6-8. 3DStructGen: an interactively web-based 3D structure generation software

Chen Pin, Wang Yu, Yan Hui, Xu Zexin, Li Yangzhong, Gao Sen, Li Jiahui, Pan Gechuanqi, Mo Qing, Tao Jun, Du Yunfei

National Supercomputer Center in Guangzhou, School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, 510006, China

Abstract: Material structure generation and computational input file preparation are the important components for high-throughput (including single-throughput) material calculations. Recently, structured data generation software based on command line mode, such as Pymatgen, Aflow and ASE (Atom Simulation Environment), has met the need to generate input files in batches under high-throughput calculations. However, in the single-throughput debugging process, when there are problems such as unreasonable structure and parameter errors, it is impossible to perform interactive editing and input parameter debugging for the 3-dimensional complex structure. Therefore, we developed an advanced structure visualization and editor program by using web standard techniques with HTML5, CSS and JavaScript that provides the following features. Firstly, both non-periodic organic molecule and crystal structure can be visualized, built and edited. Secondly, a wide range of cheminformatics algorithms for crystal structure are provided, such as cleaving surface, establishing vacuum layer, and identifying space-group type. Thirdly, it is a lightweight library coded entirely on JavaScript, and easy to interface with other software. Finally, the initial input files for VASP and Gaussian are supported for generating by interacting with dialog boxes. 3DStructGen may play a vital role in the fields of cloud computing, single-throughput calculation parameter debugging and material structure visualization in batches. It also maybe an important part of completing the whole process material simulation (including pre-processing, calculation and post-processing analysis) on the webpage.

Keyword: Web-based visualization; Structure editor; HTML5

图1. 3DStructGen界面展示图.

3DStructGen：基于网页的可交互3维结构生成软件

陈品，王煜，颜辉，许泽鑫，李杨中，高森，李家辉，潘格川崎，莫晴，陶钧，杜云飞^*

国家超算广州中心，数据科学与计算机学院，中山大学，广州51006，中国

摘要：材料结构生成与计算输入文件准备是进行高通量材料计算（包括单通量计算）的重要组成部分。近年来，基于命令行模式的结构数据生成软件如Pymatgen，Aflow和ASE (Atom Simulation Environment) 满足了高通量计算下批量生成输入文件的需求，但是在单通量调试过程中针对结构不合理、参数谬误等问题，无法对3维的复杂结构进行可交互式编辑和输入参数调试。因此，我们采用标准的网页编程（HTML5，CSS, JavaScript）技术开发了一款3维结构编辑以及可视化软件-3DStructGen。该软件特色如下：1). 支持非周期性分子、晶体结构的构建、编辑以及可视化；2). 我们开发了一系列算法处理晶体结构，如建立切面、建立真空层、确定空间群等；3). 核心代码采用JavaScript编写的轻量级库文件，容易集成到其他软件或平台；4). 通过在网页对话框的交互操作，可生成VASP、Gaussian软件的输入文件。3DStructGen可能将在云计算、单通量计算参数调试以及批量材料结构可视化等领域发挥支撑作用，是在网页端完成全流程材料模拟过程中(包括前处理、计算以及后处理分析)的重要组成部分。

关键词：网页可视化；结构编辑；HTML5