arXiv subjects

Haikuan Dong

Publications and source records attributed to Haikuan Dong.

At least 19 recordsLinked to original sources

arXiv2026

NEP89: Universal neuroevolution potential for inorganic and organic materials across 89 elements

While machine-learned interatomic potentials offer near-quantum-mechanical accuracy for atomistic simulations, many are material-specific or computationally intensive, limiting their broader use. Here, we introduce NEP89, a foundation model based on neuroevolution potential architecture, delivering near-empirical-potential speed and high accuracy across 89 elements. A compact yet comprehensive training dataset covering inorganic and organic materials was curated through descriptor-space subsampling and iterative refinement across multiple datasets. NEP89 achieves competitive accuracy compared to representative foundation models while being three to four orders of magnitude more computationally efficient, enabling previously impractical large-scale atomistic simulations of inorganic and organic systems. In addition to its out-of-the-box applicability to diverse scenarios, including million-atom-scale compression of compositionally complex alloys, ion diffusion in solid-state electrolytes and water, rocksalt dissolution, methane combustion, and protein-ligand dynamics, NEP89 also supports fine-tuning for rapid adaptation to user-specific applications, such as mechanical, thermal, structural, and spectral properties of two-dimensional materials, metallic glasses, and organic crystals.

cond-mat.mtrl-sci↗

arXiv2026

NEP-CG and NEP-AACG: Efficient coarse-grained and multiscale all-atom-coarse-grained neuroevolution potentials

Machine-learned coarse-grained (CG) models often suffer from noisy training data, limiting their accuracy and transferability. We propose a method to generate low-noise training data based on the potential of mean force by constraining CG beads during atomistic simulations and accumulating time-averaged forces. Implemented within the neuroevolution potential (NEP) framework, our approach achieves training accuracy comparable to atomistic models trained on density functional theory data. For liquid water, the NEP-CG model accurately reproduces densities from 1 bar to 1 GPa, successfully extrapolating beyond the 0.5 GPa training limit, with a virial correction essential for the correct equation of state. For an anisotropic C$_{60}$ monolayer, distinguishing crystallographically distinct bead types reduces stress errors by an order of magnitude and captures directional thermal conductivity. We further introduce a multiscale NEP-AACG model integrating all-atom (AA) and CG degrees of freedom, demonstrated for gold nanowire fracture at an experimentally relevant strain rate. Computational speeds for NEP-CG models reach hundreds to thousands of ns/day using a single consumer-grade GPU. This work provides a robust framework for constructing accurate, transferable, and efficient CG models across diverse systems.

physics.comp-ph↗

arXiv2026

qNEP: A highly efficient neuroevolution potential with dynamic charges for large-scale atomistic simulations

Although electrostatics can be incorporated into machine-learned interatomic potentials, existing approaches are computationally very demanding, limiting large-scale, long-time simulations of electrostatics-driven phenomena such as dielectric response, infrared activity, and field-matter coupling. Here, we extend the neuroevolution potential (NEP), a highly efficient machine-learned interatomic potential, to a charge-aware framework (qNEP) by introducing explicit, environment-dependent partial charges. Each ionic partial charge is represented by a neural network as a function of the local descriptor vector, analogous to the NEP site-energy model. This formulation enables the direct prediction of the Born effective charge tensor for each ion and, consequently, the polarization. As a result, dielectric properties, infrared spectra, and coupling to external electric fields can be evaluated within a unified framework. We derive consistent expressions for the forces and virials that explicitly account for the position dependence of the partial charges. The qNEP method has been implemented in the free-and-open-source GPUMD package, with support for both Ewald summation and particle-particle particle-mesh treatments of electrostatics. We demonstrate the accuracy and efficiency of the qNEP approach through representative applications to water, Li7La3Zr2O12, BaTiO3, and a magnesium-water interface. These results show that qNEP enables accurate atomistic simulations with explicit long-range electrostatics, scalable to million-atom systems on nanosecond time scales using consumer-grade GPUs.

physics.comp-ph↗

arXiv2025

Thermal conductivities of monolayer graphene oxide from machine learning molecular dynamics simulations

