forked from lijiext/lammps
194 lines
6.8 KiB
Plaintext
194 lines
6.8 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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pair_style snap command :h3
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[Syntax:]
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pair_style snap :pre
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[Examples:]
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pair_style snap
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pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P :pre
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[Description:]
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Style {snap} computes interactions
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using the spectral neighbor analysis potential (SNAP)
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"(Thompson)"_#Thompson2014. Like the GAP framework of Bartok et al.
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"(Bartok2010)"_#Bartok2010, "(Bartok2013)"_#Bartok2013
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it uses bispectrum components
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to characterize the local neighborhood of each atom
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in a very general way. The mathematical definition of the
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bispectrum calculation used by SNAP is identical
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to that used of "compute sna/atom"_compute_sna_atom.html.
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In SNAP, the total energy is decomposed into a sum over
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atom energies. The energy of atom {i} is
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expressed as a weighted sum over bispectrum components.
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:c,image(Eqs/pair_snap.jpg)
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where {B_k^i} is the {k}-th bispectrum component of atom {i},
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and {beta_k^alpha_i} is the corresponding linear coefficient
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that depends on {alpha_i}, the SNAP element of atom {i}. The
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number of bispectrum components used and their definitions
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depend on the values of {twojmax} and {diagonalstyle}
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defined in the SNAP parameter file described below.
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The bispectrum calculation is described in more detail
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in "compute sna/atom"_compute_sna_atom.html.
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Note that unlike for other potentials, cutoffs for SNAP potentials are
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not set in the pair_style or pair_coeff command; they are specified in
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the SNAP potential files themselves.
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Only a single pair_coeff command is used with the {snap} style which
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specifies two SNAP files and the list SNAP element(s) to be
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extracted.
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The SNAP elements are mapped to LAMMPS atom types by specifying
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N additional arguments after the 2nd filename in the pair_coeff
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command, where N is the number of LAMMPS atom types:
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SNAP element file
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Elem1, Elem2, ...
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SNAP parameter file
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N element names = mapping of SNAP elements to atom types :ul
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As an example, if a LAMMPS indium phosphide simulation has 4 atoms
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types, with the first two being indium and the 3rd and 4th being
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phophorous, the pair_coeff command would look like this:
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pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P :pre
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The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
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The two filenames are for the element and parameter files, respectively.
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The 'In' and 'P' arguments (between the file names) are the two elements
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which will be extracted from the element file. The
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two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
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SNAP 'In' element. The two trailing 'P' arguments map LAMMPS atom types
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3 and 4 to the SNAP 'P' element.
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If a SNAP mapping value is
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specified as NULL, the mapping is not performed.
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This can be used when a {snap} potential is used as part of the
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{hybrid} pair style. The NULL values are placeholders for atom types
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that will be used with other potentials.
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The name of the SNAP element file usually ends in the
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".snapcoeff" extension. It may contain coefficients
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for many SNAP elements.
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Only those elements listed in the pair_coeff command are extracted.
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The name of the SNAP parameter file usually ends in the ".snapparam"
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extension. It contains a small number
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of parameters that define the overall form of the SNAP potential.
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See the "pair_coeff"_pair_coeff.html doc page for alternate ways
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to specify the path for these files.
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Quite commonly,
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SNAP potentials are combined with one or more other LAMMPS pair styles
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using the {hybrid/overlay} pair style. As an example, the SNAP
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tantalum potential provided in the LAMMPS potentials directory
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combines the {snap} and {zbl} pair styles. It is invoked
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by the following commands:
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variable zblcutinner equal 4
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variable zblcutouter equal 4.8
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variable zblz equal 73
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pair_style hybrid/overlay &
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zbl $\{zblcutinner\} $\{zblcutouter\} snap
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pair_coeff * * zbl 0.0
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pair_coeff 1 1 zbl $\{zblz\}
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pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
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../potentials/Ta06A.snapparam Ta :pre
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It is convenient to keep these commands in a separate file that can
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be inserted in any LAMMPS input script using the "include"_include.html
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command.
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The top of the SNAP element file can contain any number of blank and comment
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lines (start with #), but follows a strict
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format after that. The first non-blank non-comment
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line must contain two integers:
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nelem = Number of elements
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ncoeff = Number of coefficients :ul
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This is followed by one block for each of the {nelem} elements.
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The first line of each block contains three entries:
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Element symbol (text string)
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R = Element radius (distance units)
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w = Element weight (dimensionless) :ul
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This line is followed by {ncoeff} coefficients, one per line.
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The SNAP parameter file can contain blank and comment lines (start
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with #) anywhere. Each non-blank non-comment line must contain one
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keyword/value pair. The required keywords are {rcutfac} and
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{twojmax}. Optional keywords are {rfac0}, {rmin0}, {diagonalstyle},
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and {switchflag}.
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The default values for these keywords are
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{rfac0} = 0.99363
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{rmin0} = 0.0
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{diagonalstyle} = 3
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{switchflag} = 0 :ul
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Detailed definitions of these keywords are given on the "compute
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sna/atom"_compute_sna_atom.html doc page.
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:line
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[Mixing, shift, table, tail correction, restart, rRESPA info]:
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For atom type pairs I,J and I != J, where types I and J correspond to
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two different element types, mixing is performed by LAMMPS with
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user-specifiable parameters as described above. You never need to
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specify a pair_coeff command with I != J arguments for this style.
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This pair style does not support the "pair_modify"_pair_modify.html
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shift, table, and tail options.
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This pair style does not write its information to "binary restart
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files"_restart.html, since it is stored in potential files. Thus, you
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need to re-specify the pair_style and pair_coeff commands in an input
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script that reads a restart file.
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This pair style can only be used via the {pair} keyword of the
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"run_style respa"_run_style.html command. It does not support the
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{inner}, {middle}, {outer} keywords.
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:line
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[Restrictions:]
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This style is part of the SNAP package. It is only enabled if
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LAMMPS was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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[Related commands:]
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"compute sna/atom"_compute_sna_atom.html,
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"compute snad/atom"_compute_sna_atom.html,
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"compute snav/atom"_compute_sna_atom.html
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[Default:] none
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:line
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:link(Thompson2014)
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[(Thompson)] Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
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available at "arXiv:1409.3880"_http://arxiv.org/abs/1409.3880
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:link(Bartok2010)
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[(Bartok2010)] Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
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:link(Bartok2013)
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[(Bartok2013)] Bartok, Gillan, Manby, Csanyi, Phys Rev B 87, 184115 (2013).
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