input_commands.html
c6213f36d34clammm-devel

input_commands.html
View Options

			<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
			<HTML>
			<HEAD>
			<META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
			</HEAD>
			<BODY>
			<H2>
			LAMMPS Input Commands</H2>
			<P>
			<A HREF="README.html">Return</A> to top-level of LAMMPS documentation.</P>
			<P>
			This page contains a complete list of valid LAMMPS commands which are
			read-in from an input script. It will be easiest to understand if you
			read it while looking at sample input scripts in the examples
			directory. </P>
			<P>
			The script of input commands is read by LAMMPS, one line at a time.
			Each command causes LAMMPS to take some action. Usually it simply
			causes some internal variable(s) to be set. Or it may cause a data file
			to be read in or a simulation to be run. Note that most commands have
			default settings, which means you only need use a particular command if
			you do not want the default setting.</P>
			<P>
			Each LAMMPS input script contains exactly one "read data" (or
			"read restart") command which defines the problem to be
			simulated. All other commands can be split into three categories: (a)
			commands that (if used) must appear before the "read data"
			command because they define settings needed to correctly read-in the
			problem and allocate memory for it, (b) commands that must appear after
			the "read data" command because they act on the specified
			problem, and (c) commands that can appear either before or after the
			"read data" command. Commands in category (c) are used before
			the "read data" command if a default setting needs to be
			changed before the problem description is read-in. They can be used
			after the "read data" command if the user wishes to change a
			setting before the next "run" or "minimize" command
			is used. Other than these restrictions, commands can generally appear
			in any order in the input script, although some commands require others
			to have been previously specified.</P>
			<P>
			Each LAMMPS input script also contains one or more "run" or
			"minimize" commands. These trigger an actual dynamics or
			minimization computation to be done. Following a run, new commands from
			categories (b) and (c) can be used to change various settings, and
			additional "run" commands can then be used to continue the
			previous simulation. LAMMPS continues to read successive lines from the
			input script until the end-of-file is reached, which causes LAMMPS to
			terminate.</P>
			<P>
			This page gives examples of each command, some of which can be
			specified in multiple styles. Typically the commands take one or more
			parameters. The keyword for each command should begin in the leftmost
			column and all characters in the command and its parameters should be
			in lower-case (except the word NULL or characters in filenames).
			Parameters can be separated by arbitrary numbers of spaces and/or tabs,
			so long as the command fits on one line. The remainder of the line
			after the last parameter is ignored.</P>
			<P>
			The next section outlines the structure of a LAMMPS input script. The
			final section gives a detailed description of the commands in
			alphabetic order, each with its associated parameters and default
			settings.</P>
			<UL>
			<LI>
			<A HREF="#_cch3_951156975">Structure of a LAMMPS input script</A>
			<LI>
			<A HREF="#_cch3_931277455">Alphabetic Listing of Commands</A>
			</UL>
			<HR>
			<H3>
			<A NAME="_cch3_951156975">Structure of a LAMMPS input script</A></H3>
			<P>
			Any line starting with a # is a <A HREF="#_cch3_931276588">comment</A>.
			Comments can appear anywhere in the input script.</P>
			<P>
			(1) <A HREF="#_cch3_930960479">Initialization settings</A> (must appear
			before "read data" or "read restart")</P>
			<P>
			(2) <A HREF="#_cch3_951435622">Optional Settings</A> (can appear before
			and/or after "read data" or "read restart")</P>
			<P>
			(3) <A HREF="#_cch3_951435906">Read in a Problem</A> via a "<A
			HREF="#_cch3_931277059">read data</A>" or "<A
			HREF="#_cch3_931277070">read restart</A>" command</P>
			<P>
			(4) <A HREF="#_cch3_951435622">Optional Settings</A> (same as (2))</P>
			<P>
			(5) Problem Settings (must appear after "read data" or
			"read restart")</P>
			<UL>
			<LI>
			<A HREF="#_cch3_930960510">Velocity Creation</A>
			<LI>
			<A HREF="#_cch3_951435663">Force Field Parameters</A>
			<LI>
			<A HREF="#_cch3_930960516">Constraints</A>
			<LI>
			<A HREF="#_cch3_930960490">Ensemble Control</A>
			<LI>
			<A HREF="#_cch3_930960485">Output Control</A>
			<LI>
			<A HREF="#_cch3_951435640">Integrator Settings</A>
			<LI>
			<A HREF="#_cch3_951435646">Minimizer Settings</A>
			</UL>
			<P>
			(6) <A HREF="#_cch3_951435914">Perform a Simulation</A> via a "<A
			HREF="#_cch3_931277194">run</A>" or "<A
			HREF="#_cch3_931277212">minimize</A>" command</P>
			<P>
			Repeat (4), (5), and (6) as desired ...</P>
			<HR>
			<H3>
			<A NAME="_cch3_930960479">Initialization Settings</A></H3>
			<P>
			(if used, must appear before "read data" or "read
			restart" command)</P>
			<PRE>
			<A HREF="#_cch3_931276596">units</A> real

			<A HREF="#_cch3_951437269">extra memory</A> 2.0 1.5 2.0 2.5
			<A HREF="#_cch3_931276604">dimension</A> 3
			<A HREF="#_cch3_931276624">processor grid</A> 10 10 10
			<A HREF="#_cch3_999182956">periodicity</A> 0 0 0
			<A HREF="#_cch3_999182965">slab volume</A> 3.0
			<A HREF="#_cch3_931276632">newton flag</A> 3
			<A HREF="#_cch3_931276687">true flag</A> 0
			<A HREF="#_cch3_951437278">maximum cutoff</A> 10.0
			<A HREF="#_cch3_931276900">mixing style</A> geometric
			<A HREF="#_cch3_951437286">restart version</A> 5
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_951435622">Optional Settings</A></H3>
			<P>
			(if used, can appear before and/or after "read data" or
			"read restart" command)</P>
			<PRE>
			<A HREF="#_cch3_931276654">neighbor</A> 2.0 1 1 10 1

			<A HREF="#_cch3_931276833">nonbond style</A> none
			<A HREF="#_cch3_931276833">nonbond style</A> lj/cutoff 10.0 0
			<A HREF="#_cch3_931276833">nonbond style</A> lj/smooth 8.0 10.0
			<A HREF="#_cch3_931276833">nonbond style</A> lj/shift 10.0 0
			<A HREF="#_cch3_931276833">nonbond style</A> soft 2.5
			<A HREF="#_cch3_931276833">nonbond style</A> class2/cutoff 10.0 0
			<A HREF="#_cch3_931276833">nonbond style</A> lj/charmm 15.0 15.1

			<A HREF="#_cch3_931276910">coulomb style</A> none
			<A HREF="#_cch3_931276910">coulomb style</A> cutoff 10.0
			<A HREF="#_cch3_931276910">coulomb style</A> smooth 8.0 10.0
			<A HREF="#_cch3_931276910">coulomb style</A> ewald 10.0 1.0E-4
			<A HREF="#_cch3_931276910">coulomb style</A> pppm 10.0 1.0E-4
			<A HREF="#_cch3_931276910">coulomb style</A> charmm/switch 15.0 15.1
			<A HREF="#_cch3_931276910">coulomb style</A> debye 10.0 0.5

			<A HREF="#_cch3_931276958">bond style</A> none
			<A HREF="#_cch3_931276958">bond style</A> harmonic
			<A HREF="#_cch3_931276958">bond style</A> fene/standard
			<A HREF="#_cch3_931276958">bond style</A> fene/shift
			<A HREF="#_cch3_931276958">bond style</A> nonlinear
			<A HREF="#_cch3_931276958">bond style</A> class2

			<A HREF="#_cch3_931277007">angle style</A> none
			<A HREF="#_cch3_931277007">angle style</A> harmonic
			<A HREF="#_cch3_931277007">angle style</A> class2
			<A HREF="#_cch3_931277007">angle style</A> charmm
			<A HREF="#_cch3_931277007">angle style</A> cosine

			<A HREF="#_cch3_931277020">dihedral style</A> none
			<A HREF="#_cch3_931277020">dihedral style</A> harmonic
			<A HREF="#_cch3_931277020">dihedral style</A> mutliharmonic
			<A HREF="#_cch3_931277020">dihedral style</A> class2
			<A HREF="#_cch3_931277020">dihedral style</A> charmm

			<A HREF="#_cch3_931277042">improper style</A> none
			<A HREF="#_cch3_931277042">improper style</A> harmonic
			<A HREF="#_cch3_931277042">improper style</A> cvff
			<A HREF="#_cch3_931277042">improper style</A> class2
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_951435906">Read in a Problem</A></H3>
			<PRE>
			<A HREF="#_cch3_931277059">read data</A> data.lj
			<A HREF="#_cch3_931277070">read restart</A> restart.100000
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_930960510">Velocity Creation</A></H3>
			<P>
			(if used, must appear after "read data" or "read
			restart" command)</P>
			<PRE>
			<A HREF="#_cch3_931277080">create group</A> types 1 3
			<A HREF="#_cch3_931277080">create group</A> molecules 200 300
			<A HREF="#_cch3_931277080">create group</A> region 0.0 1.0 0.0 1.0 INF 1.0
			<A HREF="#_cch3_931277080">create group</A> remainder

			<A HREF="#_cch3_931299999">rotation zero</A> 1

			<A HREF="#_cch3_931277097">create temp</A> uniform 300.0 12345678
			<A HREF="#_cch3_931277097">create temp</A> gaussian 300.0 12345678
			<A HREF="#_cch3_931277097">create temp</A> velocity 0.0 0.0 0.0
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_951435663">Force Field Parameters</A></H3>
			<P>
			(if used, must appear after "read data" or "read
			restart" command)</P>
			<PRE>
			<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 3.45 10.0 (nonbond style lj/cutoff)
			<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 3.45 8.0 10.0 (nonbond style lj/smooth)
			<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 3.45 2.0 10.0 (nonbond style lj/shift)
			<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 30.0 2.5 (nonbond style soft)
			<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 3.45 10.0 (nonbond style class2/cutoff)
			<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 3.45 1.0 3.45 (nonbond style lj/charmm)

