arXiv subjects

Jiuyang Liang

Publications and source records attributed to Jiuyang Liang.

At least 19 recordsLinked to original sources

arXiv2026

Prolate spheroidal wave functions enable fast and exponent-aware long-range machine learning interatomic potentials

Long-range interactions such as electrostatics and dispersion remain a central bottleneck for machine learning interatomic potentials (MLIPs), especially in ionic, polar and interfacial systems. Ewald-based reciprocal-space mechanisms provide a physically grounded route for capturing these nonlocal effects, but often require dense Fourier grids and can become memory-limited at scale. This problem is particularly pronounced in molecular dynamics, where high efficiency requirements make accurate long-range modelling particularly costly. Here we introduce PSWF-LR, an exponent-aware long-range framework based on prolate spheroidal wave functions (PSWFs) that can be easily incorporated into existing model architectures. Its core components are PSWF-based mollification and atom-grid spreading, which enable compact and efficient representation of arbitrary inverse-power channels $1/r^p$ while treating the decay exponent as a physical prior. Across diverse long-range benchmarks, PSWF-LR reduces Fourier-mode requirements, improves energy and force accuracy, accelerates production-level simulations by about threefold, and extends long-range MLIP simulations beyond the memory limits of conventional MLIPs.

physics.chem-ph↗

arXiv2026

Accelerating Molecular Dynamics Simulations using Fast Ewald Summation with Prolates

The evaluation of long-range Coulomb interactions is a significant cost in molecular dynamics (MD), even when using Particle Mesh Ewald (PME) or Particle-Particle-Particle-Mesh (PPPM) methods, which rely on Ewald splitting and the fast Fourier transform to achieve near-linear scaling. We introduce ESP -- Ewald summation with prolate spheroidal wave functions (PSWFs) -- which leads to a more efficient Fourier representation and a reduction in the required grid size, global communication, and particle-grid operations, without loss of accuracy. We have integrated the ESP method into two widely-used open-source MD packages, LAMMPS and GROMACS, enabling rapid comparison and adoption. Relative to PME/PPPM baselines at error tolerances $10^{-3}$ to $10^{-4}$, ESP gives roughly a $3$-fold acceleration of electrostatic interactions, and a $2.5$-fold speed-up in the MD simulation when using about $10^3$ compute cores. At high accuracy ($10^{-5}$), these increase to $10$-fold for the far-field electrostatics and $5$-fold for MD simulation. Furthermore, we show that the accelerated codes have improved strong scaling with core count, and validate them in realistic long-time biological and material simulations. ESP thus offers a practical, drop-in path to reduce the time-to-solution and energy footprint of MD workflows.

math.NA↗

arXiv2026

Random batch sum-of-Gaussians method for molecular dynamics simulation of particle systems in the NPT ensemble

In this work, we develop a random batch sum-of-Gaussians (RBSOG) method for molecular dynamics simulations of charged systems in the isothermal-isobaric (NPT) ensemble. We introduce an SOG splitting of the pressure-related $1/r^3$ kernel, yielding a smooth short-/long-range decomposition for instantaneous pressure evaluation. The long-range part is treated in Fourier space by random-batch importance sampling. Because the radial and non-radial pressure components favor different proposals, direct sampling either increases structure-factor evaluations and communication or leads to substantial variance inflation. To address this tradeoff, we introduce a measure-recalibration strategy that reuses Fourier modes drawn from the radial proposal and corrects them for the non-radial target, producing an unbiased pressure estimator with significantly reduced variance and negligible extra cost. The resulting method mitigates pressure artifacts caused by cutoff discontinuities in traditional Ewald-based treatments while preserving near-optimal $O(N)$ complexity. We provide theoretical evidence on pressure decomposition error, consistency of stochastic approximation, and convergence of RBSOG-based MD. Numerical experiments on bulk water, LiTFSI ionic liquids, and DPPC membranes show that RBSOG accurately reproduces key structural and dynamical observables with small batch sizes ($P\sim 100$). In large-scale benchmarks up to $10^7$ atoms on $2048$ CPU cores, RBSOG achieves about an order-of-magnitude speedup over particle-particle particle-mesh in electrostatic calculations for NPT simulations, together with a consistent $4\times$ variance reduction relative to random batch Ewald and excellent weak/strong scalability. Overall, RBSOG provides a practical and scalable route to reduce time-to-solution and communication cost in large-scale NPT simulations.

