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276 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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<H3>pair_style lj/cut command
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</H3>
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<H3>pair_style lj/cut/gpu command
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</H3>
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<H3>pair_style lj/cut/opt command
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</H3>
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<H3>pair_style lj/cut/coul/cut command
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</H3>
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<H3>pair_style lj/cut/coul/debye command
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</H3>
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<H3>pair_style lj/cut/coul/long command
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</H3>
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<H3>pair_style lj/cut/coul/long/tip4p 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</I> or <I>lj/cut/gpu</I> or <I>lj/cut/opt</I> or <I>lj/cut/coul/cut</I> or <I>lj/cut/coul/debye</I> or <I>lj/cut/coul/long</I> or <I>lj/cut/coul/long/tip4p</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</I> args = cutoff
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cutoff = global cutoff for Lennard Jones interactions (distance units)
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<I>lj/cut/gpu</I> args = gpumode gpuID cutoff
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gpumode = <I>one/node</I> or <I>one/gpu</I> or <I>multi/gpu</I>
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gpuID = ID or number of GPUs
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cutoff = global cutoff for Lennard Jones interactions (distance units)
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<I>lj/cut/opt</I> args = cutoff
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cutoff = global cutoff for Lennard Jones interactions (distance units)
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<I>lj/cut/coul/cut</I> args = cutoff (cutoff2)
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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/debye</I> args = kappa cutoff (cutoff2)
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kappa = Debye length (inverse distance units)
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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</I> args = cutoff (cutoff2)
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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/tip4p</I> args = otype htype btype atype qdist 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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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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</PRE>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style lj/cut 2.5
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pair_style lj/cut/gpu one/node 0 2.5
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pair_style lj/cut/opt 2.5
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pair_coeff * * 1 1
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pair_coeff 1 1 1 1.1 2.8
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</PRE>
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<PRE>pair_style lj/cut/coul/cut 10.0
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pair_style lj/cut/coul/cut 10.0 8.0
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pair_coeff * * 100.0 3.0
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pair_coeff 1 1 100.0 3.5 9.0
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pair_coeff 1 1 100.0 3.5 9.0 9.0
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</PRE>
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<PRE>pair_style lj/cut/coul/debye 1.5 3.0
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pair_style lj/cut/coul/debye 1.5 2.5 5.0
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pair_coeff * * 1.0 1.0
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pair_coeff 1 1 1.0 1.5 2.5
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pair_coeff 1 1 1.0 1.5 2.5 5.0
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</PRE>
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<PRE>pair_style lj/cut/coul/long 10.0
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pair_style lj/cut/coul/long 10.0 8.0
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pair_coeff * * 100.0 3.0
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pair_coeff 1 1 100.0 3.5 9.0
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</PRE>
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<PRE>pair_style lj/cut/coul/long/tip4p 1 2 7 8 0.3 12.0
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pair_style lj/cut/coul/long/tip4p 1 2 7 8 0.3 12.0 10.0
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pair_coeff * * 100.0 3.0
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pair_coeff 1 1 100.0 3.5 9.0
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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</I> styles compute the standard 12/6 Lennard-Jones potential,
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given by
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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>Rc is the cutoff.
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</P>
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<P>Style <I>lj/cut/gpu</I> is a GPU-enabled version of style <I>lj/cut</I> that
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should give identical answers. Depending on system size and the GPU
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processor you have on your system, it may be 4x faster (for the
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pairwise portion of the run time). See more details below.
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</P>
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<P>Style <I>lj/cut/opt</I> is an optimized version of style <I>lj/cut</I> that
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should give identical answers. Depending on system size and the
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processor you are running on, it may be 5-25% faster (for the pairwise
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portion of the run time).
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</P>
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<P>Style <I>lj/cut/coul/cut</I> adds a Coulombic pairwise interaction given by
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</P>
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<CENTER><IMG SRC = "Eqs/pair_coulomb.jpg">
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</CENTER>
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<P>where C is an energy-conversion constant, Qi and Qj are the charges on
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the 2 atoms, and epsilon is the dielectric constant which can be set
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by the <A HREF = "dielectric.html">dielectric</A> command. If one cutoff is
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specified in the pair_style command, it is used for both the LJ and
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Coulombic terms. If two cutoffs are specified, they are used as
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cutoffs for the LJ and Coulombic terms respectively.
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</P>
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<P>Style <I>lj/cut/coul/debye</I> adds an additional exp() damping factor
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to the Coulombic term, given by
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</P>
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<CENTER><IMG SRC = "Eqs/pair_debye.jpg">
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</CENTER>
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<P>where kappa is the Debye length. This potential is another way to
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mimic the screening effect of a polar solvent.
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</P>
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<P>Style <I>lj/cut/coul/long</I> computes the same Coulombic interactions as
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style <I>lj/cut/coul/cut</I> except that an additional damping factor is
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applied to the Coulombic term so it can be used in conjunction with
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the <A HREF = "kspace_style.html">kspace_style</A> command and its <I>ewald</I> or <I>pppm</I>
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option. The Coulombic cutoff specified for this style means that
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pairwise interactions within this distance are computed directly;
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interactions outside that distance are computed in reciprocal space.
