Re: [Wien] Procedure or steps to calculate phonon

[Gavin Abo]

Step 1: Install the DFT program; learn how to do scf calculations with 
unit cells, then supercells (with WIEN2k) [1].


         - Phonon calculations use primitive cells [2].

Step 2: Research available phonon software (for WIEN2k) and decide which 
one you will use.


 - For example: PHONON by K. Parlinski [3], phonopy by A. 
Togo [4], PHON by D. Alfè [5], ThermoPhonon by N. Zarkevich [6], or any 
other one you find [7]


Step 3: Check the website for the phonon software

  - The procedure used for the phonon software is almost 
always on the specific phonon program's website in their documentation, 
tutorial, forum, or obtained by contacting the software author(s).  Or 
you might find procedures on other websites [8].


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16627.html 
, https://www.youtube.com/watch?v=hsPNLbfuFjc , 
https://www.youtube.com/watch?v=s1BY2Wi538o , 
http://susi.theochem.tuwien.ac.at/reg_user/faq/supercells.html
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11543.html 
, 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11551.html 
, 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11729.html 
, https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14219.html

[3] http://www.computingformaterials.com/phoncfm710/4contact.html
[4] https://atztogo.github.io/phonopy/index.html
[5] http://www.homepages.ucl.ac.uk/~ucfbdxa/phon/
[6] https://lib.dr.iastate.edu/ameslab_software/2/
[7] https://alamode.readthedocs.io/en/latest/intro.html , 
http://phonts.mse.ufl.edu/ , http://lmgtfy.com/?q=phonon%20codes , etc.
[8] 
http://wien2k-algerien1970.blogspot.com/2017/01/guide-about-phonon-calculations.html 
, 
http://susi.theochem.tuwien.ac.at/events/ws2017/notes/tutorial-phonons.pdf 
, https://hartree-fock.blogspot.com/2010/06/using-phonopy-with-wien2k.html



On 10/15/2018 10:42 AM, S quyoom Seh wrote:


Sir with due respect, i am a new commer in the feild of computational 
methods, but sir i need a procedure of steps to calculate phonon. If 
you can provide me or give me any lead i will be very thankful to you 
and it will be your most kindness.   (PLEASE SIR I NEED THE PROCEDURE PLZ)



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[Wien] Procedure or steps to calculate phonon

[S quyoom Seh]

Sir with due respect, i am a new commer in the feild of computational
methods, but sir i need a procedure of steps to calculate phonon. If you
can provide me or give me any lead i will be very thankful to you and it
will be your most kindness.   (PLEASE SIR I NEED THE PROCEDURE PLZ)
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[Wien] How to obtain ELNES simulation results consistent with experiments ?

[??????]

Respected Prof. Blaha ,


Thank you so much for your reply.


I did it because I read Kevin Jorissen's mail:
http://zeus.theochem.tuwien.ac.at/pipermail/wien/2006-August/007602.html



I probably never did the right thing. I'll do what you suggest.


With kind regards.


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[Wien] How to obtain ELNES simulation results consistent with experiments ?

[??????]

Respected Prof. Marks ,


Thank you so much for your reply.


'One way to minimize the effect is to tilt off the zone axis to a 
pseudo-kinematical condition', does this mean I need to change the angle a 
little bit? For example, change from 

ORIENTATION SENSITIVE 
0.0 0.0 0.0
to
ORIENTATION SENSITIVE
0.0 0.0 0.1
for minimizing dynamical diffraction effects. Am I correct?


Another question, when I  set 1/2 core hole in the labelled oxygen atom 1s 
state in case.inc file, 
i.e.  
 1 0.00  0  NUMBER OF ORBITALS (EXCLUDING SPIN), SHIFT, IPRINT 1,-1,1.5 
  ( N,KAPPA,OCCUP)


Then, do I need to set -0.5 in the case.inm file ?


With kind regards.