			<A HREF="#_cch3_931276666">special bonds</A> amber
			<A HREF="#_cch3_931276666">special bonds</A> 0.0 0.0 0.5

			<A HREF="#_cch3_931276941">pppm mesh</A> 32 32 64
			<A HREF="#_cch3_931276947">pppm order</A> 5
			<A HREF="#_cch3_931276953">dielectric</A> 1.0

			<A HREF="#_cch3_931276970">bond coeff</A> 1 100.0 3.45 (bond style harmonic)
			<A HREF="#_cch3_931276970">bond coeff</A> 1 30.0 1.5 1.0 1.0 (bond style fene/standard )
			<A HREF="#_cch3_931276970">bond coeff</A> 1 30.0 1.5 1.0 1.0 0.2 (bond style fene/shift)
			<A HREF="#_cch3_931276970">bond coeff</A> 1 28.0 0.748308 0.166667 (bond style nonlinear)
			<A HREF="#_cch3_999724447">angle coeff</A> 1 30.0 108.0 (angle style harmonic)
			<A HREF="#_cch3_999724447">angle coeff</A> 1 30.0 108.0 30.0 2.5 (angle style charmm)
			<A HREF="#_cch3_999724447">angle coeff</A> 1 30.0 (angle style cosine)
			<A HREF="#_cch3_999724456">dihedral coeff</A> 1 10.0 1 3 (dihedral style harmonic)
			<A HREF="#_cch3_999724456">dihedral coeff</A> 1 2.0 2.0 2.0 2.0 2.0 (dihedral style multiharmonic)
			<A HREF="#_cch3_999724456">dihedral coeff</A> 1 2.0 5 180.0 0.5 (dihedral style charmm)
			<A HREF="#_cch3_999724473">improper coeff</A> 1 20.0 0.0 (improper style harmonic)
			<A HREF="#_cch3_999724473">improper coeff</A> 1 20.0 10.0 (improper style cvff)
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_930960516">Constraints</A></H3>
			<P>
			(if used, must appear after "read data" or "read
			restart" command)</P>
			<PRE>
			<A HREF="#_cch3_931277114">fix style</A> none
			<A HREF="#_cch3_931277114">fix style</A> 1 setforce 0.0 NULL 0.0
			<A HREF="#_cch3_931277114">fix style</A> 1 addforce 1.0 0.0 0.0
			<A HREF="#_cch3_931277114">fix style</A> 1 aveforce 1.0 0.0 0.0
			<A HREF="#_cch3_931277114">fix style</A> 1 rescale 300.0 300.0 100 20.0 0.5
			<A HREF="#_cch3_931277114">fix style</A> 1 hoover/drag 50.0 50.0 0.001
			<A HREF="#_cch3_931277114">fix style</A> 1 langevin 50.0 50.0 0.01 12345 1 1 1
			<A HREF="#_cch3_931277114">fix style</A> 1 springforce 10.0 NULL NULL 1.0
			<A HREF="#_cch3_931277114">fix style</A> 1 dragforce 10.0 -5.0 NULL 2.0 1.0
			<A HREF="#_cch3_931277114">fix style</A> 1 shake 3 0.001 100

			<A HREF="#_cch3_931277163">assign fix</A> 1 atom 200
			<A HREF="#_cch3_931277163">assign fix</A> 1 molecule 50
			<A HREF="#_cch3_931277163">assign fix</A> 1 type 2
			<A HREF="#_cch3_931277163">assign fix</A> 1 region 0.0 1.0 INF INF 0.0 1.0
			<A HREF="#_cch3_931277163">assign fix</A> 1 bondtype 4
			<A HREF="#_cch3_931277163">assign fix</A> 1 angletype 18 10
			<A HREF="#_cch3_931277163">assign fix</A> 1 remainder
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_930960490">Ensemble Control</A></H3>
			<P>
			(if used, must appear after "read data" or "read
			restart" command)</P>
			<PRE>
			<A HREF="#_cch3_931276742">temp control</A> none
			<A HREF="#_cch3_931276742">temp control</A> rescale 300.0 300.0 100 20.0 0.5
			<A HREF="#_cch3_931276742">temp control</A> replace 300.0 300.0 50 12345678
			<A HREF="#_cch3_931276742">temp control</A> langevin 50.0 50.0 0.01 123456
			<A HREF="#_cch3_931276742">temp control</A> nose/hoover 300.0 300.0 0.01

			<A HREF="#_cch3_931276784">press control</A> none
			<A HREF="#_cch3_931276784">press control</A> nose/hoover xyz 0.0 0.0 0.001
			<A HREF="#_cch3_931276784">press control</A> nose/hoover xz 0.0 10.0 5.0 5.0 0.0 10.0 0.001
			<A HREF="#_cch3_931276784">press control</A> nose/hoover yz NULL NULL 5.0 5.0 0.0 10.0 0.001
			<A HREF="#_cch3_931276784">press control</A> nose/hoover aniso 0.0 0.0 0.0 0.0 1.0 10.0 0.001
			<A HREF="#_cch3_931276784">press control</A> nose/hoover aniso 0.0 0.0 0.0 0.0 NULL NULL 0.001

			<A HREF="#_cch3_999724492">volume control</A> none
			<A HREF="#_cch3_999724492">volume control</A> linear x 0.0 10.0
			<A HREF="#_cch3_999724492">volume control</A> linear y -1.0 15.0
			<A HREF="#_cch3_999724492">volume control</A> linear z -10.0 10.0
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_930960485">Output Control</A></H3>
			<P>
			(if used, must appear after "read data" or "read
			restart" command)</P>
			<PRE>
			<A HREF="#_cch3_931276675">thermo flag</A> 50
			<A HREF="#_cch3_931276681">thermo style</A> 0

			<A HREF="#_cch3_931276696">dump atoms</A> 100 filename
			<A HREF="#_cch3_931276703">dump velocities</A> 100 filename
			<A HREF="#_cch3_931276712">dump forces</A> 100 filename

			<A HREF="#_cch3_931276719">restart</A> 1000 1 filename
			<A HREF="#_cch3_931276719">restart</A> 1000 2 file1 file2
			<A HREF="#_cch3_931276727">diagnostic</A> diffusion 100 filename 3 1.0 -1.0 2.5
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_951435640">Integrator Settings</A></H3>
			<P>
			(if used, must appear after "read data" or "read
			restart" command)</P>
			<PRE>
			<A HREF="#_cch3_931276638">timestep</A> 1.0
			<A HREF="#_cch3_931276645">respa</A> 2 2 4
			<A HREF="#_cch3_931277185">reset timestep</A> 0
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_951435646">Minimizer Settings</A></H3>
			<P>
			(if used, must appear after "read data" or "read
			restart" command)</P>
			<PRE>
			<A HREF="#_cch3_931277200">min style</A> hftn
			<A HREF="#_cch3_1001972012">min flag</A> 10
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_951435914">Perform a Simulation</A></H3>
			<PRE>
			<A HREF="#_cch3_931277194">run</A> 10000
			<A HREF="#_cch3_931277212">minimize</A> 0.0001 9999 50000
			</PRE>
			<HR>
			<HR>
			<H3>
			<A NAME="_cch3_931277455">Alphabetic Listing of Commands:</A></H3>
			<HR>
			<H3>
			<A NAME="_cch3_999724447">angle coeff </A></H3>
			<UL>
			<LI>
			1st parameter = angle type #
			<LI>
			2nd-Nth parameters = coeffs 1 to N-1
			</UL>
			<PRE>
			coeffs: harmonic
			(1) K (energy units)
			(2) theta (degrees)
			class2
			currently not enabled for "angle coeff" command
			must be specified in data file (see "read data" command)
			charmm
			(1) K (energy units)
			(2) theta (degrees)
			(3) K_UB (energy/distance^2)
			(4) r_UB (distance)
			cosine
			(1) K (energy units)

			define (or override) angle coefficients for an individual angle type
			use appropriate number of coeffs for a particular style
			see force_fields.html for meaning of coefficients for each style
			these coefficients can also be set in data file
			by a "Angle Coeffs" entry, the most recently defined
			coefficients are used
			cannot use this command before a "read data" or "read restart" is performed,
			because memory is not yet allocated for the necessary arrays
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931277007">angle style </A></H3>
			<UL>
			<LI>
			none = compute no angles
			<LI>
			harmonic = harmonic angles (class 1)
			<LI>
			class2 = class 2 angles (and associated cross terms)
			<LI>
			charmm = harmonic + Urey-Bradley
			<LI>
			cosine = (1 + cos(theta))
			</UL>
			<PRE>
			define style of angle interactions to use for all 3-body terms
			must be used before the "read data" command (if not using the
			default) to tell the program how to read the "Angle Coeffs" entry
			in the data file
			can be used after the "read data" command to change the style to none
			coefficients for all angle types must be defined in the data (or restart)
			file by a "Angle Coeffs" entry or by "angle coeff"
			commands before a run is performed

