forked from lijiext/lammps
2139 lines
83 KiB
HTML
2139 lines
83 KiB
HTML
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
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<HTML>
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<HEAD>
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<META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
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</HEAD>
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<BODY>
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<H2>
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LAMMPS Input Commands</H2>
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<P>
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<A HREF="README.html">Return</A> to top-level of LAMMPS documentation.</P>
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<P>
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This page contains a complete list of valid LAMMPS commands which are
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read-in from an input script. It will be easiest to understand if you
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read it while looking at sample input scripts in the examples
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directory. </P>
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<P>
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The script of input commands is read by LAMMPS, one line at a time.
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Each command causes LAMMPS to take some action. Usually it simply
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causes some internal variable(s) to be set. Or it may cause a data file
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to be read in or a simulation to be run. Note that most commands have
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default settings, which means you only need use a particular command if
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you do not want the default setting.</P>
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<P>
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Each LAMMPS input script contains exactly one "read data" (or
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"read restart") command which defines the problem to be
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simulated. All other commands can be split into three categories: (a)
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commands that (if used) must appear before the "read data"
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command because they define settings needed to correctly read-in the
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problem and allocate memory for it, (b) commands that must appear after
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the "read data" command because they act on the specified
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problem, and (c) commands that can appear either before or after the
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"read data" command. Commands in category (c) are used before
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the "read data" command if a default setting needs to be
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changed before the problem description is read-in. They can be used
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after the "read data" command if the user wishes to change a
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setting before the next "run" or "minimize" command
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is used. Other than these restrictions, commands can generally appear
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in any order in the input script, although some commands require others
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to have been previously specified.</P>
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<P>
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Each LAMMPS input script also contains one or more "run" or
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"minimize" commands. These trigger an actual dynamics or
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minimization computation to be done. Following a run, new commands from
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categories (b) and (c) can be used to change various settings, and
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additional "run" commands can then be used to continue the
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previous simulation. LAMMPS continues to read successive lines from the
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input script until the end-of-file is reached, which causes LAMMPS to
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terminate.</P>
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<P>
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This page gives examples of each command, some of which can be
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specified in multiple styles. Typically the commands take one or more
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parameters. The keyword for each command should begin in the leftmost
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column and all characters in the command and its parameters should be
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in lower-case (except the word NULL or characters in filenames).
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Parameters can be separated by arbitrary numbers of spaces and/or tabs,
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so long as the command fits on one line. The remainder of the line
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after the last parameter is ignored.</P>
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<P>
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The next section outlines the structure of a LAMMPS input script. The
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final section gives a detailed description of the commands in
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alphabetic order, each with its associated parameters and default
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settings.</P>
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<UL>
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<LI>
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<A HREF="#_cch3_951156975">Structure of a LAMMPS input script</A>
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<LI>
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<A HREF="#_cch3_931277455">Alphabetic Listing of Commands</A>
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</UL>
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<HR>
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<H3>
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<A NAME="_cch3_951156975">Structure of a LAMMPS input script</A></H3>
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<P>
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Any line starting with a # is a <A HREF="#_cch3_931276588">comment</A>.
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Comments can appear anywhere in the input script.</P>
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<P>
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(1) <A HREF="#_cch3_930960479">Initialization settings</A> (must appear
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before "read data" or "read restart")</P>
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<P>
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(2) <A HREF="#_cch3_951435622">Optional Settings</A> (can appear before
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and/or after "read data" or "read restart")</P>
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<P>
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(3) <A HREF="#_cch3_951435906">Read in a Problem</A> via a "<A
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HREF="#_cch3_931277059">read data</A>" or "<A
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HREF="#_cch3_931277070">read restart</A>" command</P>
