Physics - Computational Physics Publications (50)

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Physics - Computational Physics Publications

The purpose of this work is to construct a simple, efficient and accurate well-balanced numerical scheme for one-dimensional (1D) blood flow in large arteries with varying geometrical and mechanical properties. As the steady states at rest are not relevant for blood flow, we construct two well-balanced hydrostatic reconstruction techniques designed to preserve low-Shapiro number steady states that may occur in large network simulations. The Shapiro number S h = u/c is the equivalent of the Froude number for shallow water equations and the Mach number for compressible Euler equations. Read More


In fluid dynamical simulations in astrophysics, large deformations are common and surface tracking is sometimes necessary. Smoothed Particle Hydrodynamics (SPH) method has been used in many of such simulations. Recently, however, it has been shown that SPH cannot handle contact discontinuities or free surfaces accurately. Read More


Recent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems of arbitrarily large size. The idea consists in adopting a cutoff-based method in which the cutoff is cho- sen on a particle-by-particle basis, according to the distance from the interface. Read More


Reverse Monte Carlo modeling of liquid water, based on one neutron and one X-ray diffraction data set, applying also the most popular interatomic potential for water, SPC/E, has been performed. The strictly rigid geometry of SPC/E water molecules had to be loosened somewhat, in order to be able to produce a good fit to both sets of experimental data. In the final particle configurations, regularly shaped water molecules and straight hydrogen bonding angles were found to be consistent with diffraction results. Read More


We consider implementations of high-order finite difference Weighted Essentially Non-Oscillatory (WENO) schemes for the Euler equations in cylindrical and spherical coordinate systems with radial dependence only. The main concern of this work lies in ensuring both high-order accuracy and conservation. Three different spatial discretizations are assessed: one that is shown to be high-order accurate but not conservative, one conservative but not high-order accurate, and a new approach that is both high-order accurate and conservative. Read More


It is often claimed that error cancellation plays an essential role in quantum chemistry and first-principle simulation for condensed matter physics and materials science. Indeed, while the energy of a large, or even medium-size, molecular system cannot be estimated numerically within chemical accuracy (typically 1 kcal/mol or 1 mHa), it is considered that the energy difference between two configurations of the same system can be computed in practice within the desired accuracy. The purpose of this paper is to provide a quantitative study of discretization error cancellation. Read More


First-principles calculations combining density-functional theory and continuum solvation models enable realistic theoretical modeling and design of electrochemical systems. When a reaction proceeds in such systems, the number of electrons in the portion of the system treated quantum mechanically changes continuously, with a balancing charge appearing in the continuum electrolyte. A grand-canonical ensemble of electrons at a chemical potential set by the electrode potential is therefore the ideal description of such systems that directly mimics the experimental condition. Read More


Afivo is a framework for simulations with adaptive mesh refinement (AMR) on quadtree (2D) and octree (3D) grids. The framework comes with a geometric multigrid solver, shared-memory (OpenMP) parallelism and it supports output in Silo and VTK file formats. Afivo is a generic framework without built-in functionality for specific physics applications, so users have to implement their own numerical methods. Read More


The minimum action method (MAM) is to calculate the most probable transition path in randomly perturbed stochastic dynamics, based on the idea of action minimization in the path space. However, in most non-gradient dynamics, the accuracy of the numerical path between different metastable states usually suffers from the "clustering problem" at transition states on separatrix where the so-called "uphill" and "downhill" paths meet. The adaptive minimum action method (aMAM) solves this problem by relocating image points equally along arc-length with the help of moving mesh strategy. Read More


Our computation effort is primarily concentrated on support of current and future measurements being carried out at various synchrotron radiation facilities around the globe, and photodissociation computations for astrophysical applications. In our work we solve the Schr\"odinger or Dirac equation for the appropriate collision problem using the R-matrix or R-matrix with pseudo-states approach from first principles. The time dependent close-coupling (TDCC) method is also used in our work. Read More


Multi-peaked analytically extended function (AEF), previously applied by the authors to modelling of lightning discharge currents, is used in this paper for representation of the electrostatic discharge (ESD) currents. The fitting to data is achieved by interpolation of certain data points. In order to minimize unstable behaviour, the exponents of the AEF are chosen from a certain arithmetic sequence and the interpolated points are chosen according to a D-optimal design. Read More


This paper presents smoothed combined field integral equations for the solution of Dirichlet and Neumann exterior Helmholtz problems. The integral equations introduced in this paper are smooth in the sense that they only involve continuously differentiable integrands in both Dirichlet and Neumann cases. These integral equations coincide with the well-known combined field equations and are therefore uniquely solvable for all frequencies. Read More


