From vaskarpour at yahoo.com  Fri Jan  8 03:25:01 2010
From: vaskarpour at yahoo.com (Vahid Askarpour)
Date: Thu, 7 Jan 2010 18:25:01 -0800 (PST)
Subject: [Wannier] Wannier functions outside the unit cell in xcrysden
Message-ID: <744421.47923.qm@web51507.mail.re2.yahoo.com>

Dear Wannier Users,

Running Wannier through Abinit, I obtained the following spreads and Im/Re Ratios (which I think are not bad)?but when I visualize the functions by xcrysden, the functions lie outside the unit cell. Is there a way to move the functions inside the unit cell to make it clear?to which atom or molecule?they belong? I have attached the wannier90.win file.

Thanks,

Vahid Askarpour
Physics Department,
Dalhousie University,
Halifax, Canada?


???????? Spreads (Ang^2)???????????? ?Omega I????? ?? =? ??? 5.964899925
??????? ================?????? Omega D??? ?? =?? ?? 0.002783830
??????????????????????? ?????????????????????? Omega OD???? =?? ?? 0.105160589
??? Final Spread (Ang^2)???????? ??? Omega Tota l? =?? ?? 6.072844345

????? Wannier Function Num:??? 1?????? Maximum Im/Re Ratio =??? 0.000107
????? Wannier Function Num:??? 2?????? Maximum Im/Re Ratio =??? 0.000109
????? Wannier Function Num:??? 3?????? Maximum Im/Re Ratio =??? 0.000133
????? Wannier Function Num:??? 4?????? Maximum Im/Re Ratio =??? 0.000135
????? Wannier Function Num:??? 5?????? Maximum Im/Re Ratio =??? 0.000139
????? Wannier Function Num:??? 6?????? Maximum Im/Re Ratio =??? 0.000319
????? Wannier Function Num:??? 7?????? Maximum Im/Re Ratio =??? 0.000177
????? Wannier Function Num:??? 8?????? Maximum Im/Re Ratio =??? 0.000168


num_wann 8
dis_win_max 9.7
!dis_froz_max 3.44
num_iter 2000
dis_num_iter 2000
dis_conv_tol 1.0E-10
iprint 1
!plotting
wannier_plot =true
wannier_plot_format=xcrysden
wannier_plot_supercell=3
Begin Projections
random
f= 0.297708686741,? 0.376360633394, 0.250000000003 : l=0
f= 0.636475415803, -0.062477958781, 0.750000000003 : l=0
f= 0.356596731395,? 0.621736542697, 0.622053950761 : l=0
f= 6.8164940348E-01,? 6.9549188476E-01,? 2.5000000000E-01 : l=0
f= 3.9367221010E-01,? 8.5692020515E-01,? 2.5000000000E-01 : l=0
f= 8.3181156906E-01,? 5.9119677769E-01,? 7.5000000000E-01 : l=0
f= 4.4787085232E-01,? 2.7206552633E-01,? 7.5000000000E-01 : l=0
f=7.3584804570E-01,? 1.1063720593E-01,? 7.5000000000E-01 : l=0
End Projections



      


From poilvert at mit.edu  Fri Jan  8 10:01:19 2010
From: poilvert at mit.edu (nicolas poilvert)
Date: Fri, 8 Jan 2010 10:01:19 +0100
Subject: [Wannier] Wannier functions outside the unit cell in xcrysden
In-Reply-To: <744421.47923.qm@web51507.mail.re2.yahoo.com>
References: <744421.47923.qm@web51507.mail.re2.yahoo.com>
Message-ID: <66bc743b1001080101wd5266co53eb284a8960e94a@mail.gmail.com>

Dear Vahid,

Indeed that can happen.
Your Wannier Functions seem good, so what
you can do is visualize the *.xsf file and change
by hand the translation vector to "0 0 0".
Look at the format of the xcrysden file at this
address :

http://www.xcrysden.org/doc/XSF.html#l.31

look at line 31 "l 31" = origin of the data grid
this is what you need to set to 0 0 0.

