Search

Predictive high-fidelity modeling of wind turbines with computational fluid dynamics, wherein turbine geometry is resolved in an atmospheric boundary layer, is important to understanding complex flow accounting for design strategies and operational phenomena such as blade erosion, pitch-control, stall/vortex-induced vibrations, and aftermarket add-ons. The biggest challenge with high-fidelity modeling is the realization of numerical algorithms that can capture the relevant physics in detail through effective use of high-performance computing. For modern supercomputers, that means relying on GPUs for acceleration. In this paper, we present ExaWind, a GPU-enabled open-source incompressible-flow hybrid-computational fluid dynamics framework, comprising the near-body unstructured grid solver Nalu-Wind, and the off-body block-structured-grid solver AMR-Wind, which are coupled using the Topology Independent Overset Grid Assembler. Turbine simulations employ either a pure Reynolds-averaged Navier–Stokes turbulence model or hybrid turbulence modeling wherein Reynolds-averaged Navier–Stokes is used for near-body flow and large eddy simulation is used for off-body flow. Being two-way coupled through overset grids, the two solvers enable simulation of flows across a huge range of length scales, for example, 10 orders of magnitude going from O(μm) boundary layers along the blades to O(10 km) across a wind farm. In this paper, we describe the numerical algorithms for geometry-resolved turbine simulations in atmospheric boundary layers using ExaWind. We present verification studies using canonical flow problems. Validation studies are presented using megawatt-scale turbines established in literature. Additionally presented are demonstration simulations of a small wind farm under atmospheric inflow with different stability states.

Several extensions and improvements have been made to the multilevel summation method (MSM) of computing long-range electrostatic interactions. These include pressure calculation, an improved error estimator, faster direct part calculation, extension to non-orthogonal (triclinic) systems, and parallelization using the domain decomposition method. MSM also allows fully non-periodic long-range electrostatics calculations which are not possible using traditional Ewald-based methods. In spite of these significant improvements to the MSM algorithm, the particle-particle particle-mesh (PPPM) method was still found to be faster for the periodic systems we tested on a single processor. However, the fast Fourier transforms (FFTs) that PPPM relies on represent a major scaling bottleneck for the method when running on many cores (because the many-to-many communication pattern of the FFT becomes expensive) and MSM scales better than PPPM when using a large core count for two test problems on Sandia's Redsky machine. This FFT bottleneck can be reduced by running PPPM on only a subset of the total processors. MSM is most competitive for relatively low accuracy calculations. On Sandia's Chama machine, however, PPPM is found to scale better than MSM for all core counts that we tested. These results suggest that PPPM is usually more efficient than MSM for typical problems running on current high performance computers. However, further improvements to MSM algorithm could increase its competitiveness for calculation of long-range electrostatic interactions. [ABSTRACT FROM AUTHOR]

Two-temperature models are used to represent the physics of the interaction between atoms and electrons during thermal transients such as radiation damage, laser heating, and cascade simulations. We introduce a two-temperature model applied to an insulator, α-quartz, to model heat deposition in a SiO2 lattice. Our model of the SiO2 electronic subsystem is based on quantum simulations of the electronic response in a SiO2 repeat cell. We observe how the parametrization of the electronic subsystem impacts the degree of permanent amorphization of the lattice, especially compared to a metallic electronic subsystem. The parametrization of the insulator electronic subsystem has a significant effect on the amount of residual defects in the crystal after 10 ps. While recognizing that more development in the application of two-temperature models to insulators is needed, we argue that the inclusion of a simple electronic subsystem substantially improves the realism of such radiation damage simulations. [ABSTRACT FROM AUTHOR]

Two-temperature models are used to represent the interaction between atoms and free electrons during thermal transients such as radiation damage, laser heating, and cascade simulations. In this paper, we introduce an energy-conserving version of an inhomogeneous finite reservoir two-temperature model using a Langevin thermostat to communicate energy between the electronic and atomic subsystems. This energy-conserving modification allows the inhomogeneous two-temperature model to be used for longer and larger simulations and simulations of small energy phenomena, without introducing nonphysical energy fluctuations that may affect simulation results. We test this model on the annealing of Frenkel defects. We find that Frenkel defect annealing is largely indifferent to the electronic subsystem, unless the electronic subsystem is very tightly coupled to the atomic subsystem. We also consider radiation damage due to local deposition of heat in two idealized systems. We first consider radiation damage in a large face-centered-cubic Lennard-Jones (LJ) single-component crystal that readily recrystallizes. Second, we consider radiation damage in a large binary glass-forming LJ crystal that retains permanent damage. We find that the electronic subsystem parameters can influence the way heat is transported through the system and have a significant impact on the number of defects after the heat deposition event. We also find that the two idealized systems have different responses to the electronic subsystem. The single-component LJ system anneals most rapidly with an intermediate electron-ion coupling and a high electronic thermal conductivity. If sufficiently damaged, the binary glass-forming LJ system retains the least permanent damage with both a high electron-ion coupling and a high electronic thermal conductivity. In general, we find that the presence of an electronic gas can affect short and long term material annealing. [ABSTRACT FROM AUTHOR]

