From njuxuyuehua at gmail.com  Tue Jan  8 14:41:48 2013
From: njuxuyuehua at gmail.com (Xu Yuehua)
Date: Tue, 8 Jan 2013 21:41:48 +0800
Subject: [Wannier] param_get_projection: Atom site not recognised c1
Message-ID: <CABZKPKCiVd8Wrkt498OWRk0dBfAdmpfet9UngBf-TQiueKQbqg@mail.gmail.com>

hello all:

i have a strange problem. in the input *.win, i write
*Begin Projections
C1:sp2;pz*
*C2:pz
End Projections*

the output error is:

*Wannier90 is running in LIBRARY MODE

 Setting up k-point neighbours...


 Ignoring <num_bands> in input file
 Ignoring <mp_grid> in input file
 Ignoring <unit_cell_cart> in input file
 Ignoring <kpoints> in input file
 Ignoring <atoms_frac> in input file
 Exiting.......
 **param_get_projection: Atom site not recognised c1*

**
so i am wondering,anyone can help me,because in the example 10, the C1,C2
is writen in the graphite.win. i thought it is correct.



-- 
Yuehua Xu
Group of Computational Condensed Matter Physics,
National Laboratory of Solid State Microstructures and Department of
Physics,
Nanjing University,
 Nanjing 210093,
 P. R. China
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From jonathan.yates at materials.ox.ac.uk  Thu Jan 10 01:01:32 2013
From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates)
Date: Thu, 10 Jan 2013 00:01:32 +0000
Subject: [Wannier] param_get_projection: Atom site not recognised c1
In-Reply-To: <CABZKPKCiVd8Wrkt498OWRk0dBfAdmpfet9UngBf-TQiueKQbqg@mail.gmail.com>
References: <CABZKPKCiVd8Wrkt498OWRk0dBfAdmpfet9UngBf-TQiueKQbqg@mail.gmail.com>
Message-ID: <7CB3CE6F-8B95-4F40-8AB5-8290B32F5C62@materials.ox.ac.uk>


On 8 Jan 2013, at 13:41, Xu Yuehua wrote:

> hello all:
>  
> i have a strange problem. in the input *.win, i write
> Begin Projections
> C1:sp2;pz
> C2:pz
> End Projections
>  
> Wannier90 is running in LIBRARY MODE

>  param_get_projection: Atom site not recognised c1
>  
> 
> so i am wondering,anyone can help me,because in the example 10, the C1,C2 is writen in the graphite.win. i thought it is correct.

 The error is caused when the labels used in the projections (C1, C2) do not match the labels given to the atoms. In standalone mode these are set in the win file, in library mode they are passed by the calling program.

 You haven't told us how you are running W90 - although I can see that it is in library mode. You need to get the calling program to use the labels C1 and C2. If this is not possible, other options include - giving co-ordindates of the projections directly (using f= or c=) - or put a Pz orbital on each C atom and a 's' orbital midway between bonded atoms.

 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 njuxuyuehua at gmail.com  Fri Jan 11 04:31:03 2013
From: njuxuyuehua at gmail.com (Xu Yuehua)
Date: Fri, 11 Jan 2013 11:31:03 +0800
Subject: [Wannier] Wannier Digest, Vol 61, Issue 2
In-Reply-To: <mailman.3.1357809446.14813.wannier@quantum-espresso.org>
References: <mailman.3.1357809446.14813.wannier@quantum-espresso.org>
Message-ID: <CABZKPKAfEP4g2nkzeLiM4gFMrtLTdX+RschojsgyDQYEoMu0_w@mail.gmail.com>

thank you for you reply.

i am a newer in using wannner function, so i tried to understand you
meaning, it is that so:

if: my system is graphene ,(a3=a3)
begin atoms_frac
C       a1     a2    a3
C       a4     a5    a3
begin atoms_frac
then " *put a Pz orbital on each C atom and a 's' orbital midway between
bonded atoms"*
**
begin projections
f=a1,a2,a3 :pz
f=a4,a5,a3? pz
f=(a1+a4)/2,(a2+a5)/2,a3:l=0
end projections
is it right?

thank you !


On Thu, Jan 10, 2013 at 5:17 PM, <wannier-request at quantum-espresso.org>wrote:

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>    1. Re: param_get_projection: Atom site not recognised c1
>       (Jonathan Yates)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 10 Jan 2013 00:01:32 +0000
> From: Jonathan Yates <jonathan.yates at materials.ox.ac.uk>
> Subject: Re: [Wannier] param_get_projection: Atom site not recognised
>         c1
> To: Wannier90 <wannier at quantum-espresso.org>
> Message-ID: <7CB3CE6F-8B95-4F40-8AB5-8290B32F5C62 at materials.ox.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
>
>
> On 8 Jan 2013, at 13:41, Xu Yuehua wrote:
>
> > hello all:
> >
> > i have a strange problem. in the input *.win, i write
> > Begin Projections
> > C1:sp2;pz
> > C2:pz
> > End Projections
> >
> > Wannier90 is running in LIBRARY MODE
>
> >  param_get_projection: Atom site not recognised c1
> >
> >
> > so i am wondering,anyone can help me,because in the example 10, the
> C1,C2 is writen in the graphite.win. i thought it is correct.
>
>  The error is caused when the labels used in the projections (C1, C2) do
> not match the labels given to the atoms. In standalone mode these are set
> in the win file, in library mode they are passed by the calling program.
>
>  You haven't told us how you are running W90 - although I can see that it
> is in library mode. You need to get the calling program to use the labels
> C1 and C2. If this is not possible, other options include - giving
> co-ordindates of the projections directly (using f= or c=) - or put a Pz
> orbital on each C atom and a 's' orbital midway between bonded atoms.
>
>  Jonathan
>
>
>
> --
> Department of Materials, University of Oxford, Parks Road, Oxford, OX1
> 3PH, UK
> tel: +44 (0)1865 612797                http://users.ox.ac.uk/~oums0549/
>
>
>
> ------------------------------
>
> _______________________________________________
> Wannier mailing list
> Wannier at quantum-espresso.org
> http://www.democritos.it/mailman/listinfo/wannier
>
>
> End of Wannier Digest, Vol 61, Issue 2
> **************************************
>



-- 
Yuehua Xu
Group of Computational Condensed Matter Physics,
National Laboratory of Solid State Microstructures and Department of
Physics,
Nanjing University,
 Nanjing 210093,
 P. R. China
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From gpanchap at gmail.com  Tue Jan 22 19:26:50 2013
From: gpanchap at gmail.com (Ganesh Panchapakesan)
Date: Tue, 22 Jan 2013 13:26:50 -0500
Subject: [Wannier] h(r) hoppings in AO basis
Message-ID: <CAHkyYRAdu+DQaRjmcPrQeftA3wcXchooLYZ2kt1H-a=AeeK2Ew@mail.gmail.com>

Dear All,

Does anyone know if it is possible to transform the current h(r) matrix
elements, which is in the WF-basis, to (say an atom centered)
atomic-orbital basis within wannier90?  The transformation might be lossy
(i.e. it might be a projection) depending on the system of course, but
would be good to compare with other TB-fitting codes which use such
atomic-orbital basis to represent the Hamiltonian.

Also, in the current wannier90 code, I supposed the WFs are orthogonal in
the unit cell due to periodicity i.e. WF(n,R)(r) = WF(n,0)(r-R). But I
don't see that when I print the
sum(wf(nx,ny,nz,wan_ind)*conjg(wf(nx,ny,nz,wan_ind)), where {n} is the real
space grid inside the wannier_plot_supercell, which is '1' in my test case
i.e. the unit cell.  What am I missing, is the sum needed over the
supercell corresponding to the k-mesh i.e. {n} is {kx,ky,kz}?

Thanks.
Ganesh
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From gpanchap at gmail.com  Wed Jan 23 22:50:29 2013
From: gpanchap at gmail.com (Ganesh Panchapakesan)
Date: Wed, 23 Jan 2013 16:50:29 -0500
Subject: [Wannier] h(r) hoppings in AO basis
In-Reply-To: <CAHkyYRAdu+DQaRjmcPrQeftA3wcXchooLYZ2kt1H-a=AeeK2Ew@mail.gmail.com>
References: <CAHkyYRAdu+DQaRjmcPrQeftA3wcXchooLYZ2kt1H-a=AeeK2Ew@mail.gmail.com>
Message-ID: <CAHkyYRCBfos8WpQPe_G80Gej35pNP=oFT3QWad8vrNU7Q09D-w@mail.gmail.com>

Follow up:

I now understand that the normalization factor is not '1' because each
WF(n,R) is divided by the largest value whose phase is set to be zero i.e.
it is real at this point.  But shouldn't the orthogonality still work?
unless the Lowdin orthonormalization is missing i.e. eq. 17 in the Marzari
et al review of modern physics article.  Where is it coded ?

I have traced part of the problem to the following lines of code which I
believe is wrong in plot.F.  This mistake (possibly a typo) kills the
periodicity of WF(n,R):

current lines in plot.F:


 scalfac=kpt_latt(1,loop_kpt)*real(nxx-1,dp)/real(ngx,dp)+ &
                      kpt_latt(2,loop_kpt)*real(nyy-1,dp)/real(ngy,dp)+ &
                      kpt_latt(3,loop_kpt)*real(nzz-1,dp)/real(ngz,dp)

My suggested change to the above:

scalfac=kpt_latt(1,loop_kpt)*real(nx-1,dp)/real(ngx,dp)+ &
                      kpt_latt(2,loop_kpt)*real(ny-1,dp)/real(ngy,dp)+ &
                      kpt_latt(3,loop_kpt)*real(nz-1,dp)/real(ngz,dp)

This I have confirmed brings back the periodicity of the wannier functions.
 Can one of the authors please confirm the correctness (or wrongness) of my
suggestion?

I failed to mention that I am using VASP for the ab initio part.

Thanks,
Ganesh





On Tue, Jan 22, 2013 at 1:26 PM, Ganesh Panchapakesan <gpanchap at gmail.com>wrote:

> Dear All,
>
> Does anyone know if it is possible to transform the current h(r) matrix
> elements, which is in the WF-basis, to (say an atom centered)
> atomic-orbital basis within wannier90?  The transformation might be lossy
> (i.e. it might be a projection) depending on the system of course, but
> would be good to compare with other TB-fitting codes which use such
> atomic-orbital basis to represent the Hamiltonian.
>
> Also, in the current wannier90 code, I supposed the WFs are orthogonal in
> the unit cell due to periodicity i.e. WF(n,R)(r) = WF(n,0)(r-R). But I
> don't see that when I print the
> sum(wf(nx,ny,nz,wan_ind)*conjg(wf(nx,ny,nz,wan_ind)), where {n} is the real
> space grid inside the wannier_plot_supercell, which is '1' in my test case
> i.e. the unit cell.  What am I missing, is the sum needed over the
> supercell corresponding to the k-mesh i.e. {n} is {kx,ky,kz}?
>
> Thanks.
> Ganesh
>
>
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From jonathan.yates at materials.ox.ac.uk  Thu Jan 24 02:11:34 2013
From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates)
Date: Thu, 24 Jan 2013 01:11:34 +0000
Subject: [Wannier] h(r) hoppings in AO basis
In-Reply-To: <CAHkyYRCBfos8WpQPe_G80Gej35pNP=oFT3QWad8vrNU7Q09D-w@mail.gmail.com>
References: <CAHkyYRAdu+DQaRjmcPrQeftA3wcXchooLYZ2kt1H-a=AeeK2Ew@mail.gmail.com>
	<CAHkyYRCBfos8WpQPe_G80Gej35pNP=oFT3QWad8vrNU7Q09D-w@mail.gmail.com>
Message-ID: <C85856C9-6DC0-4D7F-86AB-7FCD3530D920@materials.ox.ac.uk>

Ganesh,

 I believe the code is correct as written.
  WF are not generally periodic in the unit cell - a set of WF constructed from bloch states on a nxnxn kpoint mesh will live within a nxnxn supercell of the unit cell. There is a section on normalization conventions in the Rev. Mod. Phys. article.
 The global phase you refer to has no effect on the normalisation.

 One warning: The WF written by plot.F90 will only obey orthonormality if the Bloch states used to construct them are orthonormal. This may not be the case when using PAW or Ultrasoft potentials (ie the total charge of a WF may not sum to 1). It depends on how the electronic structure code writes UNK files. If it writes only the soft part of the wavefunction the WF will not be orthonormal - if it adds in the augmentation part they should be orthonormal. I don't know what VASP does (but I would be interested if anyone knows).

Jonathan



On 23 Jan 2013, at 21:50, Ganesh Panchapakesan wrote:

> Follow up: 
> 
> I now understand that the normalization factor is not '1' because each WF(n,R) is divided by the largest value whose phase is set to be zero i.e. it is real at this point.  But shouldn't the orthogonality still work? unless the Lowdin orthonormalization is missing i.e. eq. 17 in the Marzari et al review of modern physics article.  Where is it coded ?
> 
> I have traced part of the problem to the following lines of code which I believe is wrong in plot.F.  This mistake (possibly a typo) kills the periodicity of WF(n,R): 
> 
> current lines in plot.F: 
> 
>                        scalfac=kpt_latt(1,loop_kpt)*real(nxx-1,dp)/real(ngx,dp)+ &
>                       kpt_latt(2,loop_kpt)*real(nyy-1,dp)/real(ngy,dp)+ &
>                       kpt_latt(3,loop_kpt)*real(nzz-1,dp)/real(ngz,dp)
> 
> My suggested change to the above:
>                       scalfac=kpt_latt(1,loop_kpt)*real(nx-1,dp)/real(ngx,dp)+ &
>                       kpt_latt(2,loop_kpt)*real(ny-1,dp)/real(ngy,dp)+ &
>                       kpt_latt(3,loop_kpt)*real(nz-1,dp)/real(ngz,dp)
> 
> This I have confirmed brings back the periodicity of the wannier functions.  Can one of the authors please confirm the correctness (or wrongness) of my suggestion?  
> 
> I failed to mention that I am using VASP for the ab initio part. 
> 
> Thanks,
> Ganesh
> 
> 
> 
> 
> 
> On Tue, Jan 22, 2013 at 1:26 PM, Ganesh Panchapakesan <gpanchap at gmail.com> wrote:
> Dear All,
> 
> Does anyone know if it is possible to transform the current h(r) matrix elements, which is in the WF-basis, to (say an atom centered) atomic-orbital basis within wannier90?  The transformation might be lossy (i.e. it might be a projection) depending on the system of course, but would be good to compare with other TB-fitting codes which use such atomic-orbital basis to represent the Hamiltonian.  
> 
> Also, in the current wannier90 code, I supposed the WFs are orthogonal in the unit cell due to periodicity i.e. WF(n,R)(r) = WF(n,0)(r-R). But I don't see that when I print the sum(wf(nx,ny,nz,wan_ind)*conjg(wf(nx,ny,nz,wan_ind)), where {n} is the real space grid inside the wannier_plot_supercell, which is '1' in my test case i.e. the unit cell.  What am I missing, is the sum needed over the supercell corresponding to the k-mesh i.e. {n} is {kx,ky,kz}?
> 
> Thanks.
> Ganesh
> 
> 
> _______________________________________________
> Wannier mailing list
> Wannier at quantum-espresso.org
> http://www.democritos.it/mailman/listinfo/wannier

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



From dhv at physics.rutgers.edu  Fri Jan 25 18:07:34 2013
From: dhv at physics.rutgers.edu (David Vanderbilt)
Date: Fri, 25 Jan 2013 12:07:34 -0500 (EST)
Subject: [Wannier] h(r) hoppings in AO basis
In-Reply-To: <CAHkyYRAdu+DQaRjmcPrQeftA3wcXchooLYZ2kt1H-a=AeeK2Ew@mail.gmail.com>
References: <CAHkyYRAdu+DQaRjmcPrQeftA3wcXchooLYZ2kt1H-a=AeeK2Ew@mail.gmail.com>
Message-ID: <alpine.LFD.2.00.1301251202110.20669@magnon.physics.rutgers.edu>

Ganesh,

Regarding this part

> Does anyone know if it is possible to transform the current
> h(r) matrix elements, which is in the WF-basis, to (say
> an atom centered) atomic-orbital basis within wannier90?
> The transformation might be lossy (i.e. it might be a projection)
> depending on the system of course, but would be good to compare
> with other TB-fitting codes which use such atomic-orbital basis
> to represent the Hamiltonian.

To do this, we normally choose trial functions that have the
desired chemical symmetry, and then do zero iterations of the
maxloc procedure.  That is, we use the WFs that are obtained
just by projection on the trial functions.  We also include
unoccupied bands if needed to "complete the shell" of WFs on
each atom.  Because we skip the iterative localization, these
may not be quite as localized as the MLWFs, but they may be
good for your purposes.

David

------------------------------------------------------------------------
Prof. David Vanderbilt               Phone: (732) 445-5500 x2514
Department of Physics and Astronomy  Fax:   (732) 445-4400
Rutgers University                   Email:  dhv at physics.rutgers.edu
136 Frelinghuysen Road               http://www.physics.rutgers.edu/~dhv
Piscataway, NJ 08854-8019   USA
------------------------------------------------------------------------


From gpanchap at gmail.com  Fri Jan 25 19:37:49 2013
From: gpanchap at gmail.com (Ganesh Panchapakesan)
Date: Fri, 25 Jan 2013 13:37:49 -0500
Subject: [Wannier] h(r) hoppings in AO basis
In-Reply-To: <alpine.LFD.2.00.1301251202110.20669@magnon.physics.rutgers.edu>
References: <CAHkyYRAdu+DQaRjmcPrQeftA3wcXchooLYZ2kt1H-a=AeeK2Ew@mail.gmail.com>
	<alpine.LFD.2.00.1301251202110.20669@magnon.physics.rutgers.edu>
Message-ID: <CAHkyYRAMp5VhrRE2h4FV892kfHE3au4EbBKC4oMBe00sZ_ua8w@mail.gmail.com>

David,

Thanks.  Yes, I later realized that with zero localization step the
(U(dis)(k))^dagg.H(k).U(dis)(k)  essentially projects the bloch-states onto
the trial basis within the chosen energy window (and also diagonalises the
H in that subspace by construction), which as you mention can include
unoccupied bands as well.  This is what I needed.

Ganesh


On Fri, Jan 25, 2013 at 12:07 PM, David Vanderbilt
<dhv at physics.rutgers.edu>wrote:

> Ganesh,
>
> Regarding this part
>
>
>  Does anyone know if it is possible to transform the current
>> h(r) matrix elements, which is in the WF-basis, to (say
>> an atom centered) atomic-orbital basis within wannier90?
>> The transformation might be lossy (i.e. it might be a projection)
>> depending on the system of course, but would be good to compare
>> with other TB-fitting codes which use such atomic-orbital basis
>> to represent the Hamiltonian.
>>
>
> To do this, we normally choose trial functions that have the
> desired chemical symmetry, and then do zero iterations of the
> maxloc procedure.  That is, we use the WFs that are obtained
> just by projection on the trial functions.  We also include
> unoccupied bands if needed to "complete the shell" of WFs on
> each atom.  Because we skip the iterative localization, these
> may not be quite as localized as the MLWFs, but they may be
> good for your purposes.
>
> David
>
> ------------------------------**------------------------------**
> ------------
> Prof. David Vanderbilt               Phone: (732) 445-5500 x2514
> Department of Physics and Astronomy  Fax:   (732) 445-4400
> Rutgers University                   Email:  dhv at physics.rutgers.edu
> 136 Frelinghuysen Road               http://www.physics.rutgers.**edu/~dhv<http://www.physics.rutgers.edu/~dhv>
> Piscataway, NJ 08854-8019   USA
> ------------------------------**------------------------------**
> ------------
>
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