Numerical ‘health check’ for scientific codes: the CADNA approach

Scientific computation has unavoidable approximations built into its very fabric. One important source of error that is difficult to detect and control is round-off error propagation which originates from the use of finite precision arithmetic. We propose that there is a need to perform regular numerical `health checks' on scientific codes in order to detect the cancerous effect of round-off error propagation. This is particularly important in scientific codes that are built on legacy software. We advocate the use of the CADNA library as a suitable numerical screening tool. We present a case study to illustrate the practical use of CADNA in scientific codes that are of interest to the Computer Physics Communications readership. In doing so we hope to stimulate a greater awareness of round-off error propagation and present a practical means by which it can be analyzed and managed.

Population-based local search for protein folding simulation in the MJ energy model and cubic lattices

We present experimental results on benchmark problems in 3D cubic lattice structures with the Miyazawa-Jernigan energy function for two local search procedures that utilise the pull-move set: (i) population-based local search (PLS) that traverses the energy landscape with greedy steps towards (potential) local minima followed by upward steps up to a certain level of the objective function; (ii) simulated annealing with a logarithmic cooling schedule (LSA). The parameter settings for PLS are derived from short LSA-runs executed in pre-processing and the procedure utilises tabu lists generated for each member of the population. In terms of the total number of energy function evaluations both methods perform equally well, however. PLS has the potential of being parallelised with an expected speed-up in the region of the population size. Furthermore, both methods require a significant smaller number of function evaluations when compared to Monte Carlo simulations with kink-jump moves. (C) 2009 Elsevier Ltd. All rights reserved.

2DRMP: A suite of two-dimensional R-matrix propagation codes

The R-matrix method has proved to be a remarkably stable, robust and efficient technique for solving the close-coupling equations that arise in electron and photon collisions with atoms, ions and molecules. During the last thirty-four years a series of related R-matrix program packages have been published periodically in CPC. These packages are primarily concerned with low-energy scattering where the incident energy is insufficient to ionize the target. In this paper we describe previous term2DRMP,next term a suite of two-dimensional R-matrix propagation programs aimed at creating virtual experiments on high performance and grid architectures to enable the study of electron scattering from H-like atoms and ions at intermediate energies.

Nonlinear theory of solitary waves associated with longitudinal particle motion in lattices - Application to longitudinal grain oscillations in a dust crystal

The nonlinear aspects of longitudinal motion of interacting point masses in a lattice are revisited, with emphasis on the paradigm of charged dust grains in a dusty plasma (DP) crystal. Different types of localized excitations, predicted by nonlinear wave theories, are reviewed and conditions for their occurrence (and characteristics) in DP crystals are discussed. Making use of a general formulation, allowing for an arbitrary (e.g. the Debye electrostatic or else) analytic potential form phi(r) and arbitrarily long site-to-site range of interactions, it is shown that dust-crystals support nonlinear kink-shaped localized excitations propagating at velocities above the characteristic DP lattice sound speed v(0). Both compressive and rarefactive kink-type excitations are predicted, depending on the physical parameter values, which represent pulse- (shock-)like coherent structures for the dust grain relative displacement. Furthermore, the existence of breather-type localized oscillations, envelope-modulated wavepackets and shocks is established. The relation to previous results on atomic chains as well as to experimental results on strongly-coupled dust layers in gas discharge plasmas is discussed.

Localized excitations of charged dust grains in dusty plasma lattices

The nonlinear aspects of charged dust grain motion in a one-dimensional dusty plasma (DP) monolayer are discussed. Both horizontal (longitudinal, acoustic mode) and vertical (transverse, optic mode) displacements are considered, and various types of localized excitations are reviewed, in a continuum approximation. Dust crystals are shown to support nonlinear kink-shaped supersonic longitudinal solitary excitations, as well as modulated envelope (either longitudinal or transverse) localized modes. The possibility for Discrete Breather (DB-) type excitations (Intrinsic Localized Modes, ILMs) to occur is investigated, from first principles. These highly localized excitations owe their existence to lattice discreteness, in combination with the interaction and/or
substrate (sheath) potential nonlinearity. This possibility may open new directions in DP- related research. The relation to previous results on atomic chains as well as to experimental results on strongly-coupled dust layers in gas discharge plasmas is discussed.