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bond_quartic.cpp
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Tue, May 28, 08:10
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rLAMMPS lammps
bond_quartic.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 authors: Chris Lorenz and Mark Stevens (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "bond_quartic.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "update.h"
#include "force.h"
#include "pair.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondQuartic::BondQuartic(LAMMPS *lmp) : Bond(lmp)
{
TWO_1_3 = pow(2.0,(1.0/3.0));
}
/* ---------------------------------------------------------------------- */
BondQuartic::~BondQuartic()
{
if (allocated) {
memory->sfree(setflag);
memory->sfree(k);
memory->sfree(b1);
memory->sfree(b2);
memory->sfree(rc);
memory->sfree(u0);
}
}
/* ---------------------------------------------------------------------- */
void BondQuartic::compute(int eflag, int vflag)
{
int i1,i2,n,m,type,itype,jtype;
double delx,dely,delz,ebond,fbond,evdwl,fpair;
double r,rsq,dr,r2,ra,rb,sr2,sr6;
ebond = evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
// insure pair->ev_tally() will use bond virial contribution
if (vflag_global == 2)
force->pair->vflag_either = force->pair->vflag_global = 1;
double **cutsq = force->pair->cutsq;
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++) {
// skip bond if already broken
if (bondlist[n][2] <= 0) continue;
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;
// if bond breaks, set type to 0
// both in temporary bondlist and permanent bond_type
// if this proc owns both atoms,
// negate bond_type twice if other atom stores it
// if other proc owns 2nd atom, other proc will also break bond
if (rsq > rc[type]*rc[type]) {
bondlist[n][2] = 0;
for (m = 0; m < atom->num_bond[i1]; m++)
if (atom->bond_atom[i1][m] == atom->tag[i2])
atom->bond_type[i1][m] = 0;
if (i2 < atom->nlocal)
for (m = 0; m < atom->num_bond[i2]; m++)
if (atom->bond_atom[i2][m] == atom->tag[i1])
atom->bond_type[i2][m] = 0;
continue;
}
// quartic bond
// 1st portion is from quartic term
// 2nd portion is from LJ term cut at 2^(1/6) with eps = sigma = 1.0
r = sqrt(rsq);
dr = r - rc[type];
r2 = dr*dr;
ra = dr - b1[type];
rb = dr - b2[type];
fbond = -k[type]/r * (r2*(ra+rb) + 2.0*dr*ra*rb);
if (rsq < TWO_1_3) {
sr2 = 1.0/rsq;
sr6 = sr2*sr2*sr2;
fbond += 48.0*sr6*(sr6-0.5)/rsq;
}
if (eflag) {
ebond = k[type]*r2*ra*rb + u0[type];
if (rsq < TWO_1_3) ebond += 4.0*sr6*(sr6-1.0) + 1.0;
}
// 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);
// subtract out pairwise contribution from 2 atoms via pair->single()
// required since special_bond = 1,1,1
// tally energy/virial in pair, using newton_bond as newton flag
itype = atom->type[i1];
jtype = atom->type[i2];
if (rsq < cutsq[itype][jtype]) {
evdwl = -force->pair->single(i1,i2,itype,jtype,rsq,1.0,1.0,fpair);
fpair = -fpair;
if (newton_bond || i1 < nlocal) {
f[i1][0] += delx*fpair;
f[i1][1] += dely*fpair;
f[i1][2] += delz*fpair;
}
if (newton_bond || i2 < nlocal) {
f[i2][0] -= delx*fpair;
f[i2][1] -= dely*fpair;
f[i2][2] -= delz*fpair;
}
if (evflag) force->pair->ev_tally(i1,i2,nlocal,newton_bond,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
/* ---------------------------------------------------------------------- */
void BondQuartic::allocate()
{
allocated = 1;
int n = atom->nbondtypes;
k = (double *) memory->smalloc((n+1)*sizeof(double),"bond:k");
b1 = (double *) memory->smalloc((n+1)*sizeof(double),"bond:b1");
b2 = (double *) memory->smalloc((n+1)*sizeof(double),"bond:b2");
rc = (double *) memory->smalloc((n+1)*sizeof(double),"bond:rc");
u0 = (double *) memory->smalloc((n+1)*sizeof(double),"bond:u0");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"bond:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
void BondQuartic::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 b1_one = atof(arg[2]);
double b2_one = atof(arg[3]);
double rc_one = atof(arg[4]);
double u0_one = atof(arg[5]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
b1[i] = b1_one;
b2[i] = b2_one;
rc[i] = rc_one;
u0[i] = u0_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all("Incorrect args for bond coefficients");
}
/* ----------------------------------------------------------------------
check if pair defined and special_bond settings are valid
------------------------------------------------------------------------- */
void BondQuartic::init_style()
{
if (force->pair == NULL || force->pair->single_enable == 0)
error->all("Pair style does not support bond_style quartic");
if (force->angle)
error->all("Bond style quartic cannot be used with 3,4-body interactions");
if (force->dihedral)
error->all("Bond style quartic cannot be used with 3,4-body interactions");
if (force->improper)
error->all("Bond style quartic cannot be used with 3,4-body interactions");
// special bonds must be 1 1 1
if (force->special_lj[1] != 1.0 || force->special_lj[2] != 1.0 ||
force->special_lj[3] != 1.0)
error->all("Must use special bonds = 1,1,1 with bond style quartic");
}
/* ----------------------------------------------------------------------
return an equilbrium bond length
------------------------------------------------------------------------- */
double BondQuartic::equilibrium_distance(int i)
{
return 0.97;
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void BondQuartic::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&b1[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&b2[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&rc[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&u0[1],sizeof(double),atom->nbondtypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void BondQuartic::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nbondtypes,fp);
fread(&b1[1],sizeof(double),atom->nbondtypes,fp);
fread(&b2[1],sizeof(double),atom->nbondtypes,fp);
fread(&rc[1],sizeof(double),atom->nbondtypes,fp);
fread(&u0[1],sizeof(double),atom->nbondtypes,fp);
}
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&b1[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&b2[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&rc[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&u0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
}
/* ---------------------------------------------------------------------- */
double BondQuartic::single(int type, double rsq, int i, int j)
{
double r,dr,r2,ra,rb,sr2,sr6;
if (type <= 0) return 0.0;
double eng = 0.0;
// subtract out pairwise contribution from 2 atoms via pair->single()
// required since special_bond = 1,1,1
int itype = atom->type[i];
int jtype = atom->type[j];
if (rsq < force->pair->cutsq[itype][jtype]) {
double tmp;
eng = -force->pair->single(i,j,itype,jtype,rsq,1.0,1.0,tmp);
}
// quartic bond
// 1st portion is from quartic term
// 2nd portion is from LJ term cut at 2^(1/6) with eps = sigma = 1.0
r = sqrt(rsq);
dr = r - rc[type];
r2 = dr*dr;
ra = dr - b1[type];
rb = dr - b2[type];
eng += k[type]*r2*ra*rb + u0[type];
if (rsq < TWO_1_3) {
sr2 = 1.0/rsq;
sr6 = sr2*sr2*sr2;
eng += 4.0*sr6*(sr6-1.0) + 1.0;
}
return eng;
}
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