David Kofke - Academia.edu (original) (raw)

Papers by David Kofke

The Journal of chemical physics, Jan 21, 2015

Cluster integrals are evaluated for the coefficients of the combined temperature- and density-exp... more Cluster integrals are evaluated for the coefficients of the combined temperature- and density-expansion of pressure: Z = 1 + B2(β) η + B3(β) η(2) + B4(β) η(3) + ⋯, where Z is the compressibility factor, η is the packing fraction, and the Bi(β) coefficients are expanded as a power series in reciprocal temperature, β, about β = 0. The methodology is demonstrated for square-well spheres with λ = [1.2-2.0], where λ is the well diameter relative to the hard core. For this model, the Bi coefficients can be expressed in closed form as a function of β, and we develop appropriate expressions for i = 2-6; these expressions facilitate derivation of the coefficients of the β series. Expanding the Bi coefficients in β provides a correspondence between the power series in density (typically called the virial series) and the power series in β (typically called thermodynamic perturbation theory, TPT). The coefficients of the β series result in expressions for the Helmholtz energy that can be compar...

Journal of Nanomechanics and Micromechanics, 2011

Proceedings of the 2005 OOPSLA workshop on Eclipse technology eXchange - eclipse '05, 2005

Etomica is an extensible framework for conducting molecular simulations, and it comprises an API ... more Etomica is an extensible framework for conducting molecular simulations, and it comprises an API and a graphical IDE based on the Eclipse framework. It is written almost entirely in Java, and presently comprises about 1200 classes. In this paper we describe the general structure of the Etomica API, and discuss how we have integrated it into the Eclipse framework. Topics discussed include the design of the simulation framework and the handling of OpenGL graphics that permit real-time visualization of the simulations.

International journal of molecular sciences, 2009

Volumetric strain can be divided into two parts: strain due to bond distance change and strain du... more Volumetric strain can be divided into two parts: strain due to bond distance change and strain due to vacancy sources and sinks. In this paper, efforts are focused on studying the atomic lattice strain due to a vacancy in an FCC metal lattice with molecular dynamics simulation (MDS). The result has been compared with that from a continuum mechanics method. It is shown that using a continuum mechanics approach yields constitutive results similar to the ones obtained based purely on molecular dynamics considerations.

Journal of computational chemistry, Jan 30, 2015

We describe the design of an object-oriented library of software components that are suitable for... more We describe the design of an object-oriented library of software components that are suitable for constructing simulations of systems of interacting particles. The emphasis of the discussion is on the general design of the components and how they interact, and less on details of the programming interface or its implementation. Example code is provided as an aid to understanding object-oriented programming structures and to demonstrate how the framework is applied. © 2015 Wiley Periodicals, Inc.

13th InterSociety Conference on Thermal and Thermomechanical Phenomena in Electronic Systems, 2012

Journal of Chemical Theory and Computation, 2014

We propose a measure that quantifies the effort needed to compute a given stochastic average, con... more We propose a measure that quantifies the effort needed to compute a given stochastic average, considered in the context of molecular modeling. This "difficulty index" is defined in terms of CPU time, observed uncertainty, and a characteristic scale for the quantity being computed. This metric provides a focus for optimization and comparison of methods and, if applied broadly, could aid understanding of the impact of models, algorithms, implementations, and platforms on performance of molecular modeling techniques.

Physical Review E, 2014

Virial coefficients B(n) of three-dimensional hard spheres are reported for n=5 to 11, with preci... more Virial coefficients B(n) of three-dimensional hard spheres are reported for n=5 to 11, with precision exceeding that presently available in the literature. Calculations are performed using the recursive method due to Wheatley, and a binning approach is proposed to allow more flexibility in where computational effort is directed in the calculations. We highlight the difficulty as a general measure that quantifies performance of an algorithm that computes a stochastic average and show how it can be used as the basis for optimizing such calculations.

The Gibbs-Duhem integration method is a means for evaluating phase diagrams by molecular simulati... more The Gibbs-Duhem integration method is a means for evaluating phase diagrams by molecular simulation. Starting from a state of known phase coexistence, one applies the Clapeyron equation to trace out subsequent points on the saturation line. Each simulation yields a coexistence state, and particle exchanges are not invoked to insure equality of fugacities. We describe and demonstrate here the extension

Molecular Physics, 2015

ABSTRACT We examine cluster-series methods for the behaviour of simple fluids under confinement, ... more ABSTRACT We examine cluster-series methods for the behaviour of simple fluids under confinement, applying the Mayer-sampling Monte Carlo method to evaluate the necessary cluster integrals. We examine two series formulations, one based on the density of a bulk phase in equilibrium with the confined phase (effectively specifying the chemical potential), and another based on the density of the confined phase. The theory and methods are used to calculate the structure and properties of hard-sphere fluids confined between parallel planar hard walls. We present the effects of width of the confined region on the inhomogeneous virial coefficients, and through them, on the thermodynamics of the confined system.