Nanosurf Lab

In this section we describe how to calculatethe vibrational modes of molecules using Hessian matrix. Vibrational modes are obtained from eigen values of the Hessian matrix. The elements of the matrix are defined as second derivastive of energy with respect to geometry. The first derivatives are forces and the second derivatives are obtained from the diferent of two forces and displacement. At first calculate optimization structure of the molecule and then move with atom in first direction and do SCF calculation, after that move with the same atom but in oposit direction and do again SCF calculation. Then evaluate the matrix element.This procedure repeat for each direction andeach atom of molecule. In order to calculate vibrational modes the hessian matrix ix first mass weighted.