[Wien] scf2forces

Bichler Magdalena magdalena.bichler at tuwien.ac.at
Thu Apr 21 08:22:36 CEST 2016 

First of all you must create structS files with phonopy and calculate the forces in these files with WIEN2k, which are in the case.scf files

Von meinem iPhone gesendet

Am 21.04.2016 um 08:10 schrieb Rajneesh Chaurasiya <rajnano2012 at gmail.com<mailto:rajnano2012 at gmail.com>>:

Dear Gavin,

I have successfully installed the phonopy 1.10.0 and run the example. but when i compute phonon part of our new material then it required case-001.scf case-002.scf to generate the FORCE_SETS file.
So please suggest me how i generate the case-001.scf case-002.scf file

Thank you



On Mon, Apr 11, 2016 at 8:19 PM, Rajneesh Chaurasiya <rajnano2012 at gmail.com<mailto:rajnano2012 at gmail.com>> wrote:

Dear Sir,
I installed the phonopy version 10.0 successfully but i put the command line it showing the error like this.
Please suggest me.

[ambeshst at IITJ_HPC NaCl-wien2k]$ phonopy --wien2k -c NaCl.struct -p band.conf
        _
  _ __ | |__   ___  _ __   ___   _ __  _   _
 | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
 | |_) | | | | (_) | | | | (_) || |_) | |_| |
 | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
 |_|                            |_|    |___/
                                      1.10.0

Python version 2.7.11
Band structure mode
Settings:
  Supercell: [2 2 2]
  Primitive axis:
    [ 0.   0.5  0.5]
    [ 0.5  0.   0.5]
    [ 0.5  0.5  0. ]
Spacegroup: Fm-3m (225)
Computing force constants...
Reciprocal space paths in reduced coordinates:
[ 0.00  0.00  0.00] --> [ 0.50  0.00  0.00]
[ 0.50  0.00  0.00] --> [ 0.50  0.50  0.00]
[ 0.50  0.50  0.00] --> [-0.00 -0.00  0.00]
[ 0.00  0.00  0.00] --> [ 0.50  0.50  0.50]
Traceback (most recent call last):
  File "/home/IITJHOME/ambeshst/win2k13mpi/python/bin/phonopy", line 938, in <module>
    plot = phonon.plot_band_structure(symbols=settings.get_band_labels())
  File "/home/IITJHOME/ambeshst/win2k13mpi/python/lib/python2.7/site-packages/phonopy/api_phonopy.py", line 510, in plot_band_structure
    import matplotlib.pyplot as plt
  File "/home/IITJHOME/ambeshst/win2k13mpi/python/lib/python2.7/site-packages/matplotlib-1.5.0-py2.7-linux-x86_64.egg/matplotlib/__init__.py", line 124, in <module>
    from matplotlib.rcsetup import (defaultParams,
  File "/home/IITJHOME/ambeshst/win2k13mpi/python/lib/python2.7/site-packages/matplotlib-1.5.0-py2.7-linux-x86_64.egg/matplotlib/rcsetup.py", line 25, in <module>
    from matplotlib.fontconfig_pattern import parse_fontconfig_pattern
  File "/home/IITJHOME/ambeshst/win2k13mpi/python/lib/python2.7/site-packages/matplotlib-1.5.0-py2.7-linux-x86_64.egg/matplotlib/fontconfig_pattern.py", line 25, in <module>
    from pyparsing import Literal, ZeroOrMore, \
ImportError: No module named pyparsing


On Wed, Mar 30, 2016 at 4:15 PM, Rajneesh Chaurasiya <rajnano2012 at gmail.com<mailto:rajnano2012 at gmail.com>> wrote:
Dear Gavin.

as per your suggestion when i try to install the phonopy-1.10.5 the error looks like

File "setup.py", line 88
    with open("phonopy/version.py") as w:
            ^
SyntaxError: invalid syntax

by giving the command line
[ambeshst at IITJ_HPC phono3py-1.10.5]$ python setup.py install


On Tue, Mar 29, 2016 at 3:44 PM, Rajneesh Chaurasiya <rajnano2012 at gmail.com<mailto:rajnano2012 at gmail.com>> wrote:
Dear Gavin,

