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bond_morse.cpp
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Thu, May 23, 14:41

bond_morse.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: Jeff Greathouse (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "bond_morse.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondMorse::BondMorse(LAMMPS *lmp) : Bond(lmp) {}
/* ---------------------------------------------------------------------- */
BondMorse::~BondMorse()
{
if (allocated) {
memory->sfree(setflag);
memory->sfree(d0);
memory->sfree(alpha);
memory->sfree(r0);
}
}
/* ---------------------------------------------------------------------- */
void BondMorse::compute(int eflag, int vflag)
{
int i1,i2,n,type;
double delx,dely,delz,ebond,fbond;
double rsq,r,dr,ralpha;
ebond = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nbondlist; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
r = sqrt(rsq);
dr = r - r0[type];
ralpha = exp(-alpha[type]*dr);
// force & energy
if (r > 0.0) fbond = -2.0*d0[type]*alpha[type]*(1-ralpha)*ralpha/r;
else fbond = 0.0;
if (eflag) ebond = d0[type]*(1-ralpha)*(1-ralpha);
// apply force to each of 2 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += delx*fbond;
f[i1][1] += dely*fbond;
f[i1][2] += delz*fbond;
}
if (newton_bond || i2 < nlocal) {
f[i2][0] -= delx*fbond;
f[i2][1] -= dely*fbond;
f[i2][2] -= delz*fbond;
}
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
}
}
/* ---------------------------------------------------------------------- */
void BondMorse::allocate()
{
allocated = 1;
int n = atom->nbondtypes;
d0 = (double *) memory->smalloc((n+1)*sizeof(double),"bond:d0");
alpha = (double *) memory->smalloc((n+1)*sizeof(double),"bond:alpha");
r0 = (double *) memory->smalloc((n+1)*sizeof(double),"bond:r0");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"bond:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void BondMorse::coeff(int narg, char **arg)
{
if (narg != 4) error->all("Incorrect args for bond coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nbondtypes,ilo,ihi);
double d0_one = atof(arg[1]);
double alpha_one = atof(arg[2]);
double r0_one = atof(arg[3]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
d0[i] = d0_one;
alpha[i] = alpha_one;
r0[i] = r0_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all("Incorrect args for bond coefficients");
}
/* ----------------------------------------------------------------------
return an equilbrium bond length
------------------------------------------------------------------------- */
double BondMorse::equilibrium_distance(int i)
{
return r0[i];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void BondMorse::write_restart(FILE *fp)
{
fwrite(&d0[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&alpha[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void BondMorse::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&d0[1],sizeof(double),atom->nbondtypes,fp);
fread(&alpha[1],sizeof(double),atom->nbondtypes,fp);
fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
}
MPI_Bcast(&d0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&alpha[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
}
/* ---------------------------------------------------------------------- */
void BondMorse::single(int type, double rsq, int i, int j, double &eng)
{
double r = sqrt(rsq);
double dr = r - r0[type];
double ralpha = exp(-alpha[type]*dr);
eng = d0[type]*(1-ralpha)*(1-ralpha);
}

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