Good luck,

Nicolas

On Fri, Jan 8, 2010 at 3:25 AM, Vahid Askarpour <vaskarpour at yahoo.com>wrote:

> Dear Wannier Users,
>
> Running Wannier through Abinit, I obtained the following spreads and Im/Re
> Ratios (which I think are not bad) but when I visualize the functions by
> xcrysden, the functions lie outside the unit cell. Is there a way to move
> the functions inside the unit cell to make it clear to which atom or
> molecule they belong? I have attached the wannier90.win file.
>
> Thanks,
>
> Vahid Askarpour
> Physics Department,
> Dalhousie University,
> Halifax, Canada
>
>
>          Spreads (Ang^2)              Omega I         =      5.964899925
>         ================       Omega D       =      0.002783830
>                                                Omega OD     =
> 0.105160589
>     Final Spread (Ang^2)             Omega Tota l  =      6.072844345
>
>       Wannier Function Num:    1       Maximum Im/Re Ratio =    0.000107
>       Wannier Function Num:    2       Maximum Im/Re Ratio =    0.000109
>       Wannier Function Num:    3       Maximum Im/Re Ratio =    0.000133
>       Wannier Function Num:    4       Maximum Im/Re Ratio =    0.000135
>       Wannier Function Num:    5       Maximum Im/Re Ratio =    0.000139
>       Wannier Function Num:    6       Maximum Im/Re Ratio =    0.000319
>       Wannier Function Num:    7       Maximum Im/Re Ratio =    0.000177
>       Wannier Function Num:    8       Maximum Im/Re Ratio =    0.000168
>
>
> num_wann 8
> dis_win_max 9.7
> !dis_froz_max 3.44
> num_iter 2000
> dis_num_iter 2000
> dis_conv_tol 1.0E-10
> iprint 1
> !plotting
> wannier_plot =true
> wannier_plot_format=xcrysden
> wannier_plot_supercell=3
> Begin Projections
> random
> f= 0.297708686741,  0.376360633394, 0.250000000003 : l=0
> f= 0.636475415803, -0.062477958781, 0.750000000003 : l=0
> f= 0.356596731395,  0.621736542697, 0.622053950761 : l=0
> f= 6.8164940348E-01,  6.9549188476E-01,  2.5000000000E-01 : l=0
> f= 3.9367221010E-01,  8.5692020515E-01,  2.5000000000E-01 : l=0
> f= 8.3181156906E-01,  5.9119677769E-01,  7.5000000000E-01 : l=0
> f= 4.4787085232E-01,  2.7206552633E-01,  7.5000000000E-01 : l=0
> f=7.3584804570E-01,  1.1063720593E-01,  7.5000000000E-01 : l=0
> End Projections
>
>
>
>
> _______________________________________________
> Wannier mailing list
> Wannier at quantum-espresso.org
> http://www.democritos.it/mailman/listinfo/wannier
>



-- 
POILVERT Nicolas
PhD candidate,
Dpt of Materials Science and Engineering
Massachusetts Institute of Technology
77, Massachusetts avenue
Cambridge, MA 02139
USA
work: (617) 452-4212
nicolas.poilvert at gmail.com
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From sumanta.bhandary at fysik.uu.se  Sat Jan  9 18:45:20 2010
From: sumanta.bhandary at fysik.uu.se (SUMANTA BHANDARY)
Date: Sat, 9 Jan 2010 18:45:20 +0100
Subject: [Wannier] error
Message-ID: <ED750845-066B-4497-B47B-E3F5794D16A3@fysik.uu.se>

Dear W90 users,
                               I have got an error when I run  
pw2wannier90.x saying :
  task #         0
      from davcio : error #        10
      error while reading from file

what could be the reason ? Thanks for your help .
regards
Sumanta Bhandary
PhD Student
Uppsala University




From vaskarpour at yahoo.com  Sat Jan  9 21:52:02 2010
From: vaskarpour at yahoo.com (Vahid Askarpour)
Date: Sat, 9 Jan 2010 12:52:02 -0800 (PST)
Subject: [Wannier] Error in Plotting Si wannier functions
Message-ID: <881019.62082.qm@web51502.mail.re2.yahoo.com>

Dear Wannier Users,

I have followed the tutorial examples in tutorial_files/w90-ex1. Everything works fine until the last stage when I ask to plot the wannier functions. In the .wout file, I get:

*---------------------------------------------------------------------------*
?|?????????????????????????????? PLOTTING??????????????????????????????????? |
?*---------------------------------------------------------------------------*
?WARNING: mismatch in fileUNK00001.1
??? ix=?? 24?? iy=?? 24?? iz=??? 1?? ik=?? 12 nbnd=?? 20
?? ngx=?? 24? ngy=?? 24? ngz=??? 1? kpt=??? 1bands=?? 12
?Exiting.......
?plot_wannier


I would appreciate any comments.

