[Wien] Phonopy

Mon May 9 13:55:23 CEST 2016

Additionally I would suggest having a look at an introduction into 
phonons and phonontheory, which is eg available by A. Togo:
http://icms3.weebly.com/uploads/3/5/9/0/3590130/version2.pdf
In this slides both phonon theory and the workflow of phonopy (including 
the creation of the supercells) are well explained.
Hope that helps!

Kind regards
Magdalena

Am 08.05.2016 um 19:26 schrieb Gavin Abo:
>
>> I want to calculate the Phonon spectra of A2BB'O6, which has the Fm3m 
>> space group whose atomic position are
>> A (0.25 0.25 0.25)
>> B (0 0 0.5)
>> B' (0 0 0)
>> O (0 0 0.2376)
>> when i create the super cell and make the displacement on that atom 
>> then it gives like this
>> Number of non-equivalent atoms in BP.structS-001: 80
>> Number of non-equivalent atoms in BP.structS-002: 80
>> Number of non-equivalent atoms in BP.structS-003: 52
>> Number of non-equivalent atoms in BP.structS-004: 52
>> Number of non-equivalent atoms in BP.structS-005: 80
>> Number of non-equivalent atoms in BP.structS-006: 52
>> Number of non-equivalent atoms in BP.structS-007: 80
>> Number of non-equivalent atoms in BP.structS-008: 52
>> Number of non-equivalent atoms in BP.structS-009: 80
>> Number of non-equivalent atoms in BP.structS-010: 80
>> Number of non-equivalent atoms in BP.structS-011: 52
>> Number of non-equivalent atoms in BP.structS-012: 52
>> Number of non-equivalent atoms in BP.structS-013: 80
>> Number of non-equivalent atoms in BP.structS-014: 80
>> Number of non-equivalent atoms in BP.structS-015: 80
>> Number of non-equivalent atoms in BP.structS-016: 80
>> Number of non-equivalent atoms in BP.structS-017: 80
>> Number of non-equivalent atoms in BP.structS-018: 80
>>
>> So is it required to run the scf of all the 18 structS file?
>
> The phonopy documentation [ 
> http://atztogo.github.io/phonopy/wien2k.html ] says:
>
> /case.structS and case.structS-xxx (xxx are numbers) are the perfect 
> supercell and the supercells with displacements, respectively. Perhaps 
> these are renamed to case-xxx.struct and stored in case-xxx 
> directories, then to be calculated using Wien2k./
>
> My understanding from the above two sentences is: Yes, the scf needs 
> to be ran for all structS-xxx files.
>
>> In the case of NaCl only two structS file generate after the crating 
>> the displacement and also the same case happens in the SrTiO3.
>>
>> So please suggest me whether I am doing something is wrong?
>
> The 18 structS-xxx above look like they still might have been 
> generated from the spacegroup C2/m (12) seen in the terminal output 
> from phonopy [ 
> http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg14199.html 
> ] .  Implied from what I said before [ 
> http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg14200.html 
> , 
> http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg14219.html 
> ], I suspect that the BP.struct that you provided as input to phonopy 
> might not be correct.
>
>> which theory used to generate the structS file?
>
> I currently don't know.  However, you should be able to check the 
> structS files, phonopy source code [ 
> https://sourceforge.net/projects/phonopy/files/ ], or ask the phonopy 
> users/developers [ 
> https://lists.sourceforge.net/lists/listinfo/phonopy-users ] to 
> determine how the displacements are made.  At least in one case (i.e., 
> LiH), I read that the atoms might just be displaced by 0.01 angstrom:
>
> http://dft-blog.natanzon.eu/2010/06/using-phonopy-with-wien2k.html
>
>> Why these 18 strcutS generate in my case? While i have only four 
>> different atom.
>
> All I can currently say about that is: You gave phonopy BP.struct as 
> input and that is what the program determined that you needed as 
> output.  Though, it could be because of GIGO [ 
> https://en.wikipedia.org/wiki/Garbage_in,_garbage_out ].
>
