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bond_fene_expand.cpp
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Sun, Nov 3, 15:29

bond_fene_expand.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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.
------------------------------------------------------------------------- */
// FENE bond potential, with repulsive LJ, with shift
#include "math.h"
#include "stdlib.h"
#include "bond_fene_expand.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "update.h"
#include "force.h"
#include "memory.h"
#include "error.h"
/* ----------------------------------------------------------------------
set all global defaults
------------------------------------------------------------------------- */
BondFENEExpand::BondFENEExpand()
{
TWO_1_3 = pow(2.0,(1.0/3.0));
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
BondFENEExpand::~BondFENEExpand()
{
if (allocated) {
memory->sfree(setflag);
memory->sfree(k);
memory->sfree(r0);
memory->sfree(epsilon);
memory->sfree(sigma);
memory->sfree(shift);
}
}
/* ---------------------------------------------------------------------- */
void BondFENEExpand::compute(int eflag, int vflag)
{
int i1,i2,n,type,factor;
double delx,dely,delz,rsq,r0sq,rlogarg,fforce,sr2,sr6,rfactor;
double r,rshift,rshiftsq;
energy = 0.0;
if (vflag) for (n = 0; n < 6; n++) virial[n] = 0.0;
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];
if (newton_bond) factor = 2;
else {
factor = 0;
if (i1 < nlocal) factor++;
if (i2 < nlocal) factor++;
}
rfactor = 0.5*factor;
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);
// force from log term
rsq = delx*delx + dely*dely + delz*delz;
r = sqrt(rsq);
rshift = r - shift[type];
rshiftsq = rshift*rshift;
r0sq = r0[type] * r0[type];
rlogarg = 1.0 - rshiftsq/r0sq;
// if r -> r0, then rlogarg < 0.0 which is an error
// issue a warning and reset rlogarg = epsilon
// if r > 2*r0 something serious is wrong, abort
if (rlogarg < 0.1) {
char str[128];
sprintf(str,"FENE bond too long: %d %d %d %g",
update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
error->warning(str);
if (rlogarg <= -3.0) error->one("Bad FENE bond");
rlogarg = 0.1;
}
fforce = -k[type]*rshift/rlogarg/r;
// force from LJ term
if (rshiftsq < TWO_1_3*sigma[type]*sigma[type]) {
sr2 = sigma[type]*sigma[type]/rshiftsq;
sr6 = sr2*sr2*sr2;
fforce += 48.0*epsilon[type]*sr6*(sr6-0.5)/rshift/r;
}
// energy
if (eflag) {
energy -= 0.5*rfactor * k[type]*r0sq*log(rlogarg);
if (rshiftsq < TWO_1_3*sigma[type]*sigma[type])
energy += 0.5*factor *
(4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type]);
}
// apply force to each of 2 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += delx*fforce;
f[i1][1] += dely*fforce;
f[i1][2] += delz*fforce;
}
if (newton_bond || i2 < nlocal) {
f[i2][0] -= delx*fforce;
f[i2][1] -= dely*fforce;
f[i2][2] -= delz*fforce;
}
// virial contribution
if (vflag) {
virial[0] += rfactor * delx*delx*fforce;
virial[1] += rfactor * dely*dely*fforce;
virial[2] += rfactor * delz*delz*fforce;
virial[3] += rfactor * delx*dely*fforce;
virial[4] += rfactor * delx*delz*fforce;
virial[5] += rfactor * dely*delz*fforce;
}
}
}
/* ---------------------------------------------------------------------- */
void BondFENEExpand::allocate()
{
allocated = 1;
int n = atom->nbondtypes;
k = (double *) memory->smalloc((n+1)*sizeof(double),"bond:k");
r0 = (double *) memory->smalloc((n+1)*sizeof(double),"bond:r0");
epsilon = (double *) memory->smalloc((n+1)*sizeof(double),"bond:epsilon");
sigma = (double *) memory->smalloc((n+1)*sizeof(double),"bond:sigma");
shift = (double *) memory->smalloc((n+1)*sizeof(double),"bond:shift");
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 BondFENEExpand::coeff(int narg, char **arg)
{
if (narg != 6) error->all("Incorrect args for bond coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nbondtypes,ilo,ihi);
double k_one = atof(arg[1]);
double r0_one = atof(arg[2]);
double epsilon_one = atof(arg[3]);
double sigma_one = atof(arg[4]);
double shift_one = atof(arg[5]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
r0[i] = r0_one;
epsilon[i] = epsilon_one;
sigma[i] = sigma_one;
shift[i] = shift_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all("Incorrect args for bond coefficients");
}
/* ---------------------------------------------------------------------- */
double BondFENEExpand::equilibrium_distance(int i)
{
return 0.97*sigma[i] + shift[i];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void BondFENEExpand::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&epsilon[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&sigma[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&shift[1],sizeof(double),atom->nbondtypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void BondFENEExpand::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nbondtypes,fp);
fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
fread(&epsilon[1],sizeof(double),atom->nbondtypes,fp);
fread(&sigma[1],sizeof(double),atom->nbondtypes,fp);
fread(&shift[1],sizeof(double),atom->nbondtypes,fp);
}
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&epsilon[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&shift[1],atom->nbondtypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
}
/* ---------------------------------------------------------------------- */
void BondFENEExpand::single(int type, double rsq, int i, int j, double rfactor,
int eflag, double &fforce, double &eng)
{
double r = sqrt(rsq);
double rshift = r - shift[type];
double rshiftsq = rshift*rshift;
double r0sq = r0[type] * r0[type];
double rlogarg = 1.0 - rshiftsq/r0sq;
// if r -> r0, then rlogarg < 0.0 which is an error
// issue a warning and reset rlogarg = epsilon
// if r > 2*r0 something serious is wrong, abort
if (rlogarg < 0.1) {
char str[128];
sprintf(str,"FENE bond too long: %d %g",update->ntimestep,sqrt(rsq));
error->warning(str);
if (rlogarg <= -3.0) error->one("Bad FENE bond");
rlogarg = 0.1;
}
fforce = -k[type]*rshift/rlogarg/r;
// force from LJ term
double sr2,sr6;
if (rshiftsq < TWO_1_3*sigma[type]*sigma[type]) {
sr2 = sigma[type]*sigma[type]/rshiftsq;
sr6 = sr2*sr2*sr2;
fforce += 48.0*epsilon[type]*sr6*(sr6-0.5)/rshift/r;
}
// energy
if (eflag) {
eng = -0.5*rfactor * k[type]*r0sq*log(rlogarg);
if (rshiftsq < TWO_1_3*sigma[type]*sigma[type])
eng += rfactor * (4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type]);
}
}

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