Re: [Wannier] Abinit interface to Wannier90 code for spinor wave functions

[Giovanni Pizzi]

Hi,

I cannot comment on the specifics of the ABINIT interface. But note that the 
code, when run in library mode, ignores the value in the input (it should also 
print it in one of the outputs):

https://github.com/wannier-developers/wannier90/blob/a75344b646227c9d7f12d90af4a35a902e940dca/src/parameters.F90#L750

One needs to ensure that the library instead passes the spinors_loc variable 
from the interface fortran call.

Let me also mention that we merged last month a major refactor of the whole 
Wannier90 code, to make the library much more flexible. In the future it might 
be useful to ping the developers of the interface codes you use (if you want) 
so that they are aware of the new library mode and consider releasing a new 
interface with the new library (that will be released in the next few months 
with a new version of Wannier90). The main contact person for support on the 
library mode (who is one of those who did most of the work!) is Jerome Jackson 
at STFC.

Best,
Giovanni


On 9 Mar 2024, at 14:44, Shima Sharifi (Tyndall)  
wrote:

Dear all,
I am currently working on generating MLWFs for spinor-values wave functions 
using Wannier90 interfaced with ABINIT ver9.10.5. The version of Wannier90 
utilized as a library during the installation of Abinit is 2.0.1.1, which is 
compatible with spinor wave functions.

However, upon running the calculation, despite setting the variable "nspinor=2" 
in the Abinit input file and specifying "spinors=.true." in the Wannier90 input 
file, I encountered an error indicating that "param_get_projections: spin is 
defined but spinors=.false."

It appears that the interface program is disregarding the specified value of 
"spinors" in the Wannier90 input and defaulting to a case without spin-orbit 
coupling calculation. On the other hand, it recognized that the spin is defined 
by reading the projection section of Wannier90 input file.

Does this imply that the Abinit interface to Wannier90 code currently only 
supports cases without SOC?

Best regards,
Shima

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Re: [Wannier] how to find out the projection used in SCDM method

[Giovanni Pizzi]

Dear Bhargab Kakati,

One option to see the starting point of the Wannierisation, that is the initial 
projections orthonormalized, is to set num_iter = 0 and run the Wannierisation: 
with num_iter = 0 you do not do any Wannierisation step, essentially you do a 
projection-only Wannier-functions; then, just plot the WFs and check the result.

As a note, remember that in most (all?) cases, the projections won't be 
intuitive s, p, d-like orbitals.

Hope this helps.

Best,
Giovanni


> On 29 Feb 2024, at 12:39, Bhargab Kakati  wrote:
> 
> Dear all,
> 
> I used SCDM method in my calculation and I was wandering if there's any way 
> we can fin out the projections used in the wannierization process. Any 
> suggestion will be highly appreciated.
> 
> Thank you.
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Re: [Wannier] SCDM-k method and centering of WFs

[Giovanni Pizzi]

Dear Marco,
unfortunately it's not so easy to combine SCDM with symmetries. This is a topic 
of research, and we are working for instance on other approaches that do not 
use SCDM to get automatically WFs that are instead atom-centred with symmetries.

If you are working on specific systems, the only suggestion is to try to look 
better into the systems and get WFs in the "usual" way, specifying initial 
projections close to what you want to get.
You can also use the SLWF (selectively-localised WFs) and the SAWF 
(symmetry-adapted) routines, implemented in W90, to see if they help for your 
case (look also at the tutorials http://www.wannier.org/support/, e.g. #21, #22 
and #26).

For the delocalised orbitals, it's hard to say without knowing more details on 
the system (and even there, it requires careful testing in multiple 
configurations). But one general comment (not sure it applies to you) is that 
rather than removing the problematic ones, you might want to check if adding a 
few more bands helps, or if "playing" with the disentanglement windows helps 
(also, to check: is the disentanglement converged? Are the WFs real-values if 
you plot them in real space?)