			Default = harmonic
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931277163">assign fix </A></H3>
			<UL>
			<LI>
			1st parameter = constraint #
			<LI>
			2nd parameter = style of group of atoms or bondtype
			<LI>
			3rd-Nth parameters = coeffs 1 to N-2
			</UL>
			<PRE>
			styles:
			</PRE>
			<UL>
			<LI>
			atom = single atom
			<LI>
			molecule = all atoms in a particular molecule
			<LI>
			type = single atom type
			<LI>
			region = geometric region of atoms
			<LI>
			bondtype = bondtype (only for assigning to fix style SHAKE)
			<LI>
			angletype = angletype (only for assigning to fix style SHAKE)
			<LI>
			remainder = rest of unconstrained atoms
			</UL>
			<PRE>
			coeffs: atom
			(1) global atom #
			molecule
			(1) molecule #
			type
			(1) atom type
			region
			(1) lower x bound of region
			(2) upper x bound of region
			(3) lower y bound of region
			(4) upper y bound of region
			(5) lower z bound of region
			(6) upper z bound of region
			bondtype
			(1) bond type
			angletype
			(1) angle type
			(2) bond type used within that angle
			remainder
			no other parameters required

			assign a group of atoms or a bond type to a particular constraint
			use appropriate number of coeffs for a particular style
			the constraint itself must first be defined by a
			"fix style" command
			multiple groups of atoms or bond types can be assigned to the same constraint
			the bondtype option can only be assigned to a "fix style" of "shake",
			multiple bondtypes can be SHAKEn, so long as the size of clusters of
			atoms does not exceed the limit described in the "fix style" command
			the angletype option can only be assigned to a "fix style" of "shake",
			only a single angletype can be SHAKEn, it is designed to be used
			in conjunction with "fix style bondtype" to make clusters of size 3
			entirely rigid (e.g. water)
			the angletype option enables an additional check when SHAKE constraints
			are computed: if a cluster is of size 3 and both bonds in
			the cluster are of a bondtype specified by the 2nd paramter of
			angletype, then the cluster is SHAKEn with an additional angle
			constraint that makes it rigid, using the equilibrium angle appropriate
			to the specified angletype
			IMPORTANT NOTE: the angletype option has one additional affect, namely
			that no angle forces for any angle of type angletype are computed
			(since it is assumed those angles will be frozen by being SHAKEn), thus
			it will likely cause unintended behavior if the bonds in some atom pairs
			within angles of type angletype do not have the appropriate bondtype,
			since they will not be SHAKEn but neither will the angle force by computed
			for style region, a coeff of INF means + or - infinity (all the way
			to the boundary)
			an atom can be assigned to multiple constraints, the contraints will be
			applied in the reverse order they are assigned to that atom
			(e.g. each timestep, the last fix assigned to an atom will be applied
			to it first, then the next-to-last applied second, etc)

			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276970">bond coeff </A></H3>
			<UL>
			<LI>
			1st parameter = bond type #
			<LI>
			2nd-Nth parameters = coeffs 1 to N-1
			</UL>
			<PRE>
			coeffs: harmonic
			(1) K (energy units)
			(2) r0 (distance units)
			fene/standard
			(1) k for FENE portion (energy/distance^2 units)
			(2) r0 for FENE portion (distance units)
			(3) epsilon for LJ portion (energy units)
			(4) sigma for LJ portion (distance units)
			fene/shift
			(1) k for FENE (energy/distance^2 units)
			(2) r0 for FENE after shift is performed (distance units)
			(3) epsilon for LJ (energy units)
			(4) sigma for LJ after shift is performed (distance units)
			(5) delta shift distance (distance units)
			nonlinear
			(1) epsilon (energy units)
			(2) r0 (distance units)
			(3) lamda (distance units)
			class2
			currently not enabled for "bond coeff" command
			must be specified in data file (see "read data" command)

			define (or override) bond coefficients for an individual bond type
			use appropriate number of coeffs for a particular style
			see force_fields.html for meaning of coefficients for each style
			these coefficients can also be set in data file
			by a "Bond Coeffs" entry, the most recently defined
			coefficients are used
			cannot use this command before a "read data" or "read restart" is performed,
			because memory is not yet allocated for the necessary arrays
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276958">bond style </A></H3>
			<UL>
			<LI>
			none = compute no bonds
			<LI>
			harmonic = harmonic springs
			<LI>
			fene/standard = attractive logarithmic term, repulsive LJ
			<LI>
			fene/shift = same as fene/standard with shift of bond distance
			<LI>
			nonlinear = non-linear finite-extension spring (van Swol)
			<LI>
			class2 = class 2 bonds
			</UL>
			<PRE>
			define style of bond interactions to use between all bonded atoms
			must be used before the "read data" command (if not using the
			default) to tell the program how to read the "Bond
			Coeffs" entry in the data file (if one exists)
			can be used after the "read data" command to change the style,
			in this case "bond coeff" commands must also be used to set new
			coefficients for each bond type (unless the new style is "none")
			coefficients for all bond types must be defined in the data (or restart)
			file by a "Bond Coeffs" entry or by "bond coeff"
			commands before a run is performed

			Default = harmonic
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276588">comments </A></H3>
			<PRE>
			blank lines are ignored
			lines starting with a # are echoed into the log file
			for commands, everything on a line after the last parameter is ignored
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276910">coulomb style </A></H3>
			<UL>
			<LI>
			1st parameter = style of pairwise Coulomb interactions
			<LI>
			2nd-Nth parameters = coeffs 1 to N-1
			</UL>
			<PRE>
			styles:
			</PRE>
			<UL>
			<LI>
			none = no Coulomb interactions are computed
			<LI>
			cutoff = use a simple cutoff
			<LI>
			smooth = use a switch region that goes smoothly to zero
			<LI>
			ewald = use Ewald summations for long-range effects
			<LI>
			pppm = use particle-mesh Ewald for long-range effects
			<LI>
			charmm/switch = use the charmm switch to go smoothly to zero
			<LI>
			debye = add a Debye/Huckel screening exponential
			</UL>
			<PRE>
			coeffs: none
			no other parameters required
			cutoff
			(1) cutoff distance (distance units)
			smooth
			(1) inner cutoff (distance units)
			(2) outer cutoff (distance units)
			ewald
			(1) cutoff distance for near-field portion (distance units)
			(2) accuracy criterion
			pppm
			(1) cutoff distance for near-field portion (distance units)
			(2) accuracy criterion
			charmm/switch
			(1) inner cutoff (distance units)
			(2) outer cutoff (distance units)
			debye
			(1) cutoff distance (distance units)
			(2) kappa (inverse distance units)

			use appropriate number of coeffs for a particular style
			normally this command should be used before "read data" or "read restart"
			(if simulating a charged system) to tell LAMMPS how big a force cutoff
			is being used, the "maximum cutoff" command can also serve this
			purpose
			restart files do not store "coulomb style" choice or cutoff, so
			this should be specified in the input script when running from a restart
			file
			this command can also be used after "read data" or "read restart" to
			change the style of Coulomb interactions or the cutoff
			if simulated system has no charges, should set "coulomb style none" to
			prevent LAMMPS from doing useless nonbond work, LAMMPS will set
			this for you and issue a warning
			cutoff distance can be smaller or larger than simulation box dimensions
			accuracy criterion means "one part in value" - e.g. 1.0E-4
			Ewald and PPPM accuracy criterion are used in conjunction with cutoff
			to partition work between short-range and long-range routines
			accuracy criterion effectively determines how many k-space vectors are used
			to approximate the energy and forces
			for PPPM, accuracy criterion determines mesh spacing (see "particle mesh"
			command)
			3-d periodic boundary conditions are normally used in conjunction with
			Ewald and PPPM, see "slab volume" command for 2-d Ewald/PPPM
			cannot use any Coulomb styles other than none with nonbond style = lj/shift or
			nonbond style = soft
			Coulomb style = smooth should be used with nonbond style = lj/smooth,
			and both should use same inner and outer cutoffs
			nonbond style = lj/charmm should be used with coulomb style = charmm/switch
			for smooth and charmm/switch styles, outer cutoff must be > inner cutoff
			for smooth and charmm/switch styles, atom pairs less than the inner cutoff
			distance use usual Coulomb, pairs between inner and outer are smoothed,
			and the potential goes to 0.0 at the outer cutoff
			for smooth style, force is continuously differentiable everywhere
			for debye style, an exp(-kappa*r) screening is added to the Coulombic
			interaction

			Default = cutoff 10.0 for real units
			cutoff 2.5 for lj units
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931277080">create group </A></H3>
			<UL>
			<LI>
			1st parameter = style of group of atoms
			<LI>
			2nd-Nth parameters = coeffs 1 to N-1
			</UL>
			<PRE>
			styles:
			</PRE>
			<UL>
			<LI>
			types = range of atom types
			<LI>
			molecules = range of molecule IDs
			<LI>
			region = geometric region of atoms
			<LI>
			remainder = rest of uninitialized atoms
			</UL>
			<PRE>
			coeffs: types
			(1) lowest atom type
			(2) highest atom type
			molecules
			(1) lowest molecule ID
			(2) highest molecule ID
			region
			(1) lower x bound of region
			(2) upper x bound of region
			(3) lower y bound of region
			(4) upper y bound of region
			(5) lower z bound of region
			(6) upper z bound of region
			remainder
			no other parameters required

