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arXiv2011

Self-Avoiding Random Dynamics on Integer Complex Systems

This paper introduces a new specialized algorithm for equilibrium Monte Carlo sampling of binary-valued systems, which allows for large moves in the state space. This is achieved by constructing self-avoiding walks (SAWs) in the state space. As a consequence, many bits are flipped in a single MCMC step. We name the algorithm SARDONICS, an acronym for Self-Avoiding Random Dynamics on Integer Complex Systems. The algorithm has several free parameters, but we show that Bayesian optimization can be used to automatically tune them. SARDONICS performs remarkably well in a broad number of sampling tasks: toroidal ferromagnetic and frustrated Ising models, 3D Ising models, restricted Boltzmann machines and chimera graphs arising in the design of quantum computers.

stat.CO↗

arXiv2011

Modified Tucker Decomposition for Tensor Network and Fast Linearized Tensor Renormalization Group Algorithm for Two-Dimensional Quantum Spin Lattice Systems

We propose a novel algorithm with a modified Tucker decomposition for tensor network that allows for efficiently and precisely calculating the ground state and thermodynamic properties of two-dimensional (2D) quantum spin lattice systems, and is coined as the fast linearized tensor renormalization group (fLTRG). Its amazing efficiency and precision are examined by studying the spin-1/2 anisotropic Heisenberg antiferromagnet on a honeycomb lattice, and the results are found to be fairly in agreement with the quantum Monte Carlo calculations. It is also successfully applied to tackle a quasi-2D spin-1/2 frustrated bilayer honeycomb Heisenberg model, where a quantum phase transition from an ordered antiferromagnetic state to a gapless quantum spin liquid phase is found. The thermodynamic behaviors of this frustrated spin system are also explored. The present fLTRG algorithm could be readily extended to other quantum lattice systems.

cond-mat.str-el↗

arXiv2014

Numerical treatment of interfaces for second-order wave equations

In this article we develop a numerical scheme to deal with interfaces between touching numerical grids when solving the second-order wave equation. We show that it is possible to implement an interface scheme of "penalty" type for the second-order wave equation, similar to the ones used for first-order hyperbolic and parabolic equations, and the second-order scheme used by Mattsson et al (2008). These schemes, known as SAT schemes for finite difference approximations and penalties for spectral ones, and ours share similar properties but in our case one needs to pass at the interface a smaller amount of data than previously known schemes. This is important for multi-block parallelizations in several dimensions, for it implies that one obtains the same solution quality while sharing among different computational grids only a fraction of the data one would need for a comparable (in accuracy) SAT or Mattsson et al.'s scheme. The semi-discrete approximation used here preserves the norm and uses standard finite-difference operators satisfying summation by parts. For the time integrator we use a semi-implicit IMEX Runge-Kutta method. This is crucial, since the explicit Runge-Kutta method would be impractical given the severe restrictions that arise from the stiff parts of the equations.

physics.comp-ph↗

arXiv2011

Potential and Challenge of Ankylography

The concept of ankylography, which under certain circumstances enables 3D structure determination from a single view [1], had ignited a lively debate even before its publication [2,3]. Since then, a number of readers requested the ankylographic reconstruction codes from us. To facilitate a better understanding of ankylography, we posted the source codes of the ankylographic reconstruction on a public website and encouraged interested readers to download the codes and test the method [4]. Those who have tested our codes confirm that the principle of ankylography works. Furthermore, our mathematical analysis and numerical simulations suggest that, for a continuous object with array size of 14x14x14 voxels, its 3D structure can usually be reconstructed from the diffraction intensities sampled on a spherical shell of 1 voxel thick [4]. In some cases where the object does not have very dense structure, ankylography can be applied to reconstruct its 3D image with array size of 25x25x25 voxels [4]. What remains to be elucidated is how to extend ankylography to the reconstruction of larger objects, and what further theoretical, experimental and algorithm developments will be necessary to make ankylography a practical and useful imaging tool. Here we present our up-to-date understanding of the potential and challenge of ankylography. Further, we clarify some misconceptions on ankylography, and respond to technical comments raised by Wei [5] and Wang et al. [6] Finally, it is worthwhile to point out that the potential for recovering 3D information from the Fourier coefficients within a spherical shell may also find application in other fields.

