Re: [Phonopy-users] Phonopy_Crystal symmetry
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Re: [Phonopy-users] Phonopy_Crystal symmetry
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From: Atsushi T. <atz...@gm...> - 2026-02-21 00:51:19
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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 |
