Re: [Wien] Phonopy

[Magdalena Bichler]

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@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
...

Re: [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@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
 

Re: [Wien] Phonopy

[Rajneesh Chaurasiya]

Dear Wien2k Users,


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?
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?
which theory used to generate the structS file?
Why these 18 strcutS generate in my case? While i have only four different
atom.

Thank You

On Sun, May 1, 2016 at 1:11 PM, Rajneesh Chaurasiya 
wrote:

> Dear Gavin,
> Are you sure that after changing the space group of material it will not
> effect the phonon calculation.
> 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.
> I have verified this problem in your given examples of NaCl and SrTiO3.
>
> So can you explain this problem in more details???
>
> Thank you
>
> On Wed, Apr 27, 2016 at 2:29 PM, Rajneesh Chaurasiya <
> rajnano2...@gmail.com> wrote:
>
>> Dear Sir,
>>
>> 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?
>>
>> The procedure which i follow.
>>
>> makestruct..
>> cp init.struct BP.struct
>> init_lapw
>> phonopy --wien2k -c BP.struct -d --dim="2 2 2"
>>  at this steps the erorrs looks like...
>>
>>
>> _ __ | |__   ___  _ __   ___   _ __  _   _
>>  | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
>>  | |_) | | | | (_) | | | | (_) || |_) | |_| |
>>  | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
>>  |_||_||___/
>>   1.10.0
>>
>> Python version 2.7.11
>> Creating displacements
>> Settings:
>>   Supercell: [2 2 2]
>> Spacegroup: C2/m (12)
>> 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
>>
>> disp.yaml and supercells have been created.
>>  _
>>___ _ __   __| |
>>   / _ \ '_ \ / _` |
>>  |  __/ | | | (_| |
>>   \___|_| |_|\__,_|
>>
>>
>>
>> --
>> Thanks & Regards
>> Rajneesh Chaurasiya
>> Junior Research Fellow
>> IIT,Jodhpur, India
>> Mob. No. +91-9584499697
>>   +91-7610950803
>>
>
>
>
> --
> Thanks & Regards
> Rajneesh Chaurasiya
> Junior Research Fellow
> IIT,Jodhpur, India
> Mob. No. +91-9584499697
>   +91-7610950803
>



-- 
Thanks & Regards
Rajneesh Chaurasiya
Junior Research Fellow
IIT,Jodhpur, India
Mob. No. +91-9584499697
  +91-7610950803

Re: [Wien] Phonopy

[Gavin Abo]

Take NaCl for example.

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) [ 
http://www.ilpi.com/inorganic/structures/nacl/ ].


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:


username@computername:~/wiendata/NaCl$ sed -n 2p NaCl.struct
F   LATTICE,NONEQUIV.ATOMS:  2 225_Fm-3m
username@computername:~/wiendata/NaCl$ phonopy --wien2k -c NaCl.struct 
-d --dim="2 2 2"

...
Spacegroup: Pm-3m (221)
Number of non-equivalent atoms in NaCl.structS-001: 8
Number of non-equivalent atoms in NaCl.structS-002: 8
...

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 [ 
http://www.wien2k.at/reg_user/textbooks/WIEN2k_lecture-notes_2013/WIEN2k-getting_started.pdf 
(slide 36) ].  Thus, it is not possible to displace the NaCl atomic 
positions in the spacegroup 225 [ 
http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg00119.html 
].


Now, do it correctly by following the instructions in phonopy 
documentation [ 
http://atztogo.github.io/phonopy/wien2k.html#wien2k-interface ].


Convert NaCl having spacegroup 225 (F lattice) to its equivalent 
representation in the general P lattice:


username@computername:~/wiendata/NaCl$ sed -n 2p NaCl.struct
F   LATTICE,NONEQUIV.ATOMS:  2 225_Fm-3m
username@computername:~/wiendata/NaCl$ x supercell
 Program generates supercell from a WIEN struct file.

