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From: Antonio C. <cam...@fe...> - 2026-04-21 18:35:10
|
Hello, the U parameter enters the Hamiltonian, then the solution of the Schrödinger equation, then any physical property of your system, including the forces on the atoms which enter the calculation of the thermal conductivity. Therefore, the answer in general is yes, you should include it. However, if you know that in your system the U parameter doesn't affect the forces in a significant way, then you don't need to include it. Hope this helps. Antonio Il 21/04/26 15:25, MUMTAZSOHAIL ha scritto: > > Dear Phonopy community, > > I am calculating lattice thermal conductivity of Eu2+ (and other > rare earth) doped phosphor material using phono3py. Do i need to > include U parameter in INCAR for 3rd order force constant > calculations? what will be effect on final lattice thermal > conductivity if i don't include U parameter. > > Best Regards, > Sohail Mumtaz > > > > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users -- ______________________________________________ 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 ResearcherID: A-4883-2014 |
|
From: MUMTAZSOHAIL <soh...@ma...> - 2026-04-21 13:25:27
|
Dear Phonopy community,
I am calculating lattice thermal conductivity of Eu2+ (and other rare earth) doped phosphor material using phono3py. Do i need to include U parameter in INCAR for 3rd order force constant calculations? what will be effect on final lattice thermal conductivity if i don't include U parameter.
Best Regards,
Sohail Mumtaz |
|
From: Atsushi T. <atz...@gm...> - 2026-04-12 23:58:47
|
Hi, I don't know well about TDEP. Phonopy accepts two formats of force constants, https://phonopy.github.io/phonopy/input-files.html#force-constants-and-force-constants-hdf5 You may also perform force constants fitting using MD trajectory using symfc, https://phonopy.github.io/phonopy/random-displacements.html Togo On Mon, Apr 13, 2026 at 3:13 AM Iyad AL-QASIR <iy...@gm...> wrote: > > Dear Togo, > > I am wondering if one can use the force constants produced by TDEP in phonopy to get the phonon frequencies and polarization vectors. > > Kindest Regards, > Iyad > > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users -- Atsushi Togo |
|
From: Iyad AL-Q. <iy...@gm...> - 2026-04-12 18:13:12
|
Dear Togo, I am wondering if one can use the force constants produced by TDEP in phonopy to get the phonon frequencies and polarization vectors. Kindest Regards, *Iyad* |
|
From: Luis O. <lco...@gm...> - 2026-04-02 15:07:29
|
Dear Dr. Togo,
Thank you, anyway!
Just a quick question, is there a way to create an xmgrace graph with
Phonopy? I remember it was possible with old versions.
All the best,
Luis
Em qua., 1 de abr. de 2026 às 09:07, <
pho...@li...> escreveu:
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> Today's Topics:
>
> 1. Re: Creating FORCE_SETS from Fleur calculations (Atsushi Togo)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 31 Mar 2026 22:17:23 +0900
> From: Atsushi Togo <atz...@gm...>
> To: pho...@li...
> Subject: Re: [Phonopy-users] Creating FORCE_SETS from Fleur
> calculations
> Message-ID:
> <CAAfkA7dDXknmCG=
> zov...@ma...>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> It seems phonopy failed to parse your output file to extract forces.
> But currently there is nobody to maintain phonopy-fleur interface as
> far as I know, and I have zero knowledge on fleur. So it is very
> difficult to answer your question.
>
> Some history of the phonopy fleur interface is found here,
> https://github.com/phonopy/phonopy/pulls?q=is%3Apr+Fleur+is%3Aclosed
>
> Togo
>
> On Tue, Mar 31, 2026 at 9:04?PM Luis Ogando <lco...@gm...> wrote:
> >
> > Dear Phonopy community,
> > I am trying to calculate the phonon dispersion from Fleur results.
> > Unfortunately, when trying to create the FORCE_SETS file, after a
> converged Fleur run setting ?l_f? to ?T? and ?f_level' to ?1? in inp.xml,
> I got the following error message:
> >
> >
> =====================================================================================================================================
> > (Phonopy-3.4.0) ogando@SantoAmaro:~/Fleur/Calculos/CrTe/Teste/Phonon$
> phonopy --fleur -f disp-00{1..2}/FORCES
> > _
> > _ __ | |__ ___ _ __ ___ _ __ _ _
> > | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
> > | |_) | | | | (_) | | | | (_) || |_) | |_| |
> > | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
> > |_| |_| |___/
> > 3.4.0
> >
> > -------------------------[time 2026-03-31
> 08:47:50]-------------------------
> > Compiled with OpenMP support (max 112 threads).
> > Python version 3.14.3
> > Spglib version 2.7.0
> >
> > Calculator interface: fleur
> > Displacements were read from "phonopy_disp.yaml".
> > Number of supercell files: 2
> > Number of displacements in "phonopy_disp.yaml": 2
> > 1. Traceback (most recent call last):
> > File "/home/ogando/miniconda3/envs/Phonopy-3.4.0/bin/phonopy", line
> 11, in <module>
> > sys.exit(run())
> > ~~~^^
> > File
> "/home/ogando/miniconda3/envs/Phonopy-3.4.0/lib/python3.14/site-packages/phonopy/scripts/phonopy.py",
> line 43, in run
> > main(**argparse_control)
> > ~~~~^^^^^^^^^^^^^^^^^^^^
> > File
> "/home/ogando/miniconda3/envs/Phonopy-3.4.0/lib/python3.14/site-packages/phonopy/cui/phonopy_script.py",
> line 1879, in main
> > _create_FORCE_SETS_from_settings(settings, cell_filename, symprec,
> log_level)
> >
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> > File
> "/home/ogando/miniconda3/envs/Phonopy-3.4.0/lib/python3.14/site-packages/phonopy/cui/phonopy_script.py",
> line 649, in _create_FORCE_SETS_from_settings
> > create_FORCE_SETS(
> > ~~~~~~~~~~~~~~~~~^
> > interface_mode,
> > ^^^^^^^^^^^^^^^
> > ...<6 lines>...
> > log_level=log_level,
> > ^^^^^^^^^^^^^^^^^^^^
> > )
> > ^
> > File
> "/home/ogando/miniconda3/envs/Phonopy-3.4.0/lib/python3.14/site-packages/phonopy/cui/create_force_sets.py",
> line 147, in create_FORCE_SETS
> > calc_dataset = get_calc_dataset(
> > interface_mode,
> > ...<2 lines>...
> > verbose=(log_level > 0),
> > )
> > File
> "/home/ogando/miniconda3/envs/Phonopy-3.4.0/lib/python3.14/site-packages/phonopy/interface/calculator.py",
> line 1097, in get_calc_dataset
> > data_sets = parse_set_of_forces(num_atoms, force_filenames,
> verbose=verbose)
> > File
> "/home/ogando/miniconda3/envs/Phonopy-3.4.0/lib/python3.14/site-packages/phonopy/interface/fleur.py",
> line 71, in parse_set_of_forces
> > vec = [float(x) for x in previous_line.split()[:3]]
> > ~~~~~^^^
> > ValueError: could not convert string to float: '#'
> >
> =====================================================================================================================================
> >
> > I believe that the forces are extracted from "out" file but it is too
> big to be sent through this list.
> > I would thank you for any help and I can send any relevant file you
> need.
> > Thank you in advance!
> > All the best,
> > Luis Ogando
> > _______________________________________________
> > Phonopy-users mailing list
> > Pho...@li...
> > https://lists.sourceforge.net/lists/listinfo/phonopy-users
>
>
>
> --
> Atsushi Togo
>
>
>
> ------------------------------
>
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Phonopy-users mailing list
> Pho...@li...
> https://lists.sourceforge.net/lists/listinfo/phonopy-users
>
>
> ------------------------------
>
> End of Phonopy-users Digest, Vol 191, Issue 1
> *********************************************
>
|
|
From: Atsushi T. <atz...@gm...> - 2026-03-31 13:17:41
|
Hi, It seems phonopy failed to parse your output file to extract forces. But currently there is nobody to maintain phonopy-fleur interface as far as I know, and I have zero knowledge on fleur. So it is very difficult to answer your question. Some history of the phonopy fleur interface is found here, https://github.com/phonopy/phonopy/pulls?q=is%3Apr+Fleur+is%3Aclosed Togo On Tue, Mar 31, 2026 at 9:04 PM Luis Ogando <lco...@gm...> wrote: > > Dear Phonopy community, > I am trying to calculate the phonon dispersion from Fleur results. > Unfortunately, when trying to create the FORCE_SETS file, after a converged Fleur run setting ‘l_f’ to “T” and ‘f_level' to ”1” in inp.xml, I got the following error message: > > ===================================================================================================================================== > (Phonopy-3.4.0) ogando@SantoAmaro:~/Fleur/Calculos/CrTe/Teste/Phonon$ phonopy --fleur -f disp-00{1..2}/FORCES > _ > _ __ | |__ ___ _ __ ___ _ __ _ _ > | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | > | |_) | | | | (_) | | | | (_) || |_) | |_| | > | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | > |_| |_| |___/ > 3.4.0 > > -------------------------[time 2026-03-31 08:47:50]------------------------- > Compiled with OpenMP support (max 112 threads). > Python version 3.14.3 > Spglib version 2.7.0 > > Calculator interface: fleur > Displacements were read from "phonopy_disp.yaml". > Number of supercell files: 2 > Number of displacements in "phonopy_disp.yaml": 2 > 1. Traceback (most recent call last): > File "/home/ogando/miniconda3/envs/Phonopy-3.4.0/bin/phonopy", line 11, in <module> > sys.exit(run()) > ~~~^^ > File "/home/ogando/miniconda3/envs/Phonopy-3.4.0/lib/python3.14/site-packages/phonopy/scripts/phonopy.py", line 43, in run > main(**argparse_control) > ~~~~^^^^^^^^^^^^^^^^^^^^ > File "/home/ogando/miniconda3/envs/Phonopy-3.4.0/lib/python3.14/site-packages/phonopy/cui/phonopy_script.py", line 1879, in main > _create_FORCE_SETS_from_settings(settings, cell_filename, symprec, log_level) > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > File "/home/ogando/miniconda3/envs/Phonopy-3.4.0/lib/python3.14/site-packages/phonopy/cui/phonopy_script.py", line 649, in _create_FORCE_SETS_from_settings > create_FORCE_SETS( > ~~~~~~~~~~~~~~~~~^ > interface_mode, > ^^^^^^^^^^^^^^^ > ...<6 lines>... > log_level=log_level, > ^^^^^^^^^^^^^^^^^^^^ > ) > ^ > File "/home/ogando/miniconda3/envs/Phonopy-3.4.0/lib/python3.14/site-packages/phonopy/cui/create_force_sets.py", line 147, in create_FORCE_SETS > calc_dataset = get_calc_dataset( > interface_mode, > ...<2 lines>... > verbose=(log_level > 0), > ) > File "/home/ogando/miniconda3/envs/Phonopy-3.4.0/lib/python3.14/site-packages/phonopy/interface/calculator.py", line 1097, in get_calc_dataset > data_sets = parse_set_of_forces(num_atoms, force_filenames, verbose=verbose) > File "/home/ogando/miniconda3/envs/Phonopy-3.4.0/lib/python3.14/site-packages/phonopy/interface/fleur.py", line 71, in parse_set_of_forces > vec = [float(x) for x in previous_line.split()[:3]] > ~~~~~^^^ > ValueError: could not convert string to float: '#' > ===================================================================================================================================== > > I believe that the forces are extracted from "out" file but it is too big to be sent through this list. > I would thank you for any help and I can send any relevant file you need. > Thank you in advance! > All the best, > Luis Ogando > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users -- Atsushi Togo |
|
From: Luis O. <lco...@gm...> - 2026-03-31 12:04:10
|
Dear Phonopy community,
I am trying to calculate the phonon dispersion from Fleur results.
Unfortunately, when trying to create the FORCE_SETS file, after a
converged Fleur run setting ‘l_f’ to “T” and ‘f_level' to ”1” in inp.xml,
I got the following error message:
=====================================================================================================================================
(Phonopy-3.4.0) ogando@SantoAmaro:~/Fleur/Calculos/CrTe/Teste/Phonon$
phonopy --fleur -f disp-00{1..2}/FORCES
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
3.4.0
-------------------------[time 2026-03-31 08:47:50]-------------------------
Compiled with OpenMP support (max 112 threads).