Regards,

Vahid Askarpour
Physics Department,
Dalhousie University
Halifax, Canada


      


From jonathan.yates at materials.ox.ac.uk  Sun Jan 10 00:09:26 2010
From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates)
Date: Sat, 9 Jan 2010 23:09:26 +0000
Subject: [Wannier] error
In-Reply-To: <ED750845-066B-4497-B47B-E3F5794D16A3@fysik.uu.se>
References: <ED750845-066B-4497-B47B-E3F5794D16A3@fysik.uu.se>
Message-ID: <2B9E56B4-BD51-4DAF-AF95-822AFC9655AC@materials.ox.ac.uk>


On 9 Jan 2010, at 17:45, SUMANTA BHANDARY wrote:

> Dear W90 users,
>                               I have got an error when I run
> pw2wannier90.x saying :
>  task #         0
>      from davcio : error #        10
>      error while reading from file
>
> what could be the reason ? Thanks for your help .

Sumanta,

  The pwscf error message is rather terse - but it tells you that  
there was an error reading the wavefunction files from disk.

There are several ways to obtain this error. The most common is  
running pw.x in parallel (distributing k-points using npools) and not  
using the wf_collect option (to collect the wavefunctions in a single  
file). You need to do this as pw2wannier90 does not work when kpoints  
are distributed (only R/G parallelism works)

This has been covered on the mailing list before see eg
  http://www.democritos.it/pipermail/wannier/2008-January/000102.html

  If this doesn't solve your problem you will need to give us a bit  
more information to work with (version of pwscf/w90, instructions, etc)

  Jonathan






-- 
Department of Materials, University of Oxford, Parks Road, Oxford, OX1  
3PH, UK
tel: +44 (0)1865 612797                http://users.ox.ac.uk/~oums0549/



From jonathan.yates at materials.ox.ac.uk  Sat Jan  9 23:52:13 2010
From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates)
Date: Sat, 9 Jan 2010 22:52:13 +0000
Subject: [Wannier] Error in Plotting Si wannier functions
In-Reply-To: <881019.62082.qm@web51502.mail.re2.yahoo.com>
References: <881019.62082.qm@web51502.mail.re2.yahoo.com>
Message-ID: <3F4D5466-D314-424F-A945-DED1F496119B@materials.ox.ac.uk>


On 9 Jan 2010, at 20:52, Vahid Askarpour wrote:

> Dear Wannier Users,
>
> I have followed the tutorial examples in tutorial_files/w90-ex1.  
> Everything works fine until the last stage when I ask to plot the  
> wannier functions. In the .wout file, I get:
>
> *---------------------------------------------------------------------------*
>  |                                
> PLOTTING                                    |
>   
> *---------------------------------------------------------------------------*
>  WARNING: mismatch in fileUNK00001.1
>     ix=   24   iy=   24   iz=    1   ik=   12 nbnd=   20
>    ngx=   24  ngy=   24  ngz=    1  kpt=    1bands=   12
>  Exiting.......
>  plot_wannier
>
>
> I would appreciate any comments.

Vahid,

  It looks like you are following the tutorial from the 2007 cecam  
workshop on Wannier functions. I think you'd probably find the  
tutorial that comes with the W90 distribution better (more examples,  
more attention paid to the instructions etc).
Although in any case the example w90-ex1 should work. It seems to work  
fine for me:

pw2wannier90.x < silicon.scf  > scf.out
pw2wannier90.x < silicon.nscf > nscf.out
wannier90.x -pp silicon
pw2wannier90.x < silicon.pw2wan > pw2wan.out
wannier90.x silicon

The only changes I made to the files was to change outdir in  
silicon.scf, silicon.nscf and silicon.pw2wan and to add  
'wannier_plot=true' into silicon.win.

There is something odd about your error message. W90 opens the first  
unk file, reads the fft grid dimension (ngx, ngy, ngz), closes the  
file and allocates some arrays. It then reads each unk file in turn,  
checking that it finds the right k-point and number of bands.
  In your case it failed as it found 20 bands in unk - not the 12 it  
expected.
The odd thing is that your fft grid appears to be 24x24x1 (not  
24x24x24).

