基于第一性原理量子输运模拟的并行计算

为了解决基于第一性原理分析计算大尺度量子输运体系时遇到的耗时长久问题,挖掘密度泛函理论与非平衡格林函数相结合方法(DFT+NEGF方法)在自洽迭代过程中的计算热点,就计算电子密度矩阵时的能量点积分和计算格林函数时的矩阵求逆/乘法运算提出MPI/Open MP并行计算方案.能量点积分采用MPI多进程并行方案,在数据初始化时需要将稀疏矩阵和积分能量点依照轮询调度算法分配给各进程.矩阵求逆/乘法的并行化既可调用ScaLAPACK子程序实现又可调用IntelMKL数学库中的OpenMP多线程加速函数实现.由于不同能量点计算的独立性,能量点积分采用的MPI并行计算获得近乎线性的加速比曲线.由于Open MP多线程并行采用的是基于共享内存的数据交换机制以及线程间切换通信开销小,矩阵求逆/乘法运算的OpenMP并行实现在计算效率上要优于而在程序的可扩展性上要劣于MPI多进程并行实现.     

Reducing ghosting due to k-space discontinuities in fast spin echo (FSE) imaging by a new combination of k-space ordering and parallel imaging

In multi-echo imaging sequences like fast spin echo (FSE), the point spread function (PSF) in the phase encoding direction contains significant secondary peaks (sidebands). This is due to discontinuities in adjacent k-space data obtained at different echo times caused by T₂ decay, and leads to ghosting and hence reduced image quality. Recently, utilising multiple coils for signal reception has become the standard configuration for MR systems due to the additional flexibility that parallel imaging (PI) methods can provide. PI methods generally obtain more data than is required to reconstruct an image. Here, this redundancy in information is exploited to reduce discontinuity-related ghosting in FSE imaging. Adjacent phase encoded k-space lines are acquired at different echo times alternately in the regions of discontinuity (called ‘feathering’). This moves the resulting ghost artefacts to the edges of the field of view. This property of the ghost then makes them amenable to removal using PI methods. With ‘feathered’ array coil data it is possible to reconstruct data over the region of the discontinuity from both echo times. By combining this data, a significant reduction in ghosting can be achieved. We show this approach to be effective through simulated and acquired MRI data.     

平行摄像机阵列移位法获取视差图像的研究

平行摄像机阵列移位法是一种摄像机阵列获取三维场景的视差图像的新方法.该方法在平行摄像机阵列法的基础上,将获取的视差图像进行平移处理,获得了立体显示所需的具有正、负水平视差的视差图像,且这些视差图像没有楔形失真和垂直视差.该方法集中了会聚摄像机阵列法和平行摄像机阵列法两种常规方法各自的优点并摒弃了其缺点.实验证实,所获取的视差图像在光栅式自由立体显示器上得到了三维场景的清晰逼真再现显示效果.     

A NEW HIGH PERFORMANCE SPARSE STATIC SOLVER IN FINITE ELEMENT ANALYSIS WITH LOOP-UNROLLING

In the previous papers, a high performance sparse static solver with two-level unrolling based on a cell-sparse storage scheme was reported. Although the solver reaches quite a high efficiency for a big percentage of finite element analysis benchmark tests, the MFLOPS （million floating operations per second） of LDL^T factorization of benchmark tests vary on a Dell Pentium IV 850 MHz machine from 100 to 456 depending on the average size of the super-equations, i.e., on the average depth of unrolling. In this paper, a new sparse static solver with two-level unrolling that employs the concept of master-equations and searches for an appropriate depths of unrolling is proposed. The new solver provides higher MFLOPS for LDL^T factorization of benchmark tests, and therefore speeds up the solution process.     

Application of Euler Neural Networks with Soft Computing Paradigm to Solve Nonlinear Problems Arising in Heat Transfer

In this study, a novel application of neurocomputing technique is presented for solving nonlinear heat transfer and natural convection porous fin problems arising in almost all areas of engineering and technology, especially in mechanical engineering. The mathematical models of the problems are exploited by the intelligent strength of Euler polynomials based Euler neural networks (ENN’s), optimized with a generalized normal distribution optimization (GNDO) algorithm and Interior point algorithm (IPA). In this scheme, ENN’s based differential equation models are constructed in an unsupervised manner, in which the neurons are trained by GNDO as an effective global search technique and IPA, which enhances the local search convergence. Moreover, a temperature distribution of heat transfer and natural convection porous fin are investigated by using an ENN-GNDO-IPA algorithm under the influence of variations in specific heat, thermal conductivity, internal heat generation, and heat transfer rate, respectively. A large number of executions are performed on the proposed technique for different cases to determine the reliability and effectiveness through various performance indicators including Nash–Sutcliffe efficiency (NSE), error in Nash–Sutcliffe efficiency (ENSE), mean absolute error (MAE), and Thiel’s inequality coefficient (TIC). Extensive graphical and statistical analysis shows the dominance of the proposed algorithm with state-of-the-art algorithms and numerical solver RK-4.     

