Au-alloy-supported-on-graphene

Workflow-driven approach for stability and catalytic modulation in the evolution of single-atom catalysts to Au-alloy clusters supported on graphene, as applied in our work.

Figure 1: The SimStack workflow framework is used to manage the simulation protocol for calculating the energetic properties and electronic structure of unary and alloy clusters in both gas-phase and adsorbed conditions. The workflow involves several components, each serving a specific function in the process: Mult-It: manages and organizes data lists, UnpackMol: prepares configuration files for DFT calculations, DFT-VASP: carries out Density Functional Theory calculations, DB-Generator: compiles the results into a yml file. Additionally, the workflow pushes the yml file to a GitHub repository to link the generated data with a Colab notebook, where the results of the simulations are visualized.

Colab

• Colab notebook for data visualization

This notebook calculates and provides a preview of the adsorption energy (E_ads) and excess energy (E_exc) in function of composition for clusters in both vacuum (vac) and adsorbed on graphene (ads) conditions. Users can apply it to the data generated in this work or their own datasets, as long as the output folders are named accordingly the energy.py requirement. Feel free to modify the code as needed.

Output File Arrangement

All calculations were performed with Vienna Ab initio Simulation Package (VASP), in witch the files follows its syntax. The converged_structures folder contains the most stable configurations, written out in the CONTCAR file format. It also includes the INCAR file used for geometry optimization and the OUTCAR file containing only the final energy obtained from self-consistent field (SCF) minimization. Additionally, for evaluating covalent bond contributions through Crystal Orbital Hamilton Population (COHP) analysis, the lobsterin input files used are also provided.

A calculation folder is named as [condition]_[cluster]_[isomer]_[configuration], highlighting key aspects of the system. This structure is based organization of converged_structures, which follows:

condition: vac or ads→ atomicity: n_1 ... n_4 → composition: ni4... ni2au2...au4 → isomers: vac_ni2au2_16.

For adsorbed conditions, the folder names also include the configuration, which indicates the number of contact points (fold) and the geometry, e.g., ads_ni3au1_30_3f_tetrahedron represents a tetrahedral cluster with three contact points.

Scientific Workflow

Our data management was carried out through Workflow Active Nodes (WaNos) within the SimStack framework, facilitating the efficient handling of a large number of calculations. With the initial structures generated, the workflow proceeds as follows:

1. Mult-It WaNo

Input:

• Configure the path containing .tar file with initial structures.

Output:

• file command name files on the top of the AdvancedFor loop.

2. UnpackMol WaNo

Input:

• Configuration of the path containing .tar files with input from bom Structures.

Ouput:

• POSCAR files needed to DFT-VASP WaNo.

3. DFT-VASP WaNo

Input:

• INCAR tab: one sets all INCAR flags by selecting the popup window options.
• KPOINTS tab: one defines KPOINTS file, Kpoints_length and Kpoints_Monkhorst.
• Analysis tab: Aimed to compute charge population, COHP analysis, and density of states (DOS).

Ouput:

• OUTCAR file.

4. DB-Generator WaNo

Input:

• Imports tab: Search_in_File variable should be set as vasp_results.yml and import this file using AdvancedForEach/*/DFT-VASP/outputs/vasp_results.yml command.
• Search_Parameters: One sets variable to be search, as total energy and title.

Ouput:

• Table-dict.yml containing the variables defined in the Search_Parameters.

Citing

If you would like to cite this work, the following references can be used:

• BibTeX:

    @article{DaSilva_2025,
        title = {Workflow-driven catalytic modulation from single-atom catalysts to Au–alloy clusters on graphene},
        volume = {15},
        ISSN = {2045-2322},
        url = {http://dx.doi.org/10.1038/s41598-025-85891-6},
        DOI = {10.1038/s41598-025-85891-6},
        number = {1},
        journal = {Scientific Reports},
        publisher = {Springer Science and Business Media LLC},
        author = {Da Silva,  Gabriel Reynald and Cerqueira Felix,  João Paulo and Rego,  Celso R. C. and Dias,  Alexandre C. and de O. Bastos,  Carlos Maciel and Piotrowski,  Maurício J. and Guedes-Sobrinho,  Diego},
        year = {2025},
        month = jan
    }

License & Copyright

Developer: Celso Ricardo C. Rêgo, Multiscale Materials Modelling and Virtual Design, Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT) https://www.int.kit.edu/wenzel.php.

Licensed under the KIT License.