OO bond analysis from VASP XDATCAR trajectory Author: Yuansheng Shi Date: [2025-09-16]

This script analyzes O–O distances from an AIMD trajectory (XDATCAR). Outputs:

1. OO_pair_records.csv — per-frame O–O distances
2. OO_distance_histogram.csv — histogram data (distance vs probability)
3. OO_min_distance_vs_frame.csv — min O–O distance per frame
4. OO_pdf.csv — pair distribution function g(r)
5. Figures: histogram, time series, PDF

Usage:

1. Place XDATCAR (from VASP AIMD run) in the same folder.
2. Run: python oo_analysis.py
3. Outputs will be written in the same directory.

Dependencies:

• Python >= 3.8
• numpy, pandas, matplotlib, pymatgen, scipy

Notes:

• BOND_THRESH is set to 1.45 Å (approximate O–O bonding cutoff).
• DIST_BINS and PDF_BIN_WIDTH can be adjusted.
• The script assumes XDATCAR includes oxygen atoms.

Citation: Please cite our work if you use this script in your research project or publication: