[QE-users] occupation in biological molecules and band gap

[Kazume NISHIDATE]

> I've watched/read some tutorials about QE, and some of these showed
> that the occupation of semiconductors should be "smearing", other
> ones that it should be "fixed",

The occupancies of metals and semiconductors should be "smeared" to
obtain a good convergence of the calculation.

In the plane-wave DFT calculation for the 'cyclic systems', we use
desecrate k-point mesh where the occupancies of electrons may have
decimal point if it cross the fermi-level (HOMO).

> What value should I use for the SCF and electronic calculations of
> the crystals that I'm going to work on (amino acids, hormones,
> neurotransmitters, and drugs)?

You should use the smearing method.

> *Are there any differences when the molecule has a metal, like the
   Heme group?

You also should use the smearing method in that case.

You also should perform the spin polarized calculation for the
molecule with a metal to check if there is no significant difference
with the no-spin polarized calculation.


> Besides, I would like to ask if there is a calculation that I could
> perform to obtain the bandgap of these molecules. Is it only
> possible if I create the band structure figure and calculate the
> difference between the peaks in VB and CB?

You can obtain a 'coarsely' estimated band gap by plotting the DOS
after the scf calculation with the dense k-point mesh.  If the value
is significantly differ from that at the gamma point, the VBM-CBM
(HOMO-LUMO) gap must be located at some k-point other than gamma.



best regards
kazume NISHIDATE
敬具 西館数芽

nisidate at iwate-u.ac.jp
kazume.nishidate at gmail.com


2021年11月2日(火) 9:05 xavier neto via users <users at lists.quantum-espresso.org>:

> Dear Mahmoud Payami,
>
> Thank you for your answer. It helps me a lot.
>
> So, I can use the Fixed occupation and, if the energy levels show a small
> bandgap, I introduce the Smearing. Is it right?
>
>
> About the second question. I've read that the result of HOMO - LUMO,
> obtained after the SCF calculation, can give the bandgap. Can I obtain the
> bandgap in that way? If yes, I just have to add the nbnd function in the
> input file?
> On 11/1/21 02:04, Mahmoud Payami Shabestari wrote:
>
> Dear José Xavier,
> Hi.
> Smearing for the occupations is used when the levels near HOMO are so
> close (commonly in metals near Fermi level) that in consecutive iterations
> they may exchange positions and lead to nonconvergence. For semiconductors
> with 3-5 eV gap I think it won't help.
> Bests
> Mahmoud Payami
> NSTRI, AEOI, Tehran, Iran
>
>
>
> From: José Xavier via users <users at lists.quantum-espresso.org>
> <users at lists.quantum-espresso.org>
> To: "users at lists.quantum-espresso.org" <users at lists.quantum-espresso.org>
> <users at lists.quantum-espresso.org> <users at lists.quantum-espresso.org>
> Date: Mon, 1 Nov 2021 00:18:55 +0000 (UTC)
> Subject: [QE-users] occupation in biological molecules and band gap
>
> Dear all,
>
> I'm new in QE. The group that I'm working with usually calculates the
> properties of biologically relevant molecules, like amino acids, hormones,
> neurotransmitters, and drugs, and I would like to introduce the QE code to
> the group. Their previous papers have shown that the bandgap of these
> crystals is something between 3-5 eV, which I understand to be in the
> semiconductor range.
>
> I've watched/read some tutorials about QE, and some of these showed that
> the occupation of semiconductors should be "smearing", other ones that it
> should be "fixed", but no one showed calculations with this kind of
> molecules. What value should I use for the SCF and electronic calculations
> of the crystals that I'm going to work on (amino acids, hormones,
> neurotransmitters, and drugs)?
>
> *Are there any differences when the molecule has a metal, like the Heme
> group?
>
> Besides, I would like to ask if there is a calculation that I could
> perform to obtain the bandgap of these molecules. Is it only possible if I
> create the band structure figure and calculate the difference between the
> peaks in VB and CB?
>
> Thank you for your help,
>
> Sincerely,
> José Xavier
>
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