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1、Modelling, simulation, and visualisation together create the third branch of human knowledge on equal footing with theory and experiment. Model-Driven Development (MDD) has been proposed as a means to support the software development process through the use of a model-centric approach. The objective

2、 of this paper is to address the design of an architecture for scientific application that may execute as multithreaded computations, as well as implementations of the related shared data structures. New version program summaryProgram title: Growth09 Catalogue identifier: ADVL_v3_0 Program summary U

3、RL: http:/cpc.cs.qub.ac.uk/summaries/ADVL_v3_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http:/cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 30

4、0;940 No. of bytes in distributed program, including test data, etc.: 3 119 488 Distribution format: tar.gz Programming language: Embarcadero Delphi Computer: Intel Core Duo-based PC Operating system: Windows XP, Vista, 7 RAM: more than 1 GB Classification: 4.3, 7.2, 6.2, 8, 14 Catalogue i

5、dentifier of previous version: ADVL_v2_1 Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1219 Subprograms used: Does the new version supersede the previous version?: No Nature of problem: Molecular beam epitaxy (MBE) is a technique for epitaxial growth via the interaction of on

6、e or several molecular or atomic beams that occurs on a surface of a heated crystalline substrate. 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 films and its contro

7、l. The analysis of RHEED intensity oscillations has two purposes. One is to control the film growth, and the other is to understand the mechanism of the film growth using the MBE through the analysis of surface morphology as a function of time. Such control allows the development of structures where

8、 the electrons can be confined in space, giving quantum wells or even quantum dots. Such layers are now a critical part of 3 many modern semiconductor devices, semiconductor lasers, light-emitting diodes and new devices for the magnetic storage industry. Solution method: The present paper reports a

9、practical and pragmatic approach for MDD technology 1 that has been used during design of the Growth09 program. Growth09 is a numerical model that uses multithreaded and partially nested transactions for simulation of epitaxial growth of thin films. Reasons for new version: Responding to user feedba

10、ck the program has been upgraded to a standard that allows a slave process, carrying out computations of the RHEED intensities for a disordered surface, to be run. Also, functionality and documentation of the program have been improved. Summary of revisions: 1. The MDD technology has been used to de

11、sign a computer model that allows the user to carry out numerical calculations layers coverage during the growth of thin epitaxial films, surface roughness, and the RHEED intensities for a disordered surface. This computer model can be applied to interpret the experimental data in real time 2. 2. Th

12、e logical structure of the Platform-Specific Model of the Growth06_v2 program has been modified according to the scheme shown in Fig. 1*. The class diagram in Fig. 1* is a static view of the main platform-specific elements of the Growth09 application architecture. Fig. 2* provides a dynamic view by

13、showing the creation and destruction simplistic sequence diagram. Fig. 3* presents the Growth09 use case model. 3. As can be seen in Fig. 1, Fig. 2 and Fig. 3* the Growth09 has been designed as a master program for the slave RHEED1DProcess (see A. Daniluk, Model-Driven Development for scientific com

14、puting. Computations of RHEED intensities for a disordered surface. Part I). 4. The slave RHEED1DProcess can be run as separate thread of the Growth09. Fig. 4* depicts the Platform-Specific Model for the development elements of the new distribution. *The figures mentioned can be downloaded, see “Sup

15、plementary material” below. Unusual features: The program is distributed in the form of main project Growth09.dproj, with associated files, and should be compiled using Embarcadero RAD Studio 2010 along with Together visual modelling platform. The program should be compiled with English/USA regional

16、 and language options. Additional comments: This version of the GROWTH program is designed to run in conjunction with the RHEED1DProcess (ADUY_v4_0) program. It does not replace the previous, stand alone, GROWTH06-v2 (ADVL_v2_1) version. Running time: The typical running time is machine and user-par

