From dekoning at ifi.unicamp.br  Wed Oct  2 19:28:15 2013
From: dekoning at ifi.unicamp.br (Maurice de Koning)
Date: Wed, 2 Oct 2013 14:28:15 -0300
Subject: [Wannier] Wannier90-VASP: Dipole moment of isolated H20
In-Reply-To: <504B928A.9020406@epfl.ch>
References: <96EAA162-45F6-4EC4-BC3F-4C1D6BB8E093@ifi.unicamp.br>
	<504B928A.9020406@epfl.ch>
Message-ID: <C95C3420-43EA-447F-A220-09E2EB3464DB@ifi.unicamp.br>

Hi Nicola,

This has been a while, but I recently started looking again into the problem I had using the Wannier90-VASP interface in 
reproducing the WC's for the isolated water molecule as in the paper by Silvestrelli and Parrinello (JCP 111 3572,1999) .

Initially I was not able to reproduce the WCs, even using exactly the same calculation parameters as in Silvestrelli's paper. Now I have
found out that the results are quite sensitive to the number of bands that you include in the KS calculation and in the posterior Wannierization. 
By default VASP always includes a certain number of empty bands, unless you explicitly tell it not do so. In my first calculations, the Wannier optimization
always included a number of such empty bands and the results for the 4 WCs associated with the covalent bonds and the lone pairs did not agree with those
reported by Silvestrelli. Now, if you force VASP to work only with the 4 occupied bands and Wannierize only these, the results  then do agree with those of Silvestrelli.

So it seems, at least in this case, that one should only consider the occupied bands in the calculation. 

Cheers,

Maurice

> 
> 
> Dear Maurice,
> 
> 
> not sure if this ever had a follw up. Note that the Wannier formalism
> uses a reciprocal space representation to descrive <r> and <r^2> - so
> quantities like the spreads (very much so) and the centers (much less)
> depend on k-point sampling (or one the size of the unit cell, if using gamma sampling) much mroe that one usually expects - you could have
> used a k-point mesh fine enough to converge the electronic structure
> (or a supercell largge enough), but not enough to converge the Wannier-related quantities.
> 
> For your water molecule, you should be able to calculate its dipole in
> real space just as a charge integral in space, or using a Wannier code -
> and you could plot convergence of these quantities.
> 
> Some comments on this matter should be also in an old PRB of Umari and
> Pasquarello.
> 
> All the best,
> 	
> 		nicola
> 
> 
> 
> 
> 
> On 26/06/2012 19:25, Maurice de Koning wrote:
>> Hello all,
>> 
>> We have started using the Wannier 90 interface to VASP and as a first test case we are trying to
>> reproduce the Wannier centers for the isolated water molecule as in the paper by Silvestrelli and Parrinello (JCP 111 3572,1999).
>> 
>> Using the PAW approach, the PBE xc functional, a cubic periodic box with side 10.6 Angstrom, a plane-wave kinetic energy cut-off of 1000 eV and Gamma-point sampling, the
>> relaxed geometry of the water molecule is identical to that reported by Silvestrelli, with an O-H distance of 0.972 Angstroms and an internal angle of 104.4 degrees.
>> 
>> However, when using the Wannier90 interface to VASP, the Wannier centers that we obtain do not coincide with those reported in Silvestrelli. The position of the Wannier
>> centers corresponding to the lone pairs are reasonable. We find distances of 0.306 Angstroms from the oxygen ion, and an internal angle of 120.8 degrees, which agrees reasonably well with the  values of 0.300 Angstrom and 126.4 degrees reported by Silvestrelli.
>> 
>> The WFCs associated with the electrons in the covalent bonds, however, are very different. We find a distance from the oxygen ion of 0.47 Angstrom versus a value of 0.53 Angstrom reported by Silvestrilli. These differences lead to quite a different electric dipole moment.
>> 
>> Any suggestions as to what might be the reason for these discrepancies?
>> 
>> Cheers,
>> 
>> Maurice
>> _______________________________________________
>> Wannier mailing list
>> Wannier at quantum-espresso.org
>> http://www.democritos.it/mailman/listinfo/wannier
>> 
> 
> 
> -- 
> 
> ----------------------------------------------------------------------
> Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL



From nicola.marzari at epfl.ch  Thu Oct  3 12:50:01 2013
From: nicola.marzari at epfl.ch (Nicola Marzari)
Date: Thu, 03 Oct 2013 12:50:01 +0200
Subject: [Wannier] Wannier90-VASP: Dipole moment of isolated H20
In-Reply-To: <C95C3420-43EA-447F-A220-09E2EB3464DB@ifi.unicamp.br>
References: <96EAA162-45F6-4EC4-BC3F-4C1D6BB8E093@ifi.unicamp.br>
	<504B928A.9020406@epfl.ch>
	<C95C3420-43EA-447F-A220-09E2EB3464DB@ifi.unicamp.br>
Message-ID: <524D4BD9.1020702@epfl.ch>


Thanks Maurice for the update!

