Building a Si-Si3N4 interface Tutorial

[suri]

I am trying to build this interface as given in the tutorial under Builder tutorials on Quantumwise.com. When i tried the 3rd step under Final adjustment, the bonds between  Si- triangle and N atoms just disappeared. I have attached an image of two isolated N atoms(in selection mode) after bonds with Si-triangles have broken up.I played around with it but couldn't find a solution. So am i doing it wrong or is it something else? Any help in this regard will be greeted with a lot of appreciation. Have a blessed day..!!

[Anders Blom]

The "bonds" will not appear again until your optimize the structure. Note that bonds drawn in the GUI are just to guide the eye, and not real in any physical meaning.

[suri]

But there is nowhere mentioned in that paper that bonds will disappear. Also why all other bonds appear as before and only these new bonds just vanish. It seems a bit strange to wrap my mind around it.

[Anders Blom]

Bonds are not real. If they disappear from the picture or not is not important for the computations (which don't use them anyway). But actually, the fact that they disappear does tell you something (not always, but in this case it does), namely that the structure now needs to be optimized to again reform the bonds. There are many manipulations you can make of a structure that "break bonds" but actually bonds are not broken at all, the atoms have just been placed a bit too far apart for the rule to plot the bonds is fulfilled. This, as mentioned, can mean that a geometry optimization is needed (as in this case) but it may also be unavoidable in cases of strained structures, etc.

[Anders Blom]

Btw, the tutorial does mention that "it should be pointed out that the geometry needs to be optimized, especially the Si atoms in the interface. If you do that, you will see the formation of fully saturated bonds for all Si atoms". That's precisely the point under discussion here.

[suri]

Thanks. Got it. Now how do i set about optimizing geometry? I looked for a tutorial for optimizing a geometry but couldn't find one. Would you please explain it?