[Pw_forum] Using molecularpdos.x for adsorption on metal-doped graphene

[Guido Fratesi]

Dear Rolly,

On 12/08/2016 06:06, Rolly Ng wrote:
>
> Ef = -2.7148 eV for pristine graphene,
> 5) Pristine graphene Up, HOMO -2.7151 eV, LUMO -2.7145 eV, so |delta|
> HOMO-LUMO gap is 0.0006 eV
> 6) Same for Pristine graphene down, 0.0006 eV
>
> Ef = -2.5982 eV for single Au-doped graphene,
> 5) Single Au-doped graphene Up, HOMO -2.6046 eV, LUMO -2.5703 eV, so
> |delta| HOMO-LUMO gap is 0.0253 eV
> 6) Single Au-doped graphene Down, HOMO -2.6365 eV, LUMO -2.5864 eV, so
> |delta| HOMO-LUMO gap is 0.0501 eV
>
> So, doping by 1 Au atom at center of 72 carbon supercell does open up a
> gap? Am I correct?

Yes, you are perturbing the symmetry and opening a small gap.
(Not all changes of the symmetry do open a band gap, see for example the 
2root3x2root3 reconstruction of buckled silicene where the gap is not 
opened).

>>> I can see the substantial drop in the H0MO-LUMO gap on the full-system
>>> particularly for the Up spin configuration. Does this help to explain my
>>> previous questions Q3+Q4 on physisorption vs. chemisorption?
>> You may want not to compare the HOMO-LUMO of the molecule with the
>> HOMO-LUMO of the full system, rather, the HOMO-LUMO of the free molecule
>> with the energy difference between molecule-induced structures in the
>> DOS of the full system.
>>
> I have difficulty in understanding "rather, the HOMO-LUMO of the free
> molecule with the energy difference between molecule-induced structures
> in the DOS of the full system." How can I do that explicitly? Do you
> mean compare the DOS of free molecule to the DOS of full system?

Yes. For that, you can use projwfc.x to single out the features induced 
by the molecule if the background of the substrate states is dominant.

>> But I'm surprised the code is hanging in your case and I would check
>> something simpler as a test.
>> E.g., you could project the free molecule on the free molecule, (i.e.,
>> full system = part).
>> (BTW does the example espresso-5.4.0/PP/examples/MolDos_example runs
>> properly?)
> To my surprise, I copy the examples and run it on 1 thread but it still
> shows nothing after all? Please take a look at the screen shots attached.

So this is a problem of the specific executable/machine, not the system. 
Which version are you using? We may share the files, I'll write you 
separately.

GF