ITR: Advanced Computational Environment for Molecular and Mesoscale Modeling

该信息技术研究（ITR）项目旨在应用最先进的软件工具和方法，为分子和中尺度建模开发先进的计算环境。这项工作是为了解决特定的、有充分记录的需求，这些需求阻碍了更广泛地采用分子和多尺度建模工具来解决实际问题。该环境被设计为可扩展的（易于容纳新方法和模型）、计算效率高且易于使用。它的目标是独立于平台，但可配置以利用不同计算环境的特性，包括并行和网格架构。它是使用Java编程语言开发的，由两个不同的部分组成。首先是应用程序编程接口（API），可用于从一组通用构建块构建各种各样的模拟；例如，可以通过在文本编辑器中编程来使用该API。第二个是集成开发环境（IDE），它为复杂分子模拟的开发和应用提供了另一种图形化环境。这里执行的工作包括设计、开发和测试API和IDE，研究如何在各种单处理器和多处理器计算架构上最好地实现它们，传播它们，并开展活动以促进对它们的理解和使用。咨询了一系列专家，以协助详细实施当前使用的最佳模拟方法和模型；这种做法具有加速发展和扩大人们对它的兴趣的双重目的。开发的重点是促进在研究应用中的使用，但该活动中有重要的教育成分：(1)这些工具用于生产教学分子现象及其在产生宏观行为中的作用的辅助工具；(2)以该开发环境为基础，向布法罗地区高中学生和该校大一至大四本科生讲授分子模拟知识；(3)本科生通过重点突出的发展活动做出贡献。此外，API的面向对象结构为分子模拟的教学提供了良好的教学基础，从而促进了更广泛的应用。因此，在这项工作中开发的代码和概念被用作橡树岭国家实验室新成立的纳米材料理论研究所提供的分子模拟的定期系列国家研讨会的核心组成部分。

This Information Technology Research (ITR) project aims to apply state-of-the-art software tools and methods to develop an advanced computational environment for molecular and mesoscale modeling. This work is performed to address specific, well-documented needs that block the broader adoption of molecular and multiscale modeling tools to solve practical problems. The environment is designed to be extensible (accommodates easily new methods and models), computationally efficient, and easy to use. It aims to be platform independent yet configurable to exploit features of different computing environments, including parallel and grid architectures. It is developed using the Java programming language, and consists of two distinct parts. First is an Application Programming Interface (API) that can be used to construct a wide variety of simulations from a common set of building blocks; the API can be used, for example, by programming in a text editor. Second is an Integrated Development Environment (IDE), which provides an alternative graphical environment for the development and application of complex molecular simulations. The work performed here consists of designing, developing and testing the API and IDE, researching how they can be best implemented on a wide variety of single and multiprocessor computing architectures, disseminating them, and conducting activities to promote understanding and use of them. A range of experts are consulted to assist in the detailed implementation of the best simulation methods and models in current use; this practice serves the dual purpose of speeding the development as well as broadening the interest in it. The focus of the development is to facilitate use in research applications, but there are significant educational components to the activity: (1) the tools are used to produce aids for teaching molecular phenomena and its role in producing macroscopic behaviors; (2) the development environment is used as a basis to teach ideas about molecular simulation to students from Buffalo-area high schools and freshman- through senior-level undergraduates at the University; (3) undergraduates contribute through tightly-focused development activities. Further, the object-oriented structure of the API provides a sound pedagogical basis for teaching molecular simulation in a way that promotes broader use. Accordingly the codes and concepts developed in this work are used as a central component in a regular series of national workshops in molecular simulation offered by the newly created Nanomaterials Theory Institute at Oak Ridge National Laboratory.