Python version 3.14.3
Spglib version 2.7.0
Calculator interface: fleur
Displacements were read from "phonopy_disp.yaml".
Number of supercell files: 2
Number of displacements in "phonopy_disp.yaml": 2
1. Traceback (most recent call last):
File "/home/ogando/miniconda3/envs/Phonopy-3.4.0/bin/phonopy", line 11,
in <module>
sys.exit(run())
~~~^^
File
"/home/ogando/miniconda3/envs/Phonopy-3.4.0/lib/python3.14/site-packages/phonopy/scripts/phonopy.py",
line 43, in run
main(**argparse_control)
~~~~^^^^^^^^^^^^^^^^^^^^
File
"/home/ogando/miniconda3/envs/Phonopy-3.4.0/lib/python3.14/site-packages/phonopy/cui/phonopy_script.py",
line 1879, in main
_create_FORCE_SETS_from_settings(settings, cell_filename, symprec,
log_level)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/ogando/miniconda3/envs/Phonopy-3.4.0/lib/python3.14/site-packages/phonopy/cui/phonopy_script.py",
line 649, in _create_FORCE_SETS_from_settings
create_FORCE_SETS(
~~~~~~~~~~~~~~~~~^
interface_mode,
^^^^^^^^^^^^^^^
...<6 lines>...
log_level=log_level,
^^^^^^^^^^^^^^^^^^^^
)
^
File
"/home/ogando/miniconda3/envs/Phonopy-3.4.0/lib/python3.14/site-packages/phonopy/cui/create_force_sets.py",
line 147, in create_FORCE_SETS
calc_dataset = get_calc_dataset(
interface_mode,
...<2 lines>...
verbose=(log_level > 0),
)
File
"/home/ogando/miniconda3/envs/Phonopy-3.4.0/lib/python3.14/site-packages/phonopy/interface/calculator.py",
line 1097, in get_calc_dataset
data_sets = parse_set_of_forces(num_atoms, force_filenames,
verbose=verbose)
File
"/home/ogando/miniconda3/envs/Phonopy-3.4.0/lib/python3.14/site-packages/phonopy/interface/fleur.py",
line 71, in parse_set_of_forces
vec = [float(x) for x in previous_line.split()[:3]]
~~~~~^^^
ValueError: could not convert string to float: '#'
=====================================================================================================================================
I believe that the forces are extracted from "out" file but it is too
big to be sent through this list.
I would thank you for any help and I can send any relevant file you need.
Thank you in advance!
All the best,
Luis Ogando
|
|
From: Atsushi T. <atz...@gm...> - 2026-03-28 23:36:01
|
Hi, You need to provide more details otherwise it is not possible to comment. However, I strongly recommend you to discuss with your supervisors and colleagues before posting your question again, or the discussion will be helpful to make your question clear and better understood. Togo On Sun, Mar 29, 2026 at 4:41 AM Mahesh Verma <mah...@gm...> wrote: > > Dear Developers, > Greetings of the day > > I have querry regarding the use of phono3py for 2D material as below: > > 1. Should we use the dim for 2D material as 2 2 1 to generate supercells. > 2. Can we use oncv pseudo potentials > 3. I have followed above steps and when calculating cf3 . It shows that CF3 force has not been created, I have placed the disp.ymal file in same directory. > > Any help would be appreciated. > > Thanks and Regards > > Mahesh Verma > > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users -- Atsushi Togo |
|
From: Atsushi T. <atz...@gm...> - 2026-03-28 23:33:28
|
Hi, I cannot see the technical details of the paper. You should contact the authors. Togo On Sat, Mar 28, 2026 at 8:01 PM Gulshan Kumar via Phonopy-users <pho...@li...> wrote: > > Thank you, sir, for the reply and time > > I am curious about the recently published paper; my high-pressure lattice constants and atomic positions are identical to the values they obtained because I am also using the same pseudopotentials. > DOI: https://doi.org/10.1038/s41467-026-69772-8 name: Hidden pressure-stabilized lead reservoirs in Earth’s mantle. My concern is that they clearly stated that they used phonopy-QHA for the P-T diagram. > > Thank you > > > On Thu, 26 Mar, 2026, 6:30 am Atsushi Togo, <atz...@gm...> wrote: >> >> Hi, >> >> I don't know. But if you don't include electronic entropy in the free >> energy, you may have to consider it. >> The other possibility is due to strong anharmonicity, for which I have >> recently mentioned in the mailing list, >> https://sourceforge.net/p/phonopy/mailman/message/59313092/ >> >> For the details of the electronic calculation, it is out of the topic >> here, and you should ask it in the QE forum. But as you know, you have >> to check the convergence with respect to k-point mesh, smearing etc. >> >> Togo >> >> >> On Thu, Mar 26, 2026 at 1:51 AM Gulshan Kumar via Phonopy-users >> <pho...@li...> wrote: >> > >> > Hi, >> > >> > I hope you’re doing well. >> > >> > I’m currently working on phase transitions in PbS using the Quantum ESPRESSO + phonopy QHA workflow. The transitions I’m studying are Fm-3m → Cmcm and Cmcm → Pm-3m. >> > >> > The Fm-3m → Cmcm phase boundary matches well with the literature, but for the Cmcm → Pm-3m transition I am getting a very large negative Clapeyron slope, which seems unphysical. >> > >> > For the setup, I used conventional cells with 8 atoms for Fm-3m and Cmcm, and a primitive cell with 2 atoms for Pm-3m. The supercells are 2×2×2 for Fm-3m and Cmcm, and 4×4×4 for Pm-3m. >> > >> > One concern is that the Pm-3m phase is metallic, unlike the other phases. I’m wondering if this could affect the QHA results. I’m also not sure if special care is needed for metallic systems (e.g., smearing, k-point convergence, etc.) when calculating phonons and Gibbs free energies. >> > Additionally, since the number of atoms differs between phases, I have normalized energies accordingly, but I’m still unsure if this could be contributing to the issue. >> > >> > Could this behavior be related to treating a metallic phase within QHA, or might there be something else I should check (e.g., convergence, normalization, or phonon stability)? >> > >> > I have attached the phase diagram for reference. >> > >> > Any suggestions would be really helpful. Thanks a lot! >> > _______________________________________________ >> > Phonopy-users mailing list >> > Pho...@li... >> > https://lists.sourceforge.net/lists/listinfo/phonopy-users >> >> >> >> -- >> Atsushi Togo >> >> >> _______________________________________________ >> Phonopy-users mailing list >> Pho...@li... >> https://lists.sourceforge.net/lists/listinfo/phonopy-users > > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users -- Atsushi Togo |
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From: Mahesh V. <mah...@gm...> - 2026-03-28 19:40:47
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Dear Developers, Greetings of the day I have querry regarding the use of phono3py for 2D material as below: 1. Should we use the dim for 2D material as 2 2 1 to generate supercells. 2. Can we use oncv pseudo potentials 3. I have followed above steps and when calculating cf3 . It shows that CF3 force has not been created, I have placed the disp.ymal file in same directory. Any help would be appreciated. Thanks and Regards Mahesh Verma |
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From: Gulshan K. <kum...@ii...> - 2026-03-28 11:00:54
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Thank you, sir, for the reply and time I am curious about the recently published paper; my high-pressure lattice constants and atomic positions are identical to the values they obtained because I am also using the same pseudopotentials. DOI: *https://doi.org/10.1038/s41467-026-69772-8 <https://doi.org/10.1038/s41467-026-69772-8>* name: Hidden pressure-stabilized lead reservoirs in Earth’s mantle. My concern is that they clearly stated that they used phonopy-QHA for the P-T diagram. Thank you On Thu, 26 Mar, 2026, 6:30 am Atsushi Togo, <atz...@gm...> wrote: > Hi, > > I don't know. But if you don't include electronic entropy in the free > energy, you may have to consider it. > The other possibility is due to strong anharmonicity, for which I have > recently mentioned in the mailing list, > https://sourceforge.net/p/phonopy/mailman/message/59313092/ > > For the details of the electronic calculation, it is out of the topic > here, and you should ask it in the QE forum. But as you know, you have > to check the convergence with respect to k-point mesh, smearing etc. > > Togo > > > On Thu, Mar 26, 2026 at 1:51 AM Gulshan Kumar via Phonopy-users > <pho...@li...> wrote: > > > > Hi, > > > > I hope you’re doing well. > > > > I’m currently working on phase transitions in PbS using the Quantum > ESPRESSO + phonopy QHA workflow. The transitions I’m studying are Fm-3m → > Cmcm and Cmcm → Pm-3m. > > > > The Fm-3m → Cmcm phase boundary matches well with the literature, but > for the Cmcm → Pm-3m transition I am getting a very large negative > Clapeyron slope, which seems unphysical. > > > > For the setup, I used conventional cells with 8 atoms for Fm-3m and > Cmcm, and a primitive cell with 2 atoms for Pm-3m. The supercells are 2×2×2 > for Fm-3m and Cmcm, and 4×4×4 for Pm-3m. > > > > One concern is that the Pm-3m phase is metallic, unlike the other > phases. I’m wondering if this could affect the QHA results. I’m also not > sure if special care is needed for metallic systems (e.g., smearing, > k-point convergence, etc.) when calculating phonons and Gibbs free energies. > > Additionally, since the number of atoms differs between phases, I have > normalized energies accordingly, but I’m still unsure if this could be > contributing to the issue. > > > > Could this behavior be related to treating a metallic phase within QHA, > or might there be something else I should check (e.g., convergence, > normalization, or phonon stability)? > > > > I have attached the phase diagram for reference. > > > > Any suggestions would be really helpful. Thanks a lot! > > _______________________________________________ > > Phonopy-users mailing list > > Pho...@li... > > https://lists.sourceforge.net/lists/listinfo/phonopy-users > > > > -- > Atsushi Togo > > > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users > |
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From: Atsushi T. <atz...@gm...> - 2026-03-26 00:57:35
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Hi, I don't know. But if you don't include electronic entropy in the free energy, you may have to consider it. The other possibility is due to strong anharmonicity, for which I have recently mentioned in the mailing list, https://sourceforge.net/p/phonopy/mailman/message/59313092/ For the details of the electronic calculation, it is out of the topic here, and you should ask it in the QE forum. But as you know, you have to check the convergence with respect to k-point mesh, smearing etc. Togo On Thu, Mar 26, 2026 at 1:51 AM Gulshan Kumar via Phonopy-users <pho...@li...> wrote: > > Hi, > > I hope you’re doing well. > > I’m currently working on phase transitions in PbS using the Quantum ESPRESSO + phonopy QHA workflow. The transitions I’m studying are Fm-3m → Cmcm and Cmcm → Pm-3m. > > The Fm-3m → Cmcm phase boundary matches well with the literature, but for the Cmcm → Pm-3m transition I am getting a very large negative Clapeyron slope, which seems unphysical. > > For the setup, I used conventional cells with 8 atoms for Fm-3m and Cmcm, and a primitive cell with 2 atoms for Pm-3m. The supercells are 2×2×2 for Fm-3m and Cmcm, and 4×4×4 for Pm-3m. > > One concern is that the Pm-3m phase is metallic, unlike the other phases. I’m wondering if this could affect the QHA results. I’m also not sure if special care is needed for metallic systems (e.g., smearing, k-point convergence, etc.) when calculating phonons and Gibbs free energies. > Additionally, since the number of atoms differs between phases, I have normalized energies accordingly, but I’m still unsure if this could be contributing to the issue. > > Could this behavior be related to treating a metallic phase within QHA, or might there be something else I should check (e.g., convergence, normalization, or phonon stability)? > > I have attached the phase diagram for reference. > > Any suggestions would be really helpful. Thanks a lot! > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users -- Atsushi Togo |
