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

[reyhaneh ebrahimi]

Dear Prof. Blaha,
Thank you very much for your prompt and valuable response to my issue.
The image that I attached in
https://www.mediafire.com/file/3tqo7g10kq291jq/example-radwf.jpg/file  is
only a simple example and as you noted well " All our radial functions
are given ONLY inside RMT, outside we have plane waves, thus I can never
plot a radial wf. up to 40 bohr as given in the example that I mentioned ".
Therefore, I searched and found other papers which are similar to the goal
that I am looking for in plotting the radial part of the wave function. I
attached one of these papers which is done in your group with the name "On
the importance of local orbitals using second energy derivatives for d and
f electrons" in :
https://www.mediafire.com/file/7oekpzcc6q39zjt/radwf.pdf/file

. In fact, I would like to plot the "r*u_alpha,l" as Figures 3, 10, or 11
of your paper. I search again and find an issue in the mailing list that is
somewhat similar to what I wanted,
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg02372.html

But I still haven't figured out how can I plot figures like the Figures 3,
10, or 11 of your paper using the "case.radwf" file in terms of "r". Are
the odd columns of "case.radwf" file, which I uploaded in
https://www.mediafire.com/file/uflq7f338bdhwrp/MnO-input-output-files.zip/file
, are proportional to "r*u_alpha,l"?

Also, I don't know, using the "case.radwf" file, how can I find the r
(Bohr) for each  "r*u_alpha,l" to plot it? I know that for example, the
first line of "case.radwf" defines the jatom, jr_i(jatom), r_0(jatom),
dx(jatom), rmt (jatom). But the r_0 is constant for each atom and only has
one value. However, for plotting the "r*u_alpha,l" with respect to "r" I
need different values for "r". Would you please help me how can I calculate
or find the values of "r" corresponding to each "r*u_alpha,l"?


PS: Please let me send the correct link which unfortunately doesn't work in
my previous Email. The correct link is:
https://www.mail-archive.com/search?q=radwf&l=wien%40zeus.theochem.tuwien.ac.at
Sincerely yours,
Reyhaneh Ebrahimi


On Thu, Aug 17, 2023 at 4:53 AM Peter Blaha 
wrote:

> 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

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
> -
> ___
> 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
___
Wien mailing list
Wien@zeus.theochem.tuwien.ac.at
http://zeus.theochem.tuwie

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

[Peter Blaha]

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
-
___
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

[Wien] Plotting the radial part of wave function

[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