RNET

ReactionNet-generator

Construct intermediates and reaction networks containing C, H, O elements (up to C6 products), and genegate adsorption configurations of these intermediates on metal surface.

Table of Contents

• 0. Prerequisites
• 1. File Structure
• 2. RNet.py
  • 2.1 RNet.py Usage
    • 2.1.1 Command-Line Arguments
    • 2.1.2 Example Command
  • 2.2 Outputs for RNet.py
• 3. MakeSlab.py
  • 3.1 MakeSlab.py Usage
    • 3.1.1 Command-Line Arguments
    • 3.1.2 Example Command
  • 3.2 Outputs for RNet.py
• 4. Optimization and Plot
• 5. License
• 6. Acknowledgements

0. Prerequisites

• RNet.py
  • Python 3 (version > 3.10)
  • NetworkX (A Python package for the creation of reaction networks.)
• MakeSlab.py
  • ASE (Atomic Simulation Environment, version > 3.22)
  • Pymatgen (Python Materials Genomics, version > 2023.3.23)
  • mp-api (The Materials Project API, version > 0.41.2)

1.1 File Structure

.
├── RNet.py # Genarate  reaction network diagram
├── MakeSlab.py # Construct all possible structures for intermediats adsorption on metal surfaces
├── plot_all.py # Plot the energy changes and energy differences MAE
├── example
├── utils
│ ├── molecule_db.py # Complete molecular library containing up to C6 products
│ ├── reaction_db.txt # Potential elementary reactions between molecules cataloged in the `molecule_db.py` file, where the first molecule acts as the reactant, and the second and third (if exist) molecules represent the products.
│ ├── id2chem.txt # The correspondence between molecular ID number and chemical formula
└ └── material_db.py # Metal database for cleaveving surfaces and adsorbing intermediates

2. RNet.py

RNet.py constructs a reaction network diagram containing all possible intermediate and elementary reactions based on the specified maximum number of C and O atoms.

2.1 RNet.py Usage

1. Ensure all prerequisites are installed and configured correctly.
2. Run the script with the desired parameters.

2.1.1 Command-Line Arguments

This script supports the following command-line arguments:

• noc (type: int): The maximum number of carbon atoms.
• noo (type: int): The maximum number of oxygen atoms.
• --layout (type: str, default: spring): The layout for the network graph, choose from "spring", "circular", "shell", "kamada_kawai", "spectral" or "random".

2.1.2 Example Command

To run the script, use the following command:

python RNet.py noc noo [--layout str]

python RNet.py 1 2 --layout spring

2.2 Outputs for RNet.py

1. id2chem.txt # The correspondence between molecular ID number and chemical formula
2. molecule_db.py # Selected molecular library
3. reaction_db.txt # Potential elementary reactions between molecules cataloged in the molecule_db.py file, where the first molecule acts as the reactant, and the second and third (if exist) molecules represent the products.
4. material_db.py # Metal database for cleaveving surfaces and adsorbing intermediates
5. Reaction_Net.png # Reaction network diaram.

3. MakeSlab.py

The MakeSlab.py script generates the configurations of molecules adsorbed on metal surfaces (POSCAR format of VASP) based on the molecular and elementary reaction database generated by RNet.py.

3.1 MakeSlab.py Usage

1. Ensure all prerequisites are installed and configured correctly.
2. Ensure id2chem.txt,molecule_db.py,reaction_db.txt and material_db.py have been successfully generated by RNet.py.
3. Run the script with the desired parameters.

3.1.1 Command-Line Arguments

This script supports the following command-line arguments:

• --plot (type: bool, default: False): Enable plotting of top view of slabs and its adsorption sites
• --api-key (type: str): Materials Project API key.
• --max-index (type: int, default: 1): Maximum Miller index to consider for slab generation.
• --min-slab-size (type: float, default: 8.0): Minimum size of the slab.
• --min-vacuum-size (type: float, default: 15.0): Minimum size of the vacuum layer.
• --min-lw (type: float, default: 10.0): Minimum slab model a and b vector.
• --distance (type: float, default: 10.0): Distance between adsorbate and slab.
• --element (type: str, default: "Au"): Chemical formula of the materials to process.
• --max-slabs (type: int, default: None): Maximum number of slabs to process per material.

3.1.2 Example Command

To run the script, use the following command:

python MakeSlab.py  [--plot BOOL] [--api-key STR] [--max-index INT] [--min-slab-size FLOAT] [--min-vacuum-size FLOAT] [--min-lw FLOAT] [--distance FLOAT] [--element STR] [--max-slabs INT]

python MakeSlab.py --element Pt --max-index 1

3.2 Outputs for MakeSlab.py

[element][surface_index]_[molecule_ID]-[molecule_chemical_fomula].vasp e.g. Pt100_0-H2.vasp

4. Optimization and Plot

Optimize all possible intermedieas by flowopt.py. And plot the energy changes and energy differences MAE by plot_all.py.

python ./plot_all.py

5. License

This project is licensed under the LGPL-3.0 License.

6. Acknowledgements

• ASE: https://wiki.fysik.dtu.dk/ase/
• Pymatgen: https://pymatgen.org/
• NetworkX: https://networkx.org/