clump2 id <> 9 18
		#group clump3 id <> 18 27
		#group clump4 id <> 27 36
		#group clump5 id <> 37 45
		#group clump6 id <> 45 54
		#group clump7 id <> 54 63
		#group clump8 id <> 63 72
		#group clump9 id <> 72 81

		#fix 1 all poems group clump1 clump2 clump3 clump4
		#fix 2 all poems group clump5 clump6 clump7 clump8 clump9

		neigh_modify exclude group clump1 clump1
		neigh_modify exclude group clump2 clump2
		neigh_modify exclude group clump3 clump3
		neigh_modify exclude group clump4 clump4
		neigh_modify exclude group clump5 clump5
		neigh_modify exclude group clump6 clump6
		neigh_modify exclude group clump7 clump7
		neigh_modify exclude group clump8 clump8
		neigh_modify exclude group clump9 clump9

		thermo 100

		#dump 1 all atom 50 dump.rigid

		#dump 2 all image 100 image.*.jpg type type &
		# axes yes 0.8 0.02 view 60 -30
		#dump_modify 2 pad 5

		#dump 3 all movie 100 movie.mpg type type &
		# axes yes 0.8 0.02 view 60 -30
		#dump_modify 3 pad 5

		timestep 0.0001
		thermo 50
		run 10000

examples/rigid/in.rigid-atomvar

0 → 100644

+83 −0

Original line number	Diff line number	Diff line
		# Simple rigid body system

		units lj
		atom_style atomic
		atom_modify map array

		pair_style lj/cut 2.5

		read_data data.rigid

		velocity all create 100.0 4928459


		# unconnected bodies

		group clump1 id <> 1 9
		group clump2 id <> 10 18
		group clump3 id <> 19 27
		group clump4 id <> 28 36
		group clump5 id <> 37 45
		group clump6 id <> 46 54
		group clump7 id <> 55 63
		group clump8 id <> 64 72
		group clump9 id <> 73 81

		variable bodies atom 1.0gmask(clump1)+2.0gmask(clump2)+3.0gmask(clump3)+4.0gmask(clump4)+5.0gmask(clump5)+6.0gmask(clump6)+7.0gmask(clump7)+8.0gmask(clump8)+9.0*gmask(clump9)
		fix 1 all rigid custom v_bodies

		# 1 chain of connected bodies

		#group clump1 id <> 1 9
		#group clump2 id <> 9 18
		#group clump3 id <> 18 27
		#group clump4 id <> 27 36
		#group clump5 id <> 36 45
		#group clump6 id <> 45 54
		#group clump7 id <> 54 63
		#group clump8 id <> 63 72
		#group clump9 id <> 72 81

		#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
		# clump6 clump7 clump8 clump9

		# 2 chains of connected bodies

		#group clump1 id <> 1 9
		#group clump2 id <> 9 18
		#group clump3 id <> 18 27
		#group clump4 id <> 27 36
		#group clump5 id <> 37 45
		#group clump6 id <> 45 54
		#group clump7 id <> 54 63
		#group clump8 id <> 63 72
		#group clump9 id <> 72 81

		#fix 1 all poems group clump1 clump2 clump3 clump4
		#fix 2 all poems group clump5 clump6 clump7 clump8 clump9

		neigh_modify exclude group clump1 clump1
		neigh_modify exclude group clump2 clump2
		neigh_modify exclude group clump3 clump3
		neigh_modify exclude group clump4 clump4
		neigh_modify exclude group clump5 clump5
		neigh_modify exclude group clump6 clump6
		neigh_modify exclude group clump7 clump7
		neigh_modify exclude group clump8 clump8
		neigh_modify exclude group clump9 clump9

		thermo 100

		#dump 1 all atom 50 dump.rigid

		#dump 2 all image 100 image.*.jpg type type &
		# axes yes 0.8 0.02 view 60 -30
		#dump_modify 2 pad 5

		#dump 3 all movie 100 movie.mpg type type &
		# axes yes 0.8 0.02 view 60 -30
		#dump_modify 3 pad 5

		timestep 0.0001
		thermo 50
		run 10000

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