Search

In this paper we study from a numerical analysis perspective the Fractional Step Kinetic Monte Carlo (FS-KMC) algorithms proposed in [1] for the parallel simulation of spatially distributed particle systems on a lattice. FS-KMC are fractional step algorithms with a time-stepping window $\Delta t$, and as such they are inherently partially asynchronous since there is no processor communication during the period $\Delta t$. In this contribution we primarily focus on the error analysis of FS-KMC algorithms as approximations of conventional, serial kinetic Monte Carlo (KMC). A key aspect of our analysis relies on emphasising a goal-oriented approach for suitably defined macroscopic observables (e.g., density, energy, correlations, surface roughness), rather than focusing on strong topology estimates for individual trajectories. One of the key implications of our error analysis is that it allows us to address systematically the processor communication of different parallelization strategies for KMC by comparing their (partial) asynchrony, which in turn is measured by their respective fractional time step $\Delta t$ for a prescribed error tolerance., Comment: 32 pages, 4 figures

We propose a hierarchy of multi-level kinetic Monte Carlo methods for sampling high-dimensional, stochastic lattice particle dynamics with complex interactions. The method is based on the efficient coupling of different spatial resolution levels, taking advantage of the low sampling cost in a coarse space and by developing local reconstruction strategies from coarse-grained dynamics. Microscopic reconstruction corrects possibly significant errors introduced through coarse-graining, leading to the controlled-error approximation of the sampled stochastic process. In this manner, the proposed multi-level algorithm overcomes known shortcomings of coarse-graining of particle systems with complex interactions such as combined long and short-range particle interactions and/or complex lattice geometries. Specifically, we provide error analysis for the approximation of long-time stationary dynamics in terms of relative entropy and prove that information loss in the multi-level methods is growing linearly in time, which in turn implies that an appropriate observable in the stationary regime is the information loss of the path measures per unit time. We show that this observable can be either estimated a priori, or it can be tracked computationally a posteriori in the course of a simulation. The stationary regime is of critical importance to molecular simulations as it is relevant to long-time sampling, obtaining phase diagrams and in studying metastability properties of high-dimensional complex systems. Finally, the multi-level nature of the method provides flexibility in combining rejection-free and null-event implementations, generating a hierarchy of algorithms with an adjustable number of rejections that includes well-known rejection-free and null-event algorithms., Comment: 34 pages

In this work we propose a hierarchy of Monte Carlo methods for sampling equilibrium properties of stochastic lattice systems with competing short and long range interactions. Each Monte Carlo step is composed by two or more sub - steps efficiently coupling coarse and microscopic state spaces. The method can be designed to sample the exact or controlled-error approximations of the target distribution, providing information on levels of different resolutions, as well as at the microscopic level. In both strategies the method achieves significant reduction of the computational cost compared to conventional Markov Chain Monte Carlo methods. Applications in phase transition and pattern formation problems confirm the efficiency of the proposed methods., Comment: 37 pages

We present a mathematical framework for constructing and analyzing parallel algorithms for lattice Kinetic Monte Carlo (KMC) simulations. The resulting algorithms have the capacity to simulate a wide range of spatio-temporal scales in spatially distributed, non-equilibrium physiochemical processes with complex chemistry and transport micro-mechanisms. The algorithms can be tailored to specific hierarchical parallel architectures such as multi-core processors or clusters of Graphical Processing Units (GPUs). The proposed parallel algorithms are controlled-error approximations of kinetic Monte Carlo algorithms, departing from the predominant paradigm of creating parallel KMC algorithms with exactly the same master equation as the serial one. Our methodology relies on a spatial decomposition of the Markov operator underlying the KMC algorithm into a hierarchy of operators corresponding to the processors' structure in the parallel architecture. Based on this operator decomposition, we formulate Fractional Step Approximation schemes by employing the Trotter Theorem and its random variants; these schemes, (a) determine the communication schedule} between processors, and (b) are run independently on each processor through a serial KMC simulation, called a kernel, on each fractional step time-window. Furthermore, the proposed mathematical framework allows us to rigorously justify the numerical and statistical consistency of the proposed algorithms, showing the convergence of our approximating schemes to the original serial KMC. The approach also provides a systematic evaluation of different processor communicating schedules., Comment: 34 pages, 9 figures

