A new version of Scilab software package for the study of dynamical systems

This work presents a new version of a software package for the study of chaotic flows, maps and fractals [1]. The codes were written using Scilab, a software package for numerical computations providing a powerful open computing environment for engineering and scientific applications. It was found that Scilab provides various functions for ordinary differential equation solving, Fast Fourier Transform, autocorrelation, and excellent 2D and 3D graphical capabilities. The chaotic behaviors of the nonlinear dynamics systems were analyzed using phase-space maps, autocorrelation functions, power spectra, Lyapunov exponents and Kolmogorov-Sinai entropy. Various well-known examples are implemented, with the capability of the users inserting their own ODE or iterative equations.

New version program summary

Program title: Chaos v2.0Catalogue identifier: AEAP_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAP_v2_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.: 1275No. of bytes in distributed program, including test data, etc.: 7135Distribution format: tar.gzProgramming language: Scilab 5.1.1. Scilab 5.1.1 should be installed before running the program. Information about the installation can be found at http://wiki.scilab.org/howto/install/windows.Computer: PC-compatible running Scilab on MS Windows or LinuxOperating system: Windows XP, LinuxRAM: below 150 MegabytesClassification: 6.2Catalogue identifier of previous version: AEAP_v1_0Journal reference of previous version: Comput. Phys. Comm. 178 (2008) 788Does the new version supersede the previous version?: YesNature of problem: Any physical model containing linear or nonlinear ordinary differential equations (ODE).Solution method:

1.

Numerical solving of ordinary differential equations for the study of chaotic flows. The chaotic behavior of the nonlinear dynamical system is analyzed using Poincare sections, phase-space maps, autocorrelation functions, power spectra, Lyapunov exponents and Kolmogorov-Sinai entropies.

2.

Numerical solving of iterative equations for the study of maps and fractals.

Reasons for new version: The program has been updated to use the new version 5.1.1 of Scilab with new graphical capabilities [2]. Moreover, new use cases have been added which make the handling of the program easier and more efficient.Summary of revisions:

1.

A new use case concerning coupled predator-prey models has been added [3].

2.

Three new use cases concerning fractals (Sierpinsky gasket, Barnsley's Fern and Tree) have been added [3].

3.

The graphical user interface (GUI) of the program has been reconstructed to include the new use cases.

4.

The program has been updated to use Scilab 5.1.1 with the new graphical capabilities.

Additional comments: The program package contains 12 subprograms.

•

interface.sce - the graphical user interface (GUI) that permits the choice of a routine as follows

•

1.sci - Lorenz dynamical system

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2.sci - Chua dynamical system

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3.sci - Rosler dynamical system

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4.sci - Henon map

•

5.sci - Lyapunov exponents for Lorenz dynamical system

•

6.sci - Lyapunov exponent for the logistic map

•

7.sci - Shannon entropy for the logistic map

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8.sci - Coupled predator-prey model

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1f.sci - Sierpinsky gasket

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2f.sci - Barnsley's Fern

•

3f.sci - Barnsley's Tree

Running time: 10 to 20 seconds for problems that do not involve Lyapunov exponents calculation; 60 to 1000 seconds for problems that involve high orders ODE, Lyapunov exponents calculation and fractals.References:

[1]

C.C. Bordeianu, C. Besliu, Al. Jipa, D. Felea, I. V. Grossu, Comput. Phys. Comm. 178 (2008) 788.

[2]

S. Campbell, J.P. Chancelier, R. Nikoukhah, Modeling and Simulation in Scilab/Scicos, Springer, 2006.

[3]

R.H. Landau, M.J. Paez, C.C. Bordeianu, A Survey of Computational Physics, Introductory Computational Science, Princeton University Press, 2008.

     

A Macintosh software package for simulation of human red blood cell metabolism.

We have developed a computer software package for Macintosh to simulate the metabolism and hemoglobin binding affinity of human red blood cell. The model is capable of simulating hemoglobin binding of ligands, metabolite concentrations, and metabolic fluxes at physiological steady state and in response to extracellular parameter variations, such as pH, osmolarity, glucose, and adenine concentrations. The kinetic parameters of enzymes, extracellular conditions, and initial intracellular metabolite concentrations can be specified by the user in order to model a particular situation. The software is use friendly, utilizing menu, window, and mouse to interact with the user. It also provides a pathway map of the red cell, which allows a direct access to enzyme kinetics by clicking the enzymes in the map.     

A flux splitting method for the numerical simulation of one-dimensional compressible flow

Using the technique of flux vector splitting, it is shown that one-dimensional, inviscid, compressible-flow equations possess a split conservation form. Some attractive features of this form for the design of finite-difference solution schemes are discussed. Based on the split form, two solution chemes are designed. One is a first-order accurate ‘upwind’ scheme and the other is similar to the Lax-Wendroff scheme. A hybrid scheme, based on a nonlinear weighting of these two schemes, is demonstrated to yield results superior to either of the two in the solution of an ideal shock-tube problem.     

