LSEC, Institute of Computational Mathematics and Scientific/Engineering Computing, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China.
J Mol Graph Model. 2014 May;50:44-9. doi: 10.1016/j.jmgm.2014.03.006. Epub 2014 Mar 28.
This paper describes the design and function of a visualization tool, VCMM, for visualizing and analyzing data, and interfacing solvers for generic continuum molecular modeling. In particular, an emphasis of the program is to treat the data set based on unstructured mesh as used in finite/boundary element simulations, which largely enhances the capabilities of current visualization tools in this area that only support structured mesh. VCMM is segmented into molecular, meshing and numerical modules. The capabilities of molecular module include molecular visualization and force field assignment. Meshing module contains mesh generation, analysis and visualization tools. Numerical module currently provides a few finite/boundary element solvers of continuum molecular modeling, and contains several common visualization tools for the numerical result such as line and plane interpolations, surface probing, volume rendering and stream rendering. Three modules can exchange data with each other and carry out a complete process of modeling. Interfaces are also designed in order to facilitate usage of other mesh generation tools and numerical solvers. We develop a technique to accelerate data retrieval and have combined many graphical techniques in visualization. VCMM is highly extensible, and users can obtain more powerful functions by introducing relevant plug-ins. VCMM can also be useful in other fields such as computational quantum chemistry, image processing, and material science.
本文描述了一个可视化工具 VCMM 的设计和功能，用于可视化和分析数据，并与通用连续分子建模的求解器接口。特别是，该程序的重点是处理基于非结构网格的数据集，如有限/边界元模拟中使用的数据集，这大大增强了当前在该领域仅支持结构网格的可视化工具的功能。VCMM 分为分子、网格和数值三个模块。分子模块的功能包括分子可视化和力场分配。网格模块包含网格生成、分析和可视化工具。数值模块目前提供了几个连续分子建模的有限/边界元求解器，并包含几个用于数值结果的常见可视化工具，如线和平面插值、曲面探测、体绘制和流场绘制。三个模块可以相互交换数据，并执行完整的建模过程。还设计了接口，以方便使用其他网格生成工具和数值求解器。我们开发了一种加速数据检索的技术，并在可视化中结合了许多图形技术。VCMM 具有高度的可扩展性，用户可以通过引入相关插件来获得更强大的功能。VCMM 也可以在其他领域（如计算量子化学、图像处理和材料科学）中发挥作用。