			used with "create temp" commmand to initialize velocities of atoms
			by default, the "create temp" command initializes the velocities of all atoms,
			this command limits the initialization to a group of atoms
			this command is only in force for the next "create temp" command, any
			subsequent "create temp" command is applied to all atoms (unless the
			"create group" command is used again)
			for style types, only atoms with a type such that lo-type <= type <= hi-type
			will be initialized by "create temp"
			for style types, lo-type can equal hi-type if just want to specify one type
			for style molecules, only atoms belonging to molecules with an ID # such
			that lo-ID <= type <= hi-ID will be initialized by "create temp"
			for style molecules, lo-ID can equal hi-ID if just want to specify one molecule
			for style region, only atoms within the specified spatial region
			will be initialized by "create temp"
			for style region, a coeff of INF means + or - infinity (all the way
			to the boundary)
			for style remainder, only previously uninitialized atoms
			will be initialized by "create temp"
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931277097">create temp</A></H3>
			<UL>
			<LI>
			1st parameter = style of temperature creation
			<LI>
			2nd-Nth parameters = coeffs 1 to N-1
			</UL>
			<PRE>
			styles:
			</PRE>
			<UL>
			<LI>
			uniform = uniform distribution of velocities
			<LI>
			gaussian = gaussian distribution of velocities
			<LI>
			velocity = assign specific initial velocity to each atom
			</UL>
			<PRE>
			coeffs: uniform
			(1) target T (temperature units)
			(2) random # seed (0 < seed <= 8 digits)
			gaussian
			(1) target T (temperature units)
			(2) random # seed (0 < seed <= 8 digits)
			velocity
			(1) x velocity component (velocity units)
			(2) y velocity component (velocity units)
			(3) z velocity component (velocity units)

			initialize velocities of atoms to a specified temperature
			use appropriate number of coeffs for a particular style
			cannot be done before a data or restart file is read
			by default, velocities are created for all atoms - this can be overridden
			by first using a "create group" command
			for uniform and Gaussian styles velocities are created in
			processor-independent fashion - is slower but gives the same initial
			state independent of # of processors
			for uniform and Gaussian styles the momentum of the initialized atoms is
			also zeroed, but only if all atoms are being initialized
			for uniform and Gaussian styles, RN are generated with Park/Miller RNG
			for velocity style in 2-d simulations, still specify z velocity component,
			even though it is ignored
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276727">diagnostic</A></H3>
			<UL>
			<LI>
			1st parameter = nametag of a user routine added to diagnostic.f file
			<LI>
			2nd parameter = call this user routine every this # of timesteps
			<LI>
			3rd parameter = file name for this routine's diagnostic output
			<LI>
			4th parameter = # of remaining parameters (0 to 5)
			<LI>
			5th-9th parameters = optional parameters to pass to user routine
			</UL>
			<PRE>
			call a user-defined diagnostic routine every this many timesteps
			this command can be used multiple times to call different routines
			at different frequencies, that use different parameters, and that
			send output to different files
			value of 0 for 2nd parameter means never call this particular routine
			this command causes any previous file associated with this user routine
			to be closed
			new filename can exist, will be overwritten
			if the file name specified is "none", then no file is opened
			each routine that is added to diagnostic.f and enabled with a
			"diagnostic" command will be called at the beginning and end of
			each "run" and every so many timesteps during the run
			see *** comments in diagnostic.f for changes that must be made in
			that file to enable user diagnostics, LAMMPS must then be re-compiled
			and re-linked
			see the diagnostic.f file for further information on how to create
			routines that operate on internal LAMMPS data, do their own file output,
			perform different operations (e.g. setup and clean-up) depending
			on when they are called, etc
			the optional 5th-9th parameters are stored as internal LAMMPS variables
			which can be accessed by the diagnostic routine
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276953">dielectric </A></H3>
			<PRE>
			set dielectric constant to this value

			Default = 1.0
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_999724456">dihedral coeff </A></H3>
			<UL>
			<LI>
			1st parameter = dihedral type #
			<LI>
			2nd-Nth parameters = coeffs 1 to N-1
			</UL>
			<PRE>
			coeffs: harmonic
			(1) K (energy units)
			(2) d (+1 or -1)
			(3) n (1,2,3,4,6)
			multiharmonic
			(1) A_1 (energy units)
			(2) A_2 (energy units)
			(3) A_3 (energy units)
			(4) A_4 (energy units)
			(5) A_5 (energy units)
			class2
			currently not enabled for "dihedral coeff" command
			must be specified in data file (see "read data" command)
			charmm
			(1) K (energy units)
			(2) n (1,2,3,4,6)
			(3) d (0 or 180 degrees) (converted to radians within LAMMPS)
			(4) weighting factor to turn on/off 1-4 neighbor nonbond interactions

			define (or override) dihedral coefficients for an individual dihedral type
			use appropriate number of coeffs for a particular style
			see force_fields.html for meaning of coefficients for each style
			these coefficients can also be set in data file
			by a "Dihedral Coeffs" entry, the most recently defined
			coefficients are used
			cannot use this command before a "read data" or "read restart" is performed,
			because memory is not yet allocated for the necessary arrays
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931277020">dihedral style </A></H3>
			<UL>
			<LI>
			none = compute no dihedrals
			<LI>
			harmonic = simple harmonic dihedrals (class 1)
			<LI>
			multiharmonic = multiple simple harmonic dihedrals (class 1)
			<LI>
			class2 = class 2 dihedrals (and associated cross terms)
			<LI>
			charmm= simple harmonic dihedrals + charmm 1-4 interactions
			</UL>
			<PRE>
			define style of dihedral interactions to use for all 4-body terms
			must be used before the "read data" command (if not using the
			default) to tell the program how to read the "Dihedral
			Coeffs" entry in the data file
			can be used after the "read data" command to change the style to none
			coefficients for all dihedral types must be defined in the data (or restart)
			file by a "Dihedral Coeffs" entry or by "dihedral coeff"
			commands before a run is performed

			Default = harmonic
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276604">dimension </A></H3>
			<UL>
			<LI>
			specify 3 for 3-d or 2 for 2-d run
			</UL>
			<PRE>
			for a 2-d run, assumes all z-coords are set to 0.0 in "read data" or
			"read restart" files and program creates no z velocities
			this command sets the processor grid to default values for 2-d or 3-d
			so must be used before "processor grid" command
			must be set before data or restart file is read

			Default = 3
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276696">dump atoms </A></H3>
			<UL>
			<LI>
			1st parameter = # of timesteps
			<LI>
			2nd parameter = file name
			</UL>
			<PRE>
			dump all atom positions to a file every this many timesteps
			(every this many iteration when the minimizer is invoked)
			when rRESPA is enabled, this is steps of outermost loop (longest timesteps)
			positions are also dumped at the start and end of each run
			when dumped during minimization, all dumps will have the same timestamp
			since the timestep does not change during minimization
			value of 0 means never dump
			any previous file is closed
			new filename can exist, will be overwritten
			atom positions in dump file are in "box" units (0.0 to 1.0) in each dimension
			IMPORTANT NOTE: due to the way periodic boundary conditions are enforced
			(only when neighbor lists are rebuilt), atom coords appearing in the dump
			file can be slightly outside the specified box

			Default = 0
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276712">dump forces </A></H3>
			<UL>
			<LI>
			1st parameter = # of timesteps
			<LI>
			2nd parameter = file name
			</UL>
			<PRE>
			dump all atom forces to a file every this many timesteps
			(every this many iteration when the minimizer is invoked)
			when rRESPA is enabled, this is steps of outermost loop (longest timesteps)
			forces are also dumped at the start and end of each run
			when dumped during minimization, all dumps will have the same timestamp
			since the timestep does not change during minimization
			any previous file is closed
			new filename can exist, will be overwritten
			value of 0 means never dump

			Default = 0
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276703">dump velocities </A></H3>
			<UL>
			<LI>
			1st parameter = # of timesteps
			<LI>
			2nd parameter = file name
			</UL>
			<PRE>
			dump all atom velocities to a file every this many timesteps
			when rRESPA is enabled, this is steps of outermost loop (longest timesteps)
			velocities are also dumped at the start and end of every run
			any previous file is closed
			new filename can exist, will be overwritten
			value of 0 means never dump

			Default = 0
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_951437269">extra memory</A></H3>
			<UL>
			<LI>
			1st parameter = extra_own = padding factor on allocation of owned atom
			arrays
			<LI>
			2nd parameter = extra_ghost = padding factor on allocation of ghost
			atom arrays
			<LI>
			3rd parameter = extra_neigh = padding factor on allocation of neighbor
			lists
			<LI>
			4th parameter = extra_buf = padding factor on allocation of
			communication buffers
			</UL>
			<PRE>

			factors that affect how much extra memory is allocated when a problem is setup
			factor of 1.0 means no padding (use exactly what LAMMPS estimates is
			needed), factor of 2.0 means 2x longer arrays, etc
			typically don't need to change default settings unless LAMMPS tells you
			to "boost" some factor at run-time
			final section of log file lists optimal settings for these parameters,
			i.e. the job could have been run with those "extra memory" settings
			and would have used minimal memory
			must be set before data or restart file is read