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From: Gulshan K. <kum...@ii...> - 2026-03-25 21:16:09
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Hi, I hope you’re doing well. I’m currently working on phase transitions in PbS using the Quantum ESPRESSO + phonopy QHA workflow. The transitions I’m studying are Fm-3m → Cmcm and Cmcm → Pm-3m. The Fm-3m → Cmcm phase boundary matches well with the literature, but for the Cmcm → Pm-3m transition, I am getting a very large negative Clapeyron slope, which seems unphysical. For the setup, I used conventional cells with 8 atoms for Fm-3m and Cmcm, and a primitive cell with 2 atoms for Pm-3m. The supercells are 2×2×2 for Fm-3m and Cmcm, and 4×4×4 for Pm-3m. One concern is that the Pm-3m phase is metallic, unlike the other phases. I’m wondering if this could affect the QHA results. I’m also not sure if special care is needed for metallic systems (e.g., smearing, k-point convergence, etc.) when calculating phonons and Gibbs free energies. Additionally, since the number of atoms differs between phases, I have normalized energies accordingly, but I’m still unsure if this could be contributing to the issue. Could this behavior be related to treating a metallic phase within QHA, or might there be something else I should check (e.g., convergence, normalization, or phonon stability)? I have attached the phase diagram for reference. Any suggestions would be really helpful. Thanks a lot! |
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From: Gulshan K. <kum...@ii...> - 2026-03-25 16:50:54
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Hi, I hope you’re doing well. I’m currently working on phase transitions in PbS using the Quantum ESPRESSO + phonopy QHA workflow. The transitions I’m studying are Fm-3m → Cmcm and Cmcm → Pm-3m. The Fm-3m → Cmcm phase boundary matches well with the literature, but for the Cmcm → Pm-3m transition I am getting a very large negative Clapeyron slope, which seems unphysical. For the setup, I used conventional cells with 8 atoms for Fm-3m and Cmcm, and a primitive cell with 2 atoms for Pm-3m. The supercells are 2×2×2 for Fm-3m and Cmcm, and 4×4×4 for Pm-3m. One concern is that the Pm-3m phase is metallic, unlike the other phases. I’m wondering if this could affect the QHA results. I’m also not sure if special care is needed for metallic systems (e.g., smearing, k-point convergence, etc.) when calculating phonons and Gibbs free energies. Additionally, since the number of atoms differs between phases, I have normalized energies accordingly, but I’m still unsure if this could be contributing to the issue. Could this behavior be related to treating a metallic phase within QHA, or might there be something else I should check (e.g., convergence, normalization, or phonon stability)? I have attached the phase diagram for reference. Any suggestions would be really helpful. Thanks a lot! |
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From: Vahid A. <vh2...@da...> - 2026-03-25 14:34:03
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Hi Professor Togo, Thank you for your guidance and suggestions for PbTe. I will look into the other codes you mentioned. Best, Vahid > On Mar 24, 2026, at 10:06 PM, Atsushi Togo <atz...@gm...> wrote: > > CAUTION: The Sender of this email is not from within Dalhousie. > > Hi, > > If I understand it correctly, PbTe is a strongly anharmonic crystal, > so it is not at all recommended to employ harmonic approximation at > different volumes (QHA called in phonopy, but this word can be used in > various ways...). Now there are known computational approaches like > self-consistent phonon theory and their implementation e.g. in ALAMODE > code or SSCHA code. You can compute free energies at volumes from > which you can estimate equilibrium volumes at temperatures. > > Togo > > On Wed, Mar 25, 2026 at 1:52 AM Vahid Askarpour <vh2...@da...> wrote: >> >> Dear Phonopy Users, >> >> In doing QHA for PbTe, both LDA and PBE pseudos of QE yield negative phonons at Gamma for +1% to 5% strain of the lattice constant. There is no negative frequencies for negative strains. In Fig. 7 of J. Chem. Phys. 143, 064710 (2015) paper, PbTe does show negative frequencies for PBE but not LDA at 300K with QHA. Is there a way around these negative phonons at positive strain or can I continue with the QHA calculation by ignoring them? >> >> Thanks, >> Vahid >> >> _______________________________________________ >> Phonopy-users mailing list >> Pho...@li... >> https://lists.sourceforge.net/lists/listinfo/phonopy-users > > > > -- > Atsushi Togo > > > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users |
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From: Atsushi T. <atz...@gm...> - 2026-03-25 01:06:51
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Hi, If I understand it correctly, PbTe is a strongly anharmonic crystal, so it is not at all recommended to employ harmonic approximation at different volumes (QHA called in phonopy, but this word can be used in various ways...). Now there are known computational approaches like self-consistent phonon theory and their implementation e.g. in ALAMODE code or SSCHA code. You can compute free energies at volumes from which you can estimate equilibrium volumes at temperatures. Togo On Wed, Mar 25, 2026 at 1:52 AM Vahid Askarpour <vh2...@da...> wrote: > > Dear Phonopy Users, > > In doing QHA for PbTe, both LDA and PBE pseudos of QE yield negative phonons at Gamma for +1% to 5% strain of the lattice constant. There is no negative frequencies for negative strains. In Fig. 7 of J. Chem. Phys. 143, 064710 (2015) paper, PbTe does show negative frequencies for PBE but not LDA at 300K with QHA. Is there a way around these negative phonons at positive strain or can I continue with the QHA calculation by ignoring them? > > Thanks, > Vahid > > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users -- Atsushi Togo |
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From: Vahid A. <vh2...@da...> - 2026-03-24 16:52:13
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Dear Phonopy Users, In doing QHA for PbTe, both LDA and PBE pseudos of QE yield negative phonons at Gamma for +1% to 5% strain of the lattice constant. There is no negative frequencies for negative strains. In Fig. 7 of J. Chem. Phys. 143, 064710 (2015) paper, PbTe does show negative frequencies for PBE but not LDA at 300K with QHA. Is there a way around these negative phonons at positive strain or can I continue with the QHA calculation by ignoring them? Thanks, Vahid |
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From: Vahid A. <vh2...@da...> - 2026-03-21 14:41:33
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Thank you Professor Togo for this clarification. Vahid > On Mar 21, 2026, at 9:47 AM, Atsushi Togo <atz...@gm...> wrote: > > CAUTION: The Sender of this email is not from within Dalhousie. > > Hi, > > Those energies are supposed to be obtained from another set of total > energy calculations of primitive cells at volumes. > > Togo > > On Sat, Mar 21, 2026 at 8:23 PM Vahid Askarpour <vh2...@da...> wrote: >> >> Dear Phonopy Users, >> >> Following the NaCl-QE example for QHA with QE, at a given volume, two supercells are created by phonopy for force constant calculations. Each supercell has a different “total energy”. Do we use the average of the two energies in the e-v.dat file for the given volume? Or do we need a separate force constant calculation on the unperturbed supercell? >> >> Thanks, >> Vahid >> _______________________________________________ >> Phonopy-users mailing list >> Pho...@li... >> https://lists.sourceforge.net/lists/listinfo/phonopy-users > > > > -- > Atsushi Togo > > > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users |
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From: Atsushi T. <atz...@gm...> - 2026-03-21 12:48:05
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Hi, Those energies are supposed to be obtained from another set of total energy calculations of primitive cells at volumes. Togo On Sat, Mar 21, 2026 at 8:23 PM Vahid Askarpour <vh2...@da...> wrote: > > Dear Phonopy Users, > > Following the NaCl-QE example for QHA with QE, at a given volume, two supercells are created by phonopy for force constant calculations. Each supercell has a different “total energy”. Do we use the average of the two energies in the e-v.dat file for the given volume? Or do we need a separate force constant calculation on the unperturbed supercell? > > Thanks, > Vahid > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users -- Atsushi Togo |
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From: Vahid A. <vh2...@da...> - 2026-03-21 11:23:17
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Dear Phonopy Users, Following the NaCl-QE example for QHA with QE, at a given volume, two supercells are created by phonopy for force constant calculations. Each supercell has a different “total energy”. Do we use the average of the two energies in the e-v.dat file for the given volume? Or do we need a separate force constant calculation on the unperturbed supercell? Thanks, Vahid |
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From: Naveena P.S. <nav...@gm...> - 2026-02-24 12:17:39