Born-Oppenheimer dynamics is shown to provide an accurate approximation of time-independent Schr\"odinger observables for a molecular system with an electron spectral gap, in the limit of large ratio of nuclei and electron masses, without assuming that the nuclei are localized to vanishing domains. The derivation, based on a Hamiltonian system interpretation of the Schr\"odinger equation and stability of the corresponding Hamilton-Jacobi equation, bypasses the usual separation of nuclei and electron wave functions, includes caustic states and gives a different perspective on the Born-Oppenheimer approximation, Schr\"odinger Hamiltonian systems and numerical simulation in molecular dynamics modeling at constant energy microcanonical ensembles., Comment: 42 pages, 12 figures Changes: - added section 3.1.1 on the motivation of the WKB-method and included a paragraph on Lagrangian manifolds in section 7.2.5. - added references and illustrative figures. - corrected few typos

A new method of deriving reduced models of Hamiltonian dynamical systems is developed using techniques from optimization and statistical estimation. Given a set of resolved variables that define a model reduction, the quasi-equilibrium ensembles associated with the resolved variables are employed as a family of trial probability densities on phase space. The residual that results from submitting these trial densities to the Liouville equation is quantified by an ensemble-averaged cost function related to the information loss rate of the reduction. From an initial nonequilibrium state, the statistical state of the system at any later time is estimated by minimizing the time integral of the cost function over paths of trial densities. Statistical closure of the underresolved dynamics is obtained at the level of the value function, which equals the optimal cost of reduction with respect to the resolved variables, and the evolution of the estimated statistical state is deduced from the Hamilton-Jacobi equation satisfied by the value function. In the near-equilibrium regime, or under a local quadratic approximation in the far-from-equilibrium regime, this best-fit closure is governed by a differential equation for the estimated state vector coupled to a Riccati differential equation for the Hessian matrix of the value function. Since memory effects are not explicitly included in the trial densities, a single adjustable parameter is introduced into the cost function to capture a time-scale ratio between resolved and unresolved motions. Apart from this parameter, the closed equations for the resolved variables are completely determined by the underlying deterministic dynamics.

We propose an efficient Markov Chain Monte Carlo method for sampling equilibrium distributions for stochastic lattice models, capable of handling correctly long and short-range particle interactions. The proposed method is a Metropolis-type algorithm with the proposal probability transition matrix based on the coarse-grained approximating measures introduced in a series of works of M. Katsoulakis, A. Majda, D. Vlachos and P. Plechac, L. Rey-Bellet and D.Tsagkarogiannis,. We prove that the proposed algorithm reduces the computational cost due to energy differences and has comparable mixing properties with the classical microscopic Metropolis algorithm, controlled by the level of coarsening and reconstruction procedure. The properties and effectiveness of the algorithm are demonstrated with an exactly solvable example of a one dimensional Ising-type model, comparing efficiency of the single spin-flip Metropolis dynamics and the proposed coupled Metropolis algorithm., Comment: 20 pages, 4 figures

An implicit mass-matrix penalization (IMMP) of Hamiltonian dynamics is proposed, and associated dynamical integrators, as well as sampling Monte-Carlo schemes, are analyzed for systems with multiple time scales. The penalization is based on an extended Hamiltonian with artificial constraints associated with some selected DOFs. The penalty parameters enable arbitrary tuning of timescales for the selected DOFs. The IMMP dynamics is shown to be an interpolation between the exact Hamiltonian dynamics and the dynamics with rigid constraints. This property translates in the associated numerical integrator into a tunable trade-off between stability and dynamical modification. Moreover, a penalty that vanishes with the time-step yields order two convergent schemes for the exact dynamics. Moreover, by construction, the resulting dynamics preserves the canonical equilibrium distribution in position variables, up to a computable geometric correcting potential, leading to Metropolis-like unbiased sampling algorithms. The algorithms can be implemented with a simple modification of standard geometric integrators with algebraic constraints imposed on the selected DOFs, and has no additional complexity in terms of enforcing the constraints and force evaluations. The properties of the IMMP method are demonstrated numerically on the $N$-alkane model, showing that the time-step stability region of integrators and the sampling efficiency can be increased with a gain that grows with the size of the system. This feature is mathematically analyzed for a harmonic atomic chain model. When a large stiffness parameter is introduced, the IMMP method is shown to be asymptotically stable and to converge towards the heuristically expected Markovian effective dynamics on the slow manifold., Comment: 39 pages

