Catalyst Reconstruction Simulation

This program simulates the reconstruction phenomenon of alloy catalysts during oxidation-reduction processes to obtain basic information about active sites on the catalyst surface.

Features

• Simulates oxidation and reduction steps
• Uses a cyclic calculation strategy under different ensembles
• Generates and analyzes structures at each step
• Calculates adsorption energies
• Performs Molecular Dynamics (MD) simulations

Main Components

1. main.py: The main script that orchestrates the simulation process
2. Gen_structures.py: Generates structures for each step
3. Read_energy.py: Reads and processes energy calculations
4. add_O2_first.py: Handles the initial oxygen addition step
5. clean_finder.py: Finds adsorption sites on the surface

Usage

1. Ensure all dependencies are installed (ASE, NumPy, SciPy, Pymatgen)
2. Set up your initial structure and simulation parameters
3. Run the main script:

python main.py

Output

The program generates various files and folders for each oxidation and reduction step, including:

• Structure files (CIF, ARC)
• Energy calculations
• MD simulation results

The final reconstructed structure can be found in the final_structure.cif file.

Note

This simulation is designed for specific alloy catalyst systems. Adjust parameters in the code as needed for your particular system.