The Flexible Rare Event Sampling Harness System (FRESHS)

We present the software package FRESHS (http://www.freshs.org) for parallel simulation of rare events using sampling techniques from the ‘splitting’ family of methods. Initially, Forward Flux Sampling (FFS) and Stochastic Process Rare Event Sampling (SPRES) have been implemented. These two methods together make rare event sampling available for both quasi-static and full non-equilibrium regimes. Our framework provides a plugin system for software implementing the underlying physics of the system of interest. At present, example plugins exist for our framework to steer the popular MD packages GROMACS, LAMMPS and ESPResSo, but due to the simple interface of our plugin system, it is also easy to attach other simulation software or self-written code. Use of our framework does not require recompilation of the simulation program. The modular structure allows the flexible implementation of further sampling methods or physics engines and creates a basis for objective comparison of different sampling algorithms.     

A reference implementation of the adaptive resolution scheme in ESPResSo

We review the adaptive resolution scheme (AdResS) from a technical perspective and collect arguments from several years of research, which culminates into the implementation of AdResS into the open-source package ESPResSo. This flexible implementation allows us to repeat all previous AdResS simulations with one program. We test this reference implementation and resimulate some results of the well-studied tetrahedral fluid from various previous studies to show the functionality of the package.     

P/CL: A flexible input processor

An interactive program inevitably has a need for a user interface which exceeds the simple combination of a write and a read statement. This is necessary to prevent a program abort due to an input error from the side of the user. Also it is desirable to allow for more advanced types of input than single characters or numbers. For these reasons a general-purpose input package has been developed which allows for sophisticated command-driven programs while offering the programmer as well as the user an easy-to-use interface. The structure of the package is described and examples of its use are given.     

Software design for analysis of multichannel intracardial and body surface electrocardiograms

Analysis of multichannel ECG recordings (body surface maps (BSMs) and intracardial maps) requires special software. We created a software package and a user interface on top of a commercial data analysis package (MATLAB) by a combination of high-level and low-level programming. Our software was created to satisfy the needs of a diverse group of researchers. It can handle a large variety of recording configurations. It allows for interactive usage through a fast and robust user interface, and batch processing for the analysis of large amounts of data. The package is user-extensible, includes routines for both common and experimental data processing tasks, and works on several computer platforms. The source code is made intelligible using software for structured documentation and is available to the users. The package is currently used by more than ten research groups analysing ECG data worldwide.     

Symbolic computation of the phoretic acceleration of convex particles suspended in a non-uniform gas

A package has been developed for calculating analytic expressions for forces and torques onto an arbitrarily shaped convex tracer (aerosol) particle small compared to the mean free path of the surrounding nonequilibrium gas. The package Phoretic allows to compute analytical (and also numerical) expressions for forces and torques stemming from elastic and diffusive scattering processes parameterized by an accommodation coefficient. The method is based on calculating half-sphere integral tensors of arbitrary rank and on integrating forces and torques acting on surface elements. The surrounding gas is completely specified by an arbitrarily shaped velocity distribution function. Accordingly, Phoretic requires two inputs: A particle (surface) geometry and a velocity distribution function. For example, the particle may be a cylinder with flat end caps, and the distribution function the one of Maxwell (isotropic) or Grad (13th moment approximation). The package reproduces analytic results for spheres which were available in the literature, and the ones for other geometries (cylinders, cuboids, ellipsoids) which were, however, only partially available (some works considered only elastic collisions, others temperature, or pressure, or only velocity gradients, etc.). In addition, Phoretic takes into account angular velocities which have been usually neglected and become relevant for non-spherical particles. The package is geared towards the implementation of dynamical equations for aerosol particles suspended in dilute or semidilute gases and as such helps to obtain concentration profiles and mobilities of aerosol particles depending on their shape (distribution) and environmental conditions.