  So I suspect your UNK file is wrong, or corrupted in someway. I  
don't know how that could have happened. Try again - follow the W90  
tutorial, try other examples (A slightly more usual way this might  
possibly occur is if you used a different compiler for pwscf and  
wannier90)

If you still have this problem let us know - but tell us the version  
of pwscf/wannier90 and the exact commands you issue.

  Jonathan




-- 
Department of Materials, University of Oxford, Parks Road, Oxford, OX1  
3PH, UK
tel: +44 (0)1865 612797                http://users.ox.ac.uk/~oums0549/



From vaskarpour at yahoo.com  Sun Jan 10 01:59:44 2010
From: vaskarpour at yahoo.com (Vahid Askarpour)
Date: Sat, 9 Jan 2010 16:59:44 -0800 (PST)
Subject: [Wannier] Error in Plotting Si wannier functions
In-Reply-To: <3F4D5466-D314-424F-A945-DED1F496119B@materials.ox.ac.uk>
References: <881019.62082.qm@web51502.mail.re2.yahoo.com>
	<3F4D5466-D314-424F-A945-DED1F496119B@materials.ox.ac.uk>
Message-ID: <278385.21219.qm@web51501.mail.re2.yahoo.com>

Hi Jonathan,

You were right. The error occured because the PWSCF was compiled with F90 while I compiled wannier with gfortran. Now it is working fine.

Many thanks,

Vahid


      


From m.saghayezhian at gmail.com  Sat Jan 23 12:40:48 2010
From: m.saghayezhian at gmail.com (Mohammad Saghayezhian)
Date: Sat, 23 Jan 2010 11:40:48 +0000
Subject: [Wannier] Al Chain
Message-ID: <3540b21c1001230340w6d969c51tb9357d91942721ee@mail.gmail.com>

We have a problem with constructing well-localized wannier functions for Al
chain, According to (ab initio transport properties of nanostructures from
maximally localized wannier functions) PRB 69,035108 (Calzolari et al), we
followed the steps one by one, we took the same vacuum, lattice parameter,
kpoints, and everything, but the wanniers are not localized and the ratio of
Im/Re is rather large,
 Hence it is highly appreciated if you kindly help us with this problem.

Thank you very much in advance
With kind regards
Mohammad




-------------------------------------------------------------------
Mohammad Saghayezhian
Computational Condensed Matter Research Lab
Physics Department, Isfahan University of Technology, Isfahan, Iran

Tel lab: +98 311 391 3731     Fax Office: +98311 391 3746
-------------------------------------------------------------------
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From jonathan.yates at materials.ox.ac.uk  Sat Jan 23 13:11:29 2010
From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates)
Date: Sat, 23 Jan 2010 12:11:29 +0000
Subject: [Wannier] Al Chain
In-Reply-To: <3540b21c1001230340w6d969c51tb9357d91942721ee@mail.gmail.com>
References: <3540b21c1001230340w6d969c51tb9357d91942721ee@mail.gmail.com>
Message-ID: <462943E1-6B44-4D32-B3EA-2F7D74699B89@materials.ox.ac.uk>


On 23 Jan 2010, at 11:40, Mohammad Saghayezhian wrote:

> We have a problem with constructing well-localized wannier functions  
> for Al chain, According to (ab initio transport properties of  
> nanostructures from maximally localized wannier functions) PRB  
> 69,035108 (Calzolari et al), we followed the steps one by one, we  
> took the same vacuum, lattice parameter, kpoints, and everything,  
> but the wanniers are not localized and the ratio of Im/Re is rather  
> large,
>  Hence it is highly appreciated if you kindly help us with this  
> problem.

Mohammad,

  I haven't tried that particular calculation myself. Obviously at  
some point in time it was working fine! In order to help we really  
need more information. Post the input files for pwscf and wannier90  
*.win file. The *.wout file is also useful.

One suggestion is to compare your ab-initio bands with figure 2; and  
then check you have the energy windows in a sensible position in the  
wannier90 calculation.

