Re: [Wien] Berrypi Error

[Rubel, Oleg]

I reproduced the error on my end with Python 3.10. The GitHub version is 
updated to fix the error as Sharbano suggested and tested. To update your 
version please run those commands irrespective of the WIEN2k version:

cd $WIENROOT/SRC_BerryPI/BerryPI
git pull

This will update BerryPI to the most current version (including updates to the 
Chern number and hybrid Wannier charge center calculations for topological 
materials).

Thank you again, Sharbano!

Oleg

> -Original Message-
> From: Wien  On Behalf Of
> Rubel, Oleg
> Sent: Friday, November 17, 2023 12:24 PM
> To: A Mailing list for WIEN2k users 
> Subject: Re: [Wien] Berrypi Error
> 
> Caution: External email.
> 
> 
> Dear Sharbano,
> 
> Many thanks for sharing the fix. I will take a closer look in the next couple 
> of
> days.
> 
> Best regards
> Oleg
> 
> > -Original Message-
> > From: Wien  On Behalf Of
> > shahrbano rahimi
> > Sent: Friday, November 17, 2023 11:17 AM
> > To: A Mailing list for WIEN2k users 
> > Subject: [Wien] Berrypi Error
> >
> >   Caution: External email.
> >
> >
> > Dear Prof. Peter Blaha and Prof. Oleg Rubel,
> >
> >
> > hope this email finds you in good health and spirits. I am reaching
> > out to respectfully report a technical challenge we recently
> > encountered in our Wien2k calculations using BerrypI, and to share the
> > solution we found in hopes that it might be helpful.
> >
> > Our team has been utilizing Wien2k version 23.2, along with Python
> > version
> > 3.10.9 and Numpy version 1.23.5. Initially, the electronic part of the
> > calculations proceeded without any issues. However, we stumbled upon a
> > snag in the ionic part, which resulted in the following error message:
> >
> > “Traceback (most recent call last): File
> > "/opt/codes/wien2k/v23.2/berrypi",
> > line 1081, in  theCalc =
> > postProcBerryPhase(configFile,phasesRaw,spCalc) File
> > "/opt/codes/wien2k/v23.2/berrypi", line 72, in postProcBerryPhase
> > mainCalculation = b_PyCalc.MainCalculationContainer( File
> > "/opt/codes/wien2k/v23.2/SRC_BerryPI/BerryPI/calculations.py", line
> > 338, in init ionP = self.determineIonPolarization(wrpFn,args) File
> > "/opt/codes/wien2k/v23.2/SRC_BerryPI/BerryPI/calculations.py", line
> > 621, in determineIonPolarization if isinstance(iValence, 
> > collections.Iterable):
> > AttributeError: module 'collections' has no attribute 'Iterable'”
> >
> > In our efforts to resolve this, we made the following changes in the
> > calculations.py file:
> >
> > 1.Altered the import statement from:
> >
> >   import collections
> >
> >   to:
> >
> >   from collections.abc import Iterable
> >
> > 2.Amended the following line:
> >
> >   from:
> >
> >   if isinstance(iValence, collections.Iterable):
> >
> >   to:
> >
> >   if isinstance(iValence, Iterable):
> >
> > These modifications have thankfully resolved the
> > 'collections.Iterable' error, allowing our calculations to proceed without
> further issues.
> >
> > I thought it prudent to share this experience with you, given your
> > profound expertise and significant contributions to the development of
> > Wien2k. Your guidance and insights have always been invaluable to our
> > work, and I hope this information might be of some utility in your ongoing
> endeavors.
> >
> > Thank you very much for your time and attention to this matter. Any
> > further insights or suggestions from your esteemed perspectives would
> > be greatly appreciated.
> >
> > With sincere respect and best regards,
> >
> > Sharbano Rahimi
> 
> ___
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Re: [Wien] Berrypi Error

[Rubel, Oleg]

Dear Sharbano,

Many thanks for sharing the fix. I will take a closer look in the next couple 
of days.

Best regards
Oleg

> -Original Message-
> From: Wien  On Behalf Of
> shahrbano rahimi
> Sent: Friday, November 17, 2023 11:17 AM
> To: A Mailing list for WIEN2k users 
> Subject: [Wien] Berrypi Error
> 
>   Caution: External email.
> 
> 
> Dear Prof. Peter Blaha and Prof. Oleg Rubel,
> 
> 
> hope this email finds you in good health and spirits. I am reaching out to
> respectfully report a technical challenge we recently encountered in our
> Wien2k calculations using BerrypI, and to share the solution we found in
> hopes that it might be helpful.
> 
> Our team has been utilizing Wien2k version 23.2, along with Python version
> 3.10.9 and Numpy version 1.23.5. Initially, the electronic part of the
> calculations proceeded without any issues. However, we stumbled upon a
> snag in the ionic part, which resulted in the following error message:
> 
> “Traceback (most recent call last): File "/opt/codes/wien2k/v23.2/berrypi",
> line 1081, in  theCalc =
> postProcBerryPhase(configFile,phasesRaw,spCalc) File
> "/opt/codes/wien2k/v23.2/berrypi", line 72, in postProcBerryPhase
> mainCalculation = b_PyCalc.MainCalculationContainer( File
> "/opt/codes/wien2k/v23.2/SRC_BerryPI/BerryPI/calculations.py", line 338, in
> init ionP = self.determineIonPolarization(wrpFn,args) File
> "/opt/codes/wien2k/v23.2/SRC_BerryPI/BerryPI/calculations.py", line 621, in
> determineIonPolarization if isinstance(iValence, collections.Iterable):
> AttributeError: module 'collections' has no attribute 'Iterable'”
> 
> In our efforts to resolve this, we made the following changes in the
> calculations.py file:
> 
> 1.Altered the import statement from:
> 
>   import collections
> 
>   to:
> 
>   from collections.abc import Iterable
> 
> 2.Amended the following line:
> 
>   from:
> 
>   if isinstance(iValence, collections.Iterable):
> 
>   to:
> 
>   if isinstance(iValence, Iterable):
> 
> These modifications have thankfully resolved the 'collections.Iterable' error,
> allowing our calculations to proceed without further issues.
> 
> I thought it prudent to share this experience with you, given your profound
> expertise and significant contributions to the development of Wien2k. Your
> guidance and insights have always been invaluable to our work, and I hope
> this information might be of some utility in your ongoing endeavors.
> 
> Thank you very much for your time and attention to this matter. Any further
> insights or suggestions from your esteemed perspectives would be greatly
> appreciated.
> 
> With sincere respect and best regards,
> 
> Sharbano Rahimi

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Re: [Wien] Berrypi & w2w

[Rubel, Oleg]

P.S.: I tested spontaneous polarization in BaTiO3. With 1x1x1 k mesh we have Ps 
= 0.297 C/m2 vs the "good" result from 6x6x6 mesh of 0.305 C/m2. The difference 
is not that huge.

Oleg


From: Wien  on behalf of Rubel, Oleg 

Sent: Monday, August 24, 2020 16:17
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] Berrypi & w2w

Technically, it should work even with 1x1x1 mesh. The loop is closed in k space 
through periodic boundary conditions. For a surface, x1 mesh in the 
perpendicular direction should be sufficient.

Oleg


From: Wien  on behalf of Peter Blaha 

Sent: Monday, August 24, 2020 14:47
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] Berrypi & w2w

I'd guess that for an insulator this is not a problem.

It would be problematic for metals, but berrypi is not for metals anyway.

Am 24.08.2020 um 19:52 schrieb Laurence Marks:
> Does anyone know if berrypi /w2w require a 3D k-mesh, e.g. what will
> happen with a surface calculation where along the long direction there
> is only one k-point?
>
> --
> Professor Laurence Marks
> Department of Materials Science and Engineering
> Northwestern University
> www.numis.northwestern.edu <http://www.numis.northwestern.edu/>
> Corrosion in 4D: www.numis.northwestern.edu/MURI
> <http://www.numis.northwestern.edu/MURI>
> Co-Editor, Acta Cryst A
> "Research is to see what everybody else has seen, and to think what
> nobody else has thought"
> Albert Szent-Gyorgi
>
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--
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
WWW:
http://www.imc.tuwien.ac.at/tc_blaha-

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Re: [Wien] Berrypi & w2w

[Rubel, Oleg]

Technically, it should work even with 1x1x1 mesh. The loop is closed in k space 
through periodic boundary conditions. For a surface, x1 mesh in the 
perpendicular direction should be sufficient.

Oleg


From: Wien  on behalf of Peter Blaha 

Sent: Monday, August 24, 2020 14:47
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] Berrypi & w2w

I'd guess that for an insulator this is not a problem.

It would be problematic for metals, but berrypi is not for metals anyway.

Am 24.08.2020 um 19:52 schrieb Laurence Marks:
> Does anyone know if berrypi /w2w require a 3D k-mesh, e.g. what will
> happen with a surface calculation where along the long direction there
> is only one k-point?
>
> --
> Professor Laurence Marks
> Department of Materials Science and Engineering
> Northwestern University
> www.numis.northwestern.edu <http://www.numis.northwestern.edu/>
> Corrosion in 4D: www.numis.northwestern.edu/MURI
> <http://www.numis.northwestern.edu/MURI>
> Co-Editor, Acta Cryst A
> "Research is to see what everybody else has seen, and to think what
> nobody else has thought"
> Albert Szent-Gyorgi
>
> ___
> 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
>

--
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
WWW:
http://www.imc.tuwien.ac.at/tc_blaha-

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Re: [Wien] Berrypi & w2w

[Peter Blaha]

I'd guess that for an insulator this is not a problem.

It would be problematic for metals, but berrypi is not for metals anyway.

Am 24.08.2020 um 19:52 schrieb Laurence Marks:
Does anyone know if berrypi /w2w require a 3D k-mesh, e.g. what will 
happen with a surface calculation where along the long direction there 
is only one k-point?


--
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu 
Corrosion in 4D: www.numis.northwestern.edu/MURI 


Co-Editor, Acta Cryst A
"Research is to see what everybody else has seen, and to think what 
nobody else has thought"

Albert Szent-Gyorgi

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--
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
WWW: 
http://www.imc.tuwien.ac.at/tc_blaha- 


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Re: [Wien] BerryPI

[Ali Baghi zadeh]

Thank you very much Oleg, it worked as berrypi "-k 4:4:2" -o -p.
Best regards
Ali

-Original Message-
From: Wien [mailto:wien-boun...@zeus.theochem.tuwien.ac.at] On Behalf Of
Oleg Rubel
Sent: Thursday, 7 May 2020 22:15
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] BerryPI

Hi Ali,

the field 'k4:4:2' is probably ignored, and the code takes a default mesh
10x10x10. I suspect it is the missing dash '-'. The execution should be
'berrypi -k 4:4:2 ...'

I hope it will help
Oleg

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering McMaster University JHE 359,
1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster.ca

On 2020-05-07 3:42 p.m., Ali Baghi zadeh wrote:
> Dear Users of Wien2K
> 
> I am trying to use BerryPI to calculate the polarization of the 
> LuScFeO3 structure, considering spin polarization (AFM) and LDA+U, the 
> lattice is hexagonal  (P31m) with 14 atoms per unit cell (I already 
> got convergence in energy and charge in scf).
> 
> My problem is the number of K-points when I do execute the following
> command: berrypi k4:4:2 -o -s -p (or 5:5:3). It always switch the 
> number of k points to 10x10x10, and calculation takes many hours. I am 
> using Wine2K_19.1, on AMD Ryzen 32 cores station. What mistake am I 
> doing in executing the command and how can I force the K-points to be 
> reduced to a less number?
> 
> Best regards
> 
> Ali Baghi zadeh
> 
> Postdoc researcher
> 
> ScopeM, ETH, Zurich
> 
> 
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Re: [Wien] BerryPI

[Oleg Rubel]

Hi Ali,

the field 'k4:4:2' is probably ignored, and the code takes a default 
mesh 10x10x10. I suspect it is the missing dash '-'. The execution 
should be 'berrypi -k 4:4:2 ...'


I hope it will help
Oleg

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster.ca

On 2020-05-07 3:42 p.m., Ali Baghi zadeh wrote:

Dear Users of Wien2K

I am trying to use BerryPI to calculate the polarization of the LuScFeO3 
structure, considering spin polarization (AFM) and LDA+U, the lattice is 
hexagonal  (P31m) with 14 atoms per unit cell (I already got convergence 
in energy and charge in scf).


My problem is the number of K-points when I do execute the following 
command: berrypi k4:4:2 –o –s –p (or 5:5:3). It always switch the number 
of k points to 10x10x10, and calculation takes many hours. I am using 
Wine2K_19.1, on AMD Ryzen 32 cores station. What mistake am I doing in 
executing the command and how can I force the K-points to be reduced to 
a less number?