Program summary

Title of program:PhoreticCatalogue identifier:ADYI_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYI_v1_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions: Persons requesting the program must sign the standard CPC-non-profit use license (see license agreement printed in every issue)Computer for which the program is designed and others on which it has been tested: All platforms with a monitorOperating systems or monitors under which the program has been tested: Linux, Windows XP, Unix, Mac-OSProgram language used: Mathematica^®, version 5.2 or later. Phoretic makes use of the DiscreteMath‘Combinatorica’ Mathematica^® packageMemory required to execute with typical data: 10 MByteNo. of lines in distributed program, including test data, etc.: 22 410No. of bytes in distributed program, including test data, etc.: 114 657Distribution format:tar.gzNature of physical problem: Starting from a non-uniform velocity distribution function of a gas in terms of its moments, i.e. field variables, and field gradients such as temperature, pressure, or velocity field, the problem is to analytically calculate forces and torques acting onto arbitrarily shaped convex tracer (aerosol) particles small in size compared to the mean free path of the gas. The collision process is modeled as a superposition of elastic and diffusive scattering processes (parameterized by 0?α?1).Method of solution: We implemented the solution to this problem in the symbolic programming language Mathematica^®. The program allows to specify an arbitrary shape of the tracer particle and an arbitrary distribution function of the gas and returns symbolic or numerical expressions for forces and torques. The solution requires the calculation of half-sphere and base surface integrals and subsequent symbolic algebraic and tensorial manipulations.Restrictions on the complexity of the problem: Not known. In case the software cannot calculate surface integrals analytically it offers the possibility to proceed with a numerical evaluation of the corresponding terms.Typical running time: Typical running times mostly depend on the shape of the tracer particle. For all examples coming together with the software distribution run times are below 5 minutes on a modern single-processor platform.     

DMS-Dynamic motion simulator

DMS is a graphics program that displays the output of multibody systems programs like DYNACOMBS¹. The menu driven program supports a full range of display options to aid the user in the visualization of his or her output. A small CORE compatible graphics package is included to produce graphical output on Tektronic 4010 terminals or emulators.     

Potensoft: MATLAB-based software for potential field data processing, modeling and mapping

An open-source software including an easy-to-use graphical user interface (GUI) has been developed for processing, modeling and mapping of gravity and magnetic data. The program, called Potensoft, is a set of functions written in MATLAB. The most common application of Potensoft is spatial and frequency domain filtering of gravity and magnetic data. The GUI helps the user easily change all the required parameters. One of the major advantages of the program is to display the input and processed maps in a preview window, thereby allowing the user to track the results during the ongoing process. Source codes can be modified depending on the users' goals. This paper discusses the main features of the program and its capabilities are demonstrated by means of illustrative examples. The main objective is to introduce and ensure usage of the developed package for academic, teaching and professional purposes.     

An object-oriented C++ implementation of Davidson method for finding a few selected extreme eigenpairs of a large, sparse, real, symmetric matrix

A C++ class named Davidson is presented for determining a few eigenpairs with lowest or alternatively highest values of a large, real, symmetric matrix. The algorithm described by Stathopoulos and Fischer is used. The exception mechanism is involved to report the errors. The class is written in ANSI C++, so it is fully portable. In addition a console program as well as a program with graphical user interface for Microsoft Windows is attached, which allow one to calculate the lowest eigenstates of time-independent Schrödinger equation for a given binding potential in one, two or three spatial dimensions. The package contains the classes providing often used potential functions (model atom potential, Coulomb potential, square well potential and Kramers-Henneberger well potential) as well as a possibility to use any potential stored in a file (then any dimensionality of the problem is allowed).The described code is the subject of M.Sc. thesis of T.D. prepared under the supervision of J.M.

Program summary

Program title: DavidsonCatalogue identifier: ADZM_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZM_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.: 3 037 055No. of bytes in distributed program, including test data, etc.: 20 002 609Distribution format: tar.gzProgramming language: C++Computer: AllOperating system: AnyRAM: User's parameters dependentWord size: 32 and 64 bitsSupplementary material: Test results for the 2D and 3D cases is availableClassification: 4, 4.8Nature of problem: Finding a few extreme eigenpairs of a real, symmetric, sparse matrix. Examples in quantum optics (interaction of matter with a laser field).Solution method: Davidson algorithmRunning time: The test example included in the distribution package (1D matrix) takes approximately 30 minutes to run. 2D matrix calculations can take hours and 3D, days, to run.     

