Optimization of edge hydropassivation MoS2

[Summer]

Dear QuantumATK expert,
  Recently, I optimized  a structure of armchair MoS2 with edge hydropassovation. But  some bonds bteween S and Mo break in the final optimized structure.  I tried to change some parameters and then calculate, but the bonds are still broken. I don't know what's wrong with my script. Please give me some guidance.
  My script and the opyimized structure in the attachments.
  Thank you!
 

[Petr Khomyakov]

In the Viewer, bond definition is based on some geometrical defaults that can be modified with the Fuzz factor, Graphics->Graphics Properties-> Fuzz factor. It means that the Viewer does not really know whether bonds are really broken or not. Just increase this factor to connect the atoms in the Viewer.

You may also measure the bond length using the Measure Tools or Z-matrix in the Coordinate Tools in the Builder, so that you will see how much the bonds are stretched.