Prioritized Garbage Collection: Explicit GC Support for Software Caches

Programmers routinely trade space for time to increase performance, often in the form of caching or memoization. In managed languages like Java or JavaScript, however, this space-time tradeoff is complex. Using more space translates into higher garbage collection costs, especially at the limit of available memory. Existing runtime systems provide limited support for space-sensitive algorithms, forcing programmers into difficult and often brittle choices about provisioning. This paper presents prioritized garbage collection, a cooperative programming language and runtime solution to this problem. Prioritized GC provides an interface similar to soft references, called priority references, which identify objects that the collector can reclaim eagerly if necessary. The key difference is an API for defining the policy that governs when priority references are cleared and in what order. Application code specifies a priority value for each reference and a target memory bound. The collector reclaims references, lowest priority first, until the total memory footprint of the cache fits within the bound. We use this API to implement a space-aware least-recently-used (LRU) cache, called a Sache, that is a drop-in replacement for existing caches, such as Google's Guava library. The garbage collector automatically grows and shrinks the Sache in response to available memory and workload with minimal provisioning information from the programmer. Using a Sache, it is almost impossible for an application to experience a memory leak, memory pressure, or an out-of-memory crash caused by software caching.Comment: to appear in OOPSLA 201

Phase field modeling of electrochemistry II: Kinetics

The kinetic behavior of a phase field model of electrochemistry is explored for advancing (electrodeposition) and receding (electrodissolution) conditions in one dimension. We described the equilibrium behavior of this model in [J. E. Guyer, W. J. Boettinger, J.A. Warren, and G. B. McFadden, ``Phase field modeling of electrochemistry I: Equilibrium'', cond-mat/0308173]. We examine the relationship between the parameters of the phase field method and the more typical parameters of electrochemistry. We demonstrate ohmic conduction in the electrode and ionic conduction in the electrolyte. We find that, despite making simple, linear dynamic postulates, we obtain the nonlinear relationship between current and overpotential predicted by the classical ``Butler-Volmer'' equation and observed in electrochemical experiments. The charge distribution in the interfacial double layer changes with the passage of current and, at sufficiently high currents, we find that the diffusion limited deposition of a more noble cation leads to alloy deposition with less noble species.Comment: v3: To be published in Phys. Rev. E v2: Attempt to work around turnpage bug. Replaced color Fig. 4a with grayscale 13 pages, 7 figures in 10 files, REVTeX 4, SIunits.sty, follows cond-mat/030817

A Model for Solid 3^3He: II

We propose a simple Ginzburg-Landau free energy to describe the magnetic phase transition in solid $^3$He. The free energy is analyzed with due consideration of the hard first order transitions at low magnetic fields. The resulting phase diagram contains all of the important features of the experimentally observed ph ase diagram. The free energy also yields a critical field at which the transition from the disordered state to the high field state changes from a first order to a second order one.Comment: This paper has been accepted for publication in Journal of Low Temperature Physics. Use regular Tex, with the D. Eardley version of Macros called jnl.tex. 10 pages, 4 figs available from [email protected]

VPLanet: The Virtual Planet Simulator

We describe a software package called VPLanet that simulates fundamental aspects of planetary system evolution over Gyr timescales, with a focus on investigating habitable worlds. In this initial release, eleven physics modules are included that model internal, atmospheric, rotational, orbital, stellar, and galactic processes. Many of these modules can be coupled simultaneously to simulate the evolution of terrestrial planets, gaseous planets, and stars. The code is validated by reproducing a selection of observations and past results. VPLanet is written in C and designed so that the user can choose the physics modules to apply to an individual object at runtime without recompiling, i.e., a single executable can simulate the diverse phenomena that are relevant to a wide range of planetary and stellar systems. This feature is enabled by matrices and vectors of function pointers that are dynamically allocated and populated based on user input. The speed and modularity of VPLanet enables large parameter sweeps and the versatility to add/remove physical phenomena to assess their importance. VPLanet is publicly available from a repository that contains extensive documentation, numerous examples, Python scripts for plotting and data management, and infrastructure for community input and future development.Comment: 75 pages, 34 figures, 10 tables, accepted to the Proceedings of the Astronomical Society of the Pacific. Source code, documentation, and examples available at https://github.com/VirtualPlanetaryLaboratory/vplane

Phase field modeling of electrochemistry I: Equilibrium

A diffuse interface (phase field) model for an electrochemical system is developed. We describe the minimal set of components needed to model an electrochemical interface and present a variational derivation of the governing equations. With a simple set of assumptions: mass and volume constraints, Poisson's equation, ideal solution thermodynamics in the bulk, and a simple description of the competing energies in the interface, the model captures the charge separation associated with the equilibrium double layer at the electrochemical interface. The decay of the electrostatic potential in the electrolyte agrees with the classical Gouy-Chapman and Debye-H\"uckel theories. We calculate the surface energy, surface charge, and differential capacitance as functions of potential and find qualitative agreement between the model and existing theories and experiments. In particular, the differential capacitance curves exhibit complex shapes with multiple extrema, as exhibited in many electrochemical systems.Comment: v3: To be published in Phys. Rev. E v2: Added link to cond-mat/0308179 in References 13 pages, 6 figures in 15 files, REVTeX 4, SIUnits.sty. Precedes cond-mat/030817

Epitaxial growth in dislocation-free strained alloy films: Morphological and compositional instabilities

The mechanisms of stability or instability in the strained alloy film growth are of intense current interest to both theorists and experimentalists. We consider dislocation-free, coherent, growing alloy films which could exhibit a morphological instability without nucleation. We investigate such strained films by developing a nonequilibrium, continuum model and by performing a linear stability analysis. The couplings of film-substrate misfit strain, compositional stress, deposition rate, and growth temperature determine the stability of film morphology as well as the surface spinodal decomposition. We consider some realistic factors of epitaxial growth, in particular the composition dependence of elastic moduli and the coupling between top surface and underlying bulk of the film. The interplay of these factors leads to new stability results. In addition to the stability diagrams both above and below the coherent spinodal temperature, we also calculate the kinetic critical thickness for the onset of instability as well as its scaling behavior with respect to misfit strain and deposition rate. We apply our results to some real growth systems and discuss the implications related to some recent experimental observations.Comment: 26 pages, 13 eps figure

Order of the phase transition in models of DNA thermal denaturation

We examine the behavior of a model which describes the melting of double-stranded DNA chains. The model, with displacement-dependent stiffness constants and a Morse on-site potential, is analyzed numerically; depending on the stiffness parameter, it is shown to have either (i) a second-order transition with "nu_perpendicular" = - beta = 1, "nu_parallel" = gamma/2 = 2 (characteristic of short range attractive part of the Morse potential) or (ii) a first-order transition with finite melting entropy, discontinuous fraction of bound pairs, divergent correlation lengths, and critical exponents "nu_perpendicular" = - beta = 1/2, "nu_parallel" = gamma/2 = 1.Comment: 4 pages of Latex, including 4 Postscript figures. To be published in Phys. Rev. Let