【程序分享】SPaMD studio 程序：（VASP + LAMMPS） 原子建模、模拟、分析和可视化的集成平台

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分享一个 SPaMD studio 程序: 原子建模、模拟、分析和可视化的集成平台 。

感谢论文的原作者！

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主要内容

“该研究开发了一个集成平台，用于定制和模块化原子建模、各种功能模拟的高通量实施、稳健的原子拓扑分析以及高保真处理和可视化，称为可扩展并行分子动力学（SPaMD）工作室。模块化建模系统提供了构建特定模型（如纳米结构、位错和裂纹模型）以及复杂模型（如双层、多层和纳米复合材料模型）的快速直接方法。此外，定制建模系统通过全面的工作流程实现选择和操作的连续嵌套处理，以获得具有复杂几何形状的任意模型。通过集成自动建模工具、负载平衡任务分配系统、自适应实时数据分析和可视化方法以及强大的逻辑反馈系统，为功能模拟设计了各种高通量方案。此外，通过集成AACSD和AADIS代码，原子分析支持晶体结构、取向和位错的实时和事后定量分析。为了便于处理和模拟，为SPaMD设计了一个用户友好的图形用户界面，该界面还支持数千万个原子的高效渲染。为了展示该平台的效率和功能，通过进行多次评估和测试对其进行了严格验证，这为其在目标原子模拟中的潜在应用提供了指导和信心。”——取自文章摘要。

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AACSD和AADIS代码相关链接：

【程序分享】AADIS 程序：位错特征和分布的原子分析平台

【程序分享】AACSD 程序: 用于晶体结构和缺陷的原子分析平台

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Scalable Parallel Materials/Molecular Design/Dynamics Studio 

Updated in Ver.1.5: 

Simulation: Overhaul simulation UI for VASP. Add several implementations for VASP/Basiseries module, e.g.Structure Optimization, Single Point, Molecular Dynamics, Basic Band Structure, Fat Band Structure, 3d Band Structure, Density of States, Fermi Surface, Valence Charge Density, Partial Charge Density,Electron Local Function, Local Potential,Wave Function in real space. Add port to select default server for simulation module. Add auto download routine and preview routine for simulation result. 

Analysis: Add the on-site visualization for AADIS module: DVA, STA, SVA, IDA, NYE and NTA. Improve analysis speed and memory usage for wave function in real space module in VASPA. Add new tools for visualization: Plot Curves of Line+Symbol, Scatter+Colormap, Bubble+Colormap, Vector+Colormap. Enable adding lines to plot curves from data file in CSV format.

Updated in Ver.1.4: 

Simulation:

Add several high-throughput implementations for Simulation module, e.g. ABADE, ACOHP.

Analysis:

Add new module for VASP data analyzer: fat band structure, 3D band structure and fermi surface.

Add new module for VASP volumetric data analyzer: Wave function in real space.

Visualization:

Add new module for atomic visualization mode: polyhedral, plane, vector.

Overhaul bond definition, enable complex cutoff between atoms.

Overhaul colorbar selection, enable custom definition of colorbar.

Add new module for Brillouin zone visualization, K-path definition, and fermi surface visualization.

Add new module: colorfill surface for 3D data visualization.

Updated in Ver.1.3: Add several high-throughput implementations for Simulation module, e.g. AELAS, ADAIS, ASURF, AEDOS, ABAND, APHON; Add the analysis modules for VASP results, e.g. VASPDV for density of state (DOS) and band structure, VASPVV for charge density difference (CDD) and electron localization function (ELF); fix the bugs for modelling, Simulation and visualization modules. 

Updated in Ver.1.2: Add Surfkit for Modelling module; Add support for GUI to VASP for automatically including more functionals by other developer or users; fix the bugs for Simulation and visualization module. 

Updated in Ver.1.1: Add Cryskit for Modelling module; fix the bugs for Simulation module, support submit task to current terminal. 

SPaMD Studio includes the following features: 

1) a user-friendly GUI for operation and visualization; 

2) high-throughput first principles calculation module via VASP and VASPMATE, e.g. ABADE, ACOHP, AEDOS, ABAND, APHON, AELAS, ADAIS, ASURF, AVCDD, AWFUN etc.

3) high-resolution visualization for fat band structure, 3D band structure, fermi surface, wave function in real space, etc. And atomic visualization mode via polyhedral, plane, vector. 

4) a robust rendering system designed for several million atoms or more, supporting color-coding, camera control, atom pickup, and anti-aliasing rendering; 

5) a modular modeling system that supports the direct construction of nanoparticles, nanowires, nanosheets, polycrystals with different axial ratios, bilayers and multilayers, as well as dislocation and crack insertion; 

6) a custom modeling system called atomkit, which provides geometrical selection (e.g., slice, cubic, sphere, prism, polyhedron), multilevel region adjustment (e.g., move, deform, rotate) with boolean selection (e.g., and, or, not), and basic operations (e.g., add, delete, random displace, duplicate, deform); 

7) workflow templates that can be defined with preconfigured operations for quick access and used to perform the same operations with the same settings in different simulations; 

8) adaptive real-time analysis that supports the topological methods of CNA, BAA, CSP, CNP, OIM, and LCO that were previously implemented in our AACSD code; 

9) a post-analysis system that is packaged for vector and tensor analysis methods, i.e., DVA, STA, DDA, SVA, IDA, and NTA, which were recently released in our AADIS code; 

10)an automatic task management system for high-throughput simulation, e.g., dynamic tension/compression, shock loading, and fracture toughness calculation via the internal SPaMD Simulator or other external simulators e.g., LAMMPS;  

11) an internal robust SPaMD simulator that supports molecular dynamics simulations through various ensembles such as NVE, NVT, and NPT, as well as molecular statics methods via CG and FIRE.

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SPaMD_Visualizer_manual

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