Re: [Phonopy-users] Phonopy_Crystal symmetry

[Atsushi T. <atz...@gm...>]

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
> >>
> >>
> >>
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> >>
> >>
> >>
> >>
> >> --
> >> Atsushi Togo
> >>
> >>
> >>
> >>
> >> --
> >> Atsushi Togo
> >>
> >>
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> >>
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> >> --
> >> Atsushi Togo
> >>
> >>
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> >>
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> >
> >
> > --
> > Atsushi Togo
> >
> >
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-- 
Atsushi Togo