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eeaa221ee76bbd321d36d1ccc78747b959d16ab9
lammps/src/pair_zbl.cpp

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Stephen Foiles, Aidan Thompson (SNL)
------------------------------------------------------------------------- */
#include "pair_zbl.h"
#include <cmath>
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "pair_zbl_const.h"
// From J.F. Zeigler, J. P. Biersack and U. Littmark,
// "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985.
using namespace LAMMPS_NS;
using namespace PairZBLConstants;
/* ---------------------------------------------------------------------- */
PairZBL::PairZBL(LAMMPS *lmp) : Pair(lmp) {
writedata = 1;
}
/* ---------------------------------------------------------------------- */
PairZBL::~PairZBL()
{
if (copymode) return;
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(z);
memory->destroy(d1a);
memory->destroy(d2a);
memory->destroy(d3a);
memory->destroy(d4a);
memory->destroy(zze);
memory->destroy(sw1);
memory->destroy(sw2);
memory->destroy(sw3);
memory->destroy(sw4);
memory->destroy(sw5);
}
}
/* ---------------------------------------------------------------------- */
void PairZBL::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r,t,fswitch,eswitch;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
ev_init(eflag,vflag);
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cut_globalsq) {
r = sqrt(rsq);
fpair = dzbldr(r, itype, jtype);
if (rsq > cut_innersq) {
t = r - cut_inner;
fswitch = t*t *
(sw1[itype][jtype] + sw2[itype][jtype]*t);
fpair += fswitch;
}
fpair *= -1.0/r;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
evdwl = e_zbl(r, itype, jtype);
evdwl += sw5[itype][jtype];
if (rsq > cut_innersq) {
eswitch = t*t*t *
(sw3[itype][jtype] + sw4[itype][jtype]*t);
evdwl += eswitch;
}
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairZBL::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(z,n+1,"pair:z");
memory->create(d1a,n+1,n+1,"pair:d1a");
memory->create(d2a,n+1,n+1,"pair:d2a");
memory->create(d3a,n+1,n+1,"pair:d3a");
memory->create(d4a,n+1,n+1,"pair:d4a");
memory->create(zze,n+1,n+1,"pair:zze");
memory->create(sw1,n+1,n+1,"pair:sw1");
memory->create(sw2,n+1,n+1,"pair:sw2");
memory->create(sw3,n+1,n+1,"pair:sw3");
memory->create(sw4,n+1,n+1,"pair:sw4");
memory->create(sw5,n+1,n+1,"pair:sw5");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairZBL::settings(int narg, char **arg)
{
if (narg != 2) error->all(FLERR,"Illegal pair_style command");
cut_inner = utils::numeric(FLERR,arg[0],false,lmp);
cut_global = utils::numeric(FLERR,arg[1],false,lmp);
if (cut_inner <= 0.0 )
error->all(FLERR,"Illegal pair_style command");
if (cut_inner > cut_global)
error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairZBL::coeff(int narg, char **arg)
{
double z_one, z_two;
if (narg != 4)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi;
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
int jlo,jhi;
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
z_one = utils::numeric(FLERR,arg[2],false,lmp);
z_two = utils::numeric(FLERR,arg[3],false,lmp);
// set flag for each i-j pair
// set z-parameter only for i-i pairs
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
if (i == j) {
if (z_one != z_two)
error->all(FLERR,"Incorrect args for pair coefficients");
z[i] = z_one;
}
setflag[i][j] = 1;
set_coeff(i, j, z_one, z_two);
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairZBL::init_style()
{
neighbor->request(this,instance_me);
cut_innersq = cut_inner * cut_inner;
cut_globalsq = cut_global * cut_global;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairZBL::init_one(int i, int j)
{
if (setflag[i][j] == 0)
set_coeff(i, j, z[i], z[j]);
return cut_global;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairZBL::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i;
for (i = 1; i <= atom->ntypes; i++) {
fwrite(&setflag[i][i],sizeof(int),1,fp);
if (setflag[i][i]) fwrite(&z[i],sizeof(double),1,fp);
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairZBL::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++) {
if (me == 0) utils::sfread(FLERR,&setflag[i][i],sizeof(int),1,fp,nullptr,error);
MPI_Bcast(&setflag[i][i],1,MPI_INT,0,world);
if (setflag[i][i]) {
if (me == 0) utils::sfread(FLERR,&z[i],sizeof(double),1,fp,nullptr,error);
MPI_Bcast(&z[i],1,MPI_DOUBLE,0,world);
}
}
for (i = 1; i <= atom->ntypes; i++)
for (j = 1; j <= atom->ntypes; j++)
set_coeff(i,j,z[i],z[j]);
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairZBL::write_restart_settings(FILE *fp)
{
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&cut_inner,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
