# Browsing by Subject "physics.chem-ph"

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Item Open Access A Mathematical Theory of Optimal Milestoning (with a Detour via Exact Milestoning)(2017-04-23) Lin, L; Lu, J; Vanden-Eijnden, EMilestoning is a computational procedure that reduces the dynamics of complex systems to memoryless jumps between intermediates, or milestones, and only retains some information about the probability of these jumps and the time lags between them. Here we analyze a variant of this procedure, termed optimal milestoning, which relies on a specific choice of milestones to capture exactly some kinetic features of the original dynamical system. In particular, we prove that optimal milestoning permits the exact calculation of the mean first passage times (MFPT) between any two milestones. In so doing, we also analyze another variant of the method, called exact milestoning, which also permits the exact calculation of certain MFPTs, but at the price of retaining more information about the original system's dynamics. Finally, we discuss importance sampling strategies based on optimal and exact milestoning that can be used to bypass the simulation of the original system when estimating the statistical quantities used in these methods.Item Open Access A Surface Hopping Gaussian Beam Method for High-Dimensional Transport Systems(2017-04-23) Cai, Z; Lu, JWe propose a surface hopping Gaussian beam method to numerically solve a class of high frequency linear transport systems in high spatial dimensions, based on asymptotic analysis. The stochastic surface hopping is combined with Gaussian beam method to deal with the multiple characteristic directions of the transport system in high dimensions. The Monte Carlo nature of the proposed algorithm makes it easy for parallel implementations. We validate the performance of the algorithms for applications on the quantum-classical Liouville equations.Item Open Access Accelerated sampling by infinite swapping of path integral molecular dynamics with surface hopping(2017-11-30) Lu, Jianfeng; Zhou, ZhennanTo accelerate the thermal equilibrium sampling of multi-level quantum systems, the infinite swapping limit of a recently proposed multi-level ring polymer representation is investigated. In the infinite swapping limiting, the ring polymer evolves according to an averaged Hamiltonian with respect to all possible surface index configurations of the ring polymer. A multiscale integrator for the infinite swapping limit is also proposed to enable practical sampling based on the limiting dynamics, avoiding the enumeration of all possible surface index configurations, which grows exponentially with respect to the number of beads in the ring polymer. Numerical results demonstrate the huge improvement of sampling efficiency of the infinite swapping compared with the direct simulation of path integral molecular dynamics with surface hopping.Item Open Access Frozen Gaussian approximation with surface hopping for mixed quantum-classical dynamics: A mathematical justification of fewest switches surface hopping algorithms(2017-04-23) Lu, J; Zhou, ZWe develop a surface hopping algorithm based on frozen Gaussian approximation for semiclassical matrix Schr\"odinger equations, in the spirit of Tully's fewest switches surface hopping method. The algorithm is asymptotically derived from the Schr\"odinger equation with rigorous approximation error analysis. The resulting algorithm can be viewed as a path integral stochastic representation of the semiclassical matrix Schr\"odinger equations. Our results provide mathematical understanding to and shed new light on the important class of surface hopping methods in theoretical and computational chemistry.Item Open Access Lindblad equation and its semi-classical limit of the Anderson-Holstein model(2017-04-23) Cao, Y; Lu, JFor multi-level open quantum system, the interaction between different levels could pose challenge to understand the quantum system both analytically and numerically. In this work, we study the approximation of the dynamics of the Anderson-Holstein model, as a model of multi-level open quantum system, by Redfield and Lindblad equations. Both equations have a desirable property that if the density operators for different levels is diagonal initially, they remain to be diagonal for any time. Thanks to this nice property, the semi-classical limit of both Redfield and Lindblad equations could be derived explicitly; the resulting classical master equations share similar structures of transport and hopping terms. The Redfield and Lindblad equations are also compared from the angle of time dependent perturbation theory.Item Open Access Methodological and computational aspects of parallel tempering methods in the infinite swapping limit(2018-02-14) Lu, J; Vanden-Eijnden, EA variant of the parallel tempering method is proposed in terms of a stochastic switching process for the coupled dynamics of replica configuration and temperature permutation. This formulation is shown to facilitate the analysis of the convergence properties of parallel tempering by large deviation theory, which indicates that the method should be operated in the infinite swapping limit to maximize sampling efficiency. The effective equation for the replica alone that arises in this infinite swapping limit simply involves replacing the original potential by a mixture potential. The analysis of the geometric properties of this potential offers a new perspective on the issues of how to choose of temperature ladder, and why many temperatures should typically be introduced to boost the sampling efficiency. It is also shown how to simulate the effective equation in this many temperature regime using multiscale integrators. Finally, similar ideas are also used to discuss extensions of the infinite swapping limits to the technique of simulated tempering.Item Open Access Path integral molecular dynamics with surface hopping for thermal equilibrium sampling of nonadiabatic systems(2017-04-23) Lu, Jianfeng; Zhou, ZhennanIn this work, a novel ring polymer representation for multi-level quantum system is proposed for thermal average calculations. The proposed presentation keeps the discreteness of the electronic states: besides position and momentum, each bead in the ring polymer is also characterized by a surface index indicating the electronic energy surface. A path integral molecular dynamics with surface hopping (PIMD-SH) dynamics is also developed to sample the equilibrium distribution of ring polymer configurational space. The PIMD-SH sampling method is validated theoretically and by numerical examples.Item Open Access PEXSI-$Σ$: A Green's function embedding method for Kohn-Sham density functional theory(2017-04-23) Li, Xiantao; Lin, Lin; Lu, JianfengIn this paper, we propose a new Green's function embedding method called PEXSI-$\Sigma$ for describing complex systems within the Kohn-Sham density functional theory (KSDFT) framework, after revisiting the physics literature of Green's function embedding methods from a numerical linear algebra perspective. The PEXSI-$\Sigma$ method approximates the density matrix using a set of nearly optimally chosen Green's functions evaluated at complex frequencies. For each Green's function, the complex boundary conditions are described by a self energy matrix $\Sigma$ constructed from a physical reference Green's function, which can be computed relatively easily. In the linear regime, such treatment of the boundary condition can be numerically exact. The support of the $\Sigma$ matrix is restricted to degrees of freedom near the boundary of computational domain, and can be interpreted as a frequency dependent surface potential. This makes it possible to perform KSDFT calculations with $\mathcal{O}(N^2)$ computational complexity, where $N$ is the number of atoms within the computational domain. Green's function embedding methods are also naturally compatible with atomistic Green's function methods for relaxing the atomic configuration outside the computational domain. As a proof of concept, we demonstrate the accuracy of the PEXSI-$\Sigma$ method for graphene with divacancy and dislocation dipole type of defects using the DFTB+ software package.Item Open Access Point cloud discretization of Fokker-Planck operators for committor functions(2017-04-23) Lai, R; Lu, JThe committor functions provide useful information to the understanding of transitions of a stochastic system between disjoint regions in phase space. In this work, we develop a point cloud discretization for Fokker-Planck operators to numerically calculate the committor function, with the assumption that the transition occurs on an intrinsically low-dimensional manifold in the ambient potentially high dimensional configurational space of the stochastic system. Numerical examples on model systems validate the effectiveness of the proposed method.