ITR: Advanced Computational Environment for Molecular and Mesoscale Modeling

ITR：分子和介尺度建模的高级计算环境

• 批准号: 0219266
• 负责人: David Kofke
• 金额: $ 49.91万
• 依托单位: SUNY at Buffalo
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-09-01 至 2007-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0219266&HistoricalAwards=false
• 关键词: ITR; Advanced; Computational; Environment; Molecular

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.

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，有据可查的需求，以阻止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的（可容易适应新的方法和模型），计算上有效且易于使用。它的目的是独立于平台，但可以配置以利用不同计算环境（包括并行和网格体系结构）的功能。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），可用于从一组构建块中构造各种模拟。可以通过在文本编辑器中编程来使用API​​。第二是一个综合开发环境（IDE），它为复杂分子模拟的开发和应用提供了替代的图形环境。此处执行的工作包括设计，开发和测试API和IDE，研究如何最好地在各种单一和多处理器计算体系结构上实施它们，并进行分发，并进行活动以促进对它们的理解和使用。咨询了一系列专家，以协助当前使用中最佳的模拟方法和模型的详细实施；这种实践是二重用途的目的，即加速发展并扩大对兴趣的兴趣。该发展的重点是促进在研究应用中的使用，但是活动中有重要的教育成分：（1）工具用于生产用于教授分子现象及其在产生宏观行为中的作用的辅助工具； （2）开发环境被用作向大学的水牛区高中和新生到大学的高级本科生的学生教授有关分子模拟的想法的基础； （3）本科生通过紧密关注的发展活动做出了贡献。此外，API的面向对象的结构为教学的分子模拟提供了一个合理的教学基础，以促进更广泛的使用方式。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创建的纳米材料理论研究所提供的一系列全国性研讨会中的核心组成部分。