RDF Computation from VASP XDATCAR

This Python script computes the Radial Distribution Function (RDF) from VASP's XDATCAR file. It allows you to exclude initial dynamics (e.g., equilibration), specify time ranges, atom pairs, smearing width, and more.

🔧 Requirements

Make sure you have the following Python packages installed:

• pymatgen
• vasppy
• matplotlib

You can install them via pip (note: vasppy may require manual installation or cloning from GitHub):

pip install pymatgen matplotlib
pip install git+https://github.com/JamesAlexanderHill/vasppy.git

🚀 Usage

python compute_rdf.py --dt 2 \
                      --file XDATCAR \
                      --exclude 3 \
                      --total 10 \
                      --pairs Si-O,O-O,Si-Si \
                      --smearing 0.05 \
                      --maxpeaks 3

Parameters

Argument	Type	Description
--dt	float	Time step in femtoseconds (required)
--file	string	Path to XDATCAR file (default: XDATCAR)
--exclude	float	Time to exclude from the beginning of the trajectory (in picoseconds)
--total	float	Total time range to consider (in picoseconds)
--pairs	string	Comma-separated list of atomic pairs to compute RDFs (e.g. Si-O,O-O)
--smearing	float	Gaussian smearing width (default: 0.05)
--maxpeaks	int	Number of RDF maxima to print for each pair
--out	str	Output file name

📊 Output

• Saves the RDF plot as: rdf_aimd_filtered.png
• Prints the top local maxima of g(r) for each atomic pair in the terminal (e.g., position of peaks)

📎 Example

python compute_rdf.py --dt 2 --pairs "Si-O,O-O" --exclude 3 --total 10

This computes the RDFs for Si–O and O–O between 3 ps and 10 ps, assuming a 2 fs timestep.

🧪 Notes

• Atom types are case-sensitive and should be valid chemical symbols (e.g. Si, O, Na, not si or oxygen).
• The script automatically filters structures to only include those that contain both atoms of each specified pair.
• Local maxima are detected from unsmeared RDF data, and the smeared RDF is plotted.

📬 Contact

For improvements or bug reports, feel free to open an issue or submit a pull request.