2014-09-06 07:09:28 +08:00
|
|
|
<HTML>
|
|
|
|
|
<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>
|
|
|
|
|
</CENTER>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<H3>pair_style snap command
|
|
|
|
|
</H3>
|
|
|
|
|
<P><B>Syntax:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>pair_style snap
|
|
|
|
|
</PRE>
|
|
|
|
|
<P><B>Examples:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>pair_style snap
|
|
|
|
|
pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P
|
|
|
|
|
</PRE>
|
|
|
|
|
<P><B>Description:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>Style <I>snap</I> computes interactions
|
|
|
|
|
using the spectral neighbor analysis potential (SNAP)
|
2014-09-16 01:09:37 +08:00
|
|
|
<A HREF = "#Thompson2014">(Thompson)</A>. Like the GAP framework of Bartok et al.
|
|
|
|
|
<A HREF = "#Bartok2010">(Bartok2010)</A>, <A HREF = "#Bartok2013">(Bartok2013)</A>
|
|
|
|
|
it uses bispectrum components
|
2014-09-06 07:09:28 +08:00
|
|
|
to characterize the local neighborhood of each atom
|
|
|
|
|
in a very general way. The mathematical definition of the
|
|
|
|
|
bispectrum calculation used by SNAP is identical
|
|
|
|
|
to that used of <A HREF = "compute_sna_atom.html">compute sna/atom</A>.
|
|
|
|
|
In SNAP, the total energy is decomposed into a sum over
|
|
|
|
|
atom energies. The energy of atom <I>i</I> is
|
|
|
|
|
expressed as a weighted sum over bispectrum components.
|
|
|
|
|
</P>
|
|
|
|
|
<CENTER><IMG SRC = "Eqs/pair_snap.jpg">
|
|
|
|
|
</CENTER>
|
|
|
|
|
<P>where <I>B_k^i</I> is the <I>k</I>-th bispectrum component of atom <I>i</I>,
|
|
|
|
|
and <I>beta_k^alpha_i</I> is the corresponding linear coefficient
|
|
|
|
|
that depends on <I>alpha_i</I>, the SNAP element of atom <I>i</I>. The
|
|
|
|
|
number of bispectrum components used and their definitions
|
|
|
|
|
depend on the values of <I>twojmax</I> and <I>diagonalstyle</I>
|
|
|
|
|
defined in the SNAP parameter file described below.
|
|
|
|
|
The bispectrum calculation is described in more detail
|
|
|
|
|
in <A HREF = "compute_sna_atom.html">compute sna/atom</A>.
|
|
|
|
|
</P>
|
|
|
|
|
<P>Note that unlike for other potentials, cutoffs for SNAP potentials are
|
|
|
|
|
not set in the pair_style or pair_coeff command; they are specified in
|
|
|
|
|
the SNAP potential files themselves.
|
|
|
|
|
</P>
|
|
|
|
|
<P>Only a single pair_coeff command is used with the <I>snap</I> style which
|
|
|
|
|
specifies two SNAP files and the list SNAP element(s) to be
|
|
|
|
|
extracted.
|
|
|
|
|
The SNAP elements are mapped to LAMMPS atom types by specifying
|
|
|
|
|
N additional arguments after the 2nd filename in the pair_coeff
|
|
|
|
|
command, where N is the number of LAMMPS atom types:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>SNAP element file
|
|
|
|
|
<LI>Elem1, Elem2, ...
|
|
|
|
|
<LI>SNAP parameter file
|
|
|
|
|
<LI>N element names = mapping of SNAP elements to atom types
|
|
|
|
|
</UL>
|
|
|
|
|
<P>As an example, if a LAMMPS indium phosphide simulation has 4 atoms
|
|
|
|
|
types, with the first two being indium and the 3rd and 4th being
|
|
|
|
|
phophorous, the pair_coeff command would look like this:
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P
|
|
|
|
|
</PRE>
|
|
|
|
|
<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
|
|
|
|
|
The two filenames are for the element and parameter files, respectively.
|
|
|
|
|
The 'In' and 'P' arguments (between the file names) are the two elements
|
|
|
|
|
which will be extracted from the element file. The
|
|
|
|
|
two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
|
|
|
|
|
SNAP 'In' element. The two trailing 'P' arguments map LAMMPS atom types
|
|
|
|
|
3 and 4 to the SNAP 'P' element.
|
|
|
|
|
</P>
|
|
|
|
|
<P>If a SNAP mapping value is
|
|
|
|
|
specified as NULL, the mapping is not performed.
|
|
|
|
|
This can be used when a <I>snap</I> potential is used as part of the
|
|
|
|
|
<I>hybrid</I> pair style. The NULL values are placeholders for atom types
|
|
|
|
|
that will be used with other potentials.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The name of the SNAP element file usually ends in the
|
|
|
|
|
".snapcoeff" extension. It may contain coefficients
|
|
|
|
|
for many SNAP elements.
|
|
|
|
|
Only those elements listed in the pair_coeff command are extracted.
|
|
|
|
|
The name of the SNAP parameter file usually ends in the ".snapparam"
|
|
|
|
|
extension. It contains a small number
|
|
|
|
|
of parameters that define the overall form of the SNAP potential.
|
|
|
|
|
See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
|
|
|
|
|
to specify the path for these files.
