Developing community codes for materials modeling

For this article, we call scientific software a community code if it is freely available, written by a team of developers who welcome user input, and has attracted users beyond the developers. There are obviously many such materials modeling codes. The authors have been part of such efforts for many years in the field of atomistic simulation, specifically for two community codes, the LAMMPS and GULP packages for molecular dynamics and lattice dynamics respectively. Here we highlight lessons we have learned about how to create such codes and the pros and cons of being part of a community effort. Many of our experiences are similar, but we also have some differences of opinion (like modeling vs modelling). Our hope is that readers will find these lessons useful as they design, implement, and distribute their own materials modelling software for others to use.     

Verification of cardiac tissue electrophysiology simulators using an N-version benchmark

Ongoing developments in cardiac modelling have resulted, in particular, in the development of advanced and increasingly complex computational frameworks for simulating cardiac tissue electrophysiology. The goal of these simulations is often to represent the detailed physiology and pathologies of the heart using codes that exploit the computational potential of high-performance computing architectures. These developments have rapidly progressed the simulation capacity of cardiac virtual physiological human style models; however, they have also made it increasingly challenging to verify that a given code provides a faithful representation of the purported governing equations and corresponding solution techniques. This study provides the first cardiac tissue electrophysiology simulation benchmark to allow these codes to be verified. The benchmark was successfully evaluated on 11 simulation platforms to generate a consensus gold-standard converged solution. The benchmark definition in combination with the gold-standard solution can now be used to verify new simulation codes and numerical methods in the future.     

Biocharts: a visual formalism for complex biological systems

We address one of the central issues in devising languages, methods and tools for the modelling and analysis of complex biological systems, that of linking high-level (e.g. intercellular) information with lower-level (e.g. intracellular) information. Adequate ways of dealing with this issue are crucial for understanding biological networks and pathways, which typically contain huge amounts of data that continue to grow as our knowledge and understanding of a system increases. Trying to comprehend such data using the standard methods currently in use is often virtually impossible. We propose a two-tier compound visual language, which we call Biocharts, that is geared towards building fully executable models of biological systems. One of the main goals of our approach is to enable biologists to actively participate in the computational modelling effort, in a natural way. The high-level part of our language is a version of statecharts, which have been shown to be extremely successful in software and systems engineering. The statecharts can be combined with any appropriately well-defined language (preferably a diagrammatic one) for specifying the low-level dynamics of the pathways and networks. We illustrate the language and our general modelling approach using the well-studied process of bacterial chemotaxis.     

Intercomparison on the usage of computational codes in radiation dosimetry

'QUADOS', a Concerted Action of the European Commission, has run an intercomparison aimed at evaluating the use of computational codes for dosimetry in radiation protection and medical physics. This intercomparison was open to all users of Monte Carlo, analytic and semi-analytic codes or deterministic methods. Its main aim was to provide a snapshot of the methods and codes currently in use. It also intended to furnish information on the methods used to assess the reliability of computational results and disseminate 'good practice' throughout the radiation dosimetry community. Eight problems were selected for their relevance to the radiation dosimetry community, three of which involve neutron transport. This paper focuses on the analysis of the neutron problems.     

Agile methods in European embedded software development organisations: a survey on the actual use and usefulness of Extreme Programming and Scrum

Press releases, scientific publications and anecdotal evidence demonstrate that organisations worldwide are adopting agile software development methods at increasing speed. Little is still known about the current usefulness of agile methods in the complex environment of the embedded software development industry. Embedded devices are already commonplace in regular households. The goal of this survey is to provide first-hand knowledge of the adoption and experience of two of the most known agile methods, namely Extreme Programming and Scrum, in a number of European organisations of embedded software known to be interested and active in experimenting with agile software development methods. The survey involved 13 industrial organisations in eight European countries and 35 individual software development projects. The focus of the questionnaire was to enquire into the level of use as well as the experienced usefulness - or expected usefulness if there was no experience available - of the two agile methods and their individual practices. The results show that the embedded industry has been able to apply agile methods in its development processes. The results also indicate that the appreciation of the agile methods and their individual practices appears to increase once adopted and applied in practice.     

