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

晶体是如何从液体中形成的，在从生物学、医学、食品到具有所需性能的材料的合成等领域都很重要。然而，人们对晶体形成的方式知之甚少，这种方式将允许人们可预测地控制和优化晶体生长，以获得具有目标性质的结构。例如，被称为笼形物的复杂晶体对于碳氢化合物的提取和储存很重要，并且可能导致石油和天然气管道堵塞。另一种复杂的晶体结构，称为准晶体，预计具有独特的光学特性，对电信和新型涂层很重要。该项目将使用基于图形处理器的快速计算机来研究笼形物、准晶体和相关晶体结构中晶体的形成方式。这样的模拟是具有挑战性的，因为大系统尺寸和长时间尺度必须同时实现，因此需要非常大的计算资源，如Blue Waters提供的那些。这是第一次，研究人员期望获得结晶的数据，这将补充-甚至超越-可以通过实验获得的数据，使结晶如何发生的详细原子视图，以及不同类型的晶体的过程是否不同。经典理论假设晶体是由液体原子一个接一个原子，一层接一层地形成的。那么，我们如何解释由数十个、数百个甚至数千个原子组成的单晶晶体或没有单晶的非周期固体的形成呢？研究人员将对晶体生长进行大规模、长时间的分子动力学计算机模拟，以研究晶体复杂性与生长机制之间的关系。计划中的模拟既不会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，但是大系统尺寸和长运行时间（时间步长乘以原子数= 10^16）的组合需要Blue Water所代表的领先能力的千兆级资源。初步估计表明，该项目可能首次达到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拟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成本低廉的原子模型，该模型是他们最近为研究二十面体准晶体、笼形物和其他晶体结构而开发的（Nature Materials 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hood -Blue，这是一个开源的、公开可用的代码，是研究人员为社区开发的，并且已经移植到Blue Waters并为其进行了优化。hood - blue是目前最快的模拟代码，可用于进行拟议的研究。利用获得的模拟数据，该项目将研究单位胞对称对晶体生长的作用，并将伍尔夫形状与主要笼形物类型的空间群对称联系起来。此外，该团队将对二十面体准晶体进行相位应变分析，并将生长晶体的衍射模式与实验数据进行比较。

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.