Best regards

Ali Baghi zadeh

Postdoc researcher

ScopeM, ETH, Zurich


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Re: [Wien] BerryPI

[Dr. K. C. Bhamu]

Dear Gavin,

Yes, alias berrypi calls berrypi
alias berrypi='/usr/bin/python2.7
/home/kcbhamu/Wien2k_18/SRC_BerryPI/BerryPI/berrypi'
also, berrypi -h worked.

thanks and regards
Bhamu

On Mon, Oct 1, 2018 at 5:42 PM Gavin Abo  wrote:

> "which berrypi" returning nothing I believe is fine since it uses an alias
> instead.
>
> Maybe check if the berrypi alias is setup with the terminal command:
>
> alias berrypi
>
> Maybe check that you can call berrypi, for example its help with the
> terminal command:
>
> berrypi -h
>
> In WIEN2k 18.2, I think it is userconfig that sets up BERRYPI_PATH and
> BERRYPI_PYTHON for you instead .bashrc instead of DEFAULT_BIN_PATH and
> DEFAULT_PYTHON_PATH, respectively.  So edit those, if the berrypi paths
> need adjusted.
> On 10/1/2018 4:57 AM, Dr. K. C. Bhamu wrote:
>
> Dear Prof. Oleg,
>
> I just installed the Wien2k_18.2.
>
> I saw one of your reply [1] where you call BerriPI with "which":
>
> when I do the same, I am not getting anything.
>
> My python variables in 'usr/bin' are:  python python2
> python2.7  python3python3.6  python3.6m python3m
>
>
> and
> config.py  is:
>
> DEFAULT_BIN_PATH="/home/kcbhamu/Wien2k_18.2/SRC_BerryPI/BerryPI"
> #Fix for python path to make sure it grabs the latest version
> #DEFAULT_PYTHON_PATH = "/usr/bin/python2.7"
> DEFAULT_PYTHON_PATH = "/usr/bin/python2.7"
>
> [1]
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16327.html
>
>
> regards
> Bhamu
>
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Re: [Wien] BerryPI

[Gavin Abo]

"which berrypi" returning nothing I believe is fine since it uses an 
alias instead.


Maybe check if the berrypi alias is setup with the terminal command:

alias berrypi

Maybe check that you can call berrypi, for example its help with the 
terminal command:


berrypi -h

In WIEN2k 18.2, I think it is userconfig that sets up BERRYPI_PATH and 
BERRYPI_PYTHON for you instead .bashrc instead of DEFAULT_BIN_PATH and 
DEFAULT_PYTHON_PATH, respectively.  So edit those, if the berrypi paths 
need adjusted.


On 10/1/2018 4:57 AM, Dr. K. C. Bhamu wrote:

Dear Prof. Oleg,

I just installed the Wien2k_18.2.

I saw one of your reply [1] where you call BerriPI with "which":

when I do the same, I am not getting anything.

My python variables in 'usr/bin' are:  python python2    
python2.7  python3 python3.6  python3.6m python3m



and
config.py  is:

DEFAULT_BIN_PATH="/home/kcbhamu/Wien2k_18.2/SRC_BerryPI/BerryPI"
#Fix for python path to make sure it grabs the latest version
#DEFAULT_PYTHON_PATH = "/usr/bin/python2.7"
DEFAULT_PYTHON_PATH = "/usr/bin/python2.7"

[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16327.html



regards
Bhamu
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Re: [Wien] BerryPi

[Gavin Abo]

Yes, the WIEN2k limitations page [ 
http://susi.theochem.tuwien.ac.at/reg_user/limitations/ ] lists that the 
optic package doesn't work with RLOs.


On 10/27/2017 8:45 AM, Dr. K. C. Bhamu wrote:

Hii,

I saw it but is is not helpful. Out procedure differs in many ways.

Here the person is doing -sp+-so for Pt and he is not adding RLOs, 
using TETRA 0.000, and taking plasma frequency as such from 
outputjoint file


while I am using RLO for Pb, TETRA 101 and sqrt(2)(w_pl).

I do not know if I do not apply RLO on Pb then how it will help me, 
rest of his procedure I have followed but could not get results.




Regards
Bhamu


On Fri, Oct 27, 2017 at 11:03 AM, lokanath patra 
> wrote:


Dear Dr. Bhamu

In this tutorial video for optical properties with so coupling,
they are using x kgen with so symmetry. So I think we should use
-so tag.
https://www.youtube.com/watch?v=lDW7cy1oZR4=147s


Check page no 135 of the UG to know about changing tetra.

Regards
Lokanath



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Re: [Wien] BerryPi

[Dr. K. C. Bhamu]

Hii,

I saw it but is is not helpful. Out procedure differs in many ways.

Here the person is doing -sp+-so for Pt and he is not adding RLOs, using
TETRA 0.000, and taking plasma frequency as such from outputjoint file

while I am using RLO for Pb, TETRA 101 and sqrt(2)(w_pl).

I do not know if I do not apply RLO on Pb then how it will help me, rest of
his procedure I have followed but could not get results.



Regards
Bhamu


On Fri, Oct 27, 2017 at 11:03 AM, lokanath patra <
lokanath.patra...@gmail.com> wrote:

> Dear Dr. Bhamu
>
> In this tutorial video for optical properties with so coupling, they are
> using x kgen with so symmetry. So I think we should use -so tag.
> https://www.youtube.com/watch?v=lDW7cy1oZR4=147s
>
> Check page no 135 of the UG to know about changing tetra.
>
> Regards
> Lokanath
>
>
> 
>  Virus-free.
> www.avg.com
> 
> <#m_5823975444954967641_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
> On Thu, Oct 19, 2017 at 6:53 PM, Dr. K. C. Bhamu 
> wrote:
>
>> Dear Lokanath,
>>
>> Happy Diwali!
>>
>> Hope you are enjoying your research at CU, TU.
>>
>> I am having same structure what you have in recent past.
>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at
>> /msg16508.html
>>
>> I have three queries and looking forward your favor.
>>
>> *My first query:*
>>
>> I am not getting  the reply submitted by   Jaroslav Hamrle
>> 
>> :
>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at
>> /msg16510.html
>>
>> 2b) when you want mesh for optical calculations to be finer, do:
>>   x kgen -so (to generate finer mesh)
>>   in third line in case.in2, *change value of TETRA to be 101*   
>>  >> what does he mean by changing the value of TETRA?
>>
>>
>> *Second:*
>>
>> I have PbCrO3 system with spin polarised and spin-orbit coupling.
>> I am running the case with 8 8 6 (total 35) k-points.
>>
>>
>> *Third:*
>>
>> my next question is:   what is mean by -s in your run script
>>
>> runsp_lapw -p -so -cc 0.01 -ec 0.001 -s lapw1
>>
>>
>> Do I need to increase k-mesh using "x kgen -so" or "x kgen" is sufficient?
>>
>>
>>
>> Regards
>> Bhamu
>>
>
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Re: [Wien] BerryPi

[lokanath patra]

Dear Dr. Bhamu

In this tutorial video for optical properties with so coupling, they are
using x kgen with so symmetry. So I think we should use -so tag.
https://www.youtube.com/watch?v=lDW7cy1oZR4=147s

Check page no 135 of the UG to know about changing tetra.

Regards
Lokanath


Virus-free.
www.avg.com

<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

On Thu, Oct 19, 2017 at 6:53 PM, Dr. K. C. Bhamu 
wrote:

> Dear Lokanath,
>
> Happy Diwali!
>
> Hope you are enjoying your research at CU, TU.
>
> I am having same structure what you have in recent past.
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16508.html
>
> I have three queries and looking forward your favor.
>
> *My first query:*
>
> I am not getting  the reply submitted by   Jaroslav Hamrle
> 
> :
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16510.html
>
> 2b) when you want mesh for optical calculations to be finer, do:
>   x kgen -so (to generate finer mesh)
>   in third line in case.in2, *change value of TETRA to be 101*
> >> what does he mean by changing the value of TETRA?
>
>
> *Second:*
>
> I have PbCrO3 system with spin polarised and spin-orbit coupling.
> I am running the case with 8 8 6 (total 35) k-points.
>
>
> *Third:*
>
> my next question is:   what is mean by -s in your run script
>
> runsp_lapw -p -so -cc 0.01 -ec 0.001 -s lapw1
>
>
> Do I need to increase k-mesh using "x kgen -so" or "x kgen" is sufficient?
>
>
>
> Regards
> Bhamu
>
>
>
>
> Dr. K. C. Bhamu
> National Postdoctoral Fellow,
> Physical and Materials Chemistry Division
> Mob. No.  +91-9975238952 <+91%2099752%2038952>
>
> On Fri, Jan 29, 2016 at 4:29 PM, Dr. K. C. Bhamu 
> wrote:
>
>> What you need it to shift both position i.e. 0.5 to 0.501 and
>> 0. to 0.0010.
>>
>> Problem will be solved.
>>
>> regards
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *Dr. K. C. Bhamu(UGC-Dr.
>> D. S. Kothari Postdoc Fellow)Department of PhysicsGoa University, Goa-403
>> 206IndiaMob. No.  +91-9782911977 <+91%2097829%2011977>*
>>
>> On Fri, Jan 29, 2016 at 3:59 PM, lokanath patra <
>> lokanath.patra...@gmail.com> wrote:
>>
>>> Dear Fecher and Bhamu,
>>> I also think that the error is due to the symmetry after changing the
>>> struct file. But the tutorial says ''Do not rerun the init_lapw as it may
>>> realize a higher symmetry. The intention is to keep symmetry unchanged
>>> between subsequent runs''. Just check the 3rd and 4 points of the link.
>>> https://github.com/spichardo/BerryPI/wiki/Tutorial-3:-Non-or
>>> thogonal-lattice-vectors
>>>
>>> Thanks.
>>>
>>>
>>> On Fri, Jan 29, 2016 at 2:47 PM, Dr. K. C. Bhamu 
>>> wrote:
>>>
 Hello Lokanath
 I did a mistake in my previous mail regarding rmt issue.
 Your RMT is ok (I did a mistack in compilation).

 your *x nn* gives error so definitely something is wrong with struct
 file.


 *Experts may help you.*
 regards
 Bhamu





 On Fri, Jan 29, 2016 at 11:19 AM, lokanath patra <
 lokanath.patra...@gmail.com> wrote:

> Dear Dr Bhamu,
> Actually I have already searched for that. But as  I am changing the
> position of an atom, I guess the symmetry breaks and the error comes. With
> the struct file with unchanged atomic position, it runs fine.
>
> Dear Oleg Rubel,
>
> Here I am attaching the two struct files used in “initial” calculation
> and after the displacement is introduced.
>
> Thanks.
>
> On Thu, Jan 28, 2016 at 11:29 PM, Oleg Rubel 
> wrote:
>
>> Would it be possible to attach the structure files used in “initial”
>> calculation and after the displacement is introduced?
>>
>> Thank you
>> Oleg
>>
>> > On Jan 28, 2016, at 11:08, Dr. K. C. Bhamu 
>> wrote:
>> >
>> > Dear Lokanath
>> >
>> > Your error is wellknown if you search mailing list.
>> > You may try : https://www.mail-archive.com/w
>> i...@zeus.theochem.tuwien.ac.at/msg08405.html
>> >
>> > Some time ago I got same error and by compiling SRC_hf agin I
>> overcome the error.
>> >
>> > regards
>> >
>> >
>> >
>> > 
>> > Dr. K. C. Bhamu
>> > (UGC-Dr. D. S. Kothari Postdoc Fellow)
>> > Department of Physics
>> > Goa University, Goa-403 206
>> > India
>> > Mob. No.  +91-9782911977
>> >
>> > On Thu, Jan 28, 2016 at 8:33 PM, lokanath patra <
>> lokanath.patra...@gmail.com> wrote:

Re: [Wien] BerryPi

[Dr. K. C. Bhamu]

Dear Lokanath,

Happy Diwali!

Hope you are enjoying your research at CU, TU.

I am having same structure what you have in recent past.
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16508.html

I have three queries and looking forward your favor.

*My first query:*

I am not getting  the reply submitted by   Jaroslav Hamrle

:
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16510.html

2b) when you want mesh for optical calculations to be finer, do:
  x kgen -so (to generate finer mesh)
  in third line in case.in2, *change value of TETRA to be 101*
   >> what does he mean by changing the value of TETRA?


*Second:*

I have PbCrO3 system with spin polarised and spin-orbit coupling.
I am running the case with 8 8 6 (total 35) k-points.


*Third:*

my next question is:   what is mean by -s in your run script

runsp_lapw -p -so -cc 0.01 -ec 0.001 -s lapw1


Do I need to increase k-mesh using "x kgen -so" or "x kgen" is sufficient?