Two comments: the WFs you want should always be constructed from the 4 
lowest occupied states (of course, you can include empty states for
different "disentanglement" purposes - but let's say here you are
focused on the usual water WFs).

Then, the results should not be dependent on having a VASP calculation 
use empty states or not to converge to the ground state (depending on 
circumstances, those could help or not the speed of the convergence,
but for a crystalline insulator or a molecule with filled shells the
filled manifold at self-consistency should be identical no matter how 
many empty states you use).

				nicola


On 02/10/2013 19:28, Maurice de Koning wrote:
> Hi Nicola,
>
> This has been a while, but I recently started looking again into the problem I had using the Wannier90-VASP interface in
> reproducing the WC's for the isolated water molecule as in the paper by Silvestrelli and Parrinello (JCP 111 3572,1999) .
>
> Initially I was not able to reproduce the WCs, even using exactly the same calculation parameters as in Silvestrelli's paper. Now I have
> found out that the results are quite sensitive to the number of bands that you include in the KS calculation and in the posterior Wannierization.
> By default VASP always includes a certain number of empty bands, unless you explicitly tell it not do so. In my first calculations, the Wannier optimization
> always included a number of such empty bands and the results for the 4 WCs associated with the covalent bonds and the lone pairs did not agree with those
> reported by Silvestrelli. Now, if you force VASP to work only with the 4 occupied bands and Wannierize only these, the results  then do agree with those of Silvestrelli.
>
> So it seems, at least in this case, that one should only consider the occupied bands in the calculation.
>
> Cheers,
>
> Maurice
>
>>
>>
>> Dear Maurice,
>>
>>
>> not sure if this ever had a follw up. Note that the Wannier formalism
>> uses a reciprocal space representation to descrive <r> and <r^2> - so
>> quantities like the spreads (very much so) and the centers (much less)
>> depend on k-point sampling (or one the size of the unit cell, if using gamma sampling) much mroe that one usually expects - you could have
>> used a k-point mesh fine enough to converge the electronic structure
>> (or a supercell largge enough), but not enough to converge the Wannier-related quantities.
>>
>> For your water molecule, you should be able to calculate its dipole in
>> real space just as a charge integral in space, or using a Wannier code -
>> and you could plot convergence of these quantities.
>>
>> Some comments on this matter should be also in an old PRB of Umari and
>> Pasquarello.
>>
>> All the best,
>> 	
>> 		nicola
>>
>>
>>
>>
>>
>> On 26/06/2012 19:25, Maurice de Koning wrote:
>>> Hello all,
>>>
>>> We have started using the Wannier 90 interface to VASP and as a first test case we are trying to
>>> reproduce the Wannier centers for the isolated water molecule as in the paper by Silvestrelli and Parrinello (JCP 111 3572,1999).
>>>
>>> Using the PAW approach, the PBE xc functional, a cubic periodic box with side 10.6 Angstrom, a plane-wave kinetic energy cut-off of 1000 eV and Gamma-point sampling, the
>>> relaxed geometry of the water molecule is identical to that reported by Silvestrelli, with an O-H distance of 0.972 Angstroms and an internal angle of 104.4 degrees.
>>>
>>> However, when using the Wannier90 interface to VASP, the Wannier centers that we obtain do not coincide with those reported in Silvestrelli. The position of the Wannier
>>> centers corresponding to the lone pairs are reasonable. We find distances of 0.306 Angstroms from the oxygen ion, and an internal angle of 120.8 degrees, which agrees reasonably well with the  values of 0.300 Angstrom and 126.4 degrees reported by Silvestrelli.
>>>
>>> The WFCs associated with the electrons in the covalent bonds, however, are very different. We find a distance from the oxygen ion of 0.47 Angstrom versus a value of 0.53 Angstrom reported by Silvestrilli. These differences lead to quite a different electric dipole moment.
>>>
>>> Any suggestions as to what might be the reason for these discrepancies?
>>>
>>> Cheers,
>>>
>>> Maurice
>>> _______________________________________________
>>> Wannier mailing list
>>> Wannier at quantum-espresso.org
>>> http://www.democritos.it/mailman/listinfo/wannier
>>>
>>
>>
>> --
>>
>> ----------------------------------------------------------------------
>> Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
>


