[Wien] BerryPI

2016-01-03 Thread nilofar hadaeghi 
Dear all

I have studied the polarization of some metal and insulator cases using the
latest version of the berryPI code. We performed the scf calculations by
Wien2k14.2.  One of Our calculations for one of my cases using GGA method
show that this case is an insulator in agreement with experimental reports.
The structure of this compound is centrosymmetric in the Pm3m space group.

So based on the theoretical background of berryPI code it is expected that
the polarization value for this compound must be zero. After running the
code for this compound using this command

berrypi -k6:6:6

the results has been achieved as what was expected and copied below:


---

Electronic polarization (C/m2) sp(1)  [ 0.00e+00,  0.00e+00,
0.00e+00]

Ionic polarization (C/m2)  sp(1)  [ 1.366237e-11,  1.366237e-11,
1.366237e-11]

Tot. spin polariz.=Pion+Pel (C/m2) sp(1)  [ 1.366237e-11,  1.366237e-11,
1.366237e-11]


---

TOTAL POLARIZATION (C/m2)  both   [ 1.366237e-11,  1.366237e-11,
1.366237e-11]


---

We also performed calculations for another case. We have used the GGA+U
(U>6eV) method for this case  to obtain the suitable gap compared to
experiment.  The GGA method leads to zero gap in contrast to experiment.
The same as previous studied case, this structure is centrosymmetric(space
group :Pm3m)



 So we expect the zero polarization vector for this compound too, but the
results show the non-zero polarization for the mentioned method in contrast
to theory. Could you help me to solve this problem, please?



In the GGA+U method and ferromagnetic polarization (with  SP calculation),
after running the command:

berrypi -o -k10:10:10


---

Electronic polarization (C/m2) sp(1)  [-5.253369e-01,  5.253369e-01,
-5.253369e-01]

Ionic polarization (C/m2)  sp(1)  [ 3.304038e-11,  3.304038e-11,
3.304038e-11]

Tot. spin polariz.=Pion+Pel (C/m2) sp(1)  [-5.253369e-01,  5.253369e-01,
-5.253369e-01]


---

Electronic polarization (C/m2) sp(2)  [ 0.00e+00,  0.00e+00,
0.00e+00]

Ionic polarization (C/m2)  sp(2)  [-5.253369e-01, -5.253369e-01,
-5.253369e-01]

Tot. spin polariz.=Pion+Pel (C/m2) sp(2)  [-5.253369e-01, -5.253369e-01,
-5.253369e-01]

---
TOTAL POLARIZATION (C/m2)  both   [-1.050674e+00,  6.700285e-11,
-1.050674e+00]
==

We also performed our calculations using the GGA method without spin
polarization. after running the command

 berrypi -k10:10:10


---

Electronic polarization (C/m2) sp(1)  [-1.470943e-01,
-9.456064e-02,  2.626685e-01]

Ionic polarization (C/m2)  sp(1)  [-5.253369e-01, -5.253369e-01,
-5.253369e-01]

Tot. spin polariz.=Pion+Pel (C/m2) sp(1)  [-6.724312e-01, -6.198976e-01,
-2.626685e-01]


---

TOTAL POLARIZATION (C/m2)  both   [-6.724312e-01, -6.198976e-01,
-2.626685e-01]


---
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Re: [Wien] berryPI

2015-10-15 Thread nilofar hadaeghi 
 I am really grateful for your reply and help. To my knowledge
according to the w2w UG all the files constructed via WIEN2k calculations
are necessary for w2w.
since the flow of onsite hybrid functional is similar to the flow of LDA+U
method and the switch related to the LDA+U is -o, should I use -o switch
for the berryPI run for the onsite hybrid functional?!
Sincerely yours,


On Thu, Oct 15, 2015 at 11:00 PM, Peter Blaha <pbl...@theochem.tuwien.ac.at>
wrote:

