Re: [Phonopy-users] Create FORCE_SETS

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>Prof.Kumar
I am sorry that I mistook the way of calculating.
Your explain is very helpful for me to understand details.
VASP is not at hand so I'll try it when I go to a laboratory.
Thank you so much again.

>Prof.Togo
I am sorry it is true that I'm not familiar with unix and software and the
like.
I have no one to consult with in a laboratory,so please forgive me if I ask
another time about phonopy or phono3py.
Any way,I"ll continue trying by myself.

You don't have to reply to this message.
I appreciate your comments and documents.

2019年11月25日(月) 20:05 Atsushi Togo <atz...@gm...>:

> Hi Yuka,
>
> In my feeling from what you wrote, you may not have enough knowledge
> on unix system. Now you have asked enough questions and probably
> gotten enough information. My suggestion for you is to discuss with
> your colleagues next to you. Then I believe you will find your
> solution.
>
> Togo
>
>
> Togo
>
> On Mon, Nov 25, 2019 at 7:13 PM Manish Kumar <man...@gm...>
> wrote:
> >
> > Dear Nakamura,
> >
> > For creating force sets donot rename SPOSCAR to POSCAR.
> > Create folders.
> > mkdir 1 2 3 4 5 6 7 8
> > cd 1
> > cp ../POSCAR1 POSCAR
> > This folder should contain INCAR, KPOINTS, POTCAR
> > Then run vasp.
> >
> > Similarly
> > cd 2
> > cp ../POSCAR-2 POSCAR
> > run vasp
> >
> > At last run phonopy -f {1..8}/vasprun.xml
> > Hope you get it.
> > For more details follow the website.
> >
> >
> > On Mon, Nov 25, 2019, 3:32 PM 仲村優華 <yuk...@gm...> wrote:
> >>
> >> 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
> >>
> >> _______________________________________________
> >> 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...
>
>
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