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MOSP: Multi-scale Operando Simulation Package

Note
2024.6.10: Release Candidate 1 of MOSP 2.0 (2.0-rc.1) has been released. If you encouter any issues during usage, please contact us via a new issue or email

About MOSP

MOSP is a Multi-scale Operando Simulation Package that can be utilized to investigate the dynamic structure-property relationship of nanoparticles in catalytic reaction atmospheres. MOSP comprises two main modules: the Multiscale Structure Reconstruction (MSR) module and the Kinetic Monte Carlo (KMC) module. Users can input reaction conditions, nanoparticle size, and other parameters through through the graphical user interface (GUI). With MSR, users can obtain the structure of nanoparticles in a realistic environment within seconds, and simulate the their catalytic behavior on a macroscopic time scale using KMC. The KMC module also allows to run independently by reading in initial structure files in xyz format.

MOSP is developed and maintained by Yi Gao's group, and we welcome engaging in discussions. The major contributors: Beien Zhu, Lei Ying, Yu Han, Xiaoyan Li, Jun Meng, Yi Gao (in no particular order).

Installation

1. Install python (python3.8 is recommended)
   Install python3.8 directly from python website. Or install Anaconda and build python3.8 environment.

2. Download the project

   • Method 1: clone project using git

     git clone https://github.com/mosp-catalysis/MOSP.git  
     cd MOSP  

   • Method 2：Download Zip

   Note: In the next steps, please ensure that your working directory is the main directory of MOSP

3. Install the dependencies (If you are using a 32-bit operating system or a different version of Python, please download the corresponding .whl file for PyOpenGL from this website.)

   # (If use anaconda) create anaconda environment
   conda create -n mosp_env python=3.8
   conda activate mosp_env
   # Install PyOpenGL 
   pip install data/PyOpenGL-3.1.6-cp38-cp38-win_amd64.whl  
   pip install data/PyOpenGL_accelerate-3.1.6-cp38-cp38-win_amd64.whl  
   # Install the other dependencies
   pip install -r requirements.txt  

4. Run

   # (If using an Anaconda environment, activate it before running)
   conda activate mosp_env
   # Run main program
   python main.py

Usage

1. Demonstration of the MOSP workflow

2. MSR module
   Inputs: lattice parameters, particle size (radius), reaction atmosphere, surface parameters (surface energy, adsorption energy and entropy of each gases/adsorbates, and lateral interactions)

Outputs: nanoparticle structure (exportable as .xyz file), statistics on surface site types (stored in data/OUTPUT/faceinfo.txt)

3. KMC module、

• Inputs (using MSR structure as an initial structure) Define species (adsorbates+products) -> Define events + lateral interactions

  The adsorbate definition sub-window provides the parameters needed for calculating event rates:

  

• Outputs After KMC calculations, raw data will be stored in the data/OUTPUT/ directory. Subsequently, preliminary data processing can be done internally in MOSP, including outputs such as: Coverage and TOF trends will be displayed on the Data Visual panel, and data points can be exported in csv/xlsx/json formats.

  

  Based on GCN and the relative activity of each site (normalized site-specific TOF), particles can be colored in the Model Visual panel, and data can be exported as .xyz files, with corresponding GCN/TOF stored in the last column of the coordinate file.

4. Example Files The examples/ folder provides example input files for CO oxidation reactions on Au and Pt (in .json format). These files can be loaded via the menu bar using File -> Load. More examples will be added in future versions.

Online Tutorials

Bilibili

Version

• Version 2.0: Introduces a multi-step KMC module with customizable events, along with visualization panels and data export functionality
• Version 1.0: Basic functionalities with MSR and KMC module.

References

MSR

[1] Zhu B, Xu Z, Wang CL, Gao Y,* "Shape Evolution of Metal Nanoparticles in Water Vapor Environments." Nano Lett. 2016, 16, 2628-2632. [Link]

[2] Zhu B, Meng J, Yuan W, Zhang X, Yang H, Wang Y,* Gao Y,* "Reshaping of Metal Nanoparticles in Reaction Conditions." Angew. Chem. Int. Ed. 2020, 59, 2171-2180. (minireview) [Link]

KMC

[1] Li X, Zhu B,* Gao Y,* "Exploration of Dynamic Structure–Activity Relationship of a Platinum Nanoparticle in the CO Oxidation Reaction" J. Phys. Chem. C 2021, 125, 19756-19762. [Link]

[2] Ying L, Han Y, Zhu B,* Gao Y,* "Exploration of structure sensitivity of gold nanoparticles in low-temperature CO oxidation" Ind. Chem. Mater. 2024, 2, 321-327 [Link]

