[Wien] Problems in generating case.struct using shell script and overlapping of spheres with error in lapw1

Fecher, Gerhard fecher at uni-mainz.de
Fri Feb 17 08:43:23 CET 2012


you have a RMT of 0.74 bohr for Se how can that be in nature ?
this means youre structure is wrong

If there is a misprint in the paper you used (I did not check) then
go to any available data base for structures to find the correct one.

Ciao
Gerhard



====================================
Dr. Gerhard H. Fecher
Institut of Inorganic and Analytical Chemistry
Johannes Gutenberg - University
55099 Mainz
________________________________________
Von: wien-bounces at zeus.theochem.tuwien.ac.at [wien-bounces at zeus.theochem.tuwien.ac.at]" im Auftrag von "Madhav Ghimire [ghimire.mpg at gmail.com]
Gesendet: Freitag, 17. Februar 2012 08:30
An: A Mailing list for WIEN2k users
Betreff: Re: [Wien] Problems in generating case.struct using shell script and overlapping of spheres with error in lapw1

Dear Gerhard,
     You are right in the point that my RMT's are very small. But if you increase the RMT, you will observe error in x nn. I have used the value of Rmt for Bi as 1.75, Se 1 as 1.58 and Se (2) as 1.69 as referred in the paper of Mishra et al ; JPCM 9 (1997) 461 before using the data which I sent you all. So I could not clarify where the data was wrong. Hope you all could solve it out.
Regards
Ghimire

On Fri, Feb 17, 2012 at 4:18 PM, Fecher, Gerhard <fecher at uni-mainz.de<mailto:fecher at uni-mainz.de>> wrote:
your RMT's are too small, or in other words: youre structure is wrong

Ciao
Gerhard

====================================
Dr. Gerhard H. Fecher
Institut of Inorganic and Analytical Chemistry
Johannes Gutenberg - University
55099 Mainz
________________________________________
Von: wien-bounces at zeus.theochem.tuwien.ac.at<mailto:wien-bounces at zeus.theochem.tuwien.ac.at> [wien-bounces at zeus.theochem.tuwien.ac.at<mailto:wien-bounces at zeus.theochem.tuwien.ac.at>]&quot; im Auftrag von &quot;Madhav Ghimire [ghimire.mpg at gmail.com<mailto:ghimire.mpg at gmail.com>]
Gesendet: Freitag, 17. Februar 2012 08:02
An: A Mailing list for WIEN2k users
Betreff: Re: [Wien] Problems in generating case.struct using shell script and overlapping of spheres with error in lapw1

Dear Ghosh and wien users,
   If you leave Z blank in the structure file, then also it will be taken automatically once you save the structure file. The matter may be something else I suppose. I have tried this also as you mentioned but of no use.
Anyway, one of the wien friend  from Russia had asked for the structure file. I am attaching herewith its structure file. Could you please check. Please have a trial.
Thanks and best regards
Ghimire

2012/2/17 Ghosh SUDDHASATTWA <ssghosh at igcar.gov.in<mailto:ssghosh at igcar.gov.in><mailto:ssghosh at igcar.gov.in<mailto:ssghosh at igcar.gov.in>>>
I guess this problem is with R0 which has been discussed before in the mailing list. When you enter the atomic positions through w2web, do not mention Z for the atom. Leave it blank.


________________________________
From: wien-bounces at zeus.theochem.tuwien.ac.at<mailto:wien-bounces at zeus.theochem.tuwien.ac.at><mailto:wien-bounces at zeus.theochem.tuwien.ac.at<mailto:wien-bounces at zeus.theochem.tuwien.ac.at>> [mailto:wien-bounces at zeus.theochem.tuwien.ac.at<mailto:wien-bounces at zeus.theochem.tuwien.ac.at><mailto:wien-bounces at zeus.theochem.tuwien.ac.at<mailto:wien-bounces at zeus.theochem.tuwien.ac.at>>] On Behalf Of Madhav Ghimire
Sent: Friday, February 17, 2012 12:14 PM

To: A Mailing list for WIEN2k users
Subject: Re: [Wien] Problems in generating case.struct using shell script and overlapping of spheres with error in lapw1

