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pair_born.cpp
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pair_born.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://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 Author: Sai Jayaraman (Sandia)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_born.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
PairBorn::PairBorn(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
}
/* ---------------------------------------------------------------------- */
PairBorn::~PairBorn()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(a);
memory->destroy(rho);
memory->destroy(sigma);
memory->destroy(c);
memory->destroy(d);
memory->destroy(rhoinv);
memory->destroy(born1);
memory->destroy(born2);
memory->destroy(born3);
memory->destroy(offset);
}
}
/* ---------------------------------------------------------------------- */
void PairBorn::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,r2inv,r6inv,forceborn,factor_lj;
double r,rexp;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
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];
factor_lj = special_lj[sbmask(j)];
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 < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
r = sqrt(rsq);
rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
+ born3[itype][jtype]*r2inv*r6inv;
fpair = factor_lj*forceborn*r2inv;
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 = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
+ d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
evdwl *= factor_lj;
}
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 PairBorn::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(cut,n+1,n+1,"pair:cut");
memory->create(a,n+1,n+1,"pair:a");
memory->create(rho,n+1,n+1,"pair:rho");
memory->create(sigma,n+1,n+1,"pair:sigma");
memory->create(c,n+1,n+1,"pair:c");
memory->create(d,n+1,n+1,"pair:d");
memory->create(rhoinv,n+1,n+1,"pair:rhoinv");
memory->create(born1,n+1,n+1,"pair:born1");
memory->create(born2,n+1,n+1,"pair:born2");
memory->create(born3,n+1,n+1,"pair:born3");
memory->create(offset,n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairBorn::settings(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(FLERR,arg[0]);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairBorn::coeff(int narg, char **arg)
{
if (narg < 7 || narg > 8) error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double a_one = force->numeric(FLERR,arg[2]);
double rho_one = force->numeric(FLERR,arg[3]);
double sigma_one = force->numeric(FLERR,arg[4]);
if (rho_one <= 0) error->all(FLERR,"Incorrect args for pair coefficients");
double c_one = force->numeric(FLERR,arg[5]);
double d_one = force->numeric(FLERR,arg[6]);
double cut_one = cut_global;
if (narg == 8) cut_one = force->numeric(FLERR,arg[7]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
a[i][j] = a_one;
rho[i][j] = rho_one;
sigma[i][j] = sigma_one;
c[i][j] = c_one;
d[i][j] = d_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairBorn::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
rhoinv[i][j] = 1.0/rho[i][j];
born1[i][j] = a[i][j]/rho[i][j];
born2[i][j] = 6.0*c[i][j];
born3[i][j] = 8.0*d[i][j];
if (offset_flag) {
double rexp = exp((sigma[i][j]-cut[i][j])*rhoinv[i][j]);
offset[i][j] = a[i][j]*rexp - c[i][j]/pow(cut[i][j],6.0) +
d[i][j]/pow(cut[i][j],8.0);
} else offset[i][j] = 0.0;
a[j][i] = a[i][j];
c[j][i] = c[i][j];
d[j][i] = d[i][j];
rhoinv[j][i] = rhoinv[i][j];
sigma[j][i] = sigma[i][j];
born1[j][i] = born1[i][j];
born2[j][i] = born2[i][j];
born3[j][i] = born3[i][j];
offset[j][i] = offset[i][j];
// compute I,J contribution to long-range tail correction
// count total # of atoms of type I and J via Allreduce
if (tail_flag) {
int *type = atom->type;
int nlocal = atom->nlocal;
double count[2],all[2];
count[0] = count[1] = 0.0;
for (int k = 0; k < nlocal; k++) {
if (type[k] == i) count[0] += 1.0;
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
double rho1 = rho[i][j];
double rho2 = rho1*rho1;
double rho3 = rho2*rho1;
double rc = cut[i][j];
double rc2 = rc*rc;
double rc3 = rc2*rc;
double rc5 = rc3*rc2;
etail_ij = 2.0*MY_PI*all[0]*all[1] *
(a[i][j]*exp((sigma[i][j]-rc)/rho1)*rho1*
(rc2 + 2.0*rho1*rc + 2.0*rho2) -
c[i][j]/(3.0*rc3) + d[i][j]/(5.0*rc5));
ptail_ij = (-1/3.0)*2.0*MY_PI*all[0]*all[1] *
(-a[i][j]*exp((sigma[i][j]-rc)/rho1) *
(rc3 + 3.0*rho1*rc2 + 6.0*rho2*rc + 6.0*rho3) +
2.0*c[i][j]/rc3 - 8.0*d[i][j]/(5.0*rc5));
}
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairBorn::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&a[i][j],sizeof(double),1,fp);
fwrite(&rho[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&c[i][j],sizeof(double),1,fp);
fwrite(&d[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairBorn::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&a[i][j],sizeof(double),1,fp);
fread(&rho[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&c[i][j],sizeof(double),1,fp);
fread(&d[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&d[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairBorn::write_restart_settings(FILE *fp)
{
fwrite(&cut_global,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 PairBorn::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&tail_flag,sizeof(int),1,fp);
}
MPI_Bcast(&cut_global,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 PairBorn::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g %g %g %g\n",i,
a[i][i],rho[i][i],sigma[i][i],c[i][i],d[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairBorn::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 %g %g %g %g\n",i,j,
a[i][j],rho[i][j],sigma[i][j],c[i][j],d[i][j],cut[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairBorn::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r6inv,r,rexp,forceborn,phiborn;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
r = sqrt(rsq);
rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv +
born3[itype][jtype]*r2inv*r6inv;
fforce = factor_lj*forceborn*r2inv;
phiborn = a[itype][jtype]*rexp - c[itype][jtype]*r6inv +
d[itype][jtype]*r2inv*r6inv - offset[itype][jtype];
return factor_lj*phiborn;
}
/* ---------------------------------------------------------------------- */
void *PairBorn::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str,"a") == 0) return (void *) a;
if (strcmp(str,"c") == 0) return (void *) c;
if (strcmp(str,"d") == 0) return (void *) d;
return NULL;
}

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