Cooperative and competitive concurrency in scientific computing. A full open-source upgrade of the program for dynamical calculations of RHEED intensity oscillations

A computational model is a computer program, which attempts to simulate an abstract model of a particular system. Computational models use enormous calculations and often require supercomputer speed. As personal computers are becoming more and more powerful, more laboratory experiments can be converted into computer models that can be interactively examined by scientists and students without the risk and cost of the actual experiments. The future of programming is concurrent programming. The threaded programming model provides application programmers with a useful abstraction of concurrent execution of multiple tasks. The objective of this release is to address the design of architecture for scientific application, which may execute as multiple threads execution, as well as implementations of the related shared data structures.

New version program summary

Program title: GrowthCPCatalogue identifier: ADVL_v4_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVL_v4_0.htmlProgram obtainable from: CPC Program Library, Queen?s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 32 269No. of bytes in distributed program, including test data, etc.: 8 234 229Distribution format: tar.gzProgramming language: Free Object PascalComputer: multi-core x64-based PCOperating system: Windows XP, Vista, 7Has the code been vectorised or parallelized?: NoRAM: More than 1 GB. The program requires a 32-bit or 64-bit processor to run the generated code. Memory is addressed using 32-bit (on 32-bit processors) or 64-bit (on 64-bit processors with 64-bit addressing) pointers. The amount of addressed memory is limited only by the available amount of virtual memory.Supplementary material: The figures mentioned in the “Summary of revisions” section can be obtained here.Classification: 4.3, 7.2, 6.2, 8, 14External routines: Lazarus [1]Catalogue identifier of previous version: ADVL_v3_0Journal reference of previous version: Comput. Phys. Comm. 181 (2010) 709Does the new version supersede the previous version?: YesNature of problem: Reflection high-energy electron diffraction (RHEED) is an important in-situ analysis technique, which is capable of giving quantitative information about the growth process of thin layers and its control. It can be used to calibrate growth rate, analyze surface morphology, calibrate surface temperature, monitor the arrangement of the surface atoms, and provide information about growth kinetics. Such control allows the development of structures where the electrons can be confined in space, giving quantum wells or even quantum dots. In order to determine the atomic positions of atoms in the first few layers, the RHEED intensity must be measured as a function of the scattering angles and then compared with dynamic calculations. The objective of this release is to address the design of architecture for application that simulates the rocking curves RHEED intensities during hetero-epitaxial growth process of thin films.Solution method: The GrowthCP is a complex numerical model that uses multiple threads for simulation of epitaxial growth of thin layers. This model consists of two transactional parts. The first part is a mathematical model being based on the Runge–Kutta method with adaptive step-size control. The second part represents first-principles of the one-dimensional RHEED computational model. This model is based on solving a one-dimensional Schrödinger equation. Several problems can arise when applications contain a mixture of data access code, numerical code, and presentation code. Such applications are difficult to maintain, because interdependencies between all the components cause strong ripple effects whenever a change is made anywhere. Adding new data views often requires reimplementing a numerical code, which then requires maintenance in multiple places. In order to solve problems of this type, the computational and threading layers of the project have been implemented in the form of one design pattern as a part of Model-View-Controller architecture.Reasons for new version: Responding to the users? feedback the Growth09 project has been upgraded to a standard that allows the carrying out of sample computations of the RHEED intensities for a disordered surface for a wide range of single- and epitaxial hetero-structures. The design pattern on which the project is based has also been improved. It is shown that this model can be effectively used for multithreaded growth simulations of thin epitaxial layers and corresponding RHEED intensities for a wide range of single- and hetero-structures. Responding to the users? feedback the present release has been implemented using a well-documented free compiler [1] not requiring the special configuration and installation additional libraries.Summary of revisions:

• 1. 

  The logical structure of the Growth09 program has been modified according to the scheme showed in Fig. 1.1 The class diagram in Fig. 11 is a static view of the main platform-specific elements of the GrowthCP architecture. Fig. 21 provides a dynamic view by showing the creation and destruction simplistic sequence diagram for the process.

• 2. 

  The program requires the user to provide the appropriate parameters in the form of a knowledge base for the crystal structures under investigation. These parameters are loaded from the parameters.ini files at run-time. Instructions to prepare the .ini files can be found in the new distribution.

• 3. 

  The program enables carrying out different growth models and one-dimensional dynamical RHEED calculations for the fcc lattice with basis of three-atoms, fcc lattice with basis of two-atoms, fcc lattice with single atom basis, Zinc-Blende, Sodium Chloride, and Wurtzite crystalline structures and hetero-structures, but yet the Fourier component of the scattering potential in the TRHEEDCalculations.crystPotUgXXX() procedure can be modified and implemented according to users? specific application requirements. The Fourier component of the scattering potential of the whole crystalline hetero-structures can be determined as a sum of contributions coming from all thin slices of individual atomic layers. To carry out one-dimensional calculations of the scattering potentials, the program uses properly constructed self-consistent procedures.

• 4. 

  Each component of the system shown in Figs. 11 and 21 is fully extendable and can easily be adapted to new changeable requirements. Two essential logical elements of the system, i.e. TGrowthTransaction and TRHEEDCalculations classes, were designed and implemented in this way for them to pass the information to themselves without the need to use the data-exchange files given. In consequence each of them can be independently modified and/or extended. Implementing other types of differential equations and the different algorithm for solving them in the TGrowthTransaction class does not require another implementation of the TRHEEDCalculations class. Similarly, implementing other forms of scattering potential and different algorithm for RHEED calculation stays without the influence on the TGrowthTransaction class construction.

Unusual features: The program is distributed in the form of main project GrowthCP.lpr, with associated files, and should be compiled using Lazarus IDE. The program should be compiled with English/USA regional and language options.Running time: The typical running time is machine and user-parameters dependent.References:

• [1] 

  http://sourceforge.net/projects/lazarus/files/.

     

Optimization of Geoscience Laser Altimeter System waveform metrics to support vegetation measurements

The Geoscience Laser Altimeter System (GLAS) has collected over 250 million measurements of vegetation height over forests globally. Accurate vegetation heights can be determined using waveform metrics that include vertical extent and extent of the waveform's trailing and leading edges. All three indices are highly dependent upon the signal strength, background noise and signal-to-noise ratio of the waveform, as the background noise contribution to the waveforms has to be removed before their calculation. Over the last six years, GLAS has collected data during thirteen observation periods using illumination from three different lasers. The power levels of these lasers have changed over time, resulting in variable signal power and noise characteristics. Atmospheric conditions vary continuously, also influencing signal power and noise.To minimize these effects, we optimized a noise coefficient which could be constant or vary according to observation period or noise metric. This parameter is used with the mean and standard deviation of the background noise to determine a noise level threshold that is removed from each waveform. An optimization analysis was used with a global dataset of waveforms that are near-coincident with waveforms from other observation periods; the goal of the optimization was to minimize the difference in vertical extent between spatially overlapping GLAS observations. Optimizations based on absolute difference in height led to situations in which the total extent was minimized as well; further optimizations reduced a normalized difference in height extent. The simplest optimizations were based on a constant value to be applied to all observations; noise coefficients of 2.7, 3.2, 3.4 and 4.0 were determined for datasets consisting of global forests, global vegetation, forest in the legal Amazon basin and boreal forests respectively. Optimizations based on the power level or the signal-to-noise ratio of waveforms best minimized differences in waveform extent, decreasing the percent root mean squared height difference by 25-54% over the constant value approach. Further development of methods to ensure temporal consistency of waveform indices will be necessary to support long-term satellite lidar missions and will result in more accurate and precise estimates of canopy height.     