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Hi, I have included the required files in the attached .zip folder. I am attempting to modulate (i.e., displace) the atomic positions in a 2×2×1 supercell of a TiS₂ monolayer. For this purpose, I started from the optimised unit cell input file (TiS2_primitive_scf.in). Since I obtained a soft phonon mode at the M high-symmetry point (0.5, 0, 0), I need to construct a 2×2×1 supercell and modulate the atomic positions according to the eigenvector of this soft mode. I have included the phonon output files from Quantum ESPRESSO, which contain information about the soft mode and its eigenvectors. However, I am unsure which file should be used for this purpose, whether I should refer to the .modesfile or the corresponding .dyn* file of the soft mode. For reference, I have included all the relevant files in the folder. So far, I have used the following command: phonopy --qe -c TiS2_primitive_scf.in --readfc --dim="2 2 1" --qpoints 0.5000 0.2887 0.0000 --bi 1 --amplitude 0.03 --modulation 2 2 1, 0.5000 0.2887 0.0000 1 0.03 0 -v However, this results in an error. I would like to use the modulation command correctly, but I am not sure how to configure it properly within Phonopy. I hope this clarifies my issue and helps you understand the problem. With regards, Naveena TiS2_1.zip <https://drive.google.com/file/d/1yPfp2CqdeS0bFJOPuDqOcOOozTB8HtP1/view?usp=drive_web> On Fri, Feb 13, 2026 at 9:00 AM Atsushi Togo <atz...@gm...> wrote: > Hi, > > > Do you need the input files? > > Maybe. Please think about how you could motivate me to solve your problem. > > Togo > > On Fri, Feb 13, 2026 at 4:18 PM Naveena P.Sivam <nav...@gm...> > wrote: > >> Hi >> >> I followed the instructions in the document, but I am unable to modulate >> the atom. It shows errors. Do you need the input files? >> >> -naveena >> >> On Fri 13 Feb 2026 at 08:16, Atsushi Togo <atz...@gm...> wrote: >> >>> Hi, >>> >>> > How to perform this? >>> >>> It is written in the documentation. >>> >>> > if you need any additional input, let me know. >>> >>> I need to reproduce your issue. >>> >>> Togo >>> >>> On Fri, Feb 13, 2026 at 1:59 PM Naveena P.Sivam <nav...@gm...> >>> wrote: >>> >>>> Hi, >>>> >>>> I need help to perform atomic modulation with a specific q-point >>>> (pre-processing after DFPT calculation using QE) using phonopy. MODULATION >>>> = (command). How to perform this? >>>> >>>> if you need any additional input, let me know. >>>> >>>> with regards >>>> Naveena >>>> >>>> On Fri, Feb 13, 2026 at 4:38 AM Atsushi Togo <atz...@gm...> >>>> wrote: >>>> >>>>> Hi, >>>>> >>>>> Information is too little to see the issue. So it is difficult to >>>>> answer. >>>>> >>>>> > I found your youtube videos >>>>> >>>>> I think those are not my youtube videos. >>>>> >>>>> Togo >>>>> >>>>> >>>>> On Fri, Feb 13, 2026 at 1:22 AM Naveena P.Sivam <nav...@gm...> >>>>> wrote: >>>>> >>>>>> Hello >>>>>> I am trying to do atomic modulation (atomic displacement) with >>>>>> respect to the normal mode at the specific q point. I tried to use this >>>>>> command line: >>>>>> phonopy --qe --modulation 2 2 1, 0.000000000 0.433012702 >>>>>> 0.000000000 1 0.03 0 -c TiS2_primitive_scf.in --dim 2 2 1 -v. >>>>>> >>>>>> But it provides error like this: >>>>>> >>>>>> phonopy --qe --modulation 2 2 1, 0.000000000 0.433012702 >>>>>> 0.000000000 1 0.03 0 -c TiS2_primitive_scf.in --dim 2 2 1 -v >>>>>> _ >>>>>> _ __ | |__ ___ _ __ ___ _ __ _ _ >>>>>> | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | >>>>>> | |_) | | | | (_) | | | | (_) || |_) | |_| | >>>>>> | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | >>>>>> |_| |_| |___/ >>>>>> 2.47.1 >>>>>> >>>>>> -------------------------[time 2026-02-06 >>>>>> 16:53:41]------------------------- >>>>>> Compiled with OpenMP support (max 8 threads). >>>>>> Python version 3.11.11 >>>>>> Spglib version 2.7.0 >>>>>> >>>>>> Calculator interface: qe >>>>>> Crystal structure was read from "TiS2_primitive_scf.in". >>>>>> Unit of length: au >>>>>> Modulation mode >>>>>> Settings: >>>>>> Supercell: [2 2 1] >>>>>> Spacegroup: P-3m1 (164) >>>>>> Number of symmetry operations in supercell: 48 >>>>>> ------------------------------ primitive cell >>>>>> ------------------------------ >>>>>> Lattice vectors: >>>>>> a 6.460973493253429 0.000000000000000 0.000000000000000 >>>>>> b -3.230486746626715 5.595367178253872 0.000000000000000 >>>>>> c 0.000000000000000 0.000000000000000 34.015070466894429 >>>>>> Atomic positions (fractional): >>>>>> *1 Ti 0.00000000000000 0.00000000000000 0.50000000000000 47.867 >>>>>> *2 S 0.66666700000000 0.33333300000000 0.57891028530000 32.065 >>>>>> 3 S 0.33333300000000 0.66666700000000 0.42108971470000 32.065 >>>>>> -------------------------------- unit cell >>>>>> --------------------------------- >>>>>> Lattice vectors: >>>>>> a 6.460973493253429 0.000000000000000 0.000000000000000 >>>>>> b -3.230486746626715 5.595367178253872 0.000000000000000 >>>>>> c 0.000000000000000 0.000000000000000 34.015070466894429 >>>>>> Atomic positions (fractional): >>>>>> *1 Ti 0.00000000000000 0.00000000000000 0.50000000000000 >>>>>> 47.867 > 1 >>>>>> *2 S 0.66666700000000 0.33333300000000 0.57891028530000 >>>>>> 32.065 > 2 >>>>>> 3 S 0.33333300000000 0.66666700000000 0.42108971470000 >>>>>> 32.065 > 3 >>>>>> -------------------------------- super cell >>>>>> -------------------------------- >>>>>> Lattice vectors: >>>>>> a 12.921946986506859 0.000000000000000 0.000000000000000 >>>>>> b -6.460973493253429 11.190734356507743 0.000000000000000 >>>>>> c 0.000000000000000 0.000000000000000 34.015070466894429 >>>>>> Atomic positions (fractional): >>>>>> *1 Ti 0.00000000000000 0.00000000000000 0.50000000000000 >>>>>> 47.867 > 1 >>>>>> 2 Ti 0.50000000000000 0.00000000000000 0.50000000000000 >>>>>> 47.867 > 1 >>>>>> 3 Ti 0.00000000000000 0.50000000000000 0.50000000000000 >>>>>> 47.867 > 1 >>>>>> 4 Ti 0.50000000000000 0.50000000000000 0.50000000000000 >>>>>> 47.867 > 1 >>>>>> *5 S 0.33333350000000 0.16666650000000 0.57891028530000 >>>>>> 32.065 > 2 >>>>>> 6 S 0.83333350000000 0.16666650000000 0.57891028530000 >>>>>> 32.065 > 2 >>>>>> 7 S 0.33333350000000 0.66666650000000 0.57891028530000 >>>>>> 32.065 > 2 >>>>>> 8 S 0.83333350000000 0.66666650000000 0.57891028530000 >>>>>> 32.065 > 2 >>>>>> 9 S 0.16666650000000 0.33333350000000 0.42108971470000 >>>>>> 32.065 > 3 >>>>>> 10 S 0.66666650000000 0.33333350000000 0.42108971470000 >>>>>> 32.065 > 3 >>>>>> 11 S 0.16666650000000 0.83333350000000 0.42108971470000 >>>>>> 32.065 > 3 >>>>>> 12 S 0.66666650000000 0.83333350000000 0.42108971470000 >>>>>> 32.065 > 3 >>>>>> >>>>>> ---------------------------------------------------------------------------- >>>>>> ___ _ __ _ __ ___ _ __ >>>>>> / _ \ '__| '__/ _ \| '__| >>>>>> | __/ | | | | (_) | | >>>>>> \___|_| |_| \___/|_|. >>>>>> >>>>>> Also, it creates modulation.conf which contains: >>>>>> DIM = 2 2 1 >>>>>> MODULATION = 2 2 1, 0 0.433012702 0 1 0.03 0. >>>>>> >>>>>> Also, I found this idea from: >>>>>> https://phonopy.github.io/phonopy/setting-tags.html. >>>>>> >>>>>> Just today I started to use this package and I found your youtube >>>>>> videos discussing how to use phonopy with qe. So I thought I could ask for >>>>>> some help. kindly help me if you have any ideas. >>>>>> >>>>>> with regards >>>>>> Naveena P. >>>>>> _______________________________________________ >>>>>> Phonopy-users mailing list >>>>>> Pho...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >>>>>> >>>>> >>>>> >>>>> -- >>>>> Atsushi Togo >>>>> _______________________________________________ >>>>> Phonopy-users mailing list >>>>> Pho...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >>>>> >>>> _______________________________________________ >>>> Phonopy-users mailing list >>>> Pho...@li... >>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >>>> >>> >>> >>> -- >>> Atsushi Togo >>> _______________________________________________ >>> Phonopy-users mailing list >>> Pho...@li... >>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >>> >> _______________________________________________ >> Phonopy-users mailing list >> Pho...@li... >> https://lists.sourceforge.net/lists/listinfo/phonopy-users >> > > > -- > Atsushi Togo > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users > |
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From: Naveena P.S. <nav...@gm...> - 2026-02-23 10:28:35
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Hi, I have included the required files in the attached .zip folder. I am attempting to modulate (i.e., displace) the atomic positions in a 2×2×1 supercell of a TiS₂ monolayer. For this purpose, I started from the optimised unit cell input file (TiS2_primitive_scf.in). Since I obtained a soft phonon mode at the M high-symmetry point (0.5, 0, 0), I need to construct a 2×2×1 supercell and modulate the atomic positions according to the eigenvector of this soft mode. I have included the phonon output files from Quantum ESPRESSO, which contain information about the soft mode and its eigenvectors. However, I am unsure which file should be used for this purpose, whether I should refer to the .modesfile or the corresponding .dyn* file of the soft mode. For reference, I have included all the relevant files in the folder. So far, I have used the following command: phonopy --qe -c TiS2_primitive_scf.in --readfc --dim="2 2 1" --qpoints 0.5000 0.2887 0.0000 --bi 1 --amplitude 0.03 --modulation 2 2 1, 0.5000 0.2887 0.0000 1 0.03 0 -v However, this results in an error. I would like to use the modulation command correctly, but I am not sure how to configure it properly within Phonopy. I hope this clarifies my issue and helps you understand the problem. With regards, Naveena TiS2_1.zip <https://drive.google.com/file/d/1yPfp2CqdeS0bFJOPuDqOcOOozTB8HtP1/view?usp=drive_web> On Fri, Feb 13, 2026 at 9:00 AM Atsushi Togo <atz...@gm...> wrote: > Hi, > > > Do you need the input files? > > Maybe. Please think about how you could motivate me to solve your problem. > > Togo > > On Fri, Feb 13, 2026 at 4:18 PM Naveena P.Sivam <nav...@gm...> > wrote: > >> Hi >> >> I followed the instructions in the document, but I am unable to modulate >> the atom. It shows errors. Do you need the input files? >> >> -naveena >> >> On Fri 13 Feb 2026 at 08:16, Atsushi Togo <atz...@gm...> wrote: >> >>> Hi, >>> >>> > How to perform this? >>> >>> It is written in the documentation. >>> >>> > if you need any additional input, let me know. >>> >>> I need to reproduce your issue. >>> >>> Togo >>> >>> On Fri, Feb 13, 2026 at 1:59 PM Naveena P.Sivam <nav...@gm...> >>> wrote: >>> >>>> Hi, >>>> >>>> I need help to perform atomic modulation with a specific q-point >>>> (pre-processing after DFPT calculation using QE) using phonopy. MODULATION >>>> = (command). How to perform this? >>>> >>>> if you need any additional input, let me know. >>>> >>>> with regards >>>> Naveena >>>> >>>> On Fri, Feb 13, 2026 at 4:38 AM Atsushi Togo <atz...@gm...> >>>> wrote: >>>> >>>>> Hi, >>>>> >>>>> Information is too little to see the issue. So it is difficult to >>>>> answer. >>>>> >>>>> > I found your youtube videos >>>>> >>>>> I think those are not my youtube videos. >>>>> >>>>> Togo >>>>> >>>>> >>>>> On Fri, Feb 13, 2026 at 1:22 AM Naveena P.Sivam <nav...@gm...