<div dir="ltr"><div dir="ltr"><div><div>Hi,</div><div><br></div><div>I still think that until you just "try" to make phonon calculations with the hope they'll give you the output which you expect you'll never end up. It is completely useless that you start calculating phonons disregarding the output you had from vc-relax.</div><div><br></div><div>1) Did you have the chance to realize that your vc-relax started from the 13.54 A c parameter and ended with c = 8.29 A? c was reduced by about 40%,</div><div>is it what you need/expect? I guess the answer is no</div><div><br></div><div>2) I again guess that the reason why you started from 13.54 is that you wanted to simulate a bulk MoSe2 unit cell, didn't you? For example here</div><div><a href="https://next-gen.materialsproject.org/materials/mp-1634" target="_blank">https://next-gen.materialsproject.org/materials/mp-1634</a></div><div>one finds exactly the same lattice parameters as those of your input. However, a closer inspection shows that a "bulk" MoSe2 unit cell contains two MoSe2</div><div>layers, not just one! So the question arises: do you want to simulate an isolated MoSe2 monolayer or a bulk MoSe2 crystal? Did you use a visualization program? Did you try to visualize BOTH input and output to try to understand if the code is producing reasonable results? XCrysDen or Vesta can do this job!</div><div><br></div><div>3) Once Total force is (numerically) zero and pressure as well, this does not guarantee not imaginary frequencies, see here</div><div><a href="https://www.quantum-espresso.org/faq/faq-phonons/#7.3" target="_blank">https://www.quantum-espresso.org/faq/faq-phonons/#7.3</a></div><div>Indeed an instability of your system might cause such odd behavior. See also here:</div><div><a href="https://mattermodeling.stackexchange.com/questions/1698/phonon-calculations-for-bilayer-2d-systems" target="_blank">https://mattermodeling.stackexchange.com/questions/1698/phonon-calculations-for-bilayer-2d-systems</a></div><div><br></div><div>You can google about imaginary phonon frequencies and find a lot of valid hints and explanations.</div><div><br></div><div>In conclusion, I would definitely stop making phonon calculations on structures you're not sure about. Start with what is simple and simpler, when this becomes well established move to what is hard or harder.</div><font color="#888888"><div><br></div><div>Giovanni</div></font><div><br></div><div>PS about your point 3., just to support my above advice: if you reinstall QE, try different versions and try different computing systems and all the times you</div><div>obtain the same answer, maybe the problem is not the QE version nor QE at all!!!!</div><span class="gmail-im" style="color:rgb(80,0,80)"><div><div dir="ltr" class="gmail_signature"><div dir="ltr"><span style="color:rgb(0,0,0)">-- </span></div></div></div></span></div><div><div dir="ltr" class="gmail_signature"><div dir="ltr"><span style="color:rgb(0,0,0)">-- <br><br>Giovanni Cantele, PhD<br>CNR-SPIN<br>c/o Dipartimento di Fisica<br>Universita' di Napoli "Federico II"<br>Complesso Universitario M. S. Angelo - Ed. 6<br>Via Cintia, I-80126, Napoli, Italy<br><a href="mailto:giovanni.cantele@spin.cnr.it" style="color:rgb(17,85,204)" target="_blank">e-mail: giovanni.cantele@spin.cnr.it</a><br>Phone: +39 081 676910<br>Skype contact: giocan74<br><br>ResearcherID: <a href="http://www.researcherid.com/rid/A-1951-2009" style="color:rgb(17,85,204)" target="_blank">http://www.researcherid.com/rid/A-1951-2009</a><br>Web page: </span><a href="https://sites.google.com/view/giovanni-cantele/home" style="color:rgb(17,85,204)" target="_blank">https://sites.google.com/view/giovanni-cantele/home</a><br></div></div></div><br></div><br><div class="gmail_quote gmail_quote_container"><div dir="ltr" class="gmail_attr">Il giorno lun 2 giu 2025 alle ore 19:03 AMOGH A . <<a href="mailto:f20220890@hyderabad.bits-pilani.ac.in">f20220890@hyderabad.bits-pilani.ac.in</a>> ha scritto:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div style="font-family:tahoma,sans-serif">I have been working with the suggestions and insights both of you have provided. </div><div><ol><li style="font-family:tahoma,sans-serif">I think I understand the "busy" band structures now, thanks to Giovanni's explanation.</li><li><font face="tahoma, sans-serif">I ran </font><font face="monospace">vc-relax</font><font face="tahoma, sans-serif">, allowing all 6 axes and angles to be moved, fed the output to a </font><font face="monospace">relax</font><font face="tahoma, sans-serif"> calculation and used the final coordinates as inputs to </font><font face="monospace">scf</font><font face="tahoma, sans-serif">. This took some time, but I still ended up with large negative phonon frequencies (-4200 to <b>7000?!