[QE-users] Trouble with MoSe2

[Giovanni Cantele]

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>
> .
>
>
> The information contained in this electronic communication is intended
> solely for the individual(s) or entity to which it is addressed. It may
> contain proprietary, confidential and/or legally privileged information.
> Any review, retransmission, dissemination, printing, copying or other use
> of, or taking any action in reliance on the contents of this information by
> person(s) or entities other than the intended recipient is strictly
> prohibited and may be unlawful. If you have received this communication in
> error, please notify us by responding to this email or telephone and
> immediately and permanently delete all copies of this message and any
> attachments from your system(s). The contents of this message do not
> necessarily represent the views or policies of BITS Pilani.
>
> _______________________________________________________________________________
> 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
> https://lists.quantum-espresso.org/mailman/listinfo/users
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20250530/88d85142/attachment.html>