17、ameters dependent. References: 1 OMG, Model Driven Architecture Guide Version 1.0.1, 2003. 2 P. Mazurek, A. Daniluk, K. Paprocki, Vacuum 72 (4) (2004) 363.Article OutlineSupplementary materialSupplementary materialPurchase$ 31.5020Multithreaded transactions in scientific computing: New versions of a

18、 computer program for kinematical calculations of RHEED intensity oscillations  Original Research ArticleComputer Physics Communications, Volume 175, Issue 10, 15 November 2006, Pages 678-681Marcin Brzuszek, Andrzej Daniluk Close preview  |   Related articles 

19、 |  Related reference work articles     AbstractAbstract | ReferencesReferences AbstractWriting a concurrent program can be more difficult than writing a sequential program. Programmer needs to think about synchronisation, race conditions and shared variables. Tran

20、sactions help reduce the inconvenience of using threads. A transaction is an abstraction, which allows programmers to group a sequence of actions on the program into a logical, higher-level computation unit. This paper presents multithreaded versions of the GROWTH program, which allow to calculate t

21、he layer coverages during the growth of thin epitaxial films and the corresponding RHEED intensities according to the kinematical approximation. The presented programs also contain graphical user interfaces, which enable displaying program data at run-time. New version program summaryTitles of progr

22、ams:GROWTHGr, GROWTH06 Catalogue identifier:ADVL_v2_0 Program summary URL: http:/cpc.cs.qub.ac.uk/summaries/ADVL_v2_0 Program obtainable from:CPC Program Library, Queen's University of Belfast, N. Ireland Catalogue identifier of previous version:ADVL Does the new version supersede the original p

23、rogram:No Computer for which the new version is designed and others on which it has been tested: Pentium-based PC Operating systems or monitors under which the new version has been tested: Windows 9x, XP, NT Programming language used:Object Pascal Memory required to execute with typical data:More th

24、an 1 MB Number of bits in a word:64 bits Number of processors used:1 No. of lines in distributed program, including test data, etc.:20 931 Number of bytes in distributed program, including test data, etc.: 1 311 268 Distribution format:tar.gz Nature of physical problem: The programs c

25、ompute the RHEED intensities during the growth of thin epitaxial structures prepared using the molecular beam epitaxy (MBE). The computations are based on the use of kinematical diffraction theory P.I. Cohen, G.S. Petrich, P.R. Pukite, G.J. Whaley, A.S. Arrott, Surf. Sci. 216 (1989) 222. 1. Method o

26、f solution: Epitaxial growth ofFig. 1. Internal structure of the program.thin films is modelledFig. 2. Static classes model for graphical user interface.by a set ofFig. 3. Activity diagram for the program.non-linear differential equations P.I. Cohen, G.S. Petrich, P.R. Pukite, G.J. Wh

27、aley, A.S. Arrott, Surf. Sci. 216 (1989) 222. 1.Fig. 4. TTransaction class contents.The RungeKutta method with adaptive stepsize control was used for solving initial valueFig. 5. TGrowthTransaction class blem for non-linear differential equations W.H. Press, B.P. Flannery, S.A.

28、 Teukolsky, W.T. Vetterling, Numerical Recipes in Pascal: The Art of Scientific Computing, first ed., Cambridge University Press, 1989; See also: Numerical Recipes in C+, second ed., Cambridge University Press, 1992. 2. Reasons for the new version: According to the users' suggestions we improved

29、 functionality of the program. Moreover, we added new capabilities which make the input data design process and output even easier and more efficient than the previous one. Summary of revisions: (1) We designed fully object-oriented extensions of previous version of the program A. Daniluk, Comput. P

30、hys. Comm. 170 (2005) 265. 3. In the present form the programs enable concurrently compute and display program data at run-time through an easy-to-use graphical interface. (2) The code has been modified and optimised to compile under the Delphi IDE (integrated development environment). (3) A graphic