A program package for simulation of coupled chemical reactions in flow reactors

A program package KINSIMI for an interactive simulation of homogeneous isothermal reactor systems with an arbitrary elementary kinetics has been developed. The simulation of ideal reactors, tanks-in-series, normal axial dispersion reactors and segregated and maximum mixed tanks-in-series and axial dispersion reactors can be performed with the program package. For the ideal reactors and tanks-in-series both step responses and steady states can be computed. For the axial dispersion, segregation and maximum mixedness models the treatment is limited to a steady state stimulation. For the segregation model, empirical batch reactor kinetics can be used in the computation of continuous reactor performance. The corresponding mathematical models and the numerical algorithms are discussed. Two examples of the application of the package are given. The program package can be used for reactor design as well as for educational purposes in illustrating the influence of different reaction mechanisms and flow patterns on the conversion and product distribution.     

Automating the simulation of complex discrete-time control systems:a mathematical framework, algorithms, and a software package

With the rapid proliferation of complex control systems, such as adaptive control systems, a need has arisen to automate as much as possible of the time-consuming preparatory work needed to simulate such systems. This burden currently falls on the user. The smaller the user time required and the more effortless the process, the greater, the authors believe, will be the eventual widespread acceptability of these control systems. This paper is aimed at bridging this gap between the theoretical specification of a complex discrete-time control system as described in a typical research paper and the obtaining of a first simulation. It provides a graph theoretical formulation of the issues involved, discrete algorithms to execute these tasks, and finally describes ISIM, an interpretive simulator which incorporates these features. These algorithms automate the simulation process, as seen by the user. The net result is a package which essentially requires only that the user type in a control system more or less verbatim from a technical paper to obtain a simulation output     

OpenTracker: A flexible software design for three-dimensional interaction

Tracking is an indispensable part of any virtual reality and augmented reality application. While the need for quality of tracking, in particular for high performance and fidelity, has led to a large body of past and current research, little attention is typically paid to software engineering aspects of tracking software. To address this issue we describe a software design and implementation that applies the pipes-and-filter architectural pattern to provide a customizable and flexible way of dealing with tracking data and configurations. The contribution of this work cumulates in the development of a generic data flow network library called OpenTracker to deal specifically with tracking data. The flexibility of the data flow network approach is demonstrated in a set of development scenarios and prototype applications in the area of mobile augmented reality.     

An enhanced version of SMMP—open-source software package for simulation of proteins

We describe a revised and updated version of the program package SMMP (Simple Molecular Mechanics for Proteins) [F. Eisenmenger, U.H.E. Hansmann, Sh. Hayryan, C.-K. Hu, Comput. Phys. Comm. 138 (2001) 192-212]. SMMP is an open-source FORTRAN package for molecular simulation of proteins within the standard geometry model. It is designed as a simple and inexpensive tool for researchers and students to become familiar with protein simulation techniques. This announcement describes the first major revision of this software package and its newly added features.

Program summary

Title of program:SMMPCatalogue identifier:ADOJ₋v2₋0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADOJ_v2_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandOperating system under which the program has been tested:LINUX systemProgramming language used:FORTRANComputer:PC PentiumNumber of lines in distributed program, including test data, etc.:18 492Number of bytes in distributed program, including test data, etc.:278 995Distribution format:ASCIICard punching code:ASCIICatalogue Identifier of previous version:ADOJJournal Reference of previous version:F. Eisenmenger, U.H.E. Hansmann, Sh. Hayryan, C.-K. Hu, Comput. Phys. Comm. 138 (2001) 192-212Does the new version supersede the previous version?:YesNature of physical problem:Molecular mechanics computations and Monte Carlo simulation of proteinsReasons for the new version:Increased functionalitySummary of revisions:Changes in energy function and protein representation; differences in program structure and organization; new functionalities added; miscellaneous changes and additionsMethod of solution:Utilizes ECEPP2/3 and FLEX potentials. Includes Monte Carlo simulation algorithms for canonical, as well as for generalized ensemblesRestrictions on the complexity of the problem:The consumed CPU time increases with the size of protein moleculeTypical running time:Depends on the size of the molecule under simulationUnusual features of the program:No     

A software package for system identification in the behavioral setting

An identification problem with no a priori separation of the variables into inputs and outputs and representation invariant approximation criterion is considered. The model class consists of linear time-invariant systems of bounded complexity and the approximation criterion is the minimum of a weighted 2-norm distance between the given time series and a time series that is consistent with the model. The problem is equivalent to and is solved as a mosaic-Hankel structured low-rank approximation problem. Software implementing the approach is developed and tested on benchmark problems. Additional nonstandard features of the software are specification of exact and missing variables and identification from multiple experiments.     

