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What retards the response of graphene based gaseous sensorFeb 20 2019Graphene based sensor to gas molecules should be ultrasensitive and ultrafast because of the single-atomic thickness of graphene, while the response is not fast. Usually, the measured response time for many molecules, such as CO, NH3, SO2, CO2 and NO2 ... More

Shallow Learning for Fluid Flow Reconstruction with Limited Sensors and Limited DataFeb 20 2019In many applications, it is important to reconstruct a fluid flow field, or some other high-dimensional state, from limited measurements and limited data. In this work, we propose a shallow neural network-based learning methodology for such fluid flow ... More

Solving large-scale interior eigenvalue problems to investigate the vibrational properties of the boson peak regime in amorphous materialsFeb 19 2019Amorphous solids, like metallic glasses, exhibit an excess of low frequency vibrational states reflecting the break-up of sound due to the strong structural disorder inherent to these materials. Referred to as the boson peak regime of frequencies, how ... More

Fundamental gaps of quantum dots on the cheapFeb 19 2019We show that the fundamental gaps of quantum dots can be accurately estimated at the computational effort of a standard ground-state calculation supplemented with a non self-consistent step of negligible cost, all performed within density-functional theory ... More

Expanding the horizon of automated metamaterials discovery via quantum annealingFeb 18 2019Complexity of materials designed by machine learning is currently limited by the inefficiency of classical computers. We show how quantum annealing can be incorporated into automated materials discovery and conduct a proof-of-principle study on designing ... More

Local projection stabilized finite element modeling of viscoelastic two-phase flowsFeb 18 2019A three-field local projection stabilized finite element method is developed for computations of a 3D-axisymmetric buoyancy driven bubble rising in a liquid column in which either the bubble or the liquid column can be viscoelastic. The two-phase flow ... More

Numerical study of Bose-Einstein condensation in the Kaniadakis-Quarati model for bosonsFeb 17 2019Kaniadakis and Quarati (1994) proposed a Fokker-Planck equation with quadratic drift as a PDE model for the dynamics of Bose-Einstein condensation in a homogeneous Bose gas. It is an open question whether this equation has solutions exhibiting condensates ... More

Validation of an immersed boundary method for compressible flowsFeb 16 2019This paper sums up some recent validations of an immersed boundary method for compressible flow simulations. It has been already shown that this method is able to provide accurate results without meshing effort around more or less complex geometries. ... More

Approximate Green's Function Coupled Cluster Method Employing Effective Dimension ReductionFeb 16 2019The Green's function coupled cluster (GFCC) method is a powerful many-body tool for computing the electronic structure of molecular and periodic systems, especially when electrons of the system are strongly correlated. However, for the GFCC to be routinely ... More

Inversion-Free Evaluation of Nearest Neighbors in Method of MomentsFeb 15 2019A recently introduced technique of topology sensitivity in method of moments is extended by the possibility of adding degrees-of-freedom (reconstruct) into underlying structure. The algebraic formulation is inversion-free, suitable for parallelization ... More

Simulator-free Solution of High-Dimensional Stochastic Elliptic Partial Differential Equations using Deep Neural NetworksFeb 14 2019Stochastic partial differential equations (SPDEs) are ubiquitous in engineering and computational sciences. The stochasticity arises as a consequence of uncertainty in input parameters, constitutive relations, initial/boundary conditions, etc. Because ... More

WavePacket: A Matlab package for numerical quantum dynamics. III: Quantum-classical simulations and surface hopping trajectoriesFeb 13 2019Feb 18 2019WavePacket is an open-source program package for numerical simulations in quantum dynamics. Building on the previous Part I [Comp. Phys. Comm. 213, 223-234 (2017)] and Part II [Comp. Phys. Comm. 228, 229-244 (2018)] which dealt with quantum dynamics of ... More

