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Additionally I would suggest having a look at an introduction into
phonons and phonontheory, which is eg available by A. Togo:<br>
<a class="moz-txt-link-freetext" href="http://icms3.weebly.com/uploads/3/5/9/0/3590130/version2.pdf">http://icms3.weebly.com/uploads/3/5/9/0/3590130/version2.pdf</a> <br>
In this slides both phonon theory and the workflow of phonopy
(including the creation of the supercells) are well explained.<br>
Hope that helps!<br>
<br>
Kind regards<br>
Magdalena<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">Am 08.05.2016 um 19:26 schrieb Gavin
Abo:<br>
</div>
<blockquote cite="mid:dc5785d4-b05c-a3c6-fd05-3aefc42d54e0@crimson.ua.edu" type="cite">
<br>
<blockquote cite="mid:CAOsEhO-Cx765dDmgNVeGO6Eko5eLvYnCBySaZfgpaqMv5jfohQ@mail.gmail.com" type="cite">
<div dir="ltr">
<div>I want to calculate the Phonon spectra of A2BB'O6, which
has the Fm3m space group whose atomic position are<br>
</div>
<div>A (0.25 0.25 0.25)<br>
</div>
<div>B (0 0 0.5)<br>
</div>
<div>B' (0 0 0)<br>
</div>
<div>O (0 0 0.2376)<br>
</div>
<div>when i create the super cell and make the displacement on
that atom then it gives like this<br>
Number of non-equivalent atoms in BP.structS-001: 80<br>
Number of non-equivalent atoms in BP.structS-002: 80<br>
Number of non-equivalent atoms in BP.structS-003: 52<br>
Number of non-equivalent atoms in BP.structS-004: 52<br>
Number of non-equivalent atoms in BP.structS-005: 80<br>
Number of non-equivalent atoms in BP.structS-006: 52<br>
Number of non-equivalent atoms in BP.structS-007: 80<br>
Number of non-equivalent atoms in BP.structS-008: 52<br>
Number of non-equivalent atoms in BP.structS-009: 80<br>
Number of non-equivalent atoms in BP.structS-010: 80<br>
Number of non-equivalent atoms in BP.structS-011: 52<br>
Number of non-equivalent atoms in BP.structS-012: 52<br>
Number of non-equivalent atoms in BP.structS-013: 80<br>
Number of non-equivalent atoms in BP.structS-014: 80<br>
Number of non-equivalent atoms in BP.structS-015: 80<br>
Number of non-equivalent atoms in BP.structS-016: 80<br>
Number of non-equivalent atoms in BP.structS-017: 80<br>
Number of non-equivalent atoms in BP.structS-018: 80<br>
<br>
</div>
<div>So is it required to run the scf of all the 18 structS
file?<br>
</div>
</div>
</blockquote>
<br>
The phonopy documentation [ <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://atztogo.github.io/phonopy/wien2k.html">http://atztogo.github.io/phonopy/wien2k.html</a>
] says:<br>
<br>
<i>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.</i><br>
<br>
My understanding from the above two sentences is: Yes, the scf
needs to be ran for all structS-xxx files.<br>
<br>
<blockquote cite="mid:CAOsEhO-Cx765dDmgNVeGO6Eko5eLvYnCBySaZfgpaqMv5jfohQ@mail.gmail.com" type="cite">
<div dir="ltr">
<div>In the case of NaCl only two structS file generate after
the crating the displacement and also the same case happens
in the SrTiO3.<br>
<br>
</div>
<div>So please suggest me whether I am doing something is
wrong?<br>
</div>
</div>
</blockquote>
<br>
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 [
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg14199.html">http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg14199.html</a>
] . Implied from what I said before [
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg14200.html">http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg14200.html</a>
,
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg14219.html">http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg14219.html</a>
], I suspect that the BP.struct that you provided as input to
phonopy might not be correct.<br>
<br>
<blockquote cite="mid:CAOsEhO-Cx765dDmgNVeGO6Eko5eLvYnCBySaZfgpaqMv5jfohQ@mail.gmail.com" type="cite">
<div dir="ltr">
<div>which theory used to generate the structS file? <br>
</div>
</div>
</blockquote>
<br>
I currently don't know. However, you should be able to check the
structS files, phonopy source code [ <a moz-do-not-send="true" class="moz-txt-link-freetext" href="https://sourceforge.net/projects/phonopy/files/">https://sourceforge.net/projects/phonopy/files/</a>
], or ask the phonopy users/developers [ <a moz-do-not-send="true" class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/phonopy-users"><a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/phonopy-users">https://lists.sourceforge.net/lists/listinfo/phonopy-users</a></a>
] 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:<br>
