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pair_morse_soft.cpp
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Sat, Nov 9, 23:14

pair_morse_soft.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.
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_morse_soft.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "memory.h"
#include "math_special.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathSpecial;
/* ----------------------------------------------------------------------
Contributing author: Stefan Paquay (TU/e)
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
PairMorseSoft::~PairMorseSoft()
{
if(allocated){
memory->destroy(lambda);
}
}
/* ---------------------------------------------------------------------- */
void PairMorseSoft::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,dr,dexp,dexp2,dexp3,factor_lj;
double ea,phi,V0,iea2;
double D, a, x0, l, B, s1, llf;
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]) {
r = sqrt(rsq);
dr = r - r0[itype][jtype];
D = d0[itype][jtype];
a = alpha[itype][jtype];
x0 = r0[itype][jtype];
dexp = exp( -a * dr );
dexp2 = dexp*dexp;
dexp3 = dexp2*dexp;
l = lambda[itype][jtype];
ea = exp( a * x0 );
iea2 = exp( -2.*a*x0 );
V0 = D * dexp * ( dexp - 2.0 );
B = -2.0 * D * iea2 * ( ea - 1.0 ) / 3.0;
if (l >= shift_range){
s1 = (l - 1.0) / (shift_range - 1.0);
phi = V0 + B*dexp3 * s1;
// Force computation:
fpair = 3.0*a*B*dexp3*s1 + 2.0*a*D*(dexp2 - dexp);
fpair /= r;
}else{
llf = MathSpecial::powint( l / shift_range, nlambda );
phi = V0 + B*dexp3;
phi *= llf;
// Force computation:
if (r == 0.0){
fpair = 0.0;
}else{
fpair = 3.0*a*B*dexp3 + 2.0*a*D*(dexp2 - dexp);
fpair *= llf / r;
}
}
fpair *= factor_lj;
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 = phi*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 PairMorseSoft::allocate()
{
PairMorse::allocate();
int n = atom->ntypes;
memory->create(lambda,n+1,n+1,"pair:lambda");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairMorseSoft::coeff(int narg, char **arg)
{
if (narg < 6 || narg > 7) 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 d0_one = force->numeric(FLERR,arg[2]);
double alpha_one = force->numeric(FLERR,arg[3]);
double r0_one = force->numeric(FLERR,arg[4]);
double lambda_one = force->numeric(FLERR,arg[5]);
double cut_one = cut_global;
if (narg == 7) cut_one = force->numeric(FLERR,arg[6]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
d0[i][j] = d0_one;
alpha[i][j] = alpha_one;
r0[i][j] = r0_one;
lambda[i][j] = lambda_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
Set global stuff.
------------------------------------------------------------------------- */
void PairMorseSoft::settings(int narg, char **arg)
{
if (narg != 3) error->all(FLERR,"Illegal pair_style command");
nlambda = force->inumeric(FLERR,arg[0]);
shift_range = force->numeric(FLERR,arg[1]);
cut_global = force->numeric(FLERR,arg[2]);
// 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;
}
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairMorseSoft::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
morse1[i][j] = 2.0*d0[i][j]*alpha[i][j];
if (offset_flag) {
double l, s1, V0, B, llf;
double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]);
double D = d0[i][j];
double a = alpha[i][j];
double x0 = r0[i][j];
double dexp = exp( alpha_dr );
double dexp2 = dexp*dexp;
double dexp3 = dexp2*dexp;
l = lambda[i][j];
double ea = exp( a*x0 );
double iea2 = exp( -2.*a*x0 );
V0 = D * dexp * ( dexp - 2.0 );
B = -2.0 * D * iea2 * ( ea - 1.0 ) / 3.0;
if (l >= shift_range){
s1 = (l - 1.0) / (shift_range - 1.0);
offset[i][j] = V0 + B*dexp3 * s1;
}else{
llf = MathSpecial::powint( l / shift_range, nlambda );
offset[i][j] = V0 + B*dexp3;
offset[i][j] *= llf;
}
} else offset[i][j] = 0.0;
d0[j][i] = d0[i][j];
alpha[j][i] = alpha[i][j];
r0[j][i] = r0[i][j];
morse1[j][i] = morse1[i][j];
lambda[j][i] = lambda[i][j];
offset[j][i] = offset[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairMorseSoft::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(&d0[i][j],sizeof(double),1,fp);
fwrite(&alpha[i][j],sizeof(double),1,fp);
fwrite(&r0[i][j],sizeof(double),1,fp);
fwrite(&lambda[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairMorseSoft::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(&d0[i][j],sizeof(double),1,fp);
fread(&alpha[i][j],sizeof(double),1,fp);
fread(&r0[i][j],sizeof(double),1,fp);
fread(&lambda[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairMorseSoft::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g %g %g\n",i,d0[i][i],alpha[i][i],r0[i][i],
lambda[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairMorseSoft::write_data_all(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
fprintf(fp,"%d %g %g %g %g\n",i,d0[i][j],alpha[i][j],r0[i][j],
lambda[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairMorseSoft::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r, dr, dexp, dexp2, dexp3, phi;
double B, D, a, ea, iea2;
double x0, V0, s1, l, llf;
D = d0[itype][jtype];
a = alpha[itype][jtype];
x0 = r0[itype][jtype];
r = sqrt(rsq);
dr = r - r0[itype][jtype];
dexp = exp( -a * dr );
dexp2 = dexp*dexp;
dexp3 = dexp2*dexp;
l = lambda[itype][jtype];
ea = exp( a * x0 );
iea2 = exp( -2.*a*x0 );
V0 = D * dexp * ( dexp - 2.0 );
B = -2.0 * D * iea2 * ( ea - 1.0 ) / 3.0;
if (l >= shift_range){
s1 = (l - 1.0) / (shift_range - 1.0);
phi = V0 + B*dexp3 * s1;
// Force computation:
fforce = 3.0*a*B*dexp3*s1 + 2.0*a*D*(dexp2 - dexp);
fforce /= r;
}else{
llf = MathSpecial::powint( l / shift_range, nlambda );
phi = V0 + B*dexp3;
phi *= llf;
// Force computation:
if (r == 0.0){
fforce = 0.0;
}else{
fforce = 3.0*a*B*dexp3 + 2.0*a*D*(dexp2 - dexp);
fforce *= llf / r;
}
}
fforce *= factor_lj;
phi -= offset[itype][jtype];
return factor_lj*phi;
}
/* ---------------------------------------------------------------------- */
void *PairMorseSoft::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str,"d0") == 0) return (void *) d0;
if (strcmp(str,"r0") == 0) return (void *) r0;
if (strcmp(str,"alpha") == 0) return (void *) alpha;
if (strcmp(str,"lambda") == 0) return (void *) lambda;
return NULL;
}

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