physics.optics↗

arXiv2012

Parametrization of coarse grained force fields for dynamic property of ethylene glycol oligomers/water binary mixtures

To evaluate shear viscosity of ethylene glycol oligomers (EGO)/water binary mixture by means of coarse-grained molecular dynamics (CG-MD) simulations, we proposed the self-diffusion-coefficient-based parameterization of non-bonded interactions among CG particles. Our parameterization procedure consists of three steps: 1) determination of bonded potentials, 2) scaling for time and solvent diffusivity, and 3) optimization of Lennard-Jones parameters to reproduce experimental self-diffusion coefficient and density data. With the determined parameters and the scaling relations, we evaluated shear viscosities of aqueous solutions of EGOs with various molecular weights and concentrations. Our simulation result are in close agreement with the experimental data. The largest simulation in this article corresponds to a 1.2 microseconds atomistic simulation for 100,000 atoms. Our CG model with the parameterization scheme for CG particles may be useful to study the dynamic properties of a liquid which contains relatively low molecular weight polymers or oligomers.

math-ph↗

arXiv2011

Explicit Integration of Extremely-Stiff Reaction Networks: Asymptotic Methods

We show that, even for extremely stiff systems, explicit integration may compete in both accuracy and speed with implicit methods if algebraic methods are used to stabilize the numerical integration. The required stabilizing algebra depends on whether the system is well-removed from equilibrium or near equilibrium. This paper introduces a quantitative distinction between these two regimes and addresses the former case in depth, presenting explicit asymptotic methods appropriate when the system is extremely stiff but only weakly equilibrated. A second paper examines quasi-steady-state methods as an alternative to asymptotic methods in systems well away from equilibrium and a third paper extends these methods to equilibrium conditions in extremely stiff systems using partial equilibrium methods. All three papers present systematic evidence for timesteps competitive with implicit methods. Because an explicit method can execute a timestep faster than an implicit method, algebraically-stabilized explicit algorithms might permit integration of larger networks than have been feasible before in various disciplines.

astro-ph.SR↗

arXiv2011

Explicit Integration of Extremely-Stiff Reaction Networks: Partial Equilibrium Methods

In two preceding papers we have shown that, when reaction networks are well-removed from equilibrium, explicit asymptotic and quasi-steady-state approximations can give algebraically-stabilized integration schemes that rival standard implicit methods in accuracy and speed for extremely stiff systems. However, we also showed that these explicit methods remain accurate but are no longer competitive in speed as the network approaches equilibrium. In this paper we analyze this failure and show that it is associated with the presence of fast equilibration timescales that neither asymptotic nor quasi-steady-state approximations are able to remove efficiently from the numerical integration. Based on this understanding, we develop a partial equilibrium method to deal effectively with the approach to equilibrium and show that explicit asymptotic methods, combined with the new partial equilibrium methods, give an integration scheme that plausibly can deal with the stiffest networks, even in the approach to equilibrium, with accuracy and speed competitive with that of implicit methods. Thus we demonstrate that such explicit methods may offer alternatives to implicit integration of even extremely stiff systems, and that these methods may permit integration of much larger networks than have been possible before in a number of fields.

astro-ph.SR↗

arXiv2013

Finite-Element Approximation of One-Sided Stefan Problems with Anisotropic, Approximately Crystalline, Gibbs--Thomson Law

We present a finite-element approximation for the one-sided Stefan problem and the one-sided Mullins--Sekerka problem, respectively. The problems feature a fully anisotropic Gibbs--Thomson law, as well as kinetic undercooling. Our approximation, which couples a parametric approximation of the moving boundary with a finite element approximation of the bulk quantities, can be shown to satisfy a stability bound, and it enjoys very good mesh properties which means that no mesh smoothing is necessary in practice. In our numerical computations we concentrate on the simulation of snow crystal growth. On choosing realistic physical parameters, we are able to produce several distinctive types of snow crystal morphologies. In particular, facet breaking in approximately crystalline evolutions can be observed.

physics.comp-ph↗

arXiv2012

Impact of Dynamic Interactions on Multi-Scale Analysis of Community Structure in Networks

