Tools & Scripts
A curated collection of scripts and tools I’ve developed to streamline molecular dynamics workflows. Each tool is designed to solve specific challenges in MD simulation data processing and conversion.
Pragrammatic Interaction
A comprehensive repository of utilities for MD simulation data processing and conversion. All scripts are open-source and contributions are welcome.
Data Parsing & Analysis
LAMMPS Log Parsing
- Extract thermodynamic properties from LAMMPS simulation logs
- Jupyter notebook for interactive analysis
- Returns data as pandas DataFrames for easy downstream processing
- Handles multiple files and property filtering
- View on GitHub →
Format Conversion
XSD to LAMMPS Data File Converter
- Convert Materials Studio XSD files to LAMMPS data format
- Extracts atoms with coordinates, charges, and element types
- Automatically detects and preserves bond connectivity
- Handles complex bond types based on atom elements and bond order
- Batch conversion utility for high-throughput workflows
- View on GitHub →
Trajectory Export Tools
- Perl scripts for converting Materials Studio trajectory files to LAMMPS dump format
- Export full trajectories or specific atom sets
- Output compatible with OVITO and other visualization tools
- Supports Materials Studio 2020.1v forcite trajectories
- View on GitHub →
HPC & Simulation Management
HPC Utilities
- Scripts optimized for high-performance computing environments (IIT Delhi HPC)
- LAMMPS simulation management and monitoring tools
- Job submission templates and automation scripts
- View on GitHub →
Log Visualization
- Streamlit-based interactive app for visualizing LAMMPS simulation data
- Real-time monitoring of simulation progress
- View on GitHub →
Requirements
- Python 3.x with pandas
- Perl 5.x (for some trajectory conversion tools)
- LAMMPS (for generating and analyzing log files)
- OVITO (optional, for trajectory visualization)
Getting Started
Each tool has its own README with specific usage instructions and examples. For detailed documentation, visit the main repository.
Contributing
Found a useful script? Have improvements? Contributions, bug reports, and feature requests are welcome on GitHub!