MoS2

This document describes how to create a MoS₂ layer (Fig. 3b) and how to modify it to change one or more atoms and to have add-on atoms.

MoS₂ has a layered structure that consists of MoS₂ groups arranged in widely spaced horizontal sheets (Fig. 1b).

To create a MoS₂ model one has to select a single layer of MoS₂ groups. This is done in 2 steps by Make orthogonal (Fig. 1c) and To slices (Fig. 2).

With the MoS2 P 63mmc crystal structure create an orthorhombic cell unit cell (Fig. 1d).
Duplicate the orthorhombic cell in x and y directions to obtain a tetragonal structure of large a and b cell parameters (Fig. 2).
The layer is described by MoS₂ text file.


Figure 1a MoS₂ P 63mmc.	Figure 1b MoS₂2 layers.

Figure 1c Make orthogonal defines an orthorhombic cell.	Figure 1d MoS₂, orthorhombic description.


Figure 3a Slicing in 4 slices.	Figure 3b MoS₂ layer (from first and second sub-slices).

With the popup menu attached to the model (Fig. 3b) the projected potential, HAADF, WPOA and SAED images are readlily calculated with the current settings of the microscope, aberrations, coherence, etc. (Figures 4a, 4b, 4c, 4d).


Figure 4a Projected potential.	Figure 4b HAADF.

Figure 4c WPOA image.	Figure 4d SAED.

ADF images of the MoS₂ layer are obtained using the ADF imager. The simulations parameters are:

Accelerating voltage 300 kV.
W₄₀ (C₃₀) -0.03 mm, W₀₀ (Cc) 1 mm.
W₂₀ (C₁₀) -6.8 nm.
Electron beam energy spread 0.6 eV.
Lens current and voltage stability 0.1 ppm.
Aperture diameter 24 nm^-1.
Detector sensitiviy is uniform and by default it is centered on the optical axis (000).

Each simulation run produces 4 Bright Field images with BF detector radius 10, 30, 50, 70 nm^-1 (Figures 5a, 5b, 5c, 5d). With a negative W₄₀ (C₃₀) the first BF image is similar to the HRTEM image.


Figure 5a BF outer radius 10 nm^-1.	Figure 5b BF outer radius 30 nm^-1.

Figure 5c BF outer radius 50 nm^-1.	Figure 5d BF outer radius 70 nm^-1.

Each simulation run produces also 4 Dark Field images with detector inner and outer radii 60 to 150, 80 to 170, 100 to 190, 120 to 210 nm^-1 (Figures 6a, 6b, 6c, 6d). With a negative W₄₀ (C₃₀) the first BF image is similar to the HRTEM image.


Figure 6a DF 60 to 150 nm^-1.	Figure 6b DF 80 to 170 nm^-1.

Figure 6c DF 100 to 190 nm^-1.	Figure 6d DF 120 to 210 nm^-1.

4 sector detectors (1 to 4) are placed between the BF and DF detectors. By default the inner and outer radii of the sector detectors are set to the outer radius of the BF detector and the inner radius of the DF detector (Figures 7a, 7b, 7c, 7d).


Figure 7a Sector 1.	Figure 7b Sector 2.

Figure 7c Sector 3.	Figure 7d Sector 4.

Differential Phase Contrast imaging is an interesting feature of sector detectors. DPC images calculated using the sector images (Figures 7a, 7b, 7c, 7d) are shown below. Indeed these DPC images result of simulations, experimentally provided ones will most likely be somehow different due to non-uniformity of the detectors, etc. In spite of that simulated DPC images could provide valuable insights on the MoS₂ structure when it contains impurities like W.


Figure 8a S1 + S2 + S3 + S4.	Figure 8b S1 + S2 - S3 - S4.

Figure 8c S1 - S2 + S3 - S4.	Figure 8d -S1 + S2 - S3 + S4.


Figure 9a S1 + S2 + S3 + S4.	Figure 9b -S1 - S2 + S3 + S4.

Figure 9c S1 - S2 - S3 + S4.	Figure 9d -S1 + S2 + S3 - S4.

As noted by K. Ishizuka, A practical approach for STEM image simulation based on the FFT multislice method, Ultramicroscopy 90 (2002) 71–83, it is not necessary for accurate calculations to scan the whole periodic model. Fig. 10a shows a HAADF image calculated with Ishizuka approach. The images shown in Figures 5, 6, 7, 8, 9 and 10a, were computed on a smaller part of the model of size 512 × 512 (Fig. 10a), with a probe shape shown in Fig. 10b. The projected potential was initialized on 1024 x 1024 grid with Weickenmeier-Kohl atomic form factors.


Figure 10a HAADF Ishizuka method.	Figure 10b Scan area.

Figure 10c Probe shape and profile.	Figure 10d Probe 3-D view.

During the scanning one can observe the power spectrum, bright field, dark field and 4 sectors detectors (12a, 12b, 12c, 12d).


Figure 12a Power spectrum.	Figure 12b Bright field detector.

Figure 12c Dark field detector.	Figure 12d 4 sectors detector.

Finally the probe wave-function is shown in Fig. 13.

Adding or changing one atom can be done by modifying the MoS₂ layer using a text editor or the crystal Builder. When pointing to a Mo atom the builder will provide its fractional coordinates (Fig. 14).

Figure 14 Pointing to an atom provides its fractional coordinates.