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); }