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Theory of simulated annealing (SA), a method for equilibrium and stability analyses for Hamiltonian systems, is reviewed. The SA explained in this review is based on a double bracket formulation that derives from Hamiltonian structure. In addition to general theoretical aspects, the explicit formulation as well as numerical applications are presented. Both finite and infinite degree-of-freedom systems are treated, in particular, the heavy top, a toy model mimicking low-beta reduced magnetohydrodynamics (MHD) and low- and high-beta reduced MHD. Numerical results successfully demonstrate the usefulness of SA for equilibrium and stability analyses. At the same time, the results raise some future issues that are discussed in the paper., Comment: submitted to Reviews of Modern Plasma Physics

A simple Hamiltonian modeling framework for general models in nonlinear optics is given. This framework is specialized to describe the Hamiltonian structure of electromagnetic phenomena in cubicly nonlinear optical media. The model has a simple Poisson bracket structure with the Hamiltonian encoding all of the nonlinear coupling of the fields. The field-independence of the Poisson bracket facilitates a straightforward Hamiltonian structure-preserving discretization using finite element exterior calculus. The generality and relative simplicity of this Hamiltonian framework makes it amenable for simulating a broad class of time-domain nonlinear optical problems. The main contribution of this work is a finite element discretization of Maxwell's equations in cubicly nonlinear media which is energy-stable and exactly conserves Gauss's laws. Moreover, this approach may be readily adapted to consider more general nonlinear media in subsequent work.

A broad class of nonlinear acoustic wave models possess a Hamiltonian structure in their dissipation-free limit and a gradient flow structure for their dissipative dynamics. This structure may be exploited to design numerical methods which preserve the Hamiltonian structure in the dissipation-free limit, and which achieve the correct dissipation rate in the spatially-discrete dissipative dynamics. Moreover, by using spatial discretizations which preserve the de Rham cohomology, the non-evolving involution constraint for the vorticity may be exactly satisfied for all of time. Numerical examples are given using a mimetic finite difference spatial discretization.

For several decades now it has been known that systems with shearless invariant tori, nontwist Hamiltonian systems, possess barriers to chaotic transport. These barriers are resilient to breakage under perturbation and therefore regions where they occur are natural places to look for barriers to transport. We describe a novel kind of effective barrier that persists after the shearless torus is broken. Because phenomena are generic, for convenience we study the Standard Nontwist Map (SNM), an area-preserving map that violates the twist condition locally in the phase space. The novel barrier occurs in nontwist systems when twin even period islands are present, which happens for a broad range of parameter values in the SNM. With a phase space composed of regular and irregular orbits, the movement of chaotic trajectories is hampered by the existence of both shearless curves, total barriers, and a network of partial barriers formed by the stable and unstable manifolds of the hyperbolic points. Being a degenerate system, the SNM has twin islands and, consequently, twin hyperbolic points. We show that the structures formed by the manifolds intrinsically depend on period parity of the twin islands. For this even scenario the novel structure, named a torus free barrier, occurs because the manifolds of different hyperbolic points form an intricate chain atop a dipole configuration and the transport of chaotic trajectories through the chain becomes a rare event. This structure impacts the emergence of transport, the escape basin for chaotic trajectories, the transport mechanism and the chaotic saddle. The case of odd periodic orbits is different: we find for this case the emergence of transport immediately after the breakup of the last invariant curve, and this leads to a scenario of higher transport, with intricate escape basin boundary and a chaotic saddle with non-uniformly distributed points.

The inclusion of spatial smoothing in finite-dimensional particle-based Hamiltonian reductions of the Vlasov equation are considered. In the context of the Vlasov-Poisson equation (and other mean-field Lie-Poisson systems), smoothing amounts to a convolutive regularization of the Hamiltonian. This regularization may be interpreted as a change of the inner product structure used to identify the dual space in the Lie-Poisson Hamiltonian formulation. In particular, the shape function used for spatial smoothing may be identified as the kernel function of a reproducing kernel Hilbert space whose inner product is used to define the Lie-Poisson Hamiltonian structure. It is likewise possible to introduce smoothing in the Vlasov-Maxwell system, but in this case the Poisson bracket must be modified rather than the Hamiltonian. The smoothing applied to the Vlasov-Maxwell system is incorporated by inserting smoothing in the map from canonical to kinematic coordinates. In the filtered system, the Lorentz force law and the current, the two terms coupling the Vlasov equation with Maxwell's equations, are spatially smoothed.

