[QE-users] Trouble with MoSe2
Antonio Cammarata
cammaant at fel.cvut.cz
Fri May 30 10:16:57 CEST 2025
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 <mailto: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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Submit paper to special issue "MXenes and their hybrids for sustainable
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______________________________________________
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
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