Graphene oxide (GO) exhibits rich chemical heterogeneity that strongly influences its structural, thermal, and mechanical properties, yet quantitatively linking reduction chemistry to heat transport remains challenging. In this work, we develop a machine-learned neuroevolution potential (NEP) trained on an existing density functional theory dataset (\textit{Angew.\ Chem.\ Int.\ Ed.}, \textbf{63} , e202410088 (2024)), achieving reasonable accuracy at a computational cost much lower than the existing machine-learned and empirical potentials. Leveraging this potential, we perform large-scale molecular dynamics (MD) simulations to model the thermal reduction of GO across realistic structural domains. Using the homogeneous nonequilibrium MD method with a proper quantum-statistical correction scheme, we find that reduced GO exhibits strongly suppressed thermal conductivities, ranging from a few to tens of Wm$^{-1}$K$^{-1}$, substantially lower than pristine GO without defects and far below graphene. Moreover, the thermal conductivity of reduced GO increases moderately with increasing OH/O ratio, except at the highest oxidation level (O/C=0.5) where this trend inverts, while decreasing significantly with increasing O/C ratio, a trend strongly correlated with the fraction of recovered graphene-like structures. Our work provides a computationally tractable and predictive atomistic machine learning framework for exploring how chemical structure governs heat transport in heterogeneous carbon materials.

physics.chem-ph↗

arXiv2025

Anisotropic and isotropic elasticity and thermal transport in monolayer C$_{24}$ networks from machine-learning molecular dynamics

Two-dimensional fullerene networks have recently attracted increasing interest due to their diverse bonding topologies and mechanically robust architectures. In this work, we develop an accurate machine-learned potential NEP-C$_{24}$ for both the quasi-hexagonal phase (qHP) and the quasi-tetragonal phase (qTP) C$_{24}$ monolayers, based on the neuroevolution potential (NEP) framework. Using this NEP-C$_{24}$ model, we systematically investigate the elastic and thermal transport properties. Compared with C$_{60}$ monolayers, both C$_{24}$ phases exhibit markedly enhanced stiffness, arising from the combination of reduced molecular size and increased density of covalent bonds. The qTP C$_{24}$ monolayer shows nearly isotropic elastic properties and thermal conductivities along its two principal axes owing to its four-fold symmetry, whereas the chain-like, misaligned bonding topology of the qHP C$_{24}$ monolayer leads to pronounced in-plane anisotropy. Homogeneous nonequilibrium molecular dynamics and spectral decomposition analyses reveal that low-frequency ($<5$ THz) acoustic phonons dominate heat transport, with directional variations in phonon group velocity and mean free path governing the anisotropic response in qHP C$_{24}$. Real-space heat flow visualizations further show that, in these fullerene networks, phonon transport is dominated by strong inter-fullerene covalent bonds rather than weak van der Waals interactions. These findings establish a direct link between intermolecular bonding topology and phonon-mediated heat transport, providing guidance for the rational design of fullerene-based two-dimensional materials with tunable mechanical and thermal properties.

cond-mat.mtrl-sci↗

arXiv2025

Optimizing thermoelectric performance of graphene antidot lattices via quantum transport and machine-learning molecular dynamics simulations

Thermoelectric materials, which can convert waste heat to electricity or be utilized as solid-state coolers, hold promise for sustainable energy applications. However, optimizing thermoelectric performance remains a significant challenge due to the complex interplay between electronic and thermal transport properties. In this work, we systematically optimize $ZT$ in graphene antidot lattices (GALs), nanostructured graphene sheets with periodic nanopores characterized by two geometric parameters: the hexagonal unit cell side length $L$ and the antidot radius $R$. The lattice thermal conductivity is determined through machine-learned potential-driven molecular dynamics (MD) simulations, while electronic transport properties are computed using linear-scaling quantum transport in combination with MD trajectories based on a bond-length-dependent tight-binding model. This method is able to account for electron-phonon scattering, allowing access to diffusive transport in large-scale systems, overcoming limitations of previous methods based on nonequilibrium Green function formalism. Our results show that the introduction of the antidots effectively decouples lattice and electronic transport and lead to a favorable and significant violation of the Wiedemann-Franz law. We find that optimal $ZT$ values occur in GALs with intermediate $L$ and $R$, closely correlated with peak power factor values. Notably, thermoelectric performance peaks near room temperature, with maximal $ZT$ values approaching 2, highlighting GALs as promising candidates for high-performance thermoelectric energy conversion.