Some ideas relating to a bracket formulation for dissipative systems are considered. The formulation involves a bracket that is analogous to a generalized Poisson bracket, but possesses a symmetric component. Such a bracket is presented for the Navier-Stokes equations., Comment: re-issue in Latex of an original typed manuscript from 1984

Cahn-Hilliard-Navier-Stokes (CHNS) systems describes flows with two-phases, e.g., a liquid with bubbles. Obtaining constitutive relations for general dissipative processes for such a systems, which are thermodynamically consistent, can be a challenge. We show how the metriplectic 4-bracket formalism achieves this in a straightforward, in fact algorithmic, manner. First, from the noncanonical Hamiltonian formulation for the ideal part of a CHNS system we obtain an appropriate Casimir to serve as the entropy in the metriplectic formalism that describes the dissipation (e.g. viscosity, heat conductivity and diffusion effects). General thermodynamics with the thermodynamic conjugates of concentration and chemical potential are included. Having expressions for the Hamiltonian (energy), entropy, and Poisson bracket, we describe a procedure for obtaining a metriplectic 4-bracket that describes thermodynamically consistent dissipative effects. The 4-bracket formalism leads naturally to a general CHNS system that allows for anisotropic surface energy effects. This general CHNS system reduces to cases in the literature, to which we can compare.

The phase space of a noncanonical Hamiltonian system is partially inaccessible due to dynamical constraints (Casimir invariants) arising from the kernel of the Poisson tensor. When an ensemble of noncanonical Hamiltonian systems is allowed to interact, dissipative processes eventually break the phase space constraints, resulting in an equilibrium described by a Maxwell-Boltzmann distribution. However, the time scale required to reach Maxwell-Boltzmann statistics is often much longer than the time scale over which a given system achieves a state of thermal equilibrium. Examples include diffusion in rigid mechanical systems, as well as collisionless relaxation in magnetized plasmas and stellar systems, where the interval between binary Coulomb or gravitational collisions can be longer than the time scale over which stable structures are self-organized. Here, we focus on self-organizing phenomena over spacetime scales such that particle interactions respect the noncanonical Hamiltonian structure, but yet act to create a state of thermodynamic equilibrium. We derive a collision operator for general noncanonical Hamiltonian systems, applicable to fast, localized interactions. This collision operator depends on the interaction exchanged by colliding particles and on the Poisson tensor encoding the noncanonical phase space structure, is consistent with entropy growth and conservation of particle number and energy, preserves the interior Casimir invariants, reduces to the Landau collision operator in the limit of grazing binary Coulomb collisions in canonical phase space, and exhibits a metriplectic structure. We further show how thermodynamic equilibria depart from Maxwell-Boltzmann statistics due to the noncanonical phase space structure, and how self-organization and collisionless relaxation in magnetized plasmas and stellar systems can be described through the derived collision operator., Comment: 34 pages

In the presence of an inhomogeneous oscillatory electric field, charged particles experience a net force, averaged over the oscillatory timescale, known as the ponderomotive force. We derive a one-dimensional Hamiltonian model which self-consistently couples the electromagnetic field to a plasma which experiences the ponderomotive force. We derive a family of structure preserving discretizations of the model of varying order in space and time using conforming and broken finite element exterior calculus spectral element methods. In all variants of our discretization framework, the method is found to conserve the Casimir invariants of the continuous model to machine precision and the energy to the order of the splitting method used.

We derive axisymmetric equilibrium equations in the context of the hybrid Vlasov model with kinetic ions and massless fluid electrons, assuming isothermal electrons and deformed Maxwellian distribution functions for the kinetic ions. The equilibrium system comprises a Grad-Shafranov partial differential equation and an integral equation. These equations can be utilized to calculate the equilibrium magnetic field and ion distribution function, respectively, for given particle density or given ion and electron toroidal current density profiles. The resulting solutions describe states characterized by toroidal plasma rotation and toroidal electric current density. Additionally, due to the presence of fluid electrons, these equilibria also exhibit a poloidal current density component. This is in contrast to the fully kinetic Vlasov model, where axisymmetric Jeans equilibria can only accommodate toroidal currents and flows, given the absence of a third integral of the microscopic motion.