> I can confirm that case.vectorhf  has the same structure than case.vertor.
>
> For testing one could simply   copy   case.vectorhf case.vector and try it
> out.
>
> I don't know if there are any other input files requires for w2w or BerryPI
> (case.energy ?   there is also a hf file), ...
>
> Regards
>
>
> Am 15.10.2015 um 20:08 schrieb Oleg Rubel:
>
>> Perhaps other users, who are more experienced with hybrid functions and
>> wien2wannier can add a comment.
>>
>> There are two hypes of hybrids: onsite and full (Sec. 4.5.7 and 4.5.8 of
>> the UG).
>>
>>  From BerryPI perspective, you can probably do the onsite hybrid
>> functional the same way as the orbital potential (LDA+U). The flow of
>> "runsp_lapw -eece" looks similar to "runsp_lapw -orb".
>>
>> Regarding the “full” hybrid mode, there is no direct way to invoke “-hf”
>> switch in BerryPI. Neither "x w2w [-up/-dn -c -so -p]” has such an option.
>> My understanding is that *.vectorhf needs to be analyzed instead of the
>> *.vector file. Do both files have the same structure? If yes, will w2w be
>> able to read *.vectorhf the same way as *.vector? I do not know.
>>
>>
>> Oleg
>>
>> On Oct 14, 2015, at 06:58, nilofar hadaeghi <n.hadae...@gmail.com> wrote:
>>>
>>> Dear all,
>>>   I am wondering whether I am allowed to use BerryPI code for the
>>> calculations done by hybrid functional(specially B3LYP and B3PW91) or not
>>> and if it is going to what the suitable switch is! Would you please help
>>> me?!
>>> Best regards,
>>> ___
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>>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>>
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>>
>
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[Wien] berryPI

2015-10-14 Thread nilofar hadaeghi 
Dear all,
 I am wondering whether I am allowed to use BerryPI code for the
calculations done by hybrid functional(specially B3LYP and B3PW91) or not
and if it is going to what the suitable switch is! Would you please help
me?!
Best regards,
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Re: [Wien] berryPI

2015-09-10 Thread nilofar hadaeghi 
Dear Sheikh Jamil Ahmed
 I also think that the point of the PhysRevLett.97.267602 is exactly
what you referred. Of course previously in Phys. Rev. B *85*, 104109,
three candidate ground state had been identified but in PhysRevLett.97.267602,
I4/mcm space group has been mentioned as the ground state, and I think Dr.
Gerhard's purpose was making this point clear that calculating the
polarization using I4/mcm space group is meaningless!

On Wed, Sep 9, 2015 at 3:32 PM, nilofar hadaeghi <n.hadae...@gmail.com>
wrote:

> Dear Fecher, Gerhard
>  your recommended papers have been carefully studied.
> I understood that in this compound, different structural phases whether
> for the unstrained or strained states can be occurred among which just
> the ones whose space groups are not centrosymmetric would be meaningful to
> be used in calculating the polarization. For instance in the strained
> state, it has been allowed to calculate the polarization for the space
> group P4mm. and not I4/mcm The relation between the  oxygen octahedra
> tilting and the low energy symmetry is still unknown.
> Thank you for your attention.
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> .
>
> On Wed, Sep 9, 2015 at 2:52 PM, nilofar hadaeghi <n.hadae...@gmail.com>
> wrote:
>
>> Dear Pleg Rubel and Sheikh Jamil Ahmed
>>  I really appreciate your attention and guidance. I was really
>> confused and you helped me a lot.
>> Best regards,
>> N.Hadaeghi
>>
>>
>> On Wed, Sep 9, 2015 at 2:24 AM, Fecher, Gerhard <fec...@uni-mainz.de>
>> wrote:
>>
>>> If you check Figure 2 of PhysRevLett.109.267602, you will find that
>>> there is NO polarization in I4/mcm !
>>> and in the  PhysRevLett.97.267602 you find "... the crystallographic
>>> symmetry  becomes P4/mm", now compare this to the Fig.2 of the first
>>> reference, what do you see ?
>>>
>>>
>>> Ciao
>>> Gerhard
>>>
>>> DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
>>> "I think the problem, to be quite honest with you,
>>> is that you have never actually known what the question is."
>>>
>>> 
>>> Dr. Gerhard H. Fecher
>>> Institut of Inorganic and Analytical Chemistry
>>> Johannes Gutenberg - University
>>> 55099 Mainz
>>> and
>>> Max Planck Institute for Chemical Physics of Solids
>>> 01187 Dresden
>>> 
>>> Von: wien-boun...@zeus.theochem.tuwien.ac.at [
>>> wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Sheikh Jamil
>>> Ahmed [sahm...@lakeheadu.ca]
>>> Gesendet: Dienstag, 8. September 2015 23:06
>>> An: A Mailing list for WIEN2k users
>>> Betreff: Re: [Wien] berryPI
>>>
>>> I would like to add that EuTiO3 seems to be a multiferroic compound with
>>> ground state being antiferromagnetic- paraelectric system (I4/mcm). Then,
>>> under some compressive or tensile epitaxial strain, several types of
>>> transition is possible (For example, antiferromagnetic- ferroelectric or
>>> ferromagnetic- ferroelectric) depending on the magnitude and type of
>>> strain. The following articles address this issue very well.
>>> http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.109.267602
>>>
>>> http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.97.267602
>>>
>>>
>>> Hope that helps.
>>>
>>> Sheikh
>>>
>>> --
>>> Sheikh Jamil Ahmed
>>> PhD Student
>>> Department of Material Science and Engineering
>>> McMaster University
>>> 1280 Main Street West
>>> Hamilton, Ontario, Canada L8S 4L7
>>>
>>>
>>> On Tue, Sep 8, 2015 at 3:07 PM, Oleg Rubel <oru...@lakeheadu.ca>> oru...@lakeheadu.ca>> wrote:
>>> To address your questions...
>>>
>>> > I4/mcm is centrosymmetric. I studied the tutorial related to GaN and
>>> it helped me very much. So I conclude to calculate the difference in
>>> polarization, two structures that at least one of them should not be
>>> centrosymmetric are needed, Is it correct?
>>>
>>> That’s correct. When the structure file contains the inversion symmetry,
>>> Wien2k switches from complex to real version for wave functions. Then there
>>> is no phase information to be processed.
>>>
>>> > Would you please guide me whether it is allowed to calculate the
>>> difference in

