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QCDGPU: open-source package for Monte Carlo lattice simulations on OpenCL-compatible multi-GPU systems

The multi-GPU open-source package QCDGPU for lattice Monte Carlo simulations of pure SU(N) gluodynamics in external magnetic field at finite temperature and O(N) model is developed. The code is implemented in OpenCL, tested on AMD and NVIDIA GPUs, AMD and Intel CPUs and may run on other OpenCL-compatible devices. The package contains minimal external library dependencies and is OS platform-independent. It is optimized for heterogeneous computing due to the possibility of dividing the lattice into non-equivalent parts to hide the difference in performances of the devices used. QCDGPU has client-server part for distributed simulations. The package is designed to produce lattice gauge configurations as well as to analyze previously generated ones. QCDGPU may be executed in fault-tolerant mode. Monte Carlo procedure core is based on PRNGCL library for pseudo-random numbers generation on OpenCL-compatible devices, which contains several most popular pseudo-random number generators.

hep-lat↗

Stochastic Turing patterns: analysis of compartment-based approaches

Turing patterns can be observed in reaction-diffusion systems where chemical species have different diffusion constants. In recent years, several studies investigated the effects of noise on Turing patterns and showed that the parameter regimes, for which stochastic Turing patterns are observed, can be larger than the parameter regimes predicted by deterministic models, which are written in terms of partial differential equations for species concentrations. A common stochastic reaction-diffusion approach is written in terms of compartment-based (lattice-based) models, where the domain of interest is divided into artificial compartments and the number of molecules in each compartment is simulated. In this paper, the dependence of stochastic Turing patterns on the compartment size is investigated. It has previously been shown (for relatively simpler systems) that a modeller should not choose compartment sizes which are too small or too large, and that the optimal compartment size depends on the diffusion constant. Taking these results into account, we propose and study a compartment-based model of Turing patterns where each chemical species is described using a different set of compartments. It is shown that the parameter regions where spatial patterns form are different from the regions obtained by classical deterministic PDE-based models, but they are also different from the results obtained for the stochastic reaction-diffusion models which use a single set of compartments for all chemical species. In particular, it is argued that some previously reported results on the effect of noise on Turing patterns in biological systems need to be reinterpreted.

physics.comp-ph↗

Size dependence of the largest distance between random points

A set of $N$ points is chosen randomly in a $D$-dimensional volume $V=a^D$, with periodic boundary conditions. For each point $i$, its distance $d_i$ is found to its nearest neighbour. Then, the maximal value is found, $d_{max}=max(d_i, i=1,...,N)$. Our numerical calculations indicate, that when the density $N/V$=const, $d_{max}$ scales with the linear system size as $d^2_{max}\propto a^ϕ$, with $ϕ=0.24\pm0.04$ for $D=1,2,3,4$.

physics.comp-ph↗

Ferrimagnetos de Ising con Dilución

We perform numerical studies of a three dimensional Ising mixed model at different concentrations of quenched non magnetic impurities. Our preliminary results indicate that both, the compensation temperature and the temperature that signal the transition from an ordered to a disordered phase, decrease linearly with the concentration of impurities, for concentrations below 30%. For percentages of impurities above 30% the compensation temperature disappears.

physics.comp-ph↗

Dependencia de la Temperatura de Compensación en Modelos de Multicapas Ferrimagnéticas de tipo $3(S_{1-x} σ_x)/σ$

We investigate numerically the behavior of the compensation temperature, $T_{comp}$, in ferrimagnetic multilayer in the type $3(S_{1-x} σ_x)/σ$ with respect to the increase of the spin concentration $σ_x$, which are randomly distributive in a mix of spins $S = 0, \pm 1$ and $σ= \pm 1/2$, with ferromagnetic interaction between spins of the same type, and antiferromagnetic interaction for spins of different type. We have found that $T_{comp}$ decrease slowly with the increase of $x$, until $σ_x$ represent a little more than 40\% of the spin mixture. For higher concentration values $T_{comp}$ drops abruptly and disappears, as predicted by experimental result.