Hope this helps.
Best,
Giovanni

--
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On 7 Nov 2022, at 11:23, Marco Marino 
mailto:marco.mari...@unimi.it>> wrote:

Dear Wannier90 group,

I am working with NiO and Cr2O3 bulk systems, in their antiferromagnetic phase. 
Using the SCDM-k method and considering only the valence bands (from a DFT 
collinear calculation), I obtain WFs sufficiently localized (apart from a few 
WFs totally delocalized (3 with respect to 138 wannier functions), which 
reproduce quite well the electronic band structure (apart from those few bands 
associated with the totally delocalized WFs).

The problem is that these WFs are not completely centered on the atoms. How can 
I center my WFs? How can I decompose my WFs into angular components, in order 
to be able to do a wannier calculation with the projectors so obtained? 
Moreover, how can I solve the problem of the few delocalized WFs (removing them 
makes the results worse)?

thank you for your willingness,
best regards,
marco marino
phd student
University of Milan





La Statale per il futuro
Salute, transizione digitale, sostenibilità
Il tuo 5xmille ai nuovi progetti di ricerca dell’Università degli Studi di 
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Codice fiscale: 80012650158
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Re: [Wannier] parallel computing for plotting MLWFs

[Giovanni Pizzi]

Dear Shima,

Indeed, the plotting routines have not been parallelized yet so they will run 
only in serial.
Parallelizing them should be quite straightforward, so anyone willing to 
prepare a pull request is welcome to do so on the GitHub 
page<https://github.com/wannier-developers/wannier90>.

Regarding the interpolation of the band structure, you could use the 
`geninterp` module of postw90.x is instead parallelized - you can find 
instructions on how to use it in the documentation 
(http://www.wannier.org/support/, User Guide, page 159.
For parallel efficiency, I suggest you investigate (check the timings) of the 
use of geninterp_single_file = .false. vs the default geninterp_single_file = 
.true. (described in the documentation) that will give important performance 
improvements for small systems (but for a big system it might be less relevant).

Best,
Giovanni Pizzi

P.S.: don't forget to sign your posts with your full name and affiliation

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EPFL and NCCR MARVEL
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On 2 May 2021, at 11:21, Shima Sharifi 
mailto:shima.shar...@tyndall.ie>> wrote:

Dear Wannier90 users,
I was reading the recent paper by authors of Wannier90 code: "Wannier90 as a 
community code: new features and applications". In section 3.4 they talk about 
the parallelisation scheme for the calculation of MLWFs using MPI (Minimisation 
of the spread and so on).
For the calculation that I am doing using this code (with the interface from 
quantum Espresso 6.4.1) , these steps are quite fast. Actually, the most time 
consuming part is plotting MLWFs over a fine real space grid. I need to 
calculate MLWFs within large supercells made of 10*10*10 primitive unit cells. 
Then, I'm interested in running parallel calculation for this part, or 
interpolating the band structure or plotting Fermi surfaces.
Then, my question is that if Wannier90 v. 3.0.0 has this ability to be run in 
parallel in order to calculate these properties,
Or at the moment, one is just able to do disentanglement and Wannierisation 
processes with MPI?

Thank you in advance.

Regards,
Shima
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Re: [Wannier] Complex values in seedname.mmn from real VASP wavefunction

[Giovanni Pizzi]

Dear Espen,

thanks for your message.
First of all I'd like to remind the policy of this mailing list of signing 
posts with the official affiliation.

Then, to your issue: while having complex values in the Mmn overlaps might seem 
surprising at first, this is correct.
If you are at Gamma only, your 'first-neighbour k-points' in k-space (needed to 
compute gradients in k-space, a key part of the Wannierisation algorithm), are 
"Gamma points" in neighbouring (reciprocal) cells.

More precisely, the line
11001
means exactly that the next 4x4 block is the overlap of the (periodic part of 
the) wave functions at the Gamma point (nk=1, first integer) with the point 
(k+b) obtained as starting the Gamma point (nk=1, second integer) and shifting 
it by (0, 0, 1) in units of reciprocal vectors (last three integers). So in 
this example "b" is the third reciprocal vector "b_3".

Now, while at Gamma you can choose an appropriate phase to get real u_nk (which 
are periodic in real space), this phase can indeed be chosen *locally* in 
reciprocal space, but not globally.
That is to say, there is a non-zero phase between u_Gamma and u_b3.

