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<div class="moz-cite-prefix">Take NaCl for example.<br>
<br>
Its cubic unit cell (alpha = beta = gamma = 90 deg) has space
group 225, a lattice constant (a = b = c) of about 5.6 ang, and
two nonequivalent positions (Cl: 0, 0, 0; Na: 0.5, 0.5, 0.5) [
<a class="moz-txt-link-freetext" href="http://www.ilpi.com/inorganic/structures/nacl/">http://www.ilpi.com/inorganic/structures/nacl/</a> ].<br>
<br>
First, do it the wrong way using the NaCl unit cell struct file
having the spacegroup 225 with F lattice as the input for
phonopy. You expect phonopy to give spacegroup 225 as output in
the terminal. However, the wrong input (F lattice) was used for
phonopy, so it gives spacegroup 221 as the output:<br>
<br>
username@computername:~/wiendata/NaCl$ sed -n 2p NaCl.struct<br>
F LATTICE,NONEQUIV.ATOMS: 2 225_Fm-3m <br>
username@computername:~/wiendata/NaCl$ phonopy --wien2k -c
NaCl.struct -d --dim="2 2 2"<br>
...<br>
Spacegroup: Pm-3m (221)<br>
Number of non-equivalent atoms in NaCl.structS-001: 8<br>
Number of non-equivalent atoms in NaCl.structS-002: 8<br>
...<br>
<br>
Spacegroups can have atomic positions where atoms are free to move
and others where atoms cannot move as they are fixed. The atomic
positions for NaCl in the spacegroup 225 are fixed [
<a class="moz-txt-link-freetext" href="http://www.wien2k.at/reg_user/textbooks/WIEN2k_lecture-notes_2013/WIEN2k-getting_started.pdf">http://www.wien2k.at/reg_user/textbooks/WIEN2k_lecture-notes_2013/WIEN2k-getting_started.pdf</a>
(slide 36) ]. Thus, it is not possible to displace the NaCl
atomic positions in the spacegroup 225 [
<a class="moz-txt-link-freetext" href="http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg00119.html">http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg00119.html</a>
]. <br>
<br>
Now, do it correctly by following the instructions in phonopy
documentation [
<a class="moz-txt-link-freetext" href="http://atztogo.github.io/phonopy/wien2k.html#wien2k-interface">http://atztogo.github.io/phonopy/wien2k.html#wien2k-interface</a> ].<br>
<br>
Convert NaCl having spacegroup 225 (F lattice) to its equivalent
representation in the general P lattice: <br>
<br>
username@computername:~/wiendata/NaCl$ sed -n 2p NaCl.struct<br>
F LATTICE,NONEQUIV.ATOMS: 2 225_Fm-3m <br>
username@computername:~/wiendata/NaCl$ x supercell<br>
Program generates supercell from a WIEN struct file.<br>
<br>
Filename of struct file: <br>
NaCl.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:
NaCl_super.struct <br>
<br>
You may need to replace an atom by an impurity or distort the
positions, ....<br>
0.0u 0.0s 0:19.31 0.0% 0+0k 0+16io 0pf+0w<br>
username@computername:~/wiendata/NaCl$ cp NaCl_super.struct
NaCl.struct<br>
username@computername:~/wiendata/NaCl$ sed -n 2p NaCl.struct<br>
P LATTICE,NONEQUIV. ATOMS 8 <br>
<br>
Unlike NaCl with spacegroup 225, the 1x1x1 supercell
representation of NaCl with P lattice has no spacegroup associated
with it [ <a class="moz-txt-link-freetext" href="http://www.wien2k.at/reg_user/faq/supercells.html">http://www.wien2k.at/reg_user/faq/supercells.html</a> ].
Since the P lattice has no spacegroup, there is no longer the
restriction of the 225 spacegroup that the NaCl positions are
fixed. Thus, the NaCl positions are free and can be displaced in
the P lattice.<br>
<br>
The initial NaCl.struct with P lattice has no displacement.
