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<div style="font-size: 16px; font-family: Tahoma; color: rgb(0, 0, 0); font-weight: 400; font-style: normal;">Before any scf calculations one does not know about the levels distribution, so adding smearing may help in cases where the levels are too close near HOMO. Otherwise, it wont harm anything else.</div>
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<div style="font-size: 16px; font-family: Tahoma; color: rgb(0, 0, 0); font-weight: 400; font-style: normal;">Mahmoud</div>
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<blockquote class="as91pFk8AX8sDPOUp66RUy8IoCRjefxNG8oLk8fg" style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">From: Kazume NISHIDATE <nisidate@iwate-u.ac.jp><br />
To: xavier neto <jxln_karate@yahoo.com.br>, Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org><br />
Date: Tue, 2 Nov 2021 10:56:28 +0900<br />
Subject: Re: [QE-users] occupation in biological molecules and band gap<br />
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> I've watched/read some tutorials about QE, and some of these showed<br />
> that the occupation of semiconductors should be "smearing", other<br />
> ones that it should be "fixed",<br />
<br />
The occupancies of metals and semiconductors should be "smeared" to<br />
obtain a good convergence of the calculation.<br />
<br />
In the plane-wave DFT calculation for the 'cyclic systems', we use<br />
desecrate k-point mesh where the occupancies of electrons may have<br />
decimal point if it cross the fermi-level (HOMO).<br />
<br />
> What value should I use for the SCF and electronic calculations of<br />
> the crystals that I'm going to work on (amino acids, hormones,<br />
> neurotransmitters, and drugs)?<br />
<br />
You should use the smearing method.<br />
<br />
> *Are there any differences when the molecule has a metal, like the<br />
Heme group?<br />
<br />
You also should use the smearing method in that case.<br />
<br />
You also should perform the spin polarized calculation for the<br />
molecule with a metal to check if there is no significant difference<br />
with the no-spin polarized calculation.<br />
<br />
<br />
> Besides, I would like to ask if there is a calculation that I could<br />
> perform to obtain the bandgap of these molecules. Is it only<br />
> possible if I create the band structure figure and calculate the<br />
> difference between the peaks in VB and CB?<br />
<br />
You can obtain a 'coarsely' estimated band gap by plotting the DOS<br />
after the scf calculation with the dense k-point mesh. If the value<br />
is significantly differ from that at the gamma point, the VBM-CBM<br />
(HOMO-LUMO) gap must be located at some k-point other than gamma.
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<div dir="ltr"><span style="color:rgb(0,0,0);font-family:monospace;font-size:18px">best regards</span><br style="color:rgb(0,0,0);font-family:monospace;font-size:18px" />
<span style="color:rgb(0,0,0);font-family:monospace;font-size:18px">kazume NISHIDATE</span><br style="color:rgb(0,0,0);font-family:monospace;font-size:18px" />
<span style="color:rgb(0,0,0);font-family:monospace;font-size:18px">敬具 西館数芽</span><br style="color:rgb(0,0,0);font-family:monospace;font-size:18px" />
<br style="color:rgb(0,0,0);font-family:monospace;font-size:18px" />
<span style="color:rgb(0,0,0);font-family:monospace;font-size:18px"><a href="mailto:nisidate@iwate-u.ac.jp" target="_blank">nisidate@iwate-u.ac.jp</a></span><br style="color:rgb(0,0,0);font-family:monospace;font-size:18px" />
<span style="color:rgb(0,0,0);font-family:monospace;font-size:18px"><a href="mailto:kazume.nishidate@gmail.com" target="_blank">kazume.nishidate@gmail.com</a></span></div>
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<div class="gmail_attr" dir="ltr">2021年11月2日(火) 9:05 xavier neto via users <<a href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a>>:</div>
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<div>Dear Mahmoud Payami,</div>
<div>Thank you for your answer. It helps me a lot.</div>
<div>So, I can use the Fixed occupation and, if the energy levels show a small bandgap, I introduce the Smearing. Is it right?</div>
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<div>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?</div>
<div>On 11/1/21 02:04, Mahmoud Payami Shabestari wrote:</div>
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<div style="font-size:16px;font-family:Tahoma;color:rgb(0,0,0);font-weight:400;font-style:normal">Dear José Xavier,</div>
<div style="font-size:16px;font-family:Tahoma;color:rgb(0,0,0);font-weight:400;font-style:normal">Hi.</div>
<div style="font-size:16px;font-family:Tahoma;color:rgb(0,0,0);font-weight:400;font-style:normal">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. </div>
<div style="font-size:16px;font-family:Tahoma;color:rgb(0,0,0);font-weight:400;font-style:normal">Bests</div>
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<div style="font-family:Tahoma;color:rgb(0,0,0);font-size:16px;font-weight:400;font-style:normal">Mahmoud Payami</div>
<div style="font-family:Tahoma;color:rgb(0,0,0);font-size:16px;font-weight:400;font-style:normal">NSTRI, AEOI, Tehran, Iran</div>
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<blockquote style="padding-right:0px;padding-left:5px;margin-left:5px;border-left-width:2px;border-left-style:solid;border-left-color:rgb(0,0,0);margin-right:0px">From: José Xavier via users <a href="mailto:users@lists.quantum-espresso.org" target="_blank"><users@lists.quantum-espresso.org></a><br />
To: <a href="mailto:users@lists.quantum-espresso.org" target="_blank">"users@lists.quantum-espresso.org"</a> <a href="mailto:users@lists.quantum-espresso.org" target="_blank"><users@lists.quantum-espresso.org></a><br />
Date: Mon, 1 Nov 2021 00:18:55 +0000 (UTC)<br />
Subject: [QE-users] occupation in biological molecules and band gap<br />
<div style="font-family:monospace,"courier new",courier">Dear all,<br />
<br />
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.<br />
<br />
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)?<br />
<br />
*Are there any differences when the molecule has a metal, like the Heme group?<br />
<br />
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?<br />
<br />
Thank you for your help,<br />
<br />
Sincerely,<br />
José Xavier<br />
<br />
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