Re: [Phonopy-users] Create FORCE_SETS
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Re: [Phonopy-users] Create FORCE_SETS
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From: Manish K. <man...@gm...> - 2019-11-25 10:13:31
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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 (again the documentation is outdated, phonoy_disp.yaml is written as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
>>
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