31、al user interface (GUI) for the programs have been created. The applications are MDI (multiple document interface) projects from Delphi's object repository. Each of the MDI application spawns child windows that reside within the client window; the main form contains child objects. (4) The progra

32、ms offer the possibility to carry out computations on the basis of the model of multithreaded transactions. Transactions have four elements, known as the ACID properties: atomicity, consistency, isolation and durability S. Jagannathan, J. Vitek, A. Welc, A. Hosking, Science of Computer Programming 5

33、7 (2005) 164. 4, M. Brzuszek, MSc thesis, MCS University, Lublin, 2005 (in Polish). 5. Atomicity means that either the entire transaction completes, or it is as if the transaction never executed. Consistency means that the transaction maintains the data integrity constrains of the program. Isolation

34、 means that even if transaction executed concurrently, their results appear as if they were executed in some serial order. Durability means that all changes made by a committed transaction are permanent, i.e. the effects of transaction survive subsequent system failures. The presented programs suppo

35、rt all of properties mentioned above. Fig. 1 shows internal structure of the programs. Fig. 2 shows the static structure of classes and their possible relationships (i.e. inheritance, association and aggregation) in the code. Fig. 3 shows an activity diagram for the programs. (5) The programs have b

36、een constructed according to the systems development live cycle (SDLC) methodology J.A. Hoffer, J.F. George, J.S. Valacich, Modern Systems Analysis and Design, Addison-Wesley, 1999. 6. (6) The GROWTH06 program has been modelled using the Borland Together Architect visual-modelling platform. Figs. 4

37、and 5 show the static structure of the TTransaction and TGrowthTransaction classes. Typical running time: The typical running time is machine and user-parameters dependent. Unusual features of the programs: The programs are distributed in the form of source projects GROWTHGr.dpr and GROWTH06.bdsproj

38、 with associated files, and should be compiled using Borland Delphi compilers versions 5 or latter and Delphi Borland Developer Studio 2006, respectively.Purchase$ 31.5021ROOT A C+ framework for petabyte data storage, statistical analysis and visualization  Original Research ArticleCompute

39、r Physics Communications, Volume 180, Issue 12, December 2009, Pages 2499-2512I. Antcheva, M. Ballintijn, B. Bellenot, M. Biskup, R. Brun, N. Buncic, Ph. Canal, D. Casadei, O. Couet, V. Fine, L. Franco, G. Ganis, A. Gheata, D. Gonzalez Maline, M. Goto, J. Iwaszkiewicz, A. Kreshuk, D. Marcos Segura,

40、R. Maunder, L. Moneta, et al. Close preview  |   Related articles  |  Related reference work articles     AbstractAbstract | Figures/TablesFigures/Tables | ReferencesReferences AbstractROOT is an object-oriented C+ framework conceived

41、in the high-energy physics (HEP) community, designed for storing and analyzing petabytes of data in an efficient way. Any instance of a C+ class can be stored into a ROOT file in a machine-independent compressed binary format. In ROOT the TTree object container is optimized for statistical data anal

42、ysis over very large data sets by using vertical data storage techniques. These containers can span a large number of files on local disks, the web, or a number of different shared file systems. In order to analyze this data, the user can chose out of a wide set of mathematical and statistical funct

43、ions, including linear algebra classes, numerical algorithms such as integration and minimization, and various methods for performing regression analysis (fitting). In particular, the RooFit package allows the user to perform complex data modeling and fitting while the RooStats library provides abst

44、ractions and implementations for advanced statistical tools. Multivariate classification methods based on machine learning techniques are available via the TMVA package. A central piece in these analysis tools are the histogram classes which provide binning of one- and multi-dimensional data. Result

45、s can be saved in high-quality graphical formats like Postscript and PDF or in bitmap formats like JPG or GIF. The result can also be stored into ROOT macros that allow a full recreation and rework of the graphics. Users typically create their analysis macros step by step, making use of the interact