> >>>>> wrote: >>>>> >>>>>> Hello >>>>>> I am trying to do atomic modulation (atomic displacement) with >>>>>> respect to the normal mode at the specific q point. I tried to use this >>>>>> command line: >>>>>> phonopy --qe --modulation 2 2 1, 0.000000000 0.433012702 >>>>>> 0.000000000 1 0.03 0 -c TiS2_primitive_scf.in --dim 2 2 1 -v. >>>>>> >>>>>> But it provides error like this: >>>>>> >>>>>> phonopy --qe --modulation 2 2 1, 0.000000000 0.433012702 >>>>>> 0.000000000 1 0.03 0 -c TiS2_primitive_scf.in --dim 2 2 1 -v >>>>>> _ >>>>>> _ __ | |__ ___ _ __ ___ _ __ _ _ >>>>>> | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | >>>>>> | |_) | | | | (_) | | | | (_) || |_) | |_| | >>>>>> | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | >>>>>> |_| |_| |___/ >>>>>> 2.47.1 >>>>>> >>>>>> -------------------------[time 2026-02-06 >>>>>> 16:53:41]------------------------- >>>>>> Compiled with OpenMP support (max 8 threads). >>>>>> Python version 3.11.11 >>>>>> Spglib version 2.7.0 >>>>>> >>>>>> Calculator interface: qe >>>>>> Crystal structure was read from "TiS2_primitive_scf.in". >>>>>> Unit of length: au >>>>>> Modulation mode >>>>>> Settings: >>>>>> Supercell: [2 2 1] >>>>>> Spacegroup: P-3m1 (164) >>>>>> Number of symmetry operations in supercell: 48 >>>>>> ------------------------------ primitive cell >>>>>> ------------------------------ >>>>>> Lattice vectors: >>>>>> a 6.460973493253429 0.000000000000000 0.000000000000000 >>>>>> b -3.230486746626715 5.595367178253872 0.000000000000000 >>>>>> c 0.000000000000000 0.000000000000000 34.015070466894429 >>>>>> Atomic positions (fractional): >>>>>> *1 Ti 0.00000000000000 0.00000000000000 0.50000000000000 47.867 >>>>>> *2 S 0.66666700000000 0.33333300000000 0.57891028530000 32.065 >>>>>> 3 S 0.33333300000000 0.66666700000000 0.42108971470000 32.065 >>>>>> -------------------------------- unit cell >>>>>> --------------------------------- >>>>>> Lattice vectors: >>>>>> a 6.460973493253429 0.000000000000000 0.000000000000000 >>>>>> b -3.230486746626715 5.595367178253872 0.000000000000000 >>>>>> c 0.000000000000000 0.000000000000000 34.015070466894429 >>>>>> Atomic positions (fractional): >>>>>> *1 Ti 0.00000000000000 0.00000000000000 0.50000000000000 >>>>>> 47.867 > 1 >>>>>> *2 S 0.66666700000000 0.33333300000000 0.57891028530000 >>>>>> 32.065 > 2 >>>>>> 3 S 0.33333300000000 0.66666700000000 0.42108971470000 >>>>>> 32.065 > 3 >>>>>> -------------------------------- super cell >>>>>> -------------------------------- >>>>>> Lattice vectors: >>>>>> a 12.921946986506859 0.000000000000000 0.000000000000000 >>>>>> b -6.460973493253429 11.190734356507743 0.000000000000000 >>>>>> c 0.000000000000000 0.000000000000000 34.015070466894429 >>>>>> Atomic positions (fractional): >>>>>> *1 Ti 0.00000000000000 0.00000000000000 0.50000000000000 >>>>>> 47.867 > 1 >>>>>> 2 Ti 0.50000000000000 0.00000000000000 0.50000000000000 >>>>>> 47.867 > 1 >>>>>> 3 Ti 0.00000000000000 0.50000000000000 0.50000000000000 >>>>>> 47.867 > 1 >>>>>> 4 Ti 0.50000000000000 0.50000000000000 0.50000000000000 >>>>>> 47.867 > 1 >>>>>> *5 S 0.33333350000000 0.16666650000000 0.57891028530000 >>>>>> 32.065 > 2 >>>>>> 6 S 0.83333350000000 0.16666650000000 0.57891028530000 >>>>>> 32.065 > 2 >>>>>> 7 S 0.33333350000000 0.66666650000000 0.57891028530000 >>>>>> 32.065 > 2 >>>>>> 8 S 0.83333350000000 0.66666650000000 0.57891028530000 >>>>>> 32.065 > 2 >>>>>> 9 S 0.16666650000000 0.33333350000000 0.42108971470000 >>>>>> 32.065 > 3 >>>>>> 10 S 0.66666650000000 0.33333350000000 0.42108971470000 >>>>>> 32.065 > 3 >>>>>> 11 S 0.16666650000000 0.83333350000000 0.42108971470000 >>>>>> 32.065 > 3 >>>>>> 12 S 0.66666650000000 0.83333350000000 0.42108971470000 >>>>>> 32.065 > 3 >>>>>> >>>>>> ---------------------------------------------------------------------------- >>>>>> ___ _ __ _ __ ___ _ __ >>>>>> / _ \ '__| '__/ _ \| '__| >>>>>> | __/ | | | | (_) | | >>>>>> \___|_| |_| \___/|_|. >>>>>> >>>>>> Also, it creates modulation.conf which contains: >>>>>> DIM = 2 2 1 >>>>>> MODULATION = 2 2 1, 0 0.433012702 0 1 0.03 0. >>>>>> >>>>>> Also, I found this idea from: >>>>>> https://phonopy.github.io/phonopy/setting-tags.html. >>>>>> >>>>>> Just today I started to use this package and I found your youtube >>>>>> videos discussing how to use phonopy with qe. So I thought I could ask for >>>>>> some help. kindly help me if you have any ideas. >>>>>> >>>>>> with regards >>>>>> Naveena P. >>>>>> _______________________________________________ >>>>>> Phonopy-users mailing list >>>>>> Pho...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >>>>>> >>>>> >>>>> >>>>> -- >>>>> Atsushi Togo >>>>> _______________________________________________ >>>>> Phonopy-users mailing list >>>>> Pho...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >>>>> >>>> _______________________________________________ >>>> Phonopy-users mailing list >>>> Pho...@li... >>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >>>> >>> >>> >>> -- >>> Atsushi Togo >>> _______________________________________________ >>> Phonopy-users mailing list >>> Pho...@li... >>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >>> >> _______________________________________________ >> Phonopy-users mailing list >> Pho...@li... >> https://lists.sourceforge.net/lists/listinfo/phonopy-users >> > > > -- > Atsushi Togo > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users > |
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From: Atsushi T. <atz...@gm...> - 2026-02-23 05:44:12
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Hi, I see. The phonopy message is not kind. Togo On Mon, Feb 23, 2026 at 2:32 PM Guihyun Han <han...@gm...> wrote: > > Hi, > > Thank you for the response. > It is actually working with your command. > Sorry, I didn’t put the “-d” for the dimension command options. > > Thank you for the fixing. > > Guihyun Han > > > 2026. 2. 23. 14:07, Atsushi Togo <atz...@gm...> 작성: > > > > Hi, > > > > The following is my result. What is yours? > > > > % phonopy -c bccfe.txt --fleur -d --dim 2 2 2 > > _ > > _ __ | |__ ___ _ __ ___ _ __ _ _ > > | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | > > | |_) | | | | (_) | | | | (_) || |_) | |_| | > > | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | > > |_| |_| |___/ > > 2.48.0 > > > > -------------------------[time 2026-02-23 14:06:20]------------------------- > > Compiled with OpenMP support (max 10 threads). > > Python version 3.13.2 > > Spglib version 2.6.1 > > > > Calculator interface: fleur > > Crystal structure was read from "bccfe.txt". > > Unit of length: au > > Displacements creation mode > > Systematic displacements > > Settings: > > Supercell: [2 2 2] > > Spacegroup: Im-3m (229) > > Number of symmetry operations in supercell: 384 > > Use -v option to watch primitive cell, unit cell, and supercell structures. > > > > Generated number of supercells: 1 > > "phonopy_disp.yaml" and supercells have been created. > > > > Summary of calculation was written in "phonopy_disp.yaml". > > -------------------------[time 2026-02-23 14:06:20]------------------------- > > _ > > ___ _ __ __| | > > / _ \ '_ \ / _` | > > | __/ | | | (_| | > > \___|_| |_|\__,_| > > > > On Mon, Feb 23, 2026 at 1:19 PM Guihyun Han <han...@gm...> wrote: > >> > >> Hi, > >> > >> Sorry for the file. I misunderstood your intention. > >> The file that I sent is just for simple calculation of FLEUR not for Phonopy. > >> > >> I’ve attached bccFe.txt and inp.xml. > >> This files can be used for Phonopy but gives error. > >> > >> Thank you in advance > >> Guihyun Han > >> > >> > >> > >> > >>> 2026. 2. 21. 09:50, Atsushi Togo <atz...@gm...> 작성: > >>> > >>> Hi, > >>> > >>> &lattice latsys='cF', a0=1.8897269, a=5.43 / > >>> > >>> is not supported. > >>> > >>> The phonopy fleur interface documentation says: > >>> > >>> "An important thing to note is: The bravais matrix needs to be set > >>> directly via the second method proposed in the reference." > >>> > >>> So you have to specify basis vectors explicitly. This document was not > >>> written by me, so I don't understand the detailed format. Is this your > >>> problem? > >>> > >>> Togo > >>> > >>> On Fri, Feb 20, 2026 at 6:11 PM Guihyun Han <han...@gm...> wrote: > >>>> > >>>> Hi, > >>>> > >>>> I’d like to provide the inputs. I can provide primitive cell calculations. > >>>> I attached simple system which is diamond Si. > >>>> > >>>> The situation is following. > >>>> First, I have to make supercell with inpSi.txt using Phonopy. (supercell-00x … are expected) > >>>> Second, with supercell-00x file, inp.xml will be made then calculate the forces. > >>>> However, Phonopy does not give the supercell where I cannot start the supercell calculations. > >>>> > >>>> The basic step of primitive cell calculation is following. > >>>> 1. inpSi.txt is the basic information for making inp.xml (It can be done with %inpgen -f inp.txt) > >>>> 2. inp.xml îs the input for DFT calculations, which means FLEUR use inp.xml for input > >>>> > >>>> Thank you in advance > >>>> Guihyun Han > >>>> > >>>>> 2026. 2. 20. 16:36, Atsushi Togo <atz...@gm...> 작성: > >>>>> > >>>>> Hi, > >>>>> > >>>>>> However, it still gives error (the error has no information) and does not give the supercell with displacements. > >>>>> > >>>>> To fix your issue, I need to be able to reproduce your calculation or mimic it. > >>>>> > >>>>> Togo > >>>>> > >>>>> On Fri, Feb 20, 2026 at 4:00 PM Guihyun Han <han...@gm...> wrote: > >>>>>> > >>>>>> Hi, > >>>>>> > >>>>>> I’ve tried with the command that you sent and now the Phonopy reads the structure properly. > >>>>>> Thank you for fixing it. > >>>>>> However, it still gives error (the error has no information) and does not give the supercell with displacements. > >>>>>> > >>>>>> Guihyun Han > >>>>>> > >>>>>>> 2026. 2. 19. 15:12, Atsushi Togo <atz...@gm...> 작성: > >>>>>>> > >>>>>>> Hi, > >>>>>>> > >>>>>>> Could you try the following? But please do not expect much to me, > >>>>>>> because I am not a user of fleur. > >>>>>>> > >>>>>>> % phonopy -c Pa3_in.txt --symmetry --fleur|head -n 5 > >>>>>>> phonopy_version: '2.48.0' > >>>>>>> space_group_type: 'Pa-3' > >>>>>>> space_group_number: 205 > >>>>>>> point_group_type: 'm-3' > >>>>>>> space_group_operations: > >>>>>>> > >>>>>>> % phonopy -c bccfe_in.txt --symmetry --fleur|head -n 5 > >>>>>>> phonopy_version: '2.48.0' > >>>>>>> space_group_type: 'Im-3m' > >>>>>>> space_group_number: 229 > >>>>>>> point_group_type: 'm-3m' > >>>>>>> space_group_operations: > >>>>>>> > >>>>>>> Togo > >>>>>>> > >>>>>>> On Thu, Feb 19, 2026 at 2:28 PM Guihyun Han <han...@gm...> wrote: > >>>>>>>> > >>>>>>>> Hi, > >>>>>>>> > >>>>>>>> Thank you for the fixed version. > >>>>>>>> I’ve tried to use new version, but it still has problem. > >>>>>>>> > >>>>>>>> First, I think reading the structure still has problem. > >>>>>>>> In the file of Pa3_out.txt, it still reads Pa-3 structure as Pm-3m which is simple cubic. > >>>>>>>> > >>>>>>>> Second, for the FORCES file, in my understanding of using Phonopy, forces are obtained after supercell calculations. > >>>>>>>> As far as I know, the work flow is > >>>>>>>> 1. Generate supercell with displacement > >>>>>>>> > >>>>>>>> phonopy --fleur -c bccfe.txt --pm --dim="2 0 0 0 2 0 0 0 2" > >>>>>>>> > >>>>>>>> 2. run the calculation with generated supercell > >>>>>>>> 3. make FORCE_SETS with generated FORCES > >>>>>>>> > >>>>>>>> phonopy --fleur -f FORCE > >>>>>>>> > >>>>>>>> > >>>>>>>> However, phonopy requires FORCES in the first step which is generating supercell. > >>>>>>>> I’ve attached basic input of FLEUR for bcc Fe and Pa-3 structure. > >>>>>>>> > >>>>>>>> > >>>>>>>> Thank you in advance, > >>>>>>>> Guihyun Han > >>>>>>>> > >>>>>>>> 2026. 2. 13. 17:39, Atsushi Togo <atz...@gm...> 작성: > >>>>>>>> > >>>>>>>> Hi, > >>>>>>>> > >>>>>>>> I tried to fix it, which you can find it in the develop branch of the > >>>>>>>> phonopy github repository: > >>>>>>>> https://github.com/phonopy/phonopy/pull/722 > >>>>>>>> > >>>>>>>> Since I have no input/output data except for Al example, my fix may > >>>>>>>> not be good enough. I also don't know the format of FORCES file, too. > >>>>>>>> It seems the format has changed recently, and the current one is > >>>>>>>> https://github.com/phonopy/phonopy/pull/559. > >>>>>>>> > >>>>>>>> Togo > >>>>>>>> > >>>>>>>> On Fri, Feb 13, 2026 at 5:29 PM Guihyun Han <han...