Using Scrum and unified modelling language to analyze and design an automatic course scheduling system

This research used a case study methodology to examine large-scale software projects accomplished despite ambiguous customer requirements. This study adopted Scrum as the agile software development method and used unified modelling language (UML) diagrams to enhance design implementation documents and improve the software development process. This study presented how the case company explored a Scrum-based automatic course scheduling system for elementary and secondary schools. Through interviews, the case company incorporated customers’ requirements by using the corresponding UML diagrams, which helped the project team document the software development process and design the functions to satisfy customer demand. Then, the proposed method was introduced to the automatic elementary and secondary school course scheduling system project undertaken by the case company, verifying the feasibility of the proposed method. A few problems arose in the proposed software development process, and remedies were discussed. Software companies could use these results as a reference when implementing a large-scale software project with ambiguous customer requirements.     

Modelling for agile manufacturing systems

To address the challenges of a rapidly changing manufacturing market, a new type of manufacturing system with characteristics of reconfigurability, reusability and scalability, an agile manufacturing system (AMS) has to be developed. Reconfigurability is an essential feature of AMS. Such a system can use basic building blocks, both hardware and software, which can be reconfigured quickly and reliably. A fundamental early step in the reconfiguring process for an agile manufacturing system is to develop a model that adequately describes the proposed system, in order to be able to study and evaluate the impact of the reconfiguring decision on the system performance, before its construction. Therefore, the rapid modelling and reusable modelling capabilities are demanded. In this paper, an Object & Knowledge-based Interval Timed Petri-Net (OKITPN) approach is proposed, which provides an object-oriented and modular method of modelling manufacturing activities. It includes knowledge, interval time, modular and communication attributes. The features of object-oriented modelling allow the AMS to be modelled with the properties of classes and objects, and make the concept of software IC possible for rapid modelling of complex AMSs. Once all of the Interval Timed Petri-Net (ITPN) objects are well defined the developers need to consider only the interfaces and operations relating to the ITPN objects. In order to demonstrate the capability of the proposed OKITPN, it has been used to model rapidly AMSs that are reconfigured according to requirements.     

Computational efficiency of ultrasonic guided wave imaging algorithms

Guided wave imaging techniques employed for structural health monitoring (SHM) can be computationally demanding, especially for adaptive techniques such as minimum variance distortionless response (MVDR) imaging, which requires a matrix inversion for each pixel calculation. Instantaneous windowing has been shown in previous work to improve guided wave imaging performance. The use of instantaneous windowing has the additional benefit of significantly reducing the computational requirements of image generation. This paper derives a formulation for MVDR imaging using instantaneous windowing and shows that the matrix inversion associated with MVDR imaging can be optimized, reducing the computational complexity to that of conventional delay-and-sum imaging algorithms. Additionally, a vectorized approach is presented for implementing guided wave imaging algorithms, including delay-and-sum imaging, in matrix-based software packages. The improvements in computational efficiency are quantified by measuring computation time for different array sizes, windowing assumptions, and imaging methods.     

Comparison of different finite element formulations for 3Dmagnetostatic problems

The results obtained with several three-dimensional software packages for magnetostatic field calculation using the finite-element method (FEM) are compared with regard to their accuracy and their computational time requirements. The packages are based on the vector potential (VPOT), the reduced scalar potential (RSP), and the total and reduced scalar potential (TSP+RSP), respectively. Results for an iron cylinder immersed in the field of a cylindrical coil are given. It is found that the finite-element formulation using a total and reduced scalar potential and the direct iteration method are useful for dealing with nonlinear magnetostatic field problems     

Finding Bad Values in Factorial Designs—Revisited

An outlier in an unreplicated factorial experiment is difficult to detect, and its presence reduces the power for detecting significant effects. This poses a problem for data analysts since methods for detecting outliers and testing effects in the presence of outliers are not available in popular statistical software. In this article we compare three methods that have been proposed in the literature for detecting outliers and testing effects for significance in the presence of an outlier. We illustrate the methods with data from a real experiment, comment on the ease of implementing them in standard statistical packages, and use a simulation study to compare their performance over a wider range of circumstances. We make recommendations about when each method should be used in practice.     

