Re: [Phonopy-users] Last step of VASP_DFPT method, please help, Luke Soule
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Re: [Phonopy-users] Last step of VASP_DFPT method, please help, Luke Soule
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From: Atsushi T. <atz...@gm...> - 2016-01-23 01:18:23
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Hi,
Probably it's your VASP problem. MedeA is a commercial package. So I
guess you can ask some professional person consulted if your
vasprun.xml is well made or not, compared with a plain VASP run.
Togo
On Thu, Jan 21, 2016 at 9:04 AM, Luke Soule <ls...@gm...> wrote:
> I followed this procedure to the tee and was given the exact FORCE_CONSTANTS
> that I posted early.
>
>
>
> I should mention I am using MedeA, a graphical user interface for VASP to
> generate the vasprun.xml, but I am able to put in custom inputs along with
> the rest of the usual INCAR properties. When I check the INCAR to the
> calculation it is correct, with IBRION =8, NSW =1 and the supercell POSCAR
> used as the POSCAR for the calculation.
>
>
>
> I continue to get the error:
>
> “ValueError: could not broadcast input array from shape (3,0) into shape
> (3,3)”
>
> When I put in “phonopy –dim=”2 2 2” -c POSCAR-unitcell –readfc band.conf”
>
> Which I am guessing means that phonopy is expecting a 3 by 3 array and it
> is only reading the first line of my FORCE_CONSTANTS file.
>
>
>
> Luke
>
>
>
> From: 邵和助 [mailto:hz...@ni...]
> Sent: Wednesday, January 20, 2016 9:32 AM
>
>
> To: pho...@li...
> Subject: Re: [Phonopy-users] Last step of VASP_DFPT method, please help,
> Luke Soule
>
>
>
> Dear Luke
>
> I found that there's some problem in your file of FORCE_CONSTANTS.
> You have not generate the right FORCE_CONSTANTS. Have you done the right
> steps which the manuel provides?
>
> 1. Prepare unit cell structure named, e.g., POSCAR-unitcell.
>
> 2. Prepare a perfect supercell structure from POSCAR-unitcell, e.g.,phonopy
> -d --dim="2 2 2" -c POSCAR-unitcell
>
> 3. Rename SPOSCAR created in (2) to POSCAR (POSCAR-{number} and disp.yaml
> files will never be used.)
> % mv SPOSCAR POSCAR
>
> 4. Calculate force constants of the perfect supercell by running VASP with
> IBRION = 8 and NSW = 1. An
> example of INCAR for insulator may be such like (just an example!):
>
> PREC = Accurate
> ENCUT = 500
>
> IBRION = 8
> EDIFF = 1.0e-08
> IALGO = 38
> ISMEAR = 0; SIGMA = 0.1
> LREAL = .FALSE.
> ADDGRID = .TRUE.
> LWAVE = .FALSE.
> LCHARG = .FALSE.
>
> 5 After finishing the VASP calculation, confirm vasprun.xml contains hessian
> elements, and then create
> FORCE_CONSTANTS:
> % phonopy --fc vasprun.xml.
>
> Please notice here there is two '-'..
>
> Here you will generate the right FORCE_CONSTANTS file.
>
> 6. Run phonopy with the original unit cell POSCAR-unitcell and setting tag
> FORCE_CONSTANTS = READ
> or --readfc option, e.g., as found in example/NaCl-VASPdfpt
> % phonopy --dim="2 2 2" -c POSCAR-unitcell band.conf
>
> If you properly follow the above steps, you should got the right dispersion
> of phonon.
>
>
>
> Hezhu
>
>
>
>
>
> -----原始邮件-----
> 发件人: "Luke Soule" <ls...@gm...>
> 发送时间: 2016年1月20日 星期三
> 收件人: pho...@li...
> 抄送:
> 主题: Re: [Phonopy-users] Last step of VASP_DFPT method, please help, Luke
> Soule
>
> Yes, that would be very helpful.
>
>
>
> Thanks
>
>
>
> Luke
>
>
>
>
>
> From: 邵和助 [mailto:hz...@ni...]
> Sent: Monday, January 18, 2016 5:07 PM
> To: pho...@li...
> Subject: Re: [Phonopy-users] Last step of VASP_DFPT method, please help,
> Luke Soule
>
>
>
> Luke
>
> You could attach your FORCE_CONSTANTS, band.conf, and POSCAR and I try
> to check these files for you.
>
> hezhu
>
> -----原始邮件-----
> 发件人: "Luke Soule" <ls...@gm...>
> 发送时间: 2016年1月19日 星期二
> 收件人: pho...@li...
> 抄送:
> 主题: Re: [Phonopy-users] Last step of VASP_DFPT method, please help, Luke
> Soule
>
> I apologize, I stupidly didn’t realize I could merely alter my supercell
> number in my FORCE_CONSTANTS file. Another error arose though and this one I
> am clueless on.
>
>
>
> Can someone help a beginner to phonopy?
