Re: [Phonopy-users] Phonopy_Crystal symmetry
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Re: [Phonopy-users] Phonopy_Crystal symmetry
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From: Guihyun H. <han...@gm...> - 2026-02-19 05:28:21
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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 |
