forked from lijiext/lammps
130 lines
5.1 KiB
HTML
130 lines
5.1 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 nb3b/harmonic command
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</H3>
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<H3>pair_style nb3b/harmonic/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 nb3b/harmonic
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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 nb3b/harmonic
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pair_coeff * * MgOH.nb3bharmonic Mg O H
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>This pair style computes a nonbonded 3-body harmonic potential for the
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energy E of a system of atoms as
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</P>
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<CENTER><IMG SRC = "Eqs/pair_nb3b_harmonic.jpg">
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</CENTER>
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<P>where <I>theta_0</I> is the equilibrium value of the angle and <I>K</I> is a
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prefactor. Note that the usual 1/2 factor is included in <I>K</I>. The form
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of the potential is identical to that used in angle_style <I>harmonic</I>,
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but in this case, the atoms do not need to be explicitly bonded.
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</P>
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<P>Only a single pair_coeff command is used with this style which
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specifies a potential file with parameters for specified elements.
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These are mapped to LAMMPS atom types by specifying N additional
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arguments after the filename in the pair_coeff command, where N is the
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number of LAMMPS atom types:
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</P>
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<UL><LI>filename
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<LI>N element names = mapping of elements to atom types
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</UL>
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<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
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to specify the path for the potential file.
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</P>
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<P>As an example, imagine a file SiC.nb3b.harmonic has potential values
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for Si and C. If your LAMMPS simulation has 4 atoms types and you
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want the 1st 3 to be Si, and the 4th to be C, you would use the
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following pair_coeff command:
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</P>
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<PRE>pair_coeff * * SiC.nb3b.harmonic Si Si Si C
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</PRE>
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<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
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The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
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element in the potential file. The final C argument maps LAMMPS atom
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type 4 to the C element in the potential file. If a mapping value is
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specified as NULL, the mapping is not performed. This can be used
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when the potential is used as part of the <I>hybrid</I> pair style. The
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NULL values are placeholders for atom types that will be used with
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other potentials. An example of a pair_coeff command for use with the
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<I>hybrid</I> pair style is:
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</P>
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<P>pair_coeff * * nb3b/harmonic MgOH.nb3b.harmonic Mg O H
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</P>
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<P>Three-body nonbonded harmonic files in the <I>potentials</I> directory of
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the LAMMPS distribution have a ".nb3b.harmonic" suffix. Lines that
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are not blank or comments (starting with #) define parameters for a
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triplet of elements.
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</P>
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<P>Each entry has six arguments. The first three are atom types as
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referenced in the LAMMPS input file. The first argument specifies the
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central atom. The fourth argument indicates the <I>K</I> parameter. The
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fifth argument indicates <I>theta_0</I>. The sixth argument indicates a
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separation cutoff in Angstroms.
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</P>
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<P>For a given entry, if the second and third arguments are identical,
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then the entry is for a cutoff for the distance between types 1 and 2
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(values for <I>K</I> and <I>theta_0</I> are irrelevant in this case).
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</P>
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<P>For a given entry, if the first three arguments are all different,
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then the entry is for the <I>K</I> and <I>theta_0</I> parameters (the cutoff in
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this case is irrelevant).
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</P>
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<P>It is <I>not</I> required that the potential file contain entries for all
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of the elements listed in the pair_coeff command. It can also contain
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entries for additional elements not being used in a particular
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simulation; LAMMPS ignores those entries.
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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>Restrictions:</B>
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</P>
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<P>This pair style can only be used if LAMMPS was built with the MANYBODY
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package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info on packages.
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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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</HTML>
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