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<P>
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(4) <A HREF="#_cch3_951435622">Optional Settings</A> (same as (2))</P>
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<P>
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(5) Problem Settings (must appear after "read data" or
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"read restart")</P>
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<UL>
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<LI>
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<A HREF="#_cch3_930960510">Velocity Creation</A>
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<LI>
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<A HREF="#_cch3_951435663">Force Field Parameters</A>
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<LI>
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<A HREF="#_cch3_930960516">Constraints</A>
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<LI>
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<A HREF="#_cch3_930960490">Ensemble Control</A>
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<LI>
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<A HREF="#_cch3_930960485">Output Control</A>
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<LI>
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<A HREF="#_cch3_951435640">Integrator Settings</A>
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<LI>
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<A HREF="#_cch3_951435646">Minimizer Settings</A>
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</UL>
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<P>
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(6) <A HREF="#_cch3_951435914">Perform a Simulation</A> via a "<A
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HREF="#_cch3_931277194">run</A>" or "<A
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HREF="#_cch3_931277212">minimize</A>" command</P>
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<P>
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Repeat (4), (5), and (6) as desired ...</P>
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<HR>
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<H3>
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<A NAME="_cch3_930960479">Initialization Settings</A></H3>
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<P>
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(if used, must appear before "read data" or "read
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restart" command)</P>
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<PRE>
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<A HREF="#_cch3_931276596">units</A> real
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<A HREF="#_cch3_951437269">extra memory</A> 2.0 1.5 2.0 2.5
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<A HREF="#_cch3_931276604">dimension</A> 3
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<A HREF="#_cch3_931276624">processor grid</A> 10 10 10
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<A HREF="#_cch3_999182956">periodicity</A> 0 0 0
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<A HREF="#_cch3_999182965">slab volume</A> 3.0
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<A HREF="#_cch3_931276632">newton flag</A> 3
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<A HREF="#_cch3_931276687">true flag</A> 0
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<A HREF="#_cch3_951437278">maximum cutoff</A> 10.0
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<A HREF="#_cch3_931276900">mixing style</A> geometric
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<A HREF="#_cch3_951437286">restart version</A> 5
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</PRE>
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<HR>
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<H3>
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<A NAME="_cch3_951435622">Optional Settings</A></H3>
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<P>
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(if used, can appear before and/or after "read data" or
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"read restart" command)</P>
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<PRE>
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<A HREF="#_cch3_931276654">neighbor</A> 2.0 1 1 10 1
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<A HREF="#_cch3_931276833">nonbond style</A> none
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<A HREF="#_cch3_931276833">nonbond style</A> lj/cutoff 10.0 0
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<A HREF="#_cch3_931276833">nonbond style</A> lj/smooth 8.0 10.0
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<A HREF="#_cch3_931276833">nonbond style</A> lj/shift 10.0 0
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<A HREF="#_cch3_931276833">nonbond style</A> soft 2.5
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<A HREF="#_cch3_931276833">nonbond style</A> class2/cutoff 10.0 0
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<A HREF="#_cch3_931276833">nonbond style</A> lj/charmm 15.0 15.1
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<A HREF="#_cch3_931276910">coulomb style</A> none
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<A HREF="#_cch3_931276910">coulomb style</A> cutoff 10.0
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<A HREF="#_cch3_931276910">coulomb style</A> smooth 8.0 10.0
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<A HREF="#_cch3_931276910">coulomb style</A> ewald 10.0 1.0E-4
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<A HREF="#_cch3_931276910">coulomb style</A> pppm 10.0 1.0E-4
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<A HREF="#_cch3_931276910">coulomb style</A> charmm/switch 15.0 15.1
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<A HREF="#_cch3_931276910">coulomb style</A> debye 10.0 0.5
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<A HREF="#_cch3_931276958">bond style</A> none
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<A HREF="#_cch3_931276958">bond style</A> harmonic
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<A HREF="#_cch3_931276958">bond style</A> fene/standard
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<A HREF="#_cch3_931276958">bond style</A> fene/shift
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<A HREF="#_cch3_931276958">bond style</A> nonlinear
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<A HREF="#_cch3_931276958">bond style</A> class2
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<A HREF="#_cch3_931277007">angle style</A> none
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<A HREF="#_cch3_931277007">angle style</A> harmonic
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<A HREF="#_cch3_931277007">angle style</A> class2
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<A HREF="#_cch3_931277007">angle style</A> charmm
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<A HREF="#_cch3_931277007">angle style</A> cosine
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<A HREF="#_cch3_931277020">dihedral style</A> none
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<A HREF="#_cch3_931277020">dihedral style</A> harmonic
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<A HREF="#_cch3_931277020">dihedral style</A> mutliharmonic
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<A HREF="#_cch3_931277020">dihedral style</A> class2
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<A HREF="#_cch3_931277020">dihedral style</A> charmm
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<A HREF="#_cch3_931277042">improper style</A> none
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<A HREF="#_cch3_931277042">improper style</A> harmonic
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<A HREF="#_cch3_931277042">improper style</A> cvff
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<A HREF="#_cch3_931277042">improper style</A> class2
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</PRE>
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<HR>