Therefore, the symmetry of the supercell can be expected to reduce
to the spacegroup 225. In WIEN2k, there is "x sgroup" for
determining the spacegroup. However, phonopy has its own way of
determining the spacegroup (note: it has a built-in symmetry
finder [
<a class="moz-txt-link-freetext" href="https://sourceforge.net/p/phonopy/mailman/message/25001819/">https://sourceforge.net/p/phonopy/mailman/message/25001819/</a> ]),
and it detects the expected spacegroup 225 when NaCl.struct is
given in the P lattice format as input: <br>
<br>
username@computername:~/wiendata/NaCl$ phonopy --wien2k -c
NaCl.struct -d --dim="2 2 2"<br>
...<br>
Creating displacements<br>
Settings:<br>
Supercell: [2 2 2]<br>
Spacegroup: Fm-3m (225)<br>
Number of non-equivalent atoms in NaCl.structS-001: 24<br>
Number of non-equivalent atoms in NaCl.structS-002: 24<br>
...<br>
<br>
Togo mentioned another reason why the spacegroup 225 case.struct
file cannot be used for phonopy [
<a class="moz-txt-link-freetext" href="https://sourceforge.net/p/phonopy/mailman/message/26200243/">https://sourceforge.net/p/phonopy/mailman/message/26200243/</a> ]:<br>
<br>
<i>I didn't want to implement a full Wien2k structure parser, so I
just decided to implement only for P1.</i><br>
<br>
The files with the displacements (NaCl.structS-001 and
NaCl.structS-002) of the atomic positions have the P lattice, not
the spacegroup 225, as expected:<br>
<br>
username@computername:~/wiendata/NaCl$ sed -n 2p NaCl.structS-001<br>
P LATTICE,NONEQUIV.ATOMS: 64<br>
username@computername:~/wiendata/NaCl$ sed -n 2p NaCl.structS-002<br>
P LATTICE,NONEQUIV.ATOMS: 64<br>
<br>
So that looks fine.<br>
<br>
Of course, if the atomic position of an atom is displaced, that
could change the forces on atoms in the structure [
<a class="moz-txt-link-freetext" href="https://en.wikipedia.org/wiki/Coulomb%27s_law">https://en.wikipedia.org/wiki/Coulomb%27s_law</a> ] and the spacegroup
of the structure. Indeed, if you check NaCl.structS-001 and
NaCl.structS-002, it looks like they will have spacegroup 99
(P4mm) from the output of "x sgroup".<br>
<br>
On 5/1/2016 1:41 AM, Rajneesh Chaurasiya wrote:<br>
</div>
<blockquote
cite="mid:CAOsEhO9DmOVriSebJ+n8i9Bs2JzoJ+RHyfGWZXi0Brrcyv=n=w@mail.gmail.com"
type="cite">
<div dir="ltr">
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<div>Dear Gavin, <br>
</div>
Are you sure that after changing the space group of
material it will not effect the phonon calculation.<br>
</div>
because after changing the space group of crystal
structure all the atom position changes and calculate
forces on that atoms will not be same as the previous one
space group. <br>
</div>
I have verified this problem in your given examples of NaCl
and SrTiO3.<br>
<br>
</div>
So can you explain this problem in more details???<br>
<br>
</div>
Thank you <br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Apr 27, 2016 at 2:29 PM,
Rajneesh Chaurasiya <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:rajnano2012@gmail.com"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:rajnano2012@gmail.com">rajnano2012@gmail.com</a></a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><span class="">
<div style="font-size:12.8px">
<div>
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<div>
<div>
<div>Dear Sir,<br>
<br>
</div>
I have computed the phonon spectrum of example
of NaCl and SrTiO3 successfully now when i
started the new calculation. in that
calculation i construct the case.struct file
and after initialization i make a supercell (2
2 2) and create a displacement then it change
change the space group. initially my space
group is Fm3m and after creating the
displacement it become C2/m. I thing some
thing is happening in a unusual way so any one
can help?<br>
<br>
</div>
The procedure which i follow.<br>
<br>
</div>
makestruct..<br>
</div>
cp init.struct BP.struct<br>
</div>
init_lapw<br>
phonopy --wien2k -c BP.struct -d --dim="2 2 2" <br>
</div>
<span style="font-size:12.8px"> at this steps the erorrs
looks like...</span>
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px"><br>
</span></div>
</span>
<div>_ __ | |__ ___ _ __ ___ _ __ _ _ <br>
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |<br>
| |_) | | | | (_) | | | | (_) || |_) | |_| |<br>
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |<br>
|_| |_| |___/<br>
1.10.0<br>
<br>
Python version 2.7.11<br>
Creating displacements<br>
Settings:<br>
Supercell: [2 2 2]<br>
Spacegroup: C2/m (12)<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>
disp.yaml and supercells have been created.<br>
_ <br>
___ _ __ __| |<br>
/ _ \ '_ \ / _` |<br>
| __/ | | | (_| |<br>
\___|_| |_|\__,_|<span style="font-size:12.8px"><br>
</span></div>
<span class="">
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px"><br clear="all">
</span>
<div><br>
</div>
-- <br>
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">Thanks & Regards
<div>Rajneesh Chaurasiya</div>
<div>Junior Research Fellow</div>
<div>IIT,Jodhpur, India<br>
</div>
<div>Mob. No. +91-9584499697<br>
+91-7610950803<br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</span></div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
<div class="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">Thanks & Regards
<div>Rajneesh Chaurasiya</div>
<div>Junior Research Fellow</div>
<div>IIT,Jodhpur, India<br>
</div>
<div>Mob. No. +91-9584499697<br>
+91-7610950803<br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
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