分子动力学可视化建模系统的研究与应用

发布时间：2018-06-06 13:18

本文选题：分子动力学 + Open　；参考：《广东工业大学》2017年硕士论文

【摘要】：近几年来,仿真计算作为现代科学研究的一种方法,其作用日益重要。而随着纳米技术的广泛应用,以分子动力学为代表的微观计算模拟方法也在微纳加工等领域起着不可替代的作用,它能够模拟的尺度可以达到纳米到微米,其适用的的对象包括了工程材料和有机分子等的多种模拟场合,使得它在现代科技中涉及的领域十分广泛。但是当前很多开源分子动力学软件存在建模不便等问题,针对这一问题,开发了一款分子动力学可视化建模软件NSS(Nano Simulation System)。该软件的可视化部分以OpenGL为理论基础,UI基于Qt设计,设计了全局的交互操作,运用Open GL的基本变换实现了模型的旋转、平移、缩放等操作,支持鼠标对模型的选取等操作。几何模型的构建基于开源建模核心Open CASACDE,使用了两种模型构建方法,三维图元布尔运算以及二维图元拉伸法。可直接生成的三维图元包括球体、锥体等基本三维模型,布尔运算支持相减、融合和相交三种计算方式,能适用于大部分模型的生成要求。其模型的边界表示法包含完整的几何数据和拓扑数据,为实现离散算法提供了基础。NSS的分子动力学建模是以比较常见的几何模型为基础,通过算法计算得到离散模型的方法,几何模型的建模较容易,非常适合工程背景的使用者。该软件根据分子动力学仿真的基本特点和晶体微观结构的特征,结合几何模型的模型数据,通过算法计算使得晶体构型能有序地充满整个模型,得到适于表现材料微观构型的离散模型数据,支持体心立方、面心立方构型及六方最密堆积等晶体微观结构材料的离散,也支持自定义粒子类型的离散,提供了分子动力学中固定边界、恒温边界等边界条件处理的自动生成方法。由于目前大多数开源分子动力学软件都接收文本格式的输入这一情况,NSS设计开发了针对开源微纳仿真软件的数据传递接口,除离散模型及边界粒子信息可直接导出文本使用外,初始条件及其他条件的设定也有程序的可视化界面进行输入及导出。使用这一方法对模型实例的计算,取得了可信的计算结果,有效地解决了分子动力学仿真前处理建模繁琐的问题。NSS程序作为开发的分子动力学可视化建模软件,其功能全面,使用简单,适用范围广泛,是使用分子动力学模拟的有力工具。
[Abstract]:In recent years, as a method of modern scientific research, simulation computation is becoming more and more important. With the wide application of nanotechnology, the micro-computing simulation method, represented by molecular dynamics, also plays an irreplaceable role in the field of micro-nano machining, and it can simulate the scale of nanometers to microns. The objects of application include engineering materials and organic molecules, which make it widely used in modern science and technology. However, many open source molecular dynamics software has some problems, such as modeling inconvenience. Aiming at this problem, a molecular dynamics visualization modeling software NSS(Nano Simulation system is developed. The visualization part of the software is based on OpenGL theory and UI is designed based on QT. The global interactive operation is designed. The basic transformation of Open GL is used to realize the operation of model rotation, translation, scaling and so on, and the operation of selecting the model by mouse is supported. The construction of geometric model is based on the open source modeling core Open CASACDE. Two methods are used to construct the model, namely, 3D Boolean operation and two-dimensional drawing method. The directly generated 3D graph elements include the basic 3D models such as sphere and cone. Boolean operations support subtraction fusion and intersection which can be applied to the generation requirements of most models. The boundary representation of the model contains complete geometric data and topological data, which provides the basis for the discrete algorithm. The molecular dynamics modeling of NSS is based on the more common geometric model, and the discrete model is obtained by the algorithm. The modeling of geometric model is easy, and it is very suitable for the users of engineering background. According to the basic characteristics of molecular dynamics simulation and the characteristics of crystal microstructure, the software combines the model data of the geometric model and makes the crystal configuration fill the whole model in an orderly way through the calculation of the algorithm. The discrete model data suitable for representing the microstructure of materials are obtained, which support the discretization of crystal microstructure materials such as body-centered cubic, face-centered cubic and hexagonal most dense stacking, and also support the discretization of self-defined particle types. An automatic generation method for the treatment of fixed boundary and constant temperature boundary in molecular dynamics is presented. Due to the fact that most open source molecular dynamics software accept input of text format, NSS has designed and developed a data transfer interface for open source micro / nano simulation software, except for discrete model and boundary particle information, which can be directly exported for text use. Initial conditions and other conditions are also set with the program's visual interface for input and export. Using this method to calculate the model example, the credible calculation results are obtained, and the complicated problem of pre-processing modeling of molecular dynamics simulation. NSS program is used as the developed molecular dynamics visual modeling software, and its function is comprehensive. It is a powerful tool for molecular dynamics simulation.
【学位授予单位】：广东工业大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：TB383.1;TP311.52

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