The Denstiy Of States (DOS) and the Inverse Partitipation Ratio (IPR) are two interesting properties for understanding the electronic structure of a system.
The DOS is just a histogram counting the amount of states (molecular orbitals/wavefunctions) per energy unit, and analyzing these distributions, we can understand better the electronic behavior of our system.
The IPR is a way to analyze the “amount of localization” of these states, so that the larger the value of IPR the higher the localization around an specific covalent bond.
We used these two properties in an article published in Phys. Rev. B, named “Polymorphism in phase-change materials: melt-quenched and as-deposited amorphous structures in Ge2Sb2Te5 from“, which you can check for more information. Continue reading →
When we perform molecular dynamics (MD) simulations, sometimes we want to store a frame every time step, in order to increase the quality of the statistics (i.e. when calculating radial distribution functions). But on the other hand, due to their big size, these trajectories might be very difficult to handle by visualization programs (VMD, jmol, …), because they usually load the hole file into memory, and storing every frame (or each few frames) in a long MD with a lot of atoms can produce a trajectory file of several MB or even GB.
The solution: shrinking the big trajectory into a smaller one with my “shrink_traj” script.
This script takes a trajectory file (in xyz format) and copies each nth frame to another file, resulting on a smaller and easier to handle file specially suitable for visualization.