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pair_born_coul_dsf.cpp
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Sat, Nov 2, 09:31

pair_born_coul_dsf.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: Ariel Lozano (arielzn@gmail.com)
References: Fennell and Gezelter, JCP 124, 234104 (2006)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_born_coul_dsf.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "math_special.h"
using namespace LAMMPS_NS;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
PairBornCoulDSF::PairBornCoulDSF(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
single_enable = 0;
}
/* ---------------------------------------------------------------------- */
PairBornCoulDSF::~PairBornCoulDSF()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut_lj);
memory->destroy(cut_ljsq);
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 PairBornCoulDSF::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double r,rsq,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj;
double prefactor,erfcc,erfcd,arg;
double rexp;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
double *special_coul = force->special_coul;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
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];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
// self coulombic energy
if (eflag) {
double e_self = -(e_shift/2.0 + alpha/MY_PIS) * qtmp*qtmp*qqrd2e;
ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0);
}
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[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;
if (rsq < cut_coulsq) {
r = sqrt(rsq);
prefactor = qqrd2e*qtmp*q[j]/r;
arg = alpha * r ;
erfcd = MathSpecial::expmsq(arg);
erfcc = MathSpecial::my_erfcx(arg) * erfcd;
forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
r*f_shift) * r;
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
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;
} else forceborn = 0.0;
fpair = (forcecoul + 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) {
if (rsq < cut_coulsq) {
ecoul = prefactor * (erfcc - r*e_shift - rsq*f_shift);
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv +
d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairBornCoulDSF::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_lj,n+1,n+1,"pair:cut_lj");
memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
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 PairBornCoulDSF::settings(int narg, char **arg)
{
if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command");
alpha = force->numeric(FLERR,arg[0]);
cut_lj_global = force->numeric(FLERR,arg[1]);
if (narg == 2) cut_coul = cut_lj_global;
else cut_coul = force->numeric(FLERR,arg[2]);
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_lj[i][j] = cut_lj_global;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairBornCoulDSF::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(FLERR,arg[0],atom->ntypes,ilo,ihi);
force->bounds(FLERR,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_lj_one = cut_lj_global;
if (narg == 8) cut_lj_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_lj[i][j] = cut_lj_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairBornCoulDSF::init_style()
{
if (!atom->q_flag)
error->all(FLERR,"Pair style born/coul/dsf requires atom attribute q");
neighbor->request(this,instance_me);
cut_coulsq = cut_coul * cut_coul;
double erfcc = erfc(alpha*cut_coul);
double erfcd = exp(-alpha*alpha*cut_coul*cut_coul);
f_shift = -(erfcc/cut_coulsq + 2.0/MY_PIS*alpha*erfcd/cut_coul);
e_shift = erfcc/cut_coul - f_shift*cut_coul;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairBornCoulDSF::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
double cut = MAX(cut_lj[i][j],cut_coul);
cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
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_lj[i][j])*rhoinv[i][j]);
offset[i][j] = a[i][j]*rexp - c[i][j]/pow(cut_lj[i][j],6.0)
+ d[i][j]/pow(cut_lj[i][j],8.0);
} else offset[i][j] = 0.0;
cut_ljsq[j][i] = cut_ljsq[i][j];
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];
return cut;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairBornCoulDSF::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_lj[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairBornCoulDSF::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_lj[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_lj[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairBornCoulDSF::write_restart_settings(FILE *fp)
{
fwrite(&alpha,sizeof(double),1,fp);
fwrite(&cut_lj_global,sizeof(double),1,fp);
fwrite(&cut_coul,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairBornCoulDSF::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&alpha,sizeof(double),1,fp);
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
}
MPI_Bcast(&alpha,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairBornCoulDSF::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 PairBornCoulDSF::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_lj[i][j]);
}
/* ----------------------------------------------------------------------
only the pair part is calculated here
------------------------------------------------------------------------- */
double PairBornCoulDSF::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r6inv,r,prefactor,rexp;
double forcecoul,forceborn,phicoul,phiborn;
double erfcc,erfcd,arg;
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
r = sqrt(rsq);
prefactor = factor_coul * force->qqrd2e * atom->q[i]*atom->q[j]/r;
arg = alpha * r ;
erfcd = MathSpecial::expmsq(arg);
erfcc = MathSpecial::my_erfcx(arg) * erfcd;
forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS*erfcd +
r*f_shift) * r;
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
r = sqrt(rsq);
rexp = exp(-r*rhoinv[itype][jtype]);
forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
+ born3[itype][jtype]*r2inv*r6inv;
} else forceborn = 0.0;
fforce = (forcecoul + factor_lj*forceborn) * r2inv;
double eng = 0.0;
if (rsq < cut_coulsq) {
phicoul = prefactor * (erfcc - r*e_shift - rsq*f_shift);
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
eng += phicoul;
}
if (rsq < cut_ljsq[itype][jtype]) {
phiborn = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
+ d[itype][jtype]*r2inv*r6inv - offset[itype][jtype];
eng += factor_lj*phiborn;
}
return eng;
}

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