</b> 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 </font><font face="monospace">vc-relax, relax, scf </font><font face="tahoma, sans-serif">and </font><font face="monospace">phonon</font><font face="tahoma, sans-serif"> input files on GitHub.</font></li><li><font face="tahoma, sans-serif">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.)</font></li></ol><div><font face="tahoma, sans-serif">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. </font></div><div><font face="tahoma, sans-serif"><br></font></div><div><font face="tahoma, sans-serif"><a href="https://github.com/AmoghA4/Quantum-ESPRESSO/tree/main/Updated%20Input%20Files" target="_blank">Git repo</a></font></div><div><br></div><div>Many thanks for your help,</div><div><br></div><div>Amogh A.</div></div><div style="font-family:tahoma,sans-serif"><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, 2 Jun 2025 at 13:23, Antonio Cammarata via users <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><u></u>
<div>
<p>Hi,</p>
<p>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.</p>
<p>You may read the paper
<a href="https://doi.org/10.1016/j.diamond.2022.109237" target="_blank">https://doi.org/10.1016/j.diamond.2022.109237</a> for a discussion
about this.</p>
<p>I hope this helps.</p>
<p>Best</p>
<p>Antonio<br>
</p>
<div>Il 30. 05. 25 9:51, Giovanni Cantele ha
scritto:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Hi,</div>
<div><br>
</div>
<div>first suggestion is start with "simple" calculations, then
move to trickier ones (such as phonon dispersions). </div>
<div>Second suggestion is to follow tutorials to be fully aware
of all the main issues you may face during a specific
calculation.</div>
<div><br>
</div>
<div>This being said, some considerations about your questions:</div>
<div><br>
</div>
<div>i) it is absolutely "normal" that if you replicate a unit
cell along one or more directions the number of bands
increases</div>
<div>proportionally to the number of unit cells, even if you are
making a calculation for a "perfect" undoped crystal.</div>
<div>You might want to study, for example, what happens to a one
dimensional monoatomic chain with period a when you study it </div>
<div>in a doubled unit cell with period 2a. This is something
you might find in textbooks and in web sites as well.</div>
<div>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.</div>
<div>The explanation stands in the size of the Brillouin zone,
whose volume reduces by a factor N. However, the "perfect"
crystal with</div>
<div>its minimal primitive cell and the same with the supercell
will have exactly the same "physics". For example, you should
get</div>
<div>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</div>
<div>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)</div>
<div>can be "folded" to a different point of the new Brillouin
zone. In the monoatomic chain above mentioned, for example,
the</div>
<div>Brillouin zone extremum pi/a gets folded to the gamma
point.</div>
<div><br>
</div>
<div>ii) "<span style="font-family:tahoma,sans-serif"> </span><span style="font-family:tahoma,sans-serif">I am working with the
un-relaxed unitcell" : what does it mean? Did you optimize
the atomic positions? Calculation of phonon</span></div>
<div><span style="font-family:tahoma,sans-serif">frequencies is
based on the assumption that the starting configuration is
an equilibrium configuration, that is, zero forces.</span></div>
<div><span style="font-family:tahoma,sans-serif">So the first
step is to optimize the atomic positions, sometimes you need
to optimize them also with thresholds tighter than </span></div>
<div><span style="font-family:tahoma,sans-serif">those one
normally uses to get equilibrium geometries. Starting from a
non-equilibrium geometry means an unstable system and in
turn</span></div>
<div><span style="font-family:tahoma,sans-serif">this results in
negative phonon frequencies. Be careful to experience the
calculation of phonons on very simple systems, the
convergence</span></div>
<div><span style="font-family:tahoma,sans-serif">of the
frequencies is harder to obtain than other properties, such
as band structure or bond lengths.</span></div>
<div><span style="font-family:tahoma,sans-serif"><br>
</span></div>
<div><span style="font-family:tahoma,sans-serif">Giovanni</span></div>
<div><br>
</div>
<div>
<div dir="ltr" class="gmail_signature">
