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 11:05:32
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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 (again the documentation is outdated, phonoy_disp.yaml is written as disp.yaml)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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