Re: [Wien] No job scheduler

[Lawal Mohammed via Wien]

Dear Prof. Peter, 
Thanks a lot for your reply. 
I will try it.
Best wishes. 
Lawal 

Sent from Yahoo Mail on Android 
 
  On Mon, Jun 5, 2023 at 7:51 AM, Peter Blaha wrote:  
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[Wien] No job scheduler

[Lawal Mohammed via Wien]

Dear All,
Please I want to know if it's possible to run calculations on a cluster machine 
that doesn't have a job scheduler. If yes, please I need a guide on how to do 
it. Thanks a  lot for your time. 

Best wishes. 

Lawal
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Re: [Wien] XMCD spectra

[Lawal Mohammed]

I think in case.injoint number of columns should be 7, base on your input in 
case.inop. 

Sent from Yahoo Mail on Android 
 
  On Sat, May 4, 2019 at 12:15 PM, 
t...@theochem.tuwien.ac.at wrote:   Hi,

To which extent do the DFT and experimental spectra differ?
Is there still some very vague qualitative resemblance?

In practice DFT is an approximate method.
That means that disagreement with experiment is
always expected.

F. Tran

On Saturday 2019-05-04 12:30, KRISH wrote:

>Date: Sat, 4 May 2019 12:30:12
>From: KRISH 
>Reply-To: A Mailing list for WIEN2k users 
>To: wien@zeus.theochem.tuwien.ac.at
>Subject: [Wien] XMCD spectra
>
>Dear Wien2k Users,
>I am new to Wien2k. I am using WIEN2k 18.2 in Linux. I tried to calculated 
>XMCD spectra for US compound. 
>I have used the following steps to calculate the XMCD spectra for US (NaCl 
>structure)
>
>1. cif2cell us.cif
>2. init_lapw
>3. runsp_lapw
>4. delete brodyn files
>5. initso_lapw
>       Magnetic axis 1 1 1
>       No RLOs were used (Since optics does not work well with RLOs)
>6. us.in2 -TOT was changed to FERMI
>7. The system is metal -TETRA 101 inserted to us.in2 file
>8. IPRINT option was changed from 0 to 1 in 'us.inc' and 'us.inc_so' files
>9. Created us.indm, us.indmc, and us.inorb files (LSDA+U)
>10. runsp_lapw -so -orb -dm
>11. Using w2web -selected 
>12. Edited the us.inop file
>
>us.inop
>
> 1   number of k-points, first k-point
>-10.0 10.0  Emin, Emax for matrix elements, NBvalMAX
>XMCD 2 M45  optional line: for XMCD of 2nd atom and M45 spectrum
>7 number of choices (columns in *outmat): 2: hex or tetrag. case
>1 Re xx
>2 Re yy
>3 Re zz
>4 Re xy
>7 Im xy
>8 Im xz
>9 Im yz
>OFF   ON/OFF   writes MME to unit 4 
>
>13.  Using w2web -selected 
>14. Edited us.injoint
>
>us.injoint
>  
>1     : LOWER,UPPER and (optional) UPPER-VAL BANDINDEX
>-0.    0.00100   1. : EMIN DE EMAX FOR ENERGYGRID IN ryd
>eV    : output units  eV / ryd  / cm-1
>XMCD  : omitt these 4 lines for non-XMCD
>-255.34 -268.49   : core energies in Ry (grep :3D case.scfcup) 3d 
>and 3d*(scfcup)
>1.6  0.6  : core-hole broadening (eV) for both core states
>0.1   : spectrometer broadening (eV)
> 6    : SWITCH
> 4    : SWITCH
> 2    : NUMBER OF COLUMNS
>   0.1  0.1  0.3  : BROADENING (FOR DRUDE MODEL - switch 6,7 -
>ONLY)
>
>SWITCH:
>
>   0...JOINTDOS FOR EACH BAND COMBINATION
>   1...JOINTDOS AS SUM OVER ALL BAND COMBINATIONS
>   2...DOS FOR EACH BAND
>   3...DOS AS SUM OVER ALL BANDS
>   4...Im(EPSILON)
>   5...Im(EPSILON) for each band combination
>   6...INTRABAND contributions
>   7...INTRABAND contributions including band analysis
>
>15. Using w2web -selected 
>
> I obtained an XMCD (M4,5) spectra which does not match with the experiment. 
>Am I missing anything here? I do not understand why the calculated XMCD 
>spectra does not match with experiment. 
>Any help will be highly appreciated. 
>
>
>Thank you.
>KRISH
>
>
>
>
>  
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Re: [Wien] Need help to generate unit cell for semiconductor heterostructure

[Lawal Mohammed]

Thanks a lot Prof. Laurence Mark  and Delamora.I will study more and report 
back if there is any problem.
With kind regards.
Lawal 

 

On Monday, April 29, 2019, 1:27:18 AM GMT+8, Laurence Marks 
 wrote:  
 
 To generate such a superstructure you need to work out (aided by experiment) 
the relevant epitaxial relationship between the two, then create the 
appropriate nxm 2D semicoherent interface and extend in the third direction to 
a periodic structure.
This is a complex problem in bicrystallography. If you do not understand the 
terms above, enter "semi coherent interfaces" into Google and start reading!

_
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
On Sun, Apr 28, 2019, 17:23 delamora  wrote:

I suppose that you have TiO2 rutile, and ZnO rocksalt, so what do you mean by 
one layer?Also, they have very different unit cell parameters TiO2; 4.57, 4.57, 
2.93, ZnO; 3.81, so how can you put them one on top of the other?

Let me rewrite the question. We want to make a heterostructure of TiO2/ZnO, 
just two layers for now. Your response is highly appreciated.
Kind regards
Lawal



On Sunday, April 28, 2019, 7:01:09 AM GMT+8, delamora  wrote:

 Dear Developers and Users,
I need your help to generate unit cell of a semiconductor structure of two 
layers of different materials. Any hint is highly 
appreciated.Your question is not clear... 
There