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<H3>
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<A NAME="_cch3_951435906">Read in a Problem</A></H3>
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<PRE>
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<A HREF="#_cch3_931277059">read data</A> data.lj
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<A HREF="#_cch3_931277070">read restart</A> restart.100000
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</PRE>
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<HR>
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<H3>
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<A NAME="_cch3_930960510">Velocity Creation</A></H3>
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<P>
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(if used, must appear after "read data" or "read
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restart" command)</P>
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<PRE>
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<A HREF="#_cch3_931277080">create group</A> types 1 3
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<A HREF="#_cch3_931277080">create group</A> molecules 200 300
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<A HREF="#_cch3_931277080">create group</A> region 0.0 1.0 0.0 1.0 INF 1.0
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<A HREF="#_cch3_931277080">create group</A> remainder
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<A HREF="#_cch3_931299999">rotation zero</A> 1
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<A HREF="#_cch3_931277097">create temp</A> uniform 300.0 12345678
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<A HREF="#_cch3_931277097">create temp</A> gaussian 300.0 12345678
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<A HREF="#_cch3_931277097">create temp</A> velocity 0.0 0.0 0.0
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</PRE>
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<HR>
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<H3>
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<A NAME="_cch3_951435663">Force Field Parameters</A></H3>
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<P>
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(if used, must appear after "read data" or "read
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restart" command)</P>
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<PRE>
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<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 3.45 10.0 (nonbond style lj/cutoff)
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<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 3.45 8.0 10.0 (nonbond style lj/smooth)
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<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 3.45 2.0 10.0 (nonbond style lj/shift)
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<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 30.0 2.5 (nonbond style soft)
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<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 3.45 10.0 (nonbond style class2/cutoff)
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<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 3.45 1.0 3.45 (nonbond style lj/charmm)
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<A HREF="#_cch3_931276666">special bonds</A> amber
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<A HREF="#_cch3_931276666">special bonds</A> 0.0 0.0 0.5
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<A HREF="#_cch3_931276941">pppm mesh</A> 32 32 64
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<A HREF="#_cch3_931276947">pppm order</A> 5
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<A HREF="#_cch3_931276953">dielectric</A> 1.0
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<A HREF="#_cch3_931276970">bond coeff</A> 1 100.0 3.45 (bond style harmonic)
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<A HREF="#_cch3_931276970">bond coeff</A> 1 30.0 1.5 1.0 1.0 (bond style fene/standard )
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<A HREF="#_cch3_931276970">bond coeff</A> 1 30.0 1.5 1.0 1.0 0.2 (bond style fene/shift)
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<A HREF="#_cch3_931276970">bond coeff</A> 1 28.0 0.748308 0.166667 (bond style nonlinear)
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<A HREF="#_cch3_999724447">angle coeff</A> 1 30.0 108.0 (angle style harmonic)
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<A HREF="#_cch3_999724447">angle coeff</A> 1 30.0 108.0 30.0 2.5 (angle style charmm)
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<A HREF="#_cch3_999724447">angle coeff</A> 1 30.0 (angle style cosine)
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<A HREF="#_cch3_999724456">dihedral coeff</A> 1 10.0 1 3 (dihedral style harmonic)
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<A HREF="#_cch3_999724456">dihedral coeff</A> 1 2.0 2.0 2.0 2.0 2.0 (dihedral style multiharmonic)
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<A HREF="#_cch3_999724456">dihedral coeff</A> 1 2.0 5 180.0 0.5 (dihedral style charmm)
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<A HREF="#_cch3_999724473">improper coeff</A> 1 20.0 0.0 (improper style harmonic)
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<A HREF="#_cch3_999724473">improper coeff</A> 1 20.0 10.0 (improper style cvff)
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</PRE>
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<HR>
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<H3>
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<A NAME="_cch3_930960516">Constraints</A></H3>
|
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<P>
|
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(if used, must appear after "read data" or "read
|
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restart" command)</P>
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<PRE>
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<A HREF="#_cch3_931277114">fix style</A> none
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<A HREF="#_cch3_931277114">fix style</A> 1 setforce 0.0 NULL 0.0
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<A HREF="#_cch3_931277114">fix style</A> 1 addforce 1.0 0.0 0.0
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<A HREF="#_cch3_931277114">fix style</A> 1 aveforce 1.0 0.0 0.0
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<A HREF="#_cch3_931277114">fix style</A> 1 rescale 300.0 300.0 100 20.0 0.5
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<A HREF="#_cch3_931277114">fix style</A> 1 hoover/drag 50.0 50.0 0.001
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<A HREF="#_cch3_931277114">fix style</A> 1 langevin 50.0 50.0 0.01 12345 1 1 1
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<A HREF="#_cch3_931277114">fix style</A> 1 springforce 10.0 NULL NULL 1.0
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<A HREF="#_cch3_931277114">fix style</A> 1 dragforce 10.0 -5.0 NULL 2.0 1.0
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<A HREF="#_cch3_931277114">fix style</A> 1 shake 3 0.001 100
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<A HREF="#_cch3_931277163">assign fix</A> 1 atom 200
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<A HREF="#_cch3_931277163">assign fix</A> 1 molecule 50
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<A HREF="#_cch3_931277163">assign fix</A> 1 type 2
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<A HREF="#_cch3_931277163">assign fix</A> 1 region 0.0 1.0 INF INF 0.0 1.0
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<A HREF="#_cch3_931277163">assign fix</A> 1 bondtype 4
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<A HREF="#_cch3_931277163">assign fix</A> 1 angletype 18 10
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<A HREF="#_cch3_931277163">assign fix</A> 1 remainder
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</PRE>
|
||
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<HR>
|
||
|
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<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>
|