forked from lijiext/lammps
257 lines
11 KiB
HTML
257 lines
11 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 lj/cut/soft command
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</H3>
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<H3>pair_style lj/cut/soft/omp command
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</H3>
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<H3>pair_style lj/cut/coul/cut/soft command
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</H3>
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<H3>pair_style lj/cut/coul/cut/soft/omp command
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</H3>
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<H3>pair_style lj/cut/coul/long/soft command
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</H3>
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<H3>pair_style lj/cut/coul/long/soft/omp command
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</H3>
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<H3>pair_style lj/cut/tip4p/long/soft command
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</H3>
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<H3>pair_style lj/cut/tip4p/long/soft/omp command
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</H3>
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<H3>pair_style coul/cut/soft command
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</H3>
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<H3>pair_style coul/cut/soft/omp command
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</H3>
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<H3>pair_style coul/long/soft command
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</H3>
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<H3>pair_style coul/long/soft/omp command
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</H3>
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<H3>pair_style tip4p/long/soft command
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</H3>
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<H3>pair_style tip4p/long/soft/omp 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 style args
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</PRE>
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<UL><LI>style = <I>lj/cut/soft</I> or <I>lj/cut/coul/cut/soft</I> or <I>lj/cut/coul/long/soft</I> or <I>lj/cut/tip4p/long/soft</I> or <I>coul/cut/soft</I> or <I>coul/long/soft</I> or <I>tip4p/long/soft</I>
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<LI>args = list of arguments for a particular style
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</UL>
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<PRE> <I>lj/cut/soft</I> args = n alpha_lj cutoff
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n, alpha_LJ = parameters of soft-core potential
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cutoff = global cutoff for Lennard-Jones interactions (distance units)
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<I>lj/cut/coul/cut/soft</I> args = n alpha_LJ alpha_C cutoff (cutoff2)
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n, alpha_LJ, alpha_C = parameters of soft-core potential
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units)
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<I>lj/cut/coul/long/soft</I> args = n alpha_LJ alpha_C cutoff
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n, alpha_LJ, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units)
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<I>lj/cut/tip4p/long/soft</I> args = otype htype btype atype qdist n alpha_LJ alpha_C cutoff (cutoff2)
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otype,htype = atom types for TIP4P O and H
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btype,atype = bond and angle types for TIP4P waters
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qdist = distance from O atom to massless charge (distance units)
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n, alpha_LJ, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units)
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<I>coul/cut/soft</I> args = n alpha_C cutoff
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n, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for Coulomb interactions (distance units)
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<I>coul/long/soft</I> args = n alpha_C cutoff
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n, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for Coulomb interactions (distance units)
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<I>tip4p/long/soft</I> args = otype htype btype atype qdist n alpha_C cutoff
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otype,htype = atom types for TIP4P O and H
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btype,atype = bond and angle types for TIP4P waters
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qdist = distance from O atom to massless charge (distance units)
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n, alpha_C = parameters of the soft-core potential
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cutoff = global cutoff for Coulomb interactions (distance units)
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</PRE>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style lj/cut/soft 2.0 0.5 9.5
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pair_coeff * * 0.28 3.1 1.0
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pair_coeff 1 1 0.28 3.1 1.0 9.5
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</PRE>
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<PRE>pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5
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pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 9.5
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pair_coeff * * 0.28 3.1 1.0
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pair_coeff 1 1 0.28 3.1 0.5 10.0
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pair_coeff 1 1 0.28 3.1 0.5 10.0 9.5
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</PRE>
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<PRE>pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5
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pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 9.5
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pair_coeff * * 0.28 3.1 1.0
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pair_coeff 1 1 0.28 3.1 0.0 10.0
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pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5
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</PRE>
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<PRE>pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
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pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5
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pair_coeff * * 0.155 3.1536 1.0
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pair_coeff 1 1 0.155 3.1536 1.0 9.5
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</PRE>
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<PRE>pair_style coul/long/soft 1.0 10.0 9.5
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pair_coeff * * 1.0
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pair_coeff 1 1 1.0 9.5
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</PRE>
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<PRE>pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
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pair_coeff * * 1.0
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pair_coeff 1 1 1.0 9.5
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>The <I>lj/cut/soft</I> style and substyles compute the 12/6
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Lennard-Jones and Coulomb potential modified by a soft core, in order
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to avoid singularities during free energy calculations when sites are
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created or anihilated <A HREF = "#Beutler">(Beutler)</A>,
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</P>
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<CENTER><IMG SRC = "Eqs/pair_lj_soft.jpg">
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</CENTER>
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<P>Coulomb interactions are also damped with a soft core at short
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distance,
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</P>
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<CENTER><IMG SRC = "Eqs/pair_coul_soft.jpg">
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</CENTER>
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<P>In the Coulomb part C is an energy-conversion constant, q_i and q_j are
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the charges on the 2 atoms, and epsilon is the dielectric constant
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which can be set by the <A HREF = "dielectric.html">dielectric</A> command.
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</P>
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<P>The coefficient lambda is an activation parameter. When lambda = 1 the
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pair potentiel is identical to a Lennard-Jones term plus a Coulomb
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term. When lambda = 0 the pair interactions are deactivated. The
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transition between these two extrema is smoothed by a repulsive soft
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core in order to avoid singularities in potential energy and forces
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when sites are created or anihilated and can overlap
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<A HREF = "#Beutler">(Beutler)</A>.