> I don't know what you used for lattice parameters, A, B, and B', but 
> phonopy gave 5 structS-xxx for Ba2ZnWO6:
>
> A2BB'O6, where A = Ba, B = Zn, and B' = W [ 
> http://dx.doi.org/10.1016/j.commatsci.2013.04.053 ].
>
> username at computername:~/wiendata$ mkdir Ba2ZnWO6
> username at computername:~/wiendata$ cd Ba2ZnWO6/
> username at computername:~/wiendata/Ba2ZnWO6$ makestruct
> ...
> TITLE :Ba2ZnWO6
> ...
> Would you like to enter  Spacegroup or Lattice (S/L)(def=S)? S
> ...
> give SPACE GROUP as SYMBOL or NUMBER: 225
> ...
> Units of lattice parameters (Bohr/Angstrom) (b/A) (def=ANG):A
> Lattice PARAMETERS as a b c (3 numbers):8.11 8.11 8.11
> ANGLES BETWEEN lattice vectors, as alpha beta gamma (def=90.0 90.0 
> 90.0):90 90 90
> NUMBER INEQUEVALENT ATOMS :4
> ATOM  1 (ELEMENT): Ba
> POSITION OF ATOM Ba as X,Y,Z (def=0 0 0) :0.25 0.25 0.25
> ATOM  2 (ELEMENT): Zn
> POSITION OF ATOM Zn as X,Y,Z (def=0 0 0) :0 0 0
> ATOM  3 (ELEMENT): W
> POSITION OF ATOM W as X,Y,Z (def=0 0 0) :0.5 0.5 0.5
> ATOM  4 (ELEMENT): O
> POSITION OF ATOM O as X,Y,Z (def=0 0 0) :0.262 0 0
> ...
> SPECIFY possible REDUCTION of SPHERE RADII in % (def=0)
> 2
> ...
> rerun setrmt ?(y,N) (def=N):
> N
> ...
> username at computername:~/wiendata/Ba2ZnWO6$ cp init.struct Ba2ZnWO6.struct
> username at computername:~/wiendata/Ba2ZnWO6$ init_lapw -b
> ...
> username at computername:~/wiendata/Ba2ZnWO6$ x supercell
>  Program generates supercell from a WIEN struct file.
>
>  Filename of struct file:
> Ba2ZnWO6.struct
>
>  Number of cells in x direction:
> 1
>  Number of cells in y direction:
> 1
>  Number of cells in z direction:
> 1
>  Optional shift all atoms by the same amount (fractional coordinates).
>  Please enter x shift:
> 0
>  Please enter y shift:
> 0
>  Please enter z shift:
> 0
>
>  Current structure has lattice type F
>  Enter your target lattice type: (P,B,F)
> P
>  Target lattice type will be P
>
>  Add vacuum in x-direction for surface-slab [bohr]:
> 0
>  Add vacuum in y-direction for surface-slab [bohr]:
> 0
>  Add vacuum in z-direction for surface slab [bohr]:
> 0
>
>  Supercell generated sucessfully.
>  Stored in struct file: Ba2ZnWO6_super.struct
>
>  You may need to replace an atom by an impurity or distort the 
> positions, ....
> 0.0u 0.0s 0:52.93 0.0% 0+0k 0+32io 0pf+0w
> username at computername:~/wiendata/Ba2ZnWO6$ cp Ba2ZnWO6_super.struct 
> Ba2ZnWO6.struct
> username at computername:~/wiendata/Ba2ZnWO6$ sed -n 2p Ba2ZnWO6.struct
> P   LATTICE,NONEQUIV. ATOMS 16
> username at computername:~/wiendata/Ba2ZnWO6$ phonopy --wien2k -c 
> Ba2ZnWO6.struct -d --dim="2 2 2"
>         _
>   _ __ | |__   ___  _ __   ___   _ __  _   _
>  | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
>  | |_) | | | | (_) | | | | (_) || |_) | |_| |
>  | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
>  |_|                            |_|    |___/
>                                       1.10.5
>
> Python version 3.4.3
> Spglib version 1.9.0
> Creating displacements
> Settings:
>   Supercell: [2 2 2]
> Spacegroup: Fm-3m (225)
> Number of non-equivalent atoms in Ba2ZnWO6.structS-001: 108
> Number of non-equivalent atoms in Ba2ZnWO6.structS-002: 84
> Number of non-equivalent atoms in Ba2ZnWO6.structS-003: 84
> Number of non-equivalent atoms in Ba2ZnWO6.structS-004: 208
> Number of non-equivalent atoms in Ba2ZnWO6.structS-005: 208
>
> disp.yaml and supercells have been created.
>
>
> _______________________________________________
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> SEARCH the MAILING-LIST at:  http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20160509/3649d008/attachment.html>
-------------- next part --------------
_______________________________________________
Wien mailing list
Wien at zeus.theochem.tuwien.ac.at
http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
SEARCH the MAILING-LIST at:  http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html