Re: [Phonopy-users] Create FORCE_SETS
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Re: [Phonopy-users] Create FORCE_SETS
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From: Atsushi T. <atz...@gm...> - 2019-11-25 08:59:39
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Hi, If your folders are like disp-001, ..., disp-008, then probably on the folder where phonopy_disp.yaml exists, % phonopy -f disp-001/vasprun.xml disp-002/vasprun.xml ... disp-008/vasprun.xml https://atztogo.github.io/phonopy/vasp.html#calculation-of-sets-of-forces (again the documentation is outdated, phonoy_disp.yaml is written as disp.yaml) Togo On Mon, Nov 25, 2019 at 5:10 PM 仲村優華 <yuk...@gm...> wrote: > > >Prof.Kumar > > Thank you for your advice. > According you said, I have already put POSCAR and POSCAR-001~POSCAR-008 into different folders > I renamed SPOCAR POCAR and edit INCAR as follows. > -------------------------------- > PREC = Accurate > ENCUT = 350 > IBRION = -1 > NELMIN = 5 > EDIFF = 1.0e-08 > ALGO = Fast > ISMEAR = 0; SIGMA = 0.05 > LREAL = .FALSE. > ADDGRID = .TRUE. > LWAVE = .FALSE. > LCHARG = .FALSE. > GGA = PS > NPAR = 2 > --------------------------------- > Still,the error message is said > 'Displacements were read from "phonopy_disp.yaml". > Number of files to be read (1) don't match to > the number of displacements (8) in phonopy_disp.yaml. > FORCE_SETS could not be created.' > I also tried another INCAR such as one provided in the website,though those have the same results. > So I think it is not a cause. > I have to find the reason I can not calculate that. > > Anyway,I appreciate your comment. > > > Prof.Togo > > Thank you for your comment. > I am sorry that I did not mention details. > I could not judge what I should explain. > > Your referencears on github are always appreciated. > I'll change environment as you recommend. > > 2019年11月20日(水) 13:59 Atsushi Togo <atz...@gm...>: >> >> Hi, >> >> As Manish Kumar wrote, we don't see what you did clearly. >> You can use VASP-DFPT result or usual VASP force calculations, which >> corresponds to finite displacement approach. If you consider phono3py >> for use, I recommend the later approach to be consistent. One more >> note, if you use the later case, the option you need to create >> FORCE_SETS is not '--f' (double-dash) but '-f' (one dash). >> >> Then for the installation of phono3py, it is not recommended to mix up >> conda and pip. I recommend to follow this instruction for your >> installation, >> https://atztogo.github.io/phono3py/install.html#installation-instruction-of-latest-development-version-of-phono3py >> To use conda environment is important to isolate your python dependencies. >> >> Togo >> >> On Wed, Nov 20, 2019 at 1:49 PM Manish Kumar <man...@gm...> wrote: >> > >> > Dear Researcher, >> > Vaspdfpt (copying SPOSCAR to POSCAR) will produce FORCE_CONSTANTS. >> > >> > To produce force set, you have to run all generated poscars in different folders. INCAR is different from vaspdfpt. Example is provided in the website. >> > >> > On Wed, Nov 20, 2019, 8:32 AM 仲村優華 <yuk...@gm...> wrote: >> >> >> >> Dear Phonopy Users, >> >> >> >> I started to use phonopy for reserch characteristics of thermoelectric materials. >> >> >> >> I have difficulty of creating FORCE_SETS with use of VASP output. >> >> * Example/NaCl-VASPdfpt goes successfully. >> >> >> >> To obtain supercells(2×2×2) >> >> % phonopy -d --dim="2 2 2" >> >> The output is a file named "phonopy_disp.yaml". >> >> >> >> Then,I tried 2 ways to obtain FORCE_SETS. >> >> 1)% phonopy --f vasprun.xml >> >> or >> >> % phonopy --fc vasprun.xml >> >> shows the error as below: >> >> "Number of files to be read(1) don't match to number of displacements(8) in phonopy_disp.yaml" >> >> >> >> 2)To rename SPOCAR POSCAR >> >> % phonopy --f vasprun.xml >> >> shows the error as below: >> >> "vasprun.xml does not contain necessary information" >> >> >> >> I ran through archived email and pages such as "VASP-DFPT & phonopy calculation". >> >> I'm afraid I may overlook information,though I am stuck. >> >> >> >> Should I edit a file? Or did I input a wrong command? >> >> If there are any other particular points, please point them out. >> >> >> >> **** >> >> Eventually I would like to calculate their Grüneisen parameter and lattice thermal conductivity. >> >> So I must use phono3py. >> >> However,I've been also having trouble with its install. >> >> As Prof.Togo already mentioned, the better way to install phono3py is via conda. >> >> But I installed other packages via pip,which often seems to conflict with conda. >> >> So first I am going to complete calculations with phonopy,then to install phono3py. >> >> **** >> >> >> >> Best Regards, >> >> Yuka Nakamura >> >> _______________________________________________ >> >> 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 >> Elements Strategy Initiative for Structural Materials, Kyoto university >> E-mail: atz...@gm... >> >> >> _______________________________________________ >> Phonopy-users mailing list >> Pho...@li... >> https://lists.sourceforge.net/lists/listinfo/phonopy-users -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... |
