Analyzing and biasing simulations with PLUMEDThis chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of a collective…Giovanni Bussi, Gareth A. Tribello·Dec 19, 2018SaveLearn
EigenKernel - A middleware for parallel generalized eigenvalue solvers to attain high scalability and usabilityAn open-source middleware EigenKernel was developed for use with parallel generalized eigenvalue solvers or large-scale electronic state calculation to attain high scalability and usability. The…Kazuyuki Tanaka, Hiroto Imachi, Tomoya Fukumoto et al.·Dec 19, 2018SaveLearn
A generalized massively parallel ultra-high order FFT-based Maxwell solverDispersion-free ultra-high order FFT-based Maxwell solvers have recently proven to be paramount to a large range of applications, including the high-fidelity modeling of high-intensity laser-matter…Haithem Kallala, Jean-Luc Vay, Henri Vincenti·Dec 18, 2018SaveLearn
Learning from the Density to Correct Total Energy and Forces in First Principle SimulationsWe propose a new molecular simulation framework that combines the transferability, robustness and chemical flexibility of an ab initio method with the accuracy and efficiency of a machine learned…Sebastian Dick, Marivi Fernandez-Serra·Dec 17, 2018SaveLearn
Molecular dynamic simulation of water vapor interaction with various types of pores using hybrid computing structuresTheoretical and experimental investigations of water vapor interaction with porous materials are very needful for various fields of science and technology. Not only studies of the interaction of…V. V. Korenkov, E. G. Nikonov, M. Popovičová·Dec 17, 2018SaveLearn
The reason for the tilting of domain wall with Dzyaloshinskii-Moriya interaction from a microscopic dynamical perspectiveThe interfacial Dzyaloshinskii-Moriya interaction (DMI) of a heavy metal (HM)/ferromagnetic (FM) metal heterostructure is vital to the current-induced domain wall motion (CIDWM) at an ultrahigh…Maokang Shen, Yue Zhang, Wei Luo et al.·Dec 17, 2018SaveLearn
Pressures inside a nano-porous medium. The case of a single phase fluidWe define the pressure of a porous medium in terms of the grand potential, and compute its value in a nano-confined or nano-porous medium, meaning a medium where thermodynamic equations need be…Olav Galteland, Dick Bedeaux, Signe Kjelstrup·Dec 17, 2018SaveLearn
A fast synthetic iterative scheme for the stationary phonon Boltzmann transport equationIn this paper, a fast synthetic iterative scheme is developed to accelerate convergence for the implicit DOM based on the stationary phonon BTE. The key innovative point of the present scheme is the…Chuang Zhang, Songze Chen, Zhaoli Guo et al.·Dec 16, 2018SaveLearn
Locally and Globally Optimal Configurations of N Particles on the Sphere with Applications in the Narrow Escape and Narrow Capture ProblemsDetermination of optimal arrangements of N particles on a sphere is a well-known problem in physics. A famous example of such is the Thomson problem of finding equilibrium configurations of…Wesley J. M. Ridgway, Alexei F. Cheviakov·Dec 15, 2018SaveLearn
Numerical aspect of large-scale electronic state calculation for flexible device materialNumerical aspects of large-scale electronic state calculation are explored on flexible organic device materials. Physical theory, numerical method and real application studies are discussed in the…Takeo Hoshi, Hiroto Imachi, Akiyoshi Kuwata et al.·Dec 15, 2018SaveLearn
Fiend -- Finite Element Quantum DynamicsWe present Fiend - a simulation package for three-dimensional single-particle time-dependent Schrödinger equation for cylindrically symmetric systems. Fiend has been designed for the simulation of…Janne Solanpää, Esa Räsänen·Dec 14, 2018SaveLearn
Cornell Potential: A Neural Network ApproachIn this study, we solved Schrödinger equation with Cornell potential (Coulomb-plus-linear potential) by using neural network approach. Four different types of Cornell potential were used without a…Halil Mutuk·Dec 14, 2018SaveLearn
The Computation of Local Stress in ab initio Molecular SimulationsMotivated by the increasingly more important role of ab initio molecular dynamics models in material simulations, this work focuses on the definition of local stress, when the forces are determined…Xiantao Li·Dec 14, 2018SaveLearn