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Re: [Wien] The new method of optimizing the internal parameter

[Laurence Marks]

The only difference is that with -min the run** code will switch from MSR1
to MSR1a, minimize, then switch back to MSR1 when the forces are small and
fully converge the density. Depending on what (old ?) version of run** you
are using it may not do this switching for you.

The later run** also has a way to automatically reduce RMT if touching
spheres are encountered, although I have never used these myself.

On Mon, Oct 15, 2018 at 9:46 AM karima Physique 
wrote:

> Dear Prof. Laurence Marks
> Thank you very much for your answer
> *For the case of my calculations, I want to optimize the internal
> parameters of an atom of a **chalcopyrite**, **usually I used MSR1a
> without -min (old WIEN2k versions) :*
> *runsp -fc 1*
> *save xxx*
> *i change MSR1 to MSR1a *
> *runsp -fc 0.5 -ec 0.1 -cc 0.001 *
> *is this method better than -min option? or it's the opposite*
>
>
>
> Le lun. 15 oct. 2018 à 16:31, Laurence Marks  a
> écrit :
>
>> There is in my opinion no "right" method. The question is what are you
>> trying to do?
>>
>> Case 1: A structure with fixed positions or a problem where you "don't
>> care" about minor forces, e.g. calculating a simple bulk structure. Then
>> just "runsp -cc 0.0001 -ec 0.0001" is fine. (I prefer to use -cc as well as
>> the default -ec).
>>
>> Case 2: A simple structure where there might be minor forces that you do
>> care about. Then something like "runsp -cc 0.0001 -ec 0.0001 -fc 1" first
>> and check the forces. Iff they are too large for you, then "save -f -d
>> PreMin ; runsp -cc 0.001 -ec 0.0001 -min" or similar.
>>
>> Case 3: A more complex structure where you know the positions are not
>> quite right. I suggest using something like
>> runsp -cc 0.01 -ec 0.1 -fc 4
>> save -f -d PreMin
>> runsp -cc 0.001 -ec 0.0001 -fc 1 -min
>>
>> This avoids converging too much at first when you know the result won't
>> be right until the internal minimization has been done. In addition, MSR1a
>> often works better when started from a partial minimization where the
>> density and pseudo-charges are somewhat converged. For a large problem add
>> "-noHinv", I have had problems with -min and -it in the past.
>>
>> On Mon, Oct 15, 2018 at 9:03 AM karima Physique <
>> physique.kar...@gmail.com> wrote:
>>
>>> Dear Wien2k user;
>>>
>>> According to user guide, after a SCF cycle with runsp -fc 1 we continue
>>> with  run runsp -min
>>> I want to know which of these two methods is the correct one:
>>> 1)
>>> runsp -fc 1
>>> runsp -min
>>> runsp -min -fc 0.5 -ec 0.0001 -cc 0.001
>>>
>>> or
>>> 2)
>>> runsp -fc 1
>>> runsp -min -fc 0.5 -ec 0.0001 -cc 0.001
>>>
>>
>>
>> --
>> Professor Laurence Marks
>> "Research is to see what everybody else has seen, and to think what
>> nobody else has thought", Albert Szent-Gyorgi
>> www.numis.northwestern.edu ; Corrosion in 4D:
>> MURI4D.numis.northwestern.edu
>> Partner of the CFW 100% program for gender equity,
>> www.cfw.org/100-percent
>> 
>> Co-Editor, Acta Cryst A
>> ___
>> Wien mailing list
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>> 
>> SEARCH the MAILING-LIST at:
>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>> 
>>
>

-- 
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Gyorgi
www.numis.northwestern.edu ; Corrosion in 4D: MURI4D.numis.northwestern.edu
Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent
Co-Editor, Acta Cryst A
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Re: [Wien] The new method of optimizing the internal parameter

[karima Physique]

Dear Prof. Laurence Marks
Thank you very much for your answer
*For the case of my calculations, I want to optimize the internal
parameters of an atom of a **chalcopyrite**, **usually I used MSR1a without
-min (old WIEN2k versions) :*
*runsp -fc 1*
*save xxx*
*i change MSR1 to MSR1a *
*runsp -fc 0.5 -ec 0.1 -cc 0.001 *
*is this method better than -min option? or it's the opposite*



