Comparison of modern Langevin integrators for simulations of coarse-grained polymer melts

For a wide range of phenomena, current computational ability does not always allow for atomistic simulations of high-dimensional molecular systems to reach time scales of interest. Coarse-graining (CG) is an established approach to alleviate the impact of computational limits while retaining the same algorithms used in atomistic simulations. It is important to understand how algorithms such as Langevin integrators perform on non-trivial CG molecular systems, and in particular how large of an integration time step can be used without introducing unacceptable amounts of error into averaged quantities of interest. To investigate this, we examined three different Langevin integrators on a CG polymer melt: the recently developed BAOAB method by Leimkuhler and Matthews [J. Chem. Phys. 138 (17), 05B601_1 (2013)], the Grønbech-Jensen and Farago method [Mol. Phys. 111 (8), 983-991 (2013)], or G-JF, and the frequently used Brünger–Brooks–Karplus integrator [Chem. Phys. Lett. 105 (5), 495-500 (1984)], known as BBK. We compute and analyse key statistical properties for each. Our results indicate that the integrators perform similarly for a small friction parameter; however outside this regime, the use of large integration steps produces significant deviations from the predicted diffusivity and steady-state distributions for all methods examined with the exception of G-JF.     

Zur Theorie der Teilchenbewegung in zeitabhängigen elektromagnetischen Feldern

The Langevin equation – i.e. the equation of motion for a charged particle including a collision term proportional to the particle velocity – is solved for arbitrary time-dependent electric and magnetic fields by a new general method. Instead of the usual ansatz: particle velocity = cyclotron velocity + drift velocity the method given makes the ansatz: particle velocity = tensor = cyclotron velocity. The unknown tensor obeys a simple differential equation of the first order which can be generally solved at once. This method is a modification of the variation of constants method for inhomogeneous differential equations. The electromagnetic fields considered must be spatially homogeneous; for (weakly) inhomogeneous fields an iteration procedure of Pytte (1962) may be applied. Some examples are discussed shortly. The Langevin equation treated is completely equivalent to the equation of motion in a magnetohydrodynamic one-fluid theory.     

Foundations of quantum mechanics: The Langevin equations for QM

Stochastic derivations of the Schrödinger equation are always developed on very general and abstract grounds. Thus, one is never enlightened which specific stochastic process corresponds to some particular quantum mechanical system, that is, given the physical system—expressed by the potential function, which fluctuation structure one should impose on a Langevin equation in order to arrive at results identical to those comming from the solutions of the Schrödinger equation. We show, from first principles, how to write the Langevin stochastic equations for any particular quantum system. We also show the relation between these Langevin equations and those proposed by Bohm in 1952. We present numerical simulations of the Langevin equations for some quantum mechanical problems and compare them with the usual analytic solutions to show the adequacy of our approach. The model also allows us to address important topics on the interpretation of quantum mechanics.     

辛算法在Ba+HF反应准经典轨线计算中的应用

将辛算法应用于准经典轨线理论,模拟了Ba HF反应在扩展的London-Eyring-Polanyi-Sato (LEPS)势能面上的动力学行为.比较哈密顿体系在RK4-AMH4积分,四阶辛积分,六阶辛积分下的总能量守恒情况,结果表明六阶辛算法能最好地保持反应体系的能量守恒,且用时间最短,能够很好地节省计算资源.得到的六阶辛算法下生成物BaF的振动分布高于以前计算的结果,进一步证明六阶辛算法能最好保持能量守恒的特点.     

一维Gross-Pitaevskii方程的高阶紧致分裂步多辛格式

首先把一维Gross-Pitaevskli方程改写成多辛Hamiltonian系统的形式,把形式通过分裂变成2个子哈密尔顿系统.然后,对这些子系统用辛或者多辛算法进行离散.通过对子系统数值算法的不同组合方式,得到不同精度的具有多辛算法特征数值格式.这些格式不仅具有多辛格式、分裂步方法和高阶紧致格式的特征,而且是质量守恒的.数值实验验证了新格式的数值行为.     

Asymptotic solution of the Wang-Uhlenbeck recurrence time problem

A Langevin particle is initiated at the origin with positive velocity. Its trajectory is terminated when it returns to the origin. In 1945, Wang and Uhlenbeck posed the problem of finding the joint probability density function (PDF) of the recurrence time and velocity, naming it "the recurrence time problem". We show that the short-time asymptotics of the recurrence PDF is similar to that of the integrated Brownian motion, solved in 1963 by McKean. We recover the long-time t(-3/2) decay of the first arrival PDF of diffusion by solving asymptotically an appropriate variant of McKean's integral equation.     