Regards
Bhamu




Dr. K. C. Bhamu
National Postdoctoral Fellow,
Physical and Materials Chemistry Division
Mob. No.  +91-9975238952

On Fri, Jan 29, 2016 at 4:29 PM, Dr. K. C. Bhamu 
wrote:

> What you need it to shift both position i.e. 0.5 to 0.501 and
> 0. to 0.0010.
>
> Problem will be solved.
>
> regards
>
>
>
>
>
>
>
>
>
> *Dr. K. C. Bhamu(UGC-Dr.
> D. S. Kothari Postdoc Fellow)Department of PhysicsGoa University, Goa-403
> 206IndiaMob. No.  +91-9782911977*
>
> On Fri, Jan 29, 2016 at 3:59 PM, lokanath patra <
> lokanath.patra...@gmail.com> wrote:
>
>> Dear Fecher and Bhamu,
>> I also think that the error is due to the symmetry after changing the
>> struct file. But the tutorial says ''Do not rerun the init_lapw as it may
>> realize a higher symmetry. The intention is to keep symmetry unchanged
>> between subsequent runs''. Just check the 3rd and 4 points of the link.
>> https://github.com/spichardo/BerryPI/wiki/Tutorial-3:-Non-or
>> thogonal-lattice-vectors
>>
>> Thanks.
>>
>>
>> On Fri, Jan 29, 2016 at 2:47 PM, Dr. K. C. Bhamu 
>> wrote:
>>
>>> Hello Lokanath
>>> I did a mistake in my previous mail regarding rmt issue.
>>> Your RMT is ok (I did a mistack in compilation).
>>>
>>> your *x nn* gives error so definitely something is wrong with struct
>>> file.
>>>
>>>
>>> *Experts may help you.*
>>> regards
>>> Bhamu
>>>
>>>
>>>
>>>
>>>
>>> On Fri, Jan 29, 2016 at 11:19 AM, lokanath patra <
>>> lokanath.patra...@gmail.com> wrote:
>>>
 Dear Dr Bhamu,
 Actually I have already searched for that. But as  I am changing the
 position of an atom, I guess the symmetry breaks and the error comes. With
 the struct file with unchanged atomic position, it runs fine.

 Dear Oleg Rubel,

 Here I am attaching the two struct files used in “initial” calculation
 and after the displacement is introduced.

 Thanks.

 On Thu, Jan 28, 2016 at 11:29 PM, Oleg Rubel 
 wrote:

> Would it be possible to attach the structure files used in “initial”
> calculation and after the displacement is introduced?
>
> Thank you
> Oleg
>
> > On Jan 28, 2016, at 11:08, Dr. K. C. Bhamu 
> wrote:
> >
> > Dear Lokanath
> >
> > Your error is wellknown if you search mailing list.
> > You may try : https://www.mail-archive.com/w
> i...@zeus.theochem.tuwien.ac.at/msg08405.html
> >
> > Some time ago I got same error and by compiling SRC_hf agin I
> overcome the error.
> >
> > regards
> >
> >
> >
> > 
> > Dr. K. C. Bhamu
> > (UGC-Dr. D. S. Kothari Postdoc Fellow)
> > Department of Physics
> > Goa University, Goa-403 206
> > India
> > Mob. No.  +91-9782911977
> >
> > On Thu, Jan 28, 2016 at 8:33 PM, lokanath patra <
> lokanath.patra...@gmail.com> wrote:
> > Dear Users,
> >
> > I am trying to calculate born effective charge for Bi atom in
> BiFeO3. I followed the tutorial for GaAs as BiFeO3 is having non 
> orthogonal
> lattice vectors. I used berrypi with -s option as it consists of magnetic
> ion. But after changing the position of Bi atom by 0.001, when I put the
> command ''x dstart'' to initialize the electron density, it is showing
> 'rot-def' error. Please help.
> >
> > Thanks in advance.
> >
> > --
> > Lokanath Patra
> > Ph.D Scholar
> > Dept. of Physics
> > School of Applied and Basic Sciences
> > Central University of Tamil Nadu
> > Thiruvarur
> > Tamil Nadu - 610101
> > Ph no - +91-8675834507
> >
> > ___
> > Wien mailing list
> > 

Re: [Wien] berrypi missing -c case (in automatic)

[Laurence Marks]

You are right, I missed that.

---
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Gyorgi
http://www.numis.northwestern.edu
Corrosion in 4D http://MURI4D.numis.northwestern.edu
Partner of the CFW 100% gender equity project, www.cfw.org/100-percent
Co-Editor, Acta Cryst A

On Mar 11, 2016 18:31, "Oleg Rubel"  wrote:

> The necessity for the ‘-c’ option is not obvious. Would you please give a
> hint?
>
> BerryPI executes ‘x lapw1’ and then ‘x w2w’. I both cases, ‘x’ script is
> used that identifies complex calculation. There is no need to be more
> specific and call for ‘x lapw1 -c’ or ‘x w2w -c’ (please correct me, if I
> am wrong). Do you have a case where the complex calculation is not properly
> identified? I can take a look into that.
>
> Also, I think that there is no need to run BerryPI for a system with
> inversion symmetry explicitly present in the structure file. All electronic
> phases will be zero. Sometimes, centrosymmetric structure is a reference
> structure, whereas a perturbed structure lacks the inversion symmetry. In
> this case, I would recommend to run both calculations using identical low
> symmetry settings.
>
> Oleg
>
> > On Mar 11, 2016, at 4:04 PM, Laurence Marks 
> wrote:
> >
> > berrypi seems to need a "-c" option for the complex case, presumably can
> be hacked around.
> >
> > Similarly needed for the call of w2w that it makes (I think).
> >
> > --
> > Professor Laurence Marks
> > "Research is to see what everybody else has seen, and to think what
> nobody else has thought", Albert Szent-Gyorgi
> > www.numis.northwestern.edu ; Corrosion in 4D:
> MURI4D.numis.northwestern.edu
> > Partner of the CFW 100% program for gender equity,
> www.cfw.org/100-percent
> > Co-Editor, Acta Cryst A
>
>
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Re: [Wien] berrypi missing -c case (in automatic)

[Oleg Rubel]

The necessity for the ‘-c’ option is not obvious. Would you please give a hint?

BerryPI executes ‘x lapw1’ and then ‘x w2w’. I both cases, ‘x’ script is used 
that identifies complex calculation. There is no need to be more specific and 
call for ‘x lapw1 -c’ or ‘x w2w -c’ (please correct me, if I am wrong). Do you 
have a case where the complex calculation is not properly identified? I can 
take a look into that.

Also, I think that there is no need to run BerryPI for a system with inversion 
symmetry explicitly present in the structure file. All electronic phases will 
be zero. Sometimes, centrosymmetric structure is a reference structure, whereas 
a perturbed structure lacks the inversion symmetry. In this case, I would 
recommend to run both calculations using identical low symmetry settings.

Oleg

> On Mar 11, 2016, at 4:04 PM, Laurence Marks  wrote:
> 
> berrypi seems to need a "-c" option for the complex case, presumably can be 
> hacked around.
> 
> Similarly needed for the call of w2w that it makes (I think).
> 
> -- 
> Professor Laurence Marks
> "Research is to see what everybody else has seen, and to think what nobody 
> else has thought", Albert Szent-Gyorgi
> www.numis.northwestern.edu ; Corrosion in 4D: MURI4D.numis.northwestern.edu
> Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent
> Co-Editor, Acta Cryst A

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Re: [Wien] BerryPi

[lokanath patra]

Dear Oleg,

Thanks a lot. I can find my mistake now. I will try for an insulator.

On Mon, Feb 1, 2016 at 6:17 AM, Oleg Rubel  wrote:

> Well, the fractional occupancies indicate that this is a metal. I afraid
> you cannot proceed with he effective charge calculation. BerryPI implies
> the presence of a band gap.
>
> > So if i have understood you, I have to rerun init_lapw after the
> displacement.
>
> Not quite, you need to change the order and start with the distorted
> structure (similar to
> https://github.com/spichardo/BerryPI/wiki/Tutorial-3:-Non-orthogonal-lattice-vectors).
> Again, it makes sense only if it is not a metal. Even a semimetal works
> with a shifted k-mesh.
>
>
> Oleg
>
> > On Jan 31, 2016, at 2:03 AM, lokanath patra 
> wrote:
> >
> > Dear Oleg,
> >
> > Here I am listing the result
> >
> > :BAN00034:  340.2210690.307010  1.
> > :BAN00035:  350.2463190.307010  1.
> > :BAN00036:  360.2688320.335387  1.
> > :BAN00037:  370.2843330.339720  1.
> > :BAN00038:  380.3035260.345742  1.
> > :BAN00039:  390.3184700.383233  1.
> > :BAN00040:  400.3243830.388931  1.
> > :BAN00041:  410.3616690.412751  1.
> > :BAN00042:  420.3868300.422636  1.
> > :BAN00043:  430.5354300.570228  0.88992023
> > :BAN00044:  440.5365260.576437  0.13433882
> > :BAN00045:  450.5535270.582444  0.
> > :BAN00046:  460.5682560.585172  0.
> > :BAN00047:  470.5723390.596519  0.
> > :BAN00048:  480.5723390.604896  0.
> > :BAN00049:  490.6236560.699132  0.
> > :BAN00042:  420.3122230.353933  1.
> > :BAN00043:  430.3248150.359415  1.
> > :BAN00044:  440.3331620.375854  1.
> > :BAN00045:  450.3521200.381727  1.
> > :BAN00046:  460.3521200.391737  1.
> > :BAN00047:  470.3911940.435997  1.
> > :BAN00048:  480.4003320.435997  1.
> > :BAN00049:  490.4138160.516497  1.
> > :BAN00050:  500.4138160.516497  1.
> > :BAN00051:  510.4964440.603847  0.88561301
> > :BAN00052:  520.5164970.603974  0.09045336
> > :BAN00053:  530.6728400.832567  0.
> > :BAN00054:  540.7121050.832567  0.
> > :BAN00055:  550.7638370.869655  0.
> > :BAN00056:  560.8068160.894698  0.
> > :BAN00057:  570.8278470.894698  0.
> > :BAN00034:  340.2210800.307021  1.
> > :BAN00035:  350.2463300.307021  1.
> > :BAN00036:  360.2688430.335401  1.
> > :BAN00037:  370.2843440.339732  1.
> > :BAN00038:  380.3035360.345754  1.
> > :BAN00039:  390.3184820.383243  1.
> > :BAN00040:  400.3243940.388944  1.
> > :BAN00041:  410.3616800.412761  1.
> > :BAN00042:  420.3868400.422646  1.
> > :BAN00043:  430.5354230.570222  0.88968694
> > :BAN00044:  440.5365200.576432  0.13424669
> > :BAN00045:  450.5535220.582439  0.
> > :BAN00046:  460.5682500.585166  0.
> > :BAN00047:  470.5723350.596516  0.
> > :BAN00048:  480.5723350.604893  0.
> > :BAN00049:  490.6236500.699132  0.
> >
> > So if i have understood you, I have to rerun init_lapw after the
> displacement.
> >
> > Thanks
> >
> >
> > On Sat, Jan 30, 2016 at 4:48 AM, Oleg Rubel  wrote:
> > Just a small addition: It is a “must" to start with the least symmetric
> structure first. This implies that you need to introduce displacements,
> init_lapw, run(sp)_lapw, berrypy and then bring atoms back to the high
> symmetry position, dstart (-up/-dn), run(sp)_lapw, berrypi.
> >
> > In your structure alpha and beta are 90 deg. If you are interested in
> Z*(3,3) (i.e., along Z axis) then there is no need to worry about
> nonorthogonality of lattice vectors, similar to
> https://github.com/spichardo/BerryPI/wiki/Tutorial-4:-Polarization-in-GaN
> >
> > Please be cautious with the band occupancy. Can you list the results of
> “grep :BAN *scf”? If the structure is metallic, berrypi cannot be continued.
> >
> > Oleg
> >
> > > On Jan 29, 2016, at 05:59, Dr. K. C. Bhamu 
> wrote:
> > >
> > > What you need it to shift both position i.e. 0.5 to 0.501 and
> 0. to 0.0010.
> > >
> > > Problem will be solved.
> > >
> > > regards
> > >
> > >
> > >
> > > 
> > > Dr. K. C. Bhamu
> > > (UGC-Dr. D. S. Kothari Postdoc Fellow)
> > > Department of Physics
> > > Goa University, Goa-403 206
> > > India
> > > Mob. No.  +91-9782911977
> > >
> > > On Fri, Jan 29, 2016 at 3:59 PM, lokanath patra <
> 

Re: [Wien] BerryPi

[Oleg Rubel]

Well, the fractional occupancies indicate that this is a metal. I afraid you 
cannot proceed with he effective charge calculation. BerryPI implies the 
presence of a band gap.

> So if i have understood you, I have to rerun init_lapw after the displacement.

Not quite, you need to change the order and start with the distorted structure 
(similar to 
https://github.com/spichardo/BerryPI/wiki/Tutorial-3:-Non-orthogonal-lattice-vectors).
 Again, it makes sense only if it is not a metal. Even a semimetal works with a 
shifted k-mesh.


