[QE-users] Trouble with MoSe2

Mon Jun 2 19:02:48 CEST 2025

I have been working with the suggestions and insights both of you have
provided.

   1. I think I understand the "busy" band structures now, thanks to
   Giovanni's explanation.
   2. I ran vc-relax, allowing all 6 axes and angles to be moved, fed the
   output to a relax calculation and used the final coordinates as inputs
   to scf. This took some time, but I still ended up with large negative
   phonon frequencies (-4200 to *7000?!* cm^-1). I asked for the final
   force in the cell to be 0, and set tight convergence limits at each step. I
   have put up the updated vc-relax, relax, scf and phonon input files on
   GitHub.
   3. I re-installed QE 7.4.1 and the "string of asterisks" in the
   MoSe2.dyn1 file problem is not resolved. I ran the same input files on an
   HPC running on 6.6 and still got the same mysterious string. (See
   MoSe2.dyn1 in the GitHub folder.)

I came to similar conclusions to what Antonio suggested about unitcells,
supercells, and doping but it was great to receive validation from a more
experienced researcher.

Git repo
<https://github.com/AmoghA4/Quantum-ESPRESSO/tree/main/Updated%20Input%20Files>

Many thanks for your help,

Amogh A.

On Mon, 2 Jun 2025 at 13:23, Antonio Cammarata via users <
users at lists.quantum-espresso.org> wrote:

