pair<MatrixXd*,MatrixXd*> CutbySphere(MatrixXd &Atoms, double Radius, double x0,double y0,double z0 ){
//return ;
VectorXd Dx = Atoms.col(0).array() - x0;
VectorXd Dy = Atoms.col(1).array() - y0;
VectorXd Dz = Atoms.col(2).array() - z0;
//d2space=Dx.^2+Dy.^2+Dz.^2;
MatrixXd d2space = Dx.cwiseAbs2()+ Dy.cwiseAbs2() + Dz.cwiseAbs2();
MatrixXd D2space = d2space.array() - Radius*Radius;
MatrixXd d2plane = Dx.cwiseAbs2() + Dy.cwiseAbs2();
MatrixXd D2plane = d2plane.array() - Radius*Radius;
int range=Atoms.rows();
int j = 0, k = 0;
//need to improve here
MatrixXd* PickedAtoms = new MatrixXd(range,Atoms.cols());
MatrixXd* Unpicked = new MatrixXd(range,Atoms.cols());
for ( int i = 0 ; i < range; i ++){
//cout<<i<<" "<<Atoms(i,2)<<" "<<" "<<D2space(i,0)<<endl;
if (Atoms(i,2) > z0 && D2space(i,0) <= 0){
PickedAtoms->row(j) = Atoms.row(i);
j++;
}else if (Atoms(i,2) <= z0 && D2plane(i,0) <= 0){
PickedAtoms->row(j) = Atoms.row(i);
j++;
}else{
Unpicked->row(k) = Atoms.row(i);
k++;
}
}
PickedAtoms->conservativeResize(j,Atoms.cols());
Unpicked->conservativeResize(k,Atoms.cols());
return pair<MatrixXd*,MatrixXd*> (PickedAtoms,Unpicked);
}