An inclusive framework for joined Hamiltonian and dissipative dynamical systems, which preserve energy and produce entropy, is given. The dissipative dynamics of the framework is based on the metriplectic 4-bracket, a quantity like the Poisson bracket defined on phase space functions, but unlike the Poisson bracket has four slots with symmetries and properties motivated by Riemannian curvature. Metriplectic 4-bracket dynamics is generated using two generators, the Hamiltonian and the entropy, with the entropy being a Casimir of the Hamiltonian part of the system. The formalism includes all known previous binary bracket theories for dissipation or relaxation as special cases. Rich geometrical significance of the formalism and methods for constructing metriplectic 4-brackets are explored. Many examples of both finite and infinite dimensions are given.

In this paper, we develop a one-dimensional (1-D), quasineutral, hybrid Vlasov-Maxwell equilibrium model with kinetic ions and massless fluid electrons and derive associated solutions. The model allows for an electrostatic potential that is expressed in terms of the vector potential components through the quasineutrality condition. The equilibrium states are calculated upon solving an inhomogeneous Beltrami equation that determines the magnetic field, where the inhomogeneous term is the current density of the kinetic ions and the homogeneous term represents the electron current density. We show that the corresponding 1-D system is Hamiltonian, with position playing the role of time, and its trajectories have a regular, periodic behavior for ion distribution functions that are symmetric in the two conserved particle canonical momenta. For asymmetric distribution functions, the system is nonintegrable, resulting in irregular and chaotic behavior of the fields. The electron current density can modify the magnetic field phase space structure, inducing orbit trapping and the organization of orbits into large islands of stability. Thus the electron contribution can be responsible for the emergence of localized electric field structures that induce ion trapping. We also provide a paradigm for the analytical construction of hybrid equilibria using a rotating two-dimensional harmonic oscillator Hamiltonian, enabling the calculation of analytic magnetic fields and the construction of the corresponding distribution functions in terms of Hermite polynomials.

Three geometric formulations of the Hamiltonian structure of the macroscopic Maxwell equations are given: one in terms of the double de Rham complex, one in terms of L2 duality, and one utilizing an abstract notion of duality. The final of these is used to express the geometric and Hamiltonian structure of kinetic theories in general media. The Poisson bracket so stated is explicitly metric free. Finally, as a special case, the Lorentz covariance of such kinetic theories is investigated. We obtain a Lorentz covariant kinetic theory coupled to nonlinear electrodynamics such as Born-Infeld or Euler-Heisenberg electrodynamics.

We present a generalization of Vlasov-Maxwell kinetic theory that accounts for intense electromagnetic fields. A strongly-radiating, possibly optically-thick plasma is decomposed into fragments, each comprising a charged particle together with its self-generated electromagnetic field. Assuming weak inter-fragment correlations, but strong intra-fragment correlations, a mean-field evolution equation for the single-fragment distribution functional is derived. We also identify the equation's Hamiltonian formulation. By incorporating strong correlations between a charged particle and the field it generates, the new model captures the effects of strong radiation reaction non-perturbatively. The fragment kinetic formalism offers an attractive approach to modeling exotic light-matter interactions such as nonlinear and multiple Compton scattering., Comment: 19 pages, 1 Figure

We consider a dissipative version of the standard nontwist map. Nontwist systems present a robust transport barrier, called the shearless curve, that becomes the shearless attractor when dissipation is introduced. This attractor can be regular or chaotic depending on the control parameters. Chaotic attractors can undergo sudden and qualitative changes as a parameter is varied. These changes are called crises, and at an interior crisis the attractor suddenly expands. Chaotic saddles are nonattracting chaotic sets that play a fundamental role in the dynamics of nonlinear systems, they are responsible for chaotic transients, fractal basin boundaries, chaotic scattering and they mediate interior crises. In this work we discuss the creation of chaotic saddles in a dissipative nontwist system and the interior crises they generate. We show how the presence of two saddles increase the transient times and analyze the phenomenon of crisis induced intermittency.

