Automate

Phonopy will generate a lot of single atom displacement files depending on the symmetry of the input lattice.These are few bash script that performs several tasks, including creating directories, moving and copying those displacement files, and finally submitting job scripts to a job scheduler of the cluster.

Usage

To run the script, make sure the script file is executable (e.g., chmod 700 scf-dir.sh)

Limitations

• The script assumes that the four files POTCAR, INCAR, KPOINTS, job.sh (more info at vaspwiki) are in the current directory.
• The script assumes that the job scheduler accepts the qsub command to submit job scripts.
• The script assumes that the job scheduler uses the job.sh file as the job script file.

Quasiharmonic phonon calculation

The get_entropy-temp.py code reads in data from the file named entropy-volume.dat generated by phonopy and uses scipy's interp1d function to interpolate the data and find the entropy value at given temperature and volume. The result is then written to a csv file named temp-vol-entr.csv.

The get_e-v.sh code is a shell script that generates two files by collecting energy and volume values from files named OSZICAR and OUTCAR generated by VASP respectively. It then merges these two files into e-v.dat and deletes the original files. The new file can be used as input for phonopy qha calculation.

Thermal Properties Plotting

This repository contains a python script that uses the pandas and matplotlib libraries to plot various thermal properties from the data generated by phonopy.

Note:

All the codes were created as part of my MTech thesis. Some codes assume that you have the required files in your current working directory. Change the names of those files as per your need.