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:
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