@gm...> wrote: > >>>>>>>> > >>>>>>>> > >>>>>>>> Hi, > >>>>>>>> > >>>>>>>> Thank you for the response. > >>>>>>>> I’d be grateful if you could fix it. > >>>>>>>> And I’d like to help fixing it. > >>>>>>>> > >>>>>>>> I’ve tried calculation with bcc Fe and it worked. > >>>>>>>> I think simple structures such as bcc, fcc, hcp , simple cubic structures are working well. > >>>>>>>> The case of space group 205 Pa-3, lattice vectors are same as simple cubic but the difference is position of atoms. > >>>>>>>> And the output gives the supercell of simple cubic structure. > >>>>>>>> In my opinion, reading the position of atom has some bug. > >>>>>>>> > >>>>>>>> Thank you in advance, > >>>>>>>> Guihyun Han > >>>>>>>> > >>>>>>>> 2026. 2. 13. 12:20, Atsushi Togo <atz...@gm...> 작성: > >>>>>>>> > >>>>>>>> Hi, > >>>>>>>> > >>>>>>>> The FLEUR interface in phonopy is not written well. > >>>>>>>> I may try to fix it if you like, but I have really no idea about the > >>>>>>>> input and output file. There is one example of Al for Fluer interface, > >>>>>>>> but in fact parsing forces doesn't work. So if you are a FLEUR user > >>>>>>>> and willing to help fix it, please let me know. > >>>>>>>> > >>>>>>>> Togo > >>>>>>>> > >>>>>>>> On Thu, Feb 12, 2026 at 10:25 PM Atsushi Togo <atz...@gm...> wrote: > >>>>>>>> > >>>>>>>> > >>>>>>>> Hi, > >>>>>>>> > >>>>>>>> I am not familiar with fleur, but I guess it is a bug. > >>>>>>>> > >>>>>>>> Togo > >>>>>>>> > >>>>>>>> On Thu, Feb 12, 2026 at 3:29 PM Guihyun Han <han...@gm...> wrote: > >>>>>>>> > >>>>>>>> > >>>>>>>> Dear phonopy developers > >>>>>>>> > >>>>>>>> Hi, I’m using FLEUR for DFT calculations and trying to use phonopy for phonon dispersion > >>>>>>>> I’m writing this mail because I have one problem with making supercells. > >>>>>>>> > >>>>>>>> I made same structure file as input for FLEUR and VASP and these are attached below. > >>>>>>>> > >>>>>>>> The problem I have is that phonopy gives different out for FLEUR and VASP input files. > >>>>>>>> The structure is Pa-3 (No. 205). > >>>>>>>> > >>>>>>>> For vasp POSCAR, phonopy read the POSCAR as the Pa-3 (205). > >>>>>>>> But for FLEUR, phonopy read the input as simple cubic Pm-3m (221). > >>>>>>>> And I think because of this different symmetry, I cannot get the proper supercell for FLEUR. > >>>>>>>> > >>>>>>>> I’ve read some documentations and phonopy is using spglib and there is no reason to give different result. > >>>>>>>> I hope I’m not doing something wrong. > >>>>>>>> How can I make proper supercell with FLEUR input? > >>>>>>>> > >>>>>>>> Thank you in advance and best regards > >>>>>>>> Guihyun > >>>>>>>> > >>>>>>>> > >>>>>>>> FLEUR > >>>>>>>> > >>>>>>>> MnS2 Pa3 > >>>>>>>> > >>>>>>>> > >>>>>>>> 1.0 0.0 0.0 ! a1 > >>>>>>>> > >>>>>>>> 0.0 1.0 0.0 ! a2 > >>>>>>>> > >>>>>>>> 0.0 0.0 1.0 ! a3 > >>>>>>>> > >>>>>>>> 6.15 ! aa > >>>>>>>> > >>>>>>>> 1.0 1.0 1.0 ! scale > >>>>>>>> > >>>>>>>> > >>>>>>>> 12 ! num atoms > >>>>>>>> > >>>>>>>> 25.1 0.000 0.000 0.000 > >>>>>>>> > >>>>>>>> 25.1 0.500 0.500 0.000 > >>>>>>>> > >>>>>>>> 25.1 0.000 0.500 0.500 > >>>>>>>> > >>>>>>>> 25.1 0.500 0.000 0.500 > >>>>>>>> > >>>>>>>> 16 0.600000000 0.600000000 0.600000000 > >>>>>>>> > >>>>>>>> 16 0.400000000 0.400000000 0.400000000 > >>>>>>>> > >>>>>>>> 16 0.900000000 0.400000000 0.100000000 > >>>>>>>> > >>>>>>>> 16 0.100000000 0.600000000 0.900000000 > >>>>>>>> > >>>>>>>> 16 0.400000000 0.100000000 0.900000000 > >>>>>>>> > >>>>>>>> 16 0.600000000 0.900000000 0.100000000 > >>>>>>>> > >>>>>>>> 16 0.100000000 0.900000000 0.400000000 > >>>>>>>> > >>>>>>>> 16 0.900000000 0.100000000 0.600000000 > >>>>>>>> > >>>>>>>> VASP > >>>>>>>> > >>>>>>>> MnS2 > >>>>>>>> > >>>>>>>> 1.0 > >>>>>>>> > >>>>>>>> 6.1500000000 0.0000000000 0.0000000000 > >>>>>>>> > >>>>>>>> 0.0000000000 6.1500000000 0.0000000000 > >>>>>>>> > >>>>>>>> 0.0000000000 0.0000000000 6.1500000000 > >>>>>>>> > >>>>>>>> Mn S > >>>>>>>> > >>>>>>>> 4 8 > >>>>>>>> > >>>>>>>> Direct > >>>>>>>> > >>>>>>>> 0.000000000 0.000000000 0.000000000 > >>>>>>>> > >>>>>>>> 0.500000000 0.500000000 0.000000000 > >>>>>>>> > >>>>>>>> 0.000000000 0.500000000 0.500000000 > >>>>>>>> > >>>>>>>> 0.500000000 0.000000000 0.500000000 > >>>>>>>> > >>>>>>>> 0.600000000 0.600000000 0.600000000 > >>>>>>>> > >>>>>>>> 0.400000000 0.400000000 0.400000000 > >>>>>>>> > >>>>>>>> 0.900000000 0.400000000 0.100000000 > >>>>>>>> > >>>>>>>> 0.100000000 0.600000000 0.900000000 > >>>>>>>> > >>>>>>>> 0.400000000 0.100000000 0.900000000 > >>>>>>>> > >>>>>>>> 0.600000000 0.900000000 0.100000000 > >>>>>>>> > >>>>>>>> 0.100000000 0.900000000 0.400000000 > >>>>>>>> > >>>>>>>> 0.900000000 0.100000000 0.600000000 > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> _______________________________________________ > >>>>>>>> Phonopy-users mailing list > >>>>>>>> Pho...@li... > >>>>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> -- > >>>>>>>> Atsushi Togo > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> -- > >>>>>>>> Atsushi Togo > >>>>>>>> > >>>>>>>> > >>>>>>>> _______________________________________________ > >>>>>>>> Phonopy-users mailing list > >>>>>>>> Pho...@li... > >>>>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users > >>>>>>>> > >>>>>>>> > >>>>>>>> _______________________________________________ > >>>>>>>> Phonopy-users mailing list > >>>>>>>> Pho...@li... > >>>>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> -- > >>>>>>>> Atsushi Togo > >>>>>>>> > >>>>>>>> > >>>>>>>> _______________________________________________ > >>>>>>>> Phonopy-users mailing list > >>>>>>>> Pho...@li... > >>>>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users > >>>>>>>> > >>>>>>>> > >>>>>>>> _______________________________________________ > >>>>>>>> Phonopy-users mailing list > >>>>>>>> Pho...@li... > >>>>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> -- > >>>>>>> Atsushi Togo > >>>>>>> > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> Phonopy-users mailing list > >>>>>>> Pho...@li... > >>>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users > >>>>>> > >>>>>> > >>>>>> > >>>>>> _______________________________________________ > >>>>>> Phonopy-users mailing list > >>>>>> Pho...@li... > >>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users > >>>>> > >>>>> > >>>>> > >>>>> -- > >>>>> Atsushi Togo > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Phonopy-users mailing list > >>>>> Pho...@li... > >>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users > >>>> > >>>> _______________________________________________ > >>>> Phonopy-users mailing list > >>>> Pho...@li... > >>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users > >>> > >>> > >>> > >>> -- > >>> Atsushi Togo > >>> > >>> > >>> _______________________________________________ > >>> Phonopy-users mailing list > >>> Pho...@li... > >>> https://lists.sourceforge.net/lists/listinfo/phonopy-users > >> > >> _______________________________________________ > >> Phonopy-users mailing list > >> Pho...@li... > >> https://lists.sourceforge.net/lists/listinfo/phonopy-users > > > > > > > > -- > > Atsushi Togo > > > > > > _______________________________________________ > > Phonopy-users mailing list > > Pho...@li... > > https://lists.sourceforge.net/lists/listinfo/phonopy-users > > > > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users -- Atsushi Togo |
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From: Guihyun H. <han...@gm...> - 2026-02-23 05:32:19
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Hi, Thank you for the response. It is actually working with your command. Sorry, I didn’t put the “-d” for the dimension command options. Thank you for the fixing. Guihyun Han > 2026. 2. 23. 14:07, Atsushi Togo <atz...@gm...> 작성: > > Hi, > > The following is my result. What is yours? > > % phonopy -c bccfe.txt --fleur -d --dim 2 2 2 > _ > _ __ | |__ ___ _ __ ___ _ __ _ _ > | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | > | |_) | | | | (_) | | | | (_) || |_) | |_| | > | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | > |_| |_| |___/ > 2.48.0 > > -------------------------[time 2026-02-23 14:06:20]------------------------- > Compiled with OpenMP support (max 10 threads). > Python version 3.13.2 > Spglib version 2.6.1 > > Calculator interface: fleur > Crystal structure was read from "bccfe.txt". > Unit of length: au > Displacements creation mode > Systematic displacements > Settings: > Supercell: [2 2 2] > Spacegroup: Im-3m (229) > Number of symmetry operations in supercell: 384 > Use -v option to watch primitive cell, unit cell, and supercell structures. > > Generated number of supercells: 1 > "phonopy_disp.yaml" and supercells have been created. > > Summary of calculation was written in "phonopy_disp.yaml". > -------------------------[time 2026-02-23 14:06:20]------------------------- > _ > ___ _ __ __| | > / _ \ '_ \ / _` | > | __/ | | | (_| | > \___|_| |_|\__,_| > > On Mon, Feb 23, 2026 at 1:19 PM Guihyun Han <han...@gm...> wrote: >> >> Hi, >> >> Sorry for the file. I misunderstood your intention. >> The file that I sent is just for simple calculation of FLEUR not for Phonopy. >> >> I’ve attached bccFe.txt and inp.xml. >> This files can be used for Phonopy but gives error. >> >> Thank you in advance >> Guihyun Han >> >> >> >> >>> 2026. 2. 21. 09:50, Atsushi Togo <atz...@gm...> 작성: >>> >>> Hi, >>> >>> &lattice latsys='cF', a0=1.8897269, a=5.43 / >>> >>> is not supported. >>> >>> The phonopy fleur interface documentation says: >>> >>> "An important thing to note is: The bravais matrix needs to be set >>> directly via the second method proposed in the reference." >>> >>> So you have to specify basis vectors explicitly. This document was not >>> written by me, so I don't understand the detailed format. Is this your >>> problem? >>> >>> Togo >>> >>> On Fri, Feb 20, 2026 at 6:11 PM Guihyun Han <han...@gm...> wrote: >>>> >>>> Hi, >>>> >>>> I’d like to provide the inputs. I can provide primitive cell calculations. >>>> I attached simple system which is diamond Si. >>>> >>>> The situation is following. >>>> First, I have to make supercell with inpSi.txt using Phonopy. (supercell-00x … are expected) >>>> Second, with supercell-00x file, inp.xml will be made then calculate the forces. >>>> However, Phonopy does not give the supercell where I cannot start the supercell calculations. >>>> >>>> The basic step of primitive cell calculation is following. >>>> 1. inpSi.txt is the basic information for making inp.xml (It can be done with %inpgen -f inp.txt) >>>> 2. inp.xml îs the input for DFT calculations, which means FLEUR use inp.xml for input >>>> >>>> Thank you in advance >>>> Guihyun Han >>>> >>>>> 2026. 2. 20. 16:36, Atsushi Togo <atz...@gm...> 작성: >>>>> >>>>> Hi, >>>>> >>>>>> However, it still gives error (the error has no information) and does not give the supercell with displacements. >>>>> >>>>> To fix your issue, I need to be able to reproduce your calculation or mimic it. >>>>> >>>>> Togo >>>>> >>>>> On Fri, Feb 20, 2026 at 4:00 PM Guihyun Han <han...