I think it is instructive to read sections IV.C.3 and IV.C.4 of the 
Marzari-Vanderbilt paper (PRB 1997), which has comments that are much closely 
related to this (for the related case of functions that can be chosen real 
under inversion symmetry).
This is also commented in footnote 4 of the review of Marzari et al, Rev. Mod. 
Phys.. 84 (2012) and discussed in detail in section II.F.2 of the same review.

If you prefer to look into the code - I don't know about VASP, but for Quantum 
ESPRESSO you can check search for `zerophase` in the source code of 
pw2wannier90 (e.g. here 
https://gitlab.com/QEF/q-e/blob/86749ba053539de4785264c98fdc7f3ffdbb2b0d/PP/src/pw2wannier90.f90)
 to see when and how this phase is introduced (indeed, when the at least one of 
the last three numbers of the line discussed above is non-zero).

I hope this explanation clarifies a bit the issue.

Best,

Giovanni

--
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EPFL and NCCR MARVEL
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http://nccr-marvel.ch/en/people/profile/giovanni-pizzi


On 27 Nov 2020, at 13:00, Espen Sagvolden 
mailto:espen.sagvol...@sintef.no>> wrote:

Dear all,

Seemingly paradoxical values arise in the seedname.mmn files from wannier_setup 
with VASP: They seem to be complex-valued (alternating between purely real and 
purely imaginary), even when the underlying VASP wavefunction is real 
(gamma-point computation). Since the seedname.mmn entries should only be 
orbital overlaps, this troubles me, but I'm new to Wannier90 and there may be 
something I don't know about the overlap integrals.

Here is an excerpt from the seedname.mmn file for a subspace of the four lowest 
orbitals from a gamma-point VASP run with real orbitals:

File generated by VASP: unknown system
   4   1   4
11001
0.946270648002   -0.
   -0.0006958215460.
   -0.   -0.00278197
   -0.   -0.00195965
   -0.0006958215460.
   -0.944393397524   -0.
   -0.0.0281
   -0.   -0.1135
   -0.   -0.00278197
   -0.0.0281
0.9623942622590.
0.0265   -0.
   -0.   -0.00195965
   -0.   -0.1135
0.0265   -0.
0.9623942589750.
1111   -1
0.8103761496990.
   -0.0005963287210.
0.0.498834776389
0.0.103890215607
   -0.0005963287210.
   -0.8111642040170.
   -0.0.000205733055
   -0.0.42846592
0.0.498834776389
   -0.0.000205733055
0.648824351005   -0.
   -0.046098789574   -0.
0.0.103890215607
   -0.0.42846592
   -0.046098789574   -0.
0.860569485467   -0.
1110   -1
0.810376181990   -0.
   -0.000596328947   -0.
0.0.159445743764
0.0.483948506733
   -0.000596328947   -0.
   -0.811164196521   -0.
   -0.0.65759196
   -0.0.000199593417
0.0.159445743764
   -0.0.65759196
0.847555958915   -0.
   -0.068638884681   -0.
0.0.483948506733
   -0.0.000199593417
   -0.068638884681   -0.
0.661838058801   -0.
11011
0.810376169686   -0.
   -0.0005963281680.
0.0.339388794748
   -0. 

Re: [Wannier] Recreating radial wavefunctions from pw2wannier90 or wannier90 outputs

[Giovanni Pizzi]

Dear Erica,
I am not sure if I'm misunderstanding your question, anyway here are some 
answers based on what I think you might need:

- the initial projections are generated by the interface code (e.g. 
pw2wannier90) so you should try to have them printed there. Anyway, their 
analytical form is tabulated in the user guide so you should be able to create 
their numerical representation on a grid yourself.

- Those, anyway, are just the starting point of the Wannierisation. The code 
computes the WFs and then uses the minimised U matrices (unitary transforms), 
and the UNK files from the ab-initio code (periodic part of the Kohn-Sham 
wavefunctions) to plot the final WFs in real space (there is a flag in the 
input to have W90 print the xsf files, or also in cube format). The flags, and 
the detailed specification of the format of the various files, is explained in 
detail in the Wannier90 user guide.

