Beyond Classical Molecular Dynamics: Developing DL_POLY

DL_POLY是CCP5旗舰英国代码，是少数几个进行经典分子动力学模拟的国际代码之一。这是一种强大的计算显微镜，一个真正的拉普拉斯魔，在其中，给定一组特定的原子之间的力，根据牛顿力学，人们遵循它们变化的位置和速度。因此，人们可以在原子水平上分析和理解凝聚态物质的行为。然而，经典分子动力学有两个主要的限制，这在大多数社区对新功能的请求中占主导地位。首先，经典力场的使用限制了模型的准确性，并限制了它的适用性——例如，量子效应、键的断裂和形成以及电荷转移都不包括在内。其次，通过分子动力学获得的时间尺度（系统可以遵循的时间）太短，无法正确研究化学，物理，材料科学和生物学中的许多现象和过程，因为事件很少发生。我们的目标是解决这两个方法上的限制。我们将在DL_POLY中实现：(a)密度泛函紧密结合（DFTB）来解决精度和量子效应问题；(b)正向通量采样（FFS）来模拟罕见事件，从而解决长时间尺度现象。我们将让社区成员从项目一开始就作为顾问和早期用户参与进来。计划进行一系列测试应用，以证明新软件的强大功能：1)检查纳米结构对潜在热电体电子结构的影响，以及高度无序的铋氧化物（DFTB）中局部结构与导电性之间的联系2)非均质成核，例如由纳米颗粒促进的非均质成核，以及在癌症治疗（FFS）中利用纳米气泡增强药物输送的非均质成核。新功能将在功能材料（EPSRC优先考虑）等领域开辟无数新的应用，例如能源材料、电池材料、纳米材料、铁电体、超导体、热电体，用于信息和通信技术、能源发电存储、运输、医疗保健、国防和消费品。FFS的实施将使用户能够解决各种各样的问题，如晶体成核、蛋白质折叠、孔隙形成、蛋白质通过孔隙的易位、磁性纳米结构中的罕见开关、异构化、粗糙表面的润湿、液滴聚结和基因开关的翻转。新开发的软件将免费提供给全世界的学者。新功能将确保DL_POLY保持国际竞争力。将向学术界和工业界提供全面的手册、文件和培训。

DL_POLY is a CCP5 flagship UK code, one of a handful of international codes to carry out classical molecular dynamics simulations. These are a powerful form of computational microscope, a real Laplace's demon, in which, given a specified set of forces between atoms, one follows their changing positions and velocities by Newtonian mechanics. One can thus analyse and understand the behaviour of condensed matter at the atomic level. However, classical molecular dynamics has two major limitations which dominate the majority of community requests for new functionality. First, the use of classical force fields limits the accuracy of the model and restricts its applicability -- quantum effects, bond breaking and making and charge transfer are, for example, not included. Secondly, the timescales (the time over which the system can be followed) accessible via molecular dynamics are too short to study properly many phenomena and processes in chemistry, physics, materials science and biology where events occur only rarely. We aim to address both these methodological limitations. We shall implement in DL_POLY: (a) density functional tight binding (DFTB) to address the accuracy and quantum effects problem and (b) forward flux sampling (FFS) to enable simulations of rare events and thus address long timescale phenomena.We shall involve members of the community both as advisers and early users right from the start of the project. A number of test applications are planned to demonstrate the power of the new software: i) examination of the effects of nanostructuring on the electronic structure of potential thermoelectrics and the link between local structure and conductivity in highly disordered bismuth oxides which are among the very best superionic conductors (DFTB) ii) heterogeneous nucleations, such as those promoted by nanoparticles and exploited in enhanced drug delivery by nanobubbles in cancer treatment (FFS). The new functionality will open up a myriad of new applications in areas such as functional materials (an EPSRC priority) -- e.g., energy materials, battery materials, nanomaterials, ferroelectrics, superconductors, thermoelectrics for use in information and communications technology, energy generation storage, transport, healthcare, defence and consumer goods. FFS implementation will enable users to tackle problems as diverse as crystal nucleation, protein folding, pore formation, protein translocation through pores, rare switching in magnetic nanostructures, isomerization, wetting of rough surfaces, droplet coalescence and flipping of genetic switches. The new software produced will be freely available to academics worldwide. The new features will assure that DL_POLY remains internationally competitive. Comprehensive manuals, documentation and training will be made available to both academia and industry.