Computational micromagnetics with CommicsWe present our open-source Python module Commics for the study of the magnetization dynamics in ferromagnetic materials via micromagnetic simulations. It implements state-of-the-art unconditionally…Carl-Martin Pfeiler, Michele Ruggeri, Bernhard Stiftner et al.·Dec 14, 2018SaveLearn
Assessment of localized and randomized algorithms for electronic structureAs electronic structure simulations continue to grow in size, the system-size scaling of computational costs increases in importance relative to cost prefactors. Presently, linear-scaling costs for…Jonathan E. Moussa, Andrew D. Baczewski·Dec 13, 2018SaveLearn
Acceleration of Source Iteration using the Dynamic Mode DecompositionWe present a novel acceleration technique for improving the convergence of source iteration for discrete ordinates transport calculations. Our approach uses the idea of the dynamic mode decomposition…Ryan G. McClarren, Terry S. Haut·Dec 13, 2018SaveLearn
Arbitrary Lagrangian--Eulerian finite element method for curved and deforming surfaces. I. General theory and application to fluid interfacesAn arbitrary Lagrangian--Eulerian (ALE) finite element method for arbitrarily curved and deforming two-dimensional materials and interfaces is presented here. An ALE theory is developed by endowing…Amaresh Sahu, Yannick A. D. Omar, Roger A. Sauer et al.·Dec 12, 2018SaveLearn
sGDML: Constructing Accurate and Data Efficient Molecular Force Fields Using Machine LearningWe present an optimized implementation of the recently proposed symmetric gradient domain machine learning (sGDML) model. The sGDML model is able to faithfully reproduce global potential energy…Stefan Chmiela, Huziel E. Sauceda, Igor Poltavsky et al.·Dec 12, 2018SaveLearn
Efficient discontinuous Galerkin implementations and preconditioners for implicit unsteady compressible flow simulationsThis work presents and compares efficient implementations of high-order discontinuous Galerkin methods: a modal matrix-free discontinuous Galerkin (DG) method, a hybridizable discontinuous Galerkin…Matteo Franciolini, Krzysztof Fidkowski, Andrea Crivellini·Dec 12, 2018SaveLearn
A multi-dimensional, moment-accelerated deterministic particle method for time-dependent, multi-frequency thermal radiative transfer problemsThermal Radiative Transfer (TRT) is the dominant energy transfer mechanism in high-energy density physics with applications in inertial confinement fusion and astrophysics. The stiff interactions…Hans Hammer, HyeongKae Park, Luis Chacon·Dec 11, 2018SaveLearn
Two Relaxation Time Lattice Boltzmann Method Coupled to Fast Fourier Transform Poisson Solver: Application to Electroconvective FlowElectroconvective flow between two infinitely long parallel electrodes is investigated via a multiphysics computational model. The model solves for spatiotemporal flow properties using…Yifei Guan, Igor Novosselov·Dec 11, 2018SaveLearn
Learning representations of molecules and materials with atomistic neural networksDeep Learning has been shown to learn efficient representations for structured data such as image, text or audio. In this chapter, we present neural network architectures that are able to learn…Kristof T. Schütt, Alexandre Tkatchenko, Klaus-Robert Müller·Dec 11, 2018SaveLearn
Hybrid functional study of non-linear elasticity and internal strain in zincblende III-V materialsWe investigate the elastic properties of selected zincblende III-V semiconductors. Using hybrid functional density functional theory we calculate the second and third order elastic constants, and…Daniel S. P. Tanner, Miguel A. Caro, Stefan Schulz et al.·Dec 11, 2018SaveLearn
Scattering Field Solutions of Metasurfaces based on the Boundary Element Method (BEM) for Interconnected RegionsA methodology for determining the scattered Electromagnetic (EM) fields present for interconnected regions with common metasurface boundaries is presented. The method uses a Boundary Element Method…Scott A. Stewart, Sanam Moslemi-Tabrizi, Tom. J. Smy et al.·Dec 11, 2018SaveLearn
WENO-Wombat: Scalable Fifth-Order Constrained-Transport Magnetohydrodynamics for Astrophysical ApplicationsDue to increase in computing power, high-order Eulerian schemes will likely become instrumental for the simulations of turbulence and magnetic field amplification in astrophysical fluids in the next…J. M. F. Donnert, H. Jang, P. Mendygral et al.·Dec 11, 2018SaveLearn