23 research outputs found
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SC'11 Poster: A Highly Efficient MGPT Implementation for LAMMPS; with Strong Scaling
The MGPT potential has been implemented as a drop in package to the general molecular dynamics code LAMMPS. We implement an improved communication scheme that shrinks the communication layer thickness, and increases the load balancing. This results in unprecedented strong scaling, and speedup continuing beyond 1/8 atom/core. In addition, we have optimized the small matrix linear algebra with generic blocking (for all processors) and specific SIMD intrinsics for vectorization on Intel, AMD, and BlueGene CPUs
Efficient Reactive Brownian Dynamics
We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle
simulations of reaction-diffusion systems based on the Doi or volume reactivity
model, in which pairs of particles react with a specified Poisson rate if they
are closer than a chosen reactive distance. In our Doi model, we ensure that
the microscopic reaction rules for various association and disassociation
reactions are consistent with detailed balance (time reversibility) at
thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to
separate reaction and diffusion, and solves both the diffusion-only and
reaction-only subproblems exactly, even at high packing densities. To
efficiently process reactions without uncontrolled approximations, SRBD employs
an event-driven algorithm that processes reactions in a time-ordered sequence
over the duration of the time step. A grid of cells with size larger than all
of the reactive distances is used to schedule and process the reactions, but
unlike traditional grid-based methods such as Reaction-Diffusion Master
Equation (RDME) algorithms, the results of SRBD are statistically independent
of the size of the grid used to accelerate the processing of reactions. We use
the SRBD algorithm to compute the effective macroscopic reaction rate for both
reaction- and diffusion-limited irreversible association in three dimensions.
We also study long-time tails in the time correlation functions for reversible
association at thermodynamic equilibrium. Finally, we compare different
particle and continuum methods on a model exhibiting a Turing-like instability
and pattern formation. We find that for models in which particles diffuse off
lattice, such as the Doi model, reactions lead to a spurious enhancement of the
effective diffusion coefficients.Comment: To appear in J. Chem. Phy
Billion-atom Synchronous Parallel Kinetic Monte Carlo Simulations of Critical 3D Ising Systems
An extension of the synchronous parallel kinetic Monte Carlo (pkMC) algorithm
developed by Martinez {\it et al} [{\it J.\ Comp.\ Phys.} {\bf 227} (2008)
3804] to discrete lattices is presented. The method solves the master equation
synchronously by recourse to null events that keep all processors time clocks
current in a global sense. Boundary conflicts are rigorously solved by adopting
a chessboard decomposition into non-interacting sublattices. We find that the
bias introduced by the spatial correlations attendant to the sublattice
decomposition is within the standard deviation of the serial method, which
confirms the statistical validity of the method. We have assessed the parallel
efficiency of the method and find that our algorithm scales consistently with
problem size and sublattice partition. We apply the method to the calculation
of scale-dependent critical exponents in billion-atom 3D Ising systems, with
very good agreement with state-of-the-art multispin simulations
Improved Absolute Stability of Predictor-Corrector Methods for Retarded Differential Equations
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Atomistic Simulations of Grain Boundary Pinning in CuFe Alloys
The authors apply a hybrid Monte Carlo-molecular dynamics code to the study of grain boundary motion upon annealing of pure Cu and Cu with low concentrations of Fe. The hybrid simulations account for segregation and precipitation of the low solubility Fe, together with curvature driven grain boundary motion. Grain boundaries in two different systems, a {Sigma}7+U-shaped half-loop grain and a nanocrystalline sample, were found to be pinned in the presence of Fe concentrations exceeding 3%
Synchronous parallel kinetic Monte Carlo for continuum diffusion-reaction systems
A novel parallel kinetic Monte Carlo (kMC) algorithm formulated on the basis of perfect time synchronicity is presented. The algorithm is intended as a generalization of the standard n-fold kMC method, and is trivially implemented in parallel architectures. In its present form, the algorithm is not rigorous in the sense that boundary conflicts are ignored. We demonstrate, however, that, in their absence, or if they were correctly accounted for, our algorithm solves the same master equation as the serial method. We test the validity and parallel performance of the method by solving several pure diffusion problems (i.e. with no particle interactions) with known analytical solution. We also study diffusion-reaction systems with known asymptotic behavior and find that, for large systems with interaction radii smaller than the typical diffusion length, boundary conflicts are negligible and do not affect the global kinetic evolution, which is seen to agree with the expected analytical behavior. Our method is a controlled approximation in the sense that the error incurred by ignoring boundary conflicts can be quantified intrinsically, during the course of a simulation, and decreased arbitrarily (controlled) by modifying a few problem-dependent simulation parameters
Benchmarking CEASIOM software to predict flight control and flying qualities of the B-747
CEASIOM, the Computerized Environment for Aircraft Synthesis and Integrated Optimization Methods, is a framework that integrates discipline-specific tools for conceptual design. At this early stage of the design it is very useful to be able to predict the flying and handling qualities of the aircraft. In order to do this for the configuration being studied, the aerodynamic database needs to be computed and coupled to the stability and control tools to carry out the analysis. This paper describes how the adaptive-fidelity Computational Fluid-Dynamics module of CEASIOM computes the aerodynamic database of an aircraft configuration, and how that data is analyzed by the Flight Control System Designer Toolkit module to determine the flying qualities and the control laws of the aircraft. The paper compares the predicted flying qualities with the flight-test data of the Boeing B747 aircraft in order to verify the goodness of the overall approach