/CP2K_normal_modes

Python script to animate the normal modes found by the CP2K calculations

Primary LanguagePython

CP2K_normal_modes

Description: Python script to animate the normal modes calculated in CP2K vibrational analysis. Adapts a MOLDEN output to a multiple PDB file.

Author: Salomé Llabrés Prat, PhD

Version: 1.2

Dependencies:

  • Python3 (argparse, numpy, itertools and collections)

About:

CP2K_normal_modes is a Python3 script that reads the CP2K vibration molden output (.mol) and creates XYZ file for each vibration found by CP2K.

Usage:

usage: animation_normal_modes_CP2K.py [-h] -i INPUT -o OUTPUT -f NFRAMES

Read MOLDEN file and write a multiple XYZ for each vibration.

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        CP2K MOLDEN frequency MOL file.
  -o OUTPUT, --output OUTPUT
                        Base name for the vibration output files.
  -f NFRAMES, --nframes NFRAMES
                        Number of frames to describe the vibrations.

Output:

Number of atoms found: 24.
Number of vibrations found: 69.

Read CP2K frequency file.

Write multiple XYZ files for all the vibrations.