We propose and analyze an implicit mass-matrix penalization (IMMP) technique which enables efficient and exact sampling of the (Boltzmann/Gibbs) canonical distribution associated to Hamiltonian systems with fast degrees of freedom (fDOFs). The penalty parameters enable arbitrary tuning of the timescale for the selected fDOFs, and the method is interpreted as an interpolation between the exact Hamiltonian dynamics and the dynamics with infinitely slow fDOFs (equivalent to geometrically corrected rigid constraints). This property translates in the associated numerical methods into a tunable trade-off between stability and dynamical modification. The penalization is based on an extended Hamiltonian with artificial constraints associated with each fDOF. By construction, the resulting dynamics is statistically exact with respect to the canonical distribution in position variables. The algorithms can be easily implemented with standard geometric integrators with algebraic constraints given by the expected fDOFs, and has no additional complexity in terms of enforcing the constraint and force evaluations. The method is demonstrated on a high dimensional system with non-convex interactions. Prescribing the macroscopic dynamical timescale, it is shown that the IMMP method increases the time-step stability region with a gain that grows linearly with the size of the system. The latter property, as well as consistency of the macroscopic dynamics of the IMMP method is proved rigorously for linear interactions. Finally, when a large stiffness parameter is introduced, the IMMP method can be tuned to be asymptotically stable, converging towards the heuristically expected Markovian effective dynamics on the slow manifold., Comment: 32 pages, 5 figures

The primary objective of this work is to develop coarse-graining schemes for stochastic many-body microscopic models and quantify their effectiveness in terms of a priori and a posteriori error analysis. In this paper we focus on stochastic lattice systems of interacting particles at equilibrium. %such as Ising-type models. The proposed algorithms are derived from an initial coarse-grained approximation that is directly computable by Monte Carlo simulations, and the corresponding numerical error is calculated using the specific relative entropy between the exact and approximate coarse-grained equilibrium measures. Subsequently we carry out a cluster expansion around this first-and often inadequate-approximation and obtain more accurate coarse-graining schemes. The cluster expansions yield also sharp a posteriori error estimates for the coarse-grained approximations that can be used for the construction of adaptive coarse-graining methods. We present a number of numerical examples that demonstrate that the coarse-graining schemes developed here allow for accurate predictions of critical behavior and hysteresis in systems with intermediate and long-range interactions. We also present examples where they substantially improve predictions of earlier coarse-graining schemes for short-range interactions., Comment: 37 pages, 8 figures

In this paper we investigate the approximation properties of the coarse-graining procedure applied to kinetic Monte Carlo simulations of lattice stochastic dynamics. We provide both analytical and numerical evidence that the hierarchy of the coarse models is built in a systematic way that allows for error control in both transient and long-time simulations. We demonstrate that the numerical accuracy of the CGMC algorithm as an approximation of stochastic lattice spin flip dynamics is of order two in terms of the coarse-graining ratio and that the natural small parameter is the coarse-graining ratio over the range of particle/particle interactions. The error estimate is shown to hold in the weak convergence sense. We employ the derived analytical results to guide CGMC algorithms and we demonstrate a CPU speed-up in demanding computational regimes that involve nucleation, phase transitions and metastability., Comment: 30 pages

We study a dissipative nonlinear equation modelling certain features of the Navier-Stokes equations. We prove that the evolution of radially symmetric compactly supported initial data does not lead to singularities in dimensions $n\leq 4$. For dimensions $n>4$ we present strong numerical evidence supporting existence of blow-up solutions. Moreover, using the same techniques we numerically confirm a conjecture of Lepin regarding existence of self-similar singular solutions to a semi-linear heat equation., Comment: 16 pages

We derive an equilibrium statistical theory for the macroscopic description of a ferromagnetic material at positive finite temperatures. Our formulation describes the most-probable equilibrium macrostates that yield a coherent deterministic large-scale picture varying at the size of the domain, as well as it captures the effect of random spin fluctuations caused by the thermal noise. We discuss connections of the proposed formulation to the Landau-Lifschitz theory and to the studies of domain formation based on Monte Carlo lattice simulations., Comment: 5 pages (2-column format)

We address the open problem of existence of singularities for the complex Ginzburg-Landau equation. Using a combination of rigourous results and numerical computations, we describe a countable family of self-similar singularities. Our analysis includes the super-critical non-linear Schroedinger equation as a special case, and most of the described singularities are new even in that situation. We also consider the problem of stability of these singularities., Comment: 23 pages, 18 figures (eps)