arXiv subjects

Boyi Situ

Publications and source records attributed to Boyi Situ.

3 recordsLinked to original sources

arXiv2026

GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP

Machine-learned interatomic potentials have revolutionized molecular dynamics simulations by providing quantum-mechanical accuracy at empirical-potential speeds. The graphics processing unit molecular dynamics (GPUMD) package, featuring the highly efficient neuroevolution potential (NEP) framework, has emerged as a powerful tool in this domain. However, the complexity of force field development, active learning, and trajectory post-processing often requires extensive manual scripting, imposing a steep learning curve on new users. To address this, we present GPUMDkit, a comprehensive and user-friendly toolkit that streamlines the entire simulation workflow for GPUMD and NEP. GPUMDkit integrates a suite of essential functionalities, including format conversion, structure sampling, property calculation, and data visualization, accessible through both interactive and command-line interfaces. Its modular, extensible architecture ensures accessibility for users of all experience levels while allowing seamless integration of new features. By automating complex tasks and enhancing productivity, GPUMDkit substantially lowers the barrier to using GPUMD and NEP programs. This article describes the program architecture and demonstrates its capabilities through practical applications.

cond-mat.mtrl-sci↗

arXiv2025

Unveiling the Oxidation Mechanisms of Octa-Penta Graphene: A Multidimensional Exploration from First-Principles to Machine Learning

Octa-penta graphene (OPG), a novel carbon allotrope characterized by its distinctive arrangement of pentagonal and octagonal rings, has garnered considerable attention due to its exceptional structure and functional properties. This study systematically investigates the oxidation mechanisms of OPG and elucidates the oxygen migration patterns on the OPG monolayer through first-principles calculations and machine-learning-based molecular dynamics (MLMD) simulations. Specifically, the oxidation processes on OPG-L and OPG-Z involve exothermic chemisorption, where oxygen molecules dissociate at the surfaces, forming stable epoxy groups. Furthermore, the integrated-crystal orbital Hamilton population (ICOHP) and Bader charge analyses provide insights into the physical mechanisms of oxygen atom adsorption. Importantly, we found that oxidation also impact the electronic properties of OPG, with OPG-L retaining its metallic characteristics post-oxygen adsorption, whereas OPG-Z undergoes a transformation from a metallic to a semiconducting state due to the introduction of oxygen. Oxygen migration on OPG monolayer involves breaking and reforming of C-O bonds, with varying stability across adsorption sites and limited migration along the basal plane. MLMD simulations corroborate these migration patterns, offering detailed migration trajectories consistent with theoretical predictions. These findings enhance the understanding of oxygen migration dynamics on OPG, facilitate its experimental validations, and highlight its potential as a novel 2D material for applications in batteries, heat-resistant materials, and oxidation-resistant coatings.

cond-mat.mtrl-sci↗

arXiv2023

Locally Spontaneous Dynamic Oxygen Migration on Biphenylene: A DFT Study

The dynamic oxygen migration at the interface of carbon allotropes dominated by the periodic hexagonal rings, including graphene and carbon nanotube, has opened up a new avenue to realize dynamic covalent materials. However, for the carbon materials with hybrid carbon rings, such as biphenylene, whether the dynamic oxygen migration at its interface can still be found remains unknown. Using both density functional theory calculations and machine-learning-based molecular dynamics (MLMD) simulations, we found that the oxygen migration departing away from the four-membered carbon (C4) ring is hindered, and the oxygen atom prefers to spontaneously migrate toward/around the C4 ring. This locally spontaneous dynamic oxygen migration on the biphenylene is attributed to the high barrier of about 1.5 eV for the former process and relatively low barrier of about 0.3 eV for the latter one, originating from the enhanced activity of C-O bond near/around the C4 ring due to the hybrid carbon rings structure. Moreover, the locally spontaneous dynamic oxygen migration is further confirmed by MLMD simulations. This work sheds light on the potential of biphenylene as a catalyst for spatial-controlled energy conversion and provides the guidance for realizing the dynamic covalent interface at other carbon-based or two-dimensional materials.

cond-mat.mtrl-sci↗