EmguCV在图形分解中的应用研究

图形分解技术在图像处理中应用广泛,EmguCV是.Net平台下对OpenCV图形处理库的封装。首先简要介绍了OpenCV与EmguCV及其二者的联系,然后着重介绍了运用EmguCV进行图形分解的步骤与方法,给出了样例流程图,详细介绍了关键函数的用法和其关键参数,最后给出了部分C#关键源代码,以及运行该程序的平台环境。运用EmguCV实现了图形分解,所采用的程序在电脑键盘扫描识别中具有较大的应用价值。     

Reasoning about geological space: Coupling 3D GeoModels and topological queries as an aid to spatial data selection

Topological relationships between geological objects are of great interest for mining and petroleum exploration. Indeed, adjacency, inclusion and intersection are common relationships between geological objects such as faults, geological units, fractures, mineralized zones and reservoirs. However, in the context of 3D modeling, actual geometric data models used to store those objects are not designed to manage explicit topological relationships. For example, with Gocad^© software, topological analyses are possible but they require a series of successive manipulations and are time consuming. This paper presents the development of a 3D topological query prototype, TQuery, compatible with Gocad^© modeling platform. It allows the user to export Gocad^© objects to a data storage model that regularizes the topological relationships between objects. The development of TQuery was oriented towards the use of volumetric objects that are composed of tetrahedrons. Exported data are then retrieved and used for 3D topological and spatial queries. One of the advantages of TQuery is that different types of objects can be queried at the same time without restricting the operations to voxel regions. TQuery allows the user to analyze data more quickly and efficiently and does not require a 3D modeling specialist to use it, which is particularly attractive in the context of a decision-making aid. The prototype was tested on a 3D GeoModel of a continental red-bed copper deposit in the Silurian Robitaille Formation (Transfiguration property, Québec, Canada).     

A tool for the interactive 3D visualization of electronic structure in molecules and solids

This paper presents the Vienna ab initio simulation package (VASP) data viewer, a desktop 3D visualization application for the analysis of valence electronic structure information derived from first-principles quantum-mechanical density functional calculations. This tool allows a scientist to directly view and manipulate the calculated charge density or electron localization function (ELF) from an electronic structure calculation, providing insight into the nature of chemical bonding. Particular attention was given to the design and implementation of the user interface (UI) for the data viewer. It provides for expert and novice usage, and both natural direct manipulation and precise numerical control. The data viewer has proven useful to chemical scientists for understanding the results of electronic structure calculations.     

Model-Driven Development for scientific computing. An upgrade of the RHEEDGr program

Model-Driven Engineering (MDE) is the software engineering discipline, which considers models as the most important element for software development, and for the maintenance and evolution of software, through model transformation. Model-Driven Architecture (MDA) is the approach for software development under the Model-Driven Engineering framework. This paper surveys the core MDA technology that was used to upgrade of the RHEEDGR program to C++0x language standards.

New version program summary

Program title: RHEEDGR-09Catalogue identifier: ADUY_v3_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUY_v3_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.: 21 263No. of bytes in distributed program, including test data, etc.: 1 266 982Distribution format: tar.gzProgramming language: Code Gear C++ BuilderComputer: Intel Core Duo-based PCOperating system: Windows XP, Vista, 7RAM: more than 1 MBClassification: 4.3, 7.2, 6.2, 8, 14Does the new version supersede the previous version?: YesNature of problem: Reflection High-Energy Electron Diffraction (RHEED) is a very useful technique for studying growth and surface analysis of thin epitaxial structures prepared by the Molecular Beam Epitaxy (MBE). The RHEED technique can reveal, almost instantaneously, changes either in the coverage of the sample surface by adsorbates or in the surface structure of a thin film.Solution method: The calculations are based on the use of a dynamical diffraction theory in which the electrons are taken to be diffracted by a potential, which is periodic in the dimension perpendicular to the surface.Reasons for new version: Responding to the user feedback the graphical version of the RHEED program has been upgraded to C++0x language standards. Also, functionality and documentation of the program have been improved.Summary of revisions:

1.

Model-Driven Architecture (MDA) is the approach defined by the Object Management Group (OMG) for software development under the Model-Driven Engineering framework [1]. The MDA approach shifts the focus of software development from writing code to building models. By adapting a model-centric approach, the MDA approach hopes to automate the generation of system implementation artifacts directly from the model. The following three models are the core of the MDA: (i) the Computation Independent Model (CIM), which is focused on basic requirements of the system, (ii) the Platform Independent Model (PIM), which is used by software architects and designers, and is focused on the operational capabilities of a system outside the context of a specific platform, and (iii) the Platform Specific Model (PSM), which is used by software developers and programmers, and includes details relating to the system for a specific platform. Basic requirements for the calculation of the RHEED intensity rocking curves in the one-beam condition have been described in Ref. [2]. Fig. 1 shows the PIM for the present version of the program. Fig. 2 presents the PSM for the program.