|
|
|
|
|
</P>
|
|
|
|
|
<P>Quite commonly,
|
|
|
|
|
SNAP potentials are combined with one or more other LAMMPS pair styles
|
|
|
|
|
using the <I>hybrid/overlay</I> pair style. As an example, the SNAP
|
|
|
|
|
tantalum potential provided in the LAMMPS potentials directory
|
|
|
|
|
combines the <I>snap</I> and <I>zbl</I> pair styles. It is invoked
|
|
|
|
|
by the following commands:
|
|
|
|
|
</P>
|
|
|
|
|
<PRE> variable zblcutinner equal 4
|
|
|
|
|
variable zblcutouter equal 4.8
|
|
|
|
|
variable zblz equal 73
|
|
|
|
|
pair_style hybrid/overlay &
|
|
|
|
|
zbl ${zblcutinner} ${zblcutouter} snap
|
|
|
|
|
pair_coeff * * zbl 0.0
|
|
|
|
|
pair_coeff 1 1 zbl ${zblz}
|
|
|
|
|
pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
|
|
|
|
|
../potentials/Ta06A.snapparam Ta
|
|
|
|
|
</PRE>
|
|
|
|
|
<P>It is convenient to keep these commands in a separate file that can
|
|
|
|
|
be inserted in any LAMMPS input script using the <A HREF = "include.html">include</A>
|
|
|
|
|
command.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The top of the SNAP element file can contain any number of blank and comment
|
|
|
|
|
lines (start with #), but follows a strict
|
|
|
|
|
format after that. The first non-blank non-comment
|
|
|
|
|
line must contain two integers:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>nelem = Number of elements
|
|
|
|
|
<LI>ncoeff = Number of coefficients
|
|
|
|
|
</UL>
|
|
|
|
|
<P>This is followed by one block for each of the <I>nelem</I> elements.
|
|
|
|
|
The first line of each block contains three entries:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>Element symbol (text string)
|
|
|
|
|
<LI>R = Element radius (distance units)
|
|
|
|
|
<LI>w = Element weight (dimensionless)
|
|
|
|
|
</UL>
|
|
|
|
|
<P>This line is followed by <I>ncoeff</I> coefficients, one per line.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The SNAP parameter file can contain blank and comment lines (start
|
|
|
|
|
with #) anywhere. Each non-blank non-comment line must contain one
|
|
|
|
|
keyword/value pair. The required keywords are <I>rcutfac</I> and
|
|
|
|
|
<I>twojmax</I>. Optional keywords are <I>rfac0</I>, <I>rmin0</I>, <I>diagonalstyle</I>,
|
|
|
|
|
and <I>switchflag</I>.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The default values for these keywords are
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI><I>rfac0</I> = 0.99363
|
|
|
|
|
<LI><I>rmin0</I> = 0.0
|
|
|
|
|
<LI><I>diagonalstyle</I> = 3
|
|
|
|
|
<LI><I>switchflag</I> = 0
|
|
|
|
|
</UL>
|
|
|
|
|
<P>Detailed definitions of these keywords are given on the <A HREF = "compute_sna_atom.html">compute
|
|
|
|
|
sna/atom</A> doc page.
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
|
|
|
|
|
</P>
|
|
|
|
|
<P>For atom type pairs I,J and I != J, where types I and J correspond to
|
|
|
|
|
two different element types, mixing is performed by LAMMPS with
|
|
|
|
|
user-specifiable parameters as described above. You never need to
|
|
|
|
|
specify a pair_coeff command with I != J arguments for this style.
|
|
|
|
|
</P>
|
|
|
|
|
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
|
|
|
|
|
shift, table, and tail options.
|
|
|
|
|
</P>
|
|
|
|
|
<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
|
|
|
|
|
files</A>, since it is stored in potential files. Thus, you
|
|
|
|
|
need to re-specify the pair_style and pair_coeff commands in an input
|
|
|
|
|
script that reads a restart file.
|
|
|
|
|
</P>
|
|
|
|
|
<P>This pair style can only be used via the <I>pair</I> keyword of the
|
|
|
|
|
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
|
|
|
|
|
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><B>Restrictions:</B>
|
|
|
|
|
</P>
|
2014-09-16 01:09:37 +08:00
|
|
|
<P>This style is part of the SNAP package. It is only enabled if
|
|
|
|
|
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
|
|
|
|
|
LAMMPS</A> section for more info.
|
2014-09-06 07:09:28 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Related commands:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P><A HREF = "compute_sna_atom.html">compute sna/atom</A>,
|
|
|
|
|
<A HREF = "compute_sna_atom.html">compute snad/atom</A>,
|
|
|
|
|
<A HREF = "compute_sna_atom.html">compute snav/atom</A>
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Default:</B> none
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<A NAME = "Thompson2014"></A>
|
|
|
|
|
|
2014-09-17 22:44:47 +08:00
|
|
|
<P><B>(Thompson)</B> Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
|
|
|
|
|
available at <A HREF = "http://arxiv.org/abs/1409.3880">arXiv:1409.3880</A>
|
2014-09-06 07:09:28 +08:00
|
|
|
</P>
|
|
|
|
|
<A NAME = "Bartok2010"></A>
|
|
|
|
|
|
2014-09-16 01:09:37 +08:00
|
|
|
<P><B>(Bartok2010)</B> Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
|
|
|
|
|
</P>
|
|
|
|
|
<A NAME = "Bartok2013"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Bartok2013)</B> Bartok, Gillan, Manby, Csanyi, Phys Rev B 87, 184115 (2013).
|
2014-09-06 07:09:28 +08:00
|
|
|
</P>
|
|
|
|
|
</HTML>
|