-- 

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


From gangli.pku at gmail.com  Tue Oct  8 17:29:40 2013
From: gangli.pku at gmail.com (Gang Li)
Date: Tue, 8 Oct 2013 17:29:40 +0200
Subject: [Wannier] slab hamiltonian construction from case_hr.dat ?
Message-ID: <C7BF40B7-BB4A-4F81-B4CA-7B70E6432F1D@gmail.com>

Dear all

      I am facing a problem of constructing a slab with many atoms in it that, in the end, the total amount of numerical cost is unfortunately not affordable. I then came to the MLWFs, I tried to build the slab with the same number of atoms, but with only a few orbitals on each atom.  The interpolated band structure from MLWFs agrees well with the Bloch band structure.  My question is about the 'case_hr.dat' file.

     (1)  In 'case_hr.dat', the hopping matrix spans over all projected orbitals for given displacement of the Wigner-Seitz Cell. I guess these displacements are defined in terms of the primitive lattice vectors R1, R2, R3 (correct me, if I am wrong). In the construction of the slab, I need to use another set of lattice vectors R1', R2', R3', how can I translate the hopping matrix in 'case_hr.dat' into the coordinates defined by R1', R2', R3'. 

     (2) What does the degency really tell me? Do they modify the hopping integral listed in 'case_hr.dat'? If they do, how should I use them? 

thanks for any kind reply in advances
Gang
 



From rio10002 at gmail.com  Mon Oct 14 08:34:46 2013
From: rio10002 at gmail.com (satrio)
Date: Mon, 14 Oct 2013 02:34:46 -0400
Subject: [Wannier] Tunneling Hamiltonian in Wannier90
Message-ID: <CAE=z7Sops+UF0dXUffzHW63p=K+ciMi9567twh_Vjw=5M4UX+A@mail.gmail.com>

Dear Mr/Mrs

I have a question about the Hamiltonian that is generated by this progam.
As i read from the user guide, the control for this is from hr_plot that
will produce Hamiltonian value at seedname_hr.dat. When i see the example
of the output of this part, the data just give the Halmitonian part in WF
basis at each position R <WF,R|H|WF,R>  in real lattice space. My question,
why there is no Hamiltonian part between WF basis that are from different
R, example <WF,R+b|H|WF,R> where b is the vector to nearest neighboor of R?
Thank You

Regards
Rio
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From huanghq at phys.tsinghua.edu.cn  Mon Oct 14 14:07:29 2013
From: huanghq at phys.tsinghua.edu.cn (Hua-Qing Huang)
Date: Mon, 14 Oct 2013 20:07:29 +0800
Subject: [Wannier] Tuning Hamiltonian in Wannier90
In-Reply-To: <mailman.0.1381739036.21262.wannier@quantum-espresso.org>
References: <mailman.0.1381739036.21262.wannier@quantum-espresso.org>
Message-ID: <20131014120610.M50249@phys.tsinghua.edu.cn>

Dear Rio,

I think the Hamiltonian matrix element in seedname_hr.dat is <WF_i, 0|H|WF_j, 
b>, where b is nearest neighbour or nest nearest neighbour R.  

Regards,

Huaqing


On Mon, 14 Oct 2013 10:23:56 +0200, wannier-request wrote
> Send Wannier mailing list

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From jonathan.yates at materials.ox.ac.uk  Mon Oct 14 17:56:11 2013
From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates)
Date: Mon, 14 Oct 2013 15:56:11 +0000
Subject: [Wannier] Wannier90 v2.0.0 released
Message-ID: <78877D222077A642A4CFAB09BD0077E026EFF883@MBX10.ad.oak.ox.ac.uk>

Dear Wannier90 Users,

 Version 2.0.0 of Wannier90 is now available from www.wannier.org

 A summary of changes from v1.2 is given below. The change in major version number is due to the large amount of new functionality that has been added to the code for this release. In particular there are new parallel routines for computing properties in the wannier basis including; wannier projected dos, Boltzmann transport equation in the relaxation time approximation (Boltzwann) and Berry phase properties such as Berry Curvature, Anomalous Hall conductivity and orbital magnetisation. We hope that these routines will provide a good platform for the community to develop new functionality.

Finally, we wish to thank R. Sakuma who has made available the code used to generate symmetry-adapted wannier functions in Phys. Rev. B 87 235109 (2013). This can be downloaded from www.wannier.org Please note that this is a modified version of wannier90 v1.2, although we hope to fully integrate it to the main code in the near future.

 Jonathan Yates (on behalf of the Wannier90 developers)


* Added the new (parallel) postw90.x executable for calculations which use
  the MLWFs calculated by wannier90.x as an input.
* Added the following postw90.x modules:
  - dos
  - berry
  - kpath
  - kslice
  - BoltzWann
  - geninterp
* Added the w90chk2chk.x utility to convert the checkpoint file between
  the formatted/unformatted formats, to move it between different computers
  with different architectures
* Added the w90vdw utility to calculate van der Waals energies with MLWFs
* Added the w90pov utility to render ray-traced isosurfaces using POV-Ray
* Updated interface to PWscf v5.0 (including a minor bug fix to the 
  definition of the projection functions).
* Changed the internal format of the checkpoint file (not compatible anymore
  with v.1.2 and earlier)
* Enabled very general specification of spinor projections
* Generalized the definition of the supercell for real-space plotting of
  the Wannier functions: now the supercell size (wannier_plot_supercell)
  can be different along the three directions. Moreover, the home cell
  is left approximately at the center of the supercell, rather than near
  one of its edges.
* Now it is possible to provide both 'seedname' and 'seedname.win' on the 
  command line, both will work
* Tabs can now be present in the input file without problems
* A few bugfixes



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



From autieri at sa.infn.it  Tue Oct 15 10:57:06 2013
From: autieri at sa.infn.it (Carmine Autieri)
Date: Tue, 15 Oct 2013 10:57:06 +0200 (CEST)
Subject: [Wannier] layers polarization
In-Reply-To: <2025355964.1056292.1381827280669.JavaMail.root@sa.infn.it>
Message-ID: <659196643.1056320.1381827426283.JavaMail.root@sa.infn.it>

Dear all,

I am interested in the calculation of the layers polarization (Phys. Rev. Lett. 97, 107602 (2006)).
Is this theory implemented in wannier90? 

Thank you
Best
Carmine


From gangli.pku at gmail.com  Wed Oct 16 16:43:24 2013
From: gangli.pku at gmail.com (Gang Li)
Date: Wed, 16 Oct 2013 16:43:24 +0200
Subject: [Wannier] pw2wannier90 for QE5.03: missing argument
Message-ID: <CACcU02JSE0woti-hx558+pVp8zYxQArJxk_vfRbMh5tgBgbiyQ@mail.gmail.com>

Dear all

   I encountered one problem while compiling the latest interface of
wannier90 to quantum espresso:

pw2wannier90.f90(2820): error #6580: Name in only-list does not exist.
[IUNATSICWFC]

any suggestion to fix this?

thanks,
Gang
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From jonathan.yates at materials.ox.ac.uk  Wed Oct 16 17:38:25 2013
From: jonathan.yates at materials.ox.ac.uk (Jonathan Yates)
Date: Wed, 16 Oct 2013 15:38:25 +0000
Subject: [Wannier] pw2wannier90 for QE5.03: missing argument
In-Reply-To: <CACcU02JSE0woti-hx558+pVp8zYxQArJxk_vfRbMh5tgBgbiyQ@mail.gmail.com>
References: <CACcU02JSE0woti-hx558+pVp8zYxQArJxk_vfRbMh5tgBgbiyQ@mail.gmail.com>
Message-ID: <78877D222077A642A4CFAB09BD0077E026F1B17E@MBX10.ad.oak.ox.ac.uk>


On 16 Oct 2013, at 15:43, Gang Li wrote:

> Dear all
> 
>    I encountered one problem while compiling the latest interface of wannier90 to quantum espresso:
> 
> pw2wannier90.f90(2820): error #6580: Name in only-list does not exist.   [IUNATSICWFC]

The version of pw2wannier90.f90 supplied with v2.0 should be compatible with QE v5.0, 5.0.1, 5.0.2 and 5.0.3. In fact I just tried a fresh install of 5.0.3 and it was fine.

The variable IUNATSICWFC has been removed in the SVN version of pwscf - so perhaps you have an SVN copy, rather than an official release? We need to make a few small modifications and then we will put pw2wannier90.f90 into the QE SVN repository. (so when the next version of pwscf is released wannier will work 'out of the box')

 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 levuser at gmail.com  Wed Oct 16 19:29:50 2013
From: levuser at gmail.com (levuser at gmail.com)
Date: Wed, 16 Oct 2013 17:29:50 +0000
Subject: [Wannier] levuser@gmail.com has indicated you're a friend. Accept?
Message-ID: <0.0.2A4.8E4.1CECA95515609E2.2409@mail7.flipmailer.com>

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From levuser at gmail.com  Wed Oct 16 21:11:20 2013
From: levuser at gmail.com (levuser at gmail.com)
Date: Wed, 16 Oct 2013 19:11:20 +0000
Subject: [Wannier] levuser@gmail.com has indicated you're a friend. Accept?
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From rio10002 at gmail.com  Thu Oct 17 21:38:41 2013
From: rio10002 at gmail.com (satrio)
Date: Thu, 17 Oct 2013 15:38:41 -0400
Subject: [Wannier] Help for Hr Cutoff
Message-ID: <CAE=z7SpPCu_1EDZiAF7anNwroZU9zHhDf9jj8mmDhY10i_AoqA@mail.gmail.com>

Dear All

I need a help about how to use hr_cutoff. So basically, i tried to see the
effect of the cutoff value. But the plot result is really strange. It's not
affected by the cutoff that i used. I tried to plot in kx direction for
silicon.

The commands that i wrote are

restart = plot
bands_plot = true
hr_cutoff = 0.2
bands_plot_mode = cut
one_dim_axis = x
bands_plot_dim = 3
dist_cutoff_mode = three_dim

So i change several times the value of hr_cutoff. But the result is not
change and weird. Ive already specify the k path in kx direction.
Do you think there are some mistakes that i made here?

Thank You
Regards
Rio
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From rio10002 at gmail.com  Wed Oct 30 19:35:14 2013
From: rio10002 at gmail.com (satrio)
Date: Wed, 30 Oct 2013 14:35:14 -0400
Subject: [Wannier] Dissentanglement and Wannier Function Character
Message-ID: <CAE=z7Spu7PiTMN8mX8sgV8DYSCjdO2417-TkpHrhVOvS_LGeeA@mail.gmail.com>

Dear all

I have some questions about this progam Wannier90. First, Is there any
way to find the orbital character for the final Wannier functions that are
produced in the output? Or can we know the explicit form of Wannier
function? Example like summation formula of p orbital with s orbital. So
far as i know, it only can plot the wavefunction in XCrysden.

Second, Is it possible that we have trial function that is not in
definition of user guide?

Thank you

Regards
Rio
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From a.mostofi at imperial.ac.uk  Thu Oct 31 00:03:48 2013
From: a.mostofi at imperial.ac.uk (Arash Mostofi)
Date: Wed, 30 Oct 2013 23:03:48 +0000
Subject: [Wannier] Dissentanglement and Wannier Function Character
In-Reply-To: <CAE=z7Spu7PiTMN8mX8sgV8DYSCjdO2417-TkpHrhVOvS_LGeeA@mail.gmail.com>
References: <CAE=z7Spu7PiTMN8mX8sgV8DYSCjdO2417-TkpHrhVOvS_LGeeA@mail.gmail.com>
Message-ID: <52719054.9070505@imperial.ac.uk>

Dear Rio,

Regarding your first question, it is possible to glean some information 
about the character of the Wannier functions without explicitly plotting 
them. The idea is to consider projections of the Wannier functions onto 
simple trigonometric functions - the relative magnitude and sign of 
these integrals may enable you to determine the symmetry of the Wannier 
function. These integrals come for free once you've done the underlying 
electronic structure calculation in a plane-wave basis. With the PWscf 
interface to Wannier90, they can be written to a file by setting 
"write_unkg=.true." in the input file for pw2wannier90. More details can 
be found in the Appendix of the paper by Shelley et al: 
http://dx.doi.org/10.1016/j.cpc.2011.05.017 and in the Wannier90 User 
Guide (v2.0), Section 7.3.

Regarding your second question, not unless you add the code to the 
interface between Wannier90 and the underlying electronic structure code 
to calculate them. The PWscf interface only has the ones listed in the 
user guide. Developers of other codes may have added more.

Best wishes,

Arash

--
Dr Arash A Mostofi
Departments of Materials and Physics
Deputy Director, CDT on Theory and Simulation of Materials
Imperial College London, London SW7 2AZ, UK
+44 (0)207 594 8154 | www.cmth.ph.ic.ac.uk/people/a.mostofi

On 30/10/2013 18:35, satrio wrote:
> Dear all
> I have some questions about this progam Wannier90. First, Is there any
> way to find the orbital character for the final Wannier functions that
> are produced in the output? Or can we know the explicit form of Wannier
> function? Example like summation formula of p orbital with s orbital. So
> far as i know, it only can plot the wavefunction in XCrysden.
> Second, Is it possible that we have trial function that is not in
> definition of user guide?
> Thank you
> Regards
> Rio
>
>
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