			Default = 1.5 for all 4 parameters
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931277114">fix style </A></H3>
			<UL>
			<LI>
			1st parameter = constraint # (except for none)
			<LI>
			2nd parameter = style of that constraint
			<LI>
			3rd-Nth parameters = coeffs 1 to N-2
			</UL>
			<PRE>
			styles:
			</PRE>
			<UL>
			<LI>
			none = erase all constraints and all atom and bond assignments
			<LI>
			setforce = set force on each atom in group
			<LI>
			addforce = add a force to each atom in group
			<LI>
			aveforce = apply an external force to group of atoms such that every
			atom is accelerated the same
			<LI>
			rescale = thermostat a group of atoms by rescaling their velocities
			<LI>
			hoover/drag = thermostat a group of atoms by the Hoover method
			<LI>
			langevin = thermostat a group of atoms by the Langevin method
			<LI>
			springforce = apply a spring force to each atom in group
			<LI>
			dragforce = drag each atom in group to a specified position
			<LI>
			shake = apply bond length constraints to certain bonds, enabling longer
			timesteps
			</UL>
			<PRE>
			coeffs: none
			no other parameters required (use "none" as 1st parameter)
			setforce
			(1) x component of set force (in force units)
			(2) y component of set force (in force units)
			(3) z component of set force (in force units)
			addforce
			(1) x component of added force (in force units)
			(2) y component of added force (in force units)
			(3) z component of added force (in force units)
			aveforce
			(1) x comp of added average force per atom (in force units)
			(2) y comp of added average force per atom (in force units)
			(3) z comp of added average force per atom (in force units)
			rescale
			(1) desired T at beginning of run
			(2) desired T at end of run
			(3) check for rescaling every this many timesteps
			(4) T window outside of which velocities will be rescaled
			(5) fractional amount (0.0 to 1.0) of rescaling to perform
			hoover/drag
			(1) desired T at beginning of run
			(2) desired T at end of run
			(3) damping constant for drag (roughly inverse time units)
			langevin
			(1) desired T at beginning of run
			(2) desired T at end of run
			(3) Langevin damping parameter (inverse time units)
			(4) random seed to use for white noise (0 < seed <= 8 digits)
			(5) 0/1 = off/on x dimension
			(6) 0/1 = off/on y dimension
			(7) 0/1 = off/on z dimension
			springforce
			(1) x position of spring origin
			(2) y position
			(3) z position
			(4) force constant k (so that k*distance = force units)
			dragforce
			(1) x position to drag atom towards
			(2) y position
			(3) z position
			(4) force magnitude f (in force units)
			(5) delta outside of which to apply force (in distance units)
			shake
			(1) max # of SHAKE iterations within each atom cluster
			(2) SHAKE tolerance (accuracy of one part in tolerance)
			(3) print bond statistics every this many steps (0 = never)

			define a constraint
			cannot skip a constraint number, all must be used before a run is performed
			use appropriate number of coeffs for a particular style
			which atoms or bonds the constraint will affect is set by the
			"assign fix" command
			all of the constraints (except for rescale) are applied every timestep
			all specified temperatures are in temperature units
			for style setforce, a coeff of NULL means do not alter that force component
			for style aveforce, average force on the group of fixed atoms is computed,
			then new average force is added in and actual force on each atom is set
			to new total value -> has effect of applying same force to entire group
			of atoms
			thermostatting constraints (rescale, hoover/drag, langevin) cannot be used in
			conjuction with global "temp control", since they conflict and will
			cause atom velocities to be reset twice
			thermostatting constraints (rescale, hoover/drag, langevin) cannot be used
			when performing a minimization
			if multiple Langevin constraints are specified the Marsaglia RNG will
			only use the last RNG seed specified for initialization
			meaning of rescale and Langevin thermostatting coefficients is same as in
			"temp control" command
			for rescale style, it can be used as a coarse temperature rescaler,
			for example "rescale 200.0 300.0 100 10.0 1.0" will ramp the temperature
			up during the simulation, resetting it to the target temperatue as needed
			for rescale style, it can be used to create an instantaneous
			drag force that slowly rescales the temperature without oscillation,
			for example "rescale 300.0 300.0 1 0.0 0.0001" will force (or keep)
			the temperature to be 300.0, the time frame over which this occurs
			will become longer as the last parameter is made smaller
			for hoover/drag style, the drag force accumulates over time so some
			oscillation in temperature can occur, for example
			"rescale 300.0 300.0 1 0.0 0.0001" will force (or keep)
			the temperature to be 300.0, the time frame over which the oscillations
			occur will become longer as the last parameter is made smaller
			style springforce is designed to be applied to an entire group of atoms
			en masse (e.g. an umbrella force on an entire molecule)
			for springforce style, the center of mass r0 of the group of atoms is computed,
			then a restoring force = -k(r-r0)mass/masstotal is applied to each
			atom in the group where mass = mass of the atom and masstotal = mass of
			all the atoms in the group - thus "k" should represent the total
			force on the group of atoms (not per atom)
			for springforce style, a xyz position of NULL means do not include that
			dimension in the distance or force computation
			for dragforce style, apply a drag force of magnitude f to each atom in the
			group in the direction (r-r0) where r0 = (x,y,z) - do not apply the force if
			the atom is within a distance delta of r0
			for dragforce style, a xyz position of NULL means do not include that
			dimension in the distance or force computation
			for shake style, certain bonds in the system are constrained every timestep
			to be at their equilibrium length, this is done by applying a SHAKE-like
			constraint to the forces on the atoms so that their position at the next
			timestep will preserve the atom separations
			for shake style, only atoms in small clusters can be constrained -
			e.g. water molecules, CH3 groups, but not the C backbone of a
			long polymer chain - a cluster is defined as a central atom
			connected to others in the cluster by constrained bonds connected
			together by constrained bonds - the max size of such a cluster is
			4 atoms to enable easier parallelization
			for shake style, the max iteration count need not be large (e.g. 3) since
			iterations are only done within a cluster and converge quickly
			see the "minimize" command for what constraints are allowed for use
			with the minimizer
			see the "respa" command for how constraints are applied when rRESPA
			timestepping is enabled

			Default = none
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_999724473">improper coeff </A></H3>
			<UL>
			<LI>
			1st parameter = improper type #
			<LI>
			2nd-Nth parameters = coeffs 1 to N-1
			</UL>
			<PRE>
			coeffs: harmonic
			(1) K (energy units)
			(2) chi (degrees)
			cvff
			(1) K (energy units)
			(2) d (+1 or -1)
			(3) n (0,1,2,3,4,6)
			class2
			currently not enabled for "improper coeff" command
			must be specified in data file (see "read data" command)

			define (or override) improper coefficients for an individual improper type
			use appropriate number of coeffs for a particular style
			see force_fields.html for meaning of coefficients for each style
			these coefficients can also be set in data file
			by a "Improper Coeffs" entry, the most recently defined
			coefficients are used
			cannot use this command before a "read data" or "read restart" is performed,
			because memory is not yet allocated for the necessary arrays
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931277042">improper style </A></H3>
			<UL>
			<LI>
			none = compute no impropers
			<LI>
			harmonic = harmonic impropers
			<LI>
			cvff = cvff improper (class 1 variant)
			<LI>
			class2 = class 2 Wilson out-of-plane
			</UL>
			<PRE>
			define style of improper interactions to use for all trigonal centers
			in class2 case, dictates that angle-angle terms be included for all
			trigonal and tetrahedral centers
			angle for harmonic is improper torsion, angle for class2 is Wilson out-of-plane
			must be used before the "read data" command (if not using the
			default) to tell the program how to read the "Improper
			Coeffs" entry in the data file
			can be used after the "read data" command to change the style to none
			coefficients for all improper types must be defined in the data (or restart)
			file by a "Improper Coeffs" entry or by "improper coeff"
			commands before a run is performed

			Default = harmonic
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_951437278">maximum cutoff</A></H3>
			<PRE>
			specifies the longest force cutoff that will be used in any runs
			this value is used by LAMMPS to accurately allocate memory
			for neighbor arrays
			if the value is inaccurate (e.g. the command is not used), it is not an
			error, but LAMMPS may allocate insufficient memory for neighbor lists
			this command is not typically needed if the "nonbond style" and "coulomb style"
			commands are used before the "read data" or "read restart" command, since
			they specify the appropriate cutoffs
			an exception to this is if a short cutoff is used initially,
			but a longer cutoff will be used for a subsequent run (in the same
			input script), in this case the "maximum cutoff" command should be
			used to insure enough memory is allocated for the later run
			note that a restart file contains nonbond cutoffs (so it is not necessary
			to use a "nonbond style" command before "read restart"), but LAMMPS
			still needs to know what the maximum cutoff will be before the
			restart file is read
			must be set before data or restart file is read

			Default = cutoffs for nonbond and Coulomb styles
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_1001972012">min flag </A></H3>
			<PRE>
			write out minimization info every this many iterations
			value of 0 means never write

			Default = 1
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931277200">min style </A></H3>
			<UL>
			<LI>
			hftn = Hessian-free truncated Newton method
			</UL>
			<PRE>
			choose minimization algorithm to use when "minimize" command is performed
			currently, the hftn style is the only option available

			Default = hftn
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931277212">minimize </A></H3>
			<UL>
			<LI>
			1st parameter = stopping tolerance (in force units)
			<LI>
			2nd parameter = max iterations of minimizer
			<LI>
			3rd parameter = max number of force or energy evaluations
			</UL>
			<PRE>
			perform an energy minimization of the atomic coordinates of the system
			uses algorithm selected with "min style" command
			minimize commands can be interspersed with "run" commands
			to alternate between dynamics and relaxation of the system
			minimization stops if any of 3 criteria are met:
			(1) largest force component < stopping tolerance
			(2) # of iterations > max iterations
			(3) # of force and energy evaluations > max evaluations
			output from the minimizer is specified by the "dump atoms", "dump forces",
			and "restart" commands
			when using constraints with the minimizer, fixes are
			applied when atoms move except for the following
			fixes associated with temperature control are not allowed
			(rescale, hoover/drag, langevin)
			the minimizer does not invoke the "fix style shake" contraints on
			bond lengths
			the minimizer does not invoke pressure control or volume control settings
			for good convergence, should specify use of smooth nonbond force fields
			that have continuous second derivatives, e.g. set "coulomb style" to
			"smooth" or "pppm", set "nonbond style" to "lj/smooth" or
			use a long cutoff
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276900">mixing style </A></H3>
			<UL>
			<LI>
			1st parameter = style of mixing used to generate i-j nonbond
			interactions
			</UL>
			<PRE>
			styles:
			</PRE>
			<UL>
			<LI>
			geometric = sqrt(i*j) for both epsilon and sigma
			<LI>
			arithmetic = sqrt(i*j) for epsilon, (i+j)/2 for sigma
			<LI>
			sixthpower = see force_fields file for details
			</UL>
			<PRE>
			determine the kind of mixing rule that is applied to generate nonbond
			coefficients for interactions between type i and type j atoms
			mixing rules are applied only when nonbond coeffs are input in a "read data" file
			for nonbond style "soft", only epsilons (prefactor A) are input - they are
			always mixed geometrically, regardless of mixing style setting
			for nonbond style "lj/charmm", mixing style is always arithmetic,
			regardless of mixing style setting
			must be set before data file is read