We present all-atom molecular dynamics simulations of biologically realistic transmembrane potential gradients across a DMPC bilayer. These simulations are the first to model this gradient in all-atom detail, with the field generated solely by explicit ion dynamics. Unlike traditional bilayer simulations that have one bilayer per unit cell, we simulate a 170 mV potential gradient by using a unit cell consisting of three salt-water baths separated by two bilayers, with full three-dimensional periodicity. The study shows that current computational resources are powerful enough to generate a truly electrified interface, as we show the predicted effect of the field on the overall charge distribution. Additionally, starting from Poisson’s equation, we show a new derivation of the double integral equation for calculating the potential profile in systems with this type of periodicity. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The structure of a single, grafted polyelectrolyte, DNA, is investigated by molecular dynamics simulations. The polyelectrolyte is treated as a bead-spring model with explicit charges using parametrizations of both flexible (ssDNA) and stiff (dsDNA) polyelectrolytes. In this single chain limit with no added salt, the flexible ssDNA is always highly extended. Counterion condensation on both molecules is found to be chain length dependent. The counterion distribution is not localized to the chain volume as in related polyelectrolyte brush states. Even at large chain lengths, where the majority of counterions are condensed, a significant fraction of counterions reside far from the chain. The distributions of positions of the nongrafted end monomer for ssDNA and dsDNA differ significantly, indicating a possibility for distinguishing the two states in DNA array technologies. [ABSTRACT FROM AUTHOR]

Two methods of calculating long-range intermolecular potentials are compared for an approximately 3 M aqueous electrolyte solution confined between two charged surfaces. We investigate the ionic density profiles using the charged-sheets method and the corrected three-dimensional (3D) Ewald method at two different system sizes and also compare the Coulomb forces directly. The corrected 3D Ewald method is recommended for the calculation of long-range potentials in systems of this nature because it is less system size dependent than the charged-sheets method and the resultant forces are more consistent with periodic boundaries. However, the charged-sheets method for estimating long-range potentials in Coulombic systems may be useful for certain applications, and the corrected 3D Ewald method also shows some system size dependence. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR]

SUMMARY Performance improvements in biomolecular simulations based on molecular dynamics (MD) codes are widely desired. Unfortunately, the factors, which allowed past performance improvements, particularly the microprocessor clock frequencies, are no longer increasing. Hence, novel software and hardware solutions are being explored for accelerating performance of widely used MD codes. In this paper, we describe our efforts on porting, optimizing and tuning of Large-scale Atomic/Molecular Massively Parallel Simulator, a popular MD framework, on heterogeneous architectures: multi-core processors with graphical processing unit (GPU) accelerators. Our implementation is based on accelerating the most computationally expensive non-bonded interaction terms on the GPUs and overlapping the computation on the CPU and GPUs. This functionality is built on top of message passing interface that allows multi-level parallelism to be extracted even at the workstation level with the multi-core CPUs and allows extension of the implementation on GPU-enabled clusters. We hypothesize that the optimal benefit of heterogeneous architectures for applications will come by utilizing all possible resources (for example, CPU-cores and GPU devices on GPU-enabled clusters). Benchmarks for a range of biomolecular system sizes are provided, and an analysis is performed on four generations of NVIDIA's GPU devices. On GPU-enabled Linux clusters, by overlapping and pipelining computation and communication, we observe up to 10-folds application acceleration in multi-core and multi-GPU environments illustrating significant performance improvements. Detailed analysis of the implementation is presented that allows identification of bottlenecks in algorithm, indicating that code optimization and improvements on GPUs could allow microsecond scale simulation throughput on workstations and inexpensive GPU clusters, putting widely desired biologically relevant simulation time-scales within reach of a large user community. In order to systematically optimize simulation throughput and to enable performance prediction, we have developed a parameterized performance model that will allow developers and users to explore the performance potential of future heterogeneous systems for biological simulations. Copyright © 2012 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Rhodopsin is the prototypical G-protein coupled receptor, coupling light activation with high efficiency to signaling molecules. The dark-state X-ray structures of the protein provide a starting point for consideration of the relaxation from initial light activation to conformational changes that may lead to signaling. In this study we create an energetically unstable retinal in the light activated state and then use molecular dynamics simulations to examine the types of compensation, relaxation, and conformational changes that occur following the cis-trans light activation. The results suggest that changes occur throughout the protein, with changes in the orientation of Helices 5 and 6, a closer interaction between Ala 169 on Helix 4 and retinal, and a shift in the Schiff base counterion that also reflects changes in sidechain interactions with the retinal. Taken together, the simulation is suggestive of the types of changes that lead from local conformational change to light-activated signaling in this prototypical system. Proteins 2007. © 2006 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]