>
>
>
> File "/usr/bin/phonopy", line 638, in <module>
>
> fc = file_IO.parse_FORCE_CONSTANTS(filename="FORCE_CONSTANTS")
>
> File "/usr/lib/python2.7/dist-packages/phonopy/file_IO.py", line 197, in
> parse_FORCE_CONSTANTS
>
> force_constants[i, j] = np.array(tensor)
>
> ValueError: could not broadcast input array from shape (3,0) into shape
> (3,3)
>
>
>
> Thanks, Luke
>
>
>
> From: 邵和助 [mailto:hz...@ni...]
> Sent: Thursday, January 14, 2016 5:41 PM
> To: pho...@li...
> Subject: Re: [Phonopy-users] Last step of VASP_DFPT method, please help,
> Luke Soule
>
>
>
> hi
>
> have you run the example given in Phonopy? Maybe you could find some clues
> to resolve your problem.
>
> hezhu
>
> -----原始邮件-----
> 发件人: "Luke Soule" <ls...@gm...>
> 发送时间: 2016年1月15日 星期五
> 收件人: pho...@li...
> 抄送:
> 主题: [Phonopy-users] Last step of VASP_DFPT method, please help, Luke Soule
>
> So I have followed the VASP-DFPT manual and have generated FORCE_CONSTANTS.
> Yet it is giving me this error when I type “phonopy POSCAR-unitcell -c
> –dim=”2 2 2” –readfc”
>
>
>
> “The error Force constants are read from FORCE_CONSTANTS.
>
>
>
> Number of atoms in supercell is not consistent with the matrix shape of
>
> force constants read from FORCE_CONSTANTS.
>
> Please carefully check DIM, FORCE_CONSTANTS, and POSCAR.”
>
>
>
> Is there any way to fix this?
>
>
>
> Also, can I have some pointers on syntax? What are the steps to develop a
> density of state plot from the VASP-DFPT?
>
>
>
> From: 邵和助 [mailto:hz...@ni...]
> Sent: Wednesday, January 13, 2016 4:54 PM
> To: pho...@li...
> Subject: Re: [Phonopy-users] Help with generating FORCE_SETS
>
>
>
> hi
>
> I think there is something wrong with your incar file, check it.
>
> hezhu
>
> -----原始邮件-----
> 发件人: "Luke Soule" <ls...@gm...>
> 发送时间: 2016年1月13日 星期三
> 收件人: pho...@li...
> 抄送:
> 主题: Re: [Phonopy-users] Help with generating FORCE_SETS
>
> The file does not end with those three lines, it ends with
>
> <I type=”logical” name=”LHYPERFINE”> F </i>
>
> </incar>
>
>
>
> I’ll try to re run a vasp calculation and see if I get a different result.
> Thanks,
>
>
>
> Luke
>
>
>
>
>
> From: 邵和助 [mailto:hz...@ni...]
> Sent: Tuesday, January 12, 2016 6:02 PM
> To: pho...@li...
> Subject: Re: [Phonopy-users] Help with generating FORCE_SETS
>
>
>
> hi
>
> Maybe your vasprun.xml file is not completed. You could check the file, see
> if the final lines are like this " </varray>
> </structure>
> </modeling>"
>
> If so, you should rerun a vasp calculation to get right vasprun.xml.
>
> -----原始邮件-----
> 发件人: "Luke Soule" <ls...@gm...>
> 发送时间: 2016年1月13日 星期三
> 收件人: pho...@li...
> 抄送:
> 主题: [Phonopy-users] Help with generating FORCE_SETS
>
> Hello, I am having difficulty producing a FORCE_SETS file. When I type
>
>
>
> “phonopy -f vasprun.xml”
>
>
>
> Instead of spiting out
>
>
>
> “FORCE_SETS has been created”
>
>
>
> I am getting
>
>
>
> File "/usr/bin/phonopy", line 514, in <module>
>
> log_level)
>
> File "/usr/lib/python2.7/dist-packages/phonopy/interface/vasp.py", line
> 105, in create_FORCE_CONSTANTS
>
> fc_and_atom_types = read_force_constant_vasprun_xml(filename)
>
> File "/usr/lib/python2.7/dist-packages/phonopy/interface/vasp.py", line
> 463, in read_force_constant_vasprun_xml
>
> return get_force_constants_vasprun_xml(vasprun)
>
> File "/usr/lib/python2.7/dist-packages/phonopy/interface/vasp.py", line
> 468, in get_force_constants_vasprun_xml
>
> for event, element in vasprun:
>
> File "/usr/lib/python2.7/dist-packages/phonopy/interface/vasp.py", line
> 441, in _iterparse
>
> for event, elem in etree.iterparse(fname):
>
> File "<string>", line 107, in next
>
> cElementTree.ParseError: no element found: line 40, column 0
>
>
>
>
>
>
>
> Can anyone help?
>
>
>
> Thanks,
>
>
>
> Luke Soule
>
> New Mexico Institute of Mining and Technology
>
>
>
>
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--
Atsushi Togo
Elements Strategy Initiative for Structural Materials, Kyoto university
E-mail: atz...@gm...
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