			Default = geometric for all nonbond styles except
			arithmetic for nonbond style lj/charmm
			sixthpower for nonbond style class2/cutoff
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276654">neighbor </A></H3>
			<UL>
			<LI>
			1st parameter = skin distance in distance units
			<LI>
			2nd parameter = neighboring style: 0 = N^2, 1 = binning
			<LI>
			3rd parameter = build neighbor list every this many steps (see next
			param)
			<LI>
			4th parameter = delay building until after this many steps since last
			build
			<LI>
			5th parameter = build criteria: 0 = always build, 1 = only build if
			some atom has moved 1/2 or more of the skin thickness
			</UL>
			<PRE>
			factors that affect how and when neighbor lists are constructed
			the binning style is almost always faster than the N^2 style
			skin must be large enough that all atoms needed for bond
			interactions are also acquired by interprocessor communication
			last parameter incurs extra checking and communication to test against
			skin thickness, but may mean neighbor list is created less often
			when rRESPA is run, the 3rd and 4th parameters refer to the
			nonbond (short-range) timestepping
			normally this command should be used before the data or restart file is read,
			since the skin distance is used to estimate memory needed for
			neighbor lists
			this command can also be used after the "read data" or "read restart" command
			to change the style of neighbor list construction, but if the
			skin distance is changed it can cause LAMMPS to run out of neighbor
			list memory, the "maximum cutoff" command can be used to avoid this
			problem

			Default = 2.0 1 1 10 1 for real units
			0.3 1 1 10 1 for lj units
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276632">newton flag </A></H3>
			<PRE>
			turn off or on Newton's 3rd law for bond and non-bond force computation
			</PRE>
			<UL>
			<LI>
			value = 0 = no Newton's 3rd law for either
			<LI>
			value = 1 = Newton's 3rd law only for bonded computations
			<LI>
			value = 2 = Newton's 3rd law only for non-bonded computations
			<LI>
			value = 3 = Newton's 3rd law for both bonded and non-bonded
			computations
			</UL>
			<PRE>
			no Newton's 3rd law means more force computation and less communication
			yes Newton's 3rd law means less force computation and more communication
			which choice is faster is problem dependent on N, # of processors,
			and cutoff length(s)
			expect for round-off errors, setting this flag should not affect answers,
			only run time
			must be set before data or restart file is read

			Default = 3
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276848">nonbond coeff</A></H3>
			<UL>
			<LI>
			1st parameter = 1st atom type
			<LI>
			2nd parameter = 2nd atom type
			<LI>
			3rd-Nth parameters = coeffs 1 to N-2
			</UL>
			<PRE>
			coeffs: lj/cutoff
			(1) epsilon (energy units)
			(2) sigma (distance units)
			(3) cutoff (distance units)
			lj/smooth
			(1) epsilon (energy units)
			(2) sigma (distance units)
			(3) inner cutoff (distance units)
			(4) outer cutoff (distance units)
			lj/shift
			(1) epsilon (energy units)
			(2) sigma (distance units)
			(3) delta shift distance (distance units)
			(4) cutoff (distance units)
			soft
			(1) prefactor A at start of run (energy units)
			(2) prefactor A at end of run (energy units)
			(3) cutoff (distance units)
			class2/cutoff
			(1) epsilon (energy units)
			(2) sigma (distance units)
			(3) cutoff (distance units)
			lj/charmm
			(1) epsilon (energy units)
			(2) sigma (distance units)
			(3) epsilon for 1-4 interactions (energy units)
			(4) sigma for 1-4 interactions (distance units)

			define (or override) nonbond coefficients for an individual atom type pair
			use appropriate number of coeffs for a particular style
			1st atom type must be <= 2nd atom type
			all cutoffs are in global units, not local sigma units
			(e.g. in reduced units a setting of "lj/cutoff 1.0 1.2 2.5" means a
			cutoff of 2.5, not 1.2*2.5)
			turn off a particular type pair interaction by setting the
			cutoff to 0.0 (both cutoffs to zero for lj/smooth option)
			for soft style, prefactor A is ramped from starting value to
			ending value during run
			these coefficients (except the cutoffs) can also be set in data file
			by a "Nonbond Coeffs" entry and associated mixing rules, the cutoffs can
			be set (globally) via the "nonbond style" command, the most
			recently defined coefficients/cutoffs are used
			cannot use this command before a "read data" or "read restart" is performed,
			because memory is not yet allocated for the necessary arrays
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276833">nonbond style </A></H3>
			<UL>
			<LI>
			1st parameter = style of pairwise nonbond interactions (other than
			Coulombic)
			<LI>
			2nd-Nth parameters = coeffs 1 to N-1
			</UL>
			<PRE>
			styles:
			</PRE>
			<UL>
			<LI>
			none = no nonbond interactions are computed
			<LI>
			lj/cutoff = LJ with a cutoff
			<LI>
			lj/smooth = LJ with a switched region that goes smoothly to zero
			<LI>
			lj/shift = same as lj/cutoff with shift of interparticle distance
			<LI>
			soft = cosine potential with time-varying prefactor
			<LI>
			class2/cutoff
			<LI>
			lj/charmm = LJ with charmm switched region that goes smoothly to zero
			</UL>
			<PRE>
			coeffs: none
			no other parameters required
			lj/cutoff
			(1) cutoff (distance units)
			(2) offset flag (0 or 1)
			lj/smooth
			(1) inner cutoff (distance units)
			(2) outer cutoff (distance units)
			lj/shift
			(1) cutoff (distance units)
			(2) offset flag (0 or 1)
			soft
			(1) cutoff (distance units)
			class2/cutoff
			(1) cutoff (distance units)
			(2) offset flag (0 or 1)
			lj/charmm
			(1) inner cutoff (distance units)
			(2) outer cutoff (distance units)

			define style of pairwise nonbond interactions to use between all atom types
			use appropriate number of coeffs for a particular style
			this is separate from charge interactions (see "coulomb style" command)
			normally this command should be used before "read data"
			to tell LAMMPS how big a force cutoff is being used, the
			"maximum cutoff" command can also serve this purpose
			when running from a restart file, the restart file contains the nonbond
			style and nonbond cutoffs (but not the offset flag), so it is often
			not necessary to use a "nonbond style" command before "read restart",
			however LAMMPS still needs to know what the maximum cutoff will be
			before the restart file is read, see "maximum cutoff" command
			for more details
			this command can also be used after "read data" or "read restart" to
			change the style of nonbond interactions and/or the cutoff
			cutoff distance can be smaller or larger than simulation box dimensions
			nonbond style determines how many nonbond coefficients the program expects to
			find in a "Nonbond Coeffs" entry in the data file or when using the
			"nonbond coeff" command, thus the style must be set (if not using default)
			before using the "read data" command (if the data file contains a
			"Nonbond Coeffs" entry) or a "nonbond coeff" command
			coefficients for all atom type pairs must be defined in data (or restart)
			file by a "Nonbond Coeffs" entry or by "nonbond coeffs" commands before
			a run is performed
			this command sets the cutoff(s) for all type pair interactions, thus
			overriding any previous settings by a "nonbond coeff" command or
			that were read in from a data or restart file
			for lj/cutoff, lj/shift, class2/cutoff styles,
			offset flag only affects printout of thermodynamic energy
			(not forces or dynamics), determines whether offset energy
			is added in to LJ potential to make value at cutoff = 0.0,
			flag = 0 -> do not add in offset energy,
			flag = 1 -> add in offset energy
			for lj/smooth and lj/charmm styles, outer cutoff must be > inner cutoff
			for lj/smooth and lj/charmm styles, atom pairs less than the inner cutoff
			distance use straight LJ, pairs between inner and outer use a smoothed LJ,
			and the potential goes to 0.0 at the outer cutoff
			for lj/smooth and lj/charmm styles, energy and forces are continuous at inner
			cutoff and go smoothly to zero at outer cutoff
			for lj/shift and soft styles, must set "coulomb style" to "none"
			for lj/charmm style, must set "coulomb style" to "charmm/switch", "pppm",
			or "ewald"
			for lj/shift style, delta shift distances for each atom pair are set by
			"Nonbond Coeffs" entry in data file or by "nonbond coeffs" command
			for soft style, values of the prefactor "A", which is ramped from one
			value to another during the run, are set by "Nonbond Coeffs" entry
			in data file or by "nonbond coeffs" command

			Default = lj/cutoff 10.0 0 for real units
			lj/cutoff 2.5 0 for lj units
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_999182956">periodicity </A></H3>
			<UL>
			<LI>
			1st parameter = periodic BC in x direction (0) yes, (1) no
			<LI>
			2nd parameter = periodic BC in y direction (0) yes, (1) no
			<LI>
			3rd parameter = periodic BC in z direction (0) yes, (1) no
			</UL>
			<PRE>
			turn on/off periodicity in any of three dimensions
			used in inter-particle distance computation and when particles move
			to map (or not map) them back into periodic box
			for a 2-d run (see "dimension" command), 3rd parameter must be
			specified, but doesn't matter if it is 0 or 1
			must be set before data or restart file is read