2.

The TGraph2D.bpk package has been recompiled to Graph2D0x.bpl and upgraded according to C++0x language standards. Fig. 3 shows the PSM of the Graph2D component, which is manifested by the Graph2D0x.bpl package presently. This diagram is a graphic presentation of the static view, which shows a collection of declarative model elements and their relationships. Installation instructions of the Graph2D0x package can be found in the new distribution.

3.

The program requires the user to provide the appropriate parameters for the crystal structure under investigation. These parameters are loaded from the parameters.ini file at run-time. Instructions for the preparation of the .ini files can be found in the new distribution.

4.

The program enables carrying out one-dimensional dynamical calculations for the fcc lattice, with a two-atoms basis and fcc lattice, with one atom basis but yet the zeroth Fourier component of the scattering potential in the TRHEED1D::crystPotUg() function can be modified according to users' specific application requirements.

5.

A graphical user interface (GUI) for the program has been reconstructed.

6.

The program has been compiled with English/USA regional and language options.

Unusual features: The program is distributed in the form of main projects RHEEDGr_09.cbproj and Graph2D0x.cbproj with associated files, and should be compiled using Code Gear C++ Builder 2009 compilers.Running time: The typical running time is machine and user-parameters dependent.References:

[1]

OMG, Model Driven Architecture Guide Version 1.0.1, 2003, http://www.omg.org/cgi-bin/doc?omg/03-06-01.

[2]

A. Daniluk, Comput. Phys. Comm. 166 (2005) 123.

     

Novell网络应用程序接口技术

简述了在网络环境下开发应用程序所存在的问题，提出设计一个介于用户和网络层之间的Ｎｏｖｅｌ网络应用程序接口软件包（ＡＰＩＳＰ）的新方法，并用ＢｏｒｌａｎｄＣ＋＋开发了ＡＰＩＳＰ，该软件包向用户提供Ｎｏｖｅｌ网络环境下标准的库函数。较好地解决了一般软件工程人员难于开发网络应用程序这一问题，且能用于其它类型的网络方面。     

A general purpose adaptivity driver for FE software

This paper describes a tool that serves as an automatic mesh adaptivity driver program for general purpose finite element (FE) software packages. Many commercially available FE programs lack a feature to control the numerical solution's accuracy properly. Our tool implements a mesh adaptive method that, in conjunction with separate finite element software, allows one to fully automatically improve the quality of the numerical solution up to a user specified accuracy. We demonstrate the use of the package with selected computational examples performed with a commercial FE package, ANSYS, and with our FE program FEMEngine. Copyright © 2003 John Wiley & Sons, Ltd.     

辅助SDN节点企业实施MC的软件系统分析

大规模定制作为一种生产模式,能够很好地解决顾客个性化需求与制造成本间的矛盾。在单个企业无法实现这种生产模式时,可以由供需网其他节点企业通过软件平台来实现。该文从大规模定制的4种类型角度,系统地分析了供需网节点企业实施大规模定制的软件系统需求,即给出了该软件系统的功能需求、数据需求、用户界面、流程图及相关说明等内容。该软件系统在实现大规模定制时,体现了供需网理念及特征。     

GDF v2.0, an enhanced version of GDF

An improved version of the function estimation program GDF is presented. The main enhancements of the new version include: multi-output function estimation, capability of defining custom functions in the grammar and selection of the error function. The new version has been evaluated on a series of classification and regression datasets, that are widely used for the evaluation of such methods. It is compared to two known neural networks and outperforms them in 5 (out of 10) datasets.

Program summary

Title of program: GDF v2.0Catalogue identifier: ADXC_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXC_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.: 98 147No. of bytes in distributed program, including test data, etc.: 2 040 684Distribution format: tar.gzProgramming language: GNU C++Computer: The program is designed to be portable in all systems running the GNU C++ compilerOperating system: Linux, Solaris, FreeBSDRAM: 200000 bytesClassification: 4.9Does the new version supersede the previous version?: YesNature of problem: The technique of function estimation tries to discover from a series of input data a functional form that best describes them. This can be performed with the use of parametric models, whose parameters can adapt according to the input data.Solution method: Functional forms are being created by genetic programming which are approximations for the symbolic regression problem.Reasons for new version: The GDF package was extended in order to be more flexible and user customizable than the old package. The user can extend the package by defining his own error functions and he can extend the grammar of the package by adding new functions to the function repertoire. Also, the new version can perform function estimation of multi-output functions and it can be used for classification problems.Summary of revisions: The following features have been added to the package GDF:

•

Multi-output function approximation. The package can now approximate any function . This feature gives also to the package the capability of performing classification and not only regression.