 Filename of struct file:
NaCl.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: NaCl_super.struct

 You may need to replace an atom by an impurity or distort the 
positions, 

0.0u 0.0s 0:19.31 0.0% 0+0k 0+16io 0pf+0w
username@computername:~/wiendata/NaCl$ cp NaCl_super.struct NaCl.struct
username@computername:~/wiendata/NaCl$ sed -n 2p NaCl.struct
P   LATTICE,NONEQUIV. ATOMS  8

Unlike NaCl with spacegroup 225, the 1x1x1 supercell representation of 
NaCl with P lattice has no spacegroup associated with it [ 
http://www.wien2k.at/reg_user/faq/supercells.html ]. 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.


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 [ 
https://sourceforge.net/p/phonopy/mailman/message/25001819/ ]), and it 
detects the expected spacegroup 225 when NaCl.struct is given in the P 
lattice format as input:


username@computername:~/wiendata/NaCl$ phonopy --wien2k -c NaCl.struct 
-d --dim="2 2 2"

...
Creating displacements
Settings:
  Supercell: [2 2 2]
Spacegroup: Fm-3m (225)
Number of non-equivalent atoms in NaCl.structS-001: 24
Number of non-equivalent atoms in NaCl.structS-002: 24
...

Togo mentioned another reason why the spacegroup 225 case.struct file 
cannot be used for phonopy [ 
https://sourceforge.net/p/phonopy/mailman/message/26200243/ ]:


/I didn't want to implement a full Wien2k structure parser, so I just 
decided to implement only for P1./


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:


username@computername:~/wiendata/NaCl$ sed -n 2p NaCl.structS-001
P   LATTICE,NONEQUIV.ATOMS: 64
username@computername:~/wiendata/NaCl$ sed -n 2p NaCl.structS-002
P   LATTICE,NONEQUIV.ATOMS: 64

So that looks fine.

Of course, if the atomic position of an atom is displaced, that could 
change the forces on atoms in the structure [ 
https://en.wikipedia.org/wiki/Coulomb%27s_law ] 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".


On 5/1/2016 1:41 AM, Rajneesh Chaurasiya 

Re: [Wien] Phonopy

[Rajneesh Chaurasiya]

Dear Gavin,
Are you sure that after changing the space group of material it will not
effect the phonon calculation.
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.
I have verified this problem in your given examples of NaCl and SrTiO3.

So can you explain this problem in more details???

Thank you

On Wed, Apr 27, 2016 at 2:29 PM, Rajneesh Chaurasiya 
wrote:

> Dear Sir,
>
> 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?
>
> The procedure which i follow.
>
> makestruct..
> cp init.struct BP.struct
> init_lapw
> phonopy --wien2k -c BP.struct -d --dim="2 2 2"
>  at this steps the erorrs looks like...
>
>
> _ __ | |__   ___  _ __   ___   _ __  _   _
>  | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
>  | |_) | | | | (_) | | | | (_) || |_) | |_| |
>  | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
>  |_||_||___/
>   1.10.0
>
> Python version 2.7.11
> Creating displacements
> Settings:
>   Supercell: [2 2 2]
> Spacegroup: C2/m (12)
> 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
>
> disp.yaml and supercells have been created.
>  _
>___ _ __   __| |
>   / _ \ '_ \ / _` |
>  |  __/ | | | (_| |
>   \___|_| |_|\__,_|
>
>
>
> --
> Thanks & Regards
> Rajneesh Chaurasiya
> Junior Research Fellow
> IIT,Jodhpur, India
> Mob. No. +91-9584499697
>   +91-7610950803
>



-- 
Thanks & Regards
Rajneesh Chaurasiya
Junior Research Fellow
IIT,Jodhpur, India
Mob. No. +91-9584499697
  +91-7610950803
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Re: [Wien] Phonopy

[Gavin Abo]

initially my space group is Fm3m => Phonopy needs case.struct with P 
lattice to work correctly  [1, 2].


