Re: [Wien] Error in LAPW2DM

[Gavin Abo]

Yes, I'm creating the patches from the files.

For example, if you have a 'new' source code file with changes that were 
made to the 'old' source code file, I create the patch file with [ 
https://en.wikipedia.org/wiki/Patch_(Unix) ]:


diff old.f new.f > my.patch

So the patch just contains the text differences between the two files 
(old.f and new.f).


So I used SRC_symmetso/clmchange.f in the original WIEN2k 14.2 archive 
(WIEN2k_14.2.tar).  I saved the clmchange.f attachment from the post [ 
http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg12361.html 
] as clmchange_new.f.


Then, I generated the patch with:

diff clmchange.f clmchange_new.f > clmchange.patch

This can be convenient, because the -b option can be used to create a 
backup of the original file or -R can be used to reverse the changes 
when using patch [ 
http://manpages.ubuntu.com/manpages/hardy/man1/patch.1.html ].


If you are managing a large set of patches, there is also quilt [ 
http://manpages.ubuntu.com/manpages/hardy/man1/quilt.1.html ].


On 7/6/2015 6:59 PM, Laurence Marks wrote:


Dear Gavin,

I like the idea of a patch directory. You are creating them from the 
files?


---
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
http://www.numis.northwestern.edu
Corrosion in 4D http://MURI4D.numis.northwestern.edu
Co-Editor, Acta Cryst A
"Research is to see what everybody else has seen, and to think what 
nobody else has thought"

Albert Szent-Gyorgi

On Jul 6, 2015 19:19, "Gavin Abo" > wrote:


Did you apply the source code fix to symmetso's clmchange.f of
WIEN2k 14.2 and accept the new structure generated by symmetso
during initso [
http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg12523.html
]?

There is clmchange.f at:

http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg12361.html

or you might be interested in using clmchange.patch instead at:

https://github.com/gsabo/WIEN2k-Patches/tree/master/14.2

(click "WIEN2k-Patches" link, then "Download ZIP" button)

On 7/6/2015 4:05 AM, rahn...@hsu.ac.ir 
wrote:

Dear Wien2k users,
I tried to run GGA+U calculation with structure of EuFe4Sb12. I am having 
problem at the lapwdm step when both -so and -orb are turned on(Error in 
LAPW2DM). Also,There is not any errors if I run with only the -orb option (no 
spin-orbit coupling)or visa versa.
Your guidance to solve this problem will be greatly appreciated.
Yours,
Hossein




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Re: [Wien] Error in LAPW2DM

[Laurence Marks]

Dear Gavin,

I like the idea of a patch directory. You are creating them from the files?

---
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
http://www.numis.northwestern.edu
Corrosion in 4D http://MURI4D.numis.northwestern.edu
Co-Editor, Acta Cryst A
"Research is to see what everybody else has seen, and to think what nobody
else has thought"
Albert Szent-Gyorgi
On Jul 6, 2015 19:19, "Gavin Abo"  wrote:

>  Did you apply the source code fix to symmetso's clmchange.f of WIEN2k
> 14.2 and accept the new structure generated by symmetso during initso [
> http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg12523.html
> ]?
>
> There is clmchange.f at:
>
> http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg12361.html
>
> or you might be interested in using clmchange.patch instead at:
>
> https://github.com/gsabo/WIEN2k-Patches/tree/master/14.2
>
> (click "WIEN2k-Patches" link, then "Download ZIP" button)
>
> On 7/6/2015 4:05 AM, rahn...@hsu.ac.ir wrote:
>
>  Dear Wien2k users,
> I tried to run GGA+U calculation with structure of EuFe4Sb12. I am having 
> problem at the lapwdm step when both -so and -orb are turned on(Error in 
> LAPW2DM). Also,There is not any errors if I run with only the -orb option (no 
> spin-orbit coupling)or visa versa.
>
> Your guidance to solve this problem will be greatly appreciated.
> Yours,
> Hossein
>
>
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Re: [Wien] Error in LAPW2DM

[Gavin Abo]

Did you apply the source code fix to symmetso's clmchange.f of WIEN2k 
14.2 and accept the new structure generated by symmetso during initso [ 
http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg12523.html 
]?


There is clmchange.f at:

http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg12361.html

or you might be interested in using clmchange.patch instead at:

https://github.com/gsabo/WIEN2k-Patches/tree/master/14.2

(click "WIEN2k-Patches" link, then "Download ZIP" button)

On 7/6/2015 4:05 AM, rahn...@hsu.ac.ir wrote:

Dear Wien2k users,
I tried to run GGA+U calculation with structure of EuFe4Sb12. I am having 
problem at the lapwdm step when both -so and -orb are turned on(Error in 
LAPW2DM). Also,There is not any errors if I run with only the -orb option (no 
spin-orbit coupling)or visa versa.
Your guidance to solve this problem will be greatly appreciated.
Yours,
Hossein
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Re: [Wien] Same number of atoms in 2x2x2 and 2x2x1 supercell

[Oleg Rubel]

Attaching *struct files will certainly help to facilitate the discussion. The 
site of the supercell depends on your future plans and available computational 
resources. Do you want to model defects, composition alloy, surface?