Large scale, dynamical simulations have been performed for the two dimensional octahedron model, describing Kardar-Parisi-Zhang (KPZ) for nonlinear, or Edwards-Wilkinson for linear surface growth. The autocorrelation functions of the heights and the dimer lattice gas variables are determined with high precision. Parallel random sequential (RS) and two-sub-lattice stochastic dynamics (SCA) have been compared. Read More


To synthesize diffusion MR measurements from Monte-Carlo simulation using tissue models with sizes comparable to those of scan voxels. Larger regions enable restricting structures to be modeled in greater detail and improve accuracy and precision in synthesized diffusion-weighted measurements. We employ a localized intersection checking algorithm during substrate construction and dynamical simulation. Read More


A method of determining the optimum number of levels of decomposition in soft-thresholding wavelet denoising using Stationary Wavelet Transform is presented here. The method calculates the risk at each level of decomposition using Steins Unbiased Risk Estimate, analogous to calculating the sum square error of the denoising process. The SURE risk is found to reach minimum at the same level of decomposition as the sum square error. Read More


The distributions of size and chemical composition in the regolith on airless bodies provides clues to the evolution of the solar system. Recently, the regolith on asteroid (25143) Itokawa, visited by the JAXA Hayabusa spacecraft, was observed to contain millimeter to centimeter sized particles. Itokawa boulders commonly display well-rounded profiles and surface textures that appear inconsistent with mechanical fragmentation during meteorite impact; the rounded profiles have been hypothesized to arise from rolling and movement on the surface as a consequence of seismic shaking. Read More


The solution of a nonlinear diffusion equation is numerically investigated using the generalized Fourier transform method. This equation includes fractal dimensions and power-law dependence on the radial variable and on the diffusion function. The generalized Fourier transform approach is the extension of the Fourier transform method used for normal diffusion equation. Read More


For time integration of transient eddy current problems commonly implicit time integration methods are used, where in every time step one or several nonlinear systems of equations have to be linearized with the Newton-Raphson method due to ferromagnetic materials involved. In this paper, a generalized Schur-complement is applied to the magnetic vector potential formulation, which converts a differential-algebraic equation system of index 1 into a system of ordinary differential equations (ODE) with reduced stiffness. For the time integration of this ODE system of equations, the explicit Euler method is applied. Read More


We discuss the application of numerical linked cluster expansions (NLCEs) to study one dimensional lattice systems in thermal equilibrium and after quantum quenches from thermal equilibrium states. For the former, we calculate observables in the grand canonical ensemble, while for the latter we calculate observables in the diagonal ensemble. When converged, NLCEs provide results in the thermodynamic limit. Read More


Surface tension at free surfaces in Smoothed Particle Hydrodynamics can be modelled either by implementing pairwise particle forces mimicking molecular scale phenomena or by reconstructing a surface from particles identified as free surface particles. While these models can be implemented in the traditional Weakly Compressible SPH algorithm, such an implementation in Incompressible SPH requires unrestrained pressure gradient along the free surface. Traditional ISPH methods identify free surface particles and impose a zero pressure Dirichlet boundary condition and this makes it difficult to implement a surface tension model at the free surface. Read More


The LDA-1/2 method for self-energy correction is a powerful tool for calculating accurate band structures of semiconductors, while keeping the computational load as low as standard LDA. Nevertheless, controversies remain regarding the arbitrariness of choice between (1/2)e and (1/4)e charge stripping from the atoms in group IV semiconductors, the incorrect direct band gap predicted for Ge, and inaccurate band diagrams for III-V semiconductors. Here we propose an improved method named shell-LDA-1/2 (shLDA-1/2 for short), which is based on a shell-like trimming function for the self-energy potential. Read More


In this paper, granular segregation in a two-compartment cell in zero gravity is studied numerically by DEM simulation. In the simulation using a virtual window method we find a non-monotonic flux, a function which governs the segregation. A parameter is used to quantify the segregation. Read More


Partially-self-consistent gap-renormalization GW (grGW) is introduced to calculate quasiparticle (QP) energies within the many-body perturbation theory of Hedin. Self-consistency of the Green's function is obtained by renormalization of the band gap, removing the most significant approximation of the single-shot $\text{G}_{0}\text{W}_{0}$ approach. The formalism is performed as a post-processing step and thus, can be implemented within any GW algorithm which calculates the full frequency-dependent self-energies. Read More


Reversible in operando control of friction is an unsolved challenge crucial to industrial tribology. Recent studies show that at low sliding velocities, this control can be achieved by applying an electric field across electrolyte lubricants. However, the phenomenology at high sliding velocities is yet unknown. Read More


We present a computer simulation of entangled polymer solutions at equilibrium. The chains repel each other via a soft Gaussian potential, appropriate for semi-dilute solutions at the scale of a correlation blob. The key innovation to suppress chain crossings is to use a pseudo-continuous model of a backbone which effectively leaves no gaps between consecutive points on the chain, unlike the usual bead-and-spring model. Read More


