磁约束聚变等离子体的大规模回旋动理学模拟

文章介绍了磁约束核聚变能源科学及其密切相关的聚变等离子体物理,以及研究磁约束聚变等离子体非线性物理所必需的大规模回旋动理学模拟的方法及其前沿进展.     

MPiSIM: Massively parallel simulation tool for metallic system

We report a domain decomposition molecular dynamics (MD) for simulation on metallic systems based on distributed parallel computers. The method is a development of a spatial decomposition in 3-D space with the combination of link-cell and neighbor list techniques for enhanced efficiency. The algorithm has been successfully implemented on the Origin2000, Wolf, HP Examplar etc. various platforms. The scaling performance on these platforms will be discussed and several applications in metallic systems will also be given in the paper. This revised version was published online in June 2006 with corrections to the Cover Date.     

Statistical calibration of computer simulations

This paper surveys issues associated with the statistical calibration of physics-based computer simulators. Even in solidly physics-based models there are usually a number of parameters that are suitable targets for calibration. Statistical calibration means refining the prior distributions of such uncertain parameters based on matching some simulation outputs with data, as opposed to the practice of “tuning” or point estimation that is commonly called calibration in non-statistical contexts. Older methods for statistical calibration are reviewed before turning to recent work in which the calibration problem is embedded in a Gaussian process model. In procedures of this type, parameter estimation is carried out simultaneously with the estimation of the relationship between the calibrated simulator and truth.     

Massively parallel sample preparation for the MALDI MS analyses of tissues

Investigation of the peptidome of the nervous system containing large, often easily identifiable neurons has greatly benefited from single-cell matrix-assisted laser desorption/ionization (MALDI) mass spectrometry and has led to the discovery of hundreds of novel cell-to-cell signaling peptides. By combining new sample preparation methods and established protocols for bioanalytical mass spectrometry, a high-throughput, small-volume approach is created that allows the study of the peptidome of a variety of nervous systems. Specifically, approximately single-cell-sized samples are rapidly prepared from thin tissue slices by adhering the tissue section to a glass bead array that is anchored to a stretchable membrane. Stretching the membrane fragments the tissue slice into thousands of individual samples, their dimensions predominately governed by the size of the individual glass beads. Application of MALDI matrix, followed by the repeated condensation of liquid microdroplets on the fragmented tissue, allows for maximal analyte extraction and incorporation into MALDI matrix crystals. During extraction, analyte migration between the pieces of tissue on separate beads is prevented by the underlying hydrophobic substrate and by controlling the size of the condensation droplets. The procedure, while general in nature, may be tailored to the needs of a variety of analyses, producing mass spectra equivalent to those acquired from single-cell samples.     

High-performance parallel computing for incompressible flow simulations

High-performance parallel computer systems have been employed to compute a variety of three-dimensional incompressible fluid flows. Three different numerical methods have been used for the discretization of the Navier-Stokes equations, with domain decomposition techniques employed for the parallel resolution of the discretized equations. These parallel flow solvers have been applied to the numerical simulation of different flows, ranging from basic flow studies to industrial applications. The results of these studies show that high-performance parallel computing has evolved from its initial investigative phase into a mature technology that can be employed for large-scale numerical flow simulation.     

Variational perturbation theory compared with computer simulations

The variational perturbation theory has been applied to describe the compressibility of a 50% mixture of helium and nitrogen at room temperature and pressures up to 1 GPa. With parameters resulting from this perturbation theory, Monte Carlo simulations have been performed on model systems for these compounds as well as for the mixture. On comparison, clear restrictions are seen for the applicability of the perturbation theory combined with the one-fluid representation of mixtures.Paper presented at the Twelfth Symposium on Thermophysical Properties, June 19–24, 1994, Boulder, Colorado, U.S.A.     

State of theory and computer simulations of radiation effects in ceramics

This article presents opinions based on the presentations and discussions at a Workshop on Theory and Computer Simulations of Radiation Effects in Ceramics held in August 2002 at Pacific Northwest National Laboratory in Richland, WA, USA. The workshop was focused on the current state-of-the-art of theory, modeling and simulation of radiation effects in oxide ceramics, directions for future breakthroughs, and creating a close integration with experiment.     