physics.comp-ph↗

arXiv2026

An $O(\log N)$ Monte Carlo method for periodic Coulomb systems

Efficient Monte Carlo (MC) sampling of many-body systems with long-range electrostatics is often limited by the cost of per-move energy-difference evaluation under periodic boundary conditions. We present DMK-MC, an accelerated MC method that adapts the dual-space multilevel kernel-splitting (DMK) framework to single-particle Metropolis updates. DMK-MC computes the energy change and, upon acceptance, updates the stored incoming plane-wave fields with $O(1)$ work per tree level, yielding an overall $O(\log N)$ expected work per trial move for fixed accuracy. The method decomposes the Coulomb kernel into three components: a global, periodized smooth part; a multilevel sequence of smooth difference kernels whose interactions are restricted to same-level colleague boxes; and a singular residual kernel whose short-range interactions are evaluated directly. Benchmarks on uniform, highly nonuniform, and implicit-solvent electrolyte and colloidal configurations show that DMK-MC consistently outperforms a recent FMM-based $O(\log N)$ Monte Carlo method, delivering several-fold speedups at comparable tolerances.

physics.comp-ph↗

arXiv2026

Random Batch Sum-of-Gaussians Method for Molecular Dynamics of Born-Mayer-Huggins Systems

The Born-Mayer-Huggins (BMH) potential, which combines Coulomb interactions with dispersion and short-range exponential repulsion, is widely used for ionic materials such as molten salts. However, large-scale molecular dynamics simulations of BMH systems are often limited by computation, communication, and memory costs. We recently proposed the random batch sum-of-Gaussians (RBSOG) method, which accelerates Coulomb calculations by using a sum-of-Gaussians (SOG) decomposition to split the potential into short- and long-range parts and by applying importance sampling in Fourier space for the long-range part. In this work, we extend the RBSOG to BMH systems and incorporate a random batch list (RBL) scheme to further accelerate the short-range part, yielding a unified framework for efficient simulations with the BMH potential. The combination of the SOG decomposition and the RBL enables an efficient and scalable treatment of both long- and short-range interactions in BMH system, particularly the RBL well handles the medium-range exponential repulsion and dispersion by the random batch neighbor list. Error estimate is provided to show the theoretical convergence of the RBL force. We evaluate the framework on molten NaCl and mixed alkali halide with up to $5\times10^6$ atoms on $2048$ CPU cores. Compared to the Ewald-based particle-particle particle-mesh method and the RBSOG-only method, our method achieves approximately $4\sim10\times$ and $2\times$ speedups while using $1000$ cores, respectively, under the same level of structural and thermodynamic accuracy and with a reduced memory usage. These results demonstrate the attractive performance of our method in accuracy and scalability for MD simulations with long-range interactions.

physics.comp-ph↗

arXiv2026

Fast Ewald Summation with Prolates for Charged Systems in the NPT Ensemble

We present an NPT extension of Ewald summation with prolates (ESP), a spectrally accurate and scalable particle-mesh method for molecular dynamics simulations of periodic, charged systems. Building on the recently introduced ESP framework, this work focuses on rigorous and thermodynamically consistent pressure/stress evaluation in the isothermal--isobaric ensemble. ESP employs prolate spheroidal wave functions as both splitting and spreading kernels, reducing the Fourier grid size needed to reach a prescribed pressure accuracy compared with current widely used mesh-Ewald methods based on Gaussian splitting and B-spline spreading. We derive a unified pressure-tensor formulation applicable to isotropic, semi-isotropic, anisotropic, and fully flexible cells, and show that the long-range pressure can be evaluated with a single forward FFT followed by diagonal scaling, whereas force evaluation requires both forward and inverse transforms. We provide production implementations in LAMMPS and GROMACS and validate pressure and force accuracy on bulk water, LiTFSI ionic liquids, and a transmembrane system. Benchmarks on up to $3\times 10^3$ CPU cores demonstrate strong scaling and reduced communication cost at matched accuracy, particularly for NPT pressure evaluation.

math.NA↗

arXiv2025

Machine-Learning Interatomic Potentials for Long-Range Systems

Machine-learning interatomic potentials have emerged as a revolutionary class of force-field models in molecular simulations, delivering quantum-mechanical accuracy at a fraction of the computational cost and enabling the simulation of large-scale systems over extended timescales. However, they often focus on modeling local environments, neglecting crucial long-range interactions. We propose a Sum-of-Gaussians Neural Network (SOG-Net), a lightweight and versatile framework for integrating long-range interactions into machine learning force field. The SOG-Net employs a latent-variable learning network that seamlessly bridges short-range and long-range components, coupled with an efficient Fourier convolution layer that incorporates long-range effects. By learning sum-of-Gaussians multipliers across different convolution layers, the SOG-Net adaptively captures diverse long-range decay behaviors while maintaining close-to-linear computational complexity during training and simulation via non-uniform fast Fourier transforms. The method is demonstrated effective for a broad range of long-range systems.