A starting point for deriving the Vlasov equation is the BBGKY hierarchy that describes the dynamics of coupled marginal distribution functions. With a large value of the plasma parameter one can justify eliminating 2-point correlations in terms of the 1-point function in order to derive the Vlasov Landau Lenard Balescu (VLLB) theory. Because of the high dimensionality of the problem, numerically testing the assumptions of the VLLB theory is prohibitive. In these notes we propose a physically reasonable interaction model that lowers the dimensionality of the problem and may bring such computations within reach. We introduce a 1-dimensional (1-D) electrostatic plasma model formulated in terms of the interaction of parallelly-aligned charged disks. This model combines 1-dimensional features at short distances and 3-dimensional features at large distances.

We consider a general discretization strategy for Hamiltonian field theories generated by Lie-Poisson brackets which we call dual PIC (DPIC). This method involves prescribing two different discrete representations of the dynamical variable which are constrained as a Casimir invariant of the flow to coincide with one another via an L2 projection throughout the entire simulation. This allows one to leverage the relative advantages of each discrete representation. We begin by describing DPIC as applied to a general Lie-Poisson system and then provide illustrative examples: the discretization of the two-dimensional vorticity equations and the Vlasov-Poisson equation., Comment: 21 pages

Recent works on wall-bounded flows have corroborated the coexistence of wall-attached eddies, whose statistical features are predicted through Townsend's attached eddy hypothesis (AEH), and very-large-scale motions (VLSMs), which are not encompassed in the AEH. Furthermore, it has been shown that the presence of wall-attached eddies within the logarithmic layer is linked to the appearance of an inverse-power-law region in the streamwise velocity energy spectra, upon significant separation between outer and viscous scales. In this work, a near-neutral atmospheric surface layer (ASL) is probed with a wind LiDAR to investigate the contributions to the streamwise velocity energy associated with wall-attached and VLSMs for a very-high Reynolds-number boundary layer. Energy and linear coherence spectra (LCS) of the streamwise velocity are interrogated to identify the spectral boundaries associated with eddies of different typologies and the maximum height attained by wall-attached eddies. Inspired by the AEH, an analytical model for the LCS associated with wall-attached eddies is formulated. The experimental results show that the identification of the wall-attached-eddy energy contribution through the analysis of the energy spectra leads to an underestimate of the associated spectral range, maximum height attained, and turbulence intensity. This feature is due to the overlap of the energy associated with VLSMs obscuring the inverse-power-law region. On the other hand, the Townsend-Perry constant for the turbulence intensity seems to be properly estimated through the spectral analysis. The LCS analysis estimates wall-attached eddies with a streamwise/wall-normal ratio of about 14.3 attaining a height of about 30% of the outer scale of turbulence.

Simulated annealing (SA) is a kind of relaxation method for finding equilibria of Hamiltonian systems. A set of evolution equations is solved with SA, which is derived from the original Hamiltonian system so that the energy of the system changes monotonically while preserving Casimir invariants inherent to noncanonical Hamiltonian systems. The energy extremum reached by SA is an equilibrium. Since SA searches for an energy extremum, it can also be used for stability analysis when initiated from a state where a perturbation is added to an equilibrium. The procedure of the stability analysis is explained, and some examples are shown. Because the time evolution is computationally time consuming, efficient relaxation is necessary for SA to be practically useful. An acceleration method is developed by introducing time dependence in the symmetric kernel used in the double bracket, which is part of the SA formulation described here. An explicit formulation for low-beta reduced magnetohydrodynamics (MHD) in cylindrical geometry is presented. Since SA for low-beta reduced MHD has two advection fields that relax, it is important to balance the orders of magnitude of these advection fields., Comment: This material has been accepted by Physics of Plasmas. 27 pagges, 16 figures

The deformation of a dense carpet of hair due to Stokes flow in a channel can be described by a nonlinear integro-differential equation for the shape of a single hair, which possesses several solutions for a given choice of parameters. While being posed in a previous study and bearing resemblance to the pendulum problem from mechanics, this equation has not been analytically solved until now. Despite the presence on an integral with a nonlinear functional dependence on the dependent variable, the system is integrable. We compare the analytically obtained solution to a finite-difference numerical approach, identify the physically realizable solution branch, and briefly study the solution structure through a conserved energy-like quantity. Time-dependent fluid-structure interactions are a rich and complex subject to investigate and we argue that the solution discussed herein can be used as a basis for understanding these systems.

