Topological Framework for Analysis and Visualization of Atomistic Materials Simulations

非技术性总结该奖项支持计算研究和教育，以开发计算工具，以促进遵守牛顿定律的原子的计算机模拟。原子模拟是理解固体和液体、有机和无机材料以及生命和非生命系统行为的一种非常重要和广泛应用的方法。随着现代计算的快速发展，在这种模拟中跟踪超过万亿个原子的运动是可能的。科学家面临的一个关键挑战是确定如何从如此丰富的数据中提取含义。一种广泛适用的方法是表征原子的局部排列。 众所周知，这很难以有意义的方式做到。考虑将液体冷却通过结晶温度的例子。无序液体中的原子是如何组合成晶体的？ 以有效和有意义的方式自动化这种类型的结构分析挑战了物理，化学和生物系统的计算建模的快速增长。一个有用的解决方案将产生广泛的影响，从设计具有所需特性的材料到了解它们是如何失败的。PI将开发一种新的方法来识别模拟中每个原子周围的结构排列。 基于拓扑学的数学思想，他们将开发实用的软件工具，用于局部结构确定，该工具具有鲁棒性，准确性和足够的计算效率，可以分析即使是最大的模拟。 与其他方法相比，PI的方法可以在不将结构冷却到绝对零度的情况下应用，而这通常是在动态仿真中完成的。这个过程在计算上可能非常昂贵，并且模糊了感兴趣或所寻求的现象的签名。该软件将开放源代码，允许所有科学家免费访问，并与该领域已经广泛使用的可视化代码兼容。该项目将培养下一代开发算法和软件基础设施，使科学发现和推进前沿。技术总结该奖项支持计算研究和教育，开发用于分析原子环境中局部结构的软件，这些原子环境是在原子模拟中出现的，支持凝聚态物质中缺陷，相变和变形的理论和计算研究。 传统上，连续的“序参数”被用来表征和识别大型点状物体系统中的结构;这类数据集包括通过例如分子动力学模拟和离散粒子实验获得的粒子坐标。 连续有序参数通常用于识别晶体结构中的缺陷或测量液体和玻璃中的无序。 PI将开发一个新的数学框架为中心的Voronoi细胞拓扑结构。 这将使研究人员能够在高温下研究原子机制，而无需淬火。与当前可用的方法相比，这提供了计算和科学优势。PI将重点关注三个研究目标。 首先，发展一个适合于分析大型点集局部结构的数学框架。 特别地，Voronoi拓扑提供了可能的粒子排列的配置空间的粗粒度细分。 这个配置空间的几何和拓扑结构将提供对邻居的可能安排的洞察，这在不完美的系统中特别有价值。 将特别注意晶体结构中缺陷的有限温度结构。 第二，将开发和分发开放源码软件，使其他研究人员能够将这种自动化方法应用于自己的研究和进一步的方法开发。 该软件将被设计为与广泛用于计算材料科学和应用物理学的其他软件包一起工作。 基本算法在并行计算机上是有效的，使它们能够用于研究大规模系统。 最后，将使用开发的理论和计算工具研究计算材料科学和应用物理学中的应用。 特别是，PI将专注于高温相变的动力学，晶体环境中缺陷的迁移和演变，以及对液体和玻璃中“无序”的理解。该奖项支持培训下一代开发算法和软件基础设施，以实现科学发现和推进前沿。

NONTECHNICAL SUMMARYThis award supports computational research and education to develop computational tools to advance computer simulation of atoms that obey Newton's laws. Atomistic simulation is a very important and widely applied approach for understanding the behavior of solids and liquids, organic and inorganic materials, and living and inanimate systems. With the rapid advance of modern computation, it is possible to track the motion of over a trillion atoms in such simulations. A key challenge to scientists is determining how to extract meaning from such rich data. One widely applicable approach is to characterize the local arrangement of atoms. This is notoriously difficult to do in a meaningful way. Consider the example of cooling a liquid through the crystallization temperature. How do the atoms in the disordered liquid organize to form a crystal? Automating this type of structure analysis in an efficient and meaningful manner challenges the rapid growth of computational modeling of physical, chemical and biological systems. A useful solution would have wide ranging impact from designing materials with desired properties to understanding how they fail.The PIs will develop a novel approach to identify structural arrangements around every atom in a simulation. Building on mathematical ideas from topology, they will develop practical software tools for local structure determination that is robust, accurate and sufficiently computationally efficient to analyze even the largest simulations. In contrast to others, the PIs' approach can be applied without cooling the structure to absolute zero as is usually done in dynamic simulation. This procedure can be computationally very costly and obscure the signatures of interesting or sought phenomena. The software will be made open source to allow free access to all scientists, and compatible with visualization codes that are already widely used in the field. This project will train the next generation in developing algorithms and software infrastructure that will enable scientific discovery and advance the frontiers.TECHNICAL SUMMARYThis award supports computational research and education to develop software for the analysis of local structure in atomic environments that arise in atomistic simulation in support of theoretical and computational studies of defects, phase transitions, and deformation in condensed matter. Traditionally, continuous "order parameters" are used to characterize and identify structure in large systems of point-like objects; data sets of this kind include particle coordinates as obtained through, for example, molecular dynamics simulations and discrete particle experiments. Continuous order parameters are routinely used to identify defects in crystal structures or to measure disorder in liquids and glasses. The PIs will develop a novel mathematical framework centered on Voronoi cell topology. This will allow researchers to study atomic mechanisms at high-temperature without quenching. This provides both computational and scientific advantages over currently available methods.The PIs will focus attention on three research goals. First, the development of a mathematical framework suitable for analyzing local structure in large point sets. In particular, Voronoi topology provides a coarse-grain subdivision of the configuration space of possible particle arrangements. The geometry and topology of this configuration space will provide insight into possible arrangements of neighbors that is especially valuable in imperfect systems. Particular attention will be paid to finite-temperature structure of defects in crystal structures. Second, open source software will be developed and distributed to allow other researchers to apply this automated approach for their own studies and further method development. The software will be designed to work with other software packages that are widely used in computational materials science and applied physics. The basic algorithms are efficient on parallel computers enabling their use in studying large-scale systems. Finally, applications in computational materials science and applied physics will be investigated using the theoretical and computational tools developed. In particular, the PIs will focus on the dynamics of high-temperature phase transformations, the migration and evolution of defects in crystalline environments and to the understanding of "disorder" in liquids and glasses.This award supports training the next generation in developing algorithms and software infrastructure that will enable scientific discovery and advance the frontiers.