cond-mat.mes-hall↗

arXiv2024

Million-atom heat transport simulations of polycrystalline graphene approaching first-principles accuracy enabled by neuroevolution potential on desktop GPUs

First-principles molecular dynamics simulations of heat transport in systems with large-scale structural features are challenging due to their high computational cost. Here, using polycrystalline graphene as a case study, we demonstrate the feasibility of simulating heat transport with near first-principles accuracy in systems containing over 1.4 million atoms, achievable even with consumer desktop GPUs. This is enabled by the highly efficient neuroevolution potential (NEP) approach, as implemented in the open-source GPUMD package. Leveraging the NEP model's accuracy and efficiency, we quantify the reduction in thermal conductivity of polycrystalline graphene due to grain boundaries with varying grain sizes, resolving contributions from in-plane and out-of-plane (flexural) phonon modes. Additionally, we find that grain boundaries can lead to finite thermal conductivity even under significant tensile strain, in contrast to the divergent behavior observed in pristine graphene under similar conditions, indicating that grain boundaries may play a crucial role in thermal transport in low-dimensional momentum-conserving systems. These findings could offer insights for interpreting experimental observations, given the widespread presence of both large-scale grain boundaries and external strains in real materials. The demonstrated ability to simulate millions of atoms with near-first-principles accuracy on consumer desktop GPUs using the NEP approach will help make large-scale high-fidelity atomistic simulations more accessible to the broader research community.

cond-mat.mtrl-sci↗

arXiv2024

General-purpose machine-learned potential for 16 elemental metals and their alloys

Machine-learned potentials (MLPs) have exhibited remarkable accuracy, yet the lack of general-purpose MLPs for a broad spectrum of elements and their alloys limits their applicability. Here, we present a feasible approach for constructing a unified general-purpose MLP for numerous elements, demonstrated through a model (UNEP-v1) for 16 elemental metals and their alloys. To achieve a complete representation of the chemical space, we show, via principal component analysis and diverse test datasets, that employing one-component and two-component systems suffices. Our unified UNEP-v1 model exhibits superior performance across various physical properties compared to a widely used embedded-atom method potential, while maintaining remarkable efficiency. We demonstrate our approach's effectiveness through reproducing experimentally observed chemical order and stable phases, and large-scale simulations of plasticity and primary radiation damage in MoTaVW alloys. This work represents a significant leap towards a unified general-purpose MLP encompassing the periodic table, with profound implications for materials science.

cond-mat.mtrl-sci↗

arXiv2024

Molecular dynamics simulations of heat transport using machine-learned potentials: A mini review and tutorial on GPUMD with neuroevolution potentials

Molecular dynamics (MD) simulations play an important role in understanding and engineering heat transport properties of complex materials. An essential requirement for reliably predicting heat transport properties is the use of accurate and efficient interatomic potentials. Recently, machine-learned potentials (MLPs) have shown great promise in providing the required accuracy for a broad range of materials. In this mini review and tutorial, we delve into the fundamentals of heat transport, explore pertinent MD simulation methods, and survey the applications of MLPs in MD simulations of heat transport. Furthermore, we provide a step-by-step tutorial on developing MLPs for highly efficient and predictive heat transport simulations, utilizing the neuroevolution potentials (NEPs) as implemented in the GPUMD package. Our aim with this mini review and tutorial is to empower researchers with valuable insights into cutting-edge methodologies that can significantly enhance the accuracy and efficiency of MD simulations for heat transport studies.

cond-mat.mtrl-sci↗

arXiv2023

Combining linear-scaling quantum transport and machine-learning molecular dynamics to study thermal and electronic transports in complex materials

We propose an efficient approach for simultaneous prediction of thermal and electronic transport properties in complex materials. Firstly, a highly efficient machine-learned neuroevolution potential is trained using reference data from quantum-mechanical density-functional theory calculations. This trained potential is then applied in large-scale molecular dynamics simulations, enabling the generation of realistic structures and accurate characterization of thermal transport properties. In addition, molecular dynamics simulations of atoms and linear-scaling quantum transport calculations of electrons are coupled to account for the electron-phonon scattering and other disorders that affect the charge carriers governing the electronic transport properties. We demonstrate the usefulness of this unified approach by studying thermoelectric transport properties of a graphene antidot lattice.