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</P>
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<P>Style <I>lj/cut/coul/long/tip4p</I> implements the TIP4P water model of
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<A HREF = "#Jorgensen">(Jorgensen)</A>, which introduces a massless site located a
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short distance away from the oxygen atom along the bisector of the HOH
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angle. The atomic types of the oxygen and hydrogen atoms, the bond
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and angle types for OH and HOH interactions, and the distance to the
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massless charge site are specified as pair_style arguments.
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</P>
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<P>IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom
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IDs for the O and 2 H atoms must be consecutive, with the O atom
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first. This is to enable LAMMPS to "find" the 2 H atoms associated
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with each O atom. For example, if the atom ID of an O atom in a TIP4P
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water molecule is 500, then its 2 H atoms must have IDs 501 and 502.
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</P>
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<P>See the <A HREF = "Section_howto.html#4_8">howto section</A> for more information on
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how to use the TIP4P pair style.
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</P>
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<P>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>cutoff1 (distance units)
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<LI>cutoff2 (distance units)
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</UL>
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<P>Note that sigma is defined in the LJ formula as the zero-crossing
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distance for the potential, not as the energy minimum at 2^(1/6)
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sigma.
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</P>
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<P>The latter 2 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</I>, since it
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has no Coulombic terms.
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</P>
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<P>For <I>lj/cut/coul/long</I> and <I>lj/cut/coul/long/tip4p</I> only the LJ cutoff
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can be specified since a Coulombic cutoff cannot be specified for an
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individual I,J type pair. All type pairs use the same global
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Coulombic cutoff specified in the pair_style command.
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</P>
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<HR>
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<P>The <I>lj/cut/gpu</I> style is identical to the <I>lj/cut</I> style, except that
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each processor off-loads its pairwise calculations to a GPU chip.
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Depending on the hardware available on your system this can provide a
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speed-up. See the <A HREF = "Section_start.html#2_8">Running on GPUs</A> section of
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the manual for more details about hardware and software requirements
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for using GPUs.
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</P>
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<P>The <I>gpumode</I> and <I>gpuID</I> settings in the pair_style command refer to
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how the GPUs on your system are configured.
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</P>
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<P>Set <I>gpumode</I> to <I>one/node</I> if you have a single compute "node" on
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your system, which may have multiple cores and/or GPUs. <I>GpuID</I>
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should be set to the ID of the (first) GPU you wish to use with LAMMPS
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(another GPU might be driving your display).
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</P>
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<P>Set <I>gpumode</I> to <I>one/gpu</I> if you have multiple compute "nodes" on
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your system, with one GPU per node. <I>GpuID</I> should be set to the ID
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of the GPU.
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</P>
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<P>Set <I>gpumode</I> to <I>multi/gpu</I> if you have multiple compute "nodes" on
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your system, each with multiple GPUs. <I>GpuID</I> should be set to the
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number of GPUs per node.
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</P>
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<P>More details about these settings and various possible hardware
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configuration are in <A HREF = "Section_start.html#2_8">this section</A> of the
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manual.
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</P>
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<P>Additional requirements in your input script to run with style
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<I>lj/cut/gpu</I> are as follows:
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</P>
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<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</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>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
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and cutoff distance for all of the lj/cut pair styles 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>All of the lj/cut pair styles support the
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<A HREF = "pair_modify.html">pair_modify</A> shift option for the energy of the
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Lennard-Jones portion of the pair interaction.
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</P>
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<P>The <I>lj/cut/coul/long</I> and <I>lj/cut/coul/long/tip4p</I> pair styles
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support the <A HREF = "pair_modify.html">pair_modify</A> table option since they can
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tabulate the short-range portion of the long-range Coulombic
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interaction.
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</P>
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<P>All of the lj/cut pair styles support the
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<A HREF = "pair_modify.html">pair_modify</A> tail option for adding a long-range
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tail correction to the energy and pressure of the Lennard-Jones
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portion of the pair interaction.
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</P>
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<P>All of the lj/cut pair styles write their information to <A HREF = "restart.html">binary
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restart files</A>, so pair_style and pair_coeff commands do
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not need to be specified in an input script that reads a restart file.
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</P>
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<P>The lj/cut and lj/cut/coul/long pair styles support the use of the
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<I>inner</I>, <I>middle</I>, and <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
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respa</A> command, meaning the pairwise forces can be
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partitioned by distance at different levels of the rRESPA hierarchy.
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The other styles only support the <I>pair</I> keyword of run_style respa.
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See the <A HREF = "run_style.html">run_style</A> command for details.
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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>The <I>lj/cut/coul/long</I> and <I>lj/cut/coul/long/tip4p</I> styles are part of
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the "kspace" package. The <I>lj/cut/gpu</I> style is part of the "gpu"
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package. The <I>lj/cut/opt</I> style is part of the "opt" package. They
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are only enabled if LAMMPS was built with those packages. See the
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<A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for more info. Note
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that the "kspace" package is installed by default.
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</P>
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<P>On some 64-bit machines, compiling with -O3 appears to break the
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Coulombic tabling option used by the <I>lj/cut/coul/long</I> style. See
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the "Additional build tips" section of the Making LAMMPS documentation
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pages for workarounds on this issue.
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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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</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 = "Jorgensen"></A>
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<P><B>(Jorgensen)</B> Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
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Phys, 79, 926 (1983).
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</P>
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</HTML>
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