forked from lijiext/lammps
168 lines
6.4 KiB
HTML
168 lines
6.4 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 lj/sdk command
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</H3>
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<H3>pair_style lj/sdk/gpu command
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</H3>
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<H3>pair_style lj/sdk/omp command
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</H3>
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<H3>pair_style lj/sdk/coul/long command
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</H3>
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<H3>pair_style lj/sdk/coul/long/gpu command
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</H3>
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<H3>pair_style lj/sdk/coul/long/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/sdk</I> or <I>lj/sdk/coul/long</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/sdk</I> args = cutoff
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cutoff = global cutoff for Lennard Jones interactions (distance units)
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<I>lj/sdk/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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</PRE>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style lj/sdk 2.5
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pair_coeff 1 1 lj12_6 1 1.1 2.8
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</PRE>
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<PRE>pair_style lj/sdk/coul/long 10.0
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pair_style lj/sdk/coul/long 10.0 12.0
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pair_coeff 1 1 lj9_6 100.0 3.5 12.0
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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/sdk</I> styles compute a 9/6, 12/4, or 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_cmm.jpg">
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</CENTER>
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<P>as required for the SDK Coarse-grained MD parametrization discussed in
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<A HREF = "#Shinoda">(Shinoda)</A> and <A HREF = "#DeVane">(DeVane)</A>. Rc is the cutoff.
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</P>
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<P>Style <I>lj/sdk/coul/long</I> computes the adds Coulombic interactions
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with an additional damping factor applied so it can be used in
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conjunction with the <A HREF = "kspace_style.html">kspace_style</A> command and
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its <I>ewald</I> or <I>pppm</I> or <I>pppm/cg</I> option. The Coulombic cutoff
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specified for this style means that pairwise interactions within
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this distance are computed directly; interactions outside that
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distance are computed in reciprocal space.
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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>cg_type (lj9_6, lj12_4, or lj12_6)
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<LI>epsilon (energy units)
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<LI>sigma (distance units)
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<LI>cutoff1 (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. The prefactors
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are chosen so that the potential minimum is at -epsilon.
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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.
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</P>
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<P>For <I>lj/sdk/coul/long</I> only the LJ cutoff can be specified since a
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Coulombic cutoff cannot be specified for an individual I,J type pair.
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All type pairs use the same global Coulombic cutoff specified in the
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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>intel</I>, <I>kk</I>, <I>omp</I> or <I>opt</I> suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.
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</P>
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<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
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KOKKOS, USER-OMP, and OPT packages respectively. They are only
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enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
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LAMMPS</A> 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, table, tail correction, restart, and 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/sdk pair styles <I>cannot</I> be mixed,
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since different pairs may have different exponents. So all parameters
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for all pairs have to be specified explicitly through the "pair_coeff"
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command. Defining then in a data file is also not supported, due to
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limitations of that file format.
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</P>
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<P>All of the lj/sdk 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/sdk/coul/long</I> pair styles support the
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<A HREF = "pair_modify.html">pair_modify</A> table option since they can tabulate
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the short-range portion of the long-range Coulombic interaction.
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</P>
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<P>All of the lj/sdk 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/sdk and lj/cut/coul/long pair styles do not support
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the use of the <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.
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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>All of the lj/sdk pair styles are part of the USER-CG-CMM package.
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The <I>lj/sdk/coul/long</I> style also requires the KSPACE package to be
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built (which is enabled by default). They are only enabled if LAMMPS
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was built with that package. See the <A HREF = "Section_start.html#start_3">Making
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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 = "angle_sdk.html">angle_style sdk</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 = "Shinoda"></A>
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<P><B>(Shinoda)</B> Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
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</P>
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<A NAME = "DeVane"></A>
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<P><B>(DeVane)</B> Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
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</P>
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</HTML>
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