cond-mat.mtrl-sci↗

arXiv2023

Anisotropic and high thermal conductivity in monolayer quasi-hexagonal fullerene: A comparative study against bulk phase fullerene

Recently a novel two-dimensional (2D) C$_{60}$ based crystal called quasi-hexagonal-phase fullerene (QHPF) has been fabricated and demonstrated to be a promising candidate for 2D electronic devices [Hou et al. Nature 606, 507-510 (2022)]. We construct an accurate and transferable machine-learned potential to study heat transport and related properties of this material, with a comparison to the face-centered-cubic bulk-phase fullerene (BPF). Using the homogeneous nonequilibrium molecular dynamics and the related spectral decomposition methods, we show that the thermal conductivity in QHPF is anisotropic, which is 137(7) W/mK at 300 K in the direction parallel to the cycloaddition bonds and 102(3) W/mK in the perpendicular in-plane direction. By contrast, the thermal conductivity in BPF is isotropic and is only 0.45(5) W/mK. We show that the inter-molecular covalent bonding in QHPF plays a crucial role in enhancing the thermal conductivity in QHPF as compared to that in BPF. The heat transport properties as characterized in this work will be useful for the application of QHPF as novel 2D electronic devices.

physics.comp-ph↗

arXiv2022

Exactly equivalent thermal conductivity in finite systems from equilibrium and nonequilibrium molecular dynamics simulations

In a previous paper [Physical Review B \textbf{103}, 035417 (2021)], we showed that the equilibrium molecular dynamics (EMD) method can be used to compute the apparent thermal conductivity of finite systems. It has been shown that the apparent thermal conductivity from EMD for a system with domain length $2L$ is equal to that from nonequilibrium molecular dynamics (NEMD) for a system with domain length $L$. Taking monolayer silicence with an accurate machine learning potential as an example, here we show that the thermal conductivity values from EMD and NEMD agree for the same domain length if the NEMD is applied with periodic boundary conditions in the transport direction. Our results thus establish an exact equivalence between EMD and NEMD for thermal conductivity calculations.

cond-mat.mtrl-sci↗

arXiv2022

GPUMD: A package for constructing accurate machine-learned potentials and performing highly efficient atomistic simulations

We present our latest advancements of machine-learned potentials (MLPs) based on the neuroevolution potential (NEP) framework introduced in [Fan et al., Phys. Rev. B 104, 104309 (2021)] and their implementation in the open-source package GPUMD. We increase the accuracy of NEP models both by improving the radial functions in the atomic-environment descriptor using a linear combination of Chebyshev basis functions and by extending the angular descriptor with some four-body and five-body contributions as in the atomic cluster expansion approach. We also detail our efficient implementation of the NEP approach in graphics processing units as well as our workflow for the construction of NEP models, and we demonstrate their application in large-scale atomistic simulations. By comparing to state-of-the-art MLPs, we show that the NEP approach not only achieves above-average accuracy but also is far more computationally efficient. These results demonstrate that the GPUMD package is a promising tool for solving challenging problems requiring highly accurate, large-scale atomistic simulations. To enable the construction of MLPs using a minimal training set, we propose an active-learning scheme based on the latent space of a pre-trained NEP model. Finally, we introduce three separate Python packages, GPYUMD, CALORINE, and PYNEP, which enable the integration of GPUMD into Python workflows.

physics.comp-ph↗

arXiv2022

Neuroevolution machine learning potentials: Combining high accuracy and low cost in atomistic simulations and application to heat transport

We develop a neuroevolution-potential (NEP) framework for generating neural network based machine-learning potentials. They are trained using an evolutionary strategy for performing large-scale molecular dynamics (MD) simulations. A descriptor of the atomic environment is constructed based on Chebyshev and Legendre polynomials. The method is implemented in graphic processing units within the open-source GPUMD package, which can attain a computational speed over $10^7$ atom-step per second using one Nvidia Tesla V100. Furthermore, per-atom heat current is available in NEP, which paves the way for efficient and accurate MD simulations of heat transport in materials with strong phonon anharmonicity or spatial disorder, which usually cannot be accurately treated either with traditional empirical potentials or with perturbative methods.

