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 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 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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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

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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
>
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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_

[Wien] berryPI code

[nilofar hadaeghi]

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

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