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</P>
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<P>The paratemers n, alpha_LJ and alpha_C are set in the
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<A HREF = "pair_style.html">pair_style</A> command, before the cutoffs. Usual
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choices for the exponent are n = 2 or n = 1. For the remaining
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coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are
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appropriate choices. Plots of the LJ and Coulomb terms are shown
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below, for lambda ranging from 1 ro 0 every 0.1.
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</P>
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<CENTER><IMG SRC = "JPG/lj_soft.jpg"><IMG SRC = "JPG/coul_soft.jpg">
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</CENTER>
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<P>The <I>lj/cut/tip4p/long/soft</I> implements a soft-core version of the
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TIP4P water model. The usage of this pair style is documented in the
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<A HREF = "pair_lj.html">pair_lj</A> styles. The soft-core version introduces the
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lambda parameter to the list of arguments, after epsilon and sigma in
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the <A HREF = "pair_coeff.html">pair_coeff</A> command. The paratemers n, alpha_LJ
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and alpha_C are set in the <A HREF = "pair_style.html">pair_style</A> command,
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before the cutoffs.
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</P>
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<P>The <I>coul/cut/soft</I>, <I>coul/long/soft</I> and <I>tip4p/long/soft</I> substyles
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are designed to be combined with other pair potentials via the
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<A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> command. This is because
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they have no repulsive core. Hence, if used by themselves, there will
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be no repulsion to keep two oppositely charged particles from
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overlapping each other. In this case, if lambda = 1, a singularity may
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occur. These substyles are suitable to represent charges embedded in
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the Lennard-Jones radius of another site (for example hydrogen atoms
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in several water models).
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</P>
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<P>For the <I>lj/cut/coul/cut/soft</I> or <I>lj/cut/coul/long/soft</I> pair styles,
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the following coefficients must be defined for each pair of atoms
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types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
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above, or in the data file or restart files read by the
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<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
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commands, or by mixing as described below:
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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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<LI>lambda (activation parameter between 0 and 1)
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<LI>cutoff1 (distance units)
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<LI>cutoff2 (distance units)
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</UL>
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<P>The latter two coefficients are optional. If not specified, the global
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LJ and Coulombic cutoffs specified in the pair_style command are used.
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If only one cutoff is specified, it is used as the cutoff for both LJ
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and Coulombic interactions for this type pair. If both coefficients
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are specified, they are used as the LJ and Coulombic cutoffs for this
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type pair. You cannot specify 2 cutoffs for style <I>lj/cut/soft</I>,
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since it has no Coulombic terms. For the <I>coul/cut/soft</I> and
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<I>coul/long/soft</I> only lambda and the optional cutoff2 are to be
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specified.
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</P>
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<HR>
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<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> suffix are functionally
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the same as the corresponding style without the suffix. They have
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been optimized to run faster, depending on your available hardware, as
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discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A> of the
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manual. The accelerated styles take the same arguments and should
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produce the same results, except for round-off and precision issues.
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</P>
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<P>These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
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packages, respectively. They are only enabled if LAMMPS was built with
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those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
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section for more info.
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</P>
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<P>You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
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switch</A> when you invoke LAMMPS, or you can
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use the <A HREF = "suffix.html">suffix</A> command in your input script.
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</P>
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<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
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more instructions on how to use the accelerated styles effectively.
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</P>
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<HR>
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<P><B>Mixing, shift, tail correction, restart info</B>:
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</P>
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<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
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and cutoff distance for this pair style can be mixed.
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The default mix value is <I>geometric</I>. See the "pair_modify" command
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for details.
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</P>
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<P>These pair styles support the <A HREF = "pair_modify.html">pair_modify</A> shift
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option for the energy of the Lennard-Jones portion of the pair
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interaction.
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</P>
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<P>These pair styles support the <A HREF = "pair_modify.html">pair_modify</A> tail
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option for adding a long-range tail correction to the energy and
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pressure for the Lennard-Jones portion of the pair interaction.
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</P>
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<P>These pair styles write information to <A HREF = "restart.html">binary restart
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files</A>, so pair_style and pair_coeff commands do not 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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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>To avoid division by zero do not set sigma = 0. When sites do not
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interact though the Lennard-Jones term use epsilon = 0 and sigma = 1
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for example, or else use the <I>coul/long/soft</I> or similar substyle.
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</P>
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<P>All of the plain <I>soft</I> pair styles are part of the USER-FEP package.
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The <I>long</I> styles also requires the KSPACE package to be installed.
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They are only enabled if LAMMPS was built with that package.
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See the <A HREF = "Section_start.html#start_3">Making 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>, <A HREF = "fix_adapt.html">fix_adapt</A>,
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<A HREF = "fix_adapt_fep.html">fix_adapt/fep</A>, <A HREF = "compute_fep.html">compute_fep</A>
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</P>
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<P><B>Default:</B> none
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</P>
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<HR>
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<A NAME = "Beutler"></A>
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<P><B>(Beutler)</B> Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem
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Phys Lett, 222, 529 (1994).
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</P>
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</HTML>
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