WavePacket: A Matlab package for numerical quantum dynamics. III: Quantum-classical simulations and surface hopping trajectoriesFeb 13 2019WavePacket is an open-source program package for numerical simulations in quantum dynamics. Building on the previous Part I [Comp. Phys. Comm. 213, 223-234 (2017)] and Part II [Comp. Phys. Comm. 228, 229-244 (2018)] which dealt with quantum dynamics of ... More

Efficient geometric integrators for nonadiabatic quantum dynamics in the adiabatic basisFeb 12 2019The split-operator algorithm is popular for nonadiabatic quantum dynamics because it is explicit, easy to implement, and preserves many geometric invariants of the exact evolution; however, the algorithm can only be used in the diabatic basis, or, more ... More

Removing instabilities in the hierarchical equations of motion: exact and approximate projection approachesFeb 12 2019The hierarchical equations of motion (HEOM) provide a numerically exact approach for computing the reduced dynamics of a quantum system linearly coupled to a bath. We have found that HEOM contains temperature-dependent instabilities that grow exponentially ... More

Coordinate descent full configuration interactionFeb 12 2019We develop an efficient algorithm, coordinate descent FCI (CDFCI), for the electronic structure ground state calculation in the configuration interaction framework. CDFCI solves an unconstrained non-convex optimization problem, which is a reformulation ... More

Effective dynamics of a conditioned generalized linear Glauber modelFeb 12 2019In order to study the stochastic Markov processes conditioned on a specific value of a time-integrated observable, the concept of ensembles of trajectories has been recently used extensively. In this paper, we consider a generic reaction-diffusion process ... More

Measuring Heat Flux Beyond Fourier's lawFeb 12 2019We use nonequilibrium molecular dynamics (NEMD) to explore the effect of shear flow on heat flux. By simulating a simple fluid in a channel bounded by tethered atoms, the heat flux is computed for two systems: a temperature driven one with no flow and ... More

Conductivity and capacitance of streamers in avalanche model for streamer propagationFeb 11 2019Propagation of positive streamers, modeled by the electron avalanche mechanism, is simulated in a needle-plane gap. The streamer is modeled like an RC-circuit where the channel is a resistor and the extremities of the streamer have a capacitance towards ... More

Many-body perturbation theory calculations using the yambo codeFeb 11 2019yambo is an open source project aimed at studying excited state properties of condensed matter systems from first principles using many-body methods. As input, yambo requires ground state electronic structure data as computed by density functional theory ... More

Convergence properties of detonation simulationsFeb 11 2019We present a high-resolution convergence study of detonation initiated by a temperature gradient in a stoichiometric hydrogen-oxygen mixture using the Pencil Code. With Mach numbers reaching 10-30, a certain amount of shock viscosity is needed to remove ... More

High-Throughput Computational Studies in Catalysis and Materials Research, and their Impact on Rational DesignFeb 11 2019In the 21st century, many technology fields have become reliant on advancements in process automation. We have seen dramatic growth in areas and industries that have successfully implemented a high level of automation. In drug discovery, for example, ... More

Imaginary time density functional calculation of ground states for second-row atoms using CWDVR approachFeb 10 2019We have developed the Coulomb wave function discrete variable representation (CWDVR) method to solve the imaginary time dependent Kohn - Sham equation on the many - electronic second row atoms. The imaginary time dependent Kohn - Sham equation is numerically ... More

Momentum space calculations of the binding energies of argon dimerFeb 10 2019The binding energies of argon dimer are calculated by solving the homogeneous Lippmann-Schwinger integral equation in momentum space. Our numerical analysis using two models of argon-argon interaction developed by Patkowski {\it et al.} confirms not only ... More

Self-Consistent Electron-Nucleus Cusp Correction for Molecular OrbitalsFeb 09 2019We describe a method for imposing the correct electron-nucleus (e-n) cusp in molecular orbitals expanded as a linear combination of (cuspless) Gaussian basis functions. Enforcing the e-n cusp in trial wave functions is an important asset in quantum Monte ... More

