From zarrini at staff.uni-marburg.de  Wed Mar  4 21:19:35 2015
From: zarrini at staff.uni-marburg.de (zarrini at staff.uni-marburg.de)
Date: Wed, 04 Mar 2015 21:19:35 +0100
Subject: [Wannier] MLWF for GaAs - 3D_field
Message-ID: <20150304211935.Horde.xElCEjqc1KFt3PI2s-_oVA1@home.staff.uni-marburg.de>


Dear Wannier90 user,

I tried the first example of wannier90 plotting the MLWF for GaAs, the  
*.xsf files were produced nicely, however, I was wondering why I can  
not see the MLWF by xcrysden, but just a crystal structure of GaAs as  
defined in the very beginning of the  *.xsf files. I noticed to the  
"3D_field" after the "BEGIN_BLOCK_DATAGRID_3D" although bunch of  
numbers are coming after "BEGIN_DATAGRID_3D_UNKNOWN".

The second issue is concerning to the wannier90 mailing list, which is  
not that easy to look for a specific keyword on it, like what can be  
done easily in for example wien2k or vasp mailing list. So, it would  
be great if mailing list interface could somehow change, then, one can  
look for his/her problem in the whole mailing list before sending it  
to the mailing list.

Best regards,

Salman Zarrini



From giovanni.pizzi at epfl.ch  Wed Mar  4 21:32:15 2015
From: giovanni.pizzi at epfl.ch (Giovanni Pizzi)
Date: Wed, 4 Mar 2015 20:32:15 +0000
Subject: [Wannier] MLWF for GaAs - 3D_field
In-Reply-To: <20150304211935.Horde.xElCEjqc1KFt3PI2s-_oVA1@home.staff.uni-marburg.de>
References: <20150304211935.Horde.xElCEjqc1KFt3PI2s-_oVA1@home.staff.uni-marburg.de>
Message-ID: <E3EECE85-47C5-4445-B900-DBBF1C5FB199@epfl.ch>

Hi Salman,

to reply to both your questions in one:
use google to filter through the archives, using a query string on google like:

"WHAT YOU WANT TO QUERY FOR site:mailman.qe-forge.org/pipermail/wannier"

for instance, in your case the second hit of:
"xcrysden site:mailman.qe-forge.org/pipermail/wannier"
is

http://mailman.qe-forge.org/pipermail/wannier/2007-September/000088.html

that replies to your first question.

Best,
Giovanni

P.S.: do not forget to sign your posts with your affiliation!


--
Giovanni Pizzi
Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 340 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124




On 4 Mar 2015, at 21:19, <zarrini at staff.uni-marburg.de<mailto:zarrini at staff.uni-marburg.de>>
 wrote:


Dear Wannier90 user,

I tried the first example of wannier90 plotting the MLWF for GaAs, the *.xsf files were produced nicely, however, I was wondering why I can not see the MLWF by xcrysden, but just a crystal structure of GaAs as defined in the very beginning of the  *.xsf files. I noticed to the "3D_field" after the "BEGIN_BLOCK_DATAGRID_3D" although bunch of numbers are coming after "BEGIN_DATAGRID_3D_UNKNOWN".

The second issue is concerning to the wannier90 mailing list, which is not that easy to look for a specific keyword on it, like what can be done easily in for example wien2k or vasp mailing list. So, it would be great if mailing list interface could somehow change, then, one can look for his/her problem in the whole mailing list before sending it to the mailing list.

Best regards,

Salman Zarrini

_______________________________________________
Wannier mailing list
Wannier at quantum-espresso.org<mailto:Wannier at quantum-espresso.org>
http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier

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From giovanni.pizzi at epfl.ch  Wed Mar  4 23:08:43 2015
From: giovanni.pizzi at epfl.ch (Giovanni Pizzi)
Date: Wed, 4 Mar 2015 22:08:43 +0000
Subject: [Wannier] problem with num_exclude_bands while using
 w90chk2chk.x
In-Reply-To: <D00089A09F60514C9979B84FE1EFE6B431C3EC13@MBX13.d.ethz.ch>
References: <D00089A09F60514C9979B84FE1EFE6B431C3EC13@MBX13.d.ethz.ch>
Message-ID: <29852961-2533-41C7-AFE3-101FE951C3C2@epfl.ch>

Dear Krzysztof,

thanks a lot for the report.

Indeed, as you correctly spotted, there was a missing allocation in the specific case with num_exclude_bands > 0.
Actually, the same problem was also present in the routine reading from a formatted file, needed for the conversion in the opposite format.

I committed the correction to the Wannier CVS and this will be distributed with the next Wannier90 release.
Would you be so kind to check if the attached w90chk2chk.F90 (which is the fixed version) works for you, when converting in both directions (e.g. you can convert to formatted, then back to unformatted, and see if you are e.g. still able to restart from the chk file generated with the roundtrip and obtain the same results).

Thank you in advance,
Giovanni Pizzi


--
Giovanni Pizzi
Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 340 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124




On 28 Feb 2015, at 12:36, Dymkowski Krzysztof Pawel wrote:

Dear All,
I was recently trying to convert my seedname.chk to seedname.chk.fmt using utility tool: w90chk2chk.x. I was able to run tests provided without any errors. I also was able to produce seedname.chk.fmt for both test1 and test2.

Now  I am trying to  do NiO benchmark (paramagnetic calculations) and do later on to use of this for  DMFT calculations.  When runnig w90chk2chk.x I got segmentation fault. I have added two lines to w90chk2chk.f90:

allocate(exclude_bands(num_exclude_bands),stat=ierr) ! ****KD*****
if (ierr/=0) call io_error('Error allocating exclude_bands in param_read') !*****KD*****

And it seems to work for my benchmark. In the attachment FILES I am sending you the main inptu/output files from the run with modified w90chk2chk.f90.

