Re: [Wien] Volume optimization and Eloss function.

[Gavin Abo]

If the structure is still hexagonal after the substitution, the starting 
point could be section "5.3 Structure optimization" on lattice parameter 
optimization starting on page 87 in the WIEN2k 23.1 (or 23.2) usersguide 
[1].


There you should see that you may select between two different packages.

If using *optimize*, there is:

[5] VARY A and C (2D-case) (tetragonal or hexagonal lattice)

Or if using *optimize_abc_lapw*, there is:

optimize_abc -t 2

After that, if the structure contains any free positions for atomic 
position optimization, then there is section "5.3.2 Minimization of 
internal parameters" on page 91 of the usersguide [1].


Yes, case.eloss is for the loss function [2].  On slide 9 in [3], it 
looks to be showing that case.epsilon contains the real and imaginary 
parts for the complex dielectric tensor and case.sigmak contains the 
real and imaginary parts for the optical conductivity.


[1] 
http://www.wien2k.at/reg_user/textbooks/usersguide.pdfhttp://www.wien2k.at/reg_user/textbooks/usersguide.pdf
[2] Slide 22: 
http://www.wien2k.at/events/ws2006/Optics_Vienna_April_2006.pdf
[3] 
http://www.wien2k.at/reg_user/textbooks/WIEN2k_lecture-notes_2013/optic_handout.pdf



On 8/17/2023 11:23 AM, Pranjal Nandi wrote:


Dear All,

I have an issue with 2 different parts (not related to each other). 
They are as follows.


 1. I am having a hard time in getting a hcp structure of HfO0.7 (or
Hf605 which is close to 0.7). Therefore, what I have done is that
I have downloaded the hcp structure of HfPo and substituted the Po
with Oxygen.

Now, I want to do the structural and volumetric relaxation so that
I have the stable relaxed structure of HfO0.7. I did read the
guidebook but I need guidance on what should be the correct order
of optimisation (I am lost as I can’t understand from which
optimisation I should start).

 2. In the eloss programme, which part of the function does the eloss,
epsilon and sigmak correspond to ? I guess eloss = energy loss
function, epsilon = real part of the dielectric function , sigmaK
= imaginary part of the dielectric function. Am I right?

Looking forward to your kind guidance.

Thank you.

With warm regards,

Pranjal



Aquest missatge, i els fitxers adjunts que hi pugui haver, pot 
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[Wien] Volume optimization and Eloss function.

[Pranjal Nandi]

Dear All,

I have an issue with 2 different parts (not related to each other). They are as 
follows.


  1.  I am having a hard time in getting a hcp structure of HfO0.7 (or Hf605 
which is close to 0.7). Therefore, what I have done is that I have downloaded 
the hcp structure of HfPo and substituted the Po with Oxygen.

Now, I want to do the structural and volumetric relaxation so that I have the 
stable relaxed structure of HfO0.7. I did read the guidebook but I need 
guidance on what should be the correct order of optimisation (I am lost as I 
can’t understand from which optimisation I should start).

  2.  In the eloss programme, which part of the function does the eloss, 
epsilon and sigmak correspond to ? I guess eloss = energy loss function, 
epsilon = real part of the dielectric function , sigmaK = imaginary part of the 
dielectric function. Am I right?

Looking forward to your kind guidance.

Thank you.

With warm regards,
Pranjal





Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir 
informacio confidencial o protegida legalment i s’adreca exclusivament a la 
persona o entitat destinataria. Si no consteu com a destinatari final o no 
teniu l’encarrec de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, 
modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si l’heu 
rebut per error, informeu-ne el remitent i elimineu del sistema tant el 
missatge com els fitxers adjunts que hi pugui haver.

Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener 
informacion confidencial o legalmente protegida y esta exclusivamente dirigido 
a la persona o entidad destinataria. Si usted no consta como destinatario final 
ni es la persona encargada de recibirlo, no esta autorizado a leerlo, 
retenerlo, modificarlo, distribuirlo o copiarlo, ni a revelar su contenido. Si 
lo ha recibido por error, informe de ello al remitente y elimine del sistema 
tanto el mensaje como los ficheros adjuntos que pueda contener.

This email message and any attachments it carries may contain confidential or 
legally protected material and are intended solely for the individual or 
organization to whom they are addressed. If you are not the intended recipient 
of this message or the person responsible for processing it, then you are not 
authorized to read, save, modify, send, copy or disclose any part of it. If you 
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Re: [Wien] SOC value \zeta

[Samolyuk, German D. via Wien]

Gerhard,

I wanted to know , i.e. part added to the hamiltonian 
resulting in eigenvalues and eigenvectors in case of added SOC and calculated 
using basis of wf obtained in no SOC case. The <(\sigma * l)> part I can 
calculate from density matrix output.