[1] https://sourceforge.net/p/phonopy/mailman/message/25001819/
[2] http://atztogo.github.io/phonopy/wien2k.html

On 4/27/2016 2:59 AM, Rajneesh Chaurasiya wrote:

Dear Sir,

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?


The procedure which i follow.

makestruct..
cp init.struct BP.struct
init_lapw
phonopy --wien2k -c BP.struct -d --dim="2 2 2"
 at this steps the erorrs looks like...


_ __ | |__   ___  _ __   ___   _ __  _   _
 | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
 | |_) | | | | (_) | | | | (_) || |_) | |_| |
 | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
 |_||_||___/
  1.10.0

Python version 2.7.11
Creating displacements
Settings:
  Supercell: [2 2 2]
Spacegroup: C2/m (12)
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

disp.yaml and supercells have been created.
 _
   ___ _ __   __| |
  / _ \ '_ \ / _` |
 |  __/ | | | (_| |
  \___|_| |_|\__,_|



--
Thanks & Regards
Rajneesh Chaurasiya
Junior Research Fellow
IIT,Jodhpur, India
Mob. No. +91-9584499697
  +91-7610950803
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[Wien] Phonopy

[Rajneesh Chaurasiya]

Dear Sir,

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?

The procedure which i follow.

makestruct..
cp init.struct BP.struct
init_lapw
phonopy --wien2k -c BP.struct -d --dim="2 2 2"
 at this steps the erorrs looks like...


_ __ | |__   ___  _ __   ___   _ __  _   _
 | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
 | |_) | | | | (_) | | | | (_) || |_) | |_| |
 | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
 |_||_||___/
  1.10.0

Python version 2.7.11
Creating displacements
Settings:
  Supercell: [2 2 2]
Spacegroup: C2/m (12)
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

disp.yaml and supercells have been created.
 _
   ___ _ __   __| |
  / _ \ '_ \ / _` |
 |  __/ | | | (_| |
  \___|_| |_|\__,_|



-- 
Thanks & Regards
Rajneesh Chaurasiya
Junior Research Fellow
IIT,Jodhpur, India
Mob. No. +91-9584499697
  +91-7610950803
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SEARCH the MAILING-LIST at:  
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[Wien] Phonopy

[Rajneesh Chaurasiya]

Dear Sir,

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?

The procedure which i follow.

makestruct..
cp init.struct BP.struct
init_lapw
phonopy --wien2k -c BP.struct -d --dim="2 2 2"
 at this steps the erorrs looks like...





-- 
Thanks & Regards
Rajneesh Chaurasiya
Junior Research Fellow
IIT,Jodhpur, India
Mob. No. +91-9584499697
  +91-7610950803
___
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[Wien] phonopy

[Rajneesh Chaurasiya]

Dear gavin,

I have modified the .bashrc file, which i am attaching through this mail
and also the some one image file which contains the file inside the python
folder.

please find the attached files and give your suggestions..


bashrc
Description: Binary data
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[Wien] PHONOPY and symmetry

[Luis Ogando]

Dear WIEN2k community,

   I am trying to use PHONOPY to calculate phonon dispersion curves for InP
in the zincblend phase as a test. I used an optimized structural parameter
to build a 3x3x3 supercell using the supercell utility program. After
that, PHONOPY built two other supercells displacing atoms 1 and 109 by 0.02
Bohr along x direction.
   Now, it is important to say that PHONOPY works with P1 symmetry, what
means I can use the new cell suggested by nn, but not the one suggested
by sgroup during initialization.
   Everything went smoothly when I initialized the calculation for the
first supercell (that one with displacement for atom 1) accepting twice the
cell generated by nn, but I got the following error message for the
second cell (that one with displacement for atom 109).
   Finally, I would like to mention that if I accept the cell suggested by
sgroup, everything goes fine for the second cell, but this is not
suitable for PHONOPY as mentioned above.
   I would appreciate any help with this issue.
   The case.struct is too big for the mailing list (64 KB), but I can send
it to the personal e-mail of anyone interested in.
   The error message is at the end of this message.
   All the best,
 Luis



