Object-oriented programming paradigms for molecular modeling
Object-oriented programming paradigms for molecular modeling
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DOI：
10.1080/0892702031000065719
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发表时间：
2003-01-01
影响因子：
2.1
通讯作者：
Snurr, RQ
中科院分区：
文献类型：
--
作者：
Gupta, A;Chempath, S;Snurr, RQ
本文讨论了应用面向对象程序设计（OOP）的设计理念，分子模拟代码的开发。在过去的十年中，开发了许多新的语言，如Fortran 90（F90），支持OOP设计理念。我们简要描述了F90的突出特点和一些基本的面向对象设计原则。作为设计概念的说明，我们在F90中实现了一个通用接口，用于计算成对相互作用，可以很容易地扩展到任何数量的不同力场模型。这里提出的想法是用于开发一个多用途的模拟代码，命名为音乐。使用音乐的巨正则蒙特卡罗（GCMC）模拟的灵活的吸附分子在沸石的一个例子。这个例子说明了OOP如何允许现有的分子动力学和GCMC代码很容易地结合起来，以最小的编码工作来执行混合GCMC模拟。
This paper discusses the application of object-oriented programming (OOP) design concepts to the development of molecular simulation code. A number of new languages such as Fortran 90 (F90) have been developed over the last decade that support the OOP design philosophy. We briefly describe the salient features of F90 and some basic object-oriented design principles. As an illustration of the design concepts we implement a general interface in F90 for calculating pairwise interactions that can be extended easily to any number of different forcefield models. The ideas presented here are used in the development of a mu ltipurpose si mulation c ode, named Music. An example of the use of Music for grand canonical Monte Carlo (GCMC) simulations of flexible sorbate molecules in zeolites is given. The example illustrates how OOP allowed existing code for molecular dynamics and GCMC to be easily combined to perform hybrid GCMC simulations with minimal coding effort.