Le lun. 15 oct. 2018 à 16:31, Laurence Marks  a
écrit :

> There is in my opinion no "right" method. The question is what are you
> trying to do?
>
> Case 1: A structure with fixed positions or a problem where you "don't
> care" about minor forces, e.g. calculating a simple bulk structure. Then
> just "runsp -cc 0.0001 -ec 0.0001" is fine. (I prefer to use -cc as well as
> the default -ec).
>
> Case 2: A simple structure where there might be minor forces that you do
> care about. Then something like "runsp -cc 0.0001 -ec 0.0001 -fc 1" first
> and check the forces. Iff they are too large for you, then "save -f -d
> PreMin ; runsp -cc 0.001 -ec 0.0001 -min" or similar.
>
> Case 3: A more complex structure where you know the positions are not
> quite right. I suggest using something like
> runsp -cc 0.01 -ec 0.1 -fc 4
> save -f -d PreMin
> runsp -cc 0.001 -ec 0.0001 -fc 1 -min
>
> This avoids converging too much at first when you know the result won't be
> right until the internal minimization has been done. In addition, MSR1a
> often works better when started from a partial minimization where the
> density and pseudo-charges are somewhat converged. For a large problem add
> "-noHinv", I have had problems with -min and -it in the past.
>
> On Mon, Oct 15, 2018 at 9:03 AM karima Physique 
> wrote:
>
>> Dear Wien2k user;
>>
>> According to user guide, after a SCF cycle with runsp -fc 1 we continue
>> with  run runsp -min
>> I want to know which of these two methods is the correct one:
>> 1)
>> runsp -fc 1
>> runsp -min
>> runsp -min -fc 0.5 -ec 0.0001 -cc 0.001
>>
>> or
>> 2)
>> runsp -fc 1
>> runsp -min -fc 0.5 -ec 0.0001 -cc 0.001
>>
>
>
> --
> Professor Laurence Marks
> "Research is to see what everybody else has seen, and to think what nobody
> else has thought", Albert Szent-Gyorgi
> www.numis.northwestern.edu ; Corrosion in 4D:
> MURI4D.numis.northwestern.edu
> Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent
> Co-Editor, Acta Cryst A
> ___
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> 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
>
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Re: [Wien] The new method of optimizing the internal parameter

[Laurence Marks]

There is in my opinion no "right" method. The question is what are you
trying to do?

Case 1: A structure with fixed positions or a problem where you "don't
care" about minor forces, e.g. calculating a simple bulk structure. Then
just "runsp -cc 0.0001 -ec 0.0001" is fine. (I prefer to use -cc as well as
the default -ec).

Case 2: A simple structure where there might be minor forces that you do
care about. Then something like "runsp -cc 0.0001 -ec 0.0001 -fc 1" first
and check the forces. Iff they are too large for you, then "save -f -d
PreMin ; runsp -cc 0.001 -ec 0.0001 -min" or similar.

Case 3: A more complex structure where you know the positions are not quite
right. I suggest using something like
runsp -cc 0.01 -ec 0.1 -fc 4
save -f -d PreMin
runsp -cc 0.001 -ec 0.0001 -fc 1 -min

This avoids converging too much at first when you know the result won't be
right until the internal minimization has been done. In addition, MSR1a
often works better when started from a partial minimization where the
density and pseudo-charges are somewhat converged. For a large problem add
"-noHinv", I have had problems with -min and -it in the past.