Trajectory approach to the Schrödinger–Langevin equation with linear dissipation for ground states

The Schrödinger–Langevin equation with linear dissipation is integrated by propagating an ensemble of Bohmian trajectories for the ground state of quantum systems. Substituting the wave function expressed in terms of the complex action into the Schrödinger–Langevin equation yields the complex quantum Hamilton–Jacobi equation with linear dissipation. We transform this equation into the arbitrary Lagrangian–Eulerian version with the grid velocity matching the flow velocity of the probability fluid. The resulting equation is simultaneously integrated with the trajectory guidance equation. Then, the computational method is applied to the harmonic oscillator, the double well potential, and the ground vibrational state of methyl iodide. The excellent agreement between the computational and the exact results for the ground state energies and wave functions shows that this study provides a synthetic trajectory approach to the ground state of quantum systems.     

An impulse integrator for Langevin dynamics

The best simple method for Newtonian molecular dynamics is indisputably the leapfrog Stormer-Verlet method. The appropriate generalization to simple Langevin dynamics is unclear. An analysis is presented comparing an ‘impulse method’ (kick; fluctuate; kick), the 1982 method of van Gunsteren and Berendsen, and the Brünger-Brooks-Karplus (BBK) method. It is shown how the impulse method and the van Gunsteren-Berendsen methods can be implemented as efficiently as the BBK method. Other considerations suggest that the impulse method is the best basic method for simple Langevin dynamics, with the van Gunsteren-Berendsen method a close contender.     

On the maximal noise for stochastic and QCD travelling waves

Using the relation of a set of nonlinear Langevin equations to reaction–diffusion processes, we note the existence of a maximal strength of the noise for the stochastic travelling wave solutions of these equations. Its determination is obtained using the field-theoretical analysis of branching-annihilation random walks near the directed percolation transition. We study its consequence for the stochastic Fisher–Kolmogorov–Petrovsky–Piscounov equation. For the related Langevin equation modeling the quantum chromodynamic nonlinear evolution of gluon density with rapidity, the physical maximal-noise limit may appear before the directed percolation transition, due to a shift in the travelling-wave speed. In this regime, an exact solution is known from a coalescence process. Universality and other open problems and applications are discussed in the outlook.     

Perspective on the geometric conservation law and finite element methods for ALE simulations of incompressible flow

This paper takes a fresh look at the geometric conservation law (GCL) from the perspective of the finite element method (FEM) for incompressible flows. The GCL arises naturally in the context of Arbitrary Lagrangian Eulerian (ALE) formulations for solving problems on deforming domains. GCL compliance is traditionally interpreted as a consistency criterion for applying an unsteady flow solution algorithm to simulate exactly a uniform flow on a deforming domain. We introduce an additional requirement: the time integrator must maintain its fixed mesh accuracy when applied to deforming meshes. A review of the literature shows that while many authors use an ALE FEM, few of them discuss the GCL issues. We show how a fixed mesh unsteady FEM using high order time integrator (up to fifth order in time) can be transposed to solve problems on deforming meshes and preserve its fixed mesh high order temporal accuracy. An appropriate construction of the divergence of the mesh velocity guarantees GCL compliance while a separate construction of the mesh velocity itself allows the time-integrator to deliver its fixed mesh high order temporal accuracy on deforming domains. Analytical error analysis of problems with closed form solutions provides insight on the behavior of the time integrators. It also explains why high order temporal accuracy is achieved with a conservative formulation of the incompressible Navier–Stokes equations, while only first order time accuracy is observed with the non-conservative formulation and all time-integrators investigated here. We present thorough time-step and grid refinement studies for simple problems with closed form solutions and for a manufactured solution with a non-trivial flow on a deforming mesh. In all cases studied, the proposed reconstructions of the mesh velocity and its divergence for the conservative formulation lead to optimal time accuracy on deforming grids.     

Numerical integration of the Ostrovsky equation based on its geometric structures

We consider structure preserving numerical schemes for the Ostrovsky equation, which describes gravity waves under the influence of Coriolis force. This equation has two associated invariants: an energy function and the L² norm. It is widely accepted that structure preserving methods such as invariants-preserving and multi-symplectic integrators generally yield qualitatively better numerical results. In this paper we propose five geometric integrators for this equation: energy-preserving and norm-preserving finite difference and Galerkin schemes, and a multi-symplectic integrator based on a newly found multi-symplectic formulation. A numerical comparison of these schemes is provided, which indicates that the energy-preserving finite difference schemes are more advantageous than the other schemes.     