-- ERROR --
 ERROR: (multiplicity of atom  31 )*(number of
pointgroup-operations)
 ERROR: is NOT = (number of spacegroup-operations)
 ERROR: MULT:   2  ISYM:   1  NSYM   4
 ERROR: Check your struct file withx sgroup
 -- ERROR --
 -- ERROR --
 ERROR: (multiplicity of atom  32 )*(number of
pointgroup-operations)
 ERROR: is NOT = (number of spacegroup-operations)
 ERROR: MULT:   2  ISYM:   1  NSYM   4
 ERROR: Check your struct file withx sgroup
 -- ERROR --
 -- ERROR --
 ERROR: (multiplicity of atom  33 )*(number of
pointgroup-operations)
 ERROR: is NOT = (number of spacegroup-operations)
 ERROR: MULT:   2  ISYM:   1  NSYM   4
 ERROR: Check your struct file withx sgroup
 -- ERROR --
 -- ERROR --
 ERROR: (multiplicity of atom  37 )*(number of
pointgroup-operations)
 ERROR: is NOT = (number of spacegroup-operations)
 ERROR: MULT:   1  ISYM:   2  NSYM   4
 ERROR: Check your struct file withx sgroup
 -- ERROR --
 -- ERROR --
 ERROR: (multiplicity of atom  38 )*(number of
pointgroup-operations)
 ERROR: is NOT = (number of spacegroup-operations)
 ERROR: MULT:   1  ISYM:   2  NSYM   4
 ERROR: Check your struct file withx sgroup
 -- ERROR --
 -- ERROR --
 ERROR: (multiplicity of atom  39 )*(number of
pointgroup-operations)
 ERROR: is NOT = (number of spacegroup-operations)
 ERROR: MULT:   1  ISYM:   2  NSYM   4
 ERROR: Check your struct file withx sgroup
 -- ERROR --
 -- ERROR --
 ERROR: (multiplicity of atom  52 )*(number of
pointgroup-operations)
 ERROR: is NOT = (number of spacegroup-operations)
 ERROR: MULT:   2  ISYM:   1  NSYM   4
 ERROR: Check your struct file withx sgroup
 -- ERROR --
 -- ERROR --
 ERROR: (multiplicity of atom  53 )*(number of
pointgroup-operations)
 ERROR: is NOT = (number of spacegroup-operations)
 ERROR: MULT:   2  ISYM:   1  NSYM   4
 ERROR: Check your struct file withx sgroup
 -- ERROR --
 -- ERROR --
 ERROR: (multiplicity of atom  54 )*(number of
pointgroup-operations)
 ERROR: is NOT = (number of spacegroup-operations)
 ERROR: MULT:   2  ISYM:   1  NSYM   4
 ERROR: Check your struct file withx sgroup
 -- ERROR --
 -- ERROR --
 ERROR: (multiplicity of atom  63 )*(number of
pointgroup-operations)
 ERROR: is NOT = (number of spacegroup-operations)
 ERROR: MULT:   1  ISYM:   2  NSYM   4
 ERROR: Check your struct file withx sgroup
 -- ERROR --
 -- ERROR --
 ERROR: (multiplicity of atom  64 )*(number of
pointgroup-operations)
 ERROR: is NOT = (number of spacegroup-operations)
 ERROR: MULT:   1  ISYM:   2  NSYM   4
 ERROR: Check your struct file withx sgroup
 -- ERROR --
 -- ERROR --
 ERROR: (multiplicity of atom  65 )*(number of
pointgroup-operations)
 ERROR: is NOT = (number of spacegroup-operations)
 ERROR: MULT: