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We propose a new method for molecular dynamics and Monte Carlo simulations, which is referred to as the replica-permutation method (RPM), to realize more efficient sampling than the replica-exchange method (REM).In RPM not only exchanges…
We review several parallel tempering schemes and examine their main ingredients for accuracy and efficiency. The present study covers two selection methods of temperatures and several choices for the exchange of replicas, including a recent…
The spectral features of water clusters provide important information on their structure and dynamics and can assist in deciphering the nature of the local environment of aqueous solutions in a variety of different conditions. Accurately…
Newly developed coupled-cluster (CC) methods enable simulations of ionization potentials and spectral functions of molecular systems in a wide range of energy scales ranging from core-binding to valence. This paper discusses results…
We present a formulation of smoothed particle hydrodynamics (SPH) that utilizes a first-order consistent reproducing kernel, a smoothing function that exactly interpolates linear fields with particle tracers. Previous formulations using…
This paper develops high-order well-balanced (WB) energy stable (ES) finite difference schemes for multi-layer (the number of layers $M\geqslant 2$) shallow water equations (SWEs) on both fixed and adaptive moving meshes, extending our…
Accurately simulating the properties of liquid water remains a central challenge in molecular simulations. In this work, we use machine learning potentials to investigate how the convergence settings of electronic structure calculations…
We present an energy/entropy stable and high order accurate finite difference (FD) method for solving the nonlinear (rotating) shallow water equations (SWEs) in vector invariant form using the newly developed dual-pairing and…
We perform lengthy molecular dynamics simulations of the SPC/E model of water to investigate the dynamics under pressure at many temperatures and compare with experimental measurements. We calculate the isochrones of the diffusion constant…
We present REMIX, a smoothed particle hydrodynamics (SPH) scheme designed to alleviate effects that typically suppress mixing and instability growth at density discontinuities in SPH simulations. We approach this problem by directly…
A large number of water models exists for molecular simulations. They differ in the ability to reproduce specific features of real water instead of others, like the correct temperature for the density maximum or the diffusion coefficient.…
All the existing entropy stable (ES) schemes for relativistic hydrodynamics (RHD) in the literature were restricted to the ideal equation of state (EOS), which however is often a poor approximation for most relativistic flows due to its…
We use molecular dynamics simulations to probe the rotational dynamics of the SPC/E model of water for a range of temperatures down to 200 K, 13 K above to the mode coupling temperature. We find that rotational dynamics is spatially…
Dissipative particle dynamics is a widely used mesoscale technique for the simulation of hydrodynamics (as well as immersed particles) utilizing coarse-grained molecular dynamics. While the method is capable of describing any fluid, the…
To understand the performance of popular density-functional theory (DFT) exchange-correlation (xc) functionals in simulations of liquid water, water monomers and dimers were extracted from a PBE simulation of liquid water and examined with…
This paper proposes and validates two new particle regularization techniques for the Smoothed Particle Hydrodynamics (SPH) numerical method to improve its stability and accuracy for free surface flow simulations. We introduce a general form…
Replica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently in [Plattner et al, J. Chem. Phys. 135, 134111 (2011)] a method was proposed to implement infinite…
We present two new Lagrangian methods for hydrodynamics, in a systematic comparison with moving-mesh, SPH, and stationary (non-moving) grid methods. The new methods are designed to simultaneously capture advantages of both smoothed-particle…
We study relaxation-based approaches for conserving mass and energy in the numerical solution of Schr\"odinger-Poisson (SP) type systems. Relaxation-based methods offer a general approach that can be applied as post-time step processing to…
In this work, the exact reproduction of a moving-water steady flow via the numerical solution of the one-dimensional shallow water equations is studied. A new scheme based on a modified version of the HLLEM approximate Riemann solver…