physics.comp-ph↗

Performance of Kepler GTX Titan GPUs and Xeon Phi System

NVIDIA's new architecture, Kepler improves GPU's performance significantly with the new streaming multiprocessor SMX. Along with the performance, NVIDIA has also introduced many new technologies such as direct parallelism, hyper-Q and GPU Direct with RDMA. Apart from other usual GPUs, NVIDIA also released another Kepler 'GeForce' GPU named GTX Titan. GeForce GTX Titan is not only good for gaming but also good for high performance computing with CUDA. Nevertheless, it is remarkably cheaper than Kepler Tesla GPUs. We investigate the performance of GTX Titan and find out how to optimize a CUDA code appropriately for it. Meanwhile, Intel has launched its new many integrated core (MIC) system, Xeon Phi. A Xeon Phi coprocessor could provide similar performance with NVIDIA Kepler GPUs theoretically but, in reality, it turns out that its performance is significantly inferior to GTX Titan.

physics.comp-ph↗

An $O(N^3)$ algorithm for the calculation of far field radiation patterns

We present a new method for computing the Near-To-Far-Field (NTFF) transformation in FDTD simulations which has an overall scaling of $O(N^3)$ instead of the standard $O(N^4)$. By mapping the far field with a cartesian coordinate system the 2D surface integral can be split into two successive 1D integrals. For a near field spanned by $N_X \times N_Y$ discrete sample points, and a far field spanned by $N_θ \times N_ϕ$ points, the calculation can then be performed in $O(N_θN_X N_Y) + O(N_θN_ϕN_Y)$ operations instead of $O(N_θN_ϕN_X N_Y)$.

physics.comp-ph↗

Iterative Determination of Distributions by the Monte Carlo Method in Problems with an External Source

In the Monte Carlo (MC) method statistical noise is usually present. Statistical noise may become dominant in the calculation of a distribution, usually by iteration, but is less Important in calculating integrals. The subject of the present work is the role of statistical noise in iterations involving stochastic simulation (MC method). Convergence is checked by comparing two consecutive solutions in the iteration. The statistical noise may randomize or pervert the convergence. We study the probability of the convergence, and the correct estimation of the variance in a simplified model problem. We study the statistical properties of the solution to a deterministic problem with a stochastic source obtained from a stochastic calculation. There are iteration strategies resulting in non-convergence, or randomly stopped iteration.

physics.comp-ph↗

On the Friedel sum rule in ab initio calculations of optical properties

We investigate the influence of technical parameters in dynamic electrical conductivity calculations by the Kubo-Greenwood formula on the value of the so-called sum rule. We propose a possible explanation of the slight overestimation of the sum rule in most of our results.

physics.comp-ph↗

On the velocity space discretization for the Vlasov-Poisson system: comparison between Hermite spectral and Particle-in-Cell methods. Part 1: semi-implicit scheme

We discuss a spectral method for the numerical solution of the Vlasov-Poisson system where the velocity space is decomposed by means of an Hermite basis. We describe a semi-implicit time discretization that extends the range of numerical stability relative to an explicit scheme. We also introduce and discuss the effects of an artificial collisional operator, which is necessary to take care of the velocity space filamentation problem, unavoidable in collisionless plasmas. The computational efficiency and the cost-effectiveness of this method are compared to a Particle-in-Cell (PIC) method in the case of a two-dimensional phase space. The following examples are discussed: Langmuir wave, Landau damping, ion-acoustic wave, two-stream instability, and plasma echo. The Hermite spectral method can achieve solutions that are several orders of magnitude more accurate (at a fraction of the cost) with respect to the PIC method.

physics.plasm-ph↗

Lattice Simulations using OpenACC compilers

OpenACC compilers allow one to use Graphics Processing Units without having to write explicit CUDA codes. Programs can be modified incrementally using OpenMP like directives which causes the compiler to generate CUDA kernels to be run on the GPUs. In this article we look at the performance gain in lattice simulations with dynamical fermions using OpenACC compilers.

hep-lat↗

Towards a continuum model for particle-induced velocity fluctuations in suspension flow through a stenosed geometry