			Default = 0 0 0 (periodic in all dimensions)
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276941">pppm mesh </A></H3>
			<UL>
			<LI>
			1st parameter = # of mesh points in x direction
			<LI>
			2nd parameter = # of mesh points in y direction
			<LI>
			3rd parameter = # of mesh points in z direction
			</UL>
			<PRE>
			specify the mesh size used by "coulomb style pppm"
			mesh dimensions that are power-of-two are fastest for FFTs, but any sizes
			can be used that are supported by native machine libraries
			this command is optional - if not used, a default
			mesh size will be chosen to satisfy accuracy criterion - if used, the
			specifed mesh size will override the default
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276947">pppm order </A></H3>
			<PRE>
			specify the order of the interpolation function that is used by "coulomb
			style pppm" to map particle charge to the particle mesh
			order is roughly equivalent to how many mesh points a point charge
			overlaps onto in each dimension

			Default = 5
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276784">press control </A></H3>
			<UL>
			<LI>
			1st parameter = style of pressure control
			<LI>
			2nd parameter = pressure coupling
			<LI>
			3rd-9th parameters = coeffs 1 to 7
			</UL>
			<PRE>
			styles:
			</PRE>
			<UL>
			<LI>
			none = no control (constant volume)
			<LI>
			nose/hoover = Nose-Hoover constant P
			</UL>
			<PRE>
			coupling:
			</PRE>
			<UL>
			<LI>
			xyz = couple all 3 dimensions together (isotropic)
			<LI>
			xy or yz or xz = couple 2 dimensions together, other is independent
			<LI>
			aniso = all 3 dimensions are independent (anisotropic)
			</UL>
			<PRE>
			coeffs: none
			no other parameters required
			nose/hoover xyz
			(1) desired P at beginning of run
			(2) desired P at end of run
			nose/hoover xy or yz or xz or aniso
			(1) desired Px at beginning of run (or NULL, see below)
			(2) desired Px at end of run
			(3) desired Py at beginning of run
			(4) desired Py at end of run
			(5) desired Pz at beginning of run
			(6) desired Pz at end of run
			(7) frequency constant for volume adjust (inverse time units)

			enable constant pressure simulations
			all specified pressures are in pressure units
			any dimension being varied by pressure control must be periodic
			for xyz coupling, all 3 dimensions expand/contract together uniformly
			using total scalar pressure as the driving force
			for xy/yz/xz coupling, the 2 specified dimensions expand/contract together
			uniformly using pressure components averaged over those 2 dimensions
			as the driving force, the non-specified dimension will expand/contract
			independently using its pressure component as the driving force
			for anisotropic, all 3 dimensions expand/contract independently using
			individual pressure components as the 3 driving forces
			in all cases, the simulation box stays rectilinear (not Parinello-Rahman)
			for dimensions coupled together, their specified P values should be the same
			a non-coupled dimension (e.g. dimension z for xy option or any dimension
			for aniso option) can have 2 NULL values as specified pressures,
			which means apply no pressure control in that dimension (constant volume)
			target pressure at intermediate points during a run is a ramped value
			between the beginning and ending pressure(s)
			for nose/hoover style, frequency constant is like an inverse "piston"
			mass which determines how rapidly the pressure fluctuates in response to a
			restoring force, large frequency -> small mass -> rapid fluctations
			for nose/hoover style, units of frequency/damping constant are
			inverse time, so a value of 0.001 means relax in a timespan on the
			order of 1000 fmsec (real units) or 1000 tau (LJ units)
			IMPORTANT NOTE: the computation of P in LAMMPS does not include
			a long-range Van der Waals correction, this introduces a known
			error when performing constant P simulations since the correction
			factor changes as the box size varies

			Default = none
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276624">processor grid </A></H3>
			<UL>
			<LI>
			1st parameter = # of processors in x dimension
			<LI>
			2nd parameter = # of processors in y dimension
			<LI>
			3rd parameter = # of processors in z dimension
			</UL>
			<PRE>
			specify 3-d grid of processors to map to physical simulation domain
			for 2-d problem, specify N by M by 1 grid
			program will choose these values to best map processor grid to physical
			simulation box, only use this command if wish to override program choice
			product of 3 parameters must equal total # of processors
			must be set before data or restart file is read

			Default = none
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931277059">read data </A></H3>
			<PRE>
			read the initial atom positions and bond info from the specified file
			the format for the data file is specified in the file data_format
			if a "Velocities" entry is not in data file, all atom velocities
			are set to 0.0
			if a "Coeffs" entry is in data file, the appropriate "style" command
			command must be used first (unless default setting is used) to tell
			LAMMPS how many coefficients to expect
			a "Nonbond Coeffs" entry only contains one set of coefficients for each
			atom type, after being read-in mixing rules are applied to
			compute the cross-type coefficients, see the "mixing style" command
			and data_format file for more information
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931277070">read restart </A></H3>
			<PRE>
			read atom and force-field information from specified file
			allows continuation of a previous run
			file is binary to enable exact restarts
			do not have to restart on same # of processors, but can only do exact
			restarts on same # of processors due to roundoff
			when restart file is read, warnings are issued if certain parameters
			in the restart file do not match current settings (e.g. newton flag,
			dimension, periodicity, units) - this usually indicates an error
			the restart file stores the "nonbond style" and many-body styles and
			coefficients and cutoffs, so these do not have to be re-specified in the
			input script, unless you want to change them
			the restart file does not store "coulomb style" choice or cutoff, so
			this should be re-specified in the input script
			the restart file stores the constraint assignments for each atom generated
			by using the "assign fix" command, it does NOT store the constraint
			parameters themselves, so they must be re-specified with "fix style"
			commands after the restart file is read - one exception to this is that
			SHAKE constraints (bondtype or angletype) are not stored with the
			atoms, so they must be re-specified when performing a restart with both
			the "fix style" and "assign fix" commands
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931277185">reset timestep </A></H3>
			<PRE>
			explicitly reset the timestep to this value
			the "read data" and "read restart" commands set the timestep to zero
			and the file value respectively, so this should be done after those commands
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276645">respa</A></H3>
			<UL>
			<LI>
			1st parameter = compute bond forces this many times for every one
			3/4-body force call
			<LI>
			2nd parameter = compute 3/4-body forces this many times for every one
			nonbond (short-range) force call
			<LI>
			3rd parameter = compute nonbond (short-range) forces this many times
			for every one long-range force call
			</UL>
			<PRE>
			factors that affect sub-cycling of force calculations within rRESPA hierarchy
			bonded intramolecular forces are calculated every innermost sub-timestep
			bonded 3- and 4-body forces are computed every 1st parameter sub-timesteps
			short-range nonbond pairwise forces (LJ, Coulombic) are computed every
			(2nd parameter * 1st parameter) sub-timesteps
			long-range (Ewald, PPPM) forces are computed every
			(3rd parameter * 2nd parameter * 1st parameter) sub-timesteps
			the timestepping for all 3 inner loops (bond, 3/4-body, nonbond) is performed
			as sub-cycling within the long-range timestepping loop
			the fastest (innermost) timestep size is set by the "timestep" command
			when running rRESPA, all input commands that specify numbers of timesteps
			(e.g. run, thermo flag, restart, etc) refer to the outermost loop
			of long-range timestepping
			the only exception to this rule is the "neighbor" command, where the timestep
			parameters refer to the short-range (nonbond) timestepping
			when using constraints (via the "fix style" and "assign fix" commands)
			with rRESPA, the setforce and aveforce constraints are applied at every
			level of the hierarchy (whenever forces are computed), the other
			constraints are applied only at the short-range (nonbond) level
			when using "temp control langevin" with rRESPA, thermostatting is applied
			at the short-range (nonbond) level
			rRESPA cannot be used with "fix style shake"
			setting all 3 parameters to 1 turns off rRESPA

			Default = 1 1 1 (no rRESPA)
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276719">restart </A></H3>
			<UL>
			<LI>
			1st parameter = # of timesteps
			<LI>
			2nd parameter = 1 or 2 = naming convention for restart files
			<LI>
			3rd (and 4th) parameters = file name(s)
			</UL>
			<PRE>
			create a restart file every this many timesteps
			value of 0 means never create one
			if the style is 1, restart information will be written to files
			named filename.timestep and no 4th parameter is needed
			if the style is 2, restart information will be written alternately to files
			given by the 3rd and 4th parameters, so only 2 restart files ever exist
			when the minimizer is invoked this command means create a restart file
			at the end of the minimization with the filename filename.timestep.min
			a restart file stores atom and force-field information in binary form
			allows program to restart from where it left off (see "read restart" commmand)

			Default = 0
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_951437286">restart version</A></H3>
			<PRE>
			tell LAMMPS that a restart file from an older version of LAMMPS will be read-in
			via a "read restart" command
			this command is necessary because older restart files have a different format
			valid settings are 2001 (LAMMPS 2001), 2000 (LAMMPS 2000),
			6 (LAMMPS 99) or 5 (LAMMPS 5.0)
			restart files from earlier versions of LAMMPS are not readable without
			some source code modifications
			restart files are always written out in the current-version format
			regardless of this setting
			this must be set before the "read restart" command is executed

			Default = current version of code = 2001
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931299999">rotation zero </A></H3>
			<PRE>
			zero out angular momentum when creating velocities for a group of atoms
			value of 0 means don't zero out, value of 1 means zero it

			Default = 0
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931277194">run </A></H3>
			<PRE>
			run or continue dynamics for specified # of timesteps
			when rRESPA is enabled, this is steps of outermost loop (longest timesteps)
			must have performed "read data" or "read restart"
			command first
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_999182965">slab volume </A></H3>
			<PRE>
			invoke 2-d slab Ewald/PPPM and set extended slab volume via this ratio
			2-d slab Ewald/PPPM can be used for a system that is periodic in x-y,
			but not in z
			this ratio dampens inter-slab interactions in the z dimension
			by providing empty volume between slabs and removing
			dipole inter-slab interactions
			ratio value is the size of the extended dimension in z divided by
			the actual dimension in z
			recommended ratio value is 3.0: larger is inefficient, smaller
			risks unwanted inter-slab interactions
			when 2-d slab Ewald/PPPM is used, z-direction periodicity must be
			turned off - e.g. periodicity 0 0 1
			when 2-d slab Ewald/PPPM is used, user must prevent particle migration
			beyond initial z-bounds, typically by providing walls
			2-d slab Ewald/PPPM can only be used only with electrostatically
			neutral systems
			2-d slab Ewald/PPPM can only be used (for the moment) with constant
			volume simulations (no pressure control) - the pressure computation
			(printed as thermodynamic data) does not include any slab correction
			factor or a volume correction for the extended z direction
			must be set before data or restart file is read

