Re: [Phonopy-users] Phonopy_Crystal symmetry

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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