46、ive C+ interpreter CINT, while running over small data samples. Once the development is finished, they can run these macros at full compiled speed over large data sets, using on-the-fly compilation, or by creating a stand-alone batch program. Finally, if processing farms are available, the user can

47、reduce the execution time of intrinsically parallel tasks e.g. data mining in HEP by using PROOF, which will take care of optimally distributing the work over the available resources in a transparent way. Program summaryProgram title: ROOT Catalogue identifier: AEFA_v1_0 Program summary URL: http:/c

48、pc.cs.qub.ac.uk/summaries/AEFA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: LGPL No. of lines in distributed program, including test data, etc.: 3 044 581 No. of bytes in distributed program, including test data,

49、etc.: 36 325 133 Distribution format: tar.gz Programming language: C+ Computer: Intel i386, Intel x86-64, Motorola PPC, Sun Sparc, HP PA-RISC Operating system: GNU/Linux, Windows XP/Vista, Mac OS X, FreeBSD, OpenBSD, Solaris, HP-UX, AIX Has the code been vectorized or parallelized?: Yes RA

50、M: >55 Mbytes Classification: 4, 9, 11.9, 14 Nature of problem: Storage, analysis and visualization of scientific data Solution method: Object store, wide range of analysis algorithms and visualization methods Additional comments: For an up-to-date author list see: http:/root.cern.ch/drupal/

51、content/root-development-team and http:/root.cern.ch/drupal/content/former-root-developers Running time: Depending on the data size and complexity of analysis algorithms References: 1 http:/root.cern.ch.Article Outline1. Introduction 1.1. Discovering ROOT1.2. Typical uses of ROOT2. Description of th

52、e ROOT framework 2.1. Input/output 2.1.1. Describing C+ objects2.1.2. TFile2.1.3. TTree and I/O2.1.4. I/O formats2.2. Mathematical and statistical tools2.3. Histograms2.4. Graphics and User Interface 2.4.1. 2D graphics2.4.2. 3D graphics2.4.3. Geometry and event display2.4.4. Graphical User Interface

53、2.5. Simulation2.6. Interpreters 2.6.1. Interpreter use cases2.6.2. Automatic library builds2.7. Parallel processing using PROOF 2.7.1. PROOF architecture2.7.2. Event level parallelism2.7.3. The packetizer2.7.4. The selector framework2.7.5. Aggregation of results2.7.6. Real time monitoring and feedb

54、ack3. Installation instructions 3.1. Getting the source3.2. Compiling4. Test run descriptionAcknowledgementsReferencesPurchase$ 31.5022Software products for modelling and simulation in materials science  Original Research ArticleComputational Materials Science, Volume 28, Issue 2, October

55、2003, Pages 179-198S. Malinov, W. Sha Close preview  |   Related articles  |  Related reference work articles     AbstractAbstract | Figures/TablesFigures/Tables | ReferencesReferences AbstractModels and software products have been dev

56、eloped for modelling, simulation and prediction of different correlations in materials science, including1. the correlation between processing parameters and properties in titanium alloys and -titanium aluminides;2. timetemperaturetransformation (TTT) diagrams for titanium alloys;3. corrosion resist

57、ance of titanium alloys;4. surface hardness and microhardness profile of nitrocarburised layers;5. fatigue stress life (SN) diagrams for Ti6Al4V alloys. The programs are based on trained artificial neural networks. For each particular case appropriate combination of inputs and outputs is chosen. Ver

58、y good performances of the models are achieved. Graphical user interfaces (GUI) are created for easy use of the models. In addition interactive text versions are developed. The models designed are combined and integrated in software package that is built up on a modular fashion. The software product

59、s are available in versions for different platforms including Windows 95/98/2000/NT, UNIX and Apple Macintosh. Description of the software products is given, to demonstrate that they are convenient and powerful tools for practical applications in solving various problems in materials science. Examples for optimisation of the alloy compositions, processing parameters and working conditions are illustrated. An option for use of the software in materials selection pro