@gm...> wrote: >>>>>> >>>>>> Hi, >>>>>> >>>>>> I’ve tried with the command that you sent and now the Phonopy reads the structure properly. >>>>>> Thank you for fixing it. >>>>>> However, it still gives error (the error has no information) and does not give the supercell with displacements. >>>>>> >>>>>> Guihyun Han >>>>>> >>>>>>> 2026. 2. 19. 15:12, Atsushi Togo <atz...@gm...> 작성: >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> Could you try the following? But please do not expect much to me, >>>>>>> because I am not a user of fleur. >>>>>>> >>>>>>> % phonopy -c Pa3_in.txt --symmetry --fleur|head -n 5 >>>>>>> phonopy_version: '2.48.0' >>>>>>> space_group_type: 'Pa-3' >>>>>>> space_group_number: 205 >>>>>>> point_group_type: 'm-3' >>>>>>> space_group_operations: >>>>>>> >>>>>>> % phonopy -c bccfe_in.txt --symmetry --fleur|head -n 5 >>>>>>> phonopy_version: '2.48.0' >>>>>>> space_group_type: 'Im-3m' >>>>>>> space_group_number: 229 >>>>>>> point_group_type: 'm-3m' >>>>>>> space_group_operations: >>>>>>> >>>>>>> Togo >>>>>>> >>>>>>> On Thu, Feb 19, 2026 at 2:28 PM Guihyun Han <han...@gm...> wrote: >>>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> Thank you for the fixed version. >>>>>>>> I’ve tried to use new version, but it still has problem. >>>>>>>> >>>>>>>> First, I think reading the structure still has problem. >>>>>>>> In the file of Pa3_out.txt, it still reads Pa-3 structure as Pm-3m which is simple cubic. >>>>>>>> >>>>>>>> Second, for the FORCES file, in my understanding of using Phonopy, forces are obtained after supercell calculations. >>>>>>>> As far as I know, the work flow is >>>>>>>> 1. Generate supercell with displacement >>>>>>>> >>>>>>>> phonopy --fleur -c bccfe.txt --pm --dim="2 0 0 0 2 0 0 0 2" >>>>>>>> >>>>>>>> 2. run the calculation with generated supercell >>>>>>>> 3. make FORCE_SETS with generated FORCES >>>>>>>> >>>>>>>> phonopy --fleur -f FORCE >>>>>>>> >>>>>>>> >>>>>>>> However, phonopy requires FORCES in the first step which is generating supercell. >>>>>>>> I’ve attached basic input of FLEUR for bcc Fe and Pa-3 structure. >>>>>>>> >>>>>>>> >>>>>>>> Thank you in advance, >>>>>>>> Guihyun Han >>>>>>>> >>>>>>>> 2026. 2. 13. 17:39, Atsushi Togo <atz...@gm...> 작성: >>>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> I tried to fix it, which you can find it in the develop branch of the >>>>>>>> phonopy github repository: >>>>>>>> https://github.com/phonopy/phonopy/pull/722 >>>>>>>> >>>>>>>> Since I have no input/output data except for Al example, my fix may >>>>>>>> not be good enough. I also don't know the format of FORCES file, too. >>>>>>>> It seems the format has changed recently, and the current one is >>>>>>>> https://github.com/phonopy/phonopy/pull/559. >>>>>>>> >>>>>>>> Togo >>>>>>>> >>>>>>>> On Fri, Feb 13, 2026 at 5:29 PM Guihyun Han <han...@gm...> wrote: >>>>>>>> >>>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> Thank you for the response. >>>>>>>> I’d be grateful if you could fix it. >>>>>>>> And I’d like to help fixing it. >>>>>>>> >>>>>>>> I’ve tried calculation with bcc Fe and it worked. >>>>>>>> I think simple structures such as bcc, fcc, hcp , simple cubic structures are working well. >>>>>>>> The case of space group 205 Pa-3, lattice vectors are same as simple cubic but the difference is position of atoms. >>>>>>>> And the output gives the supercell of simple cubic structure. >>>>>>>> In my opinion, reading the position of atom has some bug. >>>>>>>> >>>>>>>> Thank you in advance, >>>>>>>> Guihyun Han >>>>>>>> >>>>>>>> 2026. 2. 13. 12:20, Atsushi Togo <atz...@gm...> 작성: >>>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> The FLEUR interface in phonopy is not written well. >>>>>>>> I may try to fix it if you like, but I have really no idea about the >>>>>>>> input and output file. There is one example of Al for Fluer interface, >>>>>>>> but in fact parsing forces doesn't work. So if you are a FLEUR user >>>>>>>> and willing to help fix it, please let me know. >>>>>>>> >>>>>>>> Togo >>>>>>>> >>>>>>>> On Thu, Feb 12, 2026 at 10:25 PM Atsushi Togo <atz...@gm...> wrote: >>>>>>>> >>>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> I am not familiar with fleur, but I guess it is a bug. >>>>>>>> >>>>>>>> Togo >>>>>>>> >>>>>>>> On Thu, Feb 12, 2026 at 3:29 PM Guihyun Han <han...@gm...> wrote: >>>>>>>> >>>>>>>> >>>>>>>> Dear phonopy developers >>>>>>>> >>>>>>>> Hi, I’m using FLEUR for DFT calculations and trying to use phonopy for phonon dispersion >>>>>>>> I’m writing this mail because I have one problem with making supercells. >>>>>>>> >>>>>>>> I made same structure file as input for FLEUR and VASP and these are attached below. >>>>>>>> >>>>>>>> The problem I have is that phonopy gives different out for FLEUR and VASP input files. >>>>>>>> The structure is Pa-3 (No. 205). >>>>>>>> >>>>>>>> For vasp POSCAR, phonopy read the POSCAR as the Pa-3 (205). >>>>>>>> But for FLEUR, phonopy read the input as simple cubic Pm-3m (221). >>>>>>>> And I think because of this different symmetry, I cannot get the proper supercell for FLEUR. >>>>>>>> >>>>>>>> I’ve read some documentations and phonopy is using spglib and there is no reason to give different result. >>>>>>>> I hope I’m not doing something wrong. >>>>>>>> How can I make proper supercell with FLEUR input? >>>>>>>> >>>>>>>> Thank you in advance and best regards >>>>>>>> Guihyun >>>>>>>> >>>>>>>> >>>>>>>> FLEUR >>>>>>>> >>>>>>>> MnS2 Pa3 >>>>>>>> >>>>>>>> >>>>>>>> 1.0 0.0 0.0 ! a1 >>>>>>>> >>>>>>>> 0.0 1.0 0.0 ! a2 >>>>>>>> >>>>>>>> 0.0 0.0 1.0 ! a3 >>>>>>>> >>>>>>>> 6.15 ! aa >>>>>>>> >>>>>>>> 1.0 1.0 1.0 ! scale >>>>>>>> >>>>>>>> >>>>>>>> 12 ! num atoms >>>>>>>> >>>>>>>> 25.1 0.000 0.000 0.000 >>>>>>>> >>>>>>>> 25.1 0.500 0.500 0.000 >>>>>>>> >>>>>>>> 25.1 0.000 0.500 0.500 >>>>>>>> >>>>>>>> 25.1 0.500 0.000 0.500 >>>>>>>> >>>>>>>> 16 0.600000000 0.600000000 0.600000000 >>>>>>>> >>>>>>>> 16 0.400000000 0.400000000 0.400000000 >>>>>>>> >>>>>>>> 16 0.900000000 0.400000000 0.100000000 >>>>>>>> >>>>>>>> 16 0.100000000 0.600000000 0.900000000 >>>>>>>> >>>>>>>> 16 0.400000000 0.100000000 0.900000000 >>>>>>>> >>>>>>>> 16 0.600000000 0.900000000 0.100000000 >>>>>>>> >>>>>>>> 16 0.100000000 0.900000000 0.400000000 >>>>>>>> >>>>>>>> 16 0.900000000 0.100000000 0.600000000 >>>>>>>> >>>>>>>> VASP >>>>>>>> >>>>>>>> MnS2 >>>>>>>> >>>>>>>> 1.0 >>>>>>>> >>>>>>>> 6.1500000000 0.0000000000 0.0000000000 >>>>>>>> >>>>>>>> 0.0000000000 6.1500000000 0.0000000000 >>>>>>>> >>>>>>>> 0.0000000000 0.0000000000 6.1500000000 >>>>>>>> >>>>>>>> Mn S >>>>>>>> >>>>>>>> 4 8 >>>>>>>> >>>>>>>> Direct >>>>>>>> >>>>>>>> 0.000000000 0.000000000 0.000000000 >>>>>>>> >>>>>>>> 0.500000000 0.500000000 0.000000000 >>>>>>>> >>>>>>>> 0.000000000 0.500000000 0.500000000 >>>>>>>> >>>>>>>> 0.500000000 0.000000000 0.500000000 >>>>>>>> >>>>>>>> 0.600000000 0.600000000 0.600000000 >>>>>>>> >>>>>>>> 0.400000000 0.400000000 0.400000000 >>>>>>>> >>>>>>>> 0.900000000 0.400000000 0.100000000 >>>>>>>> >>>>>>>> 0.100000000 0.600000000 0.900000000 >>>>>>>> >>>>>>>> 0.400000000 0.100000000 0.900000000 >>>>>>>> >>>>>>>> 0.600000000 0.900000000 0.100000000 >>>>>>>> >>>>>>>> 0.100000000 0.900000000 0.400000000 >>>>>>>> >>>>>>>> 0.900000000 0.100000000 0.600000000 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Phonopy-users mailing list >>>>>>>> Pho...@li... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Atsushi Togo >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Atsushi Togo >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Phonopy-users mailing list >>>>>>>> Pho...@li... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Phonopy-users mailing list >>>>>>>> Pho...@li... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Atsushi Togo >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Phonopy-users mailing list >>>>>>>> Pho...@li... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Phonopy-users mailing list >>>>>>>> Pho...@li... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Atsushi Togo >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Phonopy-users mailing list >>>>>>> Pho...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Phonopy-users mailing list >>>>>> Pho...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >>>>> >>>>> >>>>> >>>>> -- >>>>> Atsushi Togo >>>>> >>>>> >>>>> _______________________________________________ >>>>> Phonopy-users mailing list >>>>> Pho...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >>>> >>>> _______________________________________________ >>>> Phonopy-users mailing list >>>> Pho...@li... >>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >>> >>> >>> >>> -- >>> Atsushi Togo >>> >>> >>> _______________________________________________ >>> Phonopy-users mailing list >>> Pho...@li... >>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >> >> _______________________________________________ >> Phonopy-users mailing list >> Pho...@li... >> https://lists.sourceforge.net/lists/listinfo/phonopy-users > > > > -- > Atsushi Togo > > > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users |
|
From: Atsushi T. <atz...@gm...> - 2026-02-23 05:07:28
|
Hi,
The following is my result. What is yours?
% phonopy -c bccfe.txt --fleur -d --dim 2 2 2
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
2.48.0
-------------------------[time 2026-02-23 14:06:20]-------------------------
Compiled with OpenMP support (max 10 threads).
Python version 3.13.2
Spglib version 2.6.1
Calculator interface: fleur
Crystal structure was read from "bccfe.txt".
Unit of length: au
Displacements creation mode
Systematic displacements
Settings:
Supercell: [2 2 2]
Spacegroup: Im-3m (229)
Number of symmetry operations in supercell: 384
Use -v option to watch primitive cell, unit cell, and supercell structures.
Generated number of supercells: 1
"phonopy_disp.yaml" and supercells have been created.
Summary of calculation was written in "phonopy_disp.yaml".
-------------------------[time 2026-02-23 14:06:20]-------------------------
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
On Mon, Feb 23, 2026 at 1:19 PM Guihyun Han <han...@gm...> wrote:
>
> Hi,
>
> Sorry for the file. I misunderstood your intention.
> The file that I sent is just for simple calculation of FLEUR not for Phonopy.
>
> I’ve attached bccFe.txt and inp.xml.
> This files can be used for Phonopy but gives error.
>
> Thank you in advance
> Guihyun Han
>
>
>
>
> > 2026. 2. 21. 09:50, Atsushi Togo <atz...@gm...> 작성:
> >
> > Hi,
> >
> > &lattice latsys='cF', a0=1.8897269, a=5.43 /
> >
> > is not supported.
> >
> > The phonopy fleur interface documentation says:
> >
> > "An important thing to note is: The bravais matrix needs to be set
> > directly via the second method proposed in the reference."
> >
> > So you have to specify basis vectors explicitly. This document was not
> > written by me, so I don't understand the detailed format. Is this your
> > problem?
> >
> > Togo
> >
> > On Fri, Feb 20, 2026 at 6:11 PM Guihyun Han <han...@gm...> wrote:
> >>
> >> Hi,
> >>
> >> I’d like to provide the inputs. I can provide primitive cell calculations.