物理过程的动画演示

使用科学计算软件不仅使CAI课件具有科学性,同时还可用来介绍计算方法.Matlab具有常用的3种动画演示的方法:对图形对象编程,通过VRML接口,获取动画帧.借助这些方法,可对大量涉及常微分方程或偏微分方程的物理过程进行动画模拟.     

Quantum chemistry in parallel with PQS

This article describes the capabilities and performance of the latest release (version 4.0) of the Parallel Quantum Solutions (PQS) ab initio program package. The program was first released in 1998 and evolved from the TEXAS program package developed by Pulay and coworkers in the late 1970s. PQS was designed from the start to run on Linux‐based clusters (which at the time were just becoming popular) with all major functionality being (a) fully parallel; and (b) capable of carrying out calculations on large—by ab initio standards—molecules, our initial aim being at least 100 atoms and 1000 basis functions with only modest memory requirements. With modern hardware and recent algorithmic developments, full accuracy, high‐level calculations (DFT, MP2, CI, and Coupled‐Cluster) can be performed on systems with up to several thousand basis functions on small (4‐32 node) Linux clusters. We have also developed a graphical user interface with a model builder, job input preparation, parallel job submission, and post‐job visualization and display. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009     

Accelerating molecular dynamic simulation on the cell processor and Playstation 3

Implementation of molecular dynamics (MD) calculations on novel architectures will vastly increase its power to calculate the physical properties of complex systems. Herein, we detail algorithmic advances developed to accelerate MD simulations on the Cell processor, a commodity processor found in PlayStation 3 (PS3). In particular, we discuss issues regarding memory access versus computation and the types of calculations which are best suited for streaming processors such as the Cell, focusing on implicit solvation models. We conclude with a comparison of improved performance on the PS3's Cell processor over more traditional processors.     

电场对(4, 0)Zigzag模型单壁碳纳米管的影响

The structural and electronic properties of a (4, 0) zigzag single-walled carbon nanotube (SWCNT) under parallel and transverse electric fields with strengths of 0-1.4×10~(-2) a.u. Were studied using the density functional theory (DFT) B3LYP/6-31G~* method. Results show that the properties of the SWCNT are dependent on the external electric field. The applied external electric field strongly affects the molecular dipole moments. The induced dipole moments increase linearly with increase in the electrical field intensities. This study shows that the application of parallel and transverse electric fields results in changes in the occupied and virtual molecular orbitals (Mos) but the energy gap between the highest occupied MO (HOMO) and the lowest unoccupied MO (LUMO) of this SWCNT is less sensitive to the electric field strength. The electronic spatial extent (ESE) and length of the SWCNT show small changes over the entire range of the applied electric field strengths. The natural bond orbital (NBO) electric charges on the atoms of the SWCNT show that increase in the external electric field strength increases the separation of the center of the positive and negative electric charges of the carbon nanotube.     

Theoretical study of preparative chromatography using closed-loop recycling with an initial gradient

Complementing classical isocratic elution, several more sophisticated operating modes have been proposed and are applied in preparative chromatography in order to improve performance. One such approach is gradient elution, where the solvent strength is altered by varying the fraction of a modifier added to the mobile phase to enhance selectivity and to achieve faster elution. Another useful technique is closed-loop recycling, allowing better peak resolution and increased yields. This study focuses on a modified new scheme which incorporates the advantages of both gradient elution and closed-loop recycling for the separation of a ternary mixture where the intermediately eluting component is the target. A parametric study was carried out using typical adsorption isotherm parameters to elucidate the effects of varying loading factors and parameters specific to the two basic operational modes on production rates and yields. A comparison was also made between the proposed scheme and conventional techniques. It was found that the studied scheme could exploit increased column loadings and offers significantly higher production rates.