📊 Plot Energy vs Time

This Python script processes energy values from a VASP OSZICAR file and plots energy as a function of time. It is useful for analyzing molecular dynamics simulations by extracting clean energy trends over time, while filtering out unphysical noise.

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🔧 Features

• Parses VASP OSZICAR files
• User-defined time step (in femtoseconds)
• Automatically skips the first 3 picoseconds (equilibration)
• Analyzes energy between 3 ps and 10 ps
• Filters out 4 highest unphysical energy spikes
• Plots and saves a high-quality energy vs time curve
• Command-line interface with flexible arguments

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📦 Requirements

Make sure you have the following Python packages:

• Python 3.x
• numpy
• matplotlib

You can install the dependencies using pip:

pip install numpy matplotlib

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🚀 Usage

python plot_oszicar.py --dt <time_step_fs> [--file <OSZICAR_file>] [--out <output_image>]

Required argument:

• --dt: Time step in femtoseconds (e.g., --dt 2 for a 2 fs timestep)

Optional arguments:

• --file: Path to the OSZICAR file (default: OSZICAR)
• --out: Output image filename (default: energy_vs_time.png)

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📁 Examples

# Basic usage with 2 fs timestep
python plot_oszicar.py --dt 2

# Using a custom OSZICAR file and output image name
python plot_oszicar.py --dt 1.5 --file my_OSZICAR --out my_plot.png

This will:

• Ignore the first 3 ps (e.g. 1500 steps if dt = 2 fs)
• Extract and filter energy data between 3 ps and 10 ps
• Remove 4 extreme outliers in energy values
• Plot and save the filtered curve

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🧪 Notes

• The script looks for lines containing "E=" in the OSZICAR file to extract energy values.
• If you want to analyze a different time window or change the outlier filtering strategy, you can modify the script.

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🤝 Contributing

Pull requests are welcome! If you find a bug or have an idea for improvement, feel free to open an issue or PR.