forked from lijiext/lammps
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165 lines
6.0 KiB
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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 srp command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<P>pair_style srp cutoff bond_type dist keyword value ...
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</P>
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<UL><LI>cutoff = global cutoff for SRP interactions (distance units)
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<LI>bond_type = bond type to apply SRP interactions
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<LI>dist = <I>min</I> or <I>mid</I>
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>exclude</I>
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<PRE> <I>exclude</I> value = <I>yes</I> or <I>no</I>
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</PRE>
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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 hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes
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pair_coeff 1 1 dpd 60.0 4.5 1.0
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pair_coeff 1 2 none
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pair_coeff 2 2 srp 100.0 0.8
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</PRE>
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<PRE>pair_style hybrid srp 0.8 1 mid exclude yes
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pair_coeff 1 1 none
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pair_coeff 1 2 none
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pair_coeff 2 2 srp 100.0 0.8
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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>srp</I> computes a soft segmental repulsive potential (SRP) that
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acts between bonds. This potential is useful in preventing bonds from
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passing through one another when a soft non-bonded potential acts
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between beads in, for example, DPD polymer chains.
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An example input script that uses this command is provided
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in examples/USER/srp.
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</P>
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<P>Bonds of type <I>btype</I> interact with one another through a
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bond-pairwise potential, such that the force on bond <I>i</I> due to bond
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<I>j</I> is as follows
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</P>
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<CENTER><IMG SRC = "Eqs/pair_srp1.jpg">
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</CENTER>
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<P>where <I>r</I> and <I>rij</I> are the distance and unit vector between the two
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bonds. The <I>mid</I> option computes <I>r</I> and <I>rij</I> from the midpoint
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distance between bonds. The <I>min</I> option computes <I>r</I> and <I>rij</I> from
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the minimum distance between bonds. The force acting on a bond is
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mapped onto the two bond atoms according to the lever rule,
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</P>
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<CENTER><IMG SRC = "Eqs/pair_srp2.jpg">
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</CENTER>
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<P>where <I>L</I> is the normalized distance from the atom to the point of
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closest approach of bond <I>i</I> and <I>j</I>. The <I>mid</I> option takes <I>L</I> as
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0.5 for each interaction as described in <A HREF = "#Sirk">(Sirk)</A>.
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</P>
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<P>The following coefficients must be defined via the
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<A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above, or in
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the data file or restart file read by the <A HREF = "read_data.html">read_data</A>
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or <A HREF = "read_restart.html">read_restart</A> commands:
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</P>
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<UL><LI><I>C</I> (force units)
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<LI><I>Rc</I> (distance units)
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</UL>
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<P>The last coefficient is optional. If not specified, the global cutoff
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is used.
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</P>
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<P>IMPORTANT NOTE: Pair style srp considers each bond of type <I>btype</I> as
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a fictitious particle of type <I>bptype</I>, where <I>bptype</I> is the largest
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atom type in the system. These "bond particles" are inserted at the
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beginning of the run, and serve as placeholders that define the
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position of the bonds. This allows neighbor lists to be constructed
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and pairwise interactions to be computed in almost the same way as is
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done for point particles. Because bonds interact only with other
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bonds, <A HREF = "pair_hybrid.html">pair_style hybrid</A> should be used to turn off
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interactions between atom type <I>bptype</I> and all other types of atoms.
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An error will be flagged if <A HREF = "pair_hybrid.html">pair_style hybrid</A> is
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not used. Further, only bond particles should be given an atom type
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of <I>bptype</I>; a check is done at the beginning of the run to ensure
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there are no regular atoms of <I>bptype</I>.
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</P>
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<P>The optional <I>exclude</I> keyword determines if forces are computed
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between first neighbor (directly connected) bonds. For a setting of
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<I>yes</I> they are, for <I>no</I> they are not.
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</P>
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<P>Pair style <I>srp</I> turns off normalization of thermodynamic properties
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by particle number, as if the command <A HREF = "thermo_modify.html">thermo_modify norm
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no</A> had been issued. A warning will be given if
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this setting is overridden in the input script.
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</P>
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<P>The pairwise energy associated with style <I>srp</I> is shifted to be zero
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at the cutoff distance <I>Rc</I>.
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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 styles does not support mixing.
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</P>
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<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
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shift option for the energy of the pair interaction. Note that as
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discussed above, the energy term is already shifted to be 0.0 at the
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cutoff distance <I>rc</I>.
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</P>
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<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant for
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this pair style.
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</P>
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<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
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tail option for adding long-range tail corrections to energy and
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pressure.
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</P>
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<P>This pair style writes global and per-atom information to <A HREF = "restart.html">binary
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restart files</A>. Pair srp should be used with <A HREF = "pair_hybrid.html">pair_style
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hybrid</A>, thus the pair_coeff commands need to be
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specified in the input script when reading 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 is part of the USER-MISC package. It is only enabled
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if LAMMPS was built with that package. See the Making LAMMPS section
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for more info.
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</P>
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<P>This pair style must be used with <A HREF = "pair_hybrid.html">pair_style hybrid</A>.
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</P>
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<P>This pair style requires the <A HREF = "newton.html">newton</A> command to be <I>on</I>
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for non-bonded interactions.
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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_hybrid.html">pair_style hybrid</A>, <A HREF = "pair_coeff.html">pair_coeff</A>,
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<A HREF = "pair_dpd.html">pair dpd</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The default keyword value is exclude = yes.
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</P>
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<HR>
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<A NAME = "Sirk"></A>
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<P><B>(Sirk)</B> Sirk TW, Slizoberg YR, Brennan JK, Lisal M, Andzelm JW, J
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Chem Phys, 136 (13) 134903, 2012.
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</P>
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</HTML>
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