Generating Generalized Distributions from Dynamical Simulation

We present a general molecular-dynamics simulation scheme, based on the Nose' thermostat, for sampling according to arbitrary phase space distributions. We formulate numerical methods based on both Nose'-Hoover and Nose'-Poincare' thermostats for two specific classes of distributions; namely, those that are functions of the system Hamiltonian and those for which position and momentum are statistically independent. As an example, we propose a generalized variable temperature distribution that designed to accelerate sampling in molecular systems.Comment: 10 pages, 3 figure

A molecular-dynamics algorithm for mixed hard-core/continuous potentials

We present a new molecular-dynamics algorithm for integrating the equations of motion for a system of particles interacting with mixed continuous/impulsive forces. This method, which we call Impulsive Verlet, is constructed using operator splitting techniques similar to those that have been used successfully to generate a variety molecular-dynamics integrators. In numerical experiments, the Impulsive Verlet method is shown to be superior to previous methods with respect to stability and energy conservation in long simulations.Comment: 18 pages, 6 postscript figures, uses rotate.st

Active swarms on a sphere

Here we show that coupling to curvature has profound effects on collective motion in active systems, leading to patterns not observed in flat space. Biological examples of such active motion in curved environments are numerous: curvature and tissue folding are crucial during gastrulation, epithelial and endothelial cells move on constantly growing, curved crypts and vili in the gut, and the mammalian corneal epithelium grows in a steady-state vortex pattern. On the physics side, droplets coated with actively driven microtubule bundles show active nematic patterns. We study a model of self-propelled particles with polar alignment on a sphere. Hallmarks of these motion patterns are a polar vortex and a circulating band arising due to the incompatibility between spherical topology and uniform motion - a consequence of the hairy ball theorem. We present analytical results showing that frustration due to curvature leads to stable elastic distortions storing energy in the band.Comment: 5 pages, 4 figures plus Supporting Informatio

Optimal Constraint Projection for Hyperbolic Evolution Systems

Techniques are developed for projecting the solutions of symmetric hyperbolic evolution systems onto the constraint submanifold (the constraint-satisfying subset of the dynamical field space). These optimal projections map a field configuration to the ``nearest'' configuration in the constraint submanifold, where distances between configurations are measured with the natural metric on the space of dynamical fields. The construction and use of these projections is illustrated for a new representation of the scalar field equation that exhibits both bulk and boundary generated constraint violations. Numerical simulations on a black-hole background show that bulk constraint violations cannot be controlled by constraint-preserving boundary conditions alone, but are effectively controlled by constraint projection. Simulations also show that constraint violations entering through boundaries cannot be controlled by constraint projection alone, but are controlled by constraint-preserving boundary conditions. Numerical solutions to the pathological scalar field system are shown to converge to solutions of a standard representation of the scalar field equation when constraint projection and constraint-preserving boundary conditions are used together.Comment: final version with minor changes; 16 pages, 14 figure

Higher-order splitting algorithms for solving the nonlinear Schr\"odinger equation and their instabilities

Since the kinetic and the potential energy term of the real time nonlinear Schr\"odinger equation can each be solved exactly, the entire equation can be solved to any order via splitting algorithms. We verified the fourth-order convergence of some well known algorithms by solving the Gross-Pitaevskii equation numerically. All such splitting algorithms suffer from a latent numerical instability even when the total energy is very well conserved. A detail error analysis reveals that the noise, or elementary excitations of the nonlinear Schr\"odinger, obeys the Bogoliubov spectrum and the instability is due to the exponential growth of high wave number noises caused by the splitting process. For a continuum wave function, this instability is unavoidable no matter how small the time step. For a discrete wave function, the instability can be avoided only for \dt k_{max}^2{<\atop\sim}2 \pi, where $k_{max}=\pi/\Delta x$.Comment: 10 pages, 8 figures, submitted to Phys. Rev.

Geometric Generalisations of SHAKE and RATTLE

A geometric analysis of the Shake and Rattle methods for constrained Hamiltonian problems is carried out. The study reveals the underlying differential geometric foundation of the two methods, and the exact relation between them. In addition, the geometric insight naturally generalises Shake and Rattle to allow for a strictly larger class of constrained Hamiltonian systems than in the classical setting. In order for Shake and Rattle to be well defined, two basic assumptions are needed. First, a nondegeneracy assumption, which is a condition on the Hamiltonian, i.e., on the dynamics of the system. Second, a coisotropy assumption, which is a condition on the geometry of the constrained phase space. Non-trivial examples of systems fulfilling, and failing to fulfill, these assumptions are given

Bulgac-Kusnezov-Nos\'e-Hoover thermostats

In this paper we formulate Bulgac-Kusnezov constant temperature dynamics in phase space by means of non-Hamiltonian brackets. Two generalized versions of the dynamics are similarly defined: one where the Bulgac-Kusnezov demons are globally controlled by means of a single additional Nos\'e variable, and another where each demon is coupled to an independent Nos\'e-Hoover thermostat. Numerically stable and efficient measure-preserving time-reversible algorithms are derived in a systematic way for each case. The chaotic properties of the different phase space flows are numerically illustrated through the paradigmatic example of the one-dimensional harmonic oscillator. It is found that, while the simple Bulgac-Kusnezov thermostat is apparently not ergodic, both of the Nos\'e-Hoover controlled dynamics sample the canonical distribution correctly