Oleg

> On Jan 31, 2016, at 2:03 AM, lokanath patra  
> wrote:
> 
> Dear Oleg,
> 
> Here I am listing the result
> 
> :BAN00034:  340.2210690.307010  1.
> :BAN00035:  350.2463190.307010  1.
> :BAN00036:  360.2688320.335387  1.
> :BAN00037:  370.2843330.339720  1.
> :BAN00038:  380.3035260.345742  1.
> :BAN00039:  390.3184700.383233  1.
> :BAN00040:  400.3243830.388931  1.
> :BAN00041:  410.3616690.412751  1.
> :BAN00042:  420.3868300.422636  1.
> :BAN00043:  430.5354300.570228  0.88992023
> :BAN00044:  440.5365260.576437  0.13433882
> :BAN00045:  450.5535270.582444  0.
> :BAN00046:  460.5682560.585172  0.
> :BAN00047:  470.5723390.596519  0.
> :BAN00048:  480.5723390.604896  0.
> :BAN00049:  490.6236560.699132  0.
> :BAN00042:  420.3122230.353933  1.
> :BAN00043:  430.3248150.359415  1.
> :BAN00044:  440.3331620.375854  1.
> :BAN00045:  450.3521200.381727  1.
> :BAN00046:  460.3521200.391737  1.
> :BAN00047:  470.3911940.435997  1.
> :BAN00048:  480.4003320.435997  1.
> :BAN00049:  490.4138160.516497  1.
> :BAN00050:  500.4138160.516497  1.
> :BAN00051:  510.4964440.603847  0.88561301
> :BAN00052:  520.5164970.603974  0.09045336
> :BAN00053:  530.6728400.832567  0.
> :BAN00054:  540.7121050.832567  0.
> :BAN00055:  550.7638370.869655  0.
> :BAN00056:  560.8068160.894698  0.
> :BAN00057:  570.8278470.894698  0.
> :BAN00034:  340.2210800.307021  1.
> :BAN00035:  350.2463300.307021  1.
> :BAN00036:  360.2688430.335401  1.
> :BAN00037:  370.2843440.339732  1.
> :BAN00038:  380.3035360.345754  1.
> :BAN00039:  390.3184820.383243  1.
> :BAN00040:  400.3243940.388944  1.
> :BAN00041:  410.3616800.412761  1.
> :BAN00042:  420.3868400.422646  1.
> :BAN00043:  430.5354230.570222  0.88968694
> :BAN00044:  440.5365200.576432  0.13424669
> :BAN00045:  450.5535220.582439  0.
> :BAN00046:  460.5682500.585166  0.
> :BAN00047:  470.5723350.596516  0.
> :BAN00048:  480.5723350.604893  0.
> :BAN00049:  490.6236500.699132  0.
> 
> So if i have understood you, I have to rerun init_lapw after the displacement.
> 
> Thanks
> 
> 
> On Sat, Jan 30, 2016 at 4:48 AM, Oleg Rubel  wrote:
> Just a small addition: It is a “must" to start with the least symmetric 
> structure first. This implies that you need to introduce displacements, 
> init_lapw, run(sp)_lapw, berrypy and then bring atoms back to the high 
> symmetry position, dstart (-up/-dn), run(sp)_lapw, berrypi.
> 
> In your structure alpha and beta are 90 deg. If you are interested in Z*(3,3) 
> (i.e., along Z axis) then there is no need to worry about nonorthogonality of 
> lattice vectors, similar to 
> https://github.com/spichardo/BerryPI/wiki/Tutorial-4:-Polarization-in-GaN
> 
> Please be cautious with the band occupancy. Can you list the results of “grep 
> :BAN *scf”? If the structure is metallic, berrypi cannot be continued.
> 
> Oleg
> 
> > On Jan 29, 2016, at 05:59, Dr. K. C. Bhamu  wrote:
> >
> > What you need it to shift both position i.e. 0.5 to 0.501 and 
> > 0. to 0.0010.
> >
> > Problem will be solved.
> >
> > regards
> >
> >
> >
> > 
> > Dr. K. C. Bhamu
> > (UGC-Dr. D. S. Kothari Postdoc Fellow)
> > Department of Physics
> > Goa University, Goa-403 206
> > India
> > Mob. No.  +91-9782911977
> >
> > On Fri, Jan 29, 2016 at 3:59 PM, lokanath patra 
> >  wrote:
> > Dear Fecher and Bhamu,
> > I also think that the error is due to the symmetry after changing the 
> > struct file. But the tutorial says ''Do not rerun the init_lapw as it may 
> > realize a higher symmetry. The intention is to keep symmetry unchanged 
> > between subsequent runs''. Just check the 3rd and 

Re: [Wien] BerryPi

[lokanath patra]

Dear Oleg,

Here I am listing the result

:BAN00034:  340.2210690.307010  1.
:BAN00035:  350.2463190.307010  1.
:BAN00036:  360.2688320.335387  1.
:BAN00037:  370.2843330.339720  1.
:BAN00038:  380.3035260.345742  1.
:BAN00039:  390.3184700.383233  1.
:BAN00040:  400.3243830.388931  1.
:BAN00041:  410.3616690.412751  1.
:BAN00042:  420.3868300.422636  1.
:BAN00043:  430.5354300.570228  0.88992023
:BAN00044:  440.5365260.576437  0.13433882
:BAN00045:  450.5535270.582444  0.
:BAN00046:  460.5682560.585172  0.
:BAN00047:  470.5723390.596519  0.
:BAN00048:  480.5723390.604896  0.
:BAN00049:  490.6236560.699132  0.
:BAN00042:  420.3122230.353933  1.
:BAN00043:  430.3248150.359415  1.
:BAN00044:  440.3331620.375854  1.
:BAN00045:  450.3521200.381727  1.
:BAN00046:  460.3521200.391737  1.
:BAN00047:  470.3911940.435997  1.
:BAN00048:  480.4003320.435997  1.
:BAN00049:  490.4138160.516497  1.
:BAN00050:  500.4138160.516497  1.
:BAN00051:  510.4964440.603847  0.88561301
:BAN00052:  520.5164970.603974  0.09045336
:BAN00053:  530.6728400.832567  0.
:BAN00054:  540.7121050.832567  0.
:BAN00055:  550.7638370.869655  0.
:BAN00056:  560.8068160.894698  0.
:BAN00057:  570.8278470.894698  0.
:BAN00034:  340.2210800.307021  1.
:BAN00035:  350.2463300.307021  1.
:BAN00036:  360.2688430.335401  1.
:BAN00037:  370.2843440.339732  1.
:BAN00038:  380.3035360.345754  1.
:BAN00039:  390.3184820.383243  1.
:BAN00040:  400.3243940.388944  1.
:BAN00041:  410.3616800.412761  1.
:BAN00042:  420.3868400.422646  1.
:BAN00043:  430.5354230.570222  0.88968694
:BAN00044:  440.5365200.576432  0.13424669
:BAN00045:  450.5535220.582439  0.
:BAN00046:  460.5682500.585166  0.
:BAN00047:  470.5723350.596516  0.
:BAN00048:  480.5723350.604893  0.
:BAN00049:  490.6236500.699132  0.

So if i have understood you, I have to rerun init_lapw after the
displacement.

Thanks


On Sat, Jan 30, 2016 at 4:48 AM, Oleg Rubel  wrote:

> Just a small addition: It is a “must" to start with the least symmetric
> structure first. This implies that you need to introduce displacements,
> init_lapw, run(sp)_lapw, berrypy and then bring atoms back to the high
> symmetry position, dstart (-up/-dn), run(sp)_lapw, berrypi.
>
> In your structure alpha and beta are 90 deg. If you are interested in
> Z*(3,3) (i.e., along Z axis) then there is no need to worry about
> nonorthogonality of lattice vectors, similar to
> https://github.com/spichardo/BerryPI/wiki/Tutorial-4:-Polarization-in-GaN
>
> Please be cautious with the band occupancy. Can you list the results of
> “grep :BAN *scf”? If the structure is metallic, berrypi cannot be continued.
>
> Oleg
>
> > On Jan 29, 2016, at 05:59, Dr. K. C. Bhamu  wrote:
> >
> > What you need it to shift both position i.e. 0.5 to 0.501 and
> 0. to 0.0010.
> >
> > Problem will be solved.
> >
> > regards
> >
> >
> >
> > 
> > Dr. K. C. Bhamu
> > (UGC-Dr. D. S. Kothari Postdoc Fellow)
> > Department of Physics
> > Goa University, Goa-403 206
> > India
> > Mob. No.  +91-9782911977
> >
> > On Fri, Jan 29, 2016 at 3:59 PM, lokanath patra <
> lokanath.patra...@gmail.com> wrote:
> > Dear Fecher and Bhamu,
> > I also think that the error is due to the symmetry after changing the
> struct file. But the tutorial says ''Do not rerun the init_lapw as it may
> realize a higher symmetry. The intention is to keep symmetry unchanged
> between subsequent runs''. Just check the 3rd and 4 points of the link.
> >
> https://github.com/spichardo/BerryPI/wiki/Tutorial-3:-Non-orthogonal-lattice-vectors
> >
> > Thanks.
> >
> >
> > On Fri, Jan 29, 2016 at 2:47 PM, Dr. K. C. Bhamu 
> wrote:
> > Hello Lokanath
> > I did a mistake in my previous mail regarding rmt issue.
> > Your RMT is ok (I did a mistack in compilation).
> >
> > your x nn gives error so definitely something is wrong with struct file.
> >
> > Experts may help you.
> >
> > regards
> > Bhamu
> >
> >
> >
> >
> >
> > On Fri, Jan 29, 2016 at 11:19 AM, lokanath patra <
> lokanath.patra...@gmail.com> wrote:
> > Dear Dr Bhamu,
> > Actually I have already searched for that. But as  I am changing the
> position of an atom, I guess the symmetry breaks and the error comes. With
> 

Re: [Wien] BerryPi

[Fecher, Gerhard]

Did you change only the position ? That might be the cause of your troubles.
you also need to have the correct symmetry (space group) for the new structure 
! 

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 lokanath patra 
[lokanath.patra...@gmail.com]
Gesendet: Freitag, 29. Januar 2016 08:39
An: A Mailing list for WIEN2k users
Betreff: Re: [Wien] BerryPi

I just followed the tutorial of Born effective charge. According to that, we 
have to initialize the calculation for the unchanged material. Then we have to 
change the position and den we have to initialize the electron density only 
i.e. ''x dstart''. They have mentioned not to rerun init_lapw . So I 
initialized only the electron density and got the error.

Thanks.

On Fri, Jan 29, 2016 at 12:13 PM, Dr. K. C. Bhamu 
<kcbham...@gmail.com<mailto:kcbham...@gmail.com>> wrote:
One more thing: I dont know how to calculate born effective charge. But you see 
your new struct file there are 6 position for Bi, 6 position for O and 2 for 
Fe. So new composition is 3:1:3 while in original it is 1:1:3.

So look on the new struct file, how you changing position of Bi and why rmt get 
reduced.

regards
Bhamu




On Fri, Jan 29, 2016 at 11:19 AM, lokanath patra 
<lokanath.patra...@gmail.com<mailto:lokanath.patra...@gmail.com>> wrote:
Dear Dr Bhamu,
Actually I have already searched for that. But as  I am changing the position 
of an atom, I guess the symmetry breaks and the error comes. With the struct 
file with unchanged atomic position, it runs fine.

Dear Oleg Rubel,

Here I am attaching the two struct files used in “initial” calculation and 
after the displacement is introduced.

Thanks.

On Thu, Jan 28, 2016 at 11:29 PM, Oleg Rubel 
<oru...@lakeheadu.ca<mailto:oru...@lakeheadu.ca>> wrote:
Would it be possible to attach the structure files used in “initial” 
calculation and after the displacement is introduced?

Thank you
Oleg

> On Jan 28, 2016, at 11:08, Dr. K. C. Bhamu 
> <kcbham...@gmail.com<mailto:kcbham...@gmail.com>> wrote:
>
> Dear Lokanath
>
> Your error is wellknown if you search mailing list.
> You may try : 
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08405.html
>
> Some time ago I got same error and by compiling SRC_hf agin I overcome the 
> error.
>
> regards
>
>
>
> 
> Dr. K. C. Bhamu
> (UGC-Dr. D. S. Kothari Postdoc Fellow)
> Department of Physics
> Goa University, Goa-403 206
> India
> Mob. No.  +91-9782911977<tel:%2B91-9782911977>
>
> On Thu, Jan 28, 2016 at 8:33 PM, lokanath patra 
> <lokanath.patra...@gmail.com<mailto:lokanath.patra...@gmail.com>> wrote:
> Dear Users,
>
> I am trying to calculate born effective charge for Bi atom in BiFeO3. I 
> followed the tutorial for GaAs as BiFeO3 is having non orthogonal lattice 
> vectors. I used berrypi with -s option as it consists of magnetic ion. But 
> after changing the position of Bi atom by 0.001, when I put the command ''x 
> dstart'' to initialize the electron density, it is showing 'rot-def' error. 
> Please help.
>
> Thanks in advance.
>
> --
> Lokanath Patra
> Ph.D Scholar
> Dept. of Physics
> School of Applied and Basic Sciences
> Central University of Tamil Nadu
> Thiruvarur
> Tamil Nadu - 610101
> Ph no - +91-8675834507<tel:%2B91-8675834507>
>
> ___
> Wien mailing list
> Wien@zeus.theochem.tuwien.ac.at<mailto: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
>
>
> ___
> Wien mailing list
> Wien@zeus.theochem.tuwien.ac.at<mailto: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

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SEARCH the MAILING-LIST at:  
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Re: [Wien] BerryPi

[Dr. K. C. Bhamu]

What you need it to shift both position i.e. 0.5 to 0.501 and
0. to 0.0010.