Re: [Wien] berryPI code

2015-09-09 Thread nilofar hadaeghi 
Dear prof. Oleg Rubel and Mr.Elias Assmann
 I really thank You. I will try to find these lines in the source code
of w2w but any further help would be desirable.
BerryPI Version 1.2
Python version: 2.7.3
 Numpy version: 1.6.2
Best regards,

On Wed, Sep 9, 2015 at 7:45 AM, Elias Assmann <elias.assm...@gmail.com>
wrote:

> On 09/08/2015 11:57 PM, nilofar hadaeghi wrote:
> >  I tried to implement this run this command :x w2w -up -so
> > but I again faced the following error:
> >
> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > Image  PCRoutineLine
> > Source
> > w2wc   0042E242  almgen_   120
> almgen.F
> > w2wc   00423E21  l2mmn_ 72
> l2mmn.f
> > w2wc   004223C6  MAIN__226
> main.f
> > w2wc   004038CC  Unknown   Unknown
> Unknown
> > libc.so.6  003B06621735  Unknown   Unknown
> Unknown
> > w2wc   004037A9  Unknown   Unknown
> Unknown
>
> That is quite an unspecific error, but at least you have line numbers.
>
> Which exact version of the code are you using?  Can you post the output of
>
> grep Id: SRC_w2w/{almgen.F,l2mmn.f,main.f}
>
>
> --
> Elias Assmann
>
> Wien2Wannier: maximally localized Wannier functions
>   from linearized augmented plane waves
>
> <
> http://www.ifp.tuwien.ac.at/forschung/arbeitsgruppen/cms/software-download/wien2wannier/
> >
>
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Re: [Wien] berryPI

2015-09-09 Thread nilofar hadaeghi 
Dear Fecher, Gerhard
 your recommended papers have been carefully studied.
I understood that in this compound, different structural phases whether for
the unstrained or strained states can be occurred among which just the ones
whose space groups are not centrosymmetric would be meaningful to be used
in calculating the polarization. For instance in the strained state, it has
been allowed to calculate the polarization for the space group P4mm. and
not I4/mcm The relation between the  oxygen octahedra tilting and the low
energy symmetry is still unknown.
Thank you for your attention.














.

