pair_style snap command

Accelerator Variants: snap/kk

Syntax

pair_style snap

Examples

pair_style snap
pair_coeff * * InP.snapcoeff InP.snapparam In In P P

Description

Pair style snap defines the spectral neighbor analysis potential (SNAP), a machine-learning interatomic potential (Thompson). Like the GAP framework of Bartok et al. (Bartok2010), SNAP uses bispectrum components to characterize the local neighborhood of each atom in a very general way. The mathematical definition of the bispectrum calculation and its derivatives w.r.t. atom positions is identical to that used by compute snap, which is used to fit SNAP potentials to ab initio energy, force, and stress data. In SNAP, the total energy is decomposed into a sum over atom energies. The energy of atom i is expressed as a weighted sum over bispectrum components.

\[E^i_{SNAP}(B_1^i,...,B_K^i) = \beta^{\mu_i}_0 + \sum_{k=1}^K \beta_k^{\mu_i} B_k^i\]

where \(B_k^i\) is the k-th bispectrum component of atom i, and \(\beta_k^{\mu_i}\) is the corresponding linear coefficient that depends on \(\mu_i\), the SNAP element of atom i. The number of bispectrum components used and their definitions depend on the value of twojmax and other parameters defined in the SNAP parameter file described below. The bispectrum calculation is described in more detail in compute sna/atom.

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.

Only a single pair_coeff command is used with the snap style which specifies a SNAP coefficient file followed by a SNAP parameter file and then N additional arguments specifying the mapping of SNAP elements to LAMMPS atom types, where N is the number of LAMMPS atom types:

  • SNAP coefficient file

  • SNAP parameter file

  • N element names = mapping of SNAP elements to atom types

As an example, if a LAMMPS indium phosphide simulation has 4 atoms types, with the first two being indium and the third and fourth being phophorous, the pair_coeff command would look like this:

pair_coeff * * snap InP.snapcoeff InP.snapparam In In P P

The first 2 arguments must be * * so as to span all LAMMPS atom types. The two filenames are for the coefficient and parameter files, respectively. 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.

If a SNAP mapping value is specified as NULL, the mapping is not performed. This can be used when a snap potential is used as part of the hybrid pair style. The NULL values are placeholders for atom types that will be used with other potentials.

The name of the SNAP coefficient file usually ends in the “.snapcoeff” extension. It may contain coefficients for many SNAP elements. The only requirement is that it contain at least those element names appearing in the LAMMPS mapping list. 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 pair_coeff doc page for alternate ways to specify the path for these files.

Quite commonly, SNAP potentials are combined with one or more other LAMMPS pair styles using the hybrid/overlay pair style. As an example, the SNAP tantalum potential provided in the LAMMPS potentials directory combines the snap and zbl pair styles. It is invoked by the following commands:

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 Ta06A.snapcoeff Ta06A.snapparam Ta

It is convenient to keep these commands in a separate file that can be inserted in any LAMMPS input script using the include command.

The top of the SNAP coefficient 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:

  • nelem = Number of elements

  • ncoeff = Number of coefficients

This is followed by one block for each of the nelem elements. The first line of each block contains three entries:

  • Element symbol (text string)

  • R = Element radius (distance units)

  • w = Element weight (dimensionless)

This line is followed by ncoeff coefficients, one per line.

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 rcutfac and twojmax. Optional keywords are rfac0, rmin0, switchflag, bzeroflag, quadraticflag, chemflag, bnormflag, wselfallflag, and chunksize.

The default values for these keywords are

  • rfac0 = 0.99363

  • rmin0 = 0.0

  • switchflag = 1

  • bzeroflag = 1

  • quadraticflag = 0

  • chemflag = 0

  • bnormflag = 0

  • wselfallflag = 0

  • chunksize = 2000

If quadraticflag is set to 1, then the SNAP energy expression includes additional quadratic terms that have been shown to increase the overall accuracy of the potential without much increase in computational cost (Wood).

\[E^i_{SNAP}(\mathbf{B}^i) = \beta^{\mu_i}_0 + \boldsymbol{\beta}^{\mu_i} \cdot \mathbf{B}_i + \frac{1}{2}\mathbf{B}^t_i \cdot \boldsymbol{\alpha}^{\mu_i} \cdot \mathbf{B}_i\]

where \(\mathbf{B}_i\) is the K-vector of bispectrum components, \(\boldsymbol{\beta}^{\mu_i}\) is the K-vector of linear coefficients for element \(\mu_i\), and \(\boldsymbol{\alpha}^{\mu_i}\) is the symmetric K by K matrix of quadratic coefficients. The SNAP element file should contain K(K+1)/2 additional coefficients for each element, the upper-triangular elements of \(\boldsymbol{\alpha}^{\mu_i}\).

If chemflag is set to 1, then the energy expression is written in terms of explicit multi-element bispectrum components indexed on ordered triplets of elements, which has been shown to increase the ability of the SNAP potential to capture energy differences in chemically complex systems, at the expense of a significant increase in computational cost (Cusentino).

\[E^i_{SNAP}(\mathbf{B}^i) = \beta^{\mu_i}_0 + \sum_{\kappa,\lambda,\mu} \boldsymbol{\beta}^{\kappa\lambda\mu}_{\mu_i} \cdot \mathbf{B}^{\kappa\lambda\mu}_i\]

where \(\mathbf{B}^{\kappa\lambda\mu}_i\) is the K-vector of bispectrum components for neighbors of elements \(\kappa\), \(\lambda\), and \(\mu\) and \(\boldsymbol{\beta}^{\kappa\lambda\mu}_{\mu_i}\) is the corresponding K-vector of linear coefficients for element \(\mu_i\). The SNAP element file should contain a total of \(K N_{elem}^3\) coefficients for each of the \(N_{elem}\) elements.

The keyword chunksize is only applicable when using the pair style snap with the KOKKOS package and is ignored otherwise. This keyword controls the number of atoms in each pass used to compute the bispectrum components and is used to avoid running out of memory. For example if there are 4000 atoms in the simulation and the chunksize is set to 2000, the bispectrum calculation will be broken up into two passes.

Detailed definitions for all the other keywords are given on the compute sna/atom doc page.

Note

The previously used diagonalstyle keyword was removed in 2019, since all known SNAP potentials use the default value of 3.


Mixing, shift, table, tail correction, restart, rRESPA info

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.

This pair style does not support the pair_modify shift, table, and tail options.

This pair style does not write its information to binary restart files, 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.

This pair style can only be used via the pair keyword of the run_style respa command. It does not support the inner, middle, outer keywords.


Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the Speed packages doc page. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the Build package doc page for more info.

You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

See the Speed packages doc page for more instructions on how to use the accelerated styles effectively.


Restrictions

This style is part of the SNAP package. It is only enabled if LAMMPS was built with that package. See the Build package doc page for more info.

Default

none


(Thompson) Thompson, Swiler, Trott, Foiles, Tucker, J Comp Phys, 285, 316 (2015).

(Bartok2010) Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).

(Wood) Wood and Thompson, J Chem Phys, 148, 241721, (2018)

(Cusentino) Cusentino, Wood, and Thompson, J Phys Chem A, xxx, xxxxx, (2020)