Problem will be solved.

regards









*Dr. K. C. Bhamu(UGC-Dr. D.
S. Kothari Postdoc Fellow)Department of PhysicsGoa University, Goa-403
206IndiaMob. No.  +91-9782911977*

On Fri, Jan 29, 2016 at 3:59 PM, lokanath patra  wrote:

> Dear Fecher and Bhamu,
> I also think that the error is due to the symmetry after changing the
> struct file. But the tutorial says ''Do not rerun the init_lapw as it may
> realize a higher symmetry. The intention is to keep symmetry unchanged
> between subsequent runs''. Just check the 3rd and 4 points of the link.
>
> https://github.com/spichardo/BerryPI/wiki/Tutorial-3:-Non-orthogonal-lattice-vectors
>
> Thanks.
>
>
> On Fri, Jan 29, 2016 at 2:47 PM, Dr. K. C. Bhamu 
> wrote:
>
>> Hello Lokanath
>> I did a mistake in my previous mail regarding rmt issue.
>> Your RMT is ok (I did a mistack in compilation).
>>
>> your *x nn* gives error so definitely something is wrong with struct
>> file.
>>
>>
>> *Experts may help you.*
>> regards
>> Bhamu
>>
>>
>>
>>
>>
>> On Fri, Jan 29, 2016 at 11:19 AM, lokanath patra <
>> lokanath.patra...@gmail.com> wrote:
>>
>>> Dear Dr Bhamu,
>>> Actually I have already searched for that. But as  I am changing the
>>> position of an atom, I guess the symmetry breaks and the error comes. With
>>> the struct file with unchanged atomic position, it runs fine.
>>>
>>> Dear Oleg Rubel,
>>>
>>> Here I am attaching the two struct files used in “initial” calculation
>>> and after the displacement is introduced.
>>>
>>> Thanks.
>>>
>>> On Thu, Jan 28, 2016 at 11:29 PM, Oleg Rubel 
>>> wrote:
>>>
 Would it be possible to attach the structure files used in “initial”
 calculation and after the displacement is introduced?

 Thank you
 Oleg

 > On Jan 28, 2016, at 11:08, Dr. K. C. Bhamu 
 wrote:
 >
 > Dear Lokanath
 >
 > Your error is wellknown if you search mailing list.
 > You may try :
 https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08405.html
 >
 > Some time ago I got same error and by compiling SRC_hf agin I
 overcome the error.
 >
 > regards
 >
 >
 >
 > 
 > Dr. K. C. Bhamu
 > (UGC-Dr. D. S. Kothari Postdoc Fellow)
 > Department of Physics
 > Goa University, Goa-403 206
 > India
 > Mob. No.  +91-9782911977
 >
 > On Thu, Jan 28, 2016 at 8:33 PM, lokanath patra <
 lokanath.patra...@gmail.com> wrote:
 > Dear Users,
 >
 > I am trying to calculate born effective charge for Bi atom in BiFeO3.
 I followed the tutorial for GaAs as BiFeO3 is having non orthogonal lattice
 vectors. I used berrypi with -s option as it consists of magnetic ion. But
 after changing the position of Bi atom by 0.001, when I put the command ''x
 dstart'' to initialize the electron density, it is showing 'rot-def' error.
 Please help.
 >
 > Thanks in advance.
 >
 > --
 > Lokanath Patra
 > Ph.D Scholar
 > Dept. of Physics
 > School of Applied and Basic Sciences
 > Central University of Tamil Nadu
 > Thiruvarur
 > Tamil Nadu - 610101
 > Ph no - +91-8675834507
 >
 > ___
 > 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
 >
 >
 > ___
 > 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

 ___
 Wien mailing list
 Wien@zeus.theochem.tuwien.ac.at
 http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
 SEARCH the MAILING-LIST at:
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>>>
>>>
>>>
>>> --
>>> Lokanath Patra
>>> Ph.D Scholar
>>> Dept. of Physics
>>> School of Applied and Basic Sciences
>>> Central University of Tamil Nadu
>>> Thiruvarur
>>> Tamil Nadu - 610101
>>> Ph no - +91-8675834507
>>>
>>> ___
>>> 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
>>>
>>>
>>
>> ___
>> Wien mailing list
>> Wien@zeus.theochem.tuwien.ac.at
>> 

Re: [Wien] BerryPi

[lokanath patra]

Dear Fecher and Bhamu,
I also think that the error is due to the symmetry after changing the
struct file. But the tutorial says ''Do not rerun the init_lapw as it may
realize a higher symmetry. The intention is to keep symmetry unchanged
between subsequent runs''. Just check the 3rd and 4 points of the link.
https://github.com/spichardo/BerryPI/wiki/Tutorial-3:-Non-orthogonal-lattice-vectors

Thanks.


On Fri, Jan 29, 2016 at 2:47 PM, Dr. K. C. Bhamu 
wrote:

> Hello Lokanath
> I did a mistake in my previous mail regarding rmt issue.
> Your RMT is ok (I did a mistack in compilation).
>
> your *x nn* gives error so definitely something is wrong with struct file.
>
>
> *Experts may help you.*
> regards
> Bhamu
>
>
>
>
>
> On Fri, Jan 29, 2016 at 11:19 AM, lokanath patra <
> lokanath.patra...@gmail.com> wrote:
>
>> Dear Dr Bhamu,
>> Actually I have already searched for that. But as  I am changing the
>> position of an atom, I guess the symmetry breaks and the error comes. With
>> the struct file with unchanged atomic position, it runs fine.
>>
>> Dear Oleg Rubel,
>>
>> Here I am attaching the two struct files used in “initial” calculation
>> and after the displacement is introduced.
>>
>> Thanks.
>>
>> On Thu, Jan 28, 2016 at 11:29 PM, Oleg Rubel  wrote:
>>
>>> Would it be possible to attach the structure files used in “initial”
>>> calculation and after the displacement is introduced?
>>>
>>> Thank you
>>> Oleg
>>>
>>> > On Jan 28, 2016, at 11:08, Dr. K. C. Bhamu 
>>> wrote:
>>> >
>>> > Dear Lokanath
>>> >
>>> > Your error is wellknown if you search mailing list.
>>> > You may try :
>>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08405.html
>>> >
>>> > Some time ago I got same error and by compiling SRC_hf agin I overcome
>>> the error.
>>> >
>>> > regards
>>> >
>>> >
>>> >
>>> > 
>>> > Dr. K. C. Bhamu
>>> > (UGC-Dr. D. S. Kothari Postdoc Fellow)
>>> > Department of Physics
>>> > Goa University, Goa-403 206
>>> > India
>>> > Mob. No.  +91-9782911977
>>> >
>>> > On Thu, Jan 28, 2016 at 8:33 PM, lokanath patra <
>>> lokanath.patra...@gmail.com> wrote:
>>> > Dear Users,
>>> >
>>> > I am trying to calculate born effective charge for Bi atom in BiFeO3.
>>> I followed the tutorial for GaAs as BiFeO3 is having non orthogonal lattice
>>> vectors. I used berrypi with -s option as it consists of magnetic ion. But
>>> after changing the position of Bi atom by 0.001, when I put the command ''x
>>> dstart'' to initialize the electron density, it is showing 'rot-def' error.
>>> Please help.
>>> >
>>> > Thanks in advance.
>>> >
>>> > --
>>> > Lokanath Patra
>>> > Ph.D Scholar
>>> > Dept. of Physics
>>> > School of Applied and Basic Sciences
>>> > Central University of Tamil Nadu
>>> > Thiruvarur
>>> > Tamil Nadu - 610101
>>> > Ph no - +91-8675834507
>>> >
>>> > ___
>>> > 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
>>> >
>>> >
>>> > ___
>>> > 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
>>>
>>> ___
>>> 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
>>>
>>
>>
>>
>> --
>> Lokanath Patra
>> Ph.D Scholar
>> Dept. of Physics
>> School of Applied and Basic Sciences
>> Central University of Tamil Nadu
>> Thiruvarur
>> Tamil Nadu - 610101
>> Ph no - +91-8675834507
>>
>> ___
>> 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
>>
>>
>
> ___
> 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
>
>


-- 
Lokanath Patra
Ph.D Scholar
Dept. of Physics
School of Applied and Basic Sciences
Central University of Tamil Nadu
Thiruvarur
Tamil Nadu - 610101
Ph no - +91-8675834507
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Re: [Wien] BerryPi

[Dr. K. C. Bhamu]

Hello Lokanath
I did a mistake in my previous mail regarding rmt issue.
Your RMT is ok (I did a mistack in compilation).

your *x nn* gives error so definitely something is wrong with struct file.


*Experts may help you.*
regards
Bhamu




On Fri, Jan 29, 2016 at 11:19 AM, lokanath patra <
lokanath.patra...@gmail.com> wrote:

> Dear Dr Bhamu,
> Actually I have already searched for that. But as  I am changing the
> position of an atom, I guess the symmetry breaks and the error comes. With
> the struct file with unchanged atomic position, it runs fine.
>
> Dear Oleg Rubel,
>
> Here I am attaching the two struct files used in “initial” calculation and
> after the displacement is introduced.
>
> Thanks.
>
> On Thu, Jan 28, 2016 at 11:29 PM, Oleg Rubel  wrote:
>
>> Would it be possible to attach the structure files used in “initial”
>> calculation and after the displacement is introduced?
>>
>> Thank you
>> Oleg
>>
>> > On Jan 28, 2016, at 11:08, Dr. K. C. Bhamu  wrote:
>> >
>> > Dear Lokanath
>> >
>> > Your error is wellknown if you search mailing list.
>> > You may try :
>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08405.html
>> >
>> > Some time ago I got same error and by compiling SRC_hf agin I overcome
>> the error.
>> >
>> > regards
>> >
>> >
>> >
>> > 
>> > Dr. K. C. Bhamu
>> > (UGC-Dr. D. S. Kothari Postdoc Fellow)
>> > Department of Physics
>> > Goa University, Goa-403 206
>> > India
>> > Mob. No.  +91-9782911977
>> >
>> > On Thu, Jan 28, 2016 at 8:33 PM, lokanath patra <
>> lokanath.patra...@gmail.com> wrote:
>> > Dear Users,
>> >
>> > I am trying to calculate born effective charge for Bi atom in BiFeO3. I
>> followed the tutorial for GaAs as BiFeO3 is having non orthogonal lattice
>> vectors. I used berrypi with -s option as it consists of magnetic ion. But
>> after changing the position of Bi atom by 0.001, when I put the command ''x
>> dstart'' to initialize the electron density, it is showing 'rot-def' error.
>> Please help.
>> >
>> > Thanks in advance.
>> >
>> > --
>> > Lokanath Patra
>> > Ph.D Scholar
>> > Dept. of Physics
>> > School of Applied and Basic Sciences
>> > Central University of Tamil Nadu
>> > Thiruvarur
>> > Tamil Nadu - 610101
>> > Ph no - +91-8675834507
>> >
>> > ___
>> > 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
>> >
>> >
>> > ___
>> > 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
>>
>> ___
>> 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
>>
>
>
>
> --
> Lokanath Patra
> Ph.D Scholar
> Dept. of Physics
> School of Applied and Basic Sciences
> Central University of Tamil Nadu
> Thiruvarur
> Tamil Nadu - 610101
> Ph no - +91-8675834507
>
> ___
> Wien mailing list
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> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> SEARCH the MAILING-LIST at:
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>
>
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Re: [Wien] BerryPi

[Oleg Rubel]

Just a small addition: It is a “must" to start with the least symmetric 
structure first. This implies that you need to introduce displacements, 
init_lapw, run(sp)_lapw, berrypy and then bring atoms back to the high symmetry 
position, dstart (-up/-dn), run(sp)_lapw, berrypi.

In your structure alpha and beta are 90 deg. If you are interested in Z*(3,3) 
(i.e., along Z axis) then there is no need to worry about nonorthogonality of 
lattice vectors, similar to 
https://github.com/spichardo/BerryPI/wiki/Tutorial-4:-Polarization-in-GaN

Please be cautious with the band occupancy. Can you list the results of “grep 
:BAN *scf”? If the structure is metallic, berrypi cannot be continued.

