arXiv subjects

Jianfeng Lu

Publications and source records attributed to Jianfeng Lu.

At least 307 records · Page 17Linked to original sources

arXiv2015

Emergence of step flow from atomistic scheme of epitaxial growth in 1+1 dimensions

The Burton-Cabrera-Frank (BCF) model for the flow of line defects (steps) on crystal surfaces has offered useful insights into nanostructure evolution. This model has rested on phenomenological grounds. Our goal is to show via scaling arguments the emergence of the BCF theory for non-interacting steps from a stochastic atomistic scheme of a simplified kinetic solid-on-solid model in one spatial dimension. Our main assumptions are: adsorbed atoms (adatoms) form a dilute system, and elastic effects of the crystal lattice are absent. The step edge is treated as a front that propagates via probabilistic rules for atom attachment and detachment at the step. We formally derive a quasistatic step flow description by averaging out the stochastic scheme when terrace diffusion, adatom desorption and deposition from above are present.

cond-mat.mes-hall↗

arXiv2014

Strang Splitting Methods for a quasilinear Schrödinger equation - Convergence, Instability and Dynamics

We study the Strang splitting scheme for quasilinear Schrödinger equations. We establish the convergence of the scheme for solutions with small initial data. We analyze the linear instability of the numerical scheme, which explains the numerical blow-up of large data solutions and connects to analytical breakdown of regularity of solutions to quasilinear Schrödinger equations. Numerical tests are performed for a modified version of the superfluid thin film equation.

math.NA↗

arXiv2014

Stability of a force-based hybrid method with planar sharp interface

We study a force-based hybrid method that couples atomistic model with Cauchy-Born elasticity model with sharp transition interface. We identify stability conditions that guarantee the convergence of the hybrid scheme to the solution of the atomistic model with second order accuracy, as the ratio between lattice parameter and the characteristic length scale of the deformation tends to zero. Convergence is established for hybrid schemes with planar sharp interface for system without defects, with general finite range atomistic potential and simple lattice structure. The key ingredient of the proof is regularity and stability analysis of elliptic systems of difference equations. We apply the results to atomistic-to-continuum scheme for a 2D triangular lattice with planar interface.

math.NA↗

arXiv2014

Exact dynamical coarse-graining without time-scale separation

A family of collective variables is proposed to perform exact dynamical coarse-graining even in systems without time scale separation. More precisely, it is shown that these variables are not slow in general but they satisfy an overdamped Langevin equation that statistically preserves the sequence in which any regions in collective variable space are visited and permits to calculate exactly the mean first passage times from any such region to another. The role of the free energy and diffusion coefficient in this overdamped Langevin equation is discussed, along with the way they transform under any change of variable in collective variable space. These results apply both for systems with and without inertia, and they can be generalized to using several collective variables simultaneously. The view they offer on what makes collective variables and reaction coordinates optimal breaks from the standard notion that good collective variable must be slow variable, and it suggests new ways to interpret data from molecular dynamic simulations and experiments.

cond-mat.stat-mech↗

arXiv2014

Efficient rare event simulation for failure problems in random media

In this paper we study rare events associated to solutions of elliptic partial differential equations with spatially varying random coefficients. The random coefficients follow the lognormal distribution, which is determined by a Gaussian process. This model is employed to study the failure problem of elastic materials in random media in which the failure is characterized by that the strain field exceeds a high threshold. We propose an efficient importance sampling scheme to compute small failure probabilities in the high threshold limit. The change of measure in our scheme is parametrized by two density functions. The efficiency of the importance sampling scheme is validated by numerical examples.

math.NA↗

arXiv2014

Density matrix minimization with $\ell_1$ regularization

We propose a convex variational principle to find sparse representation of low-lying eigenspace of symmetric matrices. In the context of electronic structure calculation, this corresponds to a sparse density matrix minimization algorithm with $\ell_1$ regularization. The minimization problem can be efficiently solved by a split Bergman iteration type algorithm. We further prove that from any initial condition, the algorithm converges to a minimizer of the variational principle.

