forked from lijiext/lammps
166 lines
6.3 KiB
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166 lines
6.3 KiB
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<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 lj/gromacs command
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</H3>
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<H3>pair_style lj/gromacs/cuda command
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</H3>
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<H3>pair_style lj/gromacs/omp command
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</H3>
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<H3>pair_style lj/gromacs/coul/gromacs command
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</H3>
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<H3>pair_style lj/gromacs/coul/gromacs/cuda command
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</H3>
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<H3>pair_style lj/gromacs/coul/gromacs/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/gromacs</I> or <I>lj/gromacs/coul/gromacs</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/gromacs</I> args = inner outer
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inner, outer = global switching cutoffs for Lennard Jones
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<I>lj/gromacs/coul/gromacs</I> args = inner outer (inner2) (outer2)
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inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
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inner2, outer2 = global switching cutoffs for Coulombic (optional)
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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/gromacs 9.0 12.0
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pair_coeff * * 100.0 2.0
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pair_coeff 2 2 100.0 2.0 8.0 10.0
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</PRE>
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<PRE>pair_style lj/gromacs/coul/gromacs 9.0 12.0
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pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0
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pair_coeff * * 100.0 2.0
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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/gromacs</I> styles compute shifted LJ and Coulombic interactions
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with an additional switching function S(r) that ramps the energy and force
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smoothly to zero between an inner and outer cutoff. It is a commonly
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used potential in the <A HREF = "http://www.gromacs.org">GROMACS</A> MD code and for
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the coarse-grained models of <A HREF = "#Marrink">(Marrink)</A>.
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</P>
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<CENTER><IMG SRC = "Eqs/pair_gromacs.jpg">
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</CENTER>
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<P>R1 is the inner cutoff; Rc is the outer cutoff. The coefficients A, B,
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and C are computed by LAMMPS to perform the shifting and smoothing.
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The function
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S(r) is actually applied once to each term of the LJ formula and once
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to the Coulombic formula, so there are 2 or 3 sets of A,B,C coefficients
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depending on which pair_style is used. The boundary conditions
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applied to the smoothing function are as follows: S(r1) = S'(r1) = 0,
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S(rc) = -F(rc), S'(rc) = -F'(rc), where F(r) is the corresponding term
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in the LJ or Coulombic potential energy function and a
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single quote represents a derivative with respect to r.
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</P>
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<P>The inner and outer cutoff for the LJ and Coulombic terms can be the
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same or different depending on whether 2 or 4 arguments are used in
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the pair_style command. The inner LJ cutoff must be > 0, but the
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inner Coulombic cutoff can be >= 0.
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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>inner (distance units)
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<LI>outer (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 last 2 coefficients are optional inner and outer cutoffs for style
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<I>lj/gromacs</I>. If not specified, the global <I>inner</I> and <I>outer</I> values
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are used.
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</P>
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<P>The last 2 coefficients cannot be used with style
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<I>lj/gromacs/coul/gromacs</I> because this force field does not allow
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varying cutoffs for individual atom pairs; all pairs use the global
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cutoff(s) specified in the pair_style command.
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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,
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as discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
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The accelerated styles take the same arguments and should produce the
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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_6">-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">this section</A> of the manual for more
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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, 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>None of the GROMACS pair styles support the
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<A HREF = "pair_modify.html">pair_modify</A> shift option, since the Lennard-Jones
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portion of the pair interaction is already smoothed to 0.0 at the
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cutoff.
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</P>
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<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
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for this pair style.
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</P>
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<P>None of the GROMACS pair styles support the
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<A HREF = "pair_modify.html">pair_modify</A> tail option for adding long-range tail
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corrections to energy and pressure, since there are no corrections for
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a potential that goes to 0.0 at the cutoff.
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</P>
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<P>All of the GROMACS 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>All of the GROMACS pair styles can only be used via the <I>pair</I>
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keyword of the <A HREF = "run_style.html">run_style respa</A> command. They do not
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support the <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> none
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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 = "Marrink"></A>
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<P><B>(Marrink)</B> Marrink, de Vries, Mark, J Phys Chem B, 108, 750-760 (2004).
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</P>
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</HTML>
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