We aim to understand ongoing processes at atomic scale during SPM measurements. The detail knowledge of these processes is necessary for correct interpretation of experimental data and development of new techniques. We apply DFT total energy calculations to simulate complex interaction between SPM tip and sample But addressing these complex problems with a fully converged first-principles description would be still too computationally exigent and in many cases exceeding possibilities of nowadays high performance computers. Therefore we use a home-built fast local orbital DFT code Fireball devised with the aim of computational efficiency. Optionally, calculations are checked with more demand traditional plane-wave DFT methods. In particular, we are interested in these topics:

(i) single-atom chemical identification [1]

(ii) new procedures of atomic manipulations [2,3]

(iii) detail understanding of atomic-scale contrast [4]

(iv) energy dissipation at atomic scale [5].