Oleg

> On Jan 29, 2016, at 05:59, Dr. K. C. Bhamu  wrote:
> 
> What you need it to shift both position i.e. 0.5 to 0.501 and 
> 0. to 0.0010.
> 
> Problem will be solved.
> 
> regards
> 
> 
> 
> 
> Dr. K. C. Bhamu
> (UGC-Dr. D. S. Kothari Postdoc Fellow)
> Department of Physics
> Goa University, Goa-403 206
> India
> Mob. No.  +91-9782911977
> 
> On Fri, Jan 29, 2016 at 3:59 PM, lokanath patra  
> wrote:
> Dear Fecher and Bhamu,
> I also think that the error is due to the symmetry after changing the struct 
> file. But the tutorial says ''Do not rerun the init_lapw as it may realize a 
> higher symmetry. The intention is to keep symmetry unchanged between 
> subsequent runs''. Just check the 3rd and 4 points of the link. 
> https://github.com/spichardo/BerryPI/wiki/Tutorial-3:-Non-orthogonal-lattice-vectors
> 
> Thanks.
>  
> 
> On Fri, Jan 29, 2016 at 2:47 PM, Dr. K. C. Bhamu  wrote:
> Hello Lokanath
> I did a mistake in my previous mail regarding rmt issue.
> Your RMT is ok (I did a mistack in compilation).
> 
> your x nn gives error so definitely something is wrong with struct file.
> 
> Experts may help you.
> 
> regards
> Bhamu
> 
> 
> 
> 
> 
> On Fri, Jan 29, 2016 at 11:19 AM, lokanath patra 
>  wrote:
> Dear Dr Bhamu, 
> Actually I have already searched for that. But as  I am changing the position 
> of an atom, I guess the symmetry breaks and the error comes. With the struct 
> file with unchanged atomic position, it runs fine.
> 
> Dear Oleg Rubel,
> 
> Here I am attaching the two struct files used in “initial” calculation and 
> after the displacement is introduced.
> 
> Thanks.
> 
> On Thu, Jan 28, 2016 at 11:29 PM, Oleg Rubel  wrote:
> Would it be possible to attach the structure files used in “initial” 
> calculation and after the displacement is introduced?
> 
> Thank you
> Oleg
> 
> > On Jan 28, 2016, at 11:08, Dr. K. C. Bhamu  wrote:
> >
> > Dear Lokanath
> >
> > Your error is wellknown if you search mailing list.
> > You may try : 
> > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08405.html
> >
> > Some time ago I got same error and by compiling SRC_hf agin I overcome the 
> > error.
> >
> > regards
> >
> >
> >
> > 
> > Dr. K. C. Bhamu
> > (UGC-Dr. D. S. Kothari Postdoc Fellow)
> > Department of Physics
> > Goa University, Goa-403 206
> > India
> > Mob. No.  +91-9782911977
> >
> > On Thu, Jan 28, 2016 at 8:33 PM, lokanath patra 
> >  wrote:
> > Dear Users,
> >
> > I am trying to calculate born effective charge for Bi atom in BiFeO3. I 
> > followed the tutorial for GaAs as BiFeO3 is having non orthogonal lattice 
> > vectors. I used berrypi with -s option as it consists of magnetic ion. But 
> > after changing the position of Bi atom by 0.001, when I put the command ''x 
> > dstart'' to initialize the electron density, it is showing 'rot-def' error. 
> > Please help.
> >
> > Thanks in advance.
> >
> > --
> > Lokanath Patra
> > Ph.D Scholar
> > Dept. of Physics
> > School of Applied and Basic Sciences
> > Central University of Tamil Nadu
> > Thiruvarur
> > Tamil Nadu - 610101
> > Ph no - +91-8675834507
> >
> > ___
> > 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
> >
> >
> > ___
> > 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
> 
> ___
> 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
> 
> 
> 
> -- 
> Lokanath Patra
> Ph.D Scholar
> Dept. of Physics
> School of Applied 

Re: [Wien] BerryPi

[Dr. K. C. Bhamu]

Dear Lokanath

Your error is wellknown if you search mailing list.
You may try :
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08405.html

Some time ago I got same error and by compiling SRC_hf agin I overcome the
error.

regards









*Dr. K. C. Bhamu(UGC-Dr. D.
S. Kothari Postdoc Fellow)Department of PhysicsGoa University, Goa-403
206IndiaMob. No.  +91-9782911977*

On Thu, Jan 28, 2016 at 8:33 PM, lokanath patra  wrote:

> Dear Users,
>
> I am trying to calculate born effective charge for Bi atom in BiFeO3. I
> followed the tutorial for GaAs as BiFeO3 is having non orthogonal lattice
> vectors. I used berrypi with -s option as it consists of magnetic ion. But
> after changing the position of Bi atom by 0.001, when I put the command ''x
> dstart'' to initialize the electron density, it is showing 'rot-def' error.
> Please help.
>
> Thanks in advance.
>
> --
> Lokanath Patra
> Ph.D Scholar
> Dept. of Physics
> School of Applied and Basic Sciences
> Central University of Tamil Nadu
> Thiruvarur
> Tamil Nadu - 610101
> Ph no - +91-8675834507
>
> ___
> 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
>
>
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Re: [Wien] BerryPi

[lokanath patra]

I just followed the tutorial of Born effective charge. According to that,
we have to initialize the calculation for the unchanged material. Then we
have to change the position and den we have to initialize the electron
density only i.e. ''x dstart''. They have mentioned not to rerun init_lapw
. So I initialized only the electron density and got the error.

Thanks.

On Fri, Jan 29, 2016 at 12:13 PM, Dr. K. C. Bhamu 
wrote:

> One more thing: I dont know how to calculate born effective charge. But
> you see your new struct file there are 6 position for Bi, 6 position for O
> and 2 for Fe. So new composition is 3:1:3 while in original it is 1:1:3.
>
> So look on the new struct file, how you changing position of Bi and why
> rmt get reduced.
>
> regards
> Bhamu
>
>
>
>
> On Fri, Jan 29, 2016 at 11:19 AM, lokanath patra <
> lokanath.patra...@gmail.com> wrote:
>
>> Dear Dr Bhamu,
>> Actually I have already searched for that. But as  I am changing the
>> position of an atom, I guess the symmetry breaks and the error comes. With
>> the struct file with unchanged atomic position, it runs fine.
>>
>> Dear Oleg Rubel,
>>
>> Here I am attaching the two struct files used in “initial” calculation
>> and after the displacement is introduced.
>>
>> Thanks.
>>
>> On Thu, Jan 28, 2016 at 11:29 PM, Oleg Rubel  wrote:
>>
>>> Would it be possible to attach the structure files used in “initial”
>>> calculation and after the displacement is introduced?
>>>
>>> Thank you
>>> Oleg
>>>
>>> > On Jan 28, 2016, at 11:08, Dr. K. C. Bhamu 
>>> wrote:
>>> >
>>> > Dear Lokanath
>>> >
>>> > Your error is wellknown if you search mailing list.
>>> > You may try :
>>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08405.html
>>> >
>>> > Some time ago I got same error and by compiling SRC_hf agin I overcome
>>> the error.
>>> >
>>> > regards
>>> >
>>> >
>>> >
>>> > 
>>> > Dr. K. C. Bhamu
>>> > (UGC-Dr. D. S. Kothari Postdoc Fellow)
>>> > Department of Physics
>>> > Goa University, Goa-403 206
>>> > India
>>> > Mob. No.  +91-9782911977
>>> >
>>> > On Thu, Jan 28, 2016 at 8:33 PM, lokanath patra <
>>> lokanath.patra...@gmail.com> wrote:
>>> > Dear Users,
>>> >
>>> > I am trying to calculate born effective charge for Bi atom in BiFeO3.
>>> I followed the tutorial for GaAs as BiFeO3 is having non orthogonal lattice
>>> vectors. I used berrypi with -s option as it consists of magnetic ion. But
>>> after changing the position of Bi atom by 0.001, when I put the command ''x
>>> dstart'' to initialize the electron density, it is showing 'rot-def' error.
>>> Please help.
>>> >
>>> > Thanks in advance.
>>> >
>>> > --
>>> > Lokanath Patra
>>> > Ph.D Scholar
>>> > Dept. of Physics
>>> > School of Applied and Basic Sciences
>>> > Central University of Tamil Nadu
>>> > Thiruvarur
>>> > Tamil Nadu - 610101
>>> > Ph no - +91-8675834507
>>> >
>>> > ___
>>> > 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
>>> >
>>> >
>>> > ___
>>> > 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
>>>
>>> ___
>>> 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
>>>
>>
>>
>>
>> --
>> Lokanath Patra
>> Ph.D Scholar
>> Dept. of Physics
>> School of Applied and Basic Sciences
>> Central University of Tamil Nadu
>> Thiruvarur
>> Tamil Nadu - 610101
>> Ph no - +91-8675834507
>>
>> ___
>> 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
>>
>>
>
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>


-- 
Lokanath Patra
Ph.D Scholar
Dept. of Physics
School of Applied and Basic Sciences
Central University of Tamil Nadu
Thiruvarur
Tamil Nadu - 610101
Ph no - +91-8675834507
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Re: [Wien] BerryPi

[Dr. K. C. Bhamu]

One more thing: I dont know how to calculate born effective charge. But you
see your new struct file there are 6 position for Bi, 6 position for O and
2 for Fe. So new composition is 3:1:3 while in original it is 1:1:3.

So look on the new struct file, how you changing position of Bi and why rmt
get reduced.

regards
Bhamu



On Fri, Jan 29, 2016 at 11:19 AM, lokanath patra <
lokanath.patra...@gmail.com> wrote:

> Dear Dr Bhamu,
> Actually I have already searched for that. But as  I am changing the
> position of an atom, I guess the symmetry breaks and the error comes. With
> the struct file with unchanged atomic position, it runs fine.
>
> Dear Oleg Rubel,
>
> Here I am attaching the two struct files used in “initial” calculation and
> after the displacement is introduced.
>
> Thanks.
>
> On Thu, Jan 28, 2016 at 11:29 PM, Oleg Rubel  wrote:
>
>> Would it be possible to attach the structure files used in “initial”
>> calculation and after the displacement is introduced?
>>
>> Thank you
>> Oleg
>>
>> > On Jan 28, 2016, at 11:08, Dr. K. C. Bhamu  wrote:
>> >
>> > Dear Lokanath
>> >
>> > Your error is wellknown if you search mailing list.
>> > You may try :
>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08405.html
>> >
>> > Some time ago I got same error and by compiling SRC_hf agin I overcome
>> the error.
>> >
>> > regards
>> >
>> >
>> >
>> > 
>> > Dr. K. C. Bhamu
>> > (UGC-Dr. D. S. Kothari Postdoc Fellow)
>> > Department of Physics
>> > Goa University, Goa-403 206
>> > India
>> > Mob. No.  +91-9782911977
>> >
>> > On Thu, Jan 28, 2016 at 8:33 PM, lokanath patra <
>> lokanath.patra...@gmail.com> wrote:
>> > Dear Users,
>> >
>> > I am trying to calculate born effective charge for Bi atom in BiFeO3. I
>> followed the tutorial for GaAs as BiFeO3 is having non orthogonal lattice
>> vectors. I used berrypi with -s option as it consists of magnetic ion. But
>> after changing the position of Bi atom by 0.001, when I put the command ''x
>> dstart'' to initialize the electron density, it is showing 'rot-def' error.
>> Please help.
>> >
>> > Thanks in advance.
>> >
>> > --
>> > Lokanath Patra
>> > Ph.D Scholar
>> > Dept. of Physics
>> > School of Applied and Basic Sciences
>> > Central University of Tamil Nadu
>> > Thiruvarur
>> > Tamil Nadu - 610101
>> > Ph no - +91-8675834507
>> >
>> > ___
>> > 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
>> >
>> >
>> > ___
>> > 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
>>
>> ___
>> 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
>>
>
>
>
> --
> Lokanath Patra
> Ph.D Scholar
> Dept. of Physics
> School of Applied and Basic Sciences
> Central University of Tamil Nadu
> Thiruvarur
> Tamil Nadu - 610101
> Ph no - +91-8675834507
>
> ___
> 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
>
>
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Re: [Wien] BerryPi

[Dr. K. C. Bhamu]

Did you see any error in x nn?
I am getting nn error in your Bi-changed structure, see below:
Commandline: *x nn *
Program input is: *"2 "*

 specify nn-bondlength factor: (usually=2) [and optionally dlimit, dstmax (about
  1.d-5, 20)]
 DSTMAX:   29.087375730
 iix,iiy,iiz   5   5   5   52.79519
   52.79519131.02421500
 NAMED ATOM: Bi1   Z changed to IATNR+999 to determine equivalency
 NAMED ATOM: Fe1   Z changed to IATNR+999 to determine equivalency
 NAMED ATOM: O 1   Z changed to IATNR+999 to determine equivalency

  * ERROR !!!*
 RMT(  1)=0.01000 AND RMT(  1)=0.01000
 SUMS TO 0.02000 GT NNN-DIST= 0.01056

ATOM  2  Fe1ATOM  3  O 1
 RMT(  2)=1.96000 AND RMT(  3)=1.69000
 SUMS TO 3.65000  LT.  NN-DIST= 3.66678

ATOM  3  O 1ATOM  2  Fe1
 RMT(  3)=1.69000 AND RMT(  2)=1.96000
 SUMS TO 3.65000  LT.  NN-DIST= 3.66678
NN ENDS
0.0u 0.0s 0:00.08 100.0% 0+0k 0+288io 0pf+0w.
###

I am in doubt for your this struct file as RMT for Bi is 0.01 (too
less). If we reduce RMT upto 3 it remain same and

beyond 3% it become zero. So I (not as an expert) guess, there is
something wrong in your struct file.

