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来开发用于分子和中尺度建模的高级计算环境。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。该环境设计为可扩展(轻松适应新方法和模型)、计算效率高和易于使用。它的目标是独立于平台，但可配置以利用不同计算环境的功能，包括并行和网格体系结构。它是使用Java编程语言开发的，由两个截然不同的部分组成。首先是应用程序编程接口(API)，它可用于从一组通用的构建块构造各种模拟；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一个替代的图形环境。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体系结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；这种做法具有加速开发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，但活动中也有重要的教育组成部分：(1)这些工具被用来制作教学分子现象的辅助工具，以及它在产生宏观行为中的作用；(2)开发环境被用作向来自布法罗地区的高中的学生和大学一年级到高年级的本科生传授关于分子模拟的想法的基础；(3)本科生通过密切关注的开发活动做出贡献。此外，API面向对象的结构为以促进更广泛使用的方式教授分子模拟提供了良好的教学基础。因此，这项工作中制定的编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在分子模拟方面定期举办的一系列国家讲习班的中心组成部分。

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.