On Wed, Sep 9, 2015 at 2:52 PM, nilofar hadaeghi <n.hadae...@gmail.com>
wrote:

> Dear Pleg Rubel and Sheikh Jamil Ahmed
>  I really appreciate your attention and guidance. I was really
> confused and you helped me a lot.
> Best regards,
> N.Hadaeghi
>
>
> On Wed, Sep 9, 2015 at 2:24 AM, Fecher, Gerhard <fec...@uni-mainz.de>
> wrote:
>
>> If you check Figure 2 of PhysRevLett.109.267602, you will find that there
>> is NO polarization in I4/mcm !
>> and in the  PhysRevLett.97.267602 you find "... the crystallographic
>> symmetry  becomes P4/mm", now compare this to the Fig.2 of the first
>> reference, what do you see ?
>>
>>
>> Ciao
>> Gerhard
>>
>> DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
>> "I think the problem, to be quite honest with you,
>> is that you have never actually known what the question is."
>>
>> 
>> Dr. Gerhard H. Fecher
>> Institut of Inorganic and Analytical Chemistry
>> Johannes Gutenberg - University
>> 55099 Mainz
>> and
>> Max Planck Institute for Chemical Physics of Solids
>> 01187 Dresden
>> 
>> Von: wien-boun...@zeus.theochem.tuwien.ac.at [
>> wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Sheikh Jamil
>> Ahmed [sahm...@lakeheadu.ca]
>> Gesendet: Dienstag, 8. September 2015 23:06
>> An: A Mailing list for WIEN2k users
>> Betreff: Re: [Wien] berryPI
>>
>> I would like to add that EuTiO3 seems to be a multiferroic compound with
>> ground state being antiferromagnetic- paraelectric system (I4/mcm). Then,
>> under some compressive or tensile epitaxial strain, several types of
>> transition is possible (For example, antiferromagnetic- ferroelectric or
>> ferromagnetic- ferroelectric) depending on the magnitude and type of
>> strain. The following articles address this issue very well.
>> http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.109.267602
>>
>> http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.97.267602
>>
>>
>> Hope that helps.
>>
>> Sheikh
>>
>> --
>> Sheikh Jamil Ahmed
>> PhD Student
>> Department of Material Science and Engineering
>> McMaster University
>> 1280 Main Street West
>> Hamilton, Ontario, Canada L8S 4L7
>>
>>
>> On Tue, Sep 8, 2015 at 3:07 PM, Oleg Rubel <oru...@lakeheadu.ca> oru...@lakeheadu.ca>> wrote:
>> To address your questions...
>>
>> > I4/mcm is centrosymmetric. I studied the tutorial related to GaN and it
>> helped me very much. So I conclude to calculate the difference in
>> polarization, two structures that at least one of them should not be
>> centrosymmetric are needed, Is it correct?
>>
>> That’s correct. When the structure file contains the inversion symmetry,
>> Wien2k switches from complex to real version for wave functions. Then there
>> is no phase information to be processed.
>>
>> > Would you please guide me whether it is allowed to calculate the
>> difference in polarization between a strained and unstrained state of a
>> system by implementing the berryPI on each of them separately and then
>> subtract them ?! if it going to, what does the derived polarization
>> describe?! Piezoelectricity(since it is the difference in polarization
>> caused by strain) or spontaneous polarization?
>>
>> You are heading towards piezoelectric coefficients. There are some
>> technicalities, such as clamped vs relaxed ion approximation, proper vs
>> improper. Here is a good reference:
>> http://arxiv.org/pdf/cond-mat/9903137.pdf
>> I do not see any barriers from BerryPI perspective.
>>
>>
>> Best regards
>> Oleg
>>
>> ___
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>> SEARCH the M

Re: [Wien] berryPI code

2015-09-09 Thread nilofar hadaeghi 
The output is exactly what has been mentioned in the Gavin Abo's mail as is
copied below:

/usr/local/codes/wien2k/v14.2/SRC_w2w/almgen.F:!!! $Id: almgen.F 167
2014-02-03 09:43:33Z assmann $
/usr/local/codes/wien2k/v14.2/SRC_w2w/l2mmn.f:!!! $Id: l2mmn.f 167
2014-02-03 09:43:33Z assmann $
/usr/local/codes/wien2k/v14.2/SRC_w2w/main.f:!!! $Id: main.f 199 2014-04-11
16:18:29Z assmann $

