Spectral Neighbor Analysis Potential (SNAP)

This directory contains a spectral neighbor analysis potential (SNAP[1]) Driver. It uses bispectrum components to characterize the local neighborhood of each atom in a very general way.

SNAP model driver

The SNAP driver is written in C++ and it expects a SNAP coefficient file followed by a SNAP parameter file.

Coefficient file format

The format of the SNAP coefficient file is as follows:

Blank lines and lines beginning with the # character are ignored.

nelem, ncoeff

where, nelem is the number of elements, and ncoeff is the number of coefficients.

It follows with one block for each of the nelem elements. Where, the first line of each block contains:

Element, R, W

where, Element is the element symbol (text string), R is the element radius (in distance units), and W is the element weight (dimensionless).

Lines 2, 3,..., ncoeff+1 of each block is

coeffs

where, coeffs are SNAP coefficients, one per line.

Parameter file format

The format of the SNAP parameter file is as follows:

Blank lines and lines beginning with the # character are ignored.
Non-blank and non-comment lines must contain one keyword/value pair.

keyword value

The mandatory keywords are rcutfac and twojmax. Optional keywords are rfac0, rmin0, switchflag, bzeroflag, and quadraticflag.

Hybrid style

SNAP can be used in a hybrid style and in combination with a Ziegler-Biersack-Littmark (ZBL[2,3]) screened nuclear repulsion potential and any other two-body interaction in the table style[3,4] representation.

HYBRID parameter file format

The format of the HYBRID parameter file is as follows:

Blank lines and lines beginning with the # character are ignored.

NOTE: No mixing rule will be used here.

Each pair (i,j) or (j,i) can be assigned to one style. If you specify the same pair for the second time, it wipes out all the previous assignments of that pair and the second one will be calculated for the two interacting atoms of those types.

N

N is the number of elements in the hybrid style

Element_1 Element_2 ... Element_N

Element_1 Element_2 ... Element_N are number of elements names (atom names).

If there is any zbl interaction,

zbl  inner  outer

In the ZBL style, the inner and outer cutoff are the same for all pairs of atom types. It follows by,

Element_i  Element_j  zbl  Z_i  Z_j

where the Element_i and Element_j are the i and j element names respectively. The values of Z_i and Z_j are equal to the atomic numbers of the two atom types.

If there is any table interaction,

table  style  N

where style is the method of interpolation and one of the lookup or linear or spline or bitmap.
N means to use N values in either of the lookup, linear, spline table styles, or
N means to use 2^N values in the bitmap table style.

Element_i  Element_j  table  style_number  filename  keyword  [cutoff]

table style can be used multiple times. For example, if for the interactions between i and i atoms we use a linear table style and for the interactions between i and j atoms, we use a spline table style, then you should list the table style two times as below:

table  linear  1000
table  spline  2000

where, style indexing starts from 1. It means, that the fisrt style is numbered as 1 and the second one as 2 and so on so forth. Later in the pair interactions, the table style must be added after the i, and j atom names followed by the style number and then followed by the remaining coefficients as of filename, keyword, and/or cutoff.
The filename specifies a file containing tabulated energy and force values.
The keyword specifies a section of the file.
The cutoff is an optional coefficient in distance unit.

NOTE: keyword should be unique for each pair interaction

Example 1, where we use 2 styles

table  linear  1000
table  spline  10000
i  i  table  1  ii.table ii_keyword 4.0
i  j  table  2  ij.table ij_keyword

Example 2, we only use one style

table  spline  10000
i  i  table  1  ii.table ii_keyword 4.0
i  j  table  1  ij.table ij_keyword

Example 3, we use one style and only have one tabulated file

table  spline  10000
i  i  table  1  tablefile.txt ii_keyword 4.0
i  j  table  1  tablefile.txt ij_keyword 4.8

References

1. Thompson, Swiler, Trott, Foiles, and Tucker, "Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials," J Comp Phys, 285, 316 (2015).

2. J.F. Ziegler, J. P. Biersack, and U. Littmark, “The Stopping and Range of Ions in Matter,” Volume 1, Pergamon, 1985.

3. https://lammps.sandia.gov

4. https://lammps.sandia.gov/doc/pair_table.html

Contributing

Copyright (c) 2019, Regents of the University of Minnesota.
All rights reserved.

Contributors:
      Yaser Afshar

License

LGPLv2.1