Merge branch 'chem_snap' of https://github.com/charlessievers/lammps into chem_snap

# DATE: 2019-09-18 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019) 

# Definition of SNAP+ZBL potential.

set type 1 charge 1e-08

set type 2 charge -1e-08

variable zblcutinner equal 4

variable zblcutouter equal 4.2

variable zblz1 equal 49

variable zblz2 equal 15

variable rcoul equal 10

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

pair_style hybrid/overlay coul/long ${rcoul} &

zbl ${zblcutinner} ${zblcutouter} &

snap

pair_coeff * * coul/long

pair_coeff 1 1 zbl ${zblz1} ${zblz1}

pair_coeff 1 2 zbl ${zblz1} ${zblz2}

pair_coeff 2 2 zbl ${zblz2} ${zblz2}

pair_coeff * * snap InP_Cusentino_PRB2020.snapcoeff InP_Cusentino_PRB2020.snapparam In P 

kspace_style ewald 1.0e-5

    # required

    rcutfac 1.0

    twojmax 6

    #  optional

    rfac0 0.99363

    rmin0 0.0

    bzeroflag 1

    quadraticflag 0

    wselfallflag 1

    alloyflag 1

 No newline at end of file

# Demonstrate SNAP InP potential

# Initialize simulation

variable nsteps index 100

variable nrep equal 4

variable a equal 5.83

units           metal

atom_style      charge

# generate the box and atom positions using a FCC lattice

variable nx equal ${nrep}

variable ny equal ${nrep}

variable nz equal ${nrep}

boundary        p p p

lattice         diamond $a

region          box block 0 ${nx} 0 ${ny} 0 ${nz}

create_box      2 box

create_atoms    1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2

mass 1 114.76

mass 2 30.98

# choose potential

include InP_Cusentino_PRB2020.snap

# Setup output

thermo          10

thermo_modify norm yes

# Set up NVE run

timestep 0.5e-3

neighbor 1.0 bin

neigh_modify once no every 1 delay 0 check yes

# Run MD

velocity all create 300.0 4928459

fix 1 all nve

run             ${nsteps}

  extarray = 0;

  double rfac0, rmin0;

  int twojmax, switchflag, bzeroflag, bnormflag;

  int twojmax, switchflag, bzeroflag;

  radelem = NULL;

  wjelem = NULL;

  rmin0 = 0.0;

  switchflag = 1;

  bzeroflag = 1;

  bnormflag = 0;

  quadraticflag = 0;

  alloyflag = 0;

  wselfallflag = 0;

      quadraticflag = atoi(arg[iarg+1]);

      iarg += 2;

    } else if (strcmp(arg[iarg],"alloyflag") == 0) {

      if (iarg+2+ntypes > narg)

      if (iarg+2 > narg)

        error->all(FLERR,"Illegal compute snap command");

      alloyflag = 1;

      bnormflag = 1;

      memory->create(map,ntypes+1,"compute_snap:map");

      nelements = force->inumeric(FLERR,arg[iarg+1]);

      for(int i = 0; i < ntypes; i++) {

  memory->destroy(wjelem);

  memory->destroy(cutsq);

  delete snaptr;

  if (alloyflag) memory->destroy(map);

}

/* ---------------------------------------------------------------------- */

    sizeof(double);                                     // snapall

  bytes += nmax*size_peratom * sizeof(double);          // snap_peratom

  bytes += snaptr->memory_usage();                      // SNA object

  int n = atom->ntypes+1;

  bytes += n*sizeof(int);        // map

  return bytes;

}