On Wed, Sep 9, 2015 at 10:02 AM, Elias Assmann 
wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Thanks everybody for chiming in :-).
>
> On 09/09/2015 06:36 PM, Víctor Luaña Cabal wrote:
> > grep -B 5 -A 5 Id: SRC_w2w/{almgen.F,l2mmn.f,main.f}
>
> That is very useful in many cases (or just ‘-C 5’, FWIW), but in this
> case, the one line is really all that is needed -- it identifies the
> last svn revision the file was changed in.  Essentially it would make
> sure that Nilofar was using the version of 14.2, plus save me the
> trouble of looking up that information myself.
>
> > Notice that Elias command corresponds to a bash shell, probably.
>
> And many others.  Personally, I use (and highly recommend!) fish
> ⟨http://fishshell.com/⟩, it works there as well.
>
>
> Elias
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1
> Comment: Using GnuPG with Icedove - http://www.enigmail.net/
>
> iQIcBAEBAgAGBQJV8GYoAAoJEE/4gtQZfOqPExsP/0phlFjTsSuFTazD7KgO5Yjd
> UaeCK4DjuQ+NWzzD6srRvDFt9sVhrgmeazkyccjM3y4zkZpImCHHU2KbgsFtb2UU
> ZbVsmOC1m/o+0/lRhyIqIi8R0Rw4crUJnDsfLcLqLExsYE4vi2amaN+xGkcqLEdd
> 9/TitsQAv4Kff8I8D4aTUks2OIP6+c/FwoGgaE36m0XeOeoDPyhlPo6nzRXRdOp/
> Lfhdw7TSN/aTYsTK8cPbB6V45Sr9as8qh7etjT+GS6+eVP0ulY+G/65LoToYVKhz
> BFu8Jek4q6KPcV/CsoV2xSDdpNCAR539PRD8iDRqtG2muKoGDmVqNBx6KnmuwUji
> KMbah5B1GukgAZS0/ZCKs0yCW/dPKN806BCtbVg/FJwROg96LY7JDssCY5ay7haw
> /D92VI6jzEolTZifcM4Dn57ttIiZWNqHqmmY6hF5syoFhCliEilNxH4bLhy79RkJ
> z2pn414TfXILNaFqVV9GSsqJmYqWJ762rCueAfxgWuYs++SM3dLcSzVoDcFEIono
> 6zOs5xyJLwwtDT6l0doBv5XneSbNhLcQiNCDkRYk3/ZuTkOGVufwlIVfeN6ft1Vj
> kNK9XKoNezhdfVUs7fPqVX0NTcmZvGVgM1J2MEH8kHb8K0gDjbKet17/rI0D2M1t
> +gWQlJ7jIyf61s+Vesgf
> =k0HR
> -END PGP SIGNATURE-
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Re: [Wien] berryPI

2015-09-09 Thread nilofar hadaeghi 
Dear Pleg Rubel and Sheikh Jamil Ahmed
 I really appreciate your attention and guidance. I was really confused
and you helped me a lot.
Best regards,
N.Hadaeghi


On Wed, Sep 9, 2015 at 2:24 AM, Fecher, Gerhard  wrote:

> If you check Figure 2 of PhysRevLett.109.267602, you will find that there
> is NO polarization in I4/mcm !
> and in the  PhysRevLett.97.267602 you find "... the crystallographic
> symmetry  becomes P4/mm", now compare this to the Fig.2 of the first
> reference, what do you see ?
>
>
> Ciao
> Gerhard
>
> DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
> "I think the problem, to be quite honest with you,
> is that you have never actually known what the question is."
>
> 
> Dr. Gerhard H. Fecher
> Institut of Inorganic and Analytical Chemistry
> Johannes Gutenberg - University
> 55099 Mainz
> and
> Max Planck Institute for Chemical Physics of Solids
> 01187 Dresden
> 
> Von: wien-boun...@zeus.theochem.tuwien.ac.at [
> wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Sheikh Jamil
> Ahmed [sahm...@lakeheadu.ca]
> Gesendet: Dienstag, 8. September 2015 23:06
> An: A Mailing list for WIEN2k users
> Betreff: Re: [Wien] berryPI
>
> I would like to add that EuTiO3 seems to be a multiferroic compound with
> ground state being antiferromagnetic- paraelectric system (I4/mcm). Then,
> under some compressive or tensile epitaxial strain, several types of
> transition is possible (For example, antiferromagnetic- ferroelectric or
> ferromagnetic- ferroelectric) depending on the magnitude and type of
> strain. The following articles address this issue very well.
> http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.109.267602
>
> http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.97.267602
>
>
> Hope that helps.
>
> Sheikh
>
> --
> Sheikh Jamil Ahmed
> PhD Student
> Department of Material Science and Engineering
> McMaster University
> 1280 Main Street West
> Hamilton, Ontario, Canada L8S 4L7
>
>
> On Tue, Sep 8, 2015 at 3:07 PM, Oleg Rubel > wrote:
> To address your questions...
>
> > I4/mcm is centrosymmetric. I studied the tutorial related to GaN and it
> helped me very much. So I conclude to calculate the difference in
> polarization, two structures that at least one of them should not be
> centrosymmetric are needed, Is it correct?
>
> That’s correct. When the structure file contains the inversion symmetry,
> Wien2k switches from complex to real version for wave functions. Then there
> is no phase information to be processed.
>
> > Would you please guide me whether it is allowed to calculate the
> difference in polarization between a strained and unstrained state of a
> system by implementing the berryPI on each of them separately and then
> subtract them ?! if it going to, what does the derived polarization
> describe?! Piezoelectricity(since it is the difference in polarization
> caused by strain) or spontaneous polarization?
>
> You are heading towards piezoelectric coefficients. There are some
> technicalities, such as clamped vs relaxed ion approximation, proper vs
> improper. Here is a good reference:
> http://arxiv.org/pdf/cond-mat/9903137.pdf
> I do not see any barriers from BerryPI perspective.
>
>
> Best regards
> Oleg
>
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Re: [Wien] berryPI code