GULFHYDRO Version 2.0: A software package for hydrodynamics in the Arabian Gulf

A software package is described for modelling the hydrodynamics in the Arabian Gulf and in arbitrarily small sub-regions of this water body. The package is designed to run under Windows 95 and has user-friendly graphical interfaces for model input and for examination of the output. Examples are shown to illustrate typical input and output screens and to demonstrate the accuracy of the model.     

Calcium3D: a visual software package for the simulation of calcium buffered diffusion in neuroendocrine cells

We present Calcium3D, a user-friendly software package for simulating calcium triggered processes in neuroendocrine cells. We use Monte Carlo methods for the simulation of the basic processes involved: entry of calcium into the cytoplasm, the diffusion of ions and mobile intracellular calcium buffers inside the intracellular medium, and the kinetics of the reaction of calcium with these buffers. The outputs of the simulation are calcium and buffer concentrations as a function of time and for different depths from the cellular membrane.     

三屏幕系统图文处理软件包

为了扩大视觉范围,增加人与计算机之间交互的信息量,我校人机信息界面技术实验室建立了一个具有三个屏幕的计算机图形系统,本课题组研制了该系统的图形文字处理软件包。三个屏幕既可联合成一个大屏幕,用以显示相连的或相关的信息,如一幅大地图;又可使每个屏幕作为一个窗口显示多画面,且能同步协调地变化。用户可在任一屏幕上进行图形或文本的编辑和处理,还能表示层次图形与信息逐步加细。作者已将通常的单屏幕上的软件工具改造为支持多屏幕系统,因而熟悉IBM-PC机的用户很容易使用该系统。本文给出了该软件包的功能及实现策略,详述了将Auto CAD绘图软件改造为支持多屏幕系统的方法。     

Scilab software package for the study of dynamical systems

This work presents a new software package for the study of chaotic flows and maps. The codes were written using Scilab, a software package for numerical computations providing a powerful open computing environment for engineering and scientific applications. It was found that Scilab provides various functions for ordinary differential equation solving, Fast Fourier Transform, autocorrelation, and excellent 2D and 3D graphical capabilities. The chaotic behaviors of the nonlinear dynamics systems were analyzed using phase-space maps, autocorrelation functions, power spectra, Lyapunov exponents and Kolmogorov-Sinai entropy. Various well known examples are implemented, with the capability of the users inserting their own ODE.

Program summary

Program title: ChaosCatalogue identifier: AEAP_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAP_v1_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.: 885No. of bytes in distributed program, including test data, etc.: 5925Distribution format: tar.gzProgramming language: Scilab 3.1.1Computer: PC-compatible running Scilab on MS Windows or LinuxOperating system: Windows XP, LinuxRAM: below 100 MegabytesClassification: 6.2Nature of problem: Any physical model containing linear or nonlinear ordinary differential equations (ODE).Solution method: Numerical solving of ordinary differential equations. The chaotic behavior of the nonlinear dynamical system is analyzed using Poincaré sections, phase-space maps, autocorrelation functions, power spectra, Lyapunov exponents and Kolmogorov-Sinai entropies.Restrictions: The package routines are normally able to handle ODE systems of high orders (up to order twelve and possibly higher), depending on the nature of the problem.Running time: 10 to 20 seconds for problems that do not involve Lyapunov exponents calculation; 60 to 1000 seconds for problems that involve high orders ODE and Lyapunov exponents calculation.     

Review of the Robotica software package for robotic manipulators

Robotica is a computer-aided design package for robotic nmanipulators developed at the Coordinated Science Laboratory at the University of Illinois at Urbana- Champaign. The package is a collection of function definitions for the Mathematica symbolic mathematics program. Robotica can be used either with an X- Windows graphical user interface (GUI) on a Sun Workstation or as an included function definition file within Mathematica. The primary feature of Robotica is the ability to compute, symbolically or numerically, the kinematic and dynamic equations of arbitrary robot systems utilizing the standard Denevit-Hartenburg (DH) kinematic convention. Robotica also provides the ability to visualize these arbitrary manipulators using the X- Windows graphical interface to the Mathematica graphics routines. The paper looks at the usage of Robotica at the Air Force Institute of Technology, comments on the features of Robotica, and needs for improvement and suggestions for future development     

混凝土湿热耦合模拟分析程序软件的开发与应用

为了利用计算机技术时混凝土湿热耦合传输及变形进行数值模拟分析,并在实际工程结构变形预测中有效应用,根据提出的基于Visual Basic调用Matlab及ANSYS的软件开发策略,通过混合编程开发了混凝土湿热耦合数值模拟计算程序软件(CTMSoft).利用CTMSofl对实际工程结构中混凝土的湿热传输及变形进行了数值模拟,模拟分析结果与现场实际试验及结构监测结果一致,证实该方法和程序软件是正确有效的.