153 lines
4.7 KiB
HTML
153 lines
4.7 KiB
HTML
<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>pair_style list command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>pair_style list listfile cutoff keyword
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</PRE>
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<UL><LI>listfile = name of file with list of pairwise interactions
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<LI>cutoff = global cutoff (distance units)
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<LI>keyword = optional flag <I>nocheck</I> or <I>check</I> (default is <I>check</I>)
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style list restraints.txt 200.0
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</PRE>
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<P>pair_coeff * *
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</P>
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<PRE>pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
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pair_coeff * * lj/cut 1.0 1.0
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pair_coeff 3* 3* list
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Style <I>list</I> computes interactions between explicitly listed pairs of
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atoms with the option to select functional form and parameters different
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for each individual pair. Because the parameters are all set in the
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list file, the pair_coeff statement has to be empty (but it needs to
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be provided). The <I>check</I> and <I>nocheck</I> keyword respectively enables
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or disables a test that checks whether all listed bonds were present
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and computed.
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</P>
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<P>As a consequence, this style is a hybrid between bonded, non-bonded
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and restraint interactions and most likely to be used as an additional
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interaction with the <I>hybrid/overlay</I> pair style. It currently supports
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three interaction styles: a 12-6 Lennard-Jones, a Morse and a Harmonic
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potential.
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</P>
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<P>The format of the list file is as follows:
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</P>
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<UL><LI>one line per pair of atoms
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<LI>empty lines will be ignored
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<LI>comment text starts with a '#' character
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line syntax: ID1 ID2 style coeffs cutoff
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<PRE> ID1 = atom ID of first atom
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ID2 = atom ID of second atom
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style = style of interaction
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coeffs = list of coeffs
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cutoff = cutoff for interaction (optional)
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</PRE>
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<LI>examples:
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<P># this is a comment
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</P>
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<PRE>15 259 lj126 1.0 1.0 50.0
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15 603 morse 10.0 1.2 2.0 10.0 # and another comment
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18 470 harmonic 50.0 1.2 5.0
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</PRE>
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</UL>
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<P>The cutoff parameter is optional. If not specified, the global cutoff is used.
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</P>
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<P>The style <I>lj126</I> computes pairwise interactions with the formula
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</P>
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<CENTER><IMG SRC = "Eqs/pair_lj.jpg">
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</CENTER>
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<P>and the coefficients:
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</P>
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<UL><LI>epsilon (energy units)
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<LI>sigma (distance units)
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</UL>
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<P>The style <I>morse</I> computes pairwise interactions with the formula
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</P>
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<CENTER><IMG SRC = "Eqs/pair_morse.jpg">
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</CENTER>
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<P>and the coefficients:
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</P>
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<UL><LI>D0 (energy units)
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<LI>alpha (1/distance units)
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<LI>r0 (distance units)
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</UL>
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<P>The style <I>harmonic</I> computes pairwise interactions with the formula
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</P>
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<CENTER><IMG SRC = "Eqs/bond_harmonic.jpg">
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</CENTER>
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<P>and the coefficients:
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</P>
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<UL><LI>K (energy units)
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<LI>r0 (distance units)
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</UL>
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<P>Note that the usual 1/2 factor is included in K.
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</P>
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<HR>
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<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
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</P>
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<P>This pair style does not support mixing since all parameters are
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explicit for each pair.
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</P>
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<P>The <A HREF = "pair_modify.html">pair_modify</A> shift option is supported by this
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pair style.
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</P>
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<P>The <A HREF = "pair_modify.html">pair_modify</A> table and tail options are not
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relevant for this pair style.
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</P>
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<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
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files</A>, so pair_style and pair_coeff commands need
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to be specified in an input script that reads a restart file.
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</P>
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<P>This pair style can only be used via the <I>pair</I> keyword of the
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<A HREF = "run_style.html">run_style respa</A> command. It does not support the
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<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
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</P>
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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>This pair style does not use a neighbor list and instead identifies
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atoms by their IDs. This has two consequences: 1) The cutoff has to
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be chosen sufficiently large, so that the second atom of a pair has
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to be a ghost atom on the same node on which the first atom is local;
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otherwise the interaction will be skipped. You can use the <I>check</I>
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option to detect, if interactions are missing. 2) Unlike for the rest
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of LAMMPS, minimum image conventions apply.
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</P>
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<P>The <I>list</I> style is part of the "user-misc" package. It is only
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enabled if LAMMPS is build with that package. See the <A HREF = "Section_start.html#3">Making of
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LAMMPS</A> section for more info.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "pair_coeff.html">pair_coeff</A>,
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<A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A>,
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<A HREF = "pair_lj.html">pair_style lj/cut</A>,
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<A HREF = "pair_morse.html">pair_style morse</A>,
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<A HREF = "bond_harmonic.html">bond_style harmonic</A>
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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