2015-09-08 Thread nilofar hadaeghi 
 I tried to implement this run this command :x w2w -up -so
but I again faced the following error:

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image  PCRoutineLine
Source
w2wc   0042E242  almgen_   120  almgen.F
w2wc   00423E21  l2mmn_ 72  l2mmn.f
w2wc   004223C6  MAIN__226  main.f
w2wc   004038CC  Unknown   Unknown  Unknown
libc.so.6  003B06621735  Unknown   Unknown  Unknown
w2wc   004037A9  Unknown   Unknown  Unknown
1.859u 12.940s 0:46.40 31.8%0+0k 2884224+160888io 19pf+0w
error: command   /usr/local/codes/wien2k/v14.2/w2wc upw2w.def   failed

On Sun, Sep 6, 2015 at 6:09 AM, Oleg Rubel <oru...@lakeheadu.ca> wrote:

> The error suggests that "x w2w -so -up" did not go through. Please try to
> run this command manually in the same directory, just to confirm the error.
> Also there is a trace back information in your segfault report. I would go
> into specified lines of the sources code and look for hints.
>
> I assume that SCF cycle with SOC + orbital potential is completed error
> free prior to running BerryPI.
>
> Also the k-mesh of 10:10:10 is an overkill for the first run. Starting
> with 4:4:4 and checking convergence while increasing the mesh is more
> practical.
>
> Oleg
>
>
> > On Sep 6, 2015, at 04:12, nilofar hadaeghi <n.hadae...@gmail.com> wrote:
> >
> > Dear all
> > I am working on the berryPI code and I have faced the following error.
> > Can anyine help me please?
> > Best regards,
> > [hadaeghi@cm6 YbB6]$ berrypi -o -j -k10:10:10
> > [ BerryPI ] +++Version 1.2 (Mar 12, 2014)
> >
> > [ BerryPI ] Python version: 2.7.3
> > [ BerryPI ] Numpy version: 1.6.2
> > [ BerryPI ] Calculation with an additional orbital potential is activated
> > [ BerryPI ] Spin polarization is activated automatically with adding
> > orbital potential
> > [ BerryPI ] Calculation with spin-orbit coupling is activated
> > [ BerryPI ] Proceed with the k-mesh [10, 10, 10]
> > Please make sure that W2W is installed before trying to run BerryPI
> > [ BerryPI ] Starting BerryPI Automation for YbB6
> > [ BerryPI ] New working directory:
> > /home/hadaeghi/berry-for-thesis/YbB6/GGA/6/SE=-6/YbB6/YbB6
> > [ BerryPI ]  w2kpath = /usr/local/codes/wien2k/v14.2
> > [ BerryPI ]  pypath = /usr/bin/python2.7
> > [ BerryPI ]  bppath = /usr/local/codes/wien2k/v14.2/SRC_BerryPI/BerryPI
> > [ BerryPI ] Calling command: rm -f YbB6.broyd*
> > [ BerryPI ] Copied YbB6.struct to YbB6.ksym
> > [ BerryPI ] Calling command: echo "0 10 10 10 0" | x kgen -fbz
> >   1  symmetry operations without inversion
> >  NUMBER OF K-POINTS IN WHOLE CELL: (0 allows to specify 3 divisions of G)
> > length of reciprocal lattice vectors:   0.802   0.802   0.802   0.000
> >  0.000   0.000
> >  Specify 3 mesh-divisions (n1,n2,n3):
> >  Shift of k-mesh allowed. Do you want to shift: (0=no, 1=shift)