fwrite(&tail_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairZBL::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut_inner,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error);
utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,nullptr,error);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_inner,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairZBL::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g\n",i,z[i],z[i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairZBL::write_data_all(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
fprintf(fp,"%d %d %g %g\n",i,j,z[i],z[j]);
}
/* ---------------------------------------------------------------------- */
double PairZBL::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
double /*dummy1*/, double /*dummy2*/,
double &fforce)
{
double phi,r,t,eswitch,fswitch;
r = sqrt(rsq);
fforce = dzbldr(r, itype, jtype);
if (rsq > cut_innersq) {
t = r - cut_inner;
fswitch = t*t *
(sw1[itype][jtype] + sw2[itype][jtype]*t);
fforce += fswitch;
}
fforce *= -1.0/r;
phi = e_zbl(r, itype, jtype);
phi += sw5[itype][jtype];
if (rsq > cut_innersq) {
eswitch = t*t*t *
(sw3[itype][jtype] + sw4[itype][jtype]*t);
phi += eswitch;
}
return phi;
}
/* ----------------------------------------------------------------------
compute ZBL pair energy
------------------------------------------------------------------------- */
double PairZBL::e_zbl(double r, int i, int j) {
double d1aij = d1a[i][j];
double d2aij = d2a[i][j];
double d3aij = d3a[i][j];
double d4aij = d4a[i][j];
double zzeij = zze[i][j];
double rinv = 1.0/r;
double sum = c1*exp(-d1aij*r);
sum += c2*exp(-d2aij*r);
sum += c3*exp(-d3aij*r);
sum += c4*exp(-d4aij*r);
double result = zzeij*sum*rinv;
return result;
}
/* ----------------------------------------------------------------------
compute ZBL first derivative
------------------------------------------------------------------------- */
double PairZBL::dzbldr(double r, int i, int j) {
double d1aij = d1a[i][j];
double d2aij = d2a[i][j];
double d3aij = d3a[i][j];
double d4aij = d4a[i][j];
double zzeij = zze[i][j];
double rinv = 1.0/r;
double e1 = exp(-d1aij*r);
double e2 = exp(-d2aij*r);
double e3 = exp(-d3aij*r);
double e4 = exp(-d4aij*r);
double sum = c1*e1;
sum += c2*e2;
sum += c3*e3;
sum += c4*e4;
double sum_p = -c1*d1aij*e1;
sum_p -= c2*d2aij*e2;
sum_p -= c3*d3aij*e3;
sum_p -= c4*d4aij*e4;
double result = zzeij*(sum_p - sum*rinv)*rinv;
return result;
}
/* ----------------------------------------------------------------------
compute ZBL second derivative
------------------------------------------------------------------------- */
double PairZBL::d2zbldr2(double r, int i, int j) {
double d1aij = d1a[i][j];
double d2aij = d2a[i][j];
double d3aij = d3a[i][j];
double d4aij = d4a[i][j];
double zzeij = zze[i][j];
double rinv = 1.0/r;
double e1 = exp(-d1aij*r);
double e2 = exp(-d2aij*r);
double e3 = exp(-d3aij*r);
double e4 = exp(-d4aij*r);
double sum = c1*e1;
sum += c2*e2;
sum += c3*e3;
sum += c4*e4;
double sum_p = c1*e1*d1aij;
sum_p += c2*e2*d2aij;
sum_p += c3*e3*d3aij;
sum_p += c4*e4*d4aij;
double sum_pp = c1*e1*d1aij*d1aij;
sum_pp += c2*e2*d2aij*d2aij;
sum_pp += c3*e3*d3aij*d3aij;
sum_pp += c4*e4*d4aij*d4aij;
double result = zzeij*(sum_pp + 2.0*sum_p*rinv +
2.0*sum*rinv*rinv)*rinv;
return result;
}
/* ----------------------------------------------------------------------
calculate the i,j entries in the various coeff arrays
------------------------------------------------------------------------- */
void PairZBL::set_coeff(int i, int j, double zi, double zj)
{
double ainv = (pow(zi,pzbl) + pow(zj,pzbl))/(a0*force->angstrom);
d1a[i][j] = d1*ainv;
d2a[i][j] = d2*ainv;
d3a[i][j] = d3*ainv;
d4a[i][j] = d4*ainv;
zze[i][j] = zi*zj*force->qqr2e*force->qelectron*force->qelectron;
d1a[j][i] = d1a[i][j];
d2a[j][i] = d2a[i][j];
d3a[j][i] = d3a[i][j];
d4a[j][i] = d4a[i][j];
zze[j][i] = zze[i][j];
// e = t^3 (sw3 + sw4*t) + sw5
// = A/3*t^3 + B/4*t^4 + C
// sw3 = A/3
// sw4 = B/4
// sw5 = C
// dedr = t^2 (sw1 + sw2*t)
// = A*t^2 + B*t^3
// sw1 = A
// sw2 = B
// de2dr2 = 2*A*t + 3*B*t^2
// Require that at t = tc:
// e = -Fc
// dedr = -Fc'
// d2edr2 = -Fc''
// Hence:
// A = (-3Fc' + tc*Fc'')/tc^2
// B = ( 2Fc' - tc*Fc'')/tc^3
// C = -Fc + tc/2*Fc' - tc^2/12*Fc''
double tc = cut_global - cut_inner;
double fc = e_zbl(cut_global, i, j);
double fcp = dzbldr(cut_global, i, j);
double fcpp = d2zbldr2(cut_global, i, j);
double swa = (-3.0*fcp + tc*fcpp)/(tc*tc);
double swb = ( 2.0*fcp - tc*fcpp)/(tc*tc*tc);
double swc = -fc + (tc/2.0)*fcp - (tc*tc/12.0)*fcpp;
sw1[i][j] = swa;
sw2[i][j] = swb;
sw3[i][j] = swa/3.0;
sw4[i][j] = swb/4.0;
sw5[i][j] = swc;
sw1[j][i] = sw1[i][j];
sw2[j][i] = sw2[i][j];
sw3[j][i] = sw3[i][j];
sw4[j][i] = sw4[i][j];
sw5[j][i] = sw5[i][j];
}
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