Re: [Phonopy-users] Create FORCE_SETS
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Re: [Phonopy-users] Create FORCE_SETS
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From: 仲村優華 <yuk...@gm...> - 2019-11-25 10:02:03
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Prof.Togo
Thank you again.
I might mistook the way of spelling code.
Phonopy(phonopy -d --dim="2 2 2") generated just POSCAR-001 ~008, SPOCAR
and one phonoy_disp.yaml.
(I understood "disp.yaml" is still supported to read, but will be
deprecated.)
Then I moved to POCAR and POSCAR-001 ~008 into a different folder and
rename SPOCAR POSCAR.
% phonopy -f disp-001/vasprun.xml disp-002/vasprun.xml ...
disp-008/vasprun.xml
or % phonopy -f disp-{001..008}/vasprun.xml
now show the error message : "disp-001/vasprun.xml" was not found.
So do have to make disp file of every POSCAR-***? Or do I have not to
copy "disp-001/vasprun.xml" literally?
I'm sorry to trouble you.I know I should never take your time.
But, just for your information, someone makes the same mistake.
Best Regards,
Yuka Nakamura
2019年11月25日(月) 17:59 Atsushi Togo <atz...@gm...>:
> 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 (again the documentation is outdated, phonoy_disp.yaml is written as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...
>
>
> _______________________________________________
> Phonopy-users mailing list
> Pho...@li...
> https://lists.sourceforge.net/lists/listinfo/phonopy-users
>
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