- if what you want is just the numerical data in the XSF (so, the Wannier 
functions in real space), you can just open and parse the XSF file, the numbers 
are in there (the XSF format is well documented, just google for 'xsf 
specification'). There might even be codes around that already parse it, 
probably.

Best,
Giovanni

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

--
Giovanni Pizzi
Theory and Simulation of Materials and MARVEL, EPFL
http://people.epfl.ch/giovanni.pizzi
http://nccr-marvel.ch/en/people/profile/giovanni-pizzi

On 28 Oct 2020, at 19:40, Erica Kotta mailto:eck...@nyu.edu>> 
wrote:

Hello,

I have a Wannier90 output where I have projected a group of isolated bands onto 
a set of p- and d-orbitals.

Is it possible to see the radial wave functions used by the Wannier90 software? 
I see in the User Guide tables 3.1-3.3 they list the angular functions and then 
a possible choice of radial functions, but is there a way to see the actual 
form that was used, that represents the actual basis? Does it entail outputting 
the Umn matrices, and using the UNK...NC to recreate them as in Equations 1&2 
in Wu's paper 
(https://www.labxing.com/files/lab_data/496-1580695056-bV5W1jk8.pdf)?
(And if this is the case, how do you open/read these UNK...NC files?)

Basically, I was wondering if I could get some set of numerical data 
representing what we see when we plot the xsf files in xcrysden.

Thank you very much in advance,
Erica
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Re: [Wannier] Problem reading *.mmn file

[Giovanni Pizzi]

Hi,
The error is raised in this file
https://github.com/wannier-developers/wannier90/blob/2ab7a904e8d9b8d8eb771ad4ce6fe2d415c895b0/src/overlap.F90
(Error “103”).
This is due to a problem in the file content.

Could you open the file and check if you notice something strange, e.g. * 
instead of numbers, or NaN, or other unexpected values?
I fear this might be the problem, and if this is the case, one needs to 
understand where this happened, fix the pw2wannier90 code and then re-run the 
code… (but maybe just the Mmn if the problem appeared only in the Mmn file?)

Or maybe you will spot some other issue.

Best,
Giovanni

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Theory and Simulation of Materials and MARVEL, EPFL
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On 26 May 2020, at 09:05, Juan Jose Melendez Martinez 
mailto:melen...@unex.es>> wrote:

Dear all

I am using Wannier90 to study a heterostructure made upon InSb and Ge. The 
system is large, and I need 848 wannier functions. I am facing a quite weird 
issue. After the DFT step with QE (successful, nothing strange there), I 
generated the *nnkp file (no problem) and then run pw2wannier.x to get the amn 
and mmn files. Again, nothing apparently strange there. But upon launching 
wannier90.x I get the error

Error: Problem reading input file si_insb_111_2-10.mmn

I have not been able to find any piece of info for this error message. It 
usually means that it is either very simple or very tough to solve. I cross my 
fingers for the former, since calculating the projections took more than 4 days.

I am attaching the *win and *wout files, just in case they may help.

Thanks a lot in advance

Juanjo

Juan J. Meléndez
Department of Physics
University of Extremadura
Avda. de Elvas, s/n 06006
Badajoz 
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[Wannier] Videos of the "Virtual Edition" Wannier90 School online on Materials Cloud Learn

[Giovanni Pizzi]

Dear all,

We are glad to inform you that the video recordings of the first "Virtual 
Edition” of the Wannier90 School [1] are now all available in the Learn section 
of Materials Cloud, at this link:

https://www.materialscloud.org/learn/sections/C8ad91/wannier90-v3-0-school-virtual-edition-2020

Beside the videos, the Learn section also includes:
- the slides of the presentations;
- the list of all questions asked during the presentations, with detailed 
replies by the speakers;
- all tutorial hands-on materials.

In particular, the tutorial was run on the "Quantum Mobile" Virtual 
Machine<https://www.materialscloud.org/work/quantum-mobile> that made it very 
easy for all 30+ participants to quickly get started with the various codes 
presented (Wannier90, WannierTools, AiiDA, EPW, ...) with almost zero setup 
time.