> >1000  k-points generated, ndiv=  10  10
> 10
> > KGEN ENDS
> > 0.021u 0.001s 0:00.04 50.0%0+0k 8+1320io 0pf+0w
> > [ BerryPI ] Calling command: cp YbB6.klist YbB6.klist_w90
> > [ BerryPI ] Calling command: x lapw1 -up -orb
> > LAPW1 END
> > 508.786u 14.630s 9:19.76 93.5%0+0k 1400+1637312io 0pf+0w
> > [ BerryPI ] Calling command: x lapw1 -dn -orb
> > LAPW1 END
> > 501.829u 62.532s 10:30.68 89.4%0+0k 1376+1794624io 0pf+0w
> > [ BerryPI ] Calling command: x lapwso -up -orb
> > LAPWSO END
> > 302.212u 3.411s 6:10.04 82.5%0+0k 29552+3724216io 7pf+0w
> > [ BerryPI ] Determine number of bloch bands in spin-polarized mode
> > based on *.scf2(up/dn)
> > [ BerryPI ]   spin = up
> > [ BerryPI ] Number of bloch bands is [1, 42]
> > [ BerryPI ]   spin = dn
> > [ BerryPI ] Number of bloch bands is [1, 42]
> > [ BerryPI ] Calling command: /usr/bin/python2.7
> > /usr/local/codes/wien2k/v14.2/write_inwf -mode MMN -bands 1 42
> > [ BerryPI ] Calling command: write_win
> > [ BerryPI ] Calling command: /usr/bin/python2.7
> > /usr/local/codes/wien2k/v14.2/SRC_BerryPI/BerryPI/win2nnkp.py YbB6
> > [ BerryPI ]  file YbB6.scf2up found; will extract the Fermi energy
> > :FER  : F E R M I - ENERGY(TETRAH.M.)=   0.5478304981
> > [ BerryPI ]  Ef = 0.5478304981 Ry
> > [ BerryPI ]  YbB6.fermiup is present and will be removed
> > ... done
> > [ BerryPI ]  Fermi energy is written to YbB6.fermiup
> > [ BerryPI ] Cal

[Wien] berryPI

2015-09-07 Thread nilofar hadaeghi 
Dear all
 I have studied some papers whose authors are S.J.Ahmed or O.Rubel  in
which building the centrosymmetric and noncentrosymmetric structure for the
calculation of spontaneous polarization has been explained, but it is still
ambiguous for me.
Could you please help me whether the noncentrosymmetric structure must
exist in the nature or it is enough to apply a displacement to the central
atom of the centrosymmetric structure and then use the new structure as the
noncentrosymmetric one?!
For instance I am working on EuTiO3 in which a structural transition at
temperature 282(k) from cubic to tetragonal ( from Pm3m space group to
I4/mcm) occurs. Now, would you please help me whether I use the structure
in I4/mcm space group as the noncentrosymmetric structure or I must change
the positions of the centrosymmetric structure and use the
achieved structure as the noncentrosymmetric one?
I am using WIEN2k 14.2, Python version: 2.7.3 and Numpy version: 1.6.2.
Sincerely yours,
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[Wien] berryPI code

2015-09-06 Thread nilofar hadaeghi 
Dear all
I am working on the berryPI code and I have faced the following error.
Can anyine help me please?
Best regards,
[hadaeghi@cm6 YbB6]$ berrypi -o -j -k10:10:10
[ BerryPI ] +++Version 1.2 (Mar 12, 2014)

[ BerryPI ] Python version: 2.7.3
[ BerryPI ] Numpy version: 1.6.2
[ BerryPI ] Calculation with an additional orbital potential is activated
[ BerryPI ] Spin polarization is activated automatically with adding
orbital potential
[ BerryPI ] Calculation with spin-orbit coupling is activated
[ BerryPI ] Proceed with the k-mesh [10, 10, 10]
Please make sure that W2W is installed before trying to run BerryPI
[ BerryPI ] Starting BerryPI Automation for YbB6
[ BerryPI ] New working directory:
/home/hadaeghi/berry-for-thesis/YbB6/GGA/6/SE=-6/YbB6/YbB6
[ BerryPI ]  w2kpath = /usr/local/codes/wien2k/v14.2
[ BerryPI ]  pypath = /usr/bin/python2.7
[ BerryPI ]  bppath = /usr/local/codes/wien2k/v14.2/SRC_BerryPI/BerryPI
[ BerryPI ] Calling command: rm -f YbB6.broyd*
[ BerryPI ] Copied YbB6.struct to YbB6.ksym
[ BerryPI ] Calling command: echo "0 10 10 10 0" | x kgen -fbz
   1  symmetry operations without inversion
  NUMBER OF K-POINTS IN WHOLE CELL: (0 allows to specify 3 divisions of G)
 length of reciprocal lattice vectors:   0.802   0.802   0.802   0.000
  0.000   0.000
  Specify 3 mesh-divisions (n1,n2,n3):
  Shift of k-mesh allowed. Do you want to shift: (0=no, 1=shift)
1000  k-points generated, ndiv=  10  10  10
KGEN ENDS
0.021u 0.001s 0:00.04 50.0% 0+0k 8+1320io 0pf+0w
[ BerryPI ] Calling command: cp YbB6.klist YbB6.klist_w90
[ BerryPI ] Calling command: x lapw1 -up -orb
 LAPW1 END
508.786u 14.630s 9:19.76 93.5%  0+0k 1400+1637312io 0pf+0w
[ BerryPI ] Calling command: x lapw1 -dn -orb
 LAPW1 END
501.829u 62.532s 10:30.68 89.4% 0+0k 1376+1794624io 0pf+0w
[ BerryPI ] Calling command: x lapwso -up -orb
LAPWSO END
302.212u 3.411s 6:10.04 82.5%   0+0k 29552+3724216io 7pf+0w
[ BerryPI ] Determine number of bloch bands in spin-polarized mode
based on *.scf2(up/dn)
[ BerryPI ]   spin = up
[ BerryPI ] Number of bloch bands is [1, 42]
[ BerryPI ]   spin = dn
[ BerryPI ] Number of bloch bands is [1, 42]
[ BerryPI ] Calling command: /usr/bin/python2.7
/usr/local/codes/wien2k/v14.2/write_inwf -mode MMN -bands 1 42
[ BerryPI ] Calling command: write_win
[ BerryPI ] Calling command: /usr/bin/python2.7
/usr/local/codes/wien2k/v14.2/SRC_BerryPI/BerryPI/win2nnkp.py YbB6
[ BerryPI ]  file YbB6.scf2up found; will extract the Fermi energy
:FER  : F E R M I - ENERGY(TETRAH.M.)=   0.5478304981
[ BerryPI ]  Ef = 0.5478304981 Ry
[ BerryPI ]  YbB6.fermiup is present and will be removed
 ... done
[ BerryPI ]  Fermi energy is written to YbB6.fermiup
[ BerryPI ] Calling command: x w2w -so -up
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image  PCRoutineLine
Source
w2wc   0042D9ED  almgen_70  almgen.F
w2wc   00423E21  l2mmn_ 72  l2mmn.f
w2wc   004223C6  MAIN__226  main.f
w2wc   004038CC  Unknown   Unknown  Unknown
libc.so.6  003B06621735  Unknown   Unknown  Unknown
w2wc   004037A9  Unknown   Unknown  Unknown
2.519u 1.093s 0:04.25 84.7% 0+0k 2696+7392io 10pf+0w
error: command   /usr/local/codes/wien2k/v14.2/w2wc upw2w.def   failed
[ BerryPI ] ERROR: in automation of YbB6
[ BerryPI ] ERROR --> x w2w -so -up
Command 'x w2w -so -up' returned non-zero exit status 9
Traceback (most recent call last):
  File "/usr/local/codes/wien2k/v14.2/SRC_BerryPI/BerryPI/berrypi",
line 917, in 
[bAutomationErrorChk,phasesRaw] = rawBerryPhase(configFile)
TypeError: 'bool' object is not iterable
[hadaeghi@cm6 YbB6]$
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