NanoMaterialsCAD Ver. 1.1
G. Nikoulis, P. Grammatikopoulos, S. Steinhauer, J. Kioseoglou
NanoMaterialsCAD: Flexible Software for the Design of Nanostructures
Advanced Theory and Simulations, 4: 2000232, (2021)
Introduction
NanoMaterialsCAD is an open-source software designed to prepare crystalline structures for simulations. It offers a variety of tools to manipulate the positions of atoms in any system. The program is especially useful when it come to the construction of nanoparticles (NPs). It provides a user-friendly environment which uses a convenient method to create NPs. In this article, we will focus on the capabilities of NanoMaterialsCAD to prepare NPs and we will show a case-study of Fe NPs.
Creating Nanoparticles
NanoMaterialsCAD provides an easy way to create symmetrical NPs. In the Edit tab of the top bar menu (Figure 1) five options are offered to create NPs with specific surfaces which can be subsequently modified by the user (i.e., surface ratios and/or NP size can be changed). The structure is updated in real time so the user can immediately inspect the changes while being applied to the system. The options which can be shown in Figure 1 are namely cubic, rod like, hexagonal, sphere, and nanoscroll. Every option is adjustable and can be edited directly by the users. Figure 2 shows such an example of the cubic option in which the NP is manipulated from a cubic shape towards a truncated octahedron and finally into a rhombicuboctahedron.
Figure 1: Current menu options for the creation of various nanostructures.
Figure 2: Right to left, smooth morphing via chamfering of a NP from a cubic shape toward a truncated octahedron and a rhombicuboctahedron.
The program can also construct 1D, 2D, and bulk systems. It also provides a powerful command line with multiple commands to manipulate the structures. Some of the commands are listed below.
- cut(h, k, l, D)
Cut a parallel surface to the (hkl) facet with D Angstrom distance from the center.
- rndDisplacement(r)
Randomly displaces all atoms by r Angstrom from their positions.
- randSelection(N)
Randomly select N atoms.
- icosahedron(lattice constant, noshells)
Creates an icosahedron NP
- decahedron(p, q, r, lattice constant)
Creates a decahedron NP
There are currently more than 20 commands in the software. See the Manual for more information. The last two options are the defected icosahedron and decahedron NP which are present in Figure 3.
Figure 3: a) Icosahedron NP using the icosahedron(2,10) command and b) a decahedron NP using the decahedron(10,1,0,2) command.
Case study for Fe Nanoparticles
Prediction of NP shapes is key to various nanotechnology applications since efficiency often depends heavily on shape. For example, in catalysis dissimilar NP morphologies offer different numbers of active sites for reactionsi,ii. In this case study we determine the equilibrium shape of the Fe NP with molecular dynamics (MD) using the EAM potential developed by Mendelev et al.iii
For the NPs, we created cubic shaped NPs ranging between 1 and 8 nm in edge length, and we shaped them by edge chamfering toward truncated cubes (TRD), and eventually into rhombic dodecahedron RD NPs. More specifically, we varied the ratio between the {100} and {110} facets, starting with purely {100}-terminated cubes and ending with purely {110}-terminated RD. The number of intermediate shapes increased with the NP size, as indicated by the number of points in Figure 4c. In this figure the potential energy per atom is plotted as a function of NP size. Figure 4d shows a zoomed-in sequence for the 8 nm cube from Figure 4c, indicating that the energetically favorable structure is a chamfered cube (also describable as a non-equilateral TRD) with a surface area ratio of A110/A100=1.075. A visual representation of A110 and A100 can be seen in Figure 4a.
Figure 4b shows a comparison of the potential energies of three Fe NP shapes (sphere, cube, and non-equilateral TRD), along with equivalent results from Zhao et al.iv We notice that there is good agreement between the energies and the trends of the two studies, with the TRD being the energetically favorable shape followed by the sphere and the cube. The slightly lower values obtained in this work is because of the temperature difference between the two studies which adds a 0.04eV (room temperature) difference in the final results. Nevertheless, the trends of the curves are in agreement.
Figure 4: a) Showing the construction of the NP. If S1 is the distance from the center of the NP to the intercept of a {100} facet on the x-axis, and S2 is the distance from the center of the NP to the intercepts of a {110} facet on the z and x-axes, then as the ratio S2/S1 approaches the value 1.6 the energy of the NP approaches its minimum value, regardless of NP size. b) Comparison between potential energy values as a function of size for three different shapes between the present work and Zhao et al. Note that for the latter work equilateral TRD results are shown, whereas for the former TRD corresponds to non-equilateral TRD. c) Potential energy (in eV per atom) as a function of NP size (in number of atoms, to accommodate different NP shapes). Different chamfering sequences are marked by different colors. d) Zoom-in at the chamfering sequence for 8 nm cubes, indicating the energetically favorable structure (i.e., a specific chamfered cube or non-equilateral TRD).
Conclusion
In conclusion, we showed how NanoMaterialsCAD is useful for creating crystalline structures ready to be used in simulations. It is capable of creating symmetric and non-symmetric NPs as well as defected icosahedron and decahedron NPs. It also offers a powerful command line which can be used to edit the system. Finally, we showed a case-study in which we were capable to determine the exact energetically favorable shape of the Fe NP with the help of NanoMaterialsCAD to create multiple NPs for study.
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