void rotate(snapshot *snap, string *tags, string *vecs, char axis,
real thetax, real thetay, real thetaz)
{
matrix rmat;
bodyptr bp;
switch (tolower(axis)) {
case 'x':
xmatrix(rmat, thetax);
break;
case 'y':
ymatrix(rmat, thetay);
break;
case 'z':
zmatrix(rmat, thetaz);
break;
default:
error("%s: unknown axis %c\n", getargv0(), axis);
}
if (set_member(tags, PosTag) && set_member(vecs, PosTag))
for_all_bodies(bp, *snap)
rotatevec(Pos(bp), rmat);
if (set_member(tags, VelTag) && set_member(vecs, VelTag))
for_all_bodies(bp, *snap)
rotatevec(Vel(bp), rmat);
if (set_member(tags, AccTag) && set_member(vecs, AccTag))
for_all_bodies(bp, *snap)
rotatevec(Acc(bp), rmat);
if (set_member(tags, AuxVecTag) && set_member(vecs, AuxVecTag))
for_all_bodies(bp, *snap)
rotatevec(AuxVec(bp), rmat);
}
void kTpemHamiltonian (Geometry const &geometry, DynVars const &dynVars,
tpem_sparse *matrix,Parameters const ðer,Aux &aux,int type)
{
int row, col, volume, i = 0, p;
double a=aux.varTpem_a, b=aux.varTpem_b, tmp;
int j,k,dir;
volume = ether.linSize;
int level,gamma1,gamma2;
vector<MatType> jmatrix(36,0), ymatrix(36,0);
if (ether.isSet("adjusttpembounds")) {
a=1.0; b=0.0;
}
row=0;
for (gamma1=0;gamma1<6;gamma1++) {
for (p = 0; p < volume; p++, row++) {
auxCreateJmatrix(jmatrix,dynVars,ether,p),auxCreateYmatrix(ymatrix,dynVars,ether,p);
matrix->rowptr[row] = i;
matrix->colind[i] = row;
tmp =real(jmatrix[gamma1+6*gamma1])*double(ether.modulus[p]) + ether.potential[p]+real(ymatrix[gamma1+6*gamma1]);
// tmp =real(jmatrix[gamma1+6*gamma1])*double(ether.modulus[p]) + ether.potential[p];
matrix->values[i] = (tmp-b)/a; /* -b because it's diagonal */
i++;
for (j = 0; j < geometry.z(p); j++) {
k = geometry.neighbor(p,j);
dir = geometry.scalarDirection(p,k,j);
// for (gamma1=0;gamma1<ether.numberOfOrbitals;gamma1++) {
for (gamma2=0;gamma2<6;gamma2++) {
matrix->colind[i]=k+gamma2*volume;
matrix->values[i]=ether.bandHoppings[gamma1+gamma2*6+36*dir]/a;
i++;
}
// }
}
for (gamma2=0;gamma2<6;gamma2++) {
if (gamma1==gamma2) continue;
matrix->colind[i]=p + gamma2*volume;
matrix->values[i]=jmatrix[gamma1+6*gamma2]*double(ether.modulus[p])/a;
i++;
}
}
}
if (i!=ether.nonzero) {
cerr<<"i="<<i<<" but nonzero="<<ether.nonzero<<endl;
cerr<<"At this point: "<<__FILE__<<" "<<__LINE__<<endl;
exit(1);
}
}