Non-singular boundary integral methods for fluid mechanics applicationsFeb 09 2019A formulation of the boundary integral method for solving partial differential equations has been developed whereby the usual weakly singular integral and the Cauchy principal value integral can be removed analytically. The broad applicability of the ... More

Generalized Regular k-point Grid Generation On The FlyFeb 08 2019In the DFT community, it is common practice to use regular k-point grids (Monkhorst-Pack, MP) for Brillioun zone integration. Recently Wisesa et. al.\cite{wisesa2016efficient} and Morgan et. al.\cite{MORGAN2018424} demonstrated that generalized regular ... More

Quantitative analysis of the interaction between a dc SQUID and an integrated micromechanical doubly clamped cantileverFeb 08 2019Based on the superconducting quantum interference device (SQUID) equations described by the resistively- and capacitively-shunted junction model coupled to the equation of motion of a damped harmonic oscillator, we provide simulations to quantitatively ... More

Macroscopic Lattice Boltzmann Method for Shallow Water Equations (MacLABSWE)Feb 08 2019It is well known that there are two integral steps of streaming and collision in the lattice Boltzmann method (LBM). This concept has been changed by the author's recently proposed macroscopic lattice Boltzmann method (MacLAB) to solve the Navier-Stokes ... More

Machine learning as an improved estimator for magnetization curve and spin gapFeb 08 2019By applying a machine learning algorithm to extrapolations and the numerical differentiations, we propose a method to obtain a continuous magnetization curve out of discrete energy data. It gives an expression for the spin gap, which converges faster ... More

A robust and accurate formulation of molecular and colloidal electrostaticsFeb 08 2019This paper presents a re-formulation of the boundary integral method (BIM) for the Debye-Huckel model of molecular and colloidal electrostatics that removes the mathematical singularities that have been accepted as an intrinsic part of the conventional ... More

Boundary regularised integral equation formulation of the Helmholtz equation in acousticsFeb 08 2019A boundary integral formulation for the solution of the Helmholtz equation is developed in which all traditional singular behaviour in the boundary integrals is removed analytically. The numerical precision of this approach is illustrated with calculation ... More

Boundary regularized integral equation formulation (BRIEF) of Stokes flowFeb 07 2019Single-phase Stokes flow problems with prescribed boundary conditions can be formulated in terms of a boundary regularized integral equation that is completely free of singularities that exist in the traditional formulation. The usual mathematical singularities ... More

Influence of Bonded Interactions on Structural Phases of Flexible PolymersFeb 07 2019We introduce a novel coarse-grained bead-spring model for flexible polymers to systematically examine the effects of an adjusted bonded potential on the formation and stability of structural macrostates in a thermal environment. The density of states ... More

All-electron fully relativistic Kohn-Sham theory for solids based on the Dirac-Coulomb Hamiltonian and Gaussian-type functionsFeb 07 2019We present the first full-potential method that solves the fully relativistic 4-component Dirac-Kohn-Sham equation for materials in the solid state within the framework of atom-centered Gaussian-type orbitals (GTOs). Our GTO-based method treats one-, ... More

CORSIKA 8 - Towards a modern framework for the simulation of extensive air showersFeb 07 2019Current and future challenges in astroparticle physics require novel simulation tools to achieve higher precision and more flexibility. For three decades the FORTRAN version of CORSIKA served the community in an excellent way. However, the effort to maintain ... More

A new HLLD Riemann solver with Boris correction for reducing Alfvén speedFeb 07 2019A new Riemann solver is presented for the ideal magnetohydrodynamics (MHD) equations with the so-called Boris correction. The Boris correction is applied to reduce wave speeds, avoiding an extremely small timestep in MHD simulations. The proposed Riemann ... More

