Large-scale, long-time molecular dynamics simulation of crystal growth: From close-packing to clathrates and quasicrystals

晶体生长的大规模、长时间的分子动力学模拟：从密堆积到包合物和准晶体

基本信息

批准号：
1515306
负责人：
Sharon Glotzer
金额：
$ 1.48万
依托单位：
Regents of the University of Michigan - Ann Arbor
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2015
资助国家：
美国
起止时间：
2015-08-01 至 2017-07-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1515306&HistoricalAwards=false
关键词：
Large scale long time molecular

项目摘要

How crystals form from liquids is important in fields ranging from biology, medicine, and food to the synthesis of materials with desired properties. Yet little is understood about how crystals form in a way that would allow one to predictably control and optimize crystal growth to obtain structures with targeted properties. For example, complex crystals known as clathrates are important for hydrocarbon extraction and storage, and can cause blockage of oil and natural gas pipelines. Another complex crystal structure, called a quasicrystal, is predicted to have unique optical properties important for telecommunications and novel coatings. This project will use fast computers based on graphics processors to study how crystals form in clathrates, quasicrystals, and related crystal structures. Such simulations are challenging because large system sizes and long time scales must be achieved simultaneously, and thus very large computing resources such as those offered by Blue Waters are required. For the first time, the invetigators expect to obtain data on crystallization that will complement - and surpass - what can be obtained by experiments, enabling a detailed atomistic view of how crystallization occurs, and whether the process is different for different types of crystals.Classical theories hypothesize that crystals grow from liquids atom-by-atom, layer-by-layer. How, then, can one explain the formation of crystals with dozens, hundreds, even thousands of atoms in a unit cell or aperiodic solids with no unit cell? The investigators will conduct large-scale, long-run-time molecular dynamics computer simulations of crystal growth to investigate the relationship between crystal complexity and the growth mechanism. The planned simulations will neither approach the largest molecular dynamics simulations nor the longest molecular dynamics simulations, but the combination of large system size and long run-time (time steps times number of atoms = 10^16) requires a petascale resource of the leading-edge capability that Blue Water represents. Preliminary estimates suggest that the project might achieve or surpass the dynamical range of experimental scattering data for the first time. The computer simulations will mimic standard experimental crystal growth protocols (Czochralski and Bridgman-Stockbarger) as closely as possible. The investigators will employ a computationally inexpensive atomistic model that they recently developed for the study of icosahedral quasicrystals, clathrates, and other crystal structures (Nature Materials 14, 109 (2015)). The model is similar to a united-atom force field model. The project will use HOOMD-Blue for the entirety of the planned studies, an open source, publicly available code that the investigators develop for the community, and which has been already ported to and optimized for Blue Waters. HOOMD-Blue is currently the fastest available simulation code for carrying out the proposed studies. With the acquired simulation data the project will investigate the role of unit cell symmetry on crystal growth and relate the Wulff shape to the space group symmetry of the dominant clathrate type. Furthermore, the team will conduct a phason strain analysis of the icosahedral quasicrystal and will compare the diffraction patterns of the grown crystals with experimental data.

从生物学，药物和食物到具有所需特性的材料的合成，从液体中形成晶体的重要性。然而，关于如何以一种可以预测控制和优化晶体生长以获得具有靶向特性的结构的方式，几乎没有理解的晶体。例如，称为杂质的复杂晶体对于碳氢化合物的提取和储存很重要，并且可能导致油和天然气管道的阻塞。预计另一种称为准晶体的复杂晶体结构具有独特的光学特性，对电信和新颖的涂层很重要。该项目将使用基于图形处理器的快速计算机来研究晶体如何形成外晶，准晶体和相关的晶体结构。这样的模拟是具有挑战性的，因为必须同时实现大型系统尺寸和长时间尺度，因此需要大量的计算资源，例如蓝水提供的计算资源。 For the first time, the invetigators expect to obtain data on crystallization that will complement - and surpass - what can be obtained by experiments, enabling a detailed atomistic view of how crystallization occurs, and whether the process is different for different types of crystals.Classical theories hypothesize that crystals grow from liquids atom-by-atom, layer-by-layer.那么，如何解释晶体细胞中的数十个，数百，甚至数千个原子或没有晶胞的固体中的数十个原子的晶体形成？研究人员将对晶体生长进行大规模的，长期的分子动力学模拟，以研究晶体复杂性与生长机制之间的关系。计划的仿真既不接近最大的分子动力学模拟，也不会接近最长的分子动力学模拟，而是大型系统大小和长时间运行时间的组合（时间步长的原子= 10^16）需要蓝色水代表的前沿功能的佩塔斯卡尔资源。初步估计表明，该项目可能首次实现或超过实验散射数据的动态范围。计算机模拟将尽可能地模仿标准的实验晶体生长方案（Czochralski和Bridgman-Stockbarger）。研究人员将采用一种计算廉价的原子模型，他们最近开发了用于研究二十面体准晶体，外层和其他晶体结构的研究（自然材料14，109（2015））。该模型类似于联合原子力场模型。该项目将在整个计划研究中使用Hoomd-Blue，这是调查人员为社区开发的开源，公开可用的代码，并且已经对蓝色水域进行了移植和优化。 Hoomd-Blue目前是用于进行拟议研究的最快可用仿真代码。通过获得的模拟数据，项目将研究晶胞对称性对晶体生长的作用，并将WULFF形状与主要的覆盖类型的空间组对称性相关联。此外，该团队将对二十面体准晶体进行Phason菌株分析，并将比较生长晶体的衍射模式与实验数据。