Re: [Phonopy-users] Phonopy_Crystal symmetry

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