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In the molecular dynamics calculations for the free energy of ions and ionic molecules, we often encounter wet charged molecular systems where electrical neutrality condition is broken. This causes a problem in the evaluation of…
We introduce a scheme for molecular simulations, the Deep Potential Molecular Dynamics (DeePMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data.…
I describe a modification to the original Fast Multipole Method (FMM) of Greengard & Rokhlin that approximates the gravitation field of an FMM cell as a small uniform grid (a "gridlet") of effective masses. The effective masses on a gridlet…
This paper introduces a parallel directional fast multipole method (FMM) for solving N-body problems with highly oscillatory kernels, with a focus on the Helmholtz kernel in three dimensions. This class of oscillatory kernels requires a…
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…
The utilization of periodic structures such as photonic crystals and metasurfaces is common for light manipulation at nanoscales. One of the most widely used computational approaches to consider them and design effective optical devices is…
We propose a novel method for the efficient and accurate iterative solution of frequency domain integral equations (IEs) that are used for large/multi-scale electromagnetic scattering problems. The proposed method uses a novel…
Born-Oppenheimer Molecular Dynamics (BOMD) is a powerful but expensive technique. The main bottleneck in a density functional theory bomd calculation is the solution to the Kohn-Sham (KS) equations, that requires an iterative procedure that…
Quantum embedding schemes have the potential to significantly reduce the computational cost of first principles calculations, whilst maintaining accuracy, particularly for calculations of electronic excitations in complex systems. In this…
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…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
We develop an efficient Ewald method of molecular dynamics simulation for calculating the electrostatic interactions among charged and polar particles between parallel metallic plates, where we may apply an electric field with an arbitrary…
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…
Accurate modelling of electrostatic interactions and charge transfer is fundamental to computational chemistry, yet most machine learning interatomic potentials (MLIPs) rely on local atomic descriptors that cannot capture long-range…
The Fast Multipole Method (FMM) is an efficient numerical algorithm for computation of long-ranged forces in $N$-body problems within gravitational and electrostatic fields. This method utilizes multipole expansions of the Green's function…
A new method for Ewald summation in planar/slablike geometry, i.e. systems where periodicity applies in two dimensions and the last dimension is "free" (2P), is presented. We employ a spectral representation in terms of both Fourier series…
Optimal exploitation of supercomputing resources for the evaluation of electrostatic forces remains a challenge in molecular dynamics simulations of very large systems. The most efficient methods are currently based on particle-mesh Ewald…
In this paper, a fast multipole method (FMM) is proposed for 3-D Laplace equation in layered media. The potential due to charges embedded in layered media is decomposed into a free space component and four types of reaction field…
Distributed point charge models (DCM) and their minimal variants (MDCM) have been integrated with tools widely used for condensed-phase simulations, including a virial-based barostat and a slow-growth algorithm for thermodynamic…
The accurate description of electrostatic interactions remains a challenging problem for fitted potential-energy functions. The commonly used fixed partial-charge approximation fails to reproduce the electrostatic potential at short range…