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In this project the ab initio molecular dynamics in the Car-Parrinello formulation has been applied to study the microscopic processes in semiconducting materials and the scientific visualization tools have been developed in order to animate the emerging dynamical picture. These tools can now be offered to all CSCS users performing the MD simulations for solid state physics and materials science.The coupled evolution of the atomic positions and of the electronicdensity of the highest occupied states on the Si(001) surface have been studied by first-principles molecular dynamics. A video sequence illustrating the time-dependent changes accompanying the anharmonic flipping of dimers in the top layer has been generated. The experimental facts that at room temperature the dimers appear symmetric in scanning tunnelling microscope topographic images, whereas at low temperatures (T<120K) dimers appear tilted are confirmed. Similar molecular dynamics calculations will be extended to defects and to alkali-metal adsorbed on the same silicon surface.