math-ph↗

arXiv2013

Analysis of the Time Reversible Born-Oppenheimer Molecular Dynamics

We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD) scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition as well as the accuracy of TRBOMD for computing physical properties such as the phonon frequency obtained from the molecular dynamic simulation. We connect and compare TRBOMD with the Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one dimensional model for Kohn-Sham density functional theory.

math.NA↗

arXiv2013

Seismic modeling using the frozen Gaussian approximation

We adopt the frozen Gaussian approximation (FGA) for modeling seismic waves. The method belongs to the category of ray-based beam methods. It decomposes seismic wavefield into a set of Gaussian functions and propagates these Gaussian functions along appropriate ray paths. As opposed to the classic Gaussian-beam method, FGA keeps the Gaussians frozen (at a fixed width) during the propagation process and adjusts their amplitudes to produce an accurate approximation after summation. We perform the initial decomposition of seismic data using a fast version of the Fourier-Bros-Iagolnitzer (FBI) transform and propagate the frozen Gaussian beams numerically using ray tracing. A test using a smoothed Marmousi model confirms the validity of FGA for accurate modeling of seismic wavefields.

physics.geo-ph↗

arXiv2013

Reactive trajectories and the transition path process

We study the trajectories of a solution $X_t$ to an Itô stochastic differential equation in $\Rm^d$, as the process passes between two disjoint open sets, $A$ and $B$. These segments of the trajectory are called transition paths or reactive trajectories, and they are of interest in the study of chemical reactions and thermally activated processes. In that context, the sets $A$ and $B$ represent reactant and product states. Our main results describe the probability law of these transition paths in terms of a transition path process $Y_t$, which is a strong solution to an auxiliary SDE having a singular drift term. We also show that statistics of the transition path process may be recovered by empirical sampling of the original process $X_t$. As an application of these ideas, we prove various representation formulas for statistics of the transition paths. We also identify the density and current of transition paths. Our results fit into the framework of the transition path theory by E and Vanden-Eijnden.

math.PR↗

arXiv2013

Infinite swapping replica exchange molecular dynamics leads to a simple simulation patch using mixture potentials

Replica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently in [Plattner et al, J. Chem. Phys. 135, 134111 (2011)] a method was proposed to implement infinite swapping REMD in practice. Here we show that this method naturally leads to a reformulation in terms of molecular dynamics simulations over a mixture potential, which is both simple to implement in practice and provides a better, energy based understanding of how to choose the temperatures in REMD to optimize efficiency. It also opens the door to generalizations of REMD in which the swaps involve other parameters than the temperature.

cond-mat.stat-mech↗

arXiv2012

A variational perspective on cloaking by anomalous localized resonance

A body of literature has developed concerning "cloaking by anomalous localized resonance". The mathematical heart of the matter involves the behavior of a divergence-form elliptic equation in the plane, $\nabla\cdot (a(x)\nabla u(x)) = f(x)$. The complex-valued coefficient has a matrix-shell-core geometry, with real part equal to 1 in the matrix and the core, and -1 in the shell; one is interested in understanding the resonant behavior of the solution as the imaginary part of $a(x)$ decreases to zero (so that ellipticity is lost). Most analytical work in this area has relied on separation of variables, and has therefore been restricted to radial geometries. We introduce a new approach based on a pair of dual variational principles, and apply it to some non-radial examples. In our examples, as in the radial setting, the spatial location of the source $f$ plays a crucial role in determining whether or not resonance occurs.

math.AP↗

arXiv2012

The Landscape of Complex Networks

Topological landscape is introduced for networks with functions defined on the nodes. By extending the notion of gradient flows to the network setting, critical nodes of different indices are defined. This leads to a concise and hierarchical representation of the network. Persistent homology from computational topology is used to design efficient algorithms for performing such analysis. Applications to some examples in social and biological networks are demonstrated, which show that critical nodes carry important information about structures and dynamics of such networks.