physics.chem-ph↗

arXiv2025

Accurate Error Estimates and Optimal Parameter Selection in Ewald Summation for Dielectrically Confined Coulomb Systems

Dielectrically confined Coulomb systems are widely employed in molecular dynamics (MD) simulations. Despite extensive efforts in developing efficient and accurate algorithms for these systems, rigorous and accurate error estimates, which are crucial for optimal parameter selection for simulations, is still lacking. In this work, we present a rigorous error analysis in Ewald summation for electrostatic interactions in systems with two dielectric planar interfaces, where the polarization contribution is modeled by an infinitely reflected image charge series. Accurate error estimate is provided for the truncation error of image charge series, as well as decay rates of energy and force correction terms, as functions of system parameters such as vacuum layer thickness, dielectric contrasts, and image truncation levels. Extensive numerical tests conducted across several prototypical parameter settings validate our theoretical predictions. Additionally, our analysis elucidates the non-monotonic error convergence behavior observed in previous numerical studies. Finally, we provide an optimal parameter selection strategy derived from our theoretical insights, offering practical guidance for efficient and accurate MD simulations of dielectric-confined systems.

math.NA↗

arXiv2025

Fast Algorithm for Quasi-2D Coulomb Systems

Quasi-2D Coulomb systems are of fundamental importance and have attracted much attention in many areas nowadays. Their reduced symmetry gives rise to interesting collective behaviors, but also brings great challenges for particle-based simulations. Here, we propose a novel algorithm framework to address the $O(N^2)$ simulation complexity associated with the long-range nature of Coulomb interactions. First, we introduce an efficient Sum-of-Exponentials (SOE) approximation for the long-range kernel associated with Ewald splitting, achieving uniform convergence in terms of inter-particle distance, which reduces the complexity to $O(N^{7/5})$. We then introduce a random batch sampling method in the periodic dimensions, the stochastic approximation is proven to be both unbiased and with reduced variance via a tailored importance sampling strategy, further reducing the computational cost to $O(N)$. The performance of our algorithm is demonstrated via various numerical examples. Notably, it achieves a speedup of $2\sim 3$ orders of magnitude comparing with Ewald2D method, enabling molecular dynamics (MD) simulations with up to $10^6$ particles on a single core. The present approach is therefore well-suited for large-scale particle-based simulations of Coulomb systems under confinement, making it possible to investigate the role of Coulomb interaction in many practical situations.

math.NA↗

arXiv2025

Random batch sum-of-Gaussians algorithm for molecular dynamics simulations of Yukawa systems in three dimensions

Yukawa systems have drawn widespread interest across various applications. In this paper, we introduce a novel random batch sum-of-Gaussians (RBSOG) algorithm for molecular dynamics simulations of 3D Yukawa systems with periodic boundary conditions. We develop a sum-of-Gaussians (SOG) decomposition of the Yukawa kernel, dividing the interactions into near-field and far-field components. The near-field component, singular but compactly supported in a local domain, is calculated directly. The far-field component, represented as a sum of smooth Gaussians, is treated using the random batch approximation in Fourier space with an adaptive importance sampling strategy to reduce the variance of force calculations. Unlike the traditional Ewald decomposition, which introduces discontinuities and significant truncation error at the cutoff, the SOG decomposition achieves high-order smoothness and accuracy near the cutoff, allowing for efficient and energy-stable simulations. Additionally, by avoiding the use of the fast Fourier transform, our method achieves optimal O(N) complexity while maintaining high parallel scalability. Finally, unlike previous random batch approaches, the proposed adaptive importance sampling strategy achieves nearly optimal variance reduction across the regime of the coupling parameters. Rigorous theoretical analyses are presented. We validate the performance of RBSOG method through simulations of one-component plasma under weak and strong coupling conditions, using up to 10^6 particles and 1024 CPU cores. As a practical application in fusion ignition, we simulate high-temperature, high-density deuterium-αmixtures to study the energy exchange between deuterium and high-energy αparticles. The RBSOG method can be readily extended to other dielectric response functions, offering a promising approach for large-scale simulations.