In your original file RMT is 2.39.
I suggest plz focus on RMT for Bi in new structure.

Hope you now know the source of error.

regards











*Dr. K. C. Bhamu(UGC-Dr. D.
S. Kothari Postdoc Fellow)Department of PhysicsGoa University, Goa-403
206IndiaMob. No.  +91-9782911977*

On Fri, Jan 29, 2016 at 11:19 AM, lokanath patra <
lokanath.patra...@gmail.com> wrote:

> Dear Dr Bhamu,
> Actually I have already searched for that. But as  I am changing the
> position of an atom, I guess the symmetry breaks and the error comes. With
> the struct file with unchanged atomic position, it runs fine.
>
> Dear Oleg Rubel,
>
> Here I am attaching the two struct files used in “initial” calculation and
> after the displacement is introduced.
>
> Thanks.
>
> On Thu, Jan 28, 2016 at 11:29 PM, Oleg Rubel  wrote:
>
>> Would it be possible to attach the structure files used in “initial”
>> calculation and after the displacement is introduced?
>>
>> Thank you
>> Oleg
>>
>> > On Jan 28, 2016, at 11:08, Dr. K. C. Bhamu  wrote:
>> >
>> > Dear Lokanath
>> >
>> > Your error is wellknown if you search mailing list.
>> > You may try :
>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08405.html
>> >
>> > Some time ago I got same error and by compiling SRC_hf agin I overcome
>> the error.
>> >
>> > regards
>> >
>> >
>> >
>> > 
>> > Dr. K. C. Bhamu
>> > (UGC-Dr. D. S. Kothari Postdoc Fellow)
>> > Department of Physics
>> > Goa University, Goa-403 206
>> > India
>> > Mob. No.  +91-9782911977
>> >
>> > On Thu, Jan 28, 2016 at 8:33 PM, lokanath patra <
>> lokanath.patra...@gmail.com> wrote:
>> > Dear Users,
>> >
>> > I am trying to calculate born effective charge for Bi atom in BiFeO3. I
>> followed the tutorial for GaAs as BiFeO3 is having non orthogonal lattice
>> vectors. I used berrypi with -s option as it consists of magnetic ion. But
>> after changing the position of Bi atom by 0.001, when I put the command ''x
>> dstart'' to initialize the electron density, it is showing 'rot-def' error.
>> Please help.
>> >
>> > Thanks in advance.
>> >
>> > --
>> > Lokanath Patra
>> > Ph.D Scholar
>> > Dept. of Physics
>> > School of Applied and Basic Sciences
>> > Central University of Tamil Nadu
>> > Thiruvarur
>> > Tamil Nadu - 610101
>> > Ph no - +91-8675834507
>> >
>> > ___
>> > Wien mailing list
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>> > 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
>> >
>> >
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>
>
>
> --
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> Ph.D Scholar
> Dept. of Physics
> School of Applied and Basic Sciences
> Central University of Tamil Nadu
> Thiruvarur
> Tamil Nadu - 610101
> Ph no - +91-8675834507
>
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>

Re: [Wien] BerryPi

[Oleg Rubel]

Would it be possible to attach the structure files used in “initial” 
calculation and after the displacement is introduced?

Thank you
Oleg

> On Jan 28, 2016, at 11:08, Dr. K. C. Bhamu  wrote:
> 
> Dear Lokanath
> 
> Your error is wellknown if you search mailing list.
> You may try : 
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08405.html
> 
> Some time ago I got same error and by compiling SRC_hf agin I overcome the 
> error.
> 
> regards
> 
> 
> 
> 
> Dr. K. C. Bhamu
> (UGC-Dr. D. S. Kothari Postdoc Fellow)
> Department of Physics
> Goa University, Goa-403 206
> India
> Mob. No.  +91-9782911977
> 
> On Thu, Jan 28, 2016 at 8:33 PM, lokanath patra  
> wrote:
> Dear Users,
> 
> I am trying to calculate born effective charge for Bi atom in BiFeO3. I 
> followed the tutorial for GaAs as BiFeO3 is having non orthogonal lattice 
> vectors. I used berrypi with -s option as it consists of magnetic ion. But 
> after changing the position of Bi atom by 0.001, when I put the command ''x 
> dstart'' to initialize the electron density, it is showing 'rot-def' error. 
> Please help.
> 
> Thanks in advance.
> 
> -- 
> Lokanath Patra
> Ph.D Scholar
> Dept. of Physics
> School of Applied and Basic Sciences
> Central University of Tamil Nadu
> Thiruvarur
> Tamil Nadu - 610101
> Ph no - +91-8675834507
> 
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Re: [Wien] BerryPI

[Oleg Rubel]

The GGA+U calculation is likely affected by pi wrapping (-pi = +pi).
So -p +(-pi) = -2*pi can be different from what you expect -pi + pi =
0.

Also, I would not make conclusions based on a single calculation of
polarization for a structure. All observables (spontaneous
polarization, effective charge, piezoelectricity) are related to the
polarization change (difference). Therefore calculations often require
at least two structures.

Please do not apply BerryPI to calculation of polarization when the
band occupancy is metallic.

Thanks
Oleg


On Sun, Jan 3, 2016 at 2:58 PM, nilofar hadaeghi  wrote:
> 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 error.

[Oleg Rubel]

It can be related to python/numpy installation or compatibility issues.

BerryPi dependencies:

WIEN2k (tested against 14.2 Release 15/10/2014)
WIEN2WANNIER (part of the Wien2k distribution)
Python (tested against 2.7.4)
NumPy (tested against 1.6.2 & 1.9.2)

My suggestion would be to recreate the python & numpy enviroment as
indicated above + pull a fresh BerryPI version from githab
(https://github.com/spichardo/BerryPI)

Thanks
Oleg


On Sun, Jan 3, 2016 at 11:29 AM, lokanath patra
 wrote:
> Dear all
> I am working on the berryPI code and I have faced the following error.
> Can anyone help me please?
>
> Thank you in advance.
>
>
> Traceback (most recent call last):
>   File "/cluster/home/lokanath/lib/w215/SRC_BerryPI/BerryPI/berrypi", line
> 20, in 
> import numpy # math library
>   File
> "/cluster/software/VERSIONS/python_packages-3.5_1/cluster/software/VERSIONS/python3-3.5.0/lib/python3.5/site-packages/numpy/__init__.py",
> line 180, in 
> from . import add_newdocs
>   File
> "/cluster/software/VERSIONS/python_packages-3.5_1/cluster/software/VERSIONS/python3-3.5.0/lib/python3.5/site-packages/numpy/add_newdocs.py",
> line 13, in 
> from numpy.lib import add_newdoc
>   File
> "/cluster/software/VERSIONS/python_packages-3.5_1/cluster/software/VERSIONS/python3-3.5.0/lib/python3.5/site-packages/numpy/lib/__init__.py",
> line 8, in 
> from .type_check import *
>   File
> "/cluster/software/VERSIONS/python_packages-3.5_1/cluster/software/VERSIONS/python3-3.5.0/lib/python3.5/site-packages/numpy/lib/type_check.py",
> line 11, in 
> import numpy.core.numeric as _nx
>   File
> "/cluster/software/VERSIONS/python_packages-3.5_1/cluster/software/VERSIONS/python3-3.5.0/lib/python3.5/site-packages/numpy/core/__init__.py",
> line 14, in 
> from . import multiarray
> ImportError: cannot import name multiarray
>
>
>
> --
> Lokanath Patra
> Ph.D Scholar
> Dept. of Physics
> School of Applied and Basic Sciences
> Central University of Tamil Nadu
> Thiruvarur
> Tamil Nadu - 610101
> Ph no - +91-8675834507
>
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Re: [Wien] berryPI

[Elias Assmann]

On 10/19/2015 10:47 AM, Peter Blaha wrote:
> I'm not fully familiar with the w2wannier flow, but I can see from the
> def file, that the $file.vector file already has a $hf option.

Yes, I put that in “for completeness”, but it is so far completely untested.

> However, then it should probably be also in the $file.energy$hf line

Thanks for the pointer.  Right now we have ‘$file.energy$soupdn’; what
would be the “most correct” way?  ‘$file.energy$sc$hf$soupdn’?

> and I also see a required $file.fermi  file (I don't know when it is
> created), but that should also relate to a hf calculation.

That is the Fermi energy, which ‘prepare_w2wdir’ takes from ‘$file.scf’
or, failing that, ‘$file.scf2$updn’.

Elias

-- 
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Institute of Theoretical and Computational Physics
TU Graz   ⟨https://itp.tugraz.at/⟩
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Re: [Wien] berryPI

[Peter Blaha]

The correct energy line should be:


  ‘$file.energy$sc$hf$soupdn’?

I'll fix this in my x_lapw script for the next release.


And prepare_w2wdir   should take $file.scf   or   $file.scf2$hf$updn
(not just $file.scf2$updn)
And in addition, it should accpt a -hf switch and   set hf=hf

Peter

On 10/20/2015 02:15 PM, Elias Assmann wrote:

On 10/19/2015 10:47 AM, Peter Blaha wrote:

I'm not fully familiar with the w2wannier flow, but I can see from the
def file, that the $file.vector file already has a $hf option.


Yes, I put that in “for completeness”, but it is so far completely untested.


However, then it should probably be also in the $file.energy$hf line


Thanks for the pointer.  Right now we have ‘$file.energy$soupdn’; what
would be the “most correct” way?  ‘$file.energy$sc$hf$soupdn’?


and I also see a required $file.fermi  file (I don't know when it is
created), but that should also relate to a hf calculation.


That is the Fermi energy, which ‘prepare_w2wdir’ takes from ‘$file.scf’
or, failing that, ‘$file.scf2$updn’.

Elias



--

  P.Blaha
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
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Re: [Wien] berryPI

[Peter Blaha]

I'm not fully familiar with the w2wannier flow, but I can see from the 
def file, that the $file.vector file already has a $hf option.


However, then it should probably be also in the $file.energy$hf line

and I also see a required $file.fermi  file (I don't know when it is 
created), but that should also relate to a hf calculation.


So I suspect that only copying the vectorhf file will not be enough.

Regards


On 10/16/2015 08:09 AM, Elias Assmann wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Nilofar, Oleg, and Peter,

I cannot say for sure whether w2w will work with HF because I have
never tried it, and do not know too much about how an HF calculation
works in Wien2k.  If, as Peter says

On 10/15/2015 09:30 PM, Peter Blaha wrote:

I can confirm that case.vectorhf  has the same structure than
case.vertor.


it should probably work out.  Nilofar, maybe you can give it a try and
report back here -- I would be interested to know, and if problems do
turn up, I will try to help.


For testing one could simply   copy   case.vectorhf case.vector and
try it out.


For w2w, I believe the ‘-hf’ switch should be enough.


I don't know if there are any other input files requires for w2w or
BerryPI (case.energy ?   there is also a hf file), ...


Looking at the w2w.def file

   5,'$file.inwf','old','formatted',  0
   6,'$file.outputwf$updn',   'unknown','formatted',  0
   7,'$file.amn$w90updn', 'unknown','formatted',  0
   8,'$file.mmn$w90updn', 'unknown','formatted',  0
   9,'${scratch}$file.vector$sc$hf$soupdn', 'unknown','unformatted',9000
  10,'$file.nnkp',   'old','formatted',  0
  12,'$file.eig$updn',   'unknown','formatted',  0
  18,'$file.vsp$updn','old','formatted',  0
  20,'$file.struct', 'old','formatted',  0
  50,'$file.energy$soupdn',   'old','formatted',  0
  51,'$file.fermi$updn'   'old','formatted',  0

only ‘vector’ and ‘vsp’ is needed in the “normal” case.  What is there
in the ‘hf’ file?


Am 15.10.2015 um 20:08 schrieb Oleg Rubel:

 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".


“Onsite hybrid”/EECE is quite a different beast than “full hybrid”,
and I believe it should pose no problems to w2w/BerryPI.  Just run
lapw1 with the appropriate switches (‘-orb’?).


Elias


- --
Elias Assmann
Institute of Theoretical and Computational Physics
TU Graz   
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--
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Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
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Re: [Wien] berryPI

[Elias Assmann]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Nilofar, Oleg, and Peter,

I cannot say for sure whether w2w will work with HF because I have
never tried it, and do not know too much about how an HF calculation
works in Wien2k.  If, as Peter says

On 10/15/2015 09:30 PM, Peter Blaha wrote:
> I can confirm that case.vectorhf  has the same structure than
> case.vertor.

it should probably work out.  Nilofar, maybe you can give it a try and
report back here -- I would be interested to know, and if problems do
turn up, I will try to help.