As an additional benefit, anybody can download again the Quantum Mobile [2] and 
run the same tutorials, even if they could not attend the event.

We believe that these virtual events can be very effective and can become a 
model for the future, even when travel restrictions will be lifted, with the 
additional advantages of allowing a broader and more diverse audience, and of 
reducing our carbon footprint, under the slogan "less carbon, more silicon"!

Best regards,
Giovanni Pizzi, on behalf of all event organisers

[1] http://www.wannier.org/events/school-2020-virtual-edition/
[2] The tutorial was run using version 20.03.1: 
https://github.com/marvel-nccr/quantum-mobile/releases/tag/20.03.1

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Re: [Wannier] Unit of velocities in geninterp

[Giovanni Pizzi]

Dear Vahid,
Thanks for noting this.

Note that the units of k-points in the output are 1/ang and not 2pi/ang.
Accordingly, the derivatives are in units of (eV * ang), you can verify 
checking with finite differences in a point with non-zero derivatives.

This will be included in the documentation in the next release.
https://github.com/wannier-developers/wannier90/pull/325

Best,
Giovanni


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http://nccr-marvel.ch/en/people/profile/giovanni-pizzi

On 19 Mar 2020, at 11:28, Vahid Askarpour 
mailto:vh261...@dal.ca>> wrote:

Dear Wannier90 Users,

I have posted this on QE forum but the Wannier90 forum may be more appropriate.

In the postw90 folder, in file boltzwann.F90, it says,

\param deleig_karray with the band derivatives at the given k point
 (in eV * angstrom / (2pi) as internally given by 
the code)

So deleig_k is the electron velocity at a given k-point. When we set

geninterp=.true.
geninterp_alsofirstder=.true.

the postw90 output includes k-point coordinates (2pi/ang), energies (eV) and 
velocities (no units). Even the Wannier90 User guide does not specify the unit 
for velocities. Am I correct in assuming that these velocities are in 
eV*angstrom/(2pi)?

Thank you,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
Canada
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[Wannier] Wannier90 v3.1 released (and new paper citation)

[Giovanni Pizzi]

Dear all,

Today we have released v3.1 of Wannier90.
The code includes a number of new features together with some improvements and 
bug fixes.
You can download the code here: http://www.wannier.org/download/ where you will 
also find a change 
log<https://github.com/wannier-developers/wannier90/blob/master/CHANGELOG.md> 
with a list of all changes.

There are no backward-incompatible changes with respect to v3.1, therefore we 
suggest that you switch to this more robust version of the code.

We also use this occasion to remind you that there is a new publication for the 
v3.x series of Wannier90.
We kindly ask you to cite this newer version if you are using v3.x of the code 
(bibtex also attached to this email):

G. Pizzi, V. Vitale, R. Arita, S. Blügel, F. Freimuth, G. Géranton, M. 
Gibertini, D. Gresch, C. Johnson, T.Koretsune, J. Ibañez-Azpiroz, H. Lee, J. M. 
Lihm, D. Marchand, A. Marrazzo, Y. Mokrousov, J. I. Mustafa, Y. Nohara, Y. 
Nomura, L. Paulatto, S. Poncé, T. Ponweiser, J. Qiao, F. Thöle, S. S. Tsirkin, 
M. Wierzbowska, N. Marzari, D. Vanderbilt, I. Souza, A. A. Mostofi, and J. R. 
Yates, Wannier90 as a community code: new features and applications, J. Phys. 
Cond. Matt. 32, 165902 (2020); 
doi:10.1088/1361-648X/ab51ff<http://doi.org/10.1088/1361-648X/ab51ff>


On the home page of the website (http://www.wannier.org) you will also find the 
instructions on which paper to cite if you are using older versions of Wannier 
(v2.x or v1.x), as well as bibtex files for the corresponding publications.

Best regards,

Giovanni Pizzi, on behalf of the Wannier Developers Group




Pizzi2020.bib
Description: Pizzi2020.bib
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[Wannier] New paper for Wannier 3.0 published

[Giovanni Pizzi]

Dear all,
We are very happy to announce that the paper describing v3.0 of the Wannier90 
code, in particular how it transitioned to a community code and all new 
features, has now been published. You can find the full reference below.

