Postprocessing

1. Looking at a movie
The TRAJECTORY files contains the coordinates and the velocities. To create a movie file in the xyz-format, you have to transfer the coordinates from Bohr to Å and you have to add the symbols of the atoms in the first position. Two lines have to be at the beginning of each time step, from which the first line gives the number of the total atoms. An .xyz file can also be recorded directly during the simulation Using the TRAJECTORY keyword with the option XYZ.
Please note, that CPMD does not apply the minium image convention to these trajectory files, i.e. atoms are nor replaced by their images, if they leave the supercell.

2. Calculating radial pair distribution functions
The simplest analysis of the structure is given by the radial pair distribution function g(r). This quantity is a to unity normalized function and describes the probability of finding two atoms separated by a distance r relative to the probability expected for a completely random distribution at the same density. It is formally defined as:

$$g(r)=\rho^{-2}\left < \sum_i\sum_{i\ne j} \delta({\bf r}_i) \delta({\bf r}_j-{\bf r}) \right >$$

$$= \frac{V}{N^2}\left < \sum_i\sum_{i\ne j} \delta({\bf r}-{\bf r}_{ij}) \right >$$

with r being the atomic separation, $\rho$ the number density, N the number of atoms, V the volume, r the atomic position, and r$_{ij}$ the position of the atom i relative to the atom j. The average $<>$ is taken over particles and time. Examples of code can be found in the following references [1,4].