[QE-users] occupation in biological molecules and band gap
José Xavier
jxln_karate at yahoo.com.br
Fri Nov 5 01:07:04 CET 2021
Dear Stefano Baroni,
Thank you. Your answer helped me a lot to understand the occupation function and effect in the calculations. If I understood correctly, valence and conduction bands are not close enough to need the smearing effect. Is it possible that the Fermi energy obtained from an input with a Fixed occupation and another with Smearing occupation be different in the DOS result?
About the XC functional, I will use the PBE. Unfortunately, I didn't find the NC pseudopotential with PBE in the QE library for all the atoms. So I downloaded them from the PseudoDojo website. After this initial calculation, I'll make the calculation with the Hybrid HSE functional, as it is in the reference paper. Is it good?
Again, Thank you for your time and consideration
Best wishes,
José Xavier
Department of Biophysics and Pharmacology
Federal University of Rio Grande do Norte
Natal, Brazil
Em quinta-feira, 4 de novembro de 2021 05:40:22 BRT, Stefano Baroni <baroni at sissa.it> escreveu:
Dear José Xavier,
There is no way any reasonable smearing may affect a gap of several eV. The only effect of electronic smearing (Gaussian or otherwise) is to average the contribution of neighboring energy level to the ground-state electronic charge-density distribution (“neighbouring” means within the width of the smearing function). In “real” metals (i.e. conducting crystals) this allows one to replace the sum over occupied states enclosed by the Fermi surface (which amounts to integrating a discontinuous function: a numerically difficult task) with a more tractable integration of a continuous function over the entire Brillouin zone. For isolated molecules, smearing helps dumping the convergence oscillations arising from HOMO-LUMO level crossings. Neither of these two instances occur in your case: only a smearing of the order of (or larger than) the HOMO-LUMO gap may affect the result, and hopefully you won’t be using a smearing of 3 volts.
If no mistakes or oversights are being done, the only elements of a calculation that may affect the gap are the XC functional and the quality of the pseudo-potential. In covalent materials, the HOMO and LUMO usually derive from the same atomic orbitals, so that a pseudo-potential that accurately describes occupied states is also fit for the low-lying unoccupied ones. In molecular crystals, this is not necessarily the case and a pseudopotential that is good for the HOMO may not be as good for the LUMO. Not a frequent case, but not impossible either, I believe.
Oh, one last thing: members of this mailing list usually appreciate knowing the identity and affiliation of their correspondents.
Hope this helps — Stefano B
> On 4 Nov 2021, at 08:25, José Xavier via users <users at lists.quantum-espresso.org> wrote:
>
> Dear,
>
> Sorry.
> The group I'm working with has published some papers describing the properties of the crystal of biomolecules using castep code and I would like to introduce the QE to perform similar calculations. Then, I am now trying to reproduce a paper published by the group last year to set up the input files for the next calculation that I will perform, also with the crystal structure of a biomolecule.
>
> I do not know if I can attach the paper here, so this is the reference: R. L. Araújo et al., Chemical Physics Letters 761 (2020) 138033.
>
> The band gap for Dopamine was 3.8 eV, and the other papers published by them showed values between 3-5 eV. That is why I have asked about the better option for the occupancy of semiconductors. It is one of the points that I'm trying to understand in QE to add to the calculations.
>
> It is the input file
> &control
> calculation = 'scf',
> nstep = 1500,
> etot_conv_thr = 5.0D-7,
> forc_conv_thr = 1.0D-4,
> verbosity = 'high',
> /
>
> &system
> ibrav = 8,
> a = 10.50228,
> b = 10.89998,
> c = 7.70059,
> nat = 96,
> ntyp = 5,
> ecutwfc = 73.49,
> ecutrho = 293.99,
> input_dft = 'PBE',
> vdw_corr = 'ts',
> /
>
> &electrons
> electron_maxstep = 500,
> conv_thr = 1.0D-8,
> /
>
> &ions
> /
>
> &cell
> /
>
> ATOMIC_SPECIES
> Cl 35.452702 Cl.upf
> C 12.011000 C.upf
> N 14.006700 N.upf
> O 15.999400 O.upf
> H 1.007900 H.upf
>
>
> ATOMIC_POSITIONS (angstrom)
> Cl 0.0817992817 3.5576016812 2.0615460194