An Immersed Boundary Hierarchical B-spline method for flexoelectricityFeb 07 2019This paper develops a computational framework with unfitted meshes to solve linear piezoelectricity and flexoelectricity electromechanical boundary value problems including strain gradient elasticity at infinitesimal strains. The high-order nature of ... More

Compact representation of one-particle wavefunctions and scalar fields obtained from electronic-structure calculationsFeb 07 2019We present a code-independent compact representation of one-electron wavefunctions and other volumetric data (electron density, electrostatic potential, etc.) produced by electronic-structure calculations. The compactness of the representation insures ... More

DNS-aided explicitly filtered LESFeb 07 2019The equations for LES are formally derived by low-pass filtering the NS equations with the effect of the small scales on the larger ones captured by a SGS model. However, it is known that the LES equations usually employed in practical applications are ... More

The Effects of Intrinsic Dynamical Ghost Modes in Discrete-Time Langevin SimulationsFeb 06 2019Using the recently published GJF-2GJ Langevin thermostat, which can produce time-step-independent statistical measures even for large time steps, we analyze and discuss the causes for abrupt deviations in statistical data as the time step is increased ... More

A Hybrid Strategy for the Discovery and Design of Photonic NanostructuresFeb 06 2019Feb 07 2019Designing complex physical systems, including photonic structures, is typically a tedious trial-and-error process that requires extensive simulations with iterative sweeps in multi-dimensional parameter space. To circumvent this conventional approach ... More

Recent Advances in Maximum Entropy Biasing Techniques for Molecular DynamicsFeb 06 2019This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in molecular simulation ... More

Hyperspatial optimisation of structuresFeb 06 2019Anticipating the low energy arrangements of atoms in space is an indispensable scientific task. Modern stochastic approaches to searching for these configurations depend on the optimisation of structures to nearby local minima in the energy landscape. ... More

N-, B-, P-, Al-, As-, Ga-graphdiyne/graphyne lattices: First-principles investigation of mechanical, optical and electronic propertiesFeb 06 2019Graphdiyne and graphyne are carbon-based two-dimensional (2D) porous atomic lattices, with outstanding physics and excellent application prospects for advanced technologies, like nanoelectronics and energy storage systems. During the last year, B- and ... More

Accelerating spin-space sampling by auxiliary spin-dynamics and temperature-dependent spin-cluster expansionFeb 06 2019Atomistic simulations of thermodynamic properties of magnetic materials rely on an accurate modelling of magnetic interactions and an efficient sampling of the high-dimensional spin space. Recent years have seen significant progress with a clear trend ... More

Thick-Restart Block Lanczos Method for Large-Scale Shell-Model CalculationsFeb 06 2019We propose a thick-restart block Lanczos method, which is an extension of the thick-restart Lanczos method with the block algorithm, as an eigensolver of the large-scale shell-model calculations. This method has two advantages over the conventional Lanczos ... More

A classical field theory formulation for the numerical solution of time harmonic electromagnetic fieldsFeb 05 2019Finite element representations of Maxwell's equations pose unusual challenges inherent to the variational representation of the `curl-curl' equation for the fields. We present a variational formulation based on classical field theory. Borrowing from QED, ... More

A Multiscale Multisurface Constitutive Model for The Thermo-Plastic Behavior of PolyethyleneFeb 05 2019We present a multiscale model bridging length and time scales from molecular to continuum levels with the objective of predicting the yield behavior of amorphous glassy polyethylene (PE). Constitutive parameters are obtained from molecular dynamics (MD) ... More

Long-range dispersion forces between molecules subject to ultra-short optical pulses from ab initio calculationsFeb 05 2019London-van der Waals dispersion forces are a fundamental component of condensed matter systems, biological processes, and self-assembly. In this letter we propose a method to calculate the C6 coefficients that characterize dispersion forces in the non-retarded ... More