In this paper we present a parallelization strategy on distributed memory systems for the Fast Kinetic Scheme --- a semi-Lagrangian scheme developed in [J. Comput. Phys. Read More


A method to calculate reactions in quantum mechanics is outlined. It is advantageous, in particular, in problems with many open channels of various nature i.e. Read More


First-principles density functional theory methods are used to investigate the structure, energetics, and vibrational motions of the neutral vacancy defect in diamond. The measured optical absorption spectrum demonstrates that the tetrahedral $T_d$ point group symmetry of pristine diamond is maintained when a vacancy defect is present. This is shown to arise from the presence of a dynamic Jahn-Teller distortion that is stabilised by large vibrational anharmonicity. Read More


In recent work it was clarified that amorphous solids under strain control do not possess nonlinear elastic theory in the sense that the shear modulus exists but nonlinear moduli exhibit sample to sample fluctuations that grow without bound with the system size. More relevant however for experiments are the conditions of stress control. In the present Communication we show that also under stress control the shear modulus exists but higher order moduli show unbounded sample to sample fluctuation. Read More


In soft matter system controlling the structure of the amorphous materials have been a key challenge. In this work we have modeled irreversible diffusion limited cluster aggregation of binary colloids, which serves as a model for chemical gels. Irreversible aggregation of binary colloidal particles lead to the formation of percolating cluster of one species or both species also called bigels. Read More


Distribution of black spot defects and small clusters in 1 MeV krypton irradiated 3C-SiC has been investigated using advanced scanning transmission electron microscopy (STEM) and TEM. We find that two thirds of clusters smaller than 1 nm identified in STEM are invisible in TEM images. For clusters that are larger than 1 nm, STEM and TEM results match very well. Read More


The present panorama of HPC architectures is extremely heterogeneous, ranging from traditional multi-core CPU processors, supporting a wide class of applications but delivering moderate computing performance, to many-core GPUs, exploiting aggressive data-parallelism and delivering higher performances for streaming computing applications. In this scenario, code portability (and performance portability) become necessary for easy maintainability of applications; this is very relevant in scientific computing where code changes are very frequent, making it tedious and prone to error to keep different code versions aligned. In this work we present the design and optimization of a state-of-the-art production-level LQCD Monte Carlo application, using the directive-based OpenACC programming model. Read More


In this work, we extend the solid harmonics derivation, which was used by Ackroyd et al to derive the steady-state SP$_N$ equations, to transient problems. The derivation expands the angular flux in ordinary surface harmonics but uses harmonic polynomials to generate additional surface spherical harmonic terms to be used in Galerkin projection. The derivation shows the equivalence between the SP$_N$ and the P$_N$ approximation. Read More


We extend the model of exciton-plasmon materials to include a ro-vibrational structure of molecules using wave-packet propagations on electronic potential energy surfaces. The new model replaces conventional two-level emitters with more complex molecules allowing to examine the influence of alignment and vibrational dynamics on strong coupling with surface plasmon-polaritons. We apply the model to a hybrid system comprising a thin layer of molecules placed on top of a periodic array of slits. Read More


The paper develops a hybrid method for solving a system of advection-diffusion equations in a bulk domain coupled to advection-diffusion equations on an embedded surface. A monotone nonlinear finite volume method for equations posed in the bulk is combined with a trace finite element method for equations posed on the surface. In our approach, the surface is not fitted by the mesh and is allowed to cut through the background mesh in an arbitrary way. Read More


The general procedure underlying Hartree-Fock and Kohn-Sham density functional theory calculations consists in optimizing orbitals for a self-consistent solution of the Roothaan-Hall equations in an iterative process. It is often ignored that multiple self-consistent solutions can exist, several of which may correspond to minima of the energy functional. In addition to the difficulty sometimes encountered to converge the calculation to a self-consistent solution, one must ensure that the correct self-consistent solution was found, typically the one with the lowest electronic energy. Read More


We describe and implement iMapD, a computer-assisted approach for accelerating the exploration of uncharted effective Free Energy Surfaces (FES), and more generally for the extraction of coarse-grained, macroscopic information from atomistic or stochastic (here Molecular Dynamics, MD) simulations. The approach functionally links the MD simulator with nonlinear manifold learning techniques. The added value comes from biasing the simulator towards new, unexplored phase space regions by exploiting the smoothness of the (gradually, as the exploration progresses) revealed intrinsic low-dimensional geometry of the FES. Read More


We devise a new high order local absorbing boundary condition (ABC) for radiating problems and scattering of time-harmonic acoustic waves from obstacles of arbitrary shape. By introducing an artificial boundary $S$ enclosing the scatterer, the original unbounded domain $\Omega$ is decomposed into a bounded computational domain $\Omega^{-}$ and an exterior unbounded domain $\Omega^{+}$. Then, we define interface conditions at the artificial boundary $S$, from truncated versions of the well-known Wilcox and Karp farfield expansion representations of the exact solution in the exterior region $\Omega^{+}$. Read More


Recently, the phenomenon of quantum-classical correspondence breakdown was uncovered in optomechanics, where in the classical regime the system exhibits chaos but in the corresponding quantum regime the motion is regular - there appears to be no signature of classical chaos whatsoever in the corresponding quantum system, generating a paradox. We find that transient chaos, besides being a physically meaningful phenomenon by itself, provides a resolution. Using the method of quantum state diffusion to simulate the system dynamics subject to continuous homodyne detection, we uncover transient chaos associated with quantum trajectories. Read More


Electro-quasistatic field problems involving nonlinear materials are commonly discretized in space using finite elements. In this paper, it is proposed to solve the resulting system of ordinary differential equations by an explicit Runge-Kutta-Chebyshev time-integration scheme. This mitigates the need for Newton-Raphson iterations, as they are necessary within fully implicit time integration schemes. Read More


With the advances in low dimensional transition metal dichalcolgenides (TMDCs) based metal oxide semiconductor field effect transistor (MOSFET), the interface between semiconductors and dielectrics has received considerable attention due to its dramatic effects on the morphology and charge transport of semiconductors. In this study, first principle calculations were utilized to investigate the strain effect induced by the interface between Al2O3 (0001) and monolayer MoS2. The results indicate that Al2O3 in 1. Read More


We present a fast direct solution method for the advection-diffusion equation in one and two dimensions with non-periodic boundaries. Computational cost is reduced to $\mathcal O(N)$ by making a low-rank approximation of the Green's function without sacrificing accuracy. Implicit treatment of the diffusion term reduces stiffness in advection-dominated problems. Read More


A stand-alone App has been developed, focused on obtaining information about relevant engineering properties of magnetic levitation systems. Our modelling toolkit provides real time simulations of 2D magneto-mechanical quantities for Superconductor/Permanent Magnet structures. The source code is open and may be customized for a variety of configurations. Read More


The performance of a ring of linearly coupled, monostable nonlinear oscillators is optimized towards its goal of acting as energy harvester---through piezoelectric transduction---of mesoscopic fluctuations, which are modeled as Ornstein--Uhlenbeck noises. For a single oscillator, the maximum output voltage and overall efficiency are attained for a soft piecewise-linear potential (providing a weak attractive constant force) but they are still fairly large for a harmonic potential. When several harmonic springs are linearly and bidirectionally coupled to form a ring, it is found that counter-phase coupling can largely improve the performance while in-phase coupling worsens it. Read More


In 2012 a method to analyze N-body dark matter simulations using a tetrahedral tesselation of the three-dimensional dark matter manifold in six-dimensional phase space was introduced. This paper presents an accurate density computation approach for large N-body datasets, that is based on this technique and designed for massively parallel GPU-clusters. The densities are obtained by intersecting the tessellation with the cells of a spatially adaptive grid structure. Read More


We present a framework for the solution of Boltzmann's equation in the swarm limit for arbitrary mass ratio, allowing for solutions of electron or ion transport. An arbitrary basis set can be used in the framework, which is achieved by using appropriate quadratures to obtain the required matrix elements. We demonstrate an implementation using Burnett functions and benchmark the calculations using Monte-Carlo simulations. Read More


Quasiparticle (QP) excitations are extremely important for understanding and predicting charge transfer and transport in molecules, nanostructures and extended systems. Since density functional theory (DFT) within Kohn-Sham (KS) formulation does not provide reliable QP energies, a many-body perturbation technique within the GW approximation are essential. The steep computational scaling of GW prohibits its use in extended, open boundary, systems with thousands of electrons and more. Read More


In this paper, an existing hyperelastic membrane model of graphene is adapted to curvilinear coordinates and extended to a rotation-free shell formulation based on isogeometric finite elements. The material parameters are calibrated from recent quantum data. The obtained elastic modulus and Poisson ratio from this model are very close to experimental and full ab-initio results. Read More


We give a novel and simple proof of the DFT expression for the interatomic force field that drives the motion of atoms in classical Molecular Dynamics, based on the observation that the ground state electronic energy, seen as a functional of the external potential, is the Legendre transform of the Hohenberg-Kohn functional, which in turn is a functional of the electronic density. We show in this way that the so-called Hellmann-Feynman analytical formula, currently used in numerical simulations, actually provides the exact expression of the interatomic force. Read More