Re: [Phonopy-users] Last step of VASP_DFPT method, please help, Luke Soule

[Luke S. <ls...@gm...>]

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... <mailto:ls...@gm...> >
发送时间: 2016年1月15日 星期五
收件人: pho...@li...
<mailto: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... <mailto:hz...@ni...> ] 
Sent: Wednesday, January 13, 2016 4:54 PM
To: pho...@li...
<mailto: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... <mailto:ls...@gm...> >
发送时间: 2016年1月13日 星期三
收件人: pho...@li...
<mailto: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... <mailto:hz...@ni...> ] 
Sent: Tuesday, January 12, 2016 6:02 PM
To: pho...@li...
<mailto: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... <mailto:ls...@gm...> >
发送时间: 2016年1月13日 星期三
收件人: pho...@li...
<mailto: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 

 

 

 



--
邵和助 Hezhu Shao, Ph.D
Ningbo Institute of Materials Technology and Engineering, Chinese Academy of
Sciences
No. 1219 Zhongguan West Road, Ningbo 315201, China
Tel. 86-574-87602652，18267460602