Energy Conserving, Liouville, and Symplectic Integrators

In this paper, we construct an integrator that converves volume in phase space. We compare the results obtained using this method and a symplectic integrator. The results of our experiments do not reveal any superiority of the symplectic over strictly volume-preserving integrators. We also investigate the effect of numerically conserving energy in a numerical process by rescaling velocities to keep energy constant at every step. Our results for Henon-Heiles problem show that keeping energy constant in this way destroys ergodicity and forces the solution onto a periodic orbit.     

Study on an extended Boussinesq equation

An extended Boussinesq equation that models weakly nonlinear and weakly dispersive waves on a uniform layer of water is studied in this paper. The results show that the equation is not Painlev\'e-integrable in general. Some particular exact travelling wave solutions are obtained by using a function expansion method. An approximate solitary wave solution with physical significance is obtained by using a perturbation method. We find that the extended Boussinesq equation with a depth parameter of $1/\sqrt 2$ is able to match the Laitone's (1960) second order solitary wave solution of the Euler equations.     

Effective potential for complex Langevin equations

We construct an effective potential for the complex Langevin equation on a lattice. We show that the minimum of this effective potential gives the space–time and Langevin time average of the complex Langevin field. The loop expansion of the effective potential is matched with the derivative expansion of the associated Schwinger–Dyson equation to predict the stationary distribution to which the complex Langevin equation converges.     

Multi-symplectic Birkhoffian structure for PDEs with dissipation terms

A generalization of the multi-symplectic form for Hamiltonian systems to self-adjoint systems with dissipation terms is studied. These systems can be expressed as multi-symplectic Birkhoffian equations, which leads to a natural definition of Birkhoffian multi-symplectic structure. The concept of Birkhoffian multi-symplectic integrators for Birkhoffian PDEs is investigated. The Birkhoffian multi-symplectic structure is constructed by the continuous variational principle, and the Birkhoffian multi-symplectic integrator by the discrete variational principle. As an example, two Birkhoffian multi-symplectic integrators for the equation describing a linear damped string are given.     

On the derivation of the generalized Langevin equation for interacting Brownian particles

The main result of this paper is a derivation of a generalized nonlinear Langevin equation (GLE) forn interacting particles in a bath. A consequence of the derivation is that the exact form of the (generalized) fluctuation-dissipation theorem is obtained. We discuss also the relation between the memory kernel of the GLE and some corresponding correlation functions which can be easily obtained in a molecular dynamics computer experiment. In the same spirit it is shown that the approach applies to a Brownian particle subjected to a stationary external field. The technique presented in a previous paper to simulate generalized Brownian dynamics can be easily extended to the present case. Our derivation intends to clarify the uses and (possibly) abuses of the Langevin equation in Brownian dynamics studies.     

A discrete action principle for electrodynamics and the construction of explicit symplectic integrators for linear,non-dispersive media

In this work, we derive a discrete action principle for electrodynamics that can be used to construct explicit symplectic integrators for Maxwell’s equations. Different integrators are constructed depending on the choice of discrete Lagrangian used to approximate the action. By combining discrete Lagrangians in an explicit symplectic partitioned Runge–Kutta method, an integrator capable of achieving any order of accuracy is obtained. Using the von Neumann stability analysis, we show that the integrators greatly increase the numerical stability and reduce the numerical dispersion compared to other methods. For practical purposes, we demonstrate how to implement the integrators using many features of the finite-difference time-domain method. However, our approach is also applicable to other spatial discretizations, such as those used in finite element methods. Using this implementation, numerical examples are presented that demonstrate the ability of the integrators to efficiently reduce and maintain a minimal amount of numerical dispersion, particularly when the time-step is less than the stability limit. The integrators are therefore advantageous for modeling large, inhomogeneous computational domains.     

Traffic Flow Models Considering an Internal Degree of Freedom

We solve numerically the integrodifferential equation for the equilibrium case of Paveri–Fontana's Boltzmann-like traffic equation. Beside space and actual velocity, Paveri–Fontana used an additional phase space variable, the desired velocity, to distinguish between the various driver characters. We refine his kinetic equation by introducing a modified cross section in order to incorporate finite vehicle length. We then calculate from the equilibrium solution the mean-velocity–density relation and investigate its dependence on the imposed desired velocity distribution. A further modification is made by modeling the interaction as an imperfect showing-down process. We find that the velocity cumulants of the stationary homogeneous solution essentially only depend on the first two cumulants, but not on the exact shape of the imposed desired velocity distribution. The equilibrium solution can therefore be approximated by a bivariate Gaussian distribution which is in agreement with empirical velocity distributions. From the improved kinetic equation we then derive a macroscopic model by neglecting third and higher order cumulants. The equilibrium solution of the macroscopic model is compared with the cumulants of the kinetic equilibrium solution and shows good agreement, thus justifying the closure assumption.