A mimetic spectral element discretization, utilizing a novel Galerkin projection Hodge star operator, of the macroscopic Maxwell equations in Hamiltonian form is presented. The idea of splitting purely topological and metric dependent quantities is natural in the Hamiltonian modeling framework as the Poisson bracket is metric free with the Hamiltonian containing all metric information. This idea may be incorporated into the mimetic spectral element method by directly discretizing the Poincar\'e duality structure. This "split exterior calculus mimetic spectral element method" yields spatially discretized Maxwell's equations which are Hamiltonian and exactly and strongly conserve Gauss's laws. Moreover, the new discrete Hodge star operator is itself of interest as a partition of the purely topological and metric dependent portions of the Hodge star operator. As a simple test case, the numerical results of applying this method to a one-dimensional version of Maxwell's equations are given., Comment: 25 pages, 4 figures

A Hamiltonian field theory for the macroscopic Maxwell equations with fully general polarization and magnetization is stated in the language of differential forms. The precise procedure for translating the vector calculus formulation into differential forms is discussed in detail. We choose to distinguish between straight and twisted differential forms so that all integrals be taken over densities (i.e. twisted top forms). This ensures that the duality pairings, which are stated as integrals over densities, are orientation independent. The relationship between functional differentiation with respect to vector fields and with respect to differential forms is established using the chain rule. The theory is developed such that the Poisson bracket is metric and orientation independent with all metric dependence contained in the Hamiltonian. As is typically seen in the exterior calculus formulation of Maxwell's equations, the Hodge star operator plays a key role in modeling the constitutive relations. As a demonstration of the kind of constitutive models this theory accommodates, the paper concludes with several examples., Comment: 24 pages

We present two generalized hybrid kinetic-Hall magnetohydrodynamics (MHD) models describing the interaction of a two-fluid bulk plasma, which consists of thermal ions and electrons, with energetic, suprathermal ion populations described by Vlasov dynamics. The dynamics of the thermal components are governed by standard fluid equations in the Hall MHD limit with the electron momentum equation providing an Ohm's law with Hall and electron pressure terms involving a gyrotropic electron pressure tensor. The coupling of the bulk, low-energy plasma with the energetic particle dynamics is accomplished through the current density (current coupling scheme; CCS) and the ion pressure tensor appearing in the momentum equation (pressure coupling scheme; PCS) in the first and the second model, respectively. The CCS is a generalization of two well-known models, because in the limit of vanishing energetic and thermal ion densities we recover the standard Hall MHD and the hybrid kinetic-ions/fluid-electron model, respectively. This provides us with the capability to study in a continuous manner the global impact of the energetic particles in a regime extending from vanishing to dominant energetic particle densities. The noncanonical Hamiltonian structures of the CCS and PCS, which can be exploited to study equilibrium and stability properties through the energy-Casimir variational principle, are identified. As a first application here, we derive a generalized Hall MHD Grad--Shafranov--Bernoulli system for translationally symmetric equilibria with anisotropic electron pressure and kinetic effects owing to the presence of energetic particles using the PCS.

We propose a systematic procedure called the Clebsch canonization for obtaining a canonical Hamiltonian system that is related to a given Lie-Poisson equation via a momentum map. We describe both coordinate and geometric versions of the procedure, the latter apparently for the first time. We also find another momentum map so that the pair of momentum maps constitute a dual pair under a certain condition. The dual pair gives a concrete realization of what is commonly referred to as collectivization of Lie-Poisson systems. It also implies that solving the canonized system by symplectic Runge-Kutta methods yields so-called collective Lie-Poisson integrators that preserve the coadjoint orbits and hence the Casimirs exactly. We give a couple of examples, including the Kida vortex and the heavy top on a movable base with controls, which are Lie-Poisson systems on $\mathfrak{so}(2,1)^{*}$ and $(\mathfrak{se}(3) \ltimes \mathbb{R}^{3})^{*}$, respectively., Comment: 24 pages, 6 figures

