A velocity scaling scheme [30] is supported to perform NVT ensemble molecular dynamics simulations by the following keyword:
MD.Type NVT_VS # NOMDOptNVENVT_VSNVT_VS2NVT_NHThen, in this NVT molecular dynamics the temperature for nuclear motion can be controlled by
<MD.TempControl 3 100 2 1000.0 0.0 400 10 700.0 0.4 700 40 500.0 0.7 MD.TempControl>The beginning of the description must be 'MD.TempControl', and the last of the description must be 'MD.TempControl'. The first number '3' gives the number of the following lines to control the temperature. In this case you can see that there are three lines. Following the number '3', in the consecutive lines the first column means MD steps and the second column gives an interval of MD steps that the velocity scaling is made. For the example above, a velocity scaling is performed at every two MD steps until 100 MD steps, at every 10 MD steps from 100 to 400 MD steps, and at every 40 MD steps from 400 to 700 MD steps. The third and fourth columns give a given temperature (K) and a scaling parameter in the interval, while the temperature in the interval is given by a linear interpolation. In this velocity scaling, the velocity is scaled by
1: MD step 2: MD time 14: kinetic energy of nuclear motion, Ukc (Hartree) 15: DFT total energy, Utot (Hartree) 16: Utot + Ukc (Hartree) 17: Fermi energy (Hartree) 18: Given temperature for nuclear motion (K) 19: Calculated temperature for nuclear motion (K) 22: NoseHoover Hamiltonian (Hartree)which means that the first and second columns correspond to MD step and MD time, and so on. As an example, we show a result for the velocity scaling MD of a glycine molecule in Fig. 12 (a). We see that the temperature in a molecule oscillates around the given temperature. Also for visualization of molecular dynamics, an output file 'System.Name.md' can be easily animated using free software OpenMX Viewer [152,151] and XCrySDen [105].
