This repository contains Python code for analyzing and visualizing thermodynamic properties (energy, pressure, temperature, etc.) as a function of simulation timestep.
The notebook (thermo_property vs timestep.ipynb) provides tools to read LAMMPS log/dump data, extract relevant columns, and generate plots to understand the time evolution of system properties during molecular dynamics (MD) simulations.
In molecular dynamics, thermodynamic quantities fluctuate but approach equilibrium averages.
This notebook helps:
- Parse simulation outputs
- Plot energy, temperature, and other quantities vs time
- Detect equilibrium and transient regions
- Export clean plots for publications
The code has been tested on the following system:
- OS: Linux (Ubuntu 22.04 LTS)
- Python: 3.10+
- Core packages: NumPy, Pandas, Matplotlib
Install the required Python packages:
pip install numpy pandas matplotlib