On Mon, Oct 15, 2018 at 9:03 AM karima Physique 
wrote:

> Dear Wien2k user;
>
> According to user guide, after a SCF cycle with runsp -fc 1 we continue
> with  run runsp -min
> I want to know which of these two methods is the correct one:
> 1)
> runsp -fc 1
> runsp -min
> runsp -min -fc 0.5 -ec 0.0001 -cc 0.001
>
> or
> 2)
> runsp -fc 1
> runsp -min -fc 0.5 -ec 0.0001 -cc 0.001
>


-- 
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Gyorgi
www.numis.northwestern.edu ; Corrosion in 4D: MURI4D.numis.northwestern.edu
Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent
Co-Editor, Acta Cryst A
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[Wien] The new method of optimizing the internal parameter

[karima Physique]

Dear Wien2k user;

According to user guide, after a SCF cycle with runsp -fc 1 we continue
with  run runsp -min
I want to know which of these two methods is the correct one:
1)
runsp -fc 1
runsp -min
runsp -min -fc 0.5 -ec 0.0001 -cc 0.001

or
2)
runsp -fc 1
runsp -min -fc 0.5 -ec 0.0001 -cc 0.001
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Re: [Wien] [SPAM?] How to obtain ELNES simulation results consistent with experiments ?

[Peter Blaha]

I do not understand your statement:

> As it is supercell, I calculated every peak of unequivalent O K edge and
> summed them. I'm not sure all the steps I have done are right. The


Of course, only atom 7 has the core hole, the other atoms of the 
supercell can contribute to screening. But only the spectrum of atom 7 
is meaningful, not that of the other O atoms. So don't sum up anything, 
just calculate the spectrum for atom 7.


On 10/15/18 1:53 PM, yfding wrote:
This problem haunts me for nearly a year, and my questions are still 
unsolved after consulting a lot of literature and mailing list.


I tried to get Oxygen K edge of the 3*3*3 SrCrO3 supercell.

In my calculations, I first converted the SrCrO3 (space group P4/mmm) 
into a SrCrO3 3*3*3 supercell (space group P1) in CrystalMaker, then 
transformed the SrCrO3supercell.cif file into SrCrO3supercell.struct 
file under the Wien2k case directory, labelled one oxygen atom to make 
this atom unique, did initialization, and accepted all the queries from 
nn complaints. The initialization parameters were as follows:


   Rmt: Sr:2.40  Cr:1.78  O:1.61
   potential: GGA of PBE-96
   separation energy: -6.0 Ry
   RKmax: 7.0
   Max L in WF: 10
   number of k points in the whole BZ: 5*5*5
   number of k points in the irreducible wedge of the BZ: 18

Then I edited SrCrO3.inc and removed one core electron from the 7th 
atom, i.e. 1st Oxygen atom 1s state. Next I changed 0.0 to -1.0 in 
SrCrO3.inm. Then run SCF in parallel (energy convergence 0.0001 Ry).


Then,
-edited case.innes :

   SrCrO3 O K edge
   7            (atom)
   1, 0        (n, l core)
   532       (E-Loss of 1st edge in eV)
   200   (energy of the incident electrons in keV)
   -5.0 20.0 0.1        (minimum energy, energy step, maximum energy)
   0.37  0.75   (collection semiangle, convergence semiangle, both in mrad)
   50 1   (NR, NT, defining the integration mesh in the detector plane)
   0.7   (spectrometer broadening in eV)
   OUTPUT
   0                   (full output)
   DETECTOR POSITION
   0.0 0.0             (thetax, thetay)
   MODUS
   energy              (dscs wrt what?)
   ORIENTATION SENSITIVE
   0.0 0.0 0.0
   SELECTION RULE
   n                   (selection rule)
   LSELECTION RULE
   d
   INITIALIZATION
   y y                (dos and xdos handling)
   y y                (handling of rotation matrices)
   QGRID
   U
   END

- x lapw1
- x lapw2 -qtl
- x qtl -telnes
- x telnes3
- x broadening

As it is supercell, I calculated every peak of unequivalent O K edge and 
summed them. I'm not sure all the steps I have done are right. The 
result is different from the TEM EELS experiment (The O K edge EELS 
spectra were studied on an JEOL ARM200F Cs-corrected TEM with a FEG and 
a Gatan parallel electron-energy-loss spectroscope). The relative 
strength and position of the peaks are completely inconsistent.