A nonlinear hyperelasticity model for single layer blue phosphorus based on ab-initio calculationsFeb 04 2019A new hyperelastic membrane material model is proposed for single layer blue phosphorus ($\beta\text{-P}$), also known as blue phosphorene. The model is fully nonlinear and captures the anisotropy of $\beta\text{-P}$ at large strains. The material model ... More

ESPEI for efficient thermodynamic database development, modification, and uncertainty quantification: application to Cu-MgFeb 04 2019The software package ESPEI has been developed for efficient evaluation of thermodynamic model parameters within the CALPHAD method. ESPEI uses a linear fitting strategy to parameterize Gibbs energy functions of single phases based on their thermochemical ... More

Dissipation and plastic deformation in collisions between metallic nanoparticlesFeb 04 2019Collisions between amorphous Fe nanoparticles were studied using molecular-dynamics simulation. For head-on collisions of nanoparticles with radii $R =$ 1.4 nm, $R =$ 5.2 nm, and $R =$ 11 nm, sticking was observed at all simulated velocities. The results ... More

Path-tracing Monte Carlo Libraries for 3D Radiative Transfer in Cloudy AtmospheresFeb 04 2019Interactions between clouds and radiation are at the root of many difficulties in numerically predicting future weather and climate and in retrieving the state of the atmosphere from remote sensing observations. The large range of issues related to these ... More

Cuts for 3-D magnetic scalar potentials: visualizing unintuitive surfaces arising from trivial knotsFeb 04 2019A wealth of literature exists on computing and visualizing cuts for the magnetic scalar potential of a current carrying conductor via Finite Element Methods (FEM) and harmonic maps to the circle. By a cut we refer to an orientable surface bounded by a ... More

SpinDoctor: a Matlab toolbox for diffusion MRI simulationFeb 04 2019The complex transverse water proton magnetization subject to diffusion-encoding magnetic field gradient pulses in a heterogeneous medium can be modeled by the multiple compartment Bloch-Torrey partial differential equation (BTPDE). A mathematical model ... More

Using a lattice Boltzmann method to uncover novel phase transitions in dry polar active fluidsFeb 01 2019We simulate a dry polar active fluid with contact inhibition of locomotion in two dimensions using a simple modification of the lattice Boltzmann method. Our method enables us to explore the dense regime and uncover multiple novel phase transitions: two ... More

Parallel-in-time integration of Kinematic DynamosFeb 01 2019The precise mechanisms responsible for the natural dynamos in the Earth and Sun are still not fully understood. Numerical simulations of natural dynamos are extremely computationally intensive, and are carried out in parameter regimes many orders of magnitude ... More

Determining normal mode features from numerical simulations using CEOF analysis: I. Test case using transverse oscillations of a magnetic slabFeb 01 2019Feb 05 2019We present a method to determine approximations to a system's normal mode eigenfrequency and eigenfunctions from time-dependent numerical simulations. The method proceeds iteratively and each step consists of (i) a time-dependent numerical simulation ... More

Eliminating the fictitious frequency problem in BEM solutions of the external Helmholtz equationFeb 01 2019The problem of the spurious frequency spectrum resulting from numerical implementations of the boundary element method for the exterior Helmholtz problem is revisited. When the ordinary 3D free space Green's function is replaced by a modified Green's ... More

Advances of Machine Learning in Molecular Modeling and SimulationFeb 01 2019In this review, we highlight recent developments in the application of machine learning for molecular modeling and simulation. After giving a brief overview of the foundations, components, and workflow of a typical supervised learning approach for chemical ... More

Perdew-Zunger self-interaction correction: How wrong for uniform densities and large-Z atoms?Jan 31 2019Semi-local density functionals for the exchange-correlation energy of a many-electron system cannot be exact for all one-electron densities. In 1981, Perdew and Zunger (PZ) subtracted the fully-nonlocal self-interaction error orbital-by-orbital, making ... More