Oleg


> On Jul 6, 2015, at 12:55, Alpa Dashora  wrote:
> 
> Dear Wien2k users and Prof. Blaha,
> 
> I have generated 2x2x2 and 2x2x1 supercell of anatase TiO2 (space group: I 
> 41/a m d (No. 141)) with tetragonal structure. In both the cases the number 
> of atoms in supercell are 48.
> 
> Which supercell I should use for further calculation? Is there any formula to 
> calculate number of atoms in supercell for tetragonal bodycentered structure?
> 
> I have one more query: the number of atom will remain same if I construct 
> these supercells with some other band structure code.
> 
> Please guide me to understand it.
> 
> With regards,
> -- 
> Alpa Dashora
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[Wien] Same number of atoms in 2x2x2 and 2x2x1 supercell

[Alpa Dashora]

Dear Wien2k users and Prof. Blaha,

I have generated 2x2x2 and 2x2x1 supercell of anatase TiO2 (space group: I
41/a m d (No. 141)) with tetragonal structure. In both the cases the number
of atoms in supercell are 48.

Which supercell I should use for further calculation? Is there any formula
to calculate number of atoms in supercell for tetragonal bodycentered
structure?

I have one more query: the number of atom will remain same if I construct
these supercells with some other band structure code.

Please guide me to understand it.

With regards,
-- 
Alpa Dashora
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Re: [Wien] (no subject)

[Laurence Marks]

One comment (a pet peeve). Not to be harsh about these tools, but if you
are looking at an oxide it is very unlikely that anything you generate with
a simple tool such as any of these methods will be close to reality. Even
with semiconductors this is often not the case, as is well established for
Si and the III-V compounds. I suggest looking at the experimental
literature first before doing surface GIGO, of which there is alas rather a
lot at the moment.

On Mon, Jul 6, 2015 at 10:55 AM, Oleg Rubel  wrote:

> There are two possibilities: use structure editor (an octave tool, which
> is a part of Wien2k) or VESTA package. See this thread for details
> http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg12541.html
>
> Once you have the surface, layers can be removed manually to achieve a
> desired termination. If the material is an insulator, the surface
> terminated with one type of atoms may be metallic and not stable; it will
> undergo a surface reconstruction.
>
> I hope it will help
> Oleg
>
> > On Jul 6, 2015, at 11:17, chin Sansu  wrote:
> >
> > Dear Wien2k users
> >
> > Is there any way to terminate atomic-layer of a surface with particular
> atomic layers in 2D cases?
> > Like in ABC compound I want to terminate my surface layer once with A, B
> and then C.
> > I looked around previous mails but no specific approach found.
> > Any help will be acknowledged.
> >
> > best
> > Chin
> > ___
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>
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>



-- 
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu
Corrosion in 4D: MURI4D.numis.northwestern.edu
Co-Editor, Acta Cryst A
"Research is to see what everybody else has seen, and to think what nobody
else has thought"
Albert Szent-Gyorgi
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Re: [Wien] Change in Si structure

[Peter Blaha]

This cif file for Si is in the "wrong setting".

As written in the UG, if a spacegroup supports two settings, the one 
with inversion symmetry must be chosen.


Si is FCC cubic with atoms in +-(1/8,1/8,1/8)


On 07/06/2015 02:41 PM, Muhammad Sajjad wrote:

Dear Users

I uploaded cif file (attached herewith) in Wine2k 14 and after
initialization it changes (attached in .struct formate) completely. What
will be reason behind it? I have followed the post
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg02749.html

--
Kind Regards
Muhammad Sajjad
Post Doctoral Fellow
KAUST, KSA.


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--

  P.Blaha
--
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Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
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Re: [Wien] E-cut-off

[Peter Blaha]

Leave E-cut at -6.0 Ry.

A charge leakage of 0.0001 is not a problem, but treating these states 
at -7.5 Ry as valence requires huge RKmax for convergence and still 
neglects spin-orbit coupling, which is sizable as you can see from the 
energy difference of 3P* and 3p



On 07/06/2015 03:27 PM, Seyyed Amir Abbas Emami wrote:

​dear users

I suppose to run Mn2NiGa heusler compound. I have a problem in
determination of Energy cut-off in l-start step. I have a doubt to set
Energy cut-off to -6 Ry or -7.5 Ry. Actually charge leakage and atomic
energy of Mn and Ni  are not verySensitive to choosing of -6 Ry or
-7.5.In Ga, charge leakage for -7.5Ry is less than -6 but is that
correct to select 3P as valence state. (can the charge leakage be a good
criteria for determination of Energy cut-off or valence and core states
must be considered)