> For testing one could simply   copy   case.vectorhf case.vector and
> try it out.

For w2w, I believe the ‘-hf’ switch should be enough.

> I don't know if there are any other input files requires for w2w or
> BerryPI (case.energy ?   there is also a hf file), ...

Looking at the w2w.def file

  5,'$file.inwf','old','formatted',  0
  6,'$file.outputwf$updn',   'unknown','formatted',  0
  7,'$file.amn$w90updn', 'unknown','formatted',  0
  8,'$file.mmn$w90updn', 'unknown','formatted',  0
  9,'${scratch}$file.vector$sc$hf$soupdn', 'unknown','unformatted',9000
 10,'$file.nnkp','old','formatted',  0
 12,'$file.eig$updn','unknown','formatted',  0
 18,'$file.vsp$updn','old','formatted',  0
 20,'$file.struct',  'old','formatted',  0
 50,'$file.energy$soupdn',   'old','formatted',  0
 51,'$file.fermi$updn'   'old','formatted',  0

only ‘vector’ and ‘vsp’ is needed in the “normal” case.  What is there
in the ‘hf’ file?

> Am 15.10.2015 um 20:08 schrieb Oleg Rubel:
>> 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".

“Onsite hybrid”/EECE is quite a different beast than “full hybrid”,
and I believe it should pose no problems to w2w/BerryPI.  Just run
lapw1 with the appropriate switches (‘-orb’?).


Elias


- -- 
Elias Assmann
Institute of Theoretical and Computational Physics
TU Graz   
-BEGIN PGP SIGNATURE-
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Re: [Wien] berryPI

[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 
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  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,
>>> ___
>>> 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
>>>
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>
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Re: [Wien] berryPI

[Peter Blaha]

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  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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Re: [Wien] berryPI

[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  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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> SEARCH the MAILING-LIST at:  
> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html

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Re: [Wien] berryPI

[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

[Fecher, Gerhard]

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<mailto: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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Re: [Wien] berryPI code

[Elias Assmann]

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



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Re: [Wien] berryPI code

[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 
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

[Sheikh Jamil Ahmed]

Dear Gerhard,

If I understand correctly, the assumption about the structures of
EuTiO3 in PhysRevLett.97.267602
is not accurate enough. The only consider the ground state to be Pm3_m and
then do a compression study with P4/mm. PhysRevLett.109.267602 on the other
hand pointed that the structure of bulk EuTiO3  in ground state should
be I4/mcm. Then, under compression the transition goes from I4/mcm to I4cm
to P4mm.

Sheikh

On Wed, Sep 9, 2015 at 5:24 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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>
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Re: [Wien] berryPI code

[Gavin Abo]

My guess is that the problem is coming from an inconsistency in the 
input files (case.energysoup or ?) or a code bug is causing I to become 
larger than the size nmat of BKX(I), BKY(I), or BZX(I), such that it is 
indexing out of an array.


To check if that is what is happening, I would try compiling with 
"-check bounds" [ 
https://software.intel.com/en-us/articles/determining-root-cause-of-segmentation-faults-sigsegv-or-sigbus-errors 
(Possible Cause #4) ]


and/or

I would put a print or write statement between lines 119 and 120 in 
SRC_w2w/almgen.F.  For example,


   i=i+1 <= Line 119
   if(i.gt.nmat) then
   write(unit_out,*)'dbg:i=',i,' nmat=',nmat,' n=',n, ' nlov=',nlov
   end if
   BK(1)=BKX(I)*BR1(1,1)+BKY(I)*BR1(1,2)+BKZ(I)*BR1(1,3) <= 
Line 120


The arrays BKX, BKY, and BKZ are allocated with nmat (SRC_w2w/modules.F 
and SRC_w2w/main.f).  The 'if statement' will check to see if i (from 
line 119) becomes greater than nmat.  If it does, then it should print a 
debug (dbg) line to case.outputwfup (for x w2w -up -so).


However, this is probably only helpful if you know Fortran programming.  
If you don't know Fortran programming, then the struct file and init 
parameters are needed as Elias previously mentioned [ 
http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12950.html ].

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Re: [Wien] berryPI

[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
>>
>> ___
>> Wien mailing list
>> Wien@zeus.theochem.tuwien.ac.at<mailto:Wien@zeus.theochem.tuwien.ac.at>
>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>> SEARCH the M

Re: [Wien] berryPI code

[Gavin Abo]

What is the output of Elias's grep command on your system?

For example, in a terminal, you should see something like:

username@computername:~/Desktop$ grep Id: 
$WIENROOT/SRC_w2w/{almgen.F,l2mmn.f,main.f}
/home/username/WIEN2k/SRC_w2w/almgen.F:!!! $Id: almgen.F 167 2014-02-03 
09:43:33Z assmann $
/home/username/WIEN2k/SRC_w2w/l2mmn.f:!!! $Id: l2mmn.f 167 2014-02-03 
09:43:33Z assmann $
/home/username/WIEN2k/SRC_w2w/main.f:!!! $Id: main.f 199 2014-04-11 
16:18:29Z assmann $


On 9/9/2015 10:22 AM, nilofar hadaeghi wrote:

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 > 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  PCRoutine   Line
> 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




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Re: [Wien] berryPI code

[Elias Assmann]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

On 09/09/2015 06:22 PM, nilofar hadaeghi wrote:
> 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

At least on the first level, this is a problem in w2w, so I do not
think the BerryPI version is relevant, much less Python of numpy.

Assuming you are using the latest Wien2k version (WIEN2k_14.2 (Release
15/10/2014)) and the wien2wannier version distributed with it, the
‘Id:’ lines I asked for (which give the precise version of the file)
would be

> grep Id: almgen.F main.f l2mmn.f
almgen.F:!!! $Id: almgen.F 167 2014-02-03 09:43:33Z assmann $
main.f:!!! $Id: main.f 199 2014-04-11 16:18:29Z assmann $
l2mmn.f:!!! $Id: l2mmn.f 167 2014-02-03 09:43:33Z assmann $

Please tell me if that is correct.

I looked at the differences between those versions and my most recent
ones, but I did not find any differences that seem relevant to your
error, which would mean that the error should still occur in the
development version.

Bottom line: if you are not using the Wien2k 14.2, please upgrade and
try again.  If you are, please send me the struct file and init
parameters for which the error happens, so I can try to reproduce it.


Elias

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Version: GnuPG v1
Comment: Using GnuPG with Icedove - http://www.enigmail.net/

iQIcBAEBAgAGBQJV8GKRAAoJEE/4gtQZfOqPjCYQAIBzi/MhBsCl0XjcTwH/TzR9
1ZdtEHapQue85JCwfaI5+gJYf5F3hPGSH4j8uTvIa5nABmmD3Fmq1UPIUpxbfAt3
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bnzF8D667POkRjeG5Rof
=vH91
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Re: [Wien] berryPI code

[Elias Assmann]

-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
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/D92VI6jzEolTZifcM4Dn57ttIiZWNqHqmmY6hF5syoFhCliEilNxH4bLhy79RkJ
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kNK9XKoNezhdfVUs7fPqVX0NTcmZvGVgM1J2MEH8kHb8K0gDjbKet17/rI0D2M1t
+gWQlJ7jIyf61s+Vesgf
=k0HR
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Re: [Wien] berryPI code

[Víctor Luaña Cabal]

>> grep Id: SRC_w2w/{almgen.F,l2mmn.f,main.f}

Let me explain a little the command by Elias:

grep Id: SRC_w2w/{almgen.F,l2mmn.f,main.f}
 --- -
  1 1

1: text to find
2: set of files to explore. Three files in this case.

A even improved serach would be

grep -B 5 -A 5 Id: SRC_w2w/{almgen.F,l2mmn.f,main.f}

that provides 5 lines of context before and after the pattern that
it is searched for. If you don't know much about the routines Elias
advise is *a minimal*. A search with some context would provide some
more datail, useful to a programmer.

Notice that Elias command corresponds to a bash shell, probably.

Regards,
  Víctor Luaña
--
 .  ."In science a person can be convinced by a good argument.
/ `' \   That is almost impossible in politics or religion"
   /(o)(o)\  (Adapted from Carl Sagan)
  /`. \/ .'\  "Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud" -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. !"I have two kinds of problems,
! Departamento de Química Física y Analítica ! the urgent and the important.
! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not important,
! e-mail:   vic...@fluor.quimica.uniovi.es   ! and the important are never
! phone: +34-985-103491  fax: +34-985-103125 ! urgent.
++(Dwight D. Eisenhower)
 GroupPage : http://azufre.quimica.uniovi.es/ 
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Re: [Wien] berryPI code

[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

[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 <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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Re: [Wien] berryPI

[Oleg Rubel]

That seems to be the case 
(http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list?gnum=140).
If both structures possess the inversion symmetry, it will be pointless to 
calculate polarization.

Oleg

> On Sep 8, 2015, at 03:48, Fecher, Gerhard <fec...@uni-mainz.de> wrote:
> 
> I thought that  I4/mcm  is also a centrosymmetric space group ?
> 
> 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 Oleg Rubel 
> [oru...@lakeheadu.ca]
> Gesendet: Dienstag, 8. September 2015 01:03
> An: A Mailing list for WIEN2k users
> Betreff: Re: [Wien] berryPI
> 
> The essence of electronic polarization is that it is a “relative” quantity, 
> i.e., its calculation (and measurement too) requires a reference point. The 
> reference structure is not always centrosymmetric. An example of 
> non-centrosymmetric reference structure is zinc-blende GaN that is taken as 
> P=0 in computing the spontaneous polarization of the wurtzite GaN (see 
> https://github.com/spichardo/BerryPI/wiki/Tutorial-4:-Polarization-in-GaN).
> 
> For the second part of the question on EuTiO3, enclosed structure files would 
> certainly help. One possible strategy would be to explore a gradual evolution 
> of the polarization between cubic and tetragonal structures.
> 
> 
> I hope this will help
> Oleg
> 
> 
> 
>> On Sep 7, 2015, at 3:42 AM, nilofar hadaeghi <n.hadae...@gmail.com> wrote:
>> 
>> 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,
>> ___
>> 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
> 
> ___
> 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
> ___
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> Wien@zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> SEARCH the MAILING-LIST at:  
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Re: [Wien] berryPI

[Oleg Rubel]

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

[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  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  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 ] 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   

Re: [Wien] berryPI code

[Oleg Rubel]

I afraid you need to dig into the source code of w2w and see what is going on 
in these lines.

Oleg

> On Sep 8, 2015, at 17:57, 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  PCRoutineLineSource
>  
> 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  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  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 ] Calling command: x w2w -so -up
> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > Image  PCRoutineLine
> > Source
> > w2wc   0042D9ED  almgen_

Re: [Wien] berryPI

[Sheikh Jamil Ahmed]

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
>
> ___
> 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
>
___
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Re: [Wien] berryPI

[ddsfu]

符徳勝

2015/09/09 1:39、nilofar hadaeghi <n.hadae...@gmail.com> のメッセージ:

>  I really appreciate your help.
> 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?
> 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?
> Best regards,
> 
>> On Tue, Sep 8, 2015 at 5:07 AM, Oleg Rubel <oru...@lakeheadu.ca> wrote:
>> That seems to be the case 
>> (http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list?gnum=140).
>> If both structures possess the inversion symmetry, it will be pointless to 
>> calculate polarization.
>> 
>> Oleg
>> 
>> > On Sep 8, 2015, at 03:48, Fecher, Gerhard <fec...@uni-mainz.de> wrote:
>> >
>> > I thought that  I4/mcm  is also a centrosymmetric space group ?
>> >
>> > 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 Oleg Rubel 
>> > [oru...@lakeheadu.ca]
>> > Gesendet: Dienstag, 8. September 2015 01:03
>> > An: A Mailing list for WIEN2k users
>> > Betreff: Re: [Wien] berryPI
>> >
>> > The essence of electronic polarization is that it is a “relative” 
>> > quantity, i.e., its calculation (and measurement too) requires a reference 
>> > point. The reference structure is not always centrosymmetric. An example 
>> > of non-centrosymmetric reference structure is zinc-blende GaN that is 
>> > taken as P=0 in computing the spontaneous polarization of the wurtzite GaN 
>> > (see 
>> > https://github.com/spichardo/BerryPI/wiki/Tutorial-4:-Polarization-in-GaN).
>> >
>> > For the second part of the question on EuTiO3, enclosed structure files 
>> > would certainly help. One possible strategy would be to explore a gradual 
>> > evolution of the polarization between cubic and tetragonal structures.
>> >
>> >
>> > I hope this will help
>> > Oleg
>> >
>> >
>> >
>> >> On Sep 7, 2015, at 3:42 AM, nilofar hadaeghi <n.hadae...@gmail.com> wrote:
>> >>
>> >> 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,
>> >> ___
>> >> Wien mailing list
>> >> Wien@zeus.theochem.tuwien.ac.at
>> >> http://zeus.theochem.tuwi

Re: [Wien] berryPI code

[Oleg Rubel]

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  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 ] 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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