physics.comp-ph↗

arXiv2025

Error estimate of the u-series method for molecular dynamics simulations

This paper provides an error estimate for the u-series method of the Coulomb interaction in molecular dynamics simulations. We show that the number of truncated Gaussians $M$ in the u-series and the base of interpolation nodes $b$ in the bilateral serial approximation are two key parameters for the algorithm accuracy, and that the errors converge as $\mathcal{O}(b^{-M})$ for the energy and $\mathcal{O}(b^{-3M})$ for the force. Error bounds due to numerical quadrature and cutoff in both the electrostatic energy and forces are obtained. Closed-form formulae are also provided, which are useful in the parameter setup for simulations under a given accuracy. The results are verified by analyzing the errors of two practical systems.

math.NA↗

arXiv2024

A fast spectral sum-of-Gaussians method for electrostatic summation in quasi-2D systems

The quasi-2D electrostatic systems, characterized by periodicity in two dimensions with a free third dimension, have garnered significant interest in many fields. We apply the sum-of-Gaussians (SOG) approximation to the Laplace kernel, dividing the interactions into near-field, mid-range, and long-range components. The near-field component, singular but compactly supported in a local domain, is directly calculated. The mid-range component is managed using a procedure similar to nonuniform fast Fourier transforms in three dimensions. The long-range component, which includes Gaussians of large variance, is treated with polynomial interpolation/anterpolation in the free dimension and Fourier spectral solver in the other two dimensions on proxy points. Unlike the fast Ewald summation, which requires extensive zero padding in the case of high aspect ratios, the separability of Gaussians allows us to handle such case without any zero padding in the free direction. Furthermore, while NUFFTs typically rely on certain upsampling in each dimension, and the truncated kernel method introduces an additional factor of upsampling due to kernel oscillation, our scheme eliminates the need for upsampling in any direction due to the smoothness of Gaussians, significantly reducing computational cost for large-scale problems. Finally, whereas all periodic fast multipole methods require dividing the periodic tiling into a smooth far part and a near part containing its nearest neighboring cells, our scheme operates directly on the fundamental cell, resulting in better performance with simpler implementation. We provide a rigorous error analysis showing that upsampling is not required in NUFFT-like steps, achieving $O(N\log N)$ complexity with a small prefactor. The performance of the scheme is demonstrated via extensive numerical experiments.

math.NA↗

arXiv2024

RBMD: A molecular dynamics package enabling to simulate 10 million all-atom particles in a single graphics processing unit

This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of particle systems. The long-range part of Coulomb interactions is calculated in Fourier space by the random batch Ewald algorithm, which achieves linear complexity and superscalability, surpassing classical lattice-based Ewald methods. For the short-range part, the random batch list algorithm is used to construct neighbor lists, significantly reducing both computational and memory costs. The RBMD is implemented on GPU-CPU heterogeneous architectures, with classical force fields for all-atom systems. Benchmark systems are used to validate accuracy and performance of the package. Comparison with the particle-particle particle-mesh method and the Verlet list method in the LAMMPS package is performed on three different NVIDIA GPUs, demonstrating high efficiency of the RBMD on heterogeneous architectures. Our results also show that the RBMD enables simulations on a single GPU with a CPU core up to 10 million particles. Typically, for systems of one million particles, the RBMD allows simulating all-atom systems with a high efficiency of 8.20 ms per step, demonstrating the attractive feature for running large-scale simulations of practical applications on a desktop machine.

physics.comp-ph↗

arXiv2024

A note on accurate pressure calculations of Coulomb systems with periodic boundary conditions

In this note, we address some issues concerning the accurate pressure calculation of Coulomb systems with periodic boundary conditions. First, we prove that the formulas for the excess part of the pressure with Ewald summation also reduce to the ensemble average of one-third of the ratio between the potential energy and the volume so that the comments on our previous work in a recent paper by [Onegin~\emph{et al}.,~J. Phys. A: Math.~Theor.~57 (2024) 205002] are incorrect. Second, we demonstrate that in charge non-neutral systems, the pressure expression must be corrected to include interactions with the neutralizing background. This addresses the issues about pressure computation in LAMMPS raised in the paper by Onegin {\it et al.}. Numerical experiments are performed to verify that the pressure obtained via Ewald summation with corrected terms agrees with the average pressure using thermodynamics for the non-neutral OCP system, and are independent of the splitting parameter in the Ewald summation.

