A suite of scalable atomistic simulation programs has been developed for materials research based on space-time multiresolution algorithms. Design and analysis of parallel algorithms are presented for molecular dynamics (MD) simulations and quantum-mechanical (QM) calculations based on the density functional theory. Performance tests have been carried out on 1,088-processor Cray T3E and 1,280-processor IBM SP3 computers. The linear-scaling algorithms have enabled 6.44-billion-atom MD and 111,000-atom QM calculations on 1,024 SP3 processors with parallel efficiency well over 90%. The production-quality programs also feature wavelet-based computational-space decomposition for adaptive load balancing, spacefilling-curve-based adaptive data compression with user-defined error bound for scalable I/O, and octree-based fast visibility culling for immersive and interactive visualization of massive simulation data.

In this study, a technique has been proposed for developing constitutive models for polymer composite systems reinforced with single-walled carbon nanotubes (SWNT). Since the polymer molecules are on the same size scale as the nanotubes, the interaction at the polymer/nanotube interface is highly dependent on the local molecular structure and bonding. At these small length scales, the lattice structures of the nanotube and polymer chains cannot be considered continuous, and the bulk mechanical properties of the SWNT/polymer composites can no longer be determined through traditional micromechanical approaches that are formulated using continuum mechanics. It is proposed herein that the nanotube, the local polymer near the nanotube, and the nanotube/polymer interface can be modeled as an effective continuum fiber using an equivalentcontinuum modeling method. The effective fiber retains the local molecular structure and bonding information and serves as a means for incorporating micromechanical analyses for the prediction of bulk mechanical properties of SWNT/polymer composites with various nanotube sizes and orientations. As an example, the proposed approach is used for the constitutive modeling of two SWNT/polyethylene composite systems, one with continuous and aligned SWNT and the other with discontinuous and randomly aligned nanotubes.

Accepted for publication in Handbook of Theoretical and Computational

The structural, dynamical, and thermodynamic properties of a model potassium channel are studied using molecular dynamics simulations. We use the recently unveiled protein structure for the KcsA potassium channel from Streptomyces lividans. Total and free energy profiles of potassium and sodium ions reveal a considerable preference for the larger potassium ions. The selectivity of the channel arises from its ability to completely solvate the potassium ions, but not the smaller sodium ions. Self-diffusion of water within the narrow selectivity filter is found to be reduced by an order of magnitude from bulk levels, whereas the wider hydrophobic section of the pore maintains near-bulk self-diffusion. Simulations examining multiple ion configurations suggest a two-ion channel. Ion diffusion is found to be reduced to # 1 /3 of bulk diffusion within the selectivity filter. The reduced ion mobility does not hinder the passage of ions, as permeation appears to be driven by Coulomb repulsion...

Abstract. In this paper we evaluate the possibilities of one-sided communication, a new feature of the MPI-2 standard, on the Origin2000 for relatively short-range molecular dynamics (MD) simulations. Our algorithm is based on an asynchronous message-passing multi-cell approach using MPI as message-passing layer and the Leap-Frog/Verlet algorithm for the time integration. We compare one-sided with two different twosided communication approaches for typical production runs (10 5 − 10 9 atoms) where we discuss the communication vs. computation time for increasing number of processes. We also show how the partitioning of the problem affects the different communication approaches. Using one-sided communication we achieved 10-70 % better performance over two-sided. 1

Abstract: FPGA-based acceleration of molecular dynamics (MD) has been the subject of several recent studies. Here we describe a new non-bonded force computation pipeline implemented on a 2004era COTS FPGA board and its integration into the ProtoMol MD code. There are several innovations: a novel interpolation strategy; the introduction of a “semi-floating point ” format; and various issues related to system integration. As a result, we are able to model far more particle types, without relying on complex buffering, and obtain higher accuracy than previously. A two pipeline accelerator has been implemented on a Xilinx VirtexII Pro VP70, integrated into ProtoMol, and tested with an enzyme inhibitor model having 8000 particles and 26 particle types. Despite performing all O(n) work on the host PC, as well as the data conversion and communication overhead, this implementation yields a 5.5x speed-up over a 2.8GHz PC, and with accuracy comparable to the serial code. 1

We have performed parallel large-scale molecular-dynamics simulations on the QSCmachine at Los Alamos. The good scalability of the SPaSM code is demonstrated together with its capability of efficient data analysis for enormous system sizes up to 19 000 416 964 particles. Furthermore, we introduce a newly-developed graphics package that renders in a very efficient parallel way a huge number of spheres necessary for the visualization of atomistic simulations. These abilities pave the way for future atomistic large-scale simulations of physical problems with system sizes on the µ-scale. Keywords: Large-scale; molecular-dynamics simulations; data analysis; sphere rendering. 1.

In this paper, we present an algorithm for computing a partial sum of eigenvalues of a large symmetric positive definite matrix pair. We show that this computational task is intimately connected to compute a bilinear form u T f(A)u for a properly defined matrix A, a vector u and a function f(\Delta). Compared to existing techniques which compute individual eigenvalues and then sum them up, the new algorithm is generally less accurate, but requires significantly less memory and CPU time. In the application of electronic structure calculations in molecular dynamics, the new algorithm has achieved a speedup factor of 2 for small size problems to 20 for large size problems. Relative accuracy within 0.1% to 2% is satisfactory. Previously intractable large size problems have been solved. Key words: partial eigenvalue sum, bilinear form, Gauss quadrature, Lanczos method, generalized eigenvalue problem, tight-binding molecular dynamics, Monte Carlo simulation AMS subject classifications: 6...

In this paper the exact analytical solution of the motion of a rigid body with arbitrary mass distribution is derived in the absence of forces or torques. The resulting expressions are cast into a form where the dependence of the motion on initial conditions is explicit and the equations governing the orientation of the body involve only real numbers. Based on these results, an efficient method to calculate the location and orientation of the rigid body at arbitrary times is presented. This implementation can be used to verify the accuracy of numerical integration schemes for rigid bodies, to serve as a building block for event-driven discontinuous molecular dynamics simulations of general rigid bodies, and for constructing symplectic integrators for rigid body dynamics. 1

The ultimate goal of grid technologies is to materialize the vision of grids as virtual supercomputers of unprecedented power, through utilization of geographically disperse distributively owned resources. Despite the overwhelming success of grids in running pleasantly parallel tasks, there still exists a large set of demanding applications considered the exclusive prerogative of real supercomputers. A few examples include complex systems and weather simulations, computational fluid dynamics and other tightly coupled parallel applications. These rely on a static execution environment with predictable performance, provided through efficient co-allocation of a large number of reliable homogeneously interconnected resources. In this paper, we describe a novel quasiopportunistic supercomputer system that enables execution of demanding parallel applications in grids through identification and implementation of the set of key technologies required to bridge the gap between grids and supercomputers. These technologies include an economic incentive-based framework for establishing and maintaining grid-wise allocation agreements; a co-allocation subsystem that is integrated with the economic framework and enhanced by communication topology-aware allocation mechanisms; a fault tolerant message passing library that hides the failures of the underlying resources; and data pre-staging orchestration.