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

[Rolly Ng]

Dear Guido,

Here are my updates.


On 08/11/2016 05:57 PM, Guido Fratesi wrote:
> Dear Rolly,

>> 3) Full-system Up, HOMO -2.1696 eV, LUMO -2.1449 eV, so |delta|
>> HOMO-LUMO gap is 0.0247 eV
>> 4) Full-system Down, HOMO -2.1935 eV, LUMO -2.1177 eV, so |delta|
>> HOMO-LUMO gap is 0.0758 eV
> Uhm, your system is a molecule on graphene if I remember correctly, so
> why are you expecting a gap?
> (beside the opening of a small gap occurring because of finite system size?)
>
> It may be useful to think of molecules adsorbed on a metal surface, like
> Al(001).
> What would then be the gap of the full system? --> 0
> Would this change if you chemisorb / physisorb your molecule? --> no
> What is the resulting HOMO-LUMO gap if no molecule at all is present, in
> principle? --> 0, it is a metal surface
> What is the resulting HOMO-LUMO gap of the full system from the
> calculations? --> it will be "small" and depend on the K-point sampling;
> such dependence is mitigated by the smearing technique.
> Would looking at the eigenvalues at K=\overline{Gamma} the correct way
> to find it? --> you would have to look at the full BZ. A band gap at
> Gamma could indeed be present also for a metal surface.

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?

>> 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?

>> I am running molecularpdos.x but it seems run for more than 10 hours on
>> a 12 cores/24 thread system without stopping and output as shown in the
>> attached screenshot?
> It should not be so long. At maximum it has taken few minutes for the
> largest cases I considered.
> Notice, molecularpdos.x is a serial code so just run it on one CPU core.
>
>
>> However can I select fewer bands so it may help to reduce the
>> computation time? Is this i_bnd_beg_full = 1 refers to -28.1982 eV the
>> first one? or 2.1629 eV the last one?
> Yes, you could reduce the size of the calculation by not looking at deep
> bands. Suppose you have 400 electrons (~200 filled states per spin), and
> that the lowest 100 states are below the energy range of your interest,
> you could then put i_bnd_beg_full = 101.
>
> 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.

>
> Kind regards,
> Guido
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

Thank you,
Rolly

-- 
PhD. Research Fellow,
Dept. of Physics & Materials Science,
City University of Hong Kong
Tel: +852 3442 4000
Fax: +852 3442 0538