Complexity

Volume 2018, Article ID 5083247, 16 pages

https://doi.org/10.1155/2018/5083247

## Integrated Modeling, Simulation, and Visualization for Nanomaterials

^{1}School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, China^{2}State Key Laboratory of CAD&CG, Zhejiang University, Hangzhou, China^{3}School of Media and Design, Hangzhou Dianzi University, Hangzhou, China

Correspondence should be addressed to Feiwei Qin; nc.ude.udh@iewiefniq

Received 23 October 2017; Accepted 19 March 2018; Published 24 April 2018

Academic Editor: Vittorio Loreto

Copyright © 2018 Feiwei Qin et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

#### Abstract

Computer aided modeling and simulation of nanomaterials can describe the correlation between the material’s microstructure and its macroscopic properties quantitatively. In this paper, we propose an integrated modeling, simulation, and visualization approach for designing nanomaterials. Firstly, a fast parametric modeling method for important nanomaterials such as graphene, nanotubes, and MOFs is proposed; secondly, the material model could be edited adaptively without affecting the validity of the model on the physical level; thirdly a preliminary calculation for nanomaterials’ energy is implemented based on the theory of surface fitting; finally, an integrated framework of nanomaterials modeling, simulation, and visualization is designed and implemented. Experimental results show that the proposed approach is feasible and effective.

#### 1. Introduction

Design and optimization of materials are eternal and new problems; almost all matter is made up of materials. The emerging nanotechnology which changes the distribution and arrangement of atoms to get materials of different properties has brought significant revolution for materials’ design. Nowadays nanotechnology has been extensively applied in various fields such as medical, aerospace, and energy [1–3].

Computer modeling and simulation of nanomaterials quantitatively describe the correlation between the materials’ microstructure and macroproperties to a certain extent [4]. The strong computing power provided by computer overcomes the shortcomings of traditional material design and reduces the material production cycle [5–7]. In the 21st century, computer aided design is playing a huge role in designing nanomaterials [8, 9]. However, the existing nanomaterials structure modeling software and simulation software have some problems. On one hand, the modeling and simulation systems have their respective emphases. The modeling software often lacks material simulation, and the simulation software lacks effective modeling [10–12]. On the other hand, structure modeling and material simulation are integral parts for material research. Researchers usually need to transfer data between the two systems iteratively, which is time-consuming [13]. Hence it is vital to develop an integrated modeling and simulation platform for nanomaterials.

The primary target of our research is to optimize the design of the material structure through modeling and simulation in nanoscale. We propose an integrated modeling and simulation approach for nanomaterials’ design, to assist researching on nanomaterials’ structure and macroperformance.

#### 2. Related work

Currently nanomaterials’ modeling and simulation have become necessary tools for predicting molecular motion. There are many related commercial software programs and tools. However, the existing software programs are not functionally complete enough. Some of them are modeling systems, and the others are visualization software programs. Meanwhile, these software programs are very expensive.

*Structure Modeling*. Researchers build geometric models of different structures firstly, then validate the performance of materials through computer simulation, and finally optimize materials’ geometric structures. Overvelde et al. [14] design different pore materials by changing holes’ shape, size, and arrangement and verify materials’ properties by employing finite element analysis and physical experiments. Also, though atom reconstruction is essentially a problem of nearest neighbor search, some algorithms such as KD-tree and octree are studied for modeling atoms. Lou et al. [18] use KD-tree based space partitioning algorithm to merge finite element triangle meshes for fast prototyping. Muja [19] approximates nearest neighbors with automatic algorithm configuration. The adopted algorithm is based on hierarchical -means trees. Ooi et al. [20] use KD-tree for indexing spatial databases.

*Simulation*. Material Studio is a relative mature modeling and simulation software for nanomaterials [15]. Some nanomaterials could be modeled and simple attribute calculation can be carried out on this software. However most simulation functions need to be purchased. The compatibility between Material Studio and other software programs is also a big problem. LAMMPS [16] is a molecular dynamics simulation software developed by Sandia laboratory with C++ language. It supports simulation for millions of molecules in form of gas, liquid, and solid. However, visualization interface is not provided. The user cannot watch the entire modeling process intuitively. In addition, interactive operation modeling is not supported.

Recently some researchers use GPU to accelerate the modeling and simulation for nanomaterials. Stone et al. [21] concluded that the era of accelerating molecular simulation by utilizing GPU has come. The effects of simulation for nanoscale molecule are very well with the aid of GPU’s parallel computing ability.

*Visualization*. RasMol is a commonly used software for visualizing nanomolecular model [17]. It provides powerful and convenient display interface for operation. A variety of types of files such as proteins, DNA, and big molecule can be loaded into this software. Some simple calculation such as counting numbers of amino and carboxy can also be proceeded. However the simulation of nanomaterials cannot be carried out. Hence RasMol is just a display tool. Similar toolkits such as VMD [22] and ICMLite also provide well displayed interfaces. The designer can draw sketches based on these toolkits. However the function of material simulation is absent.

There are some visualization and analysis software programs focusing on some special material’s molecule. For example, ANTHEPROT [23] and VHMPT are used for analyzing proteins, and RNAstructure and RnaViz are used for analyzing RNA. These software programs have powerful visualization abilities and provide simple functions for calculating attributes. However they are only used for some special materials; the applicability is not comprehensive.

#### 3. Structure Modeling for Nanomaterials

Structure modeling is the basis for researching correlation between nanomaterials’ structure and properties. The main problem is that analyzing the structural rule of complicated nanomaterials is difficult. Hence modeling many nanomaterials automatically by program is hard; furthermore, the number of nanomolecules is huge, which can reach hundreds of millions. The algorithm and the performance of the computer are very demanding. Aiming at the aforementioned problem, we use adjacency list to provide parametric modeling for common nanomaterials, supporting the construction of macromolecular material model.

##### 3.1. Modeling Based on Adjacency List

For supporting macromolecular model and interactive modeling, data structure of molecular nanomaterials must have these functions: finding adjacent atoms quickly; assembling and constructing nanomaterials model rapidly; mapping geometric structure and topological structure rapidly. Hence we design nanomolecules’ data structure based on adjacency list. It stores the relevant physical information of the atom, and mappings between geometric model and materials’ internal structure, and supports to reconstruct macromolecular model quickly. The main idea is: each vertex represents an atom and each edge represents the chemical bond between atoms, as shown in Figure 1. The concrete structure is as follows:(i)Nanomolecule is composed of atoms and chemical bonds.(ii)Each molecule uses two continuous spaces (AtomList and BondList) to save all the atoms and bonds, respectively.(iii)Each atom has a type, and a BondList to save all the chemical bonds and other related information.(iv)Each bond has a type, and the two connected atoms.