•

User defined function can be added to the repertoire of the grammar, extending the regression capabilities of the package. This feature is limited to 3 functions, but easily this number can be increased.

•

Capability of selecting the error function. The package offers now to the user apart from the mean square error other error functions such as: mean absolute square error, maximum square error. Also, user defined error functions can be added to the set of error functions.

•

More verbose output. The main program displays more information to the user as well as the default values for the parameters. Also, the package gives to the user the capability to define an output file, where the output of the gdf program for the testing set will be stored after the termination of the process.

Additional comments: A technical report describing the revisions, experiments and test runs is packaged with the source code.Running time: Depending on the train data.     

Vscape V1.1.0. An interactive tool for metastable vacua

Vscape is an interactive tool for studying the one-loop effective potential of an ungauged supersymmetric model of chiral multiplets. The program allows the user to define a supersymmetric model by specifying the superpotential. The F-terms and the scalar and fermionic mass matrices are calculated symbolically. The program then allows you to search numerically for (meta)stable minima of the one-loop effective potential. Additional commands enable you to further study specific minima, by, e.g., computing the mass spectrum for those vacua. Vscape combines the flexibility of symbolic software, with the speed of a numerical package.

Program summary

Program title:Vscape 1.1.1Catalogue identifier: ADZW_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZW_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.: 80 507No. of bytes in distributed program, including test data, etc.: 6 708 938Distribution format: tar.gzProgramming language: C++Computer: Pentium 4 PC Computers: need (GNU) C++ compiler, Linux standard GNU installation (./configure; make; make install). A precompiled Windows XP version is included in the distribution packageOperating system: Linux, Windows XP using cygwinRAM: 10 MBWord size: 32 bitsClassification: 11.6External routines: GSL (http://www.gnu.org/software/gsl/), CLN (http://www.ginac.de/CLN/), GiNaC (http://directory.fsf.org/GiNaC.html)Nature of problem:Vscape is an interactive tool for studying the one-loop effective potential of an ungauged supersymmetric model of chiral multiplets. The program allows the user to define a supersymmetric model by specifying the superpotential. The F-terms and the scalar and fermionic mass matrices are calculated symbolically. The program then allows you to search numerically for (meta)stable minima of the one-loop effective potential. Additional commands enable you to further study specific minima, by, e.g., computing the mass spectrum for those vacua. Vscape combines the flexibility of symbolic software with the speed of a numerical package.Solution method: Coleman-Weinberg potential is computed using numerical matrix diagonalization. Minima of the one-loop effective potential are found using the Nelder and Mead simplex algorithm. The one-loop effective potential can be studied using numerical differentiation. Symbolic users interface implemented using flex and bison.Restrictions:N=1 supersymmetric chiral models onlyUnusual features: GiNaC (+CLN), GSL, ReadLib (not essential)Running time: Interactive users interface. Most commands execute in a few ms. Computationally intensive commands execute in order of minutes, depending on the complexity of the user defined model.     

Shading evaluations with general three-dimensional models

The SHADOWPACK package of computer programs has been developed to facilitate shading evaluations, for the direct component of solar radiation, with general 3D models. An interactive solid modelling program allows the user to construct and view the 3D model before saving it for further analysis and display. Other programs permit the graphical display of the shading situation throughout the year, the quantitative assessment of energy received on different faces of the model, and the display of the distribution of energy received on particular faces by means of contour plots. The use of the computer graphics approach has proved particularly convenient because of the similarity between the techniques used for graphical and numerical algorithms.     

Mixed Monte Carlo/Molecular Dynamics simulations of the prion protein

In this paper we present the results of mixed Monte Carlo/Molecular Dynamics (MC/MD) simulations of the D178N mutant of the human prion protein. We have used the MC moves for polypeptide sampling known as Concerted Rotations with Angles (CRA) to selectively sample the region of the prion protein comprising the β-sheet and one of the α-helices. The results indicate that the MC/MD simulations sample the phase space substantially faster than regular Molecular Dynamics simulations starting with the same initial conditions. This work further indicates the MC/MD technique as a potentially powerful simulation tool, allowing the selective sampling of a region of a physical system that is deemed important.