> Hi,
>
> besides the reply i) of Giovanni to your question 1), I would like to add
> something about doped systems. The doping concentration is defined by how
> many dopant atoms you have in your unit cell; for this you might need to
> use supercells of the primitive one, for sure if you substitute the Mo
> site. This means that your doped system can be seen as a supercell of your
> primitive undoped system; but this "supercell" is now a primitive unit
> cell, as it fixes the dopant concentration and cannot be reduced to a
> smaller unit cell. Since the matrix hosting the dopant is obtained by
> replicating the undoped primitive cell, the band structure (electronic or
> phononic) will show band folding features that Giovanni mentioned. However,
> since now the unit cell is primitive (again, because it is the minimum
> volume you need to have the chosen dopant concentration), any possible
> change of the band gap character from indirect to direct (and vice versa)
> is real and not an artifact due to the band folding.
>
> You may read the paper https://doi.org/10.1016/j.diamond.2022.109237 for
> a discussion about this.
>
> I hope this helps.
>
> Best
>
> Antonio
> Il 30. 05. 25 9:51, Giovanni Cantele ha scritto:
>
> Hi,
>
> first suggestion is start with "simple" calculations, then move to
> trickier ones (such as phonon dispersions).
> Second suggestion is to follow tutorials to be fully aware of all the main
> issues you may face during a specific calculation.
>
> This being said, some considerations about your questions:
>
> i) it is absolutely "normal" that if you replicate a unit cell along one
> or more directions the number of bands increases
> proportionally to the number of unit cells, even if you are making a
> calculation for a "perfect" undoped crystal.
> You might want to study, for example, what happens to a one dimensional
> monoatomic chain with period a when you study it
> in a doubled unit cell with period 2a. This is something you might find in
> textbooks and in web sites as well.
> If your supercell is composed of N supercells of the original lattice, for
> each band of the latter you will get N bands of the former.
> The explanation stands in the size of the Brillouin zone, whose volume
> reduces by a factor N. However, the "perfect" crystal with
> its minimal primitive cell and the same with the supercell will have
> exactly the same "physics". For example, you should get
> the same density of states, except for a factor N. What I've explained is
> generally referred to as "band folding". The change in the
> volume and possibly the shape of the Brillouin zone also explain the fact
> that some point of the original Brillouin zone (e.g. K, M)
> can be "folded" to a different point of the new Brillouin zone. In the
> monoatomic chain above mentioned, for example, the
> Brillouin zone extremum pi/a gets folded to the gamma point.
>
> ii) " I am working with the un-relaxed unitcell" : what does it mean? Did
> you optimize the atomic positions? Calculation of phonon
> frequencies is based on the assumption that the starting configuration is
> an equilibrium configuration, that is, zero forces.
> So the first step is to optimize the atomic positions, sometimes you need
> to optimize them also with thresholds tighter than
> those one normally uses to get equilibrium geometries. Starting from a
> non-equilibrium geometry means an unstable system and in turn
> this results in negative phonon frequencies. Be careful to experience the
> calculation of phonons on very simple systems, the convergence
> of the frequencies is harder to obtain than other properties, such as band
> structure or bond lengths.
>
> Giovanni
>
> --
>
> Giovanni Cantele, PhD
> CNR-SPIN
> c/o Dipartimento di Fisica
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> e-mail: giovanni.cantele at spin.cnr.it <giovanni.cantele at spin.cnr.it>
> Phone: +39 081 676910
> Skype contact: giocan74
>
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: https://sites.google.com/view/giovanni-cantele/home
>
>
> Il giorno gio 29 mag 2025 alle ore 23:52 AMOGH A . <
> f20220890 at hyderabad.bits-pilani.ac.in> ha scritto:
>
>> Hello folks!
>>
>> I am having 3 problems with MoSe2.
>>
>>    1. I got the correct electronic band structure of the MoSe2 unitcell,
>>    but when I try it for the supercell (3x3 or 5x5), or some doped version,
>>    the band plots look very "busy" and messed up (plots attached). The direct
>>    bandgap at the K-point also disappears. Nothing except *nat* and
>>    *atomic_positions* changed in the input files. Is this typical of
>>    large atomic systems? Is there a way to reduce the "business"? I read about
>>    "unfolding" the Brillouin zone but not too sure how it might help.
>>    2. I am trying to get the phonon dispersion and PhDOS for the
>>    monolayer. I am working with the un-relaxed unitcell having 3 atoms. I have
>>    been getting frequencies from -3000 cm^-1 to 2000 cm^-1 (plots attached).
>>    Can someone please tell me why I am getting such large negative frequencies
>>    and how to get the correct plot? I tried changing almost all parameters in
>>    the input file to no avail.
>>    3. MoSe2.dyn(i) files for some values of i, will have a string of
>>    asterisks in place of a few numbers which gives me a Fortran compiler error
>>    when I run q2r.x (QE version 7.4.1). Thus far, I have been going to the
>>    files, finding the asterisks where numbers *should* be, and replacing
>>    them with 0.000. Any idea why that happens (and how to fix it)?
>>
>> Thanks for your help in advance!
>> Amogh A
>> Undergrad student at BITS Pilani, Hyderabad.
>>
>> (GitHub and Google Drive links)
>> Github rep containing all the input files.
>> <https://github.com/AmoghA4/Quantum-ESPRESSO>
>> Unitcell band structure
>> <https://drive.google.com/file/d/1C_7zDhHir8eiHbNe2YyJhbrPSw7mSYjs/view?usp=sharing>
>>  v.s. supercell band structure
>> <https://drive.google.com/file/d/1Dfxv2r9vj9FsLcI3cq3QVpkys2_ePyii/view?usp=sharing>
>>  and oxygen-doped
>> <https://drive.google.com/file/d/1XtAbmdGoNS8EklQ6GuJADlz6fLZREHmP/view?usp=sharing>
>> .
>> Phonon dispersion plot I got
>> <https://drive.google.com/file/d/1plCzIl364o0ZEIkLxQujZ3Sg7hZpRHwU/view?usp=sharing>
>>  v.s. the correct one
>> <https://www.researchgate.net/figure/The-phonon-dispersion-of-monolayer-a-MoS2-b-MoSe2-b-and-c-MoTe2-Non-negative_fig3_377939317>
>> .
>>
>>
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>
> _______________________________________________________________________________
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> --------------------------------------------------------------------------------
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> --
> [image: Submit paper to special issue "MXenes and their hybrids for
> sustainable applications"]
> <https://www.sciencedirect.com/special-issue/316397/mxenes-and-their-hybrids-for-sustainable-applications>
>
> ______________________________________________
> doc. Antonio Cammarata, PhD in Physics
> Associate Professor in Applied Physics
> Advanced Materials Group
> Department of Control Engineering - KN:G-204
> Faculty of Electrical Engineering
> Czech Technical University in Prague
> Karlovo Náměstí, 13
> 121 35, Prague 2, Czech Republic
> Phone: +420 224 35 5713
> Fax:   +420 224 91 8646
> ORCID: orcid.org/0000-0002-5691-0682
> ResercherID: A-4883-2014
>
> _______________________________________________________________________________
> The Quantum ESPRESSO Foundation stands in solidarity with all civilians
> worldwide who are victims of terrorism, military aggression, and
> indiscriminate warfare.
>
> --------------------------------------------------------------------------------
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users at lists.quantum-espresso.org
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