stat.ME↗

arXiv2011

Optimized local basis set for Kohn-Sham density functional theory

We develop a technique for generating a set of optimized local basis functions to solve models in the Kohn-Sham density functional theory for both insulating and metallic systems. The optimized local basis functions are obtained by solving a minimization problem in an admissible set determined by a large number of primitive basis functions. Using the optimized local basis set, the electron energy and the atomic force can be calculated accurately with a small number of basis functions. The Pulay force is systematically controlled and is not required to be calculated, which makes the optimized local basis set an ideal tool for ab initio molecular dynamics and structure optimization. We also propose a preconditioned Newton-GMRES method to obtain the optimized local basis functions in practice. The optimized local basis set is able to achieve high accuracy with a small number of basis functions per atom when applied to a one dimensional model problem.

physics.comp-ph↗

arXiv2011

Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework I: Total energy calculation

Kohn-Sham density functional theory is one of the most widely used electronic structure theories. In the pseudopotential framework, uniform discretization of the Kohn-Sham Hamiltonian generally results in a large number of basis functions per atom in order to resolve the rapid oscillations of the Kohn-Sham orbitals around the nuclei. Previous attempts to reduce the number of basis functions per atom include the usage of atomic orbitals and similar objects, but the atomic orbitals generally require fine tuning in order to reach high accuracy. We present a novel discretization scheme that adaptively and systematically builds the rapid oscillations of the Kohn-Sham orbitals around the nuclei as well as environmental effects into the basis functions. The resulting basis functions are localized in the real space, and are discontinuous in the global domain. The continuous Kohn-Sham orbitals and the electron density are evaluated from the discontinuous basis functions using the discontinuous Galerkin (DG) framework. Our method is implemented in parallel and the current implementation is able to handle systems with at least thousands of atoms. Numerical examples indicate that our method can reach very high accuracy (less than 1meV) with a very small number ($4\sim 40$) of basis functions per atom.

math.NA↗

arXiv2011

Frozen Gaussian approximation for general linear strictly hyperbolic system: formulation and Eulerian methods

The frozen Gaussian approximation, proposed in [Lu and Yang, [15]], is an efficient computational tool for high frequency wave propagation. We continue in this paper the development of frozen Gaussian approximation. The frozen Gaussian approximation is extended to general linear strictly hyperbolic systems. Eulerian methods based on frozen Gaussian approximation are developed to overcome the divergence problem of Lagrangian methods. The proposed Eulerian methods can also be used for the Herman-Kluk propagator in quantum mechanics. Numerical examples verify the performance of the proposed methods.

math.NA↗

arXiv2011

Convergence of a force-based hybrid method for atomistic and continuum models in three dimension

We study a force-based hybrid method that couples atomistic models with nonlinear Cauchy-Born elasticity models. We show that the proposed scheme converges quadratically to the solution of the atomistic model, as the ratio between lattice parameter and the characteristic length scale of the deformation tends to zero. Convergence is established for general short-ranged atomistic potential and for simple lattices in three dimension. The convergence is based on consistency and stability analysis. General tools are developed in the framework of pseudo-difference operators for stability analysis in arbitrary dimension of the multiscale atomistic and continuum coupling methods.

math.NA↗

arXiv2011

Frozen Gaussian approximation for high frequency wave propagation

We propose the frozen Gaussian approximation for computation of high frequency wave propagation. This method approximates the solution to the wave equation by an integral representation. It provides a highly efficient computational tool based on the asymptotic analysis on the phase plane. Compared to geometric optics, it provides a valid solution around caustics. Compared to the Gaussian beam method, it not only overcomes the drawback of beam spreading but also improves the asymptotic accuracy. We give several numerical examples to verify that the frozen Gaussian approximation performs well in the presence of caustics and when the Gaussian beam spreads.

math.NA↗

arXiv2011

Cauchy-Born rule and spin density wave for the spin-polarized Thomas-Fermi-Dirac-von Weizsacker model

The electronic structure (electron charges and spins) of a perfect crystal under external magnetic field is analyzed using the spin-polarized Thomas-Fermi-Dirac-von Weizsacker model. An extension of the classical Cauchy-Born rule for crystal lattices is established for the electronic structure under sharp stability conditions on charge density wave and spin density wave. A Landau-Lifschitz type micromagnetic energy functional is derived.

math-ph↗