Without modification I get the following error while runnig w90chk2chk.x:

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source
w90chk2chk.x       00000000005C3FE1  Unknown               Unknown  Unknown
w90chk2chk.x       00000000005C2737  Unknown               Unknown  Unknown
w90chk2chk.x       000000000056FE64  Unknown               Unknown  Unknown
w90chk2chk.x       000000000056FC76  Unknown               Unknown  Unknown
w90chk2chk.x       000000000052892F  Unknown               Unknown  Unknown
w90chk2chk.x       000000000052C92D  Unknown               Unknown  Unknown
libpthread.so.0    00007FABA32A40A0  Unknown               Unknown  Unknown
w90chk2chk.x       00000000005D2D26  Unknown               Unknown  Unknown
w90chk2chk.x       0000000000548D2D  Unknown               Unknown  Unknown
w90chk2chk.x       0000000000546026  Unknown               Unknown  Unknown
w90chk2chk.x       0000000000405A57  w90_conv_mp_conv_         115  w90chk2chk.F90
w90chk2chk.x       00000000004040B8  MAIN__                    593  w90chk2chk.F90
w90chk2chk.x       0000000000403AFE  Unknown               Unknown  Unknown
libc.so.6          00007FABA2AA2EAD  Unknown               Unknown  Unknown
w90chk2chk.x       00000000004039E9  Unknown               Unknown  Unknown

I have attached log file from w90chk2chk  (w90chk2chk_vannila.log?) from run without any modifications. It stops at work after reading bands.


I have compiled wannier90 using the following settings:
F90 = /opt/intel/bin/ifort
#COMMS=
MPIF90=/opt/intel/impi/5.0.3.048/bin64/mpif90
FCOPTS=-O2 -heap-arrays  -g -traceback
LDOPTS=-O2 -g -traceback

LIBDIR = /opt/intel/mkl/lib/intel64
LIBS   =  -L$(LIBDIR) -lmkl_core -lmkl_intel_lp64 -lmkl_sequential -lpthread

Is there a problem with my compilation or have  I  found a bug?

Regards,
Krzysztof Dymkowski



<FILES.tar.bz2><w90chk2chk_vannila.log>_______________________________________________
Wannier mailing list
Wannier at quantum-espresso.org<mailto:Wannier at quantum-espresso.org>
http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier

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From krzysztof.dymkowski at mat.ethz.ch  Fri Mar  6 17:07:11 2015
From: krzysztof.dymkowski at mat.ethz.ch (Dymkowski  Krzysztof Pawel)
Date: Fri, 6 Mar 2015 16:07:11 +0000
Subject: [Wannier] ODP: problem with num_exclude_bands while using
 w90chk2chk.x
In-Reply-To: <29852961-2533-41C7-AFE3-101FE951C3C2@epfl.ch>
References: <D00089A09F60514C9979B84FE1EFE6B431C3EC13@MBX13.d.ethz.ch>,
 <29852961-2533-41C7-AFE3-101FE951C3C2@epfl.ch>
Message-ID: <D00089A09F60514C9979B84FE1EFE6B431C4D900@MBX13.d.ethz.ch>

Dear Giovanni,
I checked and now works like charm.  I did both export and import.

Thanks for your help!,
Krzysztof
________________________________
Od: Giovanni Pizzi [giovanni.pizzi at epfl.ch]
Wys?ano: 4 marca 2015 22:08
Do: Dymkowski Krzysztof Pawel
DW: wannier at quantum-espresso.org
Temat: Re: [Wannier] problem with num_exclude_bands while using w90chk2chk.x

Dear Krzysztof,

thanks a lot for the report.

Indeed, as you correctly spotted, there was a missing allocation in the specific case with num_exclude_bands > 0.
Actually, the same problem was also present in the routine reading from a formatted file, needed for the conversion in the opposite format.

I committed the correction to the Wannier CVS and this will be distributed with the next Wannier90 release.
Would you be so kind to check if the attached w90chk2chk.F90 (which is the fixed version) works for you, when converting in both directions (e.g. you can convert to formatted, then back to unformatted, and see if you are e.g. still able to restart from the chk file generated with the roundtrip and obtain the same results).

Thank you in advance,
Giovanni Pizzi


--
Giovanni Pizzi
Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 340 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124




On 28 Feb 2015, at 12:36, Dymkowski Krzysztof Pawel wrote:

Dear All,
I was recently trying to convert my seedname.chk to seedname.chk.fmt using utility tool: w90chk2chk.x. I was able to run tests provided without any errors. I also was able to produce seedname.chk.fmt for both test1 and test2.

Now  I am trying to  do NiO benchmark (paramagnetic calculations) and do later on to use of this for  DMFT calculations.  When runnig w90chk2chk.x I got segmentation fault. I have added two lines to w90chk2chk.f90:

allocate(exclude_bands(num_exclude_bands),stat=ierr) ! ****KD*****
if (ierr/=0) call io_error('Error allocating exclude_bands in param_read') !*****KD*****

And it seems to work for my benchmark. In the attachment FILES I am sending you the main inptu/output files from the run with modified w90chk2chk.f90.

Without modification I get the following error while runnig w90chk2chk.x:

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source
w90chk2chk.x       00000000005C3FE1  Unknown               Unknown  Unknown
w90chk2chk.x       00000000005C2737  Unknown               Unknown  Unknown
w90chk2chk.x       000000000056FE64  Unknown               Unknown  Unknown
w90chk2chk.x       000000000056FC76  Unknown               Unknown  Unknown
w90chk2chk.x       000000000052892F  Unknown               Unknown  Unknown
w90chk2chk.x       000000000052C92D  Unknown               Unknown  Unknown
libpthread.so.0    00007FABA32A40A0  Unknown               Unknown  Unknown
w90chk2chk.x       00000000005D2D26  Unknown               Unknown  Unknown
w90chk2chk.x       0000000000548D2D  Unknown               Unknown  Unknown
w90chk2chk.x       0000000000546026  Unknown               Unknown  Unknown
w90chk2chk.x       0000000000405A57  w90_conv_mp_conv_         115  w90chk2chk.F90
w90chk2chk.x       00000000004040B8  MAIN__                    593  w90chk2chk.F90
w90chk2chk.x       0000000000403AFE  Unknown               Unknown  Unknown
libc.so.6          00007FABA2AA2EAD  Unknown               Unknown  Unknown
w90chk2chk.x       00000000004039E9  Unknown               Unknown  Unknown

I have attached log file from w90chk2chk  (w90chk2chk_vannila.log?) from run without any modifications. It stops at work after reading bands.


I have compiled wannier90 using the following settings:
F90 = /opt/intel/bin/ifort
#COMMS=
MPIF90=/opt/intel/impi/5.0.3.048/bin64/mpif90
FCOPTS=-O2 -heap-arrays  -g -traceback
LDOPTS=-O2 -g -traceback

LIBDIR = /opt/intel/mkl/lib/intel64
LIBS   =  -L$(LIBDIR) -lmkl_core -lmkl_intel_lp64 -lmkl_sequential -lpthread

Is there a problem with my compilation or have  I  found a bug?

Regards,
Krzysztof Dymkowski



<FILES.tar.bz2><w90chk2chk_vannila.log>_______________________________________________
Wannier mailing list
Wannier at quantum-espresso.org<mailto:Wannier at quantum-espresso.org>
http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier

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From zhyhku at gmail.com  Tue Mar 10 22:04:48 2015
From: zhyhku at gmail.com (Yu Zhang)
Date: Tue, 10 Mar 2015 16:04:48 -0500
Subject: [Wannier] momentum operator matrix
Message-ID: <CAD5=Mwm9R3r1in=hOE5aBDETsdWeSP=CumQWOzzALVBw53GXLA@mail.gmail.com>

Dear wannier90 users and developers,

I want to get the the matrix element of momentum operator, i.e., <Rn|
\nabla |0m>. I didn't find any instructions to get the matrix element from
wannier90. Does anybody know how to get the momentum operator matrix?

Thank you in advance!

Best regards,

Yu Zhang
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From zaldolam at email.uark.edu  Tue Mar 10 23:02:42 2015
From: zaldolam at email.uark.edu (Zeina Al-Dolami)
Date: Tue, 10 Mar 2015 17:02:42 -0500
Subject: [Wannier] Checking info from wannier.nnkp file-Something wrong!
Message-ID: <CA+LR5aHJaG958T_iOhRf+otVSH4voNZMHCu44t+eYZQMcgdLvA@mail.gmail.com>

Dear Wannier's owners and developers,
I posted my question more than a month ago. It was realted to running the
code pw2wannier90.x for my system that is 4 carbon atom. Below was the
error message:
  -----------------
  *** Reading nnkp
  -----------------

  Checking info from wannier.nnkp file

  Something wrong!
  rlatt(i,j) =   1.88808383092209       at(i,j)=   1.00000000000000


At that time, Dr.Giovanni answered me by posting two links related to the
same question. He also mentioned that my cell in .win file is different
from that in nscf calculation. I checked all the possibilities that were
suggested to generate such error. However, I have kept getting the same
error message. Below is my input file for nscf calculation and .win file.
Would you please help me with it? I am totally lost and new to this area.
Any comment or feedback is greatly appreciated. Thanks in advance


*nscf file *
&CONTROL
  calculation = 'nscf',
  verbosity = 'high',
  pseudo_dir  = '/share/apps/espresso/espresso-5.1/wannier90-1.2/pseudo/',
  outdir      = './',
  prefix      = '4clinear',
  tstress  = .false.,
  tprnfor  = .true.,
/
&SYSTEM
  ibrav       = 1,
  a           = 5.296375,
  b           = 10.000,
  c           = 10.000,
  cosbc       = 0.,
  cosac       = 0.,
  cosab       = 0.,
  nat         = 4,
  ntyp        = 1,
  ecutwfc     = 30.,
  ecutrho     = 240.,
  nbnd        = 8,
  occupations = 'smearing',
  smearing    = 'cold',
  degauss     = 0.03,
  nspin       = 1,
/
&ELECTRONS
   mixing_beta = 0.4,
   diago_full_acc = .t.,
   diagonalization = 'cg',
   conv_thr    = 1.D-10,
/
ATOMIC_SPECIES
C 12.0107  C.pbe-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
C        0.018367612   0.000000000   0.000000000
C        1.469108353   0.000000000   0.000000000
C        2.666542920   0.000000000   0.000000000
C        4.117280996   0.000000000   0.000000000
K_POINTS {crystal}
6
0.00000000  0.00000000  0.00000000  1.00000000
0.16666667  0.00000000  0.00000000  1.00000000
0.33333333  0.00000000  0.00000000  1.00000000
0.50000000  0.00000000  0.00000000  1.00000000
0.66666667  0.00000000  0.00000000  1.00000000
0.83333333  0.00000000  0.00000000  1.00000000

*.win file *
num_bands        =  8
num_wann        =   3
num_iter         =  100

dis_num_iter     =  100
dis_win_max     =  17.0
dis_froz_max    =   -2.2225

guiding_centres = .true.

mp_grid      = 6 1 1

iprint      =    2

num_dump_cycles  =   100
num_print_cycles =   10

transport        = true
transport_mode   = bulk
one_dim_axis     = x
dist_cutoff      =  5.5
tran_win_min     = -6.5
tran_win_max     = 6.5
tran_energy_step = 0.01
fermi_energy     = -1.06
dist_cutoff_mode = one_dim
translation_centre_frac = 0.0 0.0 0.0

bands_plot = true
bands_plot_format = gnuplot

begin kpoint_path
G 0.0 0.0 0.0  A 0.0 0.0 0.5
end kpoint_path

begin projections
random
end projections

begin unit_cell_cart
Ang
5.296375  0.00  0.00
0.000000 10.00  0.00
0.000000  0.00 10.00
end unit_cell_cart

Begin KPoints
0.00000000  0.00000000  0.00000000
0.16666667  0.00000000  0.00000000
0.33333333  0.00000000  0.00000000
0.50000000  0.00000000  0.00000000
0.66666667  0.00000000  0.00000000
0.83333333  0.00000000  0.00000000
End KPoints

begin atoms_cart
Ang
C  0.018367612   0.000000000   0.000000000
C  1.469108353   0.000000000   0.000000000
C  2.666542920   0.000000000   0.000000000
C  4.117280996   0.000000000   0.000000000
end atoms_cart




-- 
Zeina Al-Dolami
PhD Candidate
Microelectronics and Photonics Graduate Program
University of Arkansas
Fayetteville, AR 72701
Office: PHYS 244
Email: zaldolam at email.uark.edu <cxm075 at email.uark.edu>
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From nicola.marzari at epfl.ch  Tue Mar 10 23:25:12 2015
From: nicola.marzari at epfl.ch (Nicola Marzari)
Date: Tue, 10 Mar 2015 23:25:12 +0100
Subject: [Wannier] Checking info from wannier.nnkp file-Something wrong!
In-Reply-To: <CA+LR5aHJaG958T_iOhRf+otVSH4voNZMHCu44t+eYZQMcgdLvA@mail.gmail.com>
References: <CA+LR5aHJaG958T_iOhRf+otVSH4voNZMHCu44t+eYZQMcgdLvA@mail.gmail.com>
Message-ID: <54FF6F48.9080604@epfl.ch>



quick one - 1.88808383092209 seems like 1/0.529177 - so there must be a 
mess up
somewhere between the angstrom and bohr conversion? a b and c are meant 
to be
in angstrom, but maybe you could double check.

(BTW - I noted that both qe and wannier90 use as defaults CODATA 2006).

				nicola


On 10/03/2015 23:02, Zeina Al-Dolami wrote:
> Dear Wannier's owners and developers,
> I posted my question more than a month ago. It was realted to running
> the code pw2wannier90.x for my system that is 4 carbon atom. Below was
> the error message:
>    -----------------
>    *** Reading nnkp
>    -----------------
>
>    Checking info from wannier.nnkp file
>
>    Something wrong!
>    rlatt(i,j) =   1.88808383092209       at(i,j)=   1.00000000000000
>
>
> At that time, Dr.Giovanni answered me by posting two links related to
> the same question. He also mentioned that my cell in .win file is
> different from that in nscf calculation. I checked all the possibilities
> that were suggested to generate such error. However, I have kept getting
> the same error message. Below is my input file for nscf calculation and
> .win file. Would you please help me with it? I am totally lost and new
> to this area. Any comment or feedback is greatly appreciated. Thanks in
> advance
>
>
> *nscf file *
> &CONTROL
>    calculation = 'nscf',
>    verbosity = 'high',
>    pseudo_dir  = '/share/apps/espresso/espresso-5.1/wannier90-1.2/pseudo/',
>    outdir      = './',
>    prefix      = '4clinear',
>    tstress  = .false.,
>    tprnfor  = .true.,
> /
> &SYSTEM
>    ibrav       = 1,
>    a           = 5.296375,
>    b           = 10.000,
>    c           = 10.000,
>    cosbc       = 0.,
>    cosac       = 0.,
>    cosab       = 0.,
>    nat         = 4,
>    ntyp        = 1,
>    ecutwfc     = 30.,
>    ecutrho     = 240.,
>    nbnd        = 8,
>    occupations = 'smearing',
>    smearing    = 'cold',
>    degauss     = 0.03,
>    nspin       = 1,
> /
> &ELECTRONS
>     mixing_beta = 0.4,
>     diago_full_acc = .t.,
>     diagonalization = 'cg',
>     conv_thr    = 1.D-10,
> /
> ATOMIC_SPECIES
> C 12.0107  C.pbe-rrkjus.UPF
> ATOMIC_POSITIONS {angstrom}
> C        0.018367612   0.000000000   0.000000000
> C        1.469108353   0.000000000   0.000000000
> C        2.666542920   0.000000000   0.000000000
> C        4.117280996   0.000000000   0.000000000
> K_POINTS {crystal}
> 6
> 0.00000000  0.00000000  0.00000000  1.00000000
> 0.16666667  0.00000000  0.00000000  1.00000000
> 0.33333333  0.00000000  0.00000000  1.00000000
> 0.50000000  0.00000000  0.00000000  1.00000000
> 0.66666667  0.00000000  0.00000000  1.00000000
> 0.83333333  0.00000000  0.00000000  1.00000000
>
> *.win file *
> num_bands        =  8
> num_wann        =   3
> num_iter         =  100
>
> dis_num_iter     =  100
> dis_win_max     =  17.0
> dis_froz_max    =   -2.2225
>
> guiding_centres = .true.
>
> mp_grid      = 6 1 1
>
> iprint      =    2
>
> num_dump_cycles  =   100
> num_print_cycles =   10
>
> transport        = true
> transport_mode   = bulk
> one_dim_axis     = x
> dist_cutoff      =  5.5
> tran_win_min     = -6.5
> tran_win_max     = 6.5
> tran_energy_step = 0.01
> fermi_energy     = -1.06
> dist_cutoff_mode = one_dim
> translation_centre_frac = 0.0 0.0 0.0
>
> bands_plot = true
> bands_plot_format = gnuplot
>
> begin kpoint_path
> G 0.0 0.0 0.0  A 0.0 0.0 0.5
> end kpoint_path
>
> begin projections
> random
> end projections
>
> begin unit_cell_cart
> Ang
> 5.296375  0.00  0.00
> 0.000000 10.00  0.00
> 0.000000  0.00 10.00
> end unit_cell_cart
>
> Begin KPoints
> 0.00000000  0.00000000  0.00000000
> 0.16666667  0.00000000  0.00000000
> 0.33333333  0.00000000  0.00000000
> 0.50000000  0.00000000  0.00000000
> 0.66666667  0.00000000  0.00000000
> 0.83333333  0.00000000  0.00000000
> End KPoints
>
> begin atoms_cart
> Ang
> C  0.018367612   0.000000000   0.000000000
> C  1.469108353   0.000000000   0.000000000
> C  2.666542920   0.000000000   0.000000000
> C  4.117280996   0.000000000   0.000000000
> end atoms_cart
>
>
>
>
> --
> Zeina Al-Dolami
> PhD Candidate
> Microelectronics and Photonics Graduate Program
> University of Arkansas
> Fayetteville, AR 72701
> Office: PHYS 244
> Email: zaldolam at email.uark.edu
> <mailto:zaldolam at email.uark.edu><mailto:cxm075 at email.uark.edu>
>
>
> _______________________________________________
> Wannier mailing list
> Wannier at quantum-espresso.org
> http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier
>

-- 

----------------------------------------------------------------------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL


From zaldolam at email.uark.edu  Wed Mar 11 05:23:03 2015
From: zaldolam at email.uark.edu (Zeina Al-Dolami)
Date: Tue, 10 Mar 2015 23:23:03 -0500
Subject: [Wannier] Checking info from wannier.nnkp file-Something wrong!
In-Reply-To: <54FF6F48.9080604@epfl.ch>
References: <CA+LR5aHJaG958T_iOhRf+otVSH4voNZMHCu44t+eYZQMcgdLvA@mail.gmail.com>
 <54FF6F48.9080604@epfl.ch>
Message-ID: <8559427942308056943@unknownmsgid>

Dr.Nicola,
I appreciate your fast reply. I double checked the units and they seemed
fine to me. Also, 1/0.529177 does not give exactly 1.88808383092209. It
should be 1.889726877774355. Is there any other possible reason? I look
forward to hearing from any one who can help. Thanks in advance.

Zeina Al-Dolami

PhD Candidate

Microelectronics and Photonics Graduate Program

University of Arkansas

Fayetteville, AR 72701

Office: PHYS 244

Email: zaldolam at email.uark.edu



Sent from my iPhone

On Mar 10, 2015, at 5:25 PM, Nicola Marzari <nicola.marzari at epfl.ch> wrote:



quick one - 1.88808383092209 seems like 1/0.529177 - so there must be a
mess up
somewhere between the angstrom and bohr conversion? a b and c are meant to
be
in angstrom, but maybe you could double check.

(BTW - I noted that both qe and wannier90 use as defaults CODATA 2006).

               nicola


On 10/03/2015 23:02, Zeina Al-Dolami wrote:

Dear Wannier's owners and developers,

I posted my question more than a month ago. It was realted to running

the code pw2wannier90.x for my system that is 4 carbon atom. Below was

the error message:

  -----------------

  *** Reading nnkp

  -----------------


  Checking info from wannier.nnkp file


  Something wrong!

  rlatt(i,j) =   1.88808383092209       at(i,j)=   1.00000000000000



At that time, Dr.Giovanni answered me by posting two links related to

the same question. He also mentioned that my cell in .win file is

different from that in nscf calculation. I checked all the possibilities

that were suggested to generate such error. However, I have kept getting

the same error message. Below is my input file for nscf calculation and

.win file. Would you please help me with it? I am totally lost and new

to this area. Any comment or feedback is greatly appreciated. Thanks in

advance



*nscf file *

&CONTROL

  calculation = 'nscf',

  verbosity = 'high',

  pseudo_dir  = '/share/apps/espresso/espresso-5.1/wannier90-1.2/pseudo/',

  outdir      = './',

  prefix      = '4clinear',

  tstress  = .false.,

  tprnfor  = .true.,

/

&SYSTEM

  ibrav       = 1,

  a           = 5.296375,

  b           = 10.000,

  c           = 10.000,

  cosbc       = 0.,

  cosac       = 0.,

  cosab       = 0.,

  nat         = 4,

  ntyp        = 1,

  ecutwfc     = 30.,

  ecutrho     = 240.,

  nbnd        = 8,

  occupations = 'smearing',

  smearing    = 'cold',

  degauss     = 0.03,

  nspin       = 1,

/

&ELECTRONS

   mixing_beta = 0.4,

   diago_full_acc = .t.,

   diagonalization = 'cg',

   conv_thr    = 1.D-10,

/

ATOMIC_SPECIES

C 12.0107  C.pbe-rrkjus.UPF

ATOMIC_POSITIONS {angstrom}

C        0.018367612   0.000000000   0.000000000

C        1.469108353   0.000000000   0.000000000

C        2.666542920   0.000000000   0.000000000

C        4.117280996   0.000000000   0.000000000

K_POINTS {crystal}

6

0.00000000  0.00000000  0.00000000  1.00000000

0.16666667  0.00000000  0.00000000  1.00000000

0.33333333  0.00000000  0.00000000  1.00000000

0.50000000  0.00000000  0.00000000  1.00000000

0.66666667  0.00000000  0.00000000  1.00000000

0.83333333  0.00000000  0.00000000  1.00000000


*.win file *

num_bands        =  8

num_wann        =   3

num_iter         =  100


dis_num_iter     =  100

dis_win_max     =  17.0

dis_froz_max    =   -2.2225


guiding_centres = .true.


mp_grid      = 6 1 1


iprint      =    2


num_dump_cycles  =   100

num_print_cycles =   10


transport        = true

transport_mode   = bulk

one_dim_axis     = x

dist_cutoff      =  5.5

tran_win_min     = -6.5

tran_win_max     = 6.5

tran_energy_step = 0.01

fermi_energy     = -1.06

dist_cutoff_mode = one_dim

translation_centre_frac = 0.0 0.0 0.0


bands_plot = true

bands_plot_format = gnuplot


begin kpoint_path

G 0.0 0.0 0.0  A 0.0 0.0 0.5

end kpoint_path


begin projections

random

end projections


begin unit_cell_cart

Ang

5.296375  0.00  0.00

0.000000 10.00  0.00

0.000000  0.00 10.00

end unit_cell_cart


Begin KPoints

0.00000000  0.00000000  0.00000000

0.16666667  0.00000000  0.00000000

0.33333333  0.00000000  0.00000000

0.50000000  0.00000000  0.00000000

0.66666667  0.00000000  0.00000000

0.83333333  0.00000000  0.00000000

End KPoints


begin atoms_cart

Ang

C  0.018367612   0.000000000   0.000000000

C  1.469108353   0.000000000   0.000000000

C  2.666542920   0.000000000   0.000000000

C  4.117280996   0.000000000   0.000000000

end atoms_cart





--

Zeina Al-Dolami

PhD Candidate

Microelectronics and Photonics Graduate Program

University of Arkansas

Fayetteville, AR 72701

Office: PHYS 244

Email: zaldolam at email.uark.edu

<mailto:zaldolam at email.uark.edu <zaldolam at email.uark.edu>><
mailto:cxm075 at email.uark.edu <cxm075 at email.uark.edu>>



_______________________________________________

Wannier mailing list

Wannier at quantum-espresso.org

http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier



-- 

----------------------------------------------------------------------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
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From sharmajncasr at gmail.com  Wed Mar 11 07:34:26 2015
From: sharmajncasr at gmail.com (SRKC Sharma Yamijala)
Date: Wed, 11 Mar 2015 12:04:26 +0530
Subject: [Wannier] Checking info from wannier.nnkp file-Something wrong!
Message-ID: <CAJkCsLkm3e5Zv4BDbJpDZkS-idckMEiTk-36+J4XKc0UTV1vQw@mail.gmail.com>

On Wed, Mar 11, 2015 at 9:53 AM, <wannier-request at quantum-espresso.org>
wrote:

> Re: Checking info from wannier.nnkp file-Something wrong!


Hi,

You are doing wrong calculations write from the espresso and it took more
than half-an-hour to figure out this (for me). You are keeping ibrav =1 and
you are defining a,b,c etc. Also, some other problems may be there. Here is
the simple input and output, which at least is working without any errors.
See the manual and follow exactly the tutorials to decrease the number of
errors. Use kmesh.pl to generate k-points, use nosym=.true., noinv= .true.
etc. By the way, your system is also not relaxed.

&CONTROL
  calculation = 'nscf',
  verbosity = 'high',
  pseudo_dir  = './',
  outdir      = './tmp',
  prefix      = '4clinear',
  tstress  = .false.,
  tprnfor  = .true.,
/
&SYSTEM
  ibrav       = 1,
  a           = 5.296375,
!  b           = 10.000,
!  c           = 10.000,
  nat         = 4,
  ntyp        = 1,
  nosym = .true.
  noinv = .true.

  ecutwfc     = 30.,
  ecutrho     = 240.,
  nbnd        = 8,
  occupations = 'smearing',
  smearing    = 'cold',
  degauss     = 0.03,
  nspin       = 1,
/
&ELECTRONS
   mixing_beta = 0.4,
!   diago_full_acc = .t., diagonalization = 'cg', conv_thr    = 1.D-10,
/
ATOMIC_SPECIES
C 12.0107  C.pbe-rrkjus.UPF


ATOMIC_POSITIONS {angstrom}
C        0.018367612   0.000000000   0.000000000
C        1.469108353   0.000000000   0.000000000
C        2.666542920   0.000000000   0.000000000
C        4.117280996   0.000000000   0.000000000
K_POINTS {crystal}
6
0.00000000  0.00000000  0.00000000  1.00000000
0.16666667  0.00000000  0.00000000  1.00000000
0.33333333  0.00000000  0.00000000  1.00000000
0.50000000  0.00000000  0.00000000  1.00000000
0.66666667  0.00000000  0.00000000  1.00000000
0.83333333  0.00000000  0.00000000  1.00000000


win file:

num_bands        =  8
num_wann        =   4
num_iter         =  100

dis_num_iter     =  100
dis_win_max     =  17.0
dis_froz_max    =   -2.2225

#guiding_centres = .true.

bands_plot = true
bands_plot_format = gnuplot

begin projections
C:pz
end projections


begin atoms_cart
C        0.055497975  -0.000000061  -0.000000013
C        1.431961326  -0.000000069   0.000000010
C        2.703689131   0.000000069  -0.000000050
C        4.080151450   0.000000061   0.000000052
end atoms_cart

begin kpoint_path
G 0.0 0.0 0.0  A 0.0 0.0 0.5
end kpoint_path

begin unit_cell_cart
bohr
10.008698 0.0 0.0
0.0  10.008698 0.0
0.0 0.0  10.008698
end unit_cell_cart

mp_grid      = 6 1 1

begin KPoints
0.00000000  0.00000000  0.00000000
0.16666667  0.00000000  0.00000000
0.33333333  0.00000000  0.00000000
0.50000000  0.00000000  0.00000000
0.66666667  0.00000000  0.00000000
0.83333333  0.00000000  0.00000000
end KPoints

HTH,
Sharma.








********************************************************
*Chaitanya Sharma,*
*Prof. Pati'*s group,
Chemistry and Physics Materials unit,
JNCASR, BANGLORE,
Lab:: (080-2208) 2581, 2809
https://sites.google.com/site/sharmasrkcyamijala/
*********************************************************
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From giovanni.pizzi at epfl.ch  Tue Mar 17 16:00:41 2015
From: giovanni.pizzi at epfl.ch (Giovanni Pizzi)
Date: Tue, 17 Mar 2015 15:00:41 +0000
Subject: [Wannier] momentum operator matrix
In-Reply-To: <CAD5=Mwm9R3r1in=hOE5aBDETsdWeSP=CumQWOzzALVBw53GXLA@mail.gmail.com>
References: <CAD5=Mwm9R3r1in=hOE5aBDETsdWeSP=CumQWOzzALVBw53GXLA@mail.gmail.com>
Message-ID: <BA69801B-0177-4FFB-9BC9-0DD44AF2950A@epfl.ch>

Hi Yu Zhang,

there is a module 'geninterp' in postw90.x that prints in output bands and band derivatives (see also the documentation to see how it works). Band derivatives internally use the matrix elements you are asking for: you can look at the implementation (src/postw90/geninterp.F90) to see which functions are called, and then possibly modify slightly the code to print the quantities you are interested into.

Best,
Giovanni Pizzi

P.S.: remember to sign with your affiliation!

--
Giovanni Pizzi
Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 340 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124




On 10 Mar 2015, at 22:04, Yu Zhang wrote:

Dear wannier90 users and developers,

I want to get the the matrix element of momentum operator, i.e., <Rn| \nabla |0m>. I didn't find any instructions to get the matrix element from wannier90. Does anybody know how to get the momentum operator matrix?

Thank you in advance!

Best regards,

Yu Zhang
_______________________________________________
Wannier mailing list
Wannier at quantum-espresso.org<mailto:Wannier at quantum-espresso.org>
http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier

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From kimu206 at gmail.com  Thu Mar 26 14:29:48 2015
From: kimu206 at gmail.com (Khalid Ibne Masood Khalid)
Date: Thu, 26 Mar 2015 19:29:48 +0600
Subject: [Wannier] (no subject)
Message-ID: <CALoavpZedau9qSaXX3AOHaFyQFUgxCbyALjeRcxhgWsGkyaKbg@mail.gmail.com>

Dear Researchers,
I am new to wannier90, and I apologize my physics is not good enough. I
have two questions:
1) When writing wannier input file (.win file) I have found the projection
block most painful. I am not sure where and which orbitals to choose. (how
many s and p should be taken?) Does this initial approximated projection
affect the final transport result? If I take random projections, will that
be okay in transport problems ?

2) I want to consider the effect of electrical field in transport
properties, for this I can take electric field in my DFT calculations, but
I was wondering whether I take the gamma only option with electric field in
my DFT calculation, will it be allowed in wannierisation ?

Thank you.
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From szaboa at iis.ee.ethz.ch  Thu Mar 26 14:54:28 2015
From: szaboa at iis.ee.ethz.ch (Aron Szabo)
Date: Thu, 26 Mar 2015 14:54:28 +0100
Subject: [Wannier] (no subject)
In-Reply-To: <CALoavpZedau9qSaXX3AOHaFyQFUgxCbyALjeRcxhgWsGkyaKbg@mail.gmail.com>
References: <CALoavpZedau9qSaXX3AOHaFyQFUgxCbyALjeRcxhgWsGkyaKbg@mail.gmail.com>
Message-ID: <55140F94.8050702@iis.ee.ethz.ch>

Dear Khalid,

the initial projections can affect whether the wannierization process 
finds the global minimum or just a local one. So you will most likely 
get more compact functions if you use good projections than if you use 
random projections. But you can give it a try, and check what is the 
spread of the resulting Wannier functions. They should be around just a 
few Angstroms (2-3 in my experience for semiconductors, but can be more 
depending on the system). Also, the Hamiltonian should be real when you 
are at the global minimum (use hr_plot = T to check it).

If you don't know anything about the character of the electronic states 
in your system, then you should first project the Bloch functions onto 
atomic orbitals centered on the ions, and check which orbitals on which 
ions dominate in those bands that you want to reproduce with Wannier 
functions. In VASP you need to set the LORBIT = 10 tag to generate these 
orbital projections. It can give you an idea about which orbitals and 
how many of them you need.

Best,
Aron Szabo


On 03/26/2015 02:29 PM, Khalid Ibne Masood Khalid wrote:
> Dear Researchers,
> I am new to wannier90, and I apologize my physics is not good enough. 
> I have two questions:
> 1) When writing wannier input file (.win file) I have found the 
> projection block most painful. I am not sure where and which orbitals 
> to choose. (how many s and p should be taken?) Does this initial 
> approximated projection affect the final transport result? If I take 
> random projections, will that be okay in transport problems ?
>
> 2) I want to consider the effect of electrical field in transport 
> properties, for this I can take electric field in my DFT calculations, 
> but I was wondering whether I take the gamma only option with electric 
> field in my DFT calculation, will it be allowed in wannierisation ?
>
> Thank you.
>
>
> _______________________________________________
> Wannier mailing list
> Wannier at quantum-espresso.org
> http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier

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From irving at chem.ucla.edu  Fri Mar 27 17:17:58 2015
From: irving at chem.ucla.edu (Olivia)
Date: Fri, 27 Mar 2015 09:17:58 -0700
Subject: [Wannier] Question regarding pw2wannier.x and spinor projections
In-Reply-To: <1791266297.212493.1427231461562.JavaMail.root@chem.ucla.edu>
References: <1791266297.212493.1427231461562.JavaMail.root@chem.ucla.edu>
Message-ID: <ACF7C9D4-5819-4E89-B681-0643CBB8BC35@chem.ucla.edu>

Hello , 

I am using Wannier90 with quantum espresso and I keep recieving an error ' no projections found in seedname.nnkp.' 
It seems that specifically the .x file , pw2wannier90.x cannot read projections from the .nnkp files. 
I at first thought this might be due to the fact that spinors weren't incoporated into quantum espresso as the resleases of Wannier and Quantum Espresso do not coiencide. I then followed the directions for QE 5.0.3 , 5.0.2 and 5.1.1 an 5.1.2 installations with the pw2wannier90.f90 file provided on the website . I am still only able to run ./wannier90.x -pp to recieve the nnkp file but I am unable to run pw2wannier90.x and recieve the requitse files. I do have spinor projections in the nnkp file but these are not read by pw2wannier. This pw2wannier.x file works fine with spinors=.false.
I was wondering if anyone has recieved this error? 
If so is there something I can do to get pw2wannier90.x to recognize spinor projections?

Thank you

Olivia Irving
undergraduate researcher
University of California Los Angeles 
irving at chem.ucla.edu
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From giovanni.pizzi at epfl.ch  Fri Mar 27 18:57:51 2015
From: giovanni.pizzi at epfl.ch (Giovanni Pizzi)
Date: Fri, 27 Mar 2015 17:57:51 +0000
Subject: [Wannier] Question regarding pw2wannier.x and spinor projections
In-Reply-To: <ACF7C9D4-5819-4E89-B681-0643CBB8BC35@chem.ucla.edu>
References: <1791266297.212493.1427231461562.JavaMail.root@chem.ucla.edu>
 <ACF7C9D4-5819-4E89-B681-0643CBB8BC35@chem.ucla.edu>
Message-ID: <99559DA8-11A7-47EE-A69F-7E61DDF23911@epfl.ch>

Dear Olivia,

QE 5.1.x do not require any patching of pw2wannier90.f90. This means you should just download QE and compile the pw2wannier90.x provided therein.
That executable is able to read spinor projections.
After compilation, make sure that there was no error and that the pw2wannier90.x was correctly compiled; and when you run it, double-check that you are actually using the compiled version that you expected.

Best,

Giovanni Pizzi
Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 340 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124




On 27 Mar 2015, at 17:17, Olivia wrote:

Hello ,

I am using Wannier90 with quantum espresso and I keep recieving an error ' no projections found in seedname.nnkp.'
It seems that specifically the .x file , pw2wannier90.x cannot read projections from the .nnkp files.
I at first thought this might be due to the fact that spinors weren't incoporated into quantum espresso as the resleases of Wannier and Quantum Espresso do not coiencide. I then followed the directions for QE 5.0.3 , 5.0.2 and 5.1.1 an 5.1.2 installations with the pw2wannier90.f90 file provided on the website . I am still only able to run ./wannier90.x -pp to recieve the nnkp file but I am unable to run pw2wannier90.x and recieve the requitse files. I do have spinor projections in the nnkp file but these are not read by pw2wannier. This pw2wannier.x file works fine with spinors=.false.
I was wondering if anyone has recieved this error?
If so is there something I can do to get pw2wannier90.x to recognize spinor projections?

Thank you

Olivia Irving
undergraduate researcher
University of California Los Angeles
irving at chem.ucla.edu<mailto:irving at chem.ucla.edu>
_______________________________________________
Wannier mailing list
Wannier at quantum-espresso.org<mailto:Wannier at quantum-espresso.org>
http://mailman.qe-forge.org/cgi-bin/mailman/listinfo/wannier

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From yugd12 at mails.jlu.edu.cn  Tue Mar 31 20:39:43 2015
From: yugd12 at mails.jlu.edu.cn (=?gbk?B?09q5+raw?=)
Date: Tue, 31 Mar 2015 20:39:43 +0800(CST)
Subject: [Wannier] =?gbk?q?How_to_output_the_hamiltonian_matrix_after_bein?=
	=?gbk?q?g_cut_as_the_hr=5Fcutoff_and_the_dist=5Fcutoff_modes?=
Message-ID: <20150331123943.A810F25EDAD@mails1.jlu.edu.cn>

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From wjshi.phys at gmail.com  Tue Mar 31 15:03:03 2015
From: wjshi.phys at gmail.com (=?UTF-8?B?5Y+y5q2m5YabKFd1LUp1biBTaGkp?=)
Date: Tue, 31 Mar 2015 21:03:03 +0800
Subject: [Wannier] How to output the hamiltonian matrix after being cut
 as the hr_cutoff and the dist_cutoff modes
In-Reply-To: <20150331123943.A810F25EDAD@mails1.jlu.edu.cn>
References: <20150331123943.A810F25EDAD@mails1.jlu.edu.cn>
Message-ID: <CANQvZsMzEVWoFaVYYwOrnGXZpVcuW=1h8oCpSJKB5r-h=FwTOA@mail.gmail.com>

?Hi Guodong,

First, you need perform the DFT calculation from vasp or other packages to
obtain the *.mmn, *amn, and *.eig files. In this step you must set the
orbital projections in the *.win file, such as projection on the s and p
orbital of a atom, and s, p, and d orbital of b atom.
begin projections
a:s;p
b:s;p;d
end projections

Second, you need continue perform the wannier90 calculation, using
wannier90.x *.win, which will read the the generated *.mmn, *amn, and *.eig
file in the first step, and you must add the ``hr_plot = .true.'' tag in
the *.win file. ?After this calculation, you can get the *_hr.dat file,
this is the Hamiltonian matrix.

tip: the disentanglement may be helpful to repeat the DFT band structure:
this is my setting:

dis_win_min       = -9.0d0
dis_win_max       = 13.5d0
dis_froz_min      = -8.0d0
dis_froz_max      = 10.0d0
dis_num_iter      = 1000
num_iter         = 1000

regards,
Wu-Jun Shi
Department of Physics,
Tsinghua University,
Beijing, P.R. China




2015-03-31 20:39 GMT+08:00 ??? <yugd12 at mails.jlu.edu.cn>:

> Hell every wannier90 user:
>
> I am new to Wannier90. Recently, I would like to set up a tight-binding
> model with MLWF that can be obtained from Wannier90. So I just want to get
> the Hamiltonian matrix  after cutting the Hamiltonian in the dist_cutoff
> mode. It means that the hopping energy between two MLWFs will be set into 0
> if the distance between the two MLWFs is more than some distance.
> Therefore, how can i get such a Hamiltonian matrix after cutting? Thanks
> in advance!
>
> Best,
> Guodong Yu
> Jilin University, China
>
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