A fuzzy reasoning and fuzzy-analytical hierarchy process based approach to the process of railway risk information: A railway risk management system

Risk management is becoming increasingly important for railway companies in order to safeguard their passengers and employees while improving safety and reducing maintenance costs. However, in many circumstances, the application of probabilistic risk analysis tools may not give satisfactory results because the risk data are incomplete or there is a high level of uncertainty involved in the risk data. This article presents the development of a risk management system for railway risk analysis using fuzzy reasoning approach and fuzzy analytical hierarchy decision making process. In the system, fuzzy reasoning approach (FRA) is employed to estimate the risk level of each hazardous event in terms of failure frequency, consequence severity and consequence probability. This allows imprecision or approximate information in the risk analysis process. Fuzzy analytical hierarchy process (fuzzy-AHP) technique is then incorporated into the risk model to use its advantage in determining the relative importance of the risk contributions so that the risk assessment can be progressed from hazardous event level to hazard group level and finally to railway system level. This risk assessment system can evaluate both qualitative and quantitative risk data and information associated with a railway system effectively and efficiently, which will provide railway risk analysts, managers and engineers with a method and tool to improve their safety management of railway systems and set safety standards. A case study on risk assessment of shunting at Hammersmith depot is used to illustrate the application of the proposed risk assessment system.     

Assessment of the impacts of surface topography, off-nadir pointing and vegetation structure on vegetation lidar waveforms using an extended geometric optical and radiative transfer model

In order to prioritize the measurement requirements and accuracies of the two new lidar missions, a physical model is required for a fundamental understanding of the impact of surface topography, footprint size and off-nadir pointing on vegetation lidar waveforms and vegetation height retrieval. In this study, we extended a well developed Geometric Optical and Radiative Transfer (GORT) vegetation lidar model to take into account for the impacts of surface topography and off-nadir pointing on vegetation lidar waveforms and vegetation height retrieval and applied this extended model to assess the aforementioned impacts on vegetation lidar waveforms and height retrieval.Model simulation shows that surface topography and off-nadir pointing angle stretch waveforms and the stretching effect magnifies with footprint size, slope and off-nadir pointing angle. For an off-nadir pointing laser penetrating vegetation over a slope terrain, the waveform is either stretched or compressed based on the relative angle. The stretching effect also results in a disappearing ground peak return when slope or off-nadir pointing angle is larger than the “critical slope angle”, which is closely related to various vegetation structures and footprint size. Model simulation indicates that waveform shapes are affected by surface topography, off-nadir pointing angle and vegetation structure and it is difficult to remove topography effects from waveform extent based only on the shapes of waveform without knowing any surface topography information.Height error without correction of surface topography and off-nadir pointing angle is the smallest when the laser beams at the toward-slope direction and the largest from the opposite direction. Further simulation reveals within 20° of slope and off-nadir pointing angle, given the canopy height as roughly 25 m and the footprint size as 25 m, the error for vegetation height (RH100) ranges from − 2 m to greater than 12 m, and the error for the height at the medium energy return (RH50) from − 1 m to 4 m. The RH100 error caused by unknown surface topography and without correction of off-nadir pointing effect can be explained by an analytical formula as a function of vegetation height, surface topography, off-nadir pointing angle and footprint size as a first order approximation. RH50 is not much affected by topography, off-nadir pointing and footprint size. This forward model simulation can provide scientific guidance on prioritizing future lidar mission measurement requirements and accuracies.     

