DL_POLY version 4: a major shift in length- and time-scale limitations in Molecular Dynamics simulations of heterogeneous phenomena

在过去的30年里，模拟物质（如固体、液体、膜或纳米颗粒）的原子和分子分辨率一直是一个主要的增长领域。计算方法和硬件的发展意味着这种分子模拟现在可以以10年前无法想象的现实性和准确性进行。然而，在分子模拟可以探测的长度和时间尺度上仍然存在基本的限制。这些都阻碍了科学家们认识到分子模拟的全部力量。高性能计算的改进已经达到了我们可以开始消除这些限制的阶段。特别是大规模并行处理器（MPP）的出现，可以同时使用100或1000个处理器，这意味着可以使用分子模拟来模拟具有更真实长度尺度的系统。迄今为止，这种进展主要应用于分子均匀分布在整个材料中的材料：大多数常见材料（金属、陶瓷、塑料、液体）都是这种形式。然而，有许多非常重要的材料，其中分子分布不均匀/要么是因为它们涉及不同相的混合物（如在水和空气之间的界面），要么是非常不同性质的颗粒混合在一起（如发生在许多催化剂，纳米颗粒，聚合物复合材料和天然材料，如骨）。在这种不均匀的材料中，重要特性所体现的长度和时间尺度通常都很长，因此确实需要在最新的MPP计算机上快速高效的代码来准确地建模。HECToR的出现为在分子水平上模拟非均匀材料提供了一个独特的机会，从而获得迄今为止无法获得的对这些材料的性质以及如何控制其特性的见解。不幸的是，现有的分子模拟软件能够模拟各种重要的非均质材料，但没有一种软件能够充分扩展到赫克托的强大机器上。因此，如果要抓住HECToR提供的机会，迫切需要对现有的分子模拟包进行重大修改。这个项目的目的是开发这个新的代码和优化使用赫克托耳。该项目将从现有的DL_POLY包开始，该包在英国编写，并广泛用于以前的高端计算机设备，以模拟均质材料。将对DL_POLY进行几项重大修改，使该程序能够：(i)对具有或演化为高度不均匀结构的系统进行有效建模；（ii）通过一系列非常快速但非常罕见的原子跳跃（这是大多数固态系统随时间变化的基础），对实时进化非常缓慢的系统进行建模；（iii）利用HECToR的架构来获得最大的性能。新程序的力量将在计算分布在空气-水界面上的纳米粒子的特性、分子晶体和框架材料的成核、离子通过专用玻璃的迁移性以及蛋白质在控制蛋壳形成中的作用方面得到证明。

The simulation of matter/such as solids, liquids, membranes or nanoparticles/with atomic and molecular resolution has been a major growth area over the last 30 years. Developments in the computational methods and hardware have meant that such molecular simulations can now be performed with a level of realism and accuracy that was unimaginable even 10 years ago. However, there are still fundamental limits on the length- and time-scales that can be probed with molecular simulation. These are preventing scientists from realising the full power of molecular simulation.Improvements in high performance computing have got to the stage where we can begin to remove these limitations. In particular, the advent massively parallel processors (MPP), where 100s or 1000s of processors are used simultaneously, have meant that systems with much more realistic lengthscales can be modelled using molecular simulations. To date such progress has been applied mainly to materials in which the molecules are spread evenly throughout the material: most common materials (metals, ceramics, plastics, liquids) are of this form. However, there are many very important materials where the molecules are spread unevenly/either because they involve a mixture of different phases (such as at the interface between water and air) or particles of very different character are mixed together (as occurs with many catalysts, nanoparticles, polymer composites and natural materials such as bone). In such inhomogeneous materials, both the length- and time-scale on which important properties are manifest are often very long, and so really demand fast efficient code on the latest MPP computers to model accurately. The advent of HECToR opens a unique opportunity to model inhomogeneous materials at a molecular level, and thereby gain hitherto inaccessible insights into the nature of these materials and how their properties can be controlled. Unfortunately, of the existing molecular simulation software that is capable of modelling the full range of important inhomogeneous materials, none will scale adequately to a machine of the power of HECToR. Thus, major revisions of an existing molecular simulation package are needed urgently if the opportunities offered by HECToR are to be grasped.The purpose of this project is to develop this new code and optimise for use on HECToR. The project will start with an existing package, DL_POLY, written in the UK and used extensively on previous high-end computer facilities to model homogeneous materials. Several major modifications will be made to DL_POLY that will enable the program: (i) to model efficiently systems which either possess, or evolve into, highly nonuniform structures; (ii) to model systems which evolve very slowly in real time through a series of very fast but very infrequent atomic jumps (this is the basis on which most solid state systems change over time); and (iii) to exploit the architecture of HECToR to gain maximum performance. The power of the new program will be demonstrated in calculations on the properties of nanoparticles distributed on an air-water interface, nucleation of molecular crystals and framework materials, the mobility of ions through specialised glasses, and the role of proteins in controlling eggshell formation.