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，具有原子和分子分辨率的物质/例如固体、液体、膜或纳米颗粒/的模拟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甚至10年前无法想象的真实性和准确性水平进行。然而，仍然有一些基本的限制长度和时间尺度，可以探测分子模拟。这些限制阻碍了科学家们充分利用分子模拟的能力，高性能计算的发展已经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，其中同时使用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现实的长度尺度的系统。到目前为止，这种进展主要应用于分子均匀分布在整个材料中的材料：大多数常见的材料（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，其中分子不均匀地分布/因为它们涉及不同相的混合物（例如在水和空气之间的界面处）或性质非常不同的颗粒混合在一起（如许多催化剂、纳米颗粒、聚合物复合材料和天然材料如骨）。在这种非均匀材料中，重要性质表现的长度和时间尺度通常都很长，因此需要在最新的MPP计算机上快速高效的代码来精确建模。HECToR的出现为在分子水平上对非均匀材料进行建模提供了一个独特的机会，从而获得了迄今为止无法深入了解这些材料的性质以及如何控制它们的特性。不幸的是，现有的分子模拟软件，能够模拟的重要的非均匀材料的全部范围内，没有一个将充分扩展到HECToR的功率的机器。因此，现有的分子模拟包的重大修订是迫切需要的，如果HECToR所提供的机会被gradually.The目的，这个项目是开发这个新的代码和优化使用HECToR。该项目将从现有的软件包DL_POLY开始，该软件包在英国编写，并广泛用于以前的高端计算机设施，以模拟均匀材料。将对DL_POLY进行几个主要的修改，使程序能够：（i）有效地模拟具有高度非均匀结构或演化成高度非均匀结构的系统;（ii）模拟通过一系列非常快速但非常罕见的原子跳跃在真实的时间中演化非常缓慢的系统（这是大多数固态系统随时间变化的基础）;以及（iii）利用HECToR的架构以获得最大性能。新计划的力量将在计算分布在空气-水界面上的纳米颗粒的性质，分子晶体和框架材料的成核，离子通过专用玻璃的流动性以及蛋白质在控制蛋壳形成中的作用中得到证明。

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.