Parallel Brownian dynamics simulations with the message-passing and PGAS programming models

This is a post-peer-review, pre-copyedit version of an article published in Computer Physics Communications. The final authenticated version is available online at: https://doi.org/10.1016/j.cpc.2012.12.015[Abstract] The simulation of particle dynamics is among the most important mechanisms to study the behavior of molecules in a medium under specific conditions of temperature and density. Several models can be used to compute efficiently the forces that act on each particle, and also the interactions between them. This work presents the design and implementation of a parallel simulation code for the Brownian motion of particles in a fluid. Two different parallelization approaches have been followed: (1) using traditional distributed memory message-passing programming with MPI, and (2) using the Partitioned Global Address Space (PGAS) programming model, oriented towards hybrid shared/distributed memory systems, with the Unified Parallel C (UPC) language. Different techniques for domain decomposition and work distribution are analyzed in terms of efficiency and programmability, in order to select the most suitable strategy. Performance results on a supercomputer using up to 2048 cores are also presented for both MPI and UPC codes.Ministerio de Ciencia e Innovación ; TIN2010-16735Xunta de Galicia; ref. 2010/

Tumbling of polymers in semidilute solution under shear flow

The tumbling dynamics of individual polymers in semidilute solution is studied by large-scale non-equilibrium mesoscale hydrodynamic simulations. We find that the tumbling time is equal to the non-equilibrium relaxation time of the polymer end-to-end distance along the flow direction and strongly depends on concentration. In addition, the normalized tumbling frequency as well as the widths of the alignment distribution functions for a given concentration-dependent Weissenberg number exhibit a weak concentration dependence in the cross-over regime from a dilute to a semidilute solution. For semidilute solutions a universal behavior is obtained. This is a consequence of screening of hydrodynamic interactions at polymer concentrations exceeding the overlap concentration

Instantaneous Normal Mode analysis of liquid HF

We present an Instantaneous Normal Modes analysis of liquid HF aimed to clarify the origin of peculiar dynamical properties which are supposed to stem from the arrangement of molecules in linear hydrogen-bonded network. The present study shows that this approach is an unique tool for the understanding of the spectral features revealed in the analysis of both single molecule and collective quantities. For the system under investigation we demonstrate the relevance of hydrogen-bonding ``stretching'' and fast librational motion in the interpretation of these features.Comment: REVTeX, 7 pages, 5 eps figures included. Minor changes in the text and in a figure. Accepted for publication in Phys. Rev. Let

Forced oscillations of coronal loops driven by external EIT waves

Aims. We study the generation of transversal oscillations in coronal loops represented as a straight thin flux tube under the effect of an external driver modelling the global coronal EIT wave. We investigate how the generated oscillations depend on the nature of the driver, and the type of interaction between the two systems. Methods. We consider the oscillations of a magnetic straight cylinder with fixed-ends under the influence of an external driver modelling the force due to the global EIT wave. Given the uncertainties related to the nature of EIT waves, we first approximate the driver by an oscillatory force in time and later by a shock with a finite width. Results. Results show that for a harmonic driver the dominant period in the generated oscillation belongs to the driver. Depending on the period of driver, compared to the natural periods of the loop, a mixture of standing modes harmonics can be initiated. In the case of a non-harmonic driver (modelling a shock wave), the generated oscillations in the loop are the natural periods only. The amplitude of oscillations is determined by the position of the driver along the tube. The full diagnosis of generated oscillations is achieved using simple numerical methods