<div dir="ltr"><span style="color:rgb(0,0,0)">-- <br>
<br>
Giovanni Cantele, PhD<br>
CNR-SPIN<br>
c/o Dipartimento di Fisica<br>
Universita' di Napoli "Federico II"<br>
Complesso Universitario M. S. Angelo - Ed. 6<br>
Via Cintia, I-80126, Napoli, Italy<br>
<a href="mailto:giovanni.cantele@spin.cnr.it" style="color:rgb(17,85,204)" target="_blank">e-mail:
giovanni.cantele@spin.cnr.it</a><br>
Phone: +39 081 676910<br>
Skype contact: giocan74<br>
<br>
ResearcherID: <a href="http://www.researcherid.com/rid/A-1951-2009" style="color:rgb(17,85,204)" target="_blank">http://www.researcherid.com/rid/A-1951-2009</a><br>
Web page: </span><a href="https://sites.google.com/view/giovanni-cantele/home" style="color:rgb(17,85,204)" target="_blank">https://sites.google.com/view/giovanni-cantele/home</a><br>
</div>
</div>
</div>
<br>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">Il giorno gio 29 mag 2025 alle
ore 23:52 AMOGH A . <<a href="mailto:f20220890@hyderabad.bits-pilani.ac.in" target="_blank">f20220890@hyderabad.bits-pilani.ac.in</a>>
ha scritto:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div dir="ltr">
<div>
<div style="font-family:tahoma,sans-serif">Hello folks!</div>
<div style="font-family:tahoma,sans-serif"><br>
</div>
<div style="font-family:tahoma,sans-serif">I am having 3
problems with MoSe2.</div>
<div style="font-family:tahoma,sans-serif">
<ol>
<li>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 <i>nat</i> and <i>atomic_positions</i> 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.</li>
<li>
<div>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.</div>
</li>
<li>
<div>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 <i>should</i> be,
and replacing them with 0.000. Any idea why that
happens (and how to fix it)?</div>
</li>
</ol>
<div>Thanks for your help in advance!</div>
<div>
<div>Amogh A</div>
<div>Undergrad student at BITS
Pilani, Hyderabad.</div>
</div>
<div><br>
</div>
</div>
<div style="font-family:tahoma,sans-serif">(GitHub and
Google Drive links)</div>
<div style="font-family:tahoma,sans-serif"><a href="https://github.com/AmoghA4/Quantum-ESPRESSO" target="_blank">Github rep
containing all the input files.</a><br>
</div>
</div>
<div style="font-family:tahoma,sans-serif"><a href="https://drive.google.com/file/d/1C_7zDhHir8eiHbNe2YyJhbrPSw7mSYjs/view?usp=sharing" target="_blank">Unitcell band
structure</a> v.s. <a href="https://drive.google.com/file/d/1Dfxv2r9vj9FsLcI3cq3QVpkys2_ePyii/view?usp=sharing" target="_blank">supercell band
structure</a> and <a href="https://drive.google.com/file/d/1XtAbmdGoNS8EklQ6GuJADlz6fLZREHmP/view?usp=sharing" target="_blank">oxygen-doped</a>.<br>
</div>
<div style="font-family:tahoma,sans-serif"><a href="https://drive.google.com/file/d/1plCzIl364o0ZEIkLxQujZ3Sg7hZpRHwU/view?usp=sharing" target="_blank">Phonon
dispersion plot I got</a> v.s. <a href="https://www.researchgate.net/figure/The-phonon-dispersion-of-monolayer-a-MoS2-b-MoSe2-b-and-c-MoTe2-Non-negative_fig3_377939317" target="_blank">the correct one</a>.</div>
<div style="font-family:tahoma,sans-serif"><br>
</div>
<div>
<div dir="ltr" class="gmail_signature">
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<tbody>
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<tbody>
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</div>
</div>
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</div>
</blockquote><div><br><p>______________________________________________<br>
doc. Antonio Cammarata, PhD in Physics<br>
Associate Professor in Applied Physics<br>
Advanced Materials Group<br>
Department of Control Engineering - KN:G-204<br>
Faculty of Electrical Engineering<br>
Czech Technical University in Prague<br>
Karlovo Náměstí, 13<br>
121 35, Prague 2, Czech Republic<br>
Phone: +420 224 35 5713<br>
Fax: +420 224 91 8646 <br>
ORCID: <a href="http://orcid.org/0000-0002-5691-0682" target="_blank">orcid.org/0000-0002-5691-0682</a><br>
ResercherID: A-4883-2014</p>
</div>
</div>
_______________________________________________________________________________<br>
The Quantum ESPRESSO Foundation stands in solidarity with all civilians worldwide who are victims of terrorism, military aggression, and indiscriminate warfare.<br>
--------------------------------------------------------------------------------<br>
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu" rel="noreferrer" target="_blank">www.max-centre.eu</a>)<br>
users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote></div>
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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.<br></blockquote></div></div>