Integration of safety analysis in model-driven software development

Safety critical software requires integrating verification techniques in software development methods. Software architectures must guarantee that developed systems will meet safety requirements and safety analyses are frequently used in the assessment. Safety engineers and software architects must reach a common understanding on an optimal architecture from both perspectives. Currently both groups of engineers apply different modelling techniques and languages: safety analysis models and software modelling languages. The solutions proposed seek to integrate both domains coupling the languages of each domain. It constitutes a sound example of the use of language engineering to improve efficiency in a software-related domain. A model-driven development approach and the use of a platform-independent language are used to bridge the gap between safety analyses (failure mode effects and criticality analysis and fault tree analysis) and software development languages (e.g. unified modelling language). Language abstract syntaxes (metamodels), profiles, language mappings (model transformations) and language refinements, support the direct application of safety analysis to software architectures for the verification of safety requirements. Model consistency and the possibility of automation are found among the benefits.     

Numerical simulation of stress-strain state near crack tip in a compact tensile specimen

A computational scheme has been developed and a numerical simulation of the stress-strain state near the crack tip is performed at different levels of the stress intensity factor using a compact tensile specimen as an example. The authors analyze the influence of the finite element size near the crack tip and compare the results obtained in different codes (software packages) for different crack geometries. __________ Translated from Problemy Prochnosti, No. 1, pp. 134–140, January–February, 2009.     

Description of some numerical tools for solving incompressible turbulent and free surface flows

During the past ten years various methods have been devised to deal with the solution of the Navier–Stokes equations. In the meantime, different models have been worked out to represent turbulent incompressible flows. At LNH, deep participation in this enthusiastic research is still going on, together with a closely related development of physical modelling and metrology. In this paper, we will give an insight into a set of numerical codes which are now currently in use at our laboratory and some of their main applications to coastal engineering. This will include thermohydraulic internal flows and free surface flows. For each code a short presentation of the algorithm of solution is described.     

CTH: A three-dimensional shock wave physics code

CTH is a software system under development at Sandia National Laboratories Albuquerque to model multidimensional, multi-material, large deformation, strong shock wave physics. One-dimensional recti-linear, cylindrical, and spherical meshes; two-dimensional rectangular, and cylindrical meshes; and three-dimensional rectangular meshes are currently available. A two-step Eulerian solution scheme is used with these meshes. The first step is a Lagrangian step in which the cells distort to follow the material motion. The second step is a remesh step where the distorted cells are mapped back to the Eulerian mesh.

CTH has several models that are useful for simulating strong shock, large deformation events. Both tabular and analytic equations of state are available. CTH can model elastic-plastic behavior, high explosive detonation, fracture, and motion of fragments smaller than a computational cell. The elastic-plastic model is elastic-perfectly plastic with thermal softening. A programmed burn model is available for modelling high explosive detonation. The Jones-Wilkins-Lee equation of state is available for modelling high explosive reaction products. Fracture can be initiated based on pressure or principle stress. A special model is available for moving fragments smaller than a computational cell with statistically the correct velocity. This model is very useful for analyzing fragmentation experiments and experiments with witness plates.

CTH has been carefully designed to minimize the dispersion present in Eulerian codes. It has a high-resolution interface tracker that prevents breakup and distortion of material interfaces. It uses second order convection schemes to flux all quantities between cells.

This paper describes the models, and novel features of CTH. Special emphasis will be placed on the features that are novel to CTH or are not direct generalizations of two-dimensional models. Another paper by Trucano and McGlaun (1989) describes several hypervelocity impact calculations using CTH.     

Lippmann-Schwinger solvers for the explicit jump discretization for thermal computational homogenization problems

We present a variational formulation and a Lippmann-Schwinger equation for the explicit jump discretization of thermal computational homogenization problems, together with fast and memory-efficient matrix-free solvers based on the fast Fourier transform (FFT). Wiegmann and Zemitis introduced the explicit jump discretization for volumetric image-based computational homogenization of thermal conduction. In contrast to Fourier and finite difference-based discretization methods classically used in FFT-based homogenization, the explicit jump discretization is devoid of ringing and checkerboarding artifacts. Originally, the explicit jump discretization was formulated as the discrete equivalent of a boundary integral equation for the jump in the temperature gradient. The resulting equations are not symmetric positive definite, and thus solved by the BiCGSTAB method. Still, the numerical scheme exhibits stable convergence behavior, also in the presence of pores. In this work, we exploit a reformulation of the explicit jump system in terms of harmonically averaged conductivities. The resulting system is intrinsically symmetric positive definite and admits a Lippmann-Schwinger formulation. A seamless integration into existing FFT-based software packages is ensured. We demonstrate our improvements by numerical experiments.     