Dear Ghosh,
    Yes, for the space group 166, I have the converted lattice parameters to hexagonal setting. If you are giving Rmt value approx. between 1.4 to 3.0 for Be, then you observe an error in NN distances. So, for this, you must allow for Set automatically Rmt and continue editing. This will take care of your Rmt but the question is on initialization part and error in lapw1. Please have a try on this sample (of course if you find time).
Now regarding the use of w2web, yes I want to use the shell script for generating the case. struct file. Thanks for your information. But could I know where the cif file use to be (or do we need to download separately). If so, please guide.
Thanks in advance
M. P. Ghimire
2012/2/17 Ghosh SUDDHASATTWA <ssghosh at igcar.gov.in<mailto:ssghosh at igcar.gov.in><mailto:ssghosh at igcar.gov.in<mailto:ssghosh at igcar.gov.in>>>
Since the space group is 166, have you converted the lattice parameters to hexagonal setting
My limited experience with w2web is that it automatically sets the RMT. It should be around 2.50 for Bi.

If you do not want to use the graphical interface, you must have the cif file and use the cif2struct command.



________________________________
From: wien-bounces at zeus.theochem.tuwien.ac.at<mailto:wien-bounces at zeus.theochem.tuwien.ac.at><mailto:wien-bounces at zeus.theochem.tuwien.ac.at<mailto:wien-bounces at zeus.theochem.tuwien.ac.at>> [mailto:wien-bounces at zeus.theochem.tuwien.ac.at<mailto:wien-bounces at zeus.theochem.tuwien.ac.at><mailto:wien-bounces at zeus.theochem.tuwien.ac.at<mailto:wien-bounces at zeus.theochem.tuwien.ac.at>>] On Behalf Of Madhav Ghimire
Sent: Friday, February 17, 2012 11:33 AM
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] Problems in generating case.struct using shell script and overlapping of spheres with error in lapw1

Dear Jose,
    For the generation of structure file, Can I generate a case. struct file without using the graphical interface. In wien2k userguide, it ask us to use w2web to generate the structure file. I want to generate a structure file without using w2web (graphical interface).
In the meantime, as you mentioned in your last mail, I have checked the RmtKmax ranging between 3 to 8. But then also I observe the error as:
Error in LAPW1
 'INILPW' - can't open unit: 18
 'INILPW' -        filename: bise.vsp
 'INILPW' -          status: old          form: formatted
 'LAPW1' - INILPW aborted unsuccessfully.
Hope someone might have resolved this. If still there is any possibility, please kindly inform. Thanks for your kind suggestion.
Regards
M. P. Ghimire
2012/2/17 Jose Alfredo Camargo Martinez <sork8686 at yahoo.es<mailto:sork8686 at yahoo.es><mailto:sork8686 at yahoo.es<mailto:sork8686 at yahoo.es>>>
Us also appeared this error (CORE electrons leak out of MT-sphere) in earlier versions of the code (wien2k_09), was very rare, as its solution.
The solution: In the construction of  the case.struct  using  the graphical environment (w2web) do NOT enter the atomic number (Z) corresponding, simply enter only the atomic symbol. This removed the error in  lstart!!!

 For what  used old versions, if  you already have new version wien2k_11.

Now, the error in LAPW1, could be solved by adjusting the value of * RMT Kmax, considering (RMT * Kmax) / (RMTmin) = approximately 3.5 ( check mailing-list)

(excuse my bad english)
José A. Camargo Martínez
Estudiante Doctorado en Ciencias - Física
DEPARTAMENTO DE FÍSICA
CINVESTAV - MÉXICO D.F.
________________________________
De: Madhav Ghimire <ghimire.mpg at gmail.com<mailto:ghimire.mpg at gmail.com><mailto:ghimire.mpg at gmail.com<mailto:ghimire.mpg at gmail.com>>>
Para: A Mailing list for WIEN2k users <wien at zeus.theochem.tuwien.ac.at<mailto:wien at zeus.theochem.tuwien.ac.at><mailto:wien at zeus.theochem.tuwien.ac.at<mailto:wien at zeus.theochem.tuwien.ac.at>>>
Enviado: Jueves 16 de febrero de 2012 22:54
Asunto: Re: [Wien] Problems in generating case.struct using shell script and overlapping of spheres with error in lapw1

