alpha-quartz

[Dipankar Saha]

If we cleave the the alpha-quartz to a (0001)...then probably we will  obtain a surface with Oxygen (Si-O-Si) termination.... and that can further be transformed into the 'silanol' one (Si-OH)...by  hydrogen passivation. However, for siloxane ....if I wish to passivate  only the bottom layer of "Si"....how is that possible? Further, in "Custom Passivator" .... there is a drop-down menu against the "Hybridization"....how those options can effectively used?? 

[Umberto Martinez]

In the first window of the Surface (cleave) plugin, when you select Miller indices, you can also select the termination of your surface,.
You can do that by selecting the atom you wish from the configuration view or from the element list.

If you wish to passivate only the bottom layer, just select only the atoms in your bottom layer and passivation will be applied only to those atoms.

Finally, you need to know what type of hybridization you want in order to use this feature. That is up to you.

[Dipankar Saha]

Actually, what I was asking___

'O' with sp³ should be bonded with 'H' through a sigma.... isn't it??  But,  if I select sp² then also  a few of 'O' are getting passivated...!!!
Besides, there must be an analogy.... so that....... sp³ --> tetrahedral, sp² --> trigonal planar etc.  These in turn will help me to select the basis set (z= 0.75, 1.25...etc. )....for a different pseudo potential (say, FHI fractional) ... / But, my question is....why do we at all need a diff. pseudo potential for these 'atom-H' s  ?

[Umberto Martinez]

There is a pretty good and detailed explanation (with reference) in this tutorial http://quantumwise.com/documents/tutorials/latest/InAs-2D/index.html/chap.slab.html

[Dipankar Saha]

I went through that.... may be a detailed discussion on ...how to set  the 'z' value with a FHI fractional is well fully described there .... ; but I did find any clear reason....saying that what's the adv. of taking a diff. pseudo potential for 'atom-H' s ....!!!

[Dipankar Saha]

'O' with sp³ should be bonded with 'H' through a sigma.... isn't it??  But,  if I select sp² then also  a few of 'O' are getting passivated...!!!
Besides, there must be an analogy.... so that....... sp³ --> tetrahedral, sp² --> trigonal planar etc.  These in turn will help me to select the basis set (z= 0.75, 1.25...etc. )....for a different pseudo potential (say, FHI fractional) ...

Moreover,  as mentioned in the aforesaid lines..... I didn't get the point that why the no. 'O' s  getting passivated are.....different for the two cases??

[Jess Wellendorff]

I suppose this is a matter of how you want the nature of the oxygen bonding to be.

[Dipankar Saha]

Yes that's quite true..... Thank u Jess..!!! 

[Dipankar Saha]

Instead of bulk.... if I take a slab (say of two layers)....; should the B.G. be lowered at all??!!
________

Actually what that I'm getting...is something like Fig. S3  / I thought....those which are marked in green coming from surface states....; but looking into the PDOS.... I found  they were not...!!!

[Umberto Martinez]

It could be. A slab is a nano sheet with a confined dimension.

[Dipankar Saha]

But, the effect should be opposite due to confinement..!! Is it not...??
Can I push those two sets of bands away from the energy zero (something, that has been done in the example of InAs-2D ......)
Best_
Dipankar

[Umberto Martinez]

You can try passivating the O bonds at the surface.
Indeed, these can introduce localized states in the energy gap region.

SiO2 is a bit different that InAs and dangling O bonds can be of numerous nature, radicals, O(2-), ...

[Dipankar Saha]

Yes..I tried that (with the 'silanol')....
Anyways....let me send you the i/p files.... That will be much better....!!

Many thanks Umberto...for your help..!!!

Best_
Dipankar