physics.comp-ph↗

arXiv2024

Random Batch Ewald Method for Dielectrically Confined Coulomb Systems

Quasi two-dimensional Coulomb systems have drawn widespread interest. The reduced symmetry of these systems leads to complex collective behaviors, yet simultaneously poses significant challenges for particle-based simulations. In this paper, a novel method is presented for efficiently simulate a collection of charges confined in doubly-periodic slabs, with the extension to scenarios involving dielectric jumps at slab boundaries. Unlike existing methods, the method is insensitive to the aspect ratio of simulation box, and it achieves optimal O(N) complexity and strong scalability, thanks to the random batch Ewald (RBE) approach. Moreover, the additional cost for polarization contributions, represented as image reflection series, is reduced to a negligible cost via combining the RBE with an efficient structure factor coefficient re-calibration technique in k-space. Explicit formulas for optimal parameter choices of the algorithm are provided through error estimates, together with a rigorous proof. Finally, we demonstrate the accuracy, efficiency and scalability of our method, called RBE2D, via numerical tests across a variety of prototype systems. An excellent agreement between the RBE2D and the PPPM method is observed, with a significant reduction in the computational cost and strong scalability, demonstrating that it is a promising method for a broad range of charged systems under quasi-2D confinement.

math.NA↗

arXiv2024

Confined run-and-tumble model with boundary aggregation: long time behavior and convergence to the confined Fokker-Planck model

The motile micro-organisms such as E. coli, sperm, or some seaweed are usually modelled by self-propelled particles that move with the run-and-tumble process. Individual-based stochastic models are usually employed to model the aggregation phenomenon at the boundary, which is an active research field that has attracted a lot of biologists and biophysicists. Self-propelled particles at the microscale have complex behaviors, while characteristics at the population level are more important for practical applications but rely on individual behaviors. Kinetic PDE models that describe the time evolution of the probability density distribution of the motile micro-organisms are widely used. However, how to impose the appropriate boundary conditions that take into account the boundary aggregation phenomena is rarely studied. In this paper, we propose the boundary conditions for a 2D confined run-and-tumble model (CRTM) for self-propelled particle populations moving between two parallel plates with a run-and-tumble process. The proposed model satisfies the relative entropy inequality and thus long-time convergence. We establish the relation between CRTM and the confined Fokker-Planck model (CFPM) studied in [22]. We prove theoretically that when the tumble is highly forward peaked and frequent enough, CRTM converges asymptotically to the CFPM. A numerical comparison of the CRTM with aggregation and CFPM is given. The time evolution of both the deterministic PDE model and individual-based stochastic simulations are displayed, which match each other well.

math.AP↗

arXiv2023

Energy Stable Scheme for Random Batch Molecular Dynamics

The computational bottleneck of molecular dynamics is the pairwise additive long-range interactions between particles. The random batch Ewald (RBE) method provides a highly efficient and superscalable solver for long-range interactions, but the stochastic nature of this algorithm leads to unphysical self-heating effect during the simulation. We propose an energy stable scheme (ESS) for particle systems by employing a Berendsen-type energy bath. The scheme removes the notorious energy drift which exists due to the force error even when a symplectic integrator is employed. Combining the RBE and the ESS, the new method provides a perfect solution of the computational bottleneck of molecular dynamics at the microcanonical ensemble. Numerical results for primitive electrolyte and all-atom pure water systems demonstrate the attractive performance of the algorithm including its dramatically high accuracy, linear complexity and overcoming the energy drift for long-time simulations.

physics.chem-ph↗

arXiv2022

Improved random batch Ewald method in molecular dynamics simulations

The random batch Ewald (RBE) is an efficient and accurate method for molecular dynamics (MD) simulations of physical systems at the nano-/micro- scale. The method shows great potential to solve the computational bottleneck of long-range interactions, motivating a necessity to accelerating short-range components of the non-bonded interactions for a further speedup of MD simulations. In this work, we present an improved RBE method for the non-bonding interactions by introducing the random batch idea to constructing neighbor lists for the treatment of both the short-range part of the Ewald splitting and the Lennard-Jones potential. The efficiency of the novel neighbor list algorithm owes to the stochastic minibatch strategy which can significantly reduce the total number of neighbors. We obtan the error estimate and convergence by theoretical analysis and implement the improved RBE method in the LAMMPS package. Benchmark simulations are performed to demonstrate the accuracy and stability of the algorithm. Numerical tests on computer performance by conducting large-scaled MD simulations for systems including up to 0.1 billion water molecules, run on massive cluster with up to 50 thousand CPU cores, demonstrating the attractive features such as the high parallel scalability and memory-saving of the method in comparison to the existing methods.

physics.comp-ph↗