To find interesting structure in networks, community detection algorithms have to take into account not only the network topology, but also dynamics of interactions between nodes. We investigate this claim using the paradigm of synchronization in a network of coupled oscillators. As the network evolves to a global steady state, nodes belonging to the same community synchronize faster than nodes belonging to different communities. Traditionally, nodes in network synchronization models are coupled via one-to-one, or conservative interactions. However, social interactions are often one-to-many, as for example, in social media, where users broadcast messages to all their followers. We formulate a novel model of synchronization in a network of coupled oscillators in which the oscillators are coupled via one-to-many, or non-conservative interactions. We study the dynamics of different interaction models and contrast their spectral properties. To find multi-scale community structure in a network of interacting nodes, we define a similarity function that measures the degree to which nodes are synchronized and use it to hierarchically cluster nodes. We study real-world social networks, including networks of two social media providers. To evaluate the quality of the discovered communities in a social media network we propose a community quality metric based on user activity. We find that conservative and non-conservative interaction models lead to dramatically different views of community structure even within the same network. Our work offers a novel mathematical framework for exploring the relationship between network structure, topology and dynamics.

cs.SI↗

arXiv2012

On the efficiency and accuracy of interpolation methods for spectral codes

In this paper a general theory for interpolation methods on a rectangular grid is introduced. By the use of this theory an efficient B-spline based interpolation method for spectral codes is presented. The theory links the order of the interpolation method with its spectral properties. In this way many properties like order of continuity, order of convergence and magnitude of errors can be explained. Furthermore, a fast implementation of the interpolation methods is given. We show that the B-spline based interpolation method has several advantages compared to other methods. First, the order of continuity of the interpolated field is higher than for other methods. Second, only one FFT is needed whereas e.g. Hermite interpolation needs multiple FFTs for computing the derivatives. Third, the interpolation error almost matches the one of Hermite interpolation, a property not reached by other methods investigated.

physics.comp-ph↗

arXiv2012

Two-Phase Flow in Porous Media: Scaling of Steady-State Effective Permeability

A recent experiment has considered the effective permeability of two-phase flow of air and a water-glycerol solution under steady-state conditions in a two-dimensional model porous medium, and found a power law dependence with respect to capillary number. Running simulations on a two-dimensional network model a similar power law is found, for high viscosity contrast as in the experiment and also for viscosity matched fluids. Two states are found, one with stagnant clusters and one without. For the stagnant cluster state, a power law exponent 0.50 is found for viscosity matched fluids and 0.54 for large viscosity contrast. When there are no stagnant clusters the exponent depends on saturation and varies within the range of 0.67 - 0.80.

physics.flu-dyn↗

arXiv2014

Detection of a small shift in a broad distribution

Statistical methods for the extraction of a small shift in broad data distributions are examined by means of Monte Carlo simulations. This work was originally motivated by the CERN neutrino beam to Gran Sasso (CNGS) experiment for which the OPERA detector collaboration reported a time shift in a broad distribution with an accuracy of $\pm 7.8\,$ns, while the fluctuation of the average time turns with $\pm 23.8\,$ns out to be much larger. Although the physical result of a big shift has been withdrawn, statistical methods that make an identification in a broad distribution with such a small error possible remain of interest.

hep-ph↗

arXiv2014

Introduction to Perl module lb2d.pm 0.1 for basic Lattice Boltzmann simulations

The Lattice Boltzmann method has been gaining acceptance for hydrodynamic problems involving complex boundaries, non-equilibrium dynamics and interfacial phenomena in multiphase or multicomponent systems. lb2d.pm is a Perl module offering a clear framework for simple Lattice Boltzmann simulations in 2D. The syntax and some basic applications are presented. Mainly, the new version 0.1 enables solute transport and accounts for reactive boundaries leading to surface growth.

physics.flu-dyn↗

arXiv2012

A second-quantized red herring in full configuration-interaction Monte Carlo

This paper deals with the sign problem in full configuration-interaction quantum Monte Carlo. After putting this article on the arxiv, it was pointed out to us that our argument applies to a number of model Hamiltonians we considered numerically but not to the most generic case. Please see arxiv: 1209.3044, where we have a corrected comprehensive discussion of the necessary and sufficient conditions for when the sign problem for a given Hamiltonian (and basis) differ between first and second quantization.

