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

[Mahmoud Payami Shabestari]

Dear Jose,

Usually a "single-valued" question generates a single-valued answer.

But as you see, yours was not so.



Bests,

Mahmoud





From: Kazume NISHIDATE <nisidate at iwate-u.ac.jp>
To: José Xavier <jxln_karate at yahoo.com.br>
Cc: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
Date: Thu, 4 Nov 2021 15:06:17 +0900
Subject: Re: [QE-users] occupation in biological molecules and band gap


>  would like to ask if you could tell me why this question generates so 
different answers. 
It is partly because you did not provide the detailed information on your 
calculation.

I supposed it is a crystal composed of molecules and you applied some
k-point mesh to incorporate its periodicity. I thought that the system
might be in a semiconducting state since you were interested in the
gap value. In that case, you should apply the 'smearing' method.

If you are calculating an isolated molecule in vacuume with only the
gamma for the k-point, then the 'fixed' method is a good choice since
the occupancy can be defined explicitly at the gamma.

- note
The 'nbnd' is the number of band.  You should include sufficient empty
bands to draw a nice band/dos structure.






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4日(木) 14:09 José Xavier <jxln_karate at yahoo.com.br>:
Dear,

Thank you for your explanation.
I'll try both occupancies to see if the results of bandgap and DOS are very 
different. When I got the values, I can post the differences here.

I would like to ask if you could tell me why this question generates so 
different answers. As just like in the tutorials I saw, each one gave me a 
different answer.

Best wishes,
José Xavier


Em terça-feira, 2 de novembro de 2021 00:41:19 BRT, Mahmoud Payami 
Shabestari <mpayami at aeoi.org.ir> escreveu:






Dear Xavier,

 

> So, I can use the Fixed occupation and, if the energy levels show a small 
bandgap, I introduce the >Smearing. Is it right?

 

Yes, exactly.


 

>If yes, I just have to add the nbnd function in the input file?

 

Yes. It suffices to put nbnd equal to N/2 + 1 (N is number of electrons).

 

Mahmoud

> From: xavier neto via users <users at lists.quantum-espresso.org>
>
> To: Mahmoud Payami Shabestari <mpayami at aeoi.org.ir>, Quantum ESPRESSO 
users Forum <users at lists.quantum-espresso.org>
> Date: Mon, 1 Nov 2021 21:04:31 -0300
> Subject: [QE-users] occupation in biological molecules and band gap
>  
> 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>
>>> To: "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
>>>
>>> _______________________________________________
>>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
>>> users mailing list users at lists.quantum-espresso.org
>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>
>>
>>
>

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