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@computername:~/wiendata$ mkdir Ba2ZnWO6
username@computername:~/wiendata$ cd Ba2ZnWO6/
username@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@computername:~/wiendata/Ba2ZnWO6$ cp init.struct Ba2ZnWO6.struct
username@computername:~/wiendata/Ba2ZnWO6$ init_lapw -b
...
username@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@computername:~/wiendata/Ba2ZnWO6$ cp Ba2ZnWO6_super.struct
Ba2ZnWO6.struct
username@computername:~/wiendata/Ba2ZnWO6$ sed -n 2p Ba2ZnWO6.struct
P LATTICE,NONEQUIV. ATOMS 16
username@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@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