  Yours
   Jonathan



-- 
Department of Materials, University of Oxford, Parks Road, Oxford, OX1  
3PH, UK
tel: +44 (0)1865 612797                http://users.ox.ac.uk/~oums0549/



From jonathan.yates at materials.ox.ac.uk  Sat Jan 23 19:44:41 2010
From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates)
Date: Sat, 23 Jan 2010 18:44:41 +0000
Subject: [Wannier] Al Chain
In-Reply-To: <462943E1-6B44-4D32-B3EA-2F7D74699B89@materials.ox.ac.uk>
References: <3540b21c1001230340w6d969c51tb9357d91942721ee@mail.gmail.com>
	<462943E1-6B44-4D32-B3EA-2F7D74699B89@materials.ox.ac.uk>
Message-ID: <C855DAAD-5AFC-45A8-B97A-2FAB6CC9BF24@materials.ox.ac.uk>


On 23 Jan 2010, at 12:11, Jonathan Yates wrote:

>
> On 23 Jan 2010, at 11:40, Mohammad Saghayezhian wrote:
>
>> We have a problem with constructing well-localized wannier functions
>> for Al chain, According to (ab initio transport properties of
>> nanostructures from maximally localized wannier functions) PRB
>> 69,035108 (Calzolari et al), we followed the steps one by one, we
>> took the same vacuum, lattice parameter, kpoints, and everything,
>> but the wanniers are not localized and the ratio of Im/Re is rather
>> large,

[Mohammad sent his input files to me directly]

Mohammad,

  From your input files I see you are trying to extract 8 wannier  
functions from a set of 15 bands.
If you take a slightly larger set of bands (say 20) - you will find  
that the disentanglement stage converges quickly - and the final WF  
are well localised.

  To understand this look at the band-structure plot in Fig 2 of PRB  
69 035108. The set of 8 MLWF have a particular set of symmetry  
characteristics - the disentanglement routine is selecting the  
appropriate set of bloch states to capture this symmetry. At Gamma the  
routine chooses a state with quite high energy, neglecting several  
states with lower energy (but presumably with different symmetry).  
This state lies above the 15th band - hence why you initially had  
problems.

  Jonathan



-- 
Department of Materials, University of Oxford, Parks Road, Oxford, OX1  
3PH, UK
tel: +44 (0)1865 612797                http://users.ox.ac.uk/~oums0549/



From a.mostofi at imperial.ac.uk  Wed Jan 27 21:18:28 2010
From: a.mostofi at imperial.ac.uk (Arash Mostofi)
Date: Wed, 27 Jan 2010 20:18:28 +0000
Subject: [Wannier] Wannier90 v1.2 released
Message-ID: <4B609F94.2000407@imperial.ac.uk>

Dear Wannier90 users

Version 1.2 of Wannier90 is now available on http://www.wannier.org

A summary of the main changes from v1.1 is given below.

Cheers

Arash

-- 
:------------------------------------------------------------:
: Dr. Arash A. Mostofi           :: a.mostofi at imperial.ac.uk :
: Lecturer and RCUK Fellow       ::                          :
: Depts. of Materials & Physics  ::                          :
: Imperial College London        :: T  +44 (0)207 594 8154   :
: London SW7 2AZ, United Kingdom :: F  +44 (0)207 594 6757   :
:------- http://www.cmth.ph.ic.ac.uk/people/a.mostofi -------:

v1.2 (14th Jan 2010)

* The information written to the file seedname_hr.dat (the Hamiltonian
   in the WF basis) has been extended to include the number of WF
   (num_wann), the number of Wigner-Seitz points (nrpts) and the
   degeneracy of each point (ndegen).
* The information contained in seedname.chk has been extended to
   include the number of bands (num_bands), the number of excluded
   bands (num_exclude_bands), the excluded band indices (exclude_bands)
   and the Monkhorst-Pack grid dimensions (mp_grid). As a result
   v1.2 is not compatible with checkfiles written with older versions of
   the code.
* Automated lcr transport calculations from a single supercell.
   Includes robust sorting and Wannier function parity determination
   algorithms (new input variables: tran_num_cell_ll, tran_num_cell_rr,
   tran_group_threshold, tran_easy_fix)
* Added examples 14, 15 to tutorial to displaying new lcr transport
   functionality
* Updated interface to PWscf v4.1.2 (new input variable write_unkg)
* New utility: PL_assessment. Investigates principal layer size
   from bulk transport, many k-point lead calculations.
* Altered <seedname>_centres.xyz output file to include atomic
   positions in transport calculations
* Fixes for tran_num_cell_ll=1 in tran_hr_one_dim_cut
* Minor bug fixes
* Addition of Matthew Shelley and Nicolas Poilvert as contributors.
* Report of estimated memory usage
* Improved memory efficiency