int ComputeBondLocal::compute_bonds(int flag)
{
int i,m,n,nb,atom1,atom2,imol,iatom,btype;
tagint tagprev;
double dx,dy,dz,rsq;
double mass1,mass2,masstotal,invmasstotal;
double xcm[3],vcm[3];
double delr1[3],delr2[3],delv1[3],delv2[3];
double r12[3],vpar1,vpar2;
double vvib,vrotsq;
double inertia,omegasq;
double mvv2e;
double engpot,engtrans,engvib,engrot,fbond;
double *ptr;
double **x = atom->x;
double **v = atom->v;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
tagint *tag = atom->tag;
int *num_bond = atom->num_bond;
tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
int *mask = atom->mask;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
int molecular = atom->molecular;
Bond *bond = force->bond;
// communicate ghost velocities if needed
if (ghostvelflag && !initflag) comm->forward_comm_compute(this);
// loop over all atoms and their bonds
m = n = 0;
for (atom1 = 0; atom1 < nlocal; atom1++) {
if (!(mask[atom1] & groupbit)) continue;
if (molecular == 1) nb = num_bond[atom1];
else {
if (molindex[atom1] < 0) continue;
imol = molindex[atom1];
iatom = molatom[atom1];
nb = onemols[imol]->num_bond[iatom];
}
for (i = 0; i < nb; i++) {
if (molecular == 1) {
btype = bond_type[atom1][i];
atom2 = atom->map(bond_atom[atom1][i]);
} else {
tagprev = tag[atom1] - iatom - 1;
btype = onemols[imol]->bond_type[iatom][i];
atom2 = atom->map(onemols[imol]->bond_atom[iatom][i]+tagprev);
}
if (atom2 < 0 || !(mask[atom2] & groupbit)) continue;
if (newton_bond == 0 && tag[atom1] > tag[atom2]) continue;
if (btype == 0) continue;
if (!flag) {
m++;
continue;
}
dx = x[atom1][0] - x[atom2][0];
dy = x[atom1][1] - x[atom2][1];
dz = x[atom1][2] - x[atom2][2];
domain->minimum_image(dx,dy,dz);
rsq = dx*dx + dy*dy + dz*dz;
if (btype == 0) {
engpot = fbond = 0.0;
engvib = engrot = engtrans = omegasq = vvib = 0.0;
} else {
if (singleflag) engpot = bond->single(btype,rsq,atom1,atom2,fbond);
if (velflag) {
if (rmass) {
mass1 = rmass[atom1];
mass2 = rmass[atom2];
}
else {
mass1 = mass[type[atom1]];
mass2 = mass[type[atom2]];
}
masstotal = mass1+mass2;
invmasstotal = 1.0 / (masstotal);
xcm[0] = (mass1*x[atom1][0] + mass2*x[atom2][0]) * invmasstotal;
xcm[1] = (mass1*x[atom1][1] + mass2*x[atom2][1]) * invmasstotal;
xcm[2] = (mass1*x[atom1][2] + mass2*x[atom2][2]) * invmasstotal;
vcm[0] = (mass1*v[atom1][0] + mass2*v[atom2][0]) * invmasstotal;
vcm[1] = (mass1*v[atom1][1] + mass2*v[atom2][1]) * invmasstotal;
vcm[2] = (mass1*v[atom1][2] + mass2*v[atom2][2]) * invmasstotal;
engtrans = 0.5 * masstotal * MathExtra::lensq3(vcm);
// r12 = unit bond vector from atom1 to atom2
MathExtra::sub3(x[atom2],x[atom1],r12);
MathExtra::norm3(r12);
// delr = vector from COM to each atom
// delv = velocity of each atom relative to COM
MathExtra::sub3(x[atom1],xcm,delr1);
MathExtra::sub3(x[atom2],xcm,delr2);
MathExtra::sub3(v[atom1],vcm,delv1);
MathExtra::sub3(v[atom2],vcm,delv2);
// vpar = component of delv parallel to bond vector
vpar1 = MathExtra::dot3(delv1,r12);
vpar2 = MathExtra::dot3(delv2,r12);