			Default = none (normal 3-D Ewald/PPPM)
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276666">special bonds </A></H3>
			<UL>
			<LI>
			charmm (0.0 0.0 0.0)
			<LI>
			amber (0.0 0.0 0.5/0.8333)
			<LI>
			1st parameter = nonbond weight applied to 1-2 neighbors
			<LI>
			2nd parameter = nonbond weight applied to 1-3 neighbors
			<LI>
			3rd parameter = nonbond weight applied to 1-4 neighbors
			</UL>
			<PRE>
			weighting factors to turn on/off nonbond interactions of atom pairs that
			are "close" in the molecular topology
			1-2 neighbors are a pair of atoms connected by a bond
			1-3 neighbors are a pair of atoms 2 hops away, etc.
			weight values are from 0.0 to 1.0 and are used to multiply the
			energy and force interaction (both Coulombic and LJ) between the 2 atoms
			weight of 0.0 means no interaction
			weight of 1.0 means full interaction
			can either specify a single keyword (charmm, amber) or can give
			3 numeric values
			using the charmm keyword means use the CHARMM force field
			settings of 0.0 0.0 0.0, requiring that pair-specific 1-4 interactions
			be read in individually (see "dihedral style charmm" command)
			using the amber keyword means use the AMBER force field
			settings of 0.0 0.0 N, where N = 0.5 for Van der Waals 1-4 interactions
			and 1.0/1.2 for Coulombic 1-4 interactions

			Default = CHARMM force field values of 0.0 0.0 0.0
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276742">temp control </A></H3>
			<UL>
			<LI>
			1st parameter = style of temperature control
			<LI>
			2nd-Nth parameters = coeffs 1 to N-1
			</UL>
			<PRE>
			styles:
			</PRE>
			<UL>
			<LI>
			none = no control
			<LI>
			rescale = instantaneous rescaling
			<LI>
			replace = Gaussian replacement
			<LI>
			langevin = Langevin white noise
			<LI>
			nose/hoover = Nose-Hoover constant T
			</UL>
			<PRE>
			coeffs: none
			no other parameters required
			rescale
			(1) desired T at beginning of run
			(2) desired T at end of run
			(3) check for rescaling every this many timesteps
			(4) T window outside of which velocities will be rescaled
			(5) fractional amount (0.0 to 1.0) of rescaling to perform
			replace
			(1) desired T at beginning of run
			(2) desired T at end of run
			(3) do Gaussian replacement every this many timesteps
			(4) random # seed to use for replacement (0 < seed <= 8 digits)
			langevin
			(1) desired T at beginning of run
			(2) desired T at end of run
			(3) Langevin damping parameter (inverse time units)
			(4) random seed to use for white noise (0 < seed <= 8 digits)
			nose/hoover
			(1) desired T at beginning of run
			(2) desired T at end of run
			(3) frequency constant for friction force (inverse time units)

			enable constant temperature simulations
			use appropriate number of coeffs for a particular style
			all specified temperatures are in temperature units
			target temperature at intermediate points during run is a ramped value
			between the beginning and ending temperatures
			for rescale style, temperature is controlled by explicitly rescaling
			velocities towards the target temperature
			for rescale style, rescaling is only done if current temperature is
			beyond the target temperature plus or minus the window value
			for rescale style, the amount of rescaling is contfolled by the fractional
			amount (0.0 to 1.0), e.g. a value of 0.5 means set the velocities
			to halfway between the current and target temperature
			for rescale style, it can be used as a coarse temperature rescaler,
			for example "rescale 200.0 300.0 100 10.0 1.0" will ramp the temperature
			up during the simulation, resetting it to the target temperatue as needed
			for rescale style, it can be used to create an instantaneous
			drag force that slowly rescales the temperature without oscillation,
			for example "rescale 300.0 300.0 1 0.0 0.0001" will force (or keep)
			the temperature to be 300.0, the time frame over which this occurs
			will become longer as the last parameter is made smaller
			for replace style, Gaussian RNs from the Marsaglia RNG are used
			for langevin style, uniform RNs from the Marsaglia RNG are used
			for replace and langevin styles, the seed is used to initialize the
			Marsaglia RNG, on successive runs the RNG will just continue on
			for replace and langevin styles, generated RNs depend on # of processors
			so will not get same answers independent of # of processors
			for replace and langevin styles, RNG states are not saved in restart file,
			so cannot do an exact restart
			for langevin style, damping parameter means small value -> less damping
			for nose/hoover style, frequency constant is like an inverse
			"piston" mass which determines how rapidly the temperature
			fluctuates in response to a restoring force, large frequency ->
			small mass -> rapid fluctations
			for nose/hoover style, cannot use a end-of-run T of 0.0, must be finite
			for langevin and nose/hoover styles, units of frequency/damping constant are
			inverse time, so a value of 0.01 means relax in a timespan on the
			order of 100 fmsec (real units) or 100 tau (LJ units)

			Default = none
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276675">thermo flag </A></H3>
			<PRE>
			print thermodynamic info to screen and log file every this many timesteps
			value of 0 means never print

			Default = 0
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276681">thermo style </A></H3>
			<PRE>
			determines format of thermodynamic output to screen and log file
			</PRE>
			<UL>
			<LI>
			style = 0 -> standard output - about 5 lines per entry
			<LI>
			style = 1 -> reduced output - 1 line per entry
			<LI>
			style = 2 -> output with class 2 terms - about 8 lines per entry
			</UL>
			<PRE>
			Default = 0
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276638">timestep </A></H3>
			<PRE>
			timestep size for MD run (time units)
			when rRESPA is enabled, the timestep size is for the innermost (bond) loop

			Default = 1.0
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276687">true flag </A></H3>
			<PRE>
			read atom positions (see "read data" command) and dump atom positions
			(see "dump atoms" command) in one of 2 formats
			</PRE>
			<UL>
			<LI>
			flag = 0 -> read/dump only atom positions (remapped to periodic box)
			<LI>
			flag = 1 -> dump atom positions plus integer box counts
			<LI>
			flag = 2 -> read atom positions plus integer box counts
			<LI>
			flag = 3 -> read/dump atom positions plus integer box counts
			</UL>
			<PRE>
			for each dimension, box count of "n" means add that many box lengths
			to get "true" un-remapped position, "n" can be positive, negative, or zero
			must be set before data or restart file is read

			Default = 0
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_931276596">units </A></H3>
			<UL>
			<LI>
			real or lj
			</UL>
			<PRE>
			set units to one of two options for all subsequent input parameters

			option real = conventional units:
			</PRE>
			<UL>
			<LI>
			distance = Angstroms
			<LI>
			time = femtoseconds
			<LI>
			mass = grams/mole
			<LI>
			temperature = degrees K
			<LI>
			pressure = atmospheres
			<LI>
			energy = Kcal/mole
			<LI>
			velocity = Angstroms/femtosecond
			<LI>
			force = grams/mole * Angstroms/femtosecond^2
			</UL>
			<PRE>
			option lj = LJ reduced units:
			</PRE>
			<UL>
			<LI>
			distance = sigmas
			<LI>
			time = reduced LJ tau
			<LI>
			temperature = reduced LJ temp
			<LI>
			pressure = reduced LJ pressure
			<LI>
			energy = epsilons
			<LI>
			velocity = sigmas/tau
			<LI>
			force = reduced LJ force (sigmas/tau^2)
			</UL>
			<PRE>
			for LJ units, LAMMPS sets global epsilon,sigma,mass all equal to 1.0
			subsequent input numbers in data and command file must be in these units
			output numbers to screen and log and dump files will be in these units
			this command (if it appears) must be the first command (aside from
			comments) in the input script
			must be set before data or restart file is read

			Default = real
			</PRE>
			<HR>
			<H3>
			<A NAME="_cch3_999724492">volume control </A></H3>
			<UL>
			<LI>
			1st parameter = style of volume control
			<LI>
			2nd parameter = dimension to control (x,y,z)
			<LI>
			3rd-4th parameters = lo/hi simulation box boundaries in this dimension
			</UL>
			<PRE>
			styles:
			</PRE>
			<UL>
			<LI>
			none = no variation in any dimension (constant volume)
			<LI>
			linear = uniform expansion or contraction
			</UL>
			<PRE>
			enable volume changes (density changes) during a simulation
			specified box boundaries are in distance units
			each dimension is controlled separately
			dimensions not specified by a "volume control" command can be left
			alone (constant volume or nonperiodic) or controlled by
			a "press control" command
			any dimension being varied by volume control must be periodic
			the lo/hi values are the desired global simulation box boundaries at
			the end of the simulation run
			at each timestep, the box is expanded/contracted uniformly from its initial
			lo/hi values to the specified ending lo/hi values
			initial lo/hi values are specified in the data or restart file or
			inherited from the end of the previous run
			at each timestep, all atom coordinates are also scaled to the new box

			Default = none
			</PRE>
			</BODY>
			</HTML>

lammps/doc/2001/input_commands.htmlc6213f36d34clammm-devel

input_commands.htmlView Options

lammps/doc/2001/input_commands.html
c6213f36d34clammm-devel

input_commands.html
View Options