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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14149 f3b2605a-c512-4ea7-a41b-209d697bcdaa
177 lines
6.6 KiB
HTML
177 lines
6.6 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 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 btype 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>btype = bond type to apply SRP interactions to (can be wildcard, see below)
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<LI>distance = <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 dpd 1.0 1.0 12345 srp 0.8 * min exclude yes
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pair_coeff 1 1 dpd 60.0 50 1.0
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pair_coeff 1 2 none
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pair_coeff 2 2 srp 40.0
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</PRE>
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<PRE>pair_style hybrid srp 0.8 2 mid
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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 pairs of bonds. This potential is useful for preventing
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bonds from passing through one another when a soft non-bonded
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potential acts between beads in, for example, DPD polymer chains. An
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example input script that uses this command is provided in
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examples/USER/srp.
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</P>
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<P>Bonds of specified 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. Note that <I>btype</I> can be specified as an asterisk "*", which
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case the interaction is applied to all bond types. The <I>mid</I> option
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computes <I>r</I> and <I>rij</I> from the midpoint distance between bonds. The
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<I>min</I> option computes <I>r</I> and <I>rij</I> from the minimum distance between
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bonds. The force acting on a bond is mapped onto the two bond atoms
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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> to
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be a fictitious "particle" of type <I>bptype</I>, where <I>bptype</I> is the
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largest atom type in the system. There cannot be any actual particles
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assigned to this atom type. This means you must specify the number of
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types in your system to be one larger would normally be the case,
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e.g. via the <A HREF = "create_box.html">create_box</A> or
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<A HREF = "read_data.html">read_data</A> commands. These ficitious "bond particles"
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are inserted at the beginning of the run, and serve as placeholders
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that define the position of the bonds. This allows neighbor lists to
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be constructed and pairwise interactions to be computed in almost the
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same way as is done for actual particles. Because bonds interact only
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with other bonds, <A HREF = "pair_hybrid.html">pair_style hybrid</A> should be used
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to turn off interactions between atom type <I>bptype</I> and all other
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types of atoms. An error will be flagged if <A HREF = "pair_hybrid.html">pair_style
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hybrid</A> is not used.
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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>no</I>, first neighbor forces are computed; for <I>yes</I> they are not
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computed. A setting of <I>no</I> cannot be used with the <I>min</I> option for
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distance calculation because the the minimum distance between directly
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connected bonds is zero.
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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.
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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
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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, Sliozberg 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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