I think, I installed the Phonopy successfully and set the Path correctly.  but when i give the command

[ambeshst at IITJ_HPC tests]$ phonopy --wien2k -c NaCl.struct -d --dim="2 2 2"

It showing the syntax error

raceback (most recent call last):
  File "/home/IITJHOME/ambeshst/win2k13mpi/python35/bin/phonopy", line 496, in <module>
    from phonopy.interface.wien2k import write_supercells_with_displacements
  File "/home/IITJHOME/ambeshst/win2k13mpi/python35/lib/python3.5/site-packages/phonopy/interface/wien2k.py", line 65
    print "%s contains only forces of %d atoms" % (
                                              ^
SyntaxError: invalid syntax


Please give me your ideas why it is showing this error.


On Tue, Mar 29, 2016 at 11:39 AM, Rajneesh Chaurasiya <rajnano2012 at gmail.com<mailto:rajnano2012 at gmail.com>> wrote:
Dear Gavin,

I have again installed the Python 3.5 and Phonopy in my HPC as per your suggestion but it couldn't work properly.

I follow the steps as per your previous guidelines.

I got the following error


-bash: phonopy: command not found

When i give the command

[ambeshst at IITJ_HPC NaCl-wien2k]$ phonopy --wien2k -c NaCl.struct -d --dim="2 2 2"

Please aware me for my mistakes

On Sat, Feb 20, 2016 at 12:14 PM, Rajneesh Chaurasiya <rajnano2012 at gmail.com<mailto:rajnano2012 at gmail.com>> wrote:

Dear gavin,

I have modified the .bashrc file, which i am attaching through this mail and also the some one image file which contains the file inside the python folder.

please find the attached files and give your suggestions..

On Tue, Feb 16, 2016 at 3:19 PM, Rajneesh Chaurasiya <rajnano2012 at gmail.com<mailto:rajnano2012 at gmail.com>> wrote:
I have modified the file according to your suggestion but still there is same error...

Traceback (most recent call last):
  File "/home/IITJHOME/ambeshst/win2k13mpi/phonopy", line 40, in ?
    from phonopy import *
ImportError: No module named phonopy


I am attaching the .bashrc file so please check whether this is correct or not..
please suggest your suggestion..


On Sat, Feb 13, 2016 at 12:38 PM, Rajneesh Chaurasiya <rajnano2012 at gmail.com<mailto:rajnano2012 at gmail.com>> wrote:


Dear Gavin,

I have installed newer version of phonopy package https://sourceforge.net/projects/phonopy/files/phonopy/phonopy-1.10/phonopy-1.10.0.tar.gz/download and it required the scf2forces which i get from http://www.wien2k.at/reg_user/unsupported/ but it showing the error, which i have seen in the previous message. but as per your suggestion if i use he experimental support option in Phonopy 1.10.0 [ http://atztogo.github.io/phonopy/wien2k.html#wien2k-interface ]: means phonopy --wien2k -f case-001.scf case-002.scf then it showing error some error.


Traceback (most recent call last):
  File "/home/IITJHOME/ambeshst/win2k13mpi/phonopy", line 40, in ?
    from phonopy import *
ImportError: No module named phonopy


 so i dont know that the installed phonopy is compatible with the wien2k or not.

please give me your ideas why this is happening.




--
Thanks & Regards
Rajneesh Chaurasiya
Junior Research Fellow
IIT,Jodhpur, India
Mob. No. +91-9584499697
              +91-7610950803



--
Thanks & Regards
Rajneesh Chaurasiya
Junior Research Fellow
IIT,Jodhpur, India
Mob. No. +91-9584499697
              +91-7610950803



--
Thanks & Regards
Rajneesh Chaurasiya
Junior Research Fellow
IIT,Jodhpur, India
Mob. No. +91-9584499697
              +91-7610950803



--
Thanks & Regards
Rajneesh Chaurasiya
Junior Research Fellow
IIT,Jodhpur, India
Mob. No. +91-9584499697
              +91-7610950803



--
Thanks & Regards
Rajneesh Chaurasiya
Junior Research Fellow
IIT,Jodhpur, India
Mob. No. +91-9584499697
              +91-7610950803
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