Dear Jose,
  I have tried all those also. when you give that then you will observe error in nn distances. Its not possible.
2012/2/17 Jose Alfredo Camargo Martinez <sork8686 at yahoo.es<mailto:sork8686 at yahoo.es><mailto:sork8686 at yahoo.es<mailto:sork8686 at yahoo.es>>>
One solution would be to increase the radii of MT

José A. Camargo Martínez
Estudiante Doctorado en Ciencias - Física
DEPARTAMENTO DE FÍSICA
CINVESTAV - MÉXICO D.F.
________________________________
De: Madhav Ghimire <ghimire.mpg at gmail.com<mailto:ghimire.mpg at gmail.com><mailto:ghimire.mpg at gmail.com<mailto:ghimire.mpg at gmail.com>>>
Para: wien <Wien at zeus.theochem.tuwien.ac.at<mailto:Wien at zeus.theochem.tuwien.ac.at><mailto:Wien at zeus.theochem.tuwien.ac.at<mailto:Wien at zeus.theochem.tuwien.ac.at>>>
Enviado: Jueves 16 de febrero de 2012 22:24
Asunto: [Wien] Problems in generating case.struct using shell script and overlapping of spheres with error in lapw1

Dear Peter Blaha and wien users,
    I am trying to run a very simple compound Bi2Se3 with the given lattice parameters and atomic positions for space group R3m (166).
The atomic positions along (x, y, z) are as follows:
Bi = 0, 0. 0.40046
Se (1) = 0, 0, 0.2097
Se (2) = 0, 0, 0
With the above given parameters, I initiated the calculations, but when I select l start =-6 or -9 or any value between -1 to -9.9 for energy to separate core and valence states, it shows that core charge leaks out of the spheres. Then the calculations stuck there itself. The error to this is as listed below:
Commandline: x lstart
Program input is: "13 -6.0 "

 SELECT XCPOT:

 recommended: 13: GGA (Perdew-Burke-Ernzerhof 96)

               5: LSDA

              11: GGA (Wu-Cohen 2006)

 SELECT ENERGY to separate core and valence states:

 recommended: -6.0 Ry (check how much core charge leaks out of MT-sphere)

 WARNING:  0.328380476966373       CORE electrons leak out of MT-sphere !!!!

 WARNING:   1.30946564796119       CORE electrons leak out of MT-sphere !!!!

 WARNING:   1.30946564796119       CORE electrons leak out of MT-sphere !!!!

LSTART ENDS

0.537u 0.023s 0:00.59 93.2%    0+0k 8+0io 0pf+0w


 When I perform for other compounds complexer than Bi2Se3, I resolve the problem easily by changing its RMT value or lattice parameters or the energy to separate core/valence states. Here I do not understand why this case arises. This case occurs especially for wien2k 05 to 09 version. I did the same calculation using wien2k 11 version, here I got through this problem by selecting 1.0 as the alternative option given as ALTERNATIVELY: specify charge localization (between 0.97 and 1.0) to select core state. Then once I complete initialization part and give a run scf cycles, I observe error in show dayfile as:

start   (Fri Feb 17 12:32:41 JST 2012) with lapw0 (40/99 to go)



   cycle 1    (Fri Feb 17 12:32:41 JST 2012)        (40/99 to go)



>   lapw0      (12:32:41) 11.846u 0.116s 0:12.02 99.4%       0+0k 0+4712io 0pf+0w

>   lapw1  -up         (12:32:53) 150.227u 0.014s 2:30.80 99.6%      0+0k 0+1088io 0pf+0w



>   stop error
To clarify this, I checked the error file and error is observed in lapw1 as listed below:
Error in LAPW1
 'SELECT' - no energy limits found for L= 2
 'SELECT' - E-bottom  -10.46100   E-top -200.00000
I do not understand why this case is observed in this particular compound although there had been a work on the same material using wien2k code.
Apart from this, I have a question regarding "How to generate a case.struct without using the w2web". I hope the experts in wien2k generally use shell script rather than the interface so hopefully you can instruct the step by step commands for generating case. struct.
Thank you in advance
Best regards
--
M. P. Ghimire

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--
M. P. Ghimire

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