A block preconditioner for non-isothermal flow in porous mediaJan 31 2019In petroleum reservoir simulation, the industry standard preconditioner, the constrained pressure residual method (CPR), is a two-stage process which involves solving a restricted pressure system with Algebraic Multigrid (AMG). Initially designed for ... More

Inaccuracy of Spatial Derivatives in Simulations of Supersonic TurbulenceJan 31 2019We examine the accuracy of spatial derivatives computed from numerical simulations of supersonic turbulence. Two sets of simulations, carried out using a finite-volume code that evolves the hydrodynamic equations with an approximate Riemann solver and ... More

A nested Schur complement solver with mesh-independent convergence for the time domain photonics modelingJan 31 2019A nested Schur complement solver is proposed for iterative solution of linear systems arising in exponential and implicit time integration of the Maxwell equations with perfectly matched layer (PML) nonreflecting boundary conditions. These linear systems ... More

Data recovery in computational fluid dynamics through deep image priorsJan 30 2019One of the challenges encountered by computational simulations at exascale is the reliability of simulations in the face of hardware and software faults. These faults, expected to increase with the complexity of the computational systems, will lead to ... More

Excited states of molecules in strong uniform and non-uniform magnetic fieldsJan 30 2019This paper reports an implementation of Hartree-Fock linear response with complex orbitals for computing electronic spectra of molecules in a strong external magnetic fields. The implementation is completely general, allowing for spin-restricted, spin-unrestricted, ... More

Uncertainty Quantification in Molecular Signals using Polynomial Chaos ExpansionJan 30 2019Molecular signals are abundant in engineering and biological contexts, and undergo stochastic propagation in fluid dynamic channels. The received signal is sensitive to a variety of input and channel parameter variations. Currently we do not understand ... More

Machine-learning of atomic-scale properties based on physical principlesJan 30 2019We briefly summarize the kernel regression approach, as used recently in materials modelling, to fitting functions, particularly potential energy surfaces, and highlight how the linear algebra framework can be used to both predict and train from linear ... More

A discontinuous Galerkin scheme for full-potential electronic structure calculationsJan 30 2019In this paper, we construct an efficient numerical scheme for full-potential electronic structure calculations of periodic systems. In this scheme, the computational domain is decomposed into a set of atomic spheres and an interstitial region, and different ... More

Design and Analysis of Machine Learning Exchange-Correlation Functionals via Rotationally Invariant Convolutional DescriptorsJan 30 2019In this work we explore the potential of a new data-driven approach to the design of exchange-correlation (XC) functionals. The approach, inspired by convolutional filters in computer vision and surrogate functions from optimization, utilizes convolutions ... More

Single-Hessian thawed Gaussian approximation: The missing rung on the ladderJan 30 2019To alleviate the computational cost associated with on-the-fly ab initio semiclassical calculations of molecular spectra, we propose the single-Hessian thawed Gaussian approximation, in which the Hessian of the potential energy at all points along an ... More

Predicting the mechanical response of oligocrystals with deep learningJan 30 2019In this work we employ data-driven homogenization approaches to predict the particular mechanical evolution of polycrystalline aggregates with tens of individual crystals. In these oligocrystals the differences in stress response due to microstructural ... More

Finite size scaling for a first order transition where a continuous symmetry is broken: The spin-flop transition in the 3D XXZ Heisenberg antiferromagnetJan 30 2019Finite size scaling for a first order phase transition where a continuous symmetry is broken is developed using an approximation of Gaussian probability distributions with a phenomenological "degeneracy" factor included. Predictions are compared with ... More

The hardwall method of solving the radial Schrödinger equation and unmasking hidden symmetriesJan 29 2019Solving for the bound state eigenvalues of the Schr\"odinger equation is a tedious iterative process when the conventional shooting or matching method is used. In this work, we bypass the eigenvalue's dependence on the eigenfunction by simply trying out ... More