engvib = 0.5 * (mass1*vpar1*vpar1 + mass2*vpar2*vpar2);
// vvib = relative velocity of 2 atoms along bond direction
// vvib < 0 for 2 atoms moving towards each other
// vvib > 0 for 2 atoms moving apart
vvib = vpar2 - vpar1;
// vrotsq = tangential speed squared of atom1 only
// omegasq = omega squared, and is the same for atom1 and atom2
inertia = mass1*MathExtra::lensq3(delr1) +
mass2*MathExtra::lensq3(delr2);
vrotsq = MathExtra::lensq3(delv1) - vpar1*vpar1;
omegasq = vrotsq / MathExtra::lensq3(delr1);
engrot = 0.5 * inertia * omegasq;
// sanity check: engtotal = engtrans + engvib + engrot
//engtot = 0.5 * (mass1*MathExtra::lensq3(v[atom1]) +
// mass2*MathExtra::lensq3(v[atom2]));
//if (fabs(engtot-engtrans-engvib-engrot) > EPSILON)
// error->one(FLERR,"Sanity check on 3 energy components failed");
// scale energies by units
mvv2e = force->mvv2e;
engtrans *= mvv2e;
engvib *= mvv2e;
engrot *= mvv2e;
}
if (nvalues == 1) ptr = &vector[m];
else ptr = array[m];
for (n = 0; n < nvalues; n++) {
switch (bstyle[n]) {
case DIST:
ptr[n] = sqrt(rsq);
break;
case ENGPOT:
ptr[n] = engpot;
break;
case FORCE:
ptr[n] = sqrt(rsq)*fbond;
break;
case ENGVIB:
ptr[n] = engvib;
break;
case ENGROT:
ptr[n] = engrot;
break;
case ENGTRANS:
ptr[n] = engtrans;
break;
case OMEGA:
ptr[n] = sqrt(omegasq);
break;
case VELVIB:
ptr[n] = vvib;
break;
}
}
}
m++;
}
}
return m;
}
int ComputeBondLocal::compute_bonds(int flag)
{
int i,m,n,nb,atom1,atom2,imol,iatom,btype;
tagint tagprev;
double delx,dely,delz,rsq;
double *ptr;
double **x = atom->x;
tagint *tag = atom->tag;
int *num_bond = atom->num_bond;
tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
int *mask = atom->mask;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
int molecular = atom->molecular;
Bond *bond = force->bond;
double eng,fbond;
m = n = 0;
for (atom1 = 0; atom1 < nlocal; atom1++) {
if (!(mask[atom1] & groupbit)) continue;
if (molecular == 1) nb = num_bond[atom1];
else {
if (molindex[atom1] < 0) continue;
imol = molindex[atom1];
iatom = molatom[atom1];
nb = onemols[imol]->num_bond[iatom];
}
for (i = 0; i < nb; i++) {
if (molecular == 1) {
btype = bond_type[atom1][i];
atom2 = atom->map(bond_atom[atom1][i]);
} else {
tagprev = tag[atom1] - iatom - 1;
btype = atom->map(onemols[imol]->bond_type[iatom][i]);
atom2 = atom->map(onemols[imol]->bond_atom[iatom][i]+tagprev);
}
if (atom2 < 0 || !(mask[atom2] & groupbit)) continue;
if (newton_bond == 0 && tag[atom1] > tag[atom2]) continue;
if (btype == 0) continue;
if (flag) {
delx = x[atom1][0] - x[atom2][0];
dely = x[atom1][1] - x[atom2][1];
delz = x[atom1][2] - x[atom2][2];
domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
if (singleflag && (btype > 0))
eng = bond->single(btype,rsq,atom1,atom2,fbond);
else eng = fbond = 0.0;
if (nvalues == 1) ptr = &vector[m];
else ptr = array[m];
for (n = 0; n < nvalues; n++) {
switch (bstyle[n]) {
case DIST:
ptr[n] = sqrt(rsq);
break;
case ENG:
ptr[n] = eng;
break;
case FORCE:
ptr[n] = sqrt(rsq)*fbond;
break;
}
}
}
m++;
}
}
return m;
}