Gavin,

Thank you, the references help, but I'd rather don't hack the code 🙂.

Thank you,

German


Dr. German D Samolyuk
Materials Theory Group
Materials Science & Technology Division
Oak Ridge National Laboratory
Post Office Box 2008
Oak Ridge, TN 37831-6138
(865) 241-5394
(865) 241-3650 (FAX)

From: Wien  on behalf of Fecher, 
Gerhard 
Sent: Thursday, August 17, 2023 2:23 AM
To: A Mailing list for WIEN2k users 
Subject: [EXTERNAL] Re: [Wien] SOC value \zeta

I don't understand the question,
what do you like to know, \zeta (proportional to 1/r dV/dr) for each atom or 
the orbital moment (m_l) for each atom ?

The r dependence tells you already that there is no single value for 'zeta = 
zeta(r)'
SO is calculated directly from dV/dr which is not printed somewhere, however 
for a pure Coulomb potential (Z/r) it depends on the ordinal number Z of the 
atom,
This explains why the spin orbit interaction is stronger for 'heavier' atoms.
|1/r dV/dr| becomes large in the vicinity of the nucleus (infinity at r=0) for 
all atoms.
This explains why the spin-orbit splitting is large for core level (the larger 
the closer they are (in average) to the nucleus) and small for semi-core or 
valence level, as these electrons are in average farer away from the nucleus.

Check the manual how to have the orbital moments printed.

Ciao
Gerhard

DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
"I think the problem, to be quite honest with you,
is that you have never actually known what the question is."


Dr. Gerhard H. Fecher
Institut of Physics
Johannes Gutenberg - University
55099 Mainz

Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Samolyuk, 
German D. via Wien [wien@zeus.theochem.tuwien.ac.at]
Gesendet: Mittwoch, 16. August 2023 23:20
An: wien@zeus.theochem.tuwien.ac.at
Cc: Samolyuk, German D.
Betreff: [Wien] SOC value \zeta

Dear colleagues,

I'm running wien2k version WIEN2K_19_LI on linux cluster. The goal is to 
analyze magnetic anisotropy energy in YCo_5 intermetallic.

As it was explained in few presentation discussing SOC implementation in wien2K 
it's added in following form

\zeta ({\vec \sigma}{\vec l}), where \zeta = 1/(2Mc^2) 1/r^2 dV/dr.

Question: is it possible to output value \zeta for each atom, orbital moment?

I cant find it in output files and was not able to find following  discussion 
in archive.

Thank you,

German

Dr. German D Samolyuk
Materials Theory Group
Materials Science & Technology Division
Oak Ridge National Laboratory
Post Office Box 2008
Oak Ridge, TN 37831-6138
(865) 241-5394
(865) 241-3650 (FAX)
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Re: [Wien] Plotting the radial part of wave function

[Peter Blaha]

In these posts the content of the almblm and radwf files is described.

There is no tool for plotting this. You have to write your own program 
which reads these files, and creates a file suitable for plotting.


First, you need to understand the APW method. All our radial functions 
are given ONLY inside RMT, outside we have plane waves, thus you can 
never plot a radial wf. up to 40 bohr as given in the example you 
mentioned (I don't know from where this is and what "2p, H@Uc" means, 
but this is an unrealistic H-2p wf.)


Your "thinking" of an atomic radial wf. comes from a quantummechanics of 
pure atoms, but is molecules and solids you do not have ONE radial wf 
for a d-orbital, but this is energy dependent (a lower orbital with 3d 
character will have a different radial wf. than an orbital at a higher 
energy, and all (most) orbitals are mixtures of atomic basis functions 
(hybridized).


Anyway, a good approximation to what you want to plot can probably be 
done using lapw7 (real part). But as input you cannot select an atom and 
l, but can select a k-point and a certain bandnumber (eigenvalue).


I suggest you take only Gamma, and then plot the relevant wf for the 3d 
bands. But plot is


PS: The real part of the wf is NOT the radial wf (which makes no sense 
in a solid), but i) multiplied with the corresponding Y_lm and ii) a 
linear combination of all our radial basis functions and iii) in most 
cases a linear combination of several l,m values.