A threshold insensitive method for locating the forest canopy top with waveform lidar

Lidars have the unique ability to make direct, physical measurements of forest height and vertical structure in much denser canopies than is possible with passive optical or short wavelength radars. However the literature reports a consistent underestimate of tree height when using physically based methods, necessitating empirical corrections. This bias is a result of overestimating the range to the canopy top due to background noise and failing to correctly identify the ground.This paper introduces a method, referred to as “noise tracking”, to avoid biases when determining the range to the canopy top. Simulated waveforms, created with Monte-Carlo ray tracing over geometrically explicit forest models, are used to test noise tracking against simple thresholding over a range of forest and system characteristics. It was found that noise tracking almost completely removed the bias in all situations except for very high noise levels and very low (< 10%) canopy covers. In all cases noise tracking gave lower errors than simple thresholding and had a lower sensitivity to the initial noise threshold.Finite laser pulses spread out the measured signal, potentially overriding the benefit of noise tracking. In the past laser pulse length has been corrected by adding half that length to the signal start range. This investigation suggests that this is not always appropriate for simple thresholding and that the results for noise tracking were more directly related to pulse length than for simple thresholding. That this effect has not been commented on before may be due to the possible confounding impacts of instrument and survey characteristics inherent in field data. This method should help improve the accuracy of waveform lidar measurements of forests, whether using airborne or spaceborne instruments.     

A novel heuristic algorithm for QoS-aware end-to-end service composition

Many works have been carried out to find the efficient algorithms for QoS-aware service composition in recent years. Nevertheless, on one hand, some of these works only consider the local QoS attributes in Web services composition; on the other hand, some ideas derived from QoS selection algorithms for network routing are directly applied in service composition without any adaption. A service composition model with end-to-end QoS constraints has been presented in this paper. An improved heuristics HCE based on the observation of characteristic of end-to-end service composition is proposed as a novel solution. Simulation results reveal the better performance of proposed heuristic compared to the other two heuristics, HMCOP and generic CE algorithm.     

一类欠驱动系统的非线性输出跟踪控制

针对一类模型结构为非下三角的欠驱动系统,在反步法的框架下研究了其非线性输出跟踪控制问题．鉴于在此类欠驱动系统的反步法设计中,沿用一般下三角系统的偏差难以镇定全部的偏差动态,由此引入了“联系函数”的概念．在反步法设计中,构造了异于下三角系统的偏差,设计了状态反馈跟踪控制器,保证了系统偏差的全局一致渐近稳定性．仿真结果表明...     

一类切换系统的输入-状态稳定性分析与优化控制

利用驻留时间法和 Gronwall-Bellman不等式研究了一类切换系统的输入一状态稳定性分析与优化控制问题.在保证切换系统输入-状态稳定的前提下,将切换时刻和切换次数约束条件转化为线性约束,提出了一种新的切换系统优化问题目标函数的形式.与已有的方法相比,该方法无需引入新的状态变量,无需同时满足构造输入-状态稳定控制李亚普诺夫函数和所有子系统都是输入-状态稳定的条件,为控制器的优化设计提供了便利.最后,通过算例仿真证实了文中所提方法的可行性.     

能耗最优的水下滑翔机采样路径规划

研究了以能耗为优化准则的水下滑翔机海洋环境参数采样路径规划方法.首先,根据水下滑翔机的运动特点,建立了水下滑翔机采样作业过程的能耗模型;其次,基于能耗模型提出了一种能耗最小的滑翔运动参数优化方法,该方法避免了求解复杂的混合整数非线性规划问题;之后,在能耗最优的滑翔运动参数优化基础上,提出了一种基于两步链式Lin-Ker...     

Dynamic Network User Equilibrium with State-Dependent Time Lags

This paper recasts the Friesz et al. (1993) measure theoretic model of dynamic network user equibrium as a controlled variational inequality problem involving Riemann integrals. This restatement is done to make the model and its foundations accessible to a wider audience by removing the need to have a background in functional analysis. Our exposition is dependent on previously unavailable necessary conditions for optimal control problems with state-dependent time lags. These necessary conditions, derived in an Appendix, are employed to show that a particular variational inequality control problem has solutions that are dynamic network user equilibria. Our analysis also shows that use of proper flow propagation constraints obviates the need to explicitly employ the arc exit time functions that have complicated numerical implementations of the Friesz et al. (1993) model heretofore. We close by describing the computational implications of numerically determining dynamic user equilibria from formulations based on state-dependent time lags.