{"title":"tda-segmentor:提取和分析多孔材料局部结构和孔隙特征的工具","authors":"","doi":"10.1016/j.cpc.2024.109344","DOIUrl":null,"url":null,"abstract":"<div><p>Local geometrical features of a porous material such as the shape and size of a pore or the curvature of a solid ligament do often affect the macroscopic properties of the material, and their characterization is necessary to fully understand the structure-property relationships. In this contribution, we present an approach to automatically segment large porous structures into such local features. Our work takes inspiration from techniques available in Topological Data Analysis (TDA). In particular, using Morse theory, we generate Morse-Smale Complexes of our structures that segment the structure, and/or its porosity into individual features that can then be compared. We develop a tool written in C<span>++</span> that is built on the topology toolkit (TTK) library, an open source platform for the topological analysis of scalar data, with which we can perform segmentation of these structures. Our tool takes a volumetric grid representation as an input, which can be generated from atomistic or mesh structure models and any function defined on such grid, e.g. the distance to the surface or the interaction energy with a probe. We demonstrate the applicability of the tool by two examples related with analysis of porosity in zeolite materials as well as analysis of ligaments in a porous metal structure. Specifically, by segmenting the pores in the structure we demonstrate some applications to zeolites such as assessing pore-similarity between structures or evaluating the accessible volume to a target molecule such as methane that can be adsorbed to its surface. Moreover, once the Morse-Smale complexes are generated, we can construct graph representations of the void space, replacing the entire pore structure by a simply connected graph. Similarly, the same tool is used to segment and generates graphs representing the solid structure and we show how they can be used to correlate structure and mechanical properties of the material. 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引用次数: 0
摘要
多孔材料的局部几何特征(如孔隙的形状和大小或固体韧带的曲率)通常会影响材料的宏观特性,因此,要充分了解结构与特性之间的关系,就必须对这些特征进行表征。在本文中,我们提出了一种将大型多孔结构自动分割为此类局部特征的方法。我们的工作从拓扑数据分析(TDA)技术中获得灵感。特别是,利用莫尔斯理论,我们生成了结构的莫尔斯-尺度复合物,将结构和/或其孔隙率分割成可以比较的单个特征。我们开发了一种用 C++ 编写的工具,该工具基于拓扑工具包(TTK)库,这是一个用于标量数据拓扑分析的开源平台,我们可以利用它对这些结构进行分割。我们的工具将体积网格表示法作为输入,该表示法可由原子或网格结构模型以及定义在此类网格上的任何函数(如到表面的距离或与探针的相互作用能量)生成。我们通过分析沸石材料中的孔隙率以及分析多孔金属结构中的韧带这两个实例来展示该工具的适用性。具体来说,通过分割结构中的孔隙,我们展示了沸石的一些应用,如评估结构之间的孔隙相似性或评估目标分子(如可吸附在其表面的甲烷)的可及体积。此外,一旦生成莫尔斯-斯马尔复合体,我们就可以构建空隙空间的图示,用简单连接的图取代整个孔隙结构。同样,同样的工具也可用于分割和生成表示固体结构的图形,我们将展示如何利用它们来关联材料的结构和机械特性。代码以开源形式发布,可在此处访问: https://github.com/AMDatIMDEA/tda-segmentor
tda-segmentor: A tool to extract and analyze local structure and porosity features in porous materials
Local geometrical features of a porous material such as the shape and size of a pore or the curvature of a solid ligament do often affect the macroscopic properties of the material, and their characterization is necessary to fully understand the structure-property relationships. In this contribution, we present an approach to automatically segment large porous structures into such local features. Our work takes inspiration from techniques available in Topological Data Analysis (TDA). In particular, using Morse theory, we generate Morse-Smale Complexes of our structures that segment the structure, and/or its porosity into individual features that can then be compared. We develop a tool written in C++ that is built on the topology toolkit (TTK) library, an open source platform for the topological analysis of scalar data, with which we can perform segmentation of these structures. Our tool takes a volumetric grid representation as an input, which can be generated from atomistic or mesh structure models and any function defined on such grid, e.g. the distance to the surface or the interaction energy with a probe. We demonstrate the applicability of the tool by two examples related with analysis of porosity in zeolite materials as well as analysis of ligaments in a porous metal structure. Specifically, by segmenting the pores in the structure we demonstrate some applications to zeolites such as assessing pore-similarity between structures or evaluating the accessible volume to a target molecule such as methane that can be adsorbed to its surface. Moreover, once the Morse-Smale complexes are generated, we can construct graph representations of the void space, replacing the entire pore structure by a simply connected graph. Similarly, the same tool is used to segment and generates graphs representing the solid structure and we show how they can be used to correlate structure and mechanical properties of the material. The code is published as open-source and can be accessed here: https://github.com/AMDatIMDEA/tda-segmentor
期刊介绍:
The focus of CPC is on contemporary computational methods and techniques and their implementation, the effectiveness of which will normally be evidenced by the author(s) within the context of a substantive problem in physics. Within this setting CPC publishes two types of paper.
Computer Programs in Physics (CPiP)
These papers describe significant computer programs to be archived in the CPC Program Library which is held in the Mendeley Data repository. The submitted software must be covered by an approved open source licence. Papers and associated computer programs that address a problem of contemporary interest in physics that cannot be solved by current software are particularly encouraged.
Computational Physics Papers (CP)
These are research papers in, but are not limited to, the following themes across computational physics and related disciplines.
mathematical and numerical methods and algorithms;
computational models including those associated with the design, control and analysis of experiments; and
algebraic computation.
Each will normally include software implementation and performance details. The software implementation should, ideally, be available via GitHub, Zenodo or an institutional repository.In addition, research papers on the impact of advanced computer architecture and special purpose computers on computing in the physical sciences and software topics related to, and of importance in, the physical sciences may be considered.