E-up(Ry)  E-dn(Ry)   Occupancy   q/sphere  core-state
   1S-751.662733   -751.664185  1.00  1.001.  T
   2S -92.732470-92.732331  1.00  1.001.  T
   2P*-82.085471-82.086189  1.00  1.001.  T
   2P -80.052956-80.053617  2.00  2.001.  T
   3S -10.872333-10.873189  1.00  1.001.  T
   3P* -7.431922 -7.433162  1.00  1.000.  F
   3P  -7.165398 -7.166702  2.00  2.000.9998  F
   3D* -1.414753 -1.419390  2.00  2.000.9905  F
   3D  -1.380765 -1.385545  3.00  3.000.9900  F
   4S  -0.622550 -0.674284  1.00  1.000.5717  F
   4P* -0.158244 -0.214215  0.00  1.000.2778  F

Best Regards


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--

  P.Blaha
--
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Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
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Re: [Wien] (no subject)

[Peter Blaha]

Use the structeditor (see UG).

It is a very versatile tool and can create a surface from a bulk 
structure with arbitrary surface index and chosen atom at the top layer.




On 07/06/2015 05:17 PM, chin Sansu wrote:

Dear Wien2k users

Is there any way to terminate atomic-layer of a surface with particular
atomic layers in 2D cases?
Like in ABC compound I want to terminate my surface layer once with A, B
and then C.
I looked around previous mails but no specific approach found.
Any help will be acknowledged.

best
Chin


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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
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Re: [Wien] (no subject)

[Oleg Rubel]

There are two possibilities: use structure editor (an octave tool, which is a 
part of Wien2k) or VESTA package. See this thread for details
http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg12541.html

Once you have the surface, layers can be removed manually to achieve a desired 
termination. If the material is an insulator, the surface terminated with one 
type of atoms may be metallic and not stable; it will undergo a surface 
reconstruction.

I hope it will help
Oleg

> On Jul 6, 2015, at 11:17, chin Sansu  wrote:
> 
> Dear Wien2k users
> 
> Is there any way to terminate atomic-layer of a surface with particular 
> atomic layers in 2D cases?
> Like in ABC compound I want to terminate my surface layer once with A, B and 
> then C.
> I looked around previous mails but no specific approach found.
> Any help will be acknowledged. 
> 
> best
> Chin
> ___
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[Wien] (no subject)

[chin Sansu]

Dear Wien2k users
Is there any way to terminate atomic-layer of a surface with particular atomic 
layers in 2D cases?Like in ABC compound I want to terminate my surface layer 
once with A, B and then C.I looked around previous mails but no specific 
approach found.Any help will be acknowledged. 

bestChin
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[Wien] E-cut-off

[Seyyed Amir Abbas Emami]

​dear users

I suppose to run Mn2NiGa heusler compound. I have a problem in determination of 
Energy cut-off in l-start step. I have a doubt to set Energy cut-off to -6 Ry 
or -7.5 Ry. Actually charge leakage and atomic energy of Mn and Ni  are not 
very Sensitive to choosing of -6 Ry or -7.5.In Ga, charge leakage for -7.5Ry is 
less than -6 but is that correct to select 3P as valence state. (can the charge 
leakage be a good criteria for determination of Energy cut-off or valence and 
core states must be considered)

   E-up(Ry)  E-dn(Ry)   Occupancy   q/sphere  core-state
  1S-751.662733   -751.664185  1.00  1.001.  T
  2S -92.732470-92.732331  1.00  1.001.  T
  2P*-82.085471-82.086189  1.00  1.001.  T
  2P -80.052956-80.053617  2.00  2.001.  T
  3S -10.872333-10.873189  1.00  1.001.  T
  3P* -7.431922 -7.433162  1.00  1.000.  F
  3P  -7.165398 -7.166702  2.00  2.000.9998  F
  3D* -1.414753 -1.419390  2.00  2.000.9905  F
  3D  -1.380765 -1.385545  3.00  3.000.9900  F
  4S  -0.622550 -0.674284  1.00  1.000.5717  F
  4P* -0.158244 -0.214215  0.00  1.000.2778  F

Best Regards
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[Wien] Change in Si structure

[Muhammad Sajjad]

Dear Users

I uploaded cif file (attached herewith) in Wine2k 14 and after
initialization it changes (attached in .struct formate) completely. What
will be reason behind it? I have followed the post
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg02749.html

-- 
Kind Regards
Muhammad Sajjad
Post Doctoral Fellow
KAUST, KSA.


si227.cif
Description: CIF chemical test


opt12.struct
Description: Binary data
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[Wien] Error in LAPW2DM

[rahnama]

Dear Wien2k users, 
I tried to run GGA+U calculation with structure of EuFe4Sb12. I am having 
problem at the lapwdm step when both -so and -orb are turned on(Error in 
LAPW2DM). Also,There is not any errors if I run with only the -orb option (no 
spin-orbit coupling)or visa versa. 
Your guidance to solve this problem will be greatly appreciated. 
Yours, 
Hossein 
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