Modal compensation and the atmospheric-turbulence outer scale: computer simulations

The influence of the turbulence outer scale on the Strehl ratio obtained with low-order adaptive optics systems is examined by numerical simulation. The Karhunen-Loeve approach is used to generate wave-front samples. A method that allows construction of the outer-scale-dependent Karhunen-Loeve functions is described. It is shown that the Strehl ratio produced by a second-order adaptive optics correction (tip-tilt, defocus, and astigmatism) is affected quite strongly by the finite outer scale. For the higher-order correction, the effect under study is weak and appears only when the outer-scale magnitude becomes less than the aperture diameter. It is also shown that the finite outer scale has a positive effect on the Strehl ratio of the uncorrected long-exposure image.     

Coarse grain parallel finite element simulations for incompressible flows

Parallel simulation of incompressible fluid flows is considered on networks of homogeneous workstations. Coarse-grain parallelization of a Taylor–Galerkin/pressure-correction finite element algorithm are discussed, taking into account network communication costs. The main issues include the parallelization of system assembly, and iterative and direct solvers, that are of common interest to finite element and general numerical computation. The parallelization strategies are implemented on a Sun workstation cluster using the Parallel Virtual Machine (PVM) message passing library. Test results are obtained with a maximum of nineteen workstations and various PVM configurations are exhibited. Parallel efficiency close to ideal has been achieved for some strategies adopted. It is suggested that load balancing may not always be beneficial on distributed platforms with broadcasting communication connection. © 1998 John Wiley & Sons, Ltd.     

Towards parallel I/O in finite element simulations

I/O issues in finite element analysis on parallel processors are addressed. Viable solutions for both local and shared memory multiprocessors are presented. The approach is simple but limited by currently available hardware and software systems. Implementation is carried out on a CRAY-2 system. Performance results are reported.     

Million atom molecular dynamics simulations of materials on parallel computers

Recent advances in computing tecnology — parallel computer architectures, portable software and development of robust O(N) algorithms — have revolutionized the field of computer simulation. Using the space-time multiresolution molecular dynamics algorithms it is possible to carry out multimillion atom simulations of materials in different ranges of density, temperature and uniaxial strain.     

Lattice-Boltzmann simulations of three-dimensional fluid flow on a desktop computer

The lattice-Boltzmann (LB) method is a cellular automaton approach to simulating fluid flow with many advantages over conventional methods based on the Navier-Stokes equations. It is conceptually simple, amenable to a wide array of boundary conditions, and can be adapted to handle thermal, density, miscibility, and other effects. The LB approach has been used to model a number of fluid systems of interest to analytical chemists, including chromatography columns, micromixers, and electroosmotic pumps. However, widespread use of this tool has been limited, in part because virtually all large-scale 3D simulations in the literature have been executed on supercomputers. This work demonstrates that such simulations can be executed in reasonable periods of time (hours) on a desktop computer using a cross-platform software package that is easy to learn and use. This package incorporates several improvements that enhance the utility of the LB approach, including an algorithm for speeding common calculations by 2 orders of magnitude and a scheme for handling convection-diffusion equations of interest in electrochemical and surface reaction studies.     

Acoustical diffraction tomography in a finite form and its computer simulations

Until now, all acoustical diffraction reconstruction algorithms are in infinite forms. All of these algorithms have disadvantages: severe limitations on scatterers or tedious calculations. In this paper, we present a new reconstruction algorithm in a finite form using the method of formal parameter, which is very simple. This new algorithm gives an exact reconstruction when the amplitude of the scattered wave is smaller than that of the incident wave everywhere. This assumption is much less restrictive than that for the first and second-order Born approximations. Although this new algorithm is in a finite form, it is still an approximate one when the amplitude of the scattered wave is not smaller than that of the incident wave everywhere. However, it still gives a good reconstruction when the amplitude of the scattered wave is a little greater than that of the incident wave in some area. Some numerical examples have confirmed these conclusions