NanoMaterialsCAD: Flexible Software for the Design of Nanostructures

Abstract

NanoMaterialsCAD is a new open source tool dedicated to the creation, manipulation, and 3D visualization of crystalline structures at the nanoscale. It is designed for preprocessing atomistic configurations to be used as input for atomistic (e.g., molecular dynamics or Monte Carlo) or ab initio (e.g., density functional theory) computer simulations. It offers several tools for designing complex nanostructures (including nanoparticles, nanowires, nanotubes, nanoscrolls, etc., and combinations/permutations of them) which are either lacking or cumbersome in other existing packages. Through its intuitive graphical user interface (GUI) it enables facile ways to design and modify the size/shape and relative positions of nanoobjects while observing the changes in real time. NanoMaterialsCAD is written in C++, and exploits Open Graphics Library (OpenGL) (for the GUI), Win32API (for interaction with Windows), and Assembly (for fast data management). The source code and executable file are available for download from GitHub (https://github.com/cossphy/NanoMaterialsCAD). It is aspired that NanoMaterialsCAD will be adopted by the nanomaterials modeling community as a valuable resource; to this end it will be kept improving, incorporating more nanostructures, and adding extra functionalities to its toolbox.

On the melting point depression, coalescence, and chemical ordering of bimetallic nanoparticles: the miscible Ni–Pt system

“…42,43 All the bulk Ni–Pt compounds and related NPs were formed with the use of the Density Functional Theory (DFT) based structures from the Materials Project 44 and the NanomaterialsCad tool. 45 For the MD simulations a default timestep size of 0.001 ps was used, and at least 25 000 000 MD steps were performed for the smallest NPs (3 nm in diameter), corresponding to a minimum 25 ns simulation time. Visualisation was performed using OVITO; 46 Common Neighbour Analysis (CNA) 47 using adaptive CNA (a-CNA) 48 was performed within OVITO, which determines optimal cut-off radii for nearest-neighbours automatically for each individual atom in multiphase systems.…”

MoS 2 phononic crystals for advanced thermal management

“…3 (A and B). The sulfur atoms are irregularly arranged on the hole surface in the MoS 2 PnCs due to their greater mobility relative to the molybdenum atoms ( 39 ). The whole surface was partially covered with sulfur atoms.…”

CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems

“…The lack of a reliable and unified cyberinfrastructure to build complex nanobio interfaces poses major challenges to the molecular modeling and simulation community in terms of steep learning curves, risks of choosing unsuitable FF and faulty interface models, and mistakes in file conversion and input scripts that render simulations less useful or invalid. Several programs have been developed to help users to build nanomaterial model systems, including web applications, such as NanoModeler and PubVINAS, and stand-alone software packages, such as Atomic Simulation Environment (ASE), pysimm, Molecular Simulation Design Framework (MoSDeF), and NanoMaterialCAD . NanoModeler supports 16 gold nanocluster models with ligand grafting function, and PubVINAS provides 11 material types with corresponding physicochemical properties or bioactivities.…”

“…Several programs have been developed to help users to build nanomaterial model systems, including web applications, such as NanoModeler 17 and PubVINAS, 18 and stand-alone software packages, such as Atomic Simulation Environment (ASE), 19 pysimm, 20 Molecular Simulation Design Framework (MoSDeF), 21 and Nano-MaterialCAD. 22 NanoModeler supports 16 gold nanocluster models with ligand grafting function, and PubVINAS provides 11 material types with corresponding physicochemical properties or bioactivities. ASE, pysimm, and MoSDeF provide methods for preparing various nanomaterial systems and application programming interfaces (APIs) to integrate different features of existing software packages using Pythonbased scripting.…”