Am 17.08.2023 um 12:46 schrieb reyhaneh ebrahimi:

Dear Prof. Blaha, Thank you very much for your valuable reply. I
searched the relevant issues in the mailing list. I found issues for
example listed in
"https://www.mail-archive.com/search?q=radwf&l=wien%40zeus.theochem.tuwien.ac.at";.
Unfortunately, I didn't find an issue relevant to this subject on how
can I plot the radial wave function (u_l(e1,r)) with respect to r for
a special orbital of a special atom in my compound for example
d-orbital of Mn in MnO. In other words, I would like to plot the graph
such as the "example-radwf" image that I uploaded in
"https://www.mediafire.com/file/3tqo7g10kq291jq/example-radwf.jpg/file";
but for my compound. I followed the userguide of WIEN2k and after
using the "alm" switch in lapw2,the case.radwf and case.almblm files
are generated which I uploaded in
"https://www.mediafire.com/file/uflq7f338bdhwrp/MnO-input-output-files.zip/file";.
But I don't know, using the case.radwf file, how (or with which
command) I can plot the radial wave function with respect to r for
example for s, p, and d orbitals of Mn and s,p orbitals of Oxygen
separately in one graph as the "example-radwf" image and how I can
change the format of this file to the files which are compatible to
plot with xcrysden or Gnuplot?

I searched also the mailing-list to find how I can plot the radial
part of the wave function and found issues listed in
"https://www.mail-archive.com/search?l=wien%40zeus.theochem.tuwien.ac.at&q=plot+wave+function+with+lapw7&submit.x=16&submit.y=18";.
Whence, I followed the userguide for lapw7 and also generate the gpl
format of case.psink file using the
"https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13642.html";
issue. Then, I can plot the real part of the wavefunction (R_nl(r)) in
two dimensional using the "MnO.in7" that I uploaded in
"https://www.mediafire.com/file/uflq7f338bdhwrp/MnO-input-output-files.zip/file
". I attached my output graph using Gnuplot program for this
calculation with the name "MnO-Rnl" in
"https://www.mediafire.com/file/uflq7f338bdhwrp/MnO-input-output-files.zip/file";.
Is the real part of the wave function the same as the radial part of
the wave function in wien2k? If yes, how we can specify the orbital
and atom in my input files to have a figure like the figure that I
uploaded in 
https://www.mediafire.com/file/3tqo7g10kq291jq/example-radwf.jpg/file
?

I also try to plot the 1D of the real part of wave function using the
section  8.16 of the userguide and only replace the 2D with 1D in the
first line of the case.in7, the "MnO-1D.in7" file  in
"https://www.mediafire.com/file/uflq7f338bdhwrp/MnO-input-output-files.zip/file";.
However, after execute the " x lapw7" I have the  following error:
ERROR: UNKNOWN POST-PROCESSING TOOL
0.056u 0.153s 0:00.30 66.6% 0+0k 2072+32io 12pf+0w
Would you please help me to solve this error, too?


Sincerely yours,
Reyhaneh Ebrahimi

On Wed, Aug 16, 2023 at 11:15 AM Peter Blaha  wrote:

Please search the mailing list.
There were some previous post about the format of these files.
You certainly cannot plot them in xmgrace, as it does not contain x-y data.

Am 15.08.2023 um 00:02 schrieb reyhaneh ebrahimi:

Dear WIEN2k users
I'm a WIEN2k user, version 23.2.
I would like to plot the radial part of the wave function (u_l(r, E_l))
for my compound in 2D and 1D. To this end, I followed the user guide of
WIEN2k with version 23.2. Now, for 2D, I have the case.radwf and
case.almblm files, I attached my input an

Re: [Wien] Plotting the radial part of wave function

[reyhaneh ebrahimi]

Dear Prof. Blaha, Thank you very much for your valuable reply. I
searched the relevant issues in the mailing list. I found issues for
example listed in
"https://www.mail-archive.com/search?q=radwf&l=wien%40zeus.theochem.tuwien.ac.at";.
Unfortunately, I didn't find an issue relevant to this subject on how
can I plot the radial wave function (u_l(e1,r)) with respect to r for
a special orbital of a special atom in my compound for example
d-orbital of Mn in MnO. In other words, I would like to plot the graph
such as the "example-radwf" image that I uploaded in
"https://www.mediafire.com/file/3tqo7g10kq291jq/example-radwf.jpg/file";
but for my compound. I followed the userguide of WIEN2k and after
using the "alm" switch in lapw2,the case.radwf and case.almblm files
are generated which I uploaded in
"https://www.mediafire.com/file/uflq7f338bdhwrp/MnO-input-output-files.zip/file";.
But I don't know, using the case.radwf file, how (or with which
command) I can plot the radial wave function with respect to r for
example for s, p, and d orbitals of Mn and s,p orbitals of Oxygen
separately in one graph as the "example-radwf" image and how I can
change the format of this file to the files which are compatible to
plot with xcrysden or Gnuplot?