有限元/边界元方法在卡车驾驶室声学分析中的应用

利用有限元分析软件ANSYS和边界元分析软件SYSNOISE对卡车驾驶室的振动与内部声辐射做了数值计算分析研究.应用ANSYS软件建立了驾驶室有限元分析模型,说明了振动频响分析方法,动力学计算结果与声学边界元模型耦合的具体步骤.介绍了如何应用SYSNOISE软件建立驾驶室三维边界元声学分析模型,并采用直接边界元法,对驾驶室振动声学特性进行了计算分析.     

Computational aeroelastic modelling of airframes and turbomachinery: progress and challenges

Computational analyses such as computational fluid dynamics and computational structural dynamics have made major advances towards maturity as engineering tools. Computational aeroelasticity (CAE) is the integration of these disciplines. As CAE matures, it also finds an increasing role in the design and analysis of aerospace vehicles. This paper presents a survey of the current state of CAE with a discussion of recent research, success and continuing challenges in its progressive integration into multidisciplinary aerospace design. It approaches CAE from the perspective of the two main areas of application: airframe and turbomachinery design. An overview will be presented of the different prediction methods used for each field of application. Differing levels of nonlinear modelling will be discussed with insight into accuracy versus complexity and computational requirements. Subjects will include current advanced methods (linear and nonlinear), nonlinear flow models, use of order reduction techniques and future trends in incorporating structural nonlinearity. Examples in which CAE is currently being integrated into the design of airframes and turbomachinery will be presented.     

Resource allocation with project management software

We present results of a benchmark test evaluating the resource allocation capabilities of the project management software packages Acos Plus.1 8.2, CA SuperProject 5.0a, CS Project Professional 3.0, MS Project 2000, and Scitor Project Scheduler 8.0.1. The tests are based on 1560 instances of precedence– and resource–constrained project scheduling problems. For different complexity scenarios, we analyze the deviation of the makespan obtained by the software packages from the best feasible makespan known. Among the tested software packages, Acos Plus.1 and Project Scheduler show the best resource allocation performance. Moreover, our numerical analysis reveals a considerable performance gap between the implemented methods and state–of–the–art project scheduling algorithms, especially for large–sized problems. Thus, there is still a significant potential for improving solutions to resource allocation problems in practice.      

An agile manufacturing workcell design

This paper introduces a design for agile manufacturing worked Is intended for light mechanical assembly of products made from similar components (i.e., parts families). We define agile manufacturing as the ability to accomplish rapid changeover from the assembly of one product to the assembly of a different product. Rapid hardware changeover is made possible through the use of robots, flexible part feeders, modular grippers, and modular assembly hardware. The division of assembly, feeding, and unloading tasks between multiple robots is examined with prioritization based upon assembly time. Rapid software changeover will be facilitated by the use of a real-time, object-oriented software environment utilizing graphical simulations for off-line software development. An innovative dual VMEbus controller architecture permits an open software environment while accommodating the closed nature of most commercial robot controllers. These agile features permit new products to be introduced with minimal downtime and system reconfiguration.     

Building Agility for Developing Agile Design Information Systems

Agile manufacturing relies heavily on the quality of information that organizations have and on their ability to organize and reuse it. Constant inflow of information and knowledge is the fuel of agile manufacturing. In the process of forming virtual enterprises, these new organizations have to be equipped with information systems that integrate their present legacy technology and improve upon it. To support the quick formation of virtual organizations, one must have the ability to develop such systems quickly. Over the past few years we have evolved, through collaborative projects with industry, an approach composed of methods and an information infrastructure called n-dim that improves the ability of becoming agile manufacturers of information systems, by responding quickly to information needs of new and evolving organizations. Following an analysis of the requirements of information systems for agile design, we discuss this approach; describe some of the infrastructure features; and present several examples of simple applications that illustrate them. We summarize by discussing the advantages and limitations of our approach.