It's not just this example, but I've had the same problem with all the 
other materials. I thought about all the possible reasons, and looked up 
lots of literature and mailing lists, but I couldn't get the calculation 
results closer to the experiment. I want to know how to obtain ELNES 
simulation results consistent with experiments ?


Any comment(s) would be highly appreciated. Thanks in advance!



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--

  P.Blaha
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
WWW:   http://www.imc.tuwien.ac.at/TC_Blaha
--
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Re: [Wien] [SPAM?] How to obtain ELNES simulation results consistent with experiments ?

[Laurence Marks]

There are two fundamental issues:
a) How to handle the dynamical diffraction of the swift electrons.
b) How to handle the core hole.

To my knowledge no DFT code handles a) correctly. (Some details are in Chpt
5 of "High-Resolution Transmission Electron Microscopy: and Associated
Techniques" Eds Buseck, Cowley  and Eyring.) Particularly if you are on a
zone axis dynamical diffraction effects (often called channeling, but this
is not fully rigorous in my opinion) can be very strong. One way to
minimize the effect is to tilt off the zone axis to a pseudo-kinematical
condition. Of course, by doing this you lose imaging. You might (very
might) be able to reduce the issue by using a larger collection angle
making it similar to Precession (e.g. DOI 10.1016/j.ultramic.2012.11.007).
I am not sure if people have really explored this enough.

For the core hole, from what I have seen (I am not a full EELS expert)
often how much of a core hole one wants is an "adjustable parameter". At
least with Slater Transition Theory it should only be 1/2 a hole.

Not an easy problem, and I am not convinced that it has been fully solved
although I would be willing to be proved wrong.

On Mon, Oct 15, 2018 at 6:54 AM yfding  wrote:

> This problem haunts me for nearly a year, and my questions are still
> unsolved after consulting a lot of literature and mailing list.
>
> I tried to get Oxygen K edge of the 3*3*3 SrCrO3 supercell.
>
> In my calculations, I first converted the SrCrO3 (space group P4/mmm) into
> a SrCrO3 3*3*3 supercell (space group P1) in CrystalMaker, then transformed
> the SrCrO3supercell.cif file into SrCrO3supercell.struct file under the
> Wien2k case directory, labelled one oxygen atom to make this atom unique,
> did initialization, and accepted all the queries from nn complaints. The
> initialization parameters were as follows:
>
>   Rmt: Sr:2.40  Cr:1.78  O:1.61
>   potential: GGA of PBE-96
>   separation energy: -6.0 Ry
>   RKmax: 7.0
>   Max L in WF: 10
>   number of k points in the whole BZ: 5*5*5
>   number of k points in the irreducible wedge of the BZ: 18
>
> Then I edited SrCrO3.inc and removed one core electron from the 7th atom,
> i.e. 1st Oxygen atom 1s state. Next I changed 0.0 to -1.0 in SrCrO3.inm.
> Then run SCF in parallel (energy convergence 0.0001 Ry).
>
> Then,
> -edited case.innes :
>
>   SrCrO3 O K edge
>   7(atom)
>   1, 0(n, l core)
>   532   (E-Loss of 1st edge in eV)
>   200   (energy of the incident electrons in keV)
>   -5.0 20.0 0.1(minimum energy, energy step, maximum energy)
>   0.37  0.75   (collection semiangle, convergence semiangle, both in mrad)
>   50 1   (NR, NT, defining the integration mesh in the detector plane)
>   0.7   (spectrometer broadening in eV)
>   OUTPUT
>   0   (full output)
>   DETECTOR POSITION
>   0.0 0.0 (thetax, thetay)
>   MODUS
>   energy  (dscs wrt what?)
>   ORIENTATION SENSITIVE
>   0.0 0.0 0.0
>   SELECTION RULE
>   n   (selection rule)
>   LSELECTION RULE
>   d
>   INITIALIZATION
>   y y(dos and xdos handling)
>   y y(handling of rotation matrices)
>   QGRID
>   U
>   END
>
> - x lapw1
> - x lapw2 -qtl
> - x qtl -telnes
> - x telnes3
> - x broadening
>
> As it is supercell, I calculated every peak of unequivalent O K edge and
> summed them. I'm not sure all the steps I have done are right. The result
> is different from the TEM EELS experiment (The O K edge EELS spectra were
> studied on an JEOL ARM200F Cs-corrected TEM with a FEG and a Gatan parallel
> electron-energy-loss spectroscope). The relative strength and position of
> the peaks are completely inconsistent.
>
> It's not just this example, but I've had the same problem with all the
> other materials. I thought about all the possible reasons, and looked up
> lots of literature and mailing lists, but I couldn't get the calculation
> results closer to the experiment. I want to know how to obtain ELNES
> simulation results consistent with experiments ?
>
> Any comment(s) would be highly appreciated. Thanks in advance!
>
>
>

