Scalable Quantum Chemistry with Flexible Embedding Stage 2

在“具有灵活嵌入的可扩展量子化学”项目的第二阶段，我们建议改进我们在第一阶段开发的软件，用于复杂系统中反应性的分子建模，特别是在水等溶剂存在下的表面化学和多相催化。这个软件结合了量子化学（也称为第一原理）技术，它可以处理化学反应中心，嵌入在一个经验（分子力学）模型的其余部分的系统，也就是说，模拟表面的材料板和它上面的溶剂层。在第一阶段，我们扩展了我们的嵌入模型，以包括对自旋的新处理，极化系统，如磁有序材料，低成本量子方法的实现，以描述各向异性和自旋极化环境和周期性边界条件，以便在溶剂化表面上执行计算。该软件的目标科学的例子包括在存在或水的情况下工作的金属氧化物催化;污染物种类的结合（重金属或有毒有机物）转化为环境中的天然矿物质，或可将其从环境中去除的专门设计的无机材料;第二阶段的目标是使新用户能够尽可能简单地根据第一阶段开发的方法设置和运行灵活的嵌入计算，并使高级用户能够根据自己的需求调整代码。我们将通过替换用户界面的第一阶段代码来实现这一目标，该代码能够实现第一阶段的科学目标，但具有许多层次，并且依赖于传统的软件包，使用流行的脚本语言Python编写的新的直接用户界面。新的界面将从根本上简化代码的使用和开发，而不会影响第一阶段的主要目标，即在大规模并行机上实现新嵌入模型的高性能。我们将把旧代码库中的所有关键功能整合到新版本的代码中，包括设置嵌入式集群计算的实用程序，高级几何优化库，以及连接到多个量子力学和分子力学软件包的能力，特别是FHI-AIMS软件包，该软件包将与FHI-AIMS开发人员合作耦合到代码。我们还希望通过从第一阶段开始的演示应用程序中开发全面的文档、教程和案例研究，使新代码尽可能用户友好。到第二阶段结束时，我们将有一个新版本的代码，准备向社区发布，实现旧版本的所有关键功能，我们将能够将用户过渡到新代码，并将其用作我们所有未来QM/MM和多尺度开发的平台。

In stage two of the "Scalable Quantum Chemistry with Flexible Embedding" project we propose to refine the software we have developed in stage one for molecular modelling of reactivity in complex systems, in particular surface chemistry and heterogeneous catalysis in the presence of a solvent such as water. This software combines quantum chemistry (also known as first principles) techniques, which can treat the chemically reacting centres, embedded in an empirical (molecular mechanics) model for the rest of the system, i.e. the slab of material which models the surface and the solvent layers on top of it.In stage one we are extending our embedding model to include new treatments for spin-polarised systems such as magnetically ordered materials, an implementation of a low-cost quantum method to describe anisotropic and spin-polarised environments and periodic boundary conditions in order to perform calculations on solvated surfaces. Examples of the science this software targets includes metal oxide catalysis that work in the presence or water; the binding of pollutant species (heavy metals or toxic organics) to natural minerals in the environment, or specially designed inorganic materials that could potentially remove them from the environment; catalysis by more complex minerals, not well treated by existing treatments but of great industrial importance; and the design of sensors and photoelectric materials by organic layers on inorganic surfaces.The aim of stage two is to make it is as straightforward as possible for new users to set up and run flexible embedding calculations based on the methods developed in stage one, and for advanced users to adapt the code to their own needs. We will achieve this by replacing the user interface the stage one code, which is able to achieve the scientific goals of stage one but is many-layered and relies on a legacy software package, with a new direct user interface written in the popular scripting language Python. The new interface will radically simplify use and development of the code without compromising on the primary goal of stage one, namely achieving high performance for the new embedding models on large-scale parallel machines.We will incorporate all the key functionality from our legacy codebase into the new version of the code, including utilities to set up embedded cluster calculations, an advanced geometry optimisation library, and the ability to interface to multiple quantum mechanical and molecular mechanical software packages, in particular the FHI-AIMS package which will be coupled to the code in collaboration with the FHI-AIMS developers. We also aim to make the new code as user-friendly as possible through the development of comprehensive documentation, tutorials and case studies from the demonstration applications program began in stage one.By the end of stage two we will have a new version of the code that is ready for release to the community, with all the key functionality of the legacy version implemented, and we will be in a position to transition users to the new code and use it as our platform for all future QM/MM and multiscale developments.