[Wien] Phonopy

[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.
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