-- 
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Gyorgi
www.numis.northwestern.edu ; Corrosion in 4D: MURI4D.numis.northwestern.edu
Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent
Co-Editor, Acta Cryst A
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[Wien] [SPAM?] How to obtain ELNES simulation results consistent with experiments ?

[yfding]

This problem haunts me for nearly a year, and my questions are still unsolved 
after consulting a lot of literature and mailing list. 


I tried to get Oxygen K edge of the 3*3*3 SrCrO3 supercell.



In my calculations, I first converted the SrCrO3 (space group P4/mmm) into a 
SrCrO3 3*3*3 supercell (space group P1) in CrystalMaker, then transformed the 
SrCrO3supercell.cif file into SrCrO3supercell.struct file under the Wien2k case 
directory, labelled one oxygen atom to make this atom unique, did 
initialization, and accepted all the queries from nn complaints. The 
initialization parameters were as follows:


  Rmt: Sr:2.40  Cr:1.78  O:1.61 
  potential: GGA of PBE-96
  separation energy: -6.0 Ry
  RKmax: 7.0
  Max L in WF: 10
  number of k points in the whole BZ: 5*5*5
  number of k points in the irreducible wedge of the BZ: 18


Then I edited SrCrO3.inc and removed one core electron from the 7th atom, i.e. 
1st Oxygen atom 1s state. Next I changed 0.0 to -1.0 in SrCrO3.inm. Then run 
SCF in parallel (energy convergence 0.0001 Ry). 


Then, 
-edited case.innes :


  SrCrO3 O K edge
  7(atom)
  1, 0(n, l core)
  532   (E-Loss of 1st edge in eV)
  200   (energy of the incident electrons in keV)
  -5.0 20.0 0.1(minimum energy, energy step, maximum energy)
  0.37  0.75   (collection semiangle, convergence semiangle, both in mrad)
  50 1   (NR, NT, defining the integration mesh in the detector plane)
  0.7   (spectrometer broadening in eV)
  OUTPUT
  0   (full output)
  DETECTOR POSITION
  0.0 0.0 (thetax, thetay)
  MODUS
  energy  (dscs wrt what?)
  ORIENTATION SENSITIVE
  0.0 0.0 0.0
  SELECTION RULE
  n   (selection rule)
  LSELECTION RULE
  d
  INITIALIZATION
  y y(dos and xdos handling)
  y y(handling of rotation matrices)
  QGRID
  U
  END



- x lapw1
- x lapw2 -qtl  
- x qtl -telnes
- x telnes3
- x broadening


As it is supercell, I calculated every peak of unequivalent O K edge and summed 
them. I'm not sure all the steps I have done are right. The result is different 
from the TEM EELS experiment (The O K edge EELS spectra were studied on an JEOL 
ARM200F Cs-corrected TEM with a FEG and a Gatan parallel electron-energy-loss 
spectroscope). The relative strength and position of the peaks are completely 
inconsistent. 


It's not just this example, but I've had the same problem with all the other 
materials. I thought about all the possible reasons, and looked up lots of 
literature and mailing lists, but I couldn't get the calculation results closer 
to the experiment. I want to know how to obtain ELNES simulation results 
consistent with experiments ?


Any comment(s) would be highly appreciated. Thanks in advance!___
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