Re: [Phonopy-users] Phonopy_Crystal symmetry

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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