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...> - 2026-02-23 05:32:19
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Hi, Thank you for the response. It is actually working with your command. Sorry, I didn’t put the “-d” for the dimension command options. Thank you for the fixing. Guihyun Han > 2026. 2. 23. 14:07, Atsushi Togo <atz...@gm...> 작성: > > 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 > > > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users |