I searched also the mailing-list to find how I can plot the radial
part of the wave function and found issues listed in
"https://www.mail-archive.com/search?l=wien%40zeus.theochem.tuwien.ac.at&q=plot+wave+function+with+lapw7&submit.x=16&submit.y=18";.
Whence, I followed the userguide for lapw7 and also generate the gpl
format of case.psink file using the
"https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13642.html";
issue. Then, I can plot the real part of the wavefunction (R_nl(r)) in
two dimensional using the "MnO.in7" that I uploaded in
"https://www.mediafire.com/file/uflq7f338bdhwrp/MnO-input-output-files.zip/file
". I attached my output graph using Gnuplot program for this
calculation with the name "MnO-Rnl" in
"https://www.mediafire.com/file/uflq7f338bdhwrp/MnO-input-output-files.zip/file";.
Is the real part of the wave function the same as the radial part of
the wave function in wien2k? If yes, how we can specify the orbital
and atom in my input files to have a figure like the figure that I
uploaded in 
https://www.mediafire.com/file/3tqo7g10kq291jq/example-radwf.jpg/file
?

I also try to plot the 1D of the real part of wave function using the
section  8.16 of the userguide and only replace the 2D with 1D in the
first line of the case.in7, the "MnO-1D.in7" file  in
"https://www.mediafire.com/file/uflq7f338bdhwrp/MnO-input-output-files.zip/file";.
However, after execute the " x lapw7" I have the  following error:
ERROR: UNKNOWN POST-PROCESSING TOOL
0.056u 0.153s 0:00.30 66.6% 0+0k 2072+32io 12pf+0w
Would you please help me to solve this error, too?


Sincerely yours,
Reyhaneh Ebrahimi

On Wed, Aug 16, 2023 at 11:15 AM Peter Blaha  wrote:
>
> Please search the mailing list.
> There were some previous post about the format of these files.
> You certainly cannot plot them in xmgrace, as it does not contain x-y data.
>
> Am 15.08.2023 um 00:02 schrieb reyhaneh ebrahimi:
> > Dear WIEN2k users
> > I'm a WIEN2k user, version 23.2.
> > I would like to plot the radial part of the wave function (u_l(r, E_l))
> > for my compound in 2D and 1D. To this end, I followed the user guide of
> > WIEN2k with version 23.2. Now, for 2D, I have the case.radwf and
> > case.almblm files, I attached my input and output files at
> > https://www.mediafire.com/file/tw688j9t31hu897/MnO.zip/file
> > 
> > For plotting the radial part of the wave function, I used "xmgrace
> > case.radwf" command but it failed with errors such as "Error parsing
> > line 2, skipped."
> > Would you please help me, how can I plot the radial part of the wave
> > function?
> > thank you very much
> > Sincerely yours,
> > Reyhaneh Ebrahimi
> >
> > ___
> > Wien mailing list
> > Wien@zeus.theochem.tuwien.ac.at
> > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> > SEARCH the MAILING-LIST at:  
> > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>
> --
> --
> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-1-58801-165300
> Email: peter.bl...@tuwien.ac.atWIEN2k: http://www.wien2k.at
> WWW:   http://www.imc.tuwien.ac.at
> -
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Re: [Wien] XCrySDen

[Tone Kokalj]

Dear Pablo,

You only upgraded the OS, or you got a new computer with a high screen
resolution, such as Quad HD (2,560×1,440) or Ultra HD (3,840×2,160).
For such high resolutions, xcrysden appearance is indeed awkward (too
small). This annoying issue will be fixed in the next release.

Best regards,
Tone
-- 
Jožef Stefan Institute, Ljubljana, Slovenia

On Wed, 2023-08-09 at 18:36 +, delamora wrote:
> I am having problems with XCrySDen; the figures and the letters are
> very small.
> I have the Fedora Linux;
> ---
> Linux fedora 6.4.7-100.fc37.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Jul 27
> 19:56:37 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
> ---
> In earlier versions I did not have this problem
> 
> Saludos
> 
> Pablo
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