<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://dft-blog.natanzon.eu/2010/06/using-phonopy-with-wien2k.html">http://dft-blog.natanzon.eu/2010/06/using-phonopy-with-wien2k.html</a><br>
<br>
<blockquote cite="mid:CAOsEhO-Cx765dDmgNVeGO6Eko5eLvYnCBySaZfgpaqMv5jfohQ@mail.gmail.com" type="cite">
<div dir="ltr">
<div>Why these 18 strcutS generate in my case? While i have
only four different atom.<br>
</div>
</div>
</blockquote>
<br>
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 [ <a moz-do-not-send="true" class="moz-txt-link-freetext" href="https://en.wikipedia.org/wiki/Garbage_in,_garbage_out"><a class="moz-txt-link-freetext" href="https://en.wikipedia.org/wiki/Garbage_in,_garbage_out">https://en.wikipedia.org/wiki/Garbage_in,_garbage_out</a></a>
].<br>
<br>
I don't know what you used for lattice parameters, A, B, and B',
but phonopy gave 5 structS-xxx for Ba2ZnWO6:<br>
<br>
A2BB'O6, where A = Ba, B = Zn, and B' = W [ <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://dx.doi.org/10.1016/j.commatsci.2013.04.053"><a class="moz-txt-link-freetext" href="http://dx.doi.org/10.1016/j.commatsci.2013.04.053">http://dx.doi.org/10.1016/j.commatsci.2013.04.053</a></a>
].<br>
<br>
username@computername:~/wiendata$ mkdir Ba2ZnWO6<br>
username@computername:~/wiendata$ cd Ba2ZnWO6/<br>
username@computername:~/wiendata/Ba2ZnWO6$ makestruct<br>
...<br>
TITLE :Ba2ZnWO6<br>
...<br>
Would you like to enter Spacegroup or Lattice (S/L)(def=S)? S<br>
...<br>
give SPACE GROUP as SYMBOL or NUMBER: 225<br>
...<br>
Units of lattice parameters (Bohr/Angstrom) (b/A) (def=ANG):A<br>
Lattice PARAMETERS as a b c (3 numbers):8.11 8.11 8.11<br>
ANGLES BETWEEN lattice vectors, as alpha beta gamma (def=90.0 90.0
90.0):90 90 90<br>
NUMBER INEQUEVALENT ATOMS :4<br>
ATOM 1 (ELEMENT): Ba<br>
POSITION OF ATOM Ba as X,Y,Z (def=0 0 0) :0.25 0.25 0.25<br>
ATOM 2 (ELEMENT): Zn<br>
POSITION OF ATOM Zn as X,Y,Z (def=0 0 0) :0 0 0<br>
ATOM 3 (ELEMENT): W<br>
POSITION OF ATOM W as X,Y,Z (def=0 0 0) :0.5 0.5 0.5<br>
ATOM 4 (ELEMENT): O<br>
POSITION OF ATOM O as X,Y,Z (def=0 0 0) :0.262 0 0 <br>
...<br>
SPECIFY possible REDUCTION of SPHERE RADII in % (def=0)<br>
2<br>
...<br>
rerun setrmt ?(y,N) (def=N): <br>
N<br>
...<br>
username@computername:~/wiendata/Ba2ZnWO6$ cp init.struct
Ba2ZnWO6.struct<br>
username@computername:~/wiendata/Ba2ZnWO6$ init_lapw -b<br>
...<br>
username@computername:~/wiendata/Ba2ZnWO6$ x supercell<br>
Program generates supercell from a WIEN struct file.<br>
<br>
Filename of struct file: <br>
Ba2ZnWO6.struct<br>
<br>
Number of cells in x direction: <br>
1<br>
Number of cells in y direction: <br>
1<br>
Number of cells in z direction: <br>
1<br>
Optional shift all atoms by the same amount (fractional
coordinates). <br>
Please enter x shift: <br>
0<br>
Please enter y shift: <br>
0<br>
Please enter z shift: <br>
0<br>
<br>
Current structure has lattice type F <br>
Enter your target lattice type: (P,B,F)<br>
P<br>
Target lattice type will be P <br>
<br>
Add vacuum in x-direction for surface-slab [bohr]:<br>
0<br>
Add vacuum in y-direction for surface-slab [bohr]:<br>
0<br>
Add vacuum in z-direction for surface slab [bohr]:<br>
0<br>
<br>
Supercell generated sucessfully.<br>
Stored in struct file:
Ba2ZnWO6_super.struct <br>
<br>
You may need to replace an atom by an impurity or distort the
positions, ....<br>
0.0u 0.0s 0:52.93 0.0% 0+0k 0+32io 0pf+0w<br>
username@computername:~/wiendata/Ba2ZnWO6$ cp
Ba2ZnWO6_super.struct Ba2ZnWO6.struct<br>
username@computername:~/wiendata/Ba2ZnWO6$ sed -n 2p
Ba2ZnWO6.struct<br>
P LATTICE,NONEQUIV. ATOMS 16 <br>
username@computername:~/wiendata/Ba2ZnWO6$ phonopy --wien2k -c
Ba2ZnWO6.struct -d --dim="2 2 2"<br>
_ <br>
_ __ | |__ ___ _ __ ___ _ __ _ _ <br>
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |<br>
| |_) | | | | (_) | | | | (_) || |_) | |_| |<br>
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |<br>
|_| |_| |___/<br>
1.10.5<br>
<br>
Python version 3.4.3<br>
Spglib version 1.9.0<br>
Creating displacements<br>
Settings:<br>
Supercell: [2 2 2]<br>
Spacegroup: Fm-3m (225)<br>
Number of non-equivalent atoms in Ba2ZnWO6.structS-001: 108<br>
Number of non-equivalent atoms in Ba2ZnWO6.structS-002: 84<br>
Number of non-equivalent atoms in Ba2ZnWO6.structS-003: 84<br>
Number of non-equivalent atoms in Ba2ZnWO6.structS-004: 208<br>
Number of non-equivalent atoms in Ba2ZnWO6.structS-005: 208<br>
<br>
disp.yaml and supercells have been created.<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
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