Merge pull request #506 from lammps/snap

If the {quadratic} keyword value is set to 1, then additional

columns are appended to each per-atom array, corresponding to

a matrix of quantities that are products of two bispectrum components. If the

number of bispectrum components is {K}, then the number of matrix elements

is {K}^2. These are output in subblocks of {K}^2 columns, using the same

ordering of columns and sub-blocks as was used for the bispectrum

components.

the products of all distinct pairs of  bispectrum components. If the

number of bispectrum components is {K}, then the number of distinct pairs

is  {K}({K}+1)/2. These are output in subblocks of  {K}({K}+1)/2 columns, using the same

ordering of sub-blocks as was used for the bispectrum

components. Within each sub-block, the ordering is upper-triangular,

(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K})

These values can be accessed by any command that uses per-atom values

from a compute as input.  See "Section

{rmin0} = 0.0

{diagonalstyle} = 3

{switchflag} = 0

{bzeroflag} = 1 :ul

{bzeroflag} = 1

{quadraticflag} = 1 :ul

Detailed definitions of these keywords are given on the "compute

Detailed definitions for all the keywords are given on the "compute

sna/atom"_compute_sna_atom.html doc page.

If {quadraticflag} is set to 1, then the SNAP energy expression includes the quadratic term,

0.5*B^t.alpha.B, where alpha is a symmetric {K} by {K} matrix.

The SNAP element file should contain {K}({K}+1)/2 additional coefficients

for each element, the upper-triangular elements of alpha.

:line

    for (int i = 0; i < natoms; i++) type[i] = 1;

    lmp->input->one("delete_atoms group all");

    lammps_create_atoms(lmp,natoms,NULL,type,x,v);

    lammps_create_atoms(lmp,natoms,NULL,type,x,v,NULL,0);

    lmp->input->one("run 10");

  }

# optional

gamma 1

rfac0 0.99363

rmin0 0

diagonalstyle 3

bzeroflag 0

quadraticflag 0

variable zblcutouter equal 4.8

variable zblz equal 74

# Specify hybrid with SNAP, ZBL, and long-range Coulomb

# Specify hybrid with SNAP and ZBL

pair_style hybrid/overlay &

zbl ${zblcutinner} ${zblcutouter} &