RDF Analysis

This tool processes output files from various simulation software, calculates the radial distribution function (RDF) to characterize structural properties and interactions, and generates analysis-ready data files (.dat) along with corresponding RDF plots (.png).

Features

• Supports multiple molecular simulation output formats
• Calculates radial distribution functions (RDF) accurately
• Outputs both raw data files (.dat) and corresponding figures

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Installation

It is recommended to create a dedicated Conda environment:

conda create --name rdf python=3.10
conda activate rdf
pip install -r requirements.txt

Usage

Run the program with your topology and trajectory files as input:

python main.py <topology_file> <trajectory_file>

input

• VASP: (POSCAR + XDATCAR)
• LAMMPS: (.data + dump trajectory)
• GROMACS: (.tpr + .xtc/.trr)

Project Structure

• parsers/: Modules to read input files for POSCAR/XDATCAR (VASP), LAMMPS .data, and GROMACS .tpr + trajectory files
• rdf/: Functions to compute and plot RDF
• utils/: Helper functions for user interaction
• outputs/: Directory where analysis results (plots and data) are saved
• data/: (optional) Sample/test input data

Note

• Interactive mode allows selection of atom pairs for RDF calculation, or calculate all pairs at once
• Output files are automatically named with prefixes according to input type (vasp, lmp, gmx)
• Ensure all dependencies in requirements.txt are installed before running