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

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• 作者：Andrzej Daniluk ; ^a ; ^{adaniluk@tytan.umcs.lublin.pl}
• 关键词：Reflection high-energy electron diffraction (RHEED) ; Molecular beam epitaxy (MBE) ; UML ; Model-Driven Development (MDD) ; Multithreaded programming ; Free compilers
• 刊名：Computer Physics Communications
• 出版年：2011
• 出版时间：June 2011
• 年：2011
• 卷：182
• 期：6
• 页码：1389-1390
• 全文大小：93 K

文摘

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: GrowthCP

Catalogue identifier: ADVL_v4_0

Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADVL_v4_0.html

Program obtainable from: CPC Program Library, Queens 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.: 32 269

No. of bytes in distributed program, including test data, etc.: 8 234 229

Distribution format: tar.gz

Programming language: Free Object Pascal

Computer: multi-core x64-based PC

Operating system: Windows XP, Vista, 7

Has the code been vectorised or parallelized?: No

RAM: 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, 14

External routines: Lazarus [1]

Catalogue identifier of previous version: ADVL_v3_0

Journal reference of previous version: Comput. Phys. Comm. 181 (2010) 709

Does the new version supersede the previous version?: Yes

Nature 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/.