> C 5.5672207516 2.3820020182 1.5383881642
> C 6.8676172680 2.3016151531 2.0378186594
> C 7.6740917486 1.2139979213 1.7109111992
> C 7.1708614134 0.2052409474 0.8660364342
> C 5.8641017691 0.2888392074 0.3824664792
> C 5.0461091419 1.3745015880 0.7211106768
> C 3.6078113637 1.4316201905 0.2725853451
> C 2.7518815143 0.4607516679 1.0837652041
> N 1.2927740324 0.7293581046 0.9097604338
> O 8.9420606908 1.0405633732 2.1969666347
> O 7.9421528767 -0.8592157994 0.4969485133
> H 4.9507875742 3.2382085016 1.7978112316
> H 7.2567722381 3.0757711119 2.6983831238
> H 5.4944176415 -0.5103602212 -0.2609621157
> H 3.5211750076 1.1867086798 -0.7944499632
> H 3.2341044736 2.4553300348 0.4002708665
> H 2.9544617954 0.5610191735 2.1528589679
> H 2.9305129146 -0.5797510968 0.7909394044
> H 1.0163150923 0.8290194264 -0.0876428360
> H 0.7377473441 -0.0519386975 1.3201503246
> H 1.0094717266 1.6180109698 1.3674476912
> H 9.3583518315 1.9253421323 2.3588599841
> H 8.7739063725 -0.9001600265 1.0247860732
> Cl 10.4204815314 9.0075931626 2.0615460194
> C 4.9350600615 7.8319934996 1.5383881642
> C 3.6346635451 7.7516066345 2.0378186594
> C 2.8281890645 6.6639894027 1.7109111992
> C 3.3314193997 5.6552324288 0.8660364342
> C 4.6381790440 5.7388306888 0.3824664792
> C 5.4561716712 6.8244930694 0.7211106768
> C 6.8944694494 6.8816116719 0.2725853451
> C 7.7503992987 5.9107431493 1.0837652041
> N 9.2095067806 6.1793495860 0.9097604338
> O 1.5602201223 6.4905548545 2.1969666347
> O 2.5601279363 4.5907756820 0.4969485133
> H 5.5514932389 8.6881999830 1.7978112316
> H 3.2455085750 8.5257625933 2.6983831238
> H 5.0078631716 4.9396312602 -0.2609621157
> H 6.9811058055 6.6367001612 -0.7944499632
> H 7.2681763394 7.9053215162 0.4002708665
> H 7.5478190177 6.0110106549 2.1528589679
> H 7.5717678985 4.8702403846 0.7909394044
> H 9.4859657207 6.2790109078 -0.0876428360
> H 9.7645334690 5.3980527839 1.3201503246
> H 9.4928090865 7.0680024512 1.3674476912
> H 1.1439289816 7.3753336137 2.3588599841
> H 1.7283744406 4.5498314548 1.0247860732
> Cl 0.0817992817 1.8923898002 5.9118373550
> C 5.5672207516 3.0679894631 5.3886794997
> C 6.8676172680 3.1483763283 5.8881099949
> C 7.6740917486 4.2359935601 5.5612025347
> C 7.1708614134 5.2447505339 4.7163277697
> C 5.8641017691 5.1611522740 4.2327578147
> C 5.0461091419 4.0754898934 4.5714020123
> C 3.6078113637 4.0183712909 4.1228766806
> C 2.7518815143 4.9892398135 4.9340565396
> N 1.2927740324 4.7206333768 4.7600517694
> O 8.9420606908 4.4094281082 6.0472579702
> O 7.9421528767 6.3092072808 4.3472398488
> H 4.9507875742 2.2117829797 5.6481025671
> H 7.2567722381 2.3742203695 6.5486744594
> H 5.4944176415 5.9603517026 3.5893292198
> H 3.5211750076 4.2632828016 3.0558413723
> H 3.2341044736 2.9946614466 4.2505622020
> H 2.9544617954 4.8889723078 6.0031503034
> H 2.9305129146 6.0297425782 4.6412307399
> H 1.0163150923 4.6209720549 3.7626484995
> H 0.7377473441 5.5019301789 5.1704416601
> H 1.0094717266 3.8319805115 5.2177390267
> H 9.3583518315 3.5246493491 6.2091513196
> H 8.7739063725 6.3501515079 4.8750774087
> Cl 10.4204815314 7.3423812815 5.9118373550
> C 4.9350600615 8.5179809445 5.3886794997
> C 3.6346635451 8.5983678096 5.8881099949
> C 2.8281890645 9.6859850415 5.5612025347
> C 3.3314193997 10.6947420153 4.7163277697
> C 4.6381790440 10.6111437554 4.2327578147
> C 5.4561716712 9.5254813747 4.5714020123
> C 6.8944694494 9.4683627722 4.1228766806
> C 7.7503992987 10.4392312948 4.9340565396
> N 9.2095067806 10.1706248581 4.7600517694
> O 1.5602201222 9.8594195896 6.0472579702
> O 2.5601279363 11.7591987621 4.3472398488
> H 5.5514932389 7.6617744611 5.6481025671
> H 3.2455085750 7.8242118508 6.5486744594
> H 5.0078631716 11.4103431839 3.5893292198
> H 6.9811058055 9.7132742830 3.0558413723
> H 7.2681763394 8.4446529280 4.2505622020
> H 7.5478190177 10.3389637892 6.0031503034
> H 7.5717678985 11.4797340595 4.6412307399
> H 9.4859657207 10.0709635363 3.7626484995
> H 9.7645334690 10.9519216602 5.1704416601
> H 9.4928090865 9.2819719929 5.2177390267
> H 1.1439289816 8.9746408304 6.2091513196
> H 1.7283744406 11.8001429893 4.8750774087
>
>
> K_POINTS (automatic)
> 2 2 2 0 0 0
>
>
>
>
> Em quinta-feira, 4 de novembro de 2021 03:06:30 BRT, Kazume NISHIDATE <nisidate at iwate-u.ac.jp> escreveu:
>
>
>
>
>
>> 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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