> >> I attached simple system which is diamond Si.
> >>
> >> The situation is following.
> >> First, I have to make supercell with inpSi.txt using Phonopy. (supercell-00x … are expected)
> >> Second, with supercell-00x file, inp.xml will be made then calculate the forces.
> >> However, Phonopy does not give the supercell where I cannot start the supercell calculations.
> >>
> >> The basic step of primitive cell calculation is following.
> >> 1. inpSi.txt is the basic information for making inp.xml (It can be done with %inpgen -f inp.txt)
> >> 2. inp.xml îs the input for DFT calculations, which means FLEUR use inp.xml for input
> >>
> >> Thank you in advance
> >> Guihyun Han
> >>
> >>> 2026. 2. 20. 16:36, Atsushi Togo <atz...@gm...> 작성:
> >>>
> >>> Hi,
> >>>
> >>>> However, it still gives error (the error has no information) and does not give the supercell with displacements.
> >>>
> >>> To fix your issue, I need to be able to reproduce your calculation or mimic it.
> >>>
> >>> Togo
> >>>
> >>> On Fri, Feb 20, 2026 at 4:00 PM Guihyun Han <han...@gm...> wrote:
> >>>>
> >>>> Hi,
> >>>>
> >>>> I’ve tried with the command that you sent and now the Phonopy reads the structure properly.
> >>>> Thank you for fixing it.
> >>>> However, it still gives error (the error has no information) and does not give the supercell with displacements.
> >>>>
> >>>> Guihyun Han
> >>>>
> >>>>> 2026. 2. 19. 15:12, Atsushi Togo <atz...@gm...> 작성:
> >>>>>
> >>>>> Hi,
> >>>>>
> >>>>> Could you try the following? But please do not expect much to me,
> >>>>> because I am not a user of fleur.
> >>>>>
> >>>>> % phonopy -c Pa3_in.txt --symmetry --fleur|head -n 5
> >>>>> phonopy_version: '2.48.0'
> >>>>> space_group_type: 'Pa-3'
> >>>>> space_group_number: 205
> >>>>> point_group_type: 'm-3'
> >>>>> space_group_operations:
> >>>>>
> >>>>> % phonopy -c bccfe_in.txt --symmetry --fleur|head -n 5
> >>>>> phonopy_version: '2.48.0'
> >>>>> space_group_type: 'Im-3m'
> >>>>> space_group_number: 229
> >>>>> point_group_type: 'm-3m'
> >>>>> space_group_operations:
> >>>>>
> >>>>> Togo
> >>>>>
> >>>>> On Thu, Feb 19, 2026 at 2:28 PM Guihyun Han <han...@gm...> wrote:
> >>>>>>
> >>>>>> Hi,
> >>>>>>
> >>>>>> Thank you for the fixed version.
> >>>>>> I’ve tried to use new version, but it still has problem.
> >>>>>>
> >>>>>> First, I think reading the structure still has problem.
> >>>>>> In the file of Pa3_out.txt, it still reads Pa-3 structure as Pm-3m which is simple cubic.
> >>>>>>
> >>>>>> Second, for the FORCES file, in my understanding of using Phonopy, forces are obtained after supercell calculations.
> >>>>>> As far as I know, the work flow is
> >>>>>> 1. Generate supercell with displacement
> >>>>>>
> >>>>>> phonopy --fleur -c bccfe.txt --pm --dim="2 0 0 0 2 0 0 0 2"
> >>>>>>
> >>>>>> 2. run the calculation with generated supercell
> >>>>>> 3. make FORCE_SETS with generated FORCES
> >>>>>>
> >>>>>> phonopy --fleur -f FORCE
> >>>>>>
> >>>>>>
> >>>>>> However, phonopy requires FORCES in the first step which is generating supercell.
> >>>>>> I’ve attached basic input of FLEUR for bcc Fe and Pa-3 structure.
> >>>>>>
> >>>>>>
> >>>>>> Thank you in advance,
> >>>>>> Guihyun Han
> >>>>>>
> >>>>>> 2026. 2. 13. 17:39, Atsushi Togo <atz...@gm...> 작성:
> >>>>>>
> >>>>>> Hi,
> >>>>>>
> >>>>>> I tried to fix it, which you can find it in the develop branch of the
> >>>>>> phonopy github repository:
> >>>>>> https://github.com/phonopy/phonopy/pull/722
> >>>>>>
> >>>>>> Since I have no input/output data except for Al example, my fix may
> >>>>>> not be good enough. I also don't know the format of FORCES file, too.
> >>>>>> It seems the format has changed recently, and the current one is
> >>>>>> https://github.com/phonopy/phonopy/pull/559.
> >>>>>>
> >>>>>> Togo
> >>>>>>
> >>>>>> On Fri, Feb 13, 2026 at 5:29 PM Guihyun Han <han...@gm...> wrote:
> >>>>>>
> >>>>>>
> >>>>>> Hi,
> >>>>>>
> >>>>>> Thank you for the response.
> >>>>>> I’d be grateful if you could fix it.
> >>>>>> And I’d like to help fixing it.
> >>>>>>
> >>>>>> I’ve tried calculation with bcc Fe and it worked.
> >>>>>> I think simple structures such as bcc, fcc, hcp , simple cubic structures are working well.
> >>>>>> The case of space group 205 Pa-3, lattice vectors are same as simple cubic but the difference is position of atoms.
> >>>>>> And the output gives the supercell of simple cubic structure.
> >>>>>> In my opinion, reading the position of atom has some bug.
> >>>>>>
> >>>>>> Thank you in advance,
> >>>>>> Guihyun Han
> >>>>>>
> >>>>>> 2026. 2. 13. 12:20, Atsushi Togo <atz...@gm...> 작성:
> >>>>>>
> >>>>>> Hi,
> >>>>>>
> >>>>>> The FLEUR interface in phonopy is not written well.
> >>>>>> I may try to fix it if you like, but I have really no idea about the
> >>>>>> input and output file. There is one example of Al for Fluer interface,
> >>>>>> but in fact parsing forces doesn't work. So if you are a FLEUR user
> >>>>>> and willing to help fix it, please let me know.
> >>>>>>
> >>>>>> Togo
> >>>>>>
> >>>>>> On Thu, Feb 12, 2026 at 10:25 PM Atsushi Togo <atz...@gm...> wrote:
> >>>>>>
> >>>>>>
> >>>>>> Hi,
> >>>>>>
> >>>>>> I am not familiar with fleur, but I guess it is a bug.
> >>>>>>
> >>>>>> Togo
> >>>>>>
> >>>>>> On Thu, Feb 12, 2026 at 3:29 PM Guihyun Han <han...@gm...> wrote:
> >>>>>>
> >>>>>>
> >>>>>> Dear phonopy developers
> >>>>>>
> >>>>>> Hi, I’m using FLEUR for DFT calculations and trying to use phonopy for phonon dispersion
> >>>>>> I’m writing this mail because I have one problem with making supercells.
> >>>>>>
> >>>>>> I made same structure file as input for FLEUR and VASP and these are attached below.
> >>>>>>
> >>>>>> The problem I have is that phonopy gives different out for FLEUR and VASP input files.
> >>>>>> The structure is Pa-3 (No. 205).
> >>>>>>
> >>>>>> For vasp POSCAR, phonopy read the POSCAR as the Pa-3 (205).
> >>>>>> But for FLEUR, phonopy read the input as simple cubic Pm-3m (221).
> >>>>>> And I think because of this different symmetry, I cannot get the proper supercell for FLEUR.
> >>>>>>
> >>>>>> I’ve read some documentations and phonopy is using spglib and there is no reason to give different result.
> >>>>>> I hope I’m not doing something wrong.
> >>>>>> How can I make proper supercell with FLEUR input?
> >>>>>>
> >>>>>> Thank you in advance and best regards
> >>>>>> Guihyun
> >>>>>>
> >>>>>>
> >>>>>> FLEUR
> >>>>>>
> >>>>>> MnS2 Pa3
> >>>>>>
> >>>>>>
> >>>>>> 1.0 0.0 0.0 ! a1
> >>>>>>
> >>>>>> 0.0 1.0 0.0 ! a2
> >>>>>>
> >>>>>> 0.0 0.0 1.0 ! a3
> >>>>>>
> >>>>>> 6.15 ! aa
> >>>>>>
> >>>>>> 1.0 1.0 1.0 ! scale
> >>>>>>
> >>>>>>
> >>>>>> 12 ! num atoms
> >>>>>>
> >>>>>> 25.1 0.000 0.000 0.000
> >>>>>>
> >>>>>> 25.1 0.500 0.500 0.000
> >>>>>>
> >>>>>> 25.1 0.000 0.500 0.500
> >>>>>>
> >>>>>> 25.1 0.500 0.000 0.500
> >>>>>>
> >>>>>> 16 0.600000000 0.600000000 0.600000000
> >>>>>>
> >>>>>> 16 0.400000000 0.400000000 0.400000000
> >>>>>>
> >>>>>> 16 0.900000000 0.400000000 0.100000000
> >>>>>>
> >>>>>> 16 0.100000000 0.600000000 0.900000000
> >>>>>>
> >>>>>> 16 0.400000000 0.100000000 0.900000000
> >>>>>>
> >>>>>> 16 0.600000000 0.900000000 0.100000000
> >>>>>>
> >>>>>> 16 0.100000000 0.900000000 0.400000000
> >>>>>>
> >>>>>> 16 0.900000000 0.100000000 0.600000000
> >>>>>>
> >>>>>> VASP
> >>>>>>
> >>>>>> MnS2
> >>>>>>
> >>>>>> 1.0
> >>>>>>
> >>>>>> 6.1500000000 0.0000000000 0.0000000000
> >>>>>>
> >>>>>> 0.0000000000 6.1500000000 0.0000000000
> >>>>>>
> >>>>>> 0.0000000000 0.0000000000 6.1500000000
> >>>>>>
> >>>>>> Mn S
> >>>>>>
> >>>>>> 4 8
> >>>>>>
> >>>>>> Direct
> >>>>>>
> >>>>>> 0.000000000 0.000000000 0.000000000
> >>>>>>
> >>>>>> 0.500000000 0.500000000 0.000000000
> >>>>>>
> >>>>>> 0.000000000 0.500000000 0.500000000
> >>>>>>
> >>>>>> 0.500000000 0.000000000 0.500000000
> >>>>>>
> >>>>>> 0.600000000 0.600000000 0.600000000
> >>>>>>
> >>>>>> 0.400000000 0.400000000 0.400000000
> >>>>>>
> >>>>>> 0.900000000 0.400000000 0.100000000
> >>>>>>
> >>>>>> 0.100000000 0.600000000 0.900000000
> >>>>>>
> >>>>>> 0.400000000 0.100000000 0.900000000
> >>>>>>
> >>>>>> 0.600000000 0.900000000 0.100000000
> >>>>>>
> >>>>>> 0.100000000 0.900000000 0.400000000
> >>>>>>
> >>>>>> 0.900000000 0.100000000 0.600000000
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Phonopy-users mailing list
> >>>>>> Pho...@li...
> >>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> Atsushi Togo
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> Atsushi Togo
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Phonopy-users mailing list
> >>>>>> Pho...@li...
> >>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Phonopy-users mailing list
> >>>>>> Pho...@li...
> >>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> Atsushi Togo
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Phonopy-users mailing list
> >>>>>> Pho...@li...
> >>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Phonopy-users mailing list
> >>>>>> Pho...@li...
> >>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>> Atsushi Togo
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> Phonopy-users mailing list
> >>>>> Pho...@li...
> >>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Phonopy-users mailing list
> >>>> Pho...@li...
> >>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users
> >>>
> >>>
> >>>
> >>> --
> >>> Atsushi Togo
> >>>
> >>>
> >>> _______________________________________________
> >>> Phonopy-users mailing list
> >>> Pho...@li...
> >>> https://lists.sourceforge.net/lists/listinfo/phonopy-users
> >>
> >> _______________________________________________
> >> Phonopy-users mailing list
> >> Pho...@li...
> >> https://lists.sourceforge.net/lists/listinfo/phonopy-users
> >
> >
> >
> > --
> > Atsushi Togo
> >
> >
> > _______________________________________________
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Atsushi Togo
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