ScaFaCoS – A Scalable library of Fast Coulomb Solvers for particle Systems

The simulation of classical particle systems by means of molecular dynamics techniques requires the evaluation of potentials and forces between particles to explore the phase or configuration space of the system. The interactions can be classified into short-range and long-range contributions. While short-range potentials are evaluated very efficiently by means of neighbor list techniques, which reduce the computational complexity to O(N), the long range interactions must be evaluated over all particle pair contributions in the system. This increases the complexity to O(N2), limiting very often the tractable system size to a few thousand particles. In charged or polarized systems, the evaluation of Coulomb interactions between particles is the dominant part of the computation. To tame the quadratic computational complexity of the problem, a number of different methods with O(N) and O(N log(N)) have been developed over the past. Prominent examples are the linearly scaling fast multipole method and FFT-based methods, like P3M, which exhibit an N log(N) scaling but also tree methods, originally designed for strongly inhomogeneous gravitational problems as well as variants of the multigrid method. To integrate an efficient, yet accurate method into an existing simulation code is often a time consuming task, because of the level of implementation complexity. This is even more pronounced when considering scalability on parallel computers. Furthermore, different types of boundary conditions might be necessary to consider, which are not implemented in a standard way even in community codes. To tackle large particle systems, solvers of low computational complexity and good scalability have to be considered. In order to facilitate the integration of such high level implementations of Coulomb solvers into existing programs, the scalable library ScaFaCoS was developed [1], which contains various methods for treating long range interactions in complex particle systems under various boundary conditions, e.g., open boundaries or periodic boundaries in various cartesian directions [2]. Implemented algorithms comprise the fast multipole method, Barnes–Hut tree method, P3M, multigrid methods, and a newly developed Maxwell solver MEMD. Several methods allow full error control and the optimal adjustment of method parameters to reduce run time. An overview will be given about the methods, their accuracy and stability, as well as results for performance and scalability on parallel clusters. REFERENCES 1. http://www.scafacos.de 2. Arnold, A., Fahrenberger, F. Holm, Chr., Lenz, O., Bolten, M., Dachsel, H., Halver,. R., Kabadshow, I., Gähler, F., Heber, F., Iseringhausen, J., Hofmann, M., Pippig, M., Potts, D., Sutmann, G. Comparison of scalable fast methods for long-range interactions. Phys. Rev. E. 2013, 88, 063308

Multi-level load balancing for parallel particle simulations

Ideas from multi-level relaxation methods are combined with load balancing techniques to achieve a convergence acceleration for a homogeneous work load distribution over a given set of processors when the underlying work function is inhomogeneously distributed in space. The algorithm is based on an orthogonal recursive bisection ap- proach which is evaluated via a hierarchically refined coarse integration. The method only requires a minimal information transfer across processors during the tree traversal steps. It is described of how to partition the system of processors to geometrical space, when global information is needed for the spatial tesselation

Efficiency of linked cell algorithms

The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its efficiency, because a large part of CPU time is spent to identify the interacting particles. Several recent publications proposed improvements to the algorithm and investigated their efficiency by applying them to particular setups. In this publication we develop a general method to evaluate the efficiency of these algorithms, which is mostly independent of the parameters of the simulation, and test it for a number of linked cell list algorithms. We also propose a combination of linked cell reordering and interaction sorting that shows a good efficiency for a broad range of simulation setups.Comment: Submitted to Computer Physics Communications on 22 December 2009, still awaiting a referee repor

Trefftz Difference Schemes on Irregular Stencils

The recently developed Flexible Local Approximation MEthod (FLAME) produces accurate difference schemes by replacing the usual Taylor expansion with Trefftz functions -- local solutions of the underlying differential equation. This paper advances and casts in a general form a significant modification of FLAME proposed recently by Pinheiro & Webb: a least-squares fit instead of the exact match of the approximate solution at the stencil nodes. As a consequence of that, FLAME schemes can now be generated on irregular stencils with the number of nodes substantially greater than the number of approximating functions. The accuracy of the method is preserved but its robustness is improved. For demonstration, the paper presents a number of numerical examples in 2D and 3D: electrostatic (magnetostatic) particle interactions, scattering of electromagnetic (acoustic) waves, and wave propagation in a photonic crystal. The examples explore the role of the grid and stencil size, of the number of approximating functions, and of the irregularity of the stencils.Comment: 28 pages, 12 figures; to be published in J Comp Phy

Field exposed water in a nanopore: liquid or vapour?

We study the behavior of ambient temperature water under the combined effects of nanoscale confinement and applied electric field. Using molecular simulations we analyze the thermodynamic causes of field-induced expansion at some, and contraction at other conditions. Repulsion among parallel water dipoles and mild weakening of interactions between partially aligned water molecules prove sufficient to destabilize the aqueous liquid phase in isobaric systems in which all water molecules are permanently exposed to a uniform electric field. At the same time, simulations reveal comparatively weak field-induced perturbations of water structure upheld by flexible hydrogen bonding. In open systems with fixed chemical potential, these perturbations do not suffice to offset attraction of water into the field; additional water is typically driven from unperturbed bulk phase to the field-exposed region. In contrast to recent theoretical predictions in the literature, our analysis and simulations confirm that classical electrostriction characterizes usual electrowetting behavior in nanoscale channels and nanoporous materials.Comment: 20 pages, 6 figures + T.O.C. figure, in press in PCC