Bound states of the one-dimensional Schrödinger equation with arbitrary potential: a scattering matrix methodJan 29 2019This paper presents an accurate highly efficient method for solving the bound states in the one-dimensional Schr\"odinger equation with an arbitrary potential. First, we demonstrate that the bound state energies of a general potential well can be obtained ... More

Quantified Uncertainty in Thermodynamic Modeling for Materials DesignJan 29 2019Phase fractions, compositions and energies of the stable phases as a function of macroscopic composition, temperature, and pressure (X-T-P) are the principle correlations needed for the design of new materials and improvement of existing materials. They ... More

Construction of Many-Body Eigenstates with Displacement TransformationsJan 29 2019Many-body eigenstates beyond the gaussian approximation can be constructed in terms of local integrals of motion (IOM), although their actual computation has been until now a daunting task. We present a new practical computation of IOMS based on displacement ... More

Dense Fiber Modeling for 3D-Polarized Light Imaging SimulationsJan 29 20193D-Polarized Light Imaging (3D-PLI) is a neuroimaging technique used to study the structural connectivity of the human brain at the meso- and microscale. In 3D-PLI, the complex nerve fiber architecture of the brain is characterized by 3D orientation vector ... More

Time-symmetry, symplecticity and stability of Euler-Maclaurin and Lanczos-Dyche integrationJan 28 2019Numerical evolution of time-dependent differential equations via explicit Runge-Kutta or Taylor methods typically fails to preserve symmetries of a system. It is known that there exists no numerical integration method that in general preserves both the ... More

High-Resolution Simulations of Giant Impacts: Efficient Spherical Initial Conditions and Next-Generation Performance with SWIFTJan 28 2019We perform simulations of giant impacts onto the young Uranus using smoothed particle hydrodynamics (SPH) with over 100 million particles. This 100--1000$\times$ improvement in resolution passes a key threshold to reveal previously unseen details in the ... More

Data-driven acceleration of Photonic SimulationsJan 26 2019Designing modern photonic devices often involves traversing a large parameters space via an optimization procedure, gradient based or otherwise, and typically results in the designer performing electromagnetic simulations of correlated devices. In this ... More

Data-driven acceleration of Photonic SimulationsJan 26 2019Feb 17 2019Designing modern photonic devices often involves traversing a large parameter space via an optimization procedure, gradient based or otherwise, and typically results in the designer performing electromagnetic simulations of correlated devices. In this ... More

NCrystal : a library for thermal neutron transportJan 25 2019An open source software package for modelling thermal neutron transport is presented. The code facilitates Monte Carlo-based transport simulations and focuses in the initial release on interactions in both mosaic single crystals as well as polycrystalline ... More

All Equalities Are Equal, but Some Are More Equal Than Others: The Effect of Implementation Aliasing on the Numerical Solution to Conservation EquationsJan 25 2019We investigate the effect of aliasing when applied to the storage of variables, and their reconstruction for the solution of conservation equations. In particular, we investigate the effect on the error of storing primitives versus conserved variables ... More

Model dispersion with PRISM; an alternative to MCMC for rapid analysis of modelsJan 25 2019We have built PRISM, a "Probabilistic Regression Instrument for Simulating Models". PRISM uses the Bayes linear approach and history matching to construct an approximation ('emulator') of any given model, by combining limited model evaluations with advanced ... More

An Efficient Solver for Cumulative Density Function-based Solutions of Uncertain Kinematic Wave ModelsJan 24 2019We develop a numerical framework to implement the cumulative density function (CDF) method for obtaining the probability distribution of the system state described by a kinematic wave model. The approach relies on Monte Carlo Simulations (MCS) of the ... More

An immersed method based on cut-cells for the simulation of 2D incompressible fluid flows past solid structuresJan 24 2019We present a cut-cell method for the simulation of 2D incompressible flows past obstacles. It consists in using the MAC scheme on cartesian grids and imposing Dirchlet boundary conditions for the velocity field on the boundary of solid structures following ... More