Helicity, a topological degree that measures the winding and linking of vortex lines, is preserved by ideal (barotropic) fluid dynamics. In the context of the Hamiltonian description, the helicity is a Casimir invariant characterizing a foliation of the associated Poisson manifold. Casimir invariants are special invariants that depend on the Poisson bracket, not on the particular choice of the Hamiltonian. The total mass (or particle number) is another Casimir invariant, whose invariance guarantees the mass (particle) conservation (independent of any specific choice of the Hamiltonian). In a kinetic description (e.g. that of the Vlasov equation), the helicity is no longer an invariant (although the total mass remains a Casimir of the Vlasov's Poisson algebra). The implication is that some "kinetic effect" can violate the constancy of the helicity. To elucidate how the helicity constraint emerges or submerges, we examine the fluid reduction of the Vlasov system; the fluid (macroscopic) system is a "sub-algebra" of the kinetic (microscopic) Vlasov system. In the Vlasov system, the helicity can be conserved, if a special helicity symmetry condition holds. To put it another way, breaking helicity symmetry induces a change in the helicity. We delineate the geometrical meaning of helicity symmetry, and show that, for a special class of flows (so-called epi-2 dimensional flows), the helicity symmetry is written as $\partial_\gamma =0$ for a coordinate $\gamma$ of the configuration space.

Chaotic transport is a subject of paramount importance in a variety of problems in plasma physics, specially those related to anomalous transport and turbulence. On the other hand, a great deal of information on chaotic transport can be obtained from simple dynamical systems like two-dimensional area-preserving (symplectic) maps, where powerful mathematical results like KAM theory are available. In this work we review recent works on transport barriers in area-preserving maps, focusing on systems which do not obey the so-called twist property. For such systems KAM theory no longer holds everywhere and novel dynamical features show up as non-resistive reconnection, shearless curves and shearless bifurcations. After presenting some general features using a standard nontwist mapping, we consider magnetic field line maps for magnetically confined plasmas in tokamaks.

The recently proposed low degree-of-freedom model of Moffat and Kimura [1,2] for describing the approach to finite-time singularity of the incompressible Euler fluid equations is investigated. The model assumes an initial finite-energy configuration of two vortex rings placed symmetrically on two tilted planes. The Hamiltonian structure of the inviscid limit of the model is obtained. The associated noncanonical Poisson bracket [3] and two invariants, one that serves as the Hamiltonian and the other a Casimir invariant, are discovered. It is shown that the system is integrable with a solution that lies on the intersection for the two invariants, just as for the free rigid body of mechanics whose solution lies on the intersection of the kinetic energy and angular momentum surfaces. Also, a direct quadrature is given and used to demonstrate the Leray form for finite-time singularity in the model. To the extent the Moffat and Kimura model accurately represents Euler's ideal fluid equations of motion, we have shown the existence of finite-time singularity.

Exoplanet systems with multiple planets in mean motion resonances have often been hailed as a signpost of disk driven migration. Resonant chains like Kepler-223 and Kepler-80 consist of a trio of planets with the three-body resonant angle librating and/or with a two-body resonant angle librating for each pair. Here we investigate whether close-in super-Earths and mini-Neptunes forming in situ can lock into resonant chains due to dissipation from a depleted gas disk. We simulate the giant impact phase of planet formation, including eccentricity damping from a gaseous disk, followed by subsequent dynamical evolution over tens of millions of years. In a fraction of simulated systems, we find that planets naturally lock into resonant chains. These planets achieve a chain of near-integer period ratios during the gas disk stage, experience eccentricity damping that captures them into resonance, stay in resonance as the gas disk dissipates, and avoid subsequent giant impacts, eccentricity excitation, and chaotic diffusion that would dislodge the planets from resonance. Disk conditions that enable planets to complete their formation during the gas disk stage enable those planets to achieve tight period ratios <= 2 and, if they happen to be near integer period ratios, lock into resonance. Using the weighting of different disk conditions deduced by MacDonald et al. (2020) and forward modeling Kepler selection effects, we find that our simulations of in situ formation via oligarchic growth lead to a rate of observable trios with integer period ratios and librating resonant angles comparable to observed Kepler systems., Comment: 13 pages, 3 tables, 9 figures, accepted for publication in the Astrophysical Journal on October 5, 2020