We'd appreciate if you could cite this paper in all publications resulting from 
your use of Wannier90.


Here is the full reference:

G. Pizzi, V. Vitale, R. Arita, S. Blügel, F. Freimuth, G. Géranton, M. 
Gibertini, D. Gresch, C. Johnson, T.Koretsune, J. Ibañez-Azpiroz, H. Lee, J. M. 
Lihm, D. Marchand, A. Marrazzo, Y. Mokrousov, J. I. Mustafa, Y. Nohara, Y. 
Nomura, L. Paulatto, S. Poncé, T. Ponweiser, J. Qiao, F. Thöle, S. S. Tsirkin, 
M. Wierzbowska, N. Marzari, D. Vanderbilt, I. Souza, A. A. Mostofi, and J. R. 
Yates, Wannier90 as a community code: new features and applications, J. Phys. 
Cond. Matt. 32, 165902 (2020); 
doi:10.1088/1361-648X/ab51ff<http://doi.org/10.1088/1361-648X/ab51ff>


Happy Wannierisation,

Giovanni Pizzi, on behalf of all co-authors


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Re: [Wannier] Problems with SPN formatted and gw2wannier.py

[Giovanni Pizzi]

Dear Marten,
Thanks a lot.
I’ve opened an issue to keep track of this problem and its solution

https://github.com/wannier-developers/wannier90/issues/293

Just one question - which version of the code did you use? Could you report 
directly in the issue?

Thanks,
Giovanni

--
Giovanni Pizzi
Theory and Simulation of Materials and MARVEL, EPFL
http://people.epfl.ch/giovanni.pizzi
http://nccr-marvel.ch/en/people/profile/giovanni-pizzi


On 26 Sep 2019, at 12:36, Marten Richter 
mailto:marten.rich...@tu-berlin.de>> wrote:

Dear Wannier90 list,

for some reasons, I tried to use gw stuff from yambo with wannier and I
also needed spins.
I need to use the spn formatted option, since I am too stupid (or lazy)
to install the python package for FortranFile on the cluster.
So I tried to run gw2wannier90.py from the utility folder using spn
output with spn_formatted.

I ran into several issues and I am really wondering, if the spn
formatted output was tested.
Anyway I made a patch and I would be glad, if someone can look over it
(who has reference data for the unformatted option for testing)
and could integrate it.
(Special care necessary, since I can write in several programming
languages but not in python and I do not have really much data to check
the correct behaviour).
I hope, that this is the right mailing list.

Regards,

Marten Richter

--

Dr. Marten Richter
Institut für Theoretische Physik
Technische Universität Berlin
Hardenbergstr. 36 Sekr. EW 7-1
D-10623 Berlin
Germany

email: marten.rich...@tu-berlin.de<mailto:marten.rich...@tu-berlin.de>
Tel: +49-30-314-24858 (office)
Fax: +49-30-314-21130
http://www.itp.TU-Berlin.DE/knorr/



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Re: [Wannier] Segmentation fault in postw90.x

[Giovanni Pizzi]

Thanks for the report!
I just created a PR to fix this: 
https://github.com/wannier-developers/wannier90/pull/290

If all tests pass (as they should) this will get merged and be available in the 
next minor release of W90.

Thanks,
Giovanni

--
Giovanni Pizzi
Theory and Simulation of Materials and MARVEL, EPFL
http://people.epfl.ch/giovanni.pizzi
http://nccr-marvel.ch/en/people/profile/giovanni-pizzi

On 12 Sep 2019, at 11:38, Nicolas Tancogne-Dejean 
mailto:nicolas.tancogne-dej...@mpsd.mpg.de>>
 wrote:

Dear developers,

I am starting to use Wannier90 and ran into a segmentation fault problem.
After looking at the code, it is clear what is happening.

In kslice.F90, the code tries to use an array before it gets allocated.

The faulty line  is

bnddataunit(n) = io_file_unit()

It is interesting to note that bnddataunit seems to not be used in the code.

Best regards,
Nicolas
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