A fourth-order accurate compact difference scheme for solving the three-dimensional Poisson equation with arbitrary boundariesJan 24 2019Feb 04 2019This paper presents an efficient high-order sharp-interface method for solving the three-dimensional (3D) Poisson equation with Dirichlet boundary conditions on a nonuniform Cartesian grid with irregular domain boundaries. The new approach is based on ... More

Solution to partition function for macroscopic condensed matters -- the key problem of statistical physicsJan 24 2019The key problem of statistical physics standing over one hundred years is how to exactly calculate the partition function of macroscopic condensed matters, which severely hinders application of the theory to predict many properties of realistic systems. ... More

Renormalization of radiobiological response functions by energy loss fluctuations and complexities in chromosome aberration induction: deactivation theory for proton therapy from cells to tumor controlJan 24 2019We employ a multi-scale mechanistic approach to investigate radiation induced cell toxicities and deactivation mechanisms as a function of linear energy transfer in hadron therapy. Our theoretical model consists of a system of Markov chains in microscopic ... More

Betaboltz: a Monte-Carlo simulation tool for gas scattering processesJan 23 2019We present an open-source code for the simulation of electron and ion transport in arbitrary gas mixtures with static uniform electric and magnetic fields. The program provided microscopic interaction simulation and is interfaced with cross-section tables ... More

Quantized bounding volume hierarchies for neighbor search in molecular simulations on graphics processing unitsJan 23 2019We present an algorithm for neighbor search in molecular simulations on graphics processing units (GPUs) based on bounding volume hierarchies (BVHs). The BVH is compressed into a low-precision, quantized representation to increase the BVH traversal speed ... More

Single determinant approximation for ground and excited states with accuracy comparable to that of the configuration interactionJan 23 2019It was realized from the early days of Chemical Physics (Rev. Mod. Phys. 35, 496 (1963)) that the energy $E_{HF}$ of the Slater determinant (SlDet) $|\Phi _{HF}\rangle$, obtained by the single particle Hartree-Fock (HF) equation, does not coincide with ... More

Relativistic dissipation obeys Chapman-Enskog asymptotics: analytical and numerical evidence as a basis for accurate kinetic simulationsJan 23 2019We present an analytical derivation of the transport coefficients of a relativistic gas in (2+1) dimensions for both Chapman-Enskog (CE) asymptotics and Grad's expansion methods. Moreover, we develop a systematic calibration method, connecting the relaxation ... More

Gridless particle technique for the Vlasov Poisson system in problems with high degree of symmetryJan 23 2019In the paper, gridless particle techniques are presented in order to solve problems involving electrostatic, collisionless plasmas. The method makes use of computational particles having the shape of spherical shells or of rings, and can be used to study ... More

The density of states approach to the sign problemJan 22 2019Approaches to the sign problem based on the density of states have been recently revived by the introduction of the LLR algorithm, which allows us to compute the density of states itself with exponential error reduction. In this work, after a review of ... More

Planewave density interpolation methods for 3D Helmholtz boundary integral equationsJan 22 2019This paper introduces planewave density interpolation methods for the regularization of weakly singular, strongly singular, hypersingular and nearly singular integral kernels present in 3D Helmholtz surface layer potentials and associated integral operators. ... More

A DLM immersed boundary method based wave-structure interaction solver for high density ratio multiphase flowsJan 22 2019We present a robust immersed boundary (IB) method for high density ratio multiphase flows that is capable of modeling complex wave-structure interaction (WSI) problems arising in marine and coastal engineering applications. The IB/WSI methodology is enabled ... More

Performance of preconditioned iterative linear solvers for cardiovascular simulations in rigid and deformable vesselsJan 21 2019Computing the solution of linear systems of equations is invariably the most time consuming task in the numerical solutions of PDEs in many fields of computational science. In this study, we focus on the numerical simulation of cardiovascular hemodynamics ... More