physics.comp-ph↗

arXiv2021

Heat transport across graphene/hexagonal-BN tilted grain boundaries from phase-field crystal model and molecular dynamics simulations

We study the interfacial thermal conductance of grain boundaries (GBs) between monolayer graphene and hexagonal boron nitride (h-BN) sheets using a combined atomistic approach. First, realistic samples containing graphene/h-BN GBs with different tilt angles are generated using the phase-field crystal (PFC) model developed recently [P. Hirvonen \textit{et al.}, Phys. Rev. B \textbf{100}, 165412 (2019)] that captures slow diffusive relaxation inaccessible to molecular dynamics (MD) simulations. Then, large-scale MD simulations using the efficient GPUMD package are performed to assess heat transport and rectification properties across the GBs. We find that lattice mismatch between the graphene and h-BN sheets plays a less important role in determining the interfacial thermal conductance as compared to the tilt angle. In addition, we find no significant thermal rectification effects for these GBs.

cond-mat.mtrl-sci↗

arXiv2021

Ultrahigh convergent thermal conductivity of carbon nanotubes from comprehensive atomistic modeling

Anomalous heat transport in one-dimensional nanostructures, such as nanotubes and nanowires, is a widely debated problem in condensed matter and statistical physics, with contradicting pieces of evidence from experiments and simulations. Using a comprehensive modeling approach, comprised of lattice dynamics and molecular dynamics simulations, we proved that the infinite length limit of the thermal conductivity of a (10,0) single-wall carbon nanotube is finite but this limit is reached only for macroscopic lengths due to thermal phonon mean free path of several millimeters. Our calculations showed that the extremely high thermal conductivity of this system at room temperature is dictated by quantum effects. Modal analysis showed that the divergent nature of thermal conductivity, observed in one-dimensional model systems, is suppressed in carbon nanotubes by anharmonic scattering channels provided by the flexural and optical modes with polarization in the plane orthogonal to the transport direction.

cond-mat.mes-hall↗

arXiv2020

Interpretation of apparent thermal conductivity in finite systems from equilibrium molecular dynamics simulations

We propose a way to properly interpret the apparent thermal conductivity obtained for finite systems using equilibrium molecular dynamics simulations (EMD) with fixed or open boundary conditions in the transport direction. In such systems the heat current autocorrelation function develops negative values after a correlation time which is proportional to the length of the simulation cell in the transport direction. Accordingly, the running thermal conductivity develops a maximum value at the same correlation time and eventually decays to zero. By comparing EMD with nonequilibrium molecular dynamics (NEMD) simulations, we conclude that the maximum thermal conductivity from EMD in a system with domain length 2L is equal to the thermal conductivity from NEMD in a system with domain length L. This facilitates the use of nonperiodic-boundary EMD for thermal transport in finite samples in close correspondence to NEMD.

cond-mat.stat-mech↗

arXiv2020

Thermal conductivity reduction in carbon nanotube by fullerene encapsulation: A molecular dynamics study

Single-walled carbon nanotubes (SWCNTs) in their pristine form have high thermal conductivity whose further improvement has attracted a lot of interest. Some theoretical studies have suggested that the thermal conductivity of a $(10,10)$ SWCNT is dramatically enhanced by C$_{60}$ fullerene encapsulation. However, recent experiments on SWCNT bundles show that fullerene encapsulation leads to a reduction rather than an increase in thermal conductivity. Here, we employ three different molecular dynamics methods to study the influence of C$_{60}$ encapsulation on heat transport in a $(10,10)$ SWCNT. All the three methods consistently predict a reduction of the thermal conductivity of $(10,10)$ SWCNT upon C$_{60}$ encapsulation by $20\%-30\%$, in agreement with experimental results on bundles of SWCNTs. We demonstrate that there is a simulation artifact in the Green-Kubo method which gives anomalously large thermal conductivity from artificial convection. Our results show that the C$_{60}$ molecules conduct little heat compared to the outer SWCNT and reduce the phonon mean free paths of the SWCNT by inducing extra phonon scattering. We also find that the thermal conductivity of a $(10,10)$ SWCNT monotonically decreases with increasing filling ratio of C$_{60}$ molecules.

cond-mat.mtrl-sci↗