Related Publications

[1] Zhu B, Meng J, Gao Y,* "Equilibrium Shape of Metal Nanoparticles under Reactive Gas Conditions." J. Phys. Chem. C 2017, 121, 5629-5634. [Link]

[2] Zhang X, Meng J, Zhu B,* Yu J, Zou S, Zhang Z, Gao Y,* Wang Y,* "In situ TEM Studies of Shape Evolution of Pd Nanoparticles under Oxygen and Hydrogen Environment at Atmospheric Pressure." Chem. Comm. 2017, 53, 13213-13216. (back cover) [Link]

[3] Meng J, Zhu B,* Gao Y,* "Shape Evolution of Metal Nanoparticles in Binary Gas Environment." J. Phys. Chem. C 2018, 122, 6144-6150. [Link]

[4] Duan M, Yu J, Meng J, Zhu B,* Wang Y,* Gao Y,* "Reconstruction of Supported Metal Nanoparticles in Reaction Conditions." Angew. Chem. Int. Ed. 2018, 57, 6464-6469. (minireview) [Link]

[5] Zhang X, Meng J, Zhu B,* Yuan W, Yang H, Zhang Z, Gao Y,* Wang Y,* "Unexpected N₂ Induced Refacetting of Palladium Nanoparticles." Chem. Comm. 2018, 54, 8587-8590. [Link]

[6] Chmielewski A, Meng J, Zhu B, Gao Y, Guesmi H, Prunier H, Alloyeau D, Wang G, Louis C, Dalannoy L, Afanasiev P, Ricolleau C, Nelayah J,* "Reshaping Dynamics of Gold Nanoparticles under H₂ and O₂ at Atmospheric Pressure." ACS Nano 2019, 13, 2024-2033. [Link]

[7] Du J, Meng J, Li X, Zhu B, Gao Y,* "Multiscale Atomistic Simulation of Metal Nanoparticles in Working Conditions." Nanoscale Adv. 2019, 1, 2478-2484. [PDF]

[8] Yuan L, Zhu B, Zhang G,* Gao Y,* "Reshaping of Rh Nanoparticles in Operando Conditions." Catal. Today 2020, 350, 184-191. [Link]

[9] Tang M, Zhu B, Meng J, Zhang X, Yuan W, Zhang Z, Gao Y,* Wang Y,* "Pd-Pt Nanoalloy Transformation Pathways at Atomic Scale." Mater. Today Nano 2018, 1, 41-46. [Link]

[10] Li X, Zhu B, Qi R, Gao Y,* "Real-time Simulation of Nonequilibrium Nanocrystal Transformation." Adv. Theory Simul. 2019, 2, 1800127.[Link]

[11] Wu Z, Tang M, Li X, Luo S, Yuan W, Zhu B,* Zhang H, Gao Y, Wang Y,* "Surface faceting and compositional evolution of Pd@Au core−shell nanocrystals during in situ annealing." Phys. Chem. Chem. Phys. 2019, 21, 3134-3139. [Link]

[12] Zhu B, Qi R, Yuan L, Gao Y,* "Real-time Simulation of the Atomic Ostwald Ripening of TiO₂ Supported Nanoparticles." Nanoscale 2020, 12, 19142-19148. [Link]

[13] Duan X, Li X, Zhu B,* Gao Y,* "Identifying the morphology of Pt nanoparticles for the optimal catalytic activity towards CO oxidation." Nanoscale 2022, 14, 17754-17760. [Link]

[14] Han Y, Li X, Zhu B,* Gao Y,* "Unveiling the Au Surface Reconstruction in a CO Environment by Surface Dynamics and Ab Initio Thermodynamics." J.Phys. Chem. A 2022, 126, 6538-6547. [Link]

[15] Han Y, Duan X, Zhu B,* Gao Y,* "Insights into structure of metal nanomaterials in reactive environments." WIREs Comput Mol Sci. A 2022, 12:e1587. [Link]

[16] Duan X, Ying L, Li X, Zhu B,* Gao Y,* "High or Low Coordination: Insight into the Active Site of Pt Nanoparticles toward CO Oxidation." J.Phys. Chem. Lett. 2023, 14, 9848-9854. [Link]

[16] Duan X, Han Y, Zhu B,* Gao Y,* "Modelling of metal nanoparticles' structures and dynamics under reaction conditions." Materials Today Catalysis 2023, 3, 100032. [Link]

[18] Li X, Ou P, Duan X, Ying L, Meng J, Zhu B,* Gao Y,* "Dynamic Active Sites In Situ Formed in Metal Nanoparticle Reshaping under Reaction Conditions." JACS Au 2024, 4, 1892-1900. [Link]