physics.comp-ph↗

arXiv2012

User Guide for the Discrete Dipole Approximation Code DDSCAT 7.2

DDSCAT 7.2 is a freely available open-source Fortran-90 software package applying the discrete dipole approximation (DDA) to calculate scattering and absorption of electromagnetic waves by targets with arbitrary geometries and complex refractive index. The targets may be isolated entities (e.g., dust particles), but may also be 1-d or 2-d periodic arrays of "target unit cells", which can be used to study absorption, scattering, and electric fields around arrays of nanostructures. The DDA approximates the target by an array of polarizable points. The theory of the DDA and its implementation in DDSCAT is presented in Draine (1988) and Draine & Flatau (1994), and its extension to periodic structures in Draine & Flatau (2008). Efficient near-field calculations are enabled following Flatau & Draine (2012). DDSCAT 7.2 allows accurate calculations of electromagnetic scattering from targets with size parameters 2*pi*aeff/lambda < 25 provided the refractive index m is not large compared to unity (|m-1| < 2). DDSCAT 7.2 includes support for MPI, OpenMP, and the Intel Math Kernel Library (MKL). DDSCAT 7.2 supports calculations for a variety of target geometries (e.g., ellipsoids, regular tetrahedra, rectangular solids, finite cylinders, hexagonal prisms, etc.). Target materials may be both inhomogeneous and anisotropic. It is straightforward for the user to import new target geometries into the code. DDSCAT 7.2 calculates total cross sections for absorption and scattering and selected elements of the Mueller scattering intensity matrix for specified orientation of the target relative to the incident wave, and for specified scattering directions. DDSCAT 7.2 calculates E throughout a user-specified rectangular volume containing the target. A Fortran-90 code READNF to read E and P from files created by DDSCAT 7.2 is included in the distribution.

physics.comp-ph↗

arXiv2012

Conduction, diffusion and noise of electrons in amorphous chalcogenides at low electric fields

The low-field electron diffusion, noise, and the conduction in amorphous chalcogenides are investigated by means of a Monte Carlo implementation of a full three- dimensional variable-range hopping transport model between localized states. Quantities like the carrier-velocity autocorrelation function, the noise power spectrum, the diffusion coefficient and the ohmic conductivity are obtained from numerical simulations at room temperatures and lower. Some interesting features of the linear-response regime typical of hopping transport are observed and discussed for the case of the amorphous Ge2Sb2Te5.

cond-mat.mtrl-sci↗

arXiv2013

Realistic time-scale fully atomistic simulations of surface nucleation of dislocations in pristine nanopillars

We use our recently proposed accelerated dynamics algorithm (Tiwary & van de Walle, 2011) to calculate temperature and stress dependence of activation free energy for surface nucleation of dislocations in pristine Gold nanopillars under realistic loads. While maintaining fully atomistic resolution, we achieve the fraction of a second time-scale regime. We find that the activation free energy depends significantly on the driving force (stress or strain) and temperature, leading to very high activation entropies. We also perform compression tests on Gold nanopillars for strain rates varying between 7 orders of magnitudes, reaching as low as 10^3/s. Our calculations show the quantitative effects on the yield point of unrealistic strain-rate Molecular Dynamics calculations: we find that while the failure mechanism for <001> compression of Gold nanopillars remains the same across the entire strain-rate range, the elastic limit (defined as stress for nucleation of the first dislocation) depends significantly on the strain-rate. We also propose a new methodology that overcomes some of the limits in our original accelerated dynamics scheme (and accelerated dynamics methods in general). We lay out our methods in sufficient details so as to be used for understanding and predicting deformation mechanism under realistic driving forces for various problems.

cond-mat.mtrl-sci↗

arXiv2012

Mod-CSA: Modularity optimization by conformational space annealing

We propose a new modularity optimization method, Mod-CSA, based on stochastic global optimization algorithm, conformational space annealing (CSA). Our method outperforms simulated annealing in terms of both efficiency and accuracy, finding higher modularity partitions with less computational resources required. The high modularity values found by our method are higher than, or equal to, the largest values previously reported. In addition, the method can be combined with other heuristic methods, and implemented in parallel fashion, allowing it to be applicable to large graphs with more than 10000 nodes.

physics.comp-ph↗