Non-particulate continuum descriptions allow for computationally efficient modeling of suspension flows at scales that are inaccessible to more detailed particulate approaches. It is well known that the presence of particles influences the effective viscosity of a suspension and that this effect has thus to be accounted for in macroscopic continuum models. The present paper aims at developing a non-particulate model that reproduces not only the rheology but also the cell-induced velocity fluctuations, responsible for enhanced diffusivity. The results are obtained from a coarse-grained blood model based on the lattice Boltzmann method. The benchmark system comprises a flow between two parallel plates with one of them featuring a smooth obstacle imitating a stenosis. Appropriate boundary conditions are developed for the particulate model to generate equilibrated cell configurations mimicking an infinite channel in front of the stenosis. The averaged flow field in the bulk of the channel can be described well by a non-particulate simulation with a matched viscosity. We show that our proposed phenomenological model is capable to reproduce many features of the velocity fluctuations.

cond-mat.soft↗

Aliovalent Doping of CeO$_2$: DFT-study of Oxidation State and Vacancy Effects

The modification of the properties of CeO$_2$ through aliovalent doping are investigated within the \emph{ab-initio} density functional theory framework. Lattice parameters, dopant atomic radii, bulk moduli and thermal expansion coefficients of fluorite type Ce$_{1-x}$M$_{x}$O$_{2-y}$ (with M$ = $ Mg, V, Co, Cu, Zn, Nb, Ba, La, Sm, Gd, Yb, and Bi)are presented for dopant concentrations in the range $0.00 \leq x \leq 0.25$. The stability of the dopants is compared and discussed, and the influence of oxygen vacancies is investigated. It is shown that oxygen vacancies tend to increase the lattice parameter, and strongly decrease the bulk modulus. Defect formation energies are correlated with calculated crystal radii and covalent radii of the dopants, but are shown to present no simple trend. The previously observed inverse relation between the thermal expansion coefficient and the bulk modulus is shown to persist independent of the inclusion of charge compensating vacancies.

cond-mat.mtrl-sci↗

Solving the Schrodinger equation directly for a particle in one-dimensional periodic potentials

Solutions of time-independent Schrodinger equation for potentials periodic in space satisfy Bloch theorem. The theorem has been used to obtain solutions of the Schrodinger equation for periodic systems by expanding them in terms of plane waves of appropriate wave-vectors and then diagonalising the resulting Hamiltonian matrix. However, this method can give exact solutions only if an infinite number of plane-waves are used in the wavefunction. Thus the Schrodinger equation has not been solved exactly even for one-dimensional infinitely large periodic systems despite the simplification that the theorem provides. On the other hand, solutions of one-dimensional Schrodinger equation for finite systems are obtained routinely by using standard numerical techniques to integrate the Schrodinger equation directly. In this paper, we extend this approach to infinitely large systems and use Bloch theorem in a novel way to find direct exact numerical solutions of the Schrodinger equation for arbitrary one-dimensional periodic potentials. In addition to providing a different way of solving the Schrodinger equation for such systems, the simplicity of the algorithm renders it a great pedagogical value.

physics.comp-ph↗

A thermostatistical approach to scale-free networks

We describe an ensemble of growing scale-free networks in an equilibrium framework, providing insight into why the exponent of empirical scale-free networks in nature is typically robust. In an analogy to thermostatistics, to describe the canonical and microcanonical ensembles, we introduce a functional, whose maximum corresponds to a scale-free configuration. We then identify the equivalents to energy, Zeroth-law, entropy and heat capacity for scale-free networks. Discussing the merging of scale-free networks, we also establish an exact relation to predict their final "equilibrium" degree exponent. All analytic results are complemented with Monte Carlo simulations. Our approach illustrates the possibility to apply the tools of equilibrium statistical physics to study the properties of growing networks, and it also supports the recent arguments on the complementarity between equilibrium and nonequilibrium systems.

physics.soc-ph↗

Multi-Shell Ankylography

Three-dimensional (3D) imaging techniques appeal to a broad range of scientific and industrial applications. Typically, projection slice theorem enables multiple two-dimensional (2D) projections of an object to be combined in the Fourier domain to yield a 3D image. However, traditional techniques require a significant number of projections. The significant number of views required in conventional tomography not only complicates such imaging modalities, but also limits their ability to image samples that are sensitive to radiation dose or are otherwise unstable in time. In this work, we demonstrate through numerical simulations and an eigenvalue analysis that a recently developed technique called ankylography enables 3D image reconstruction using much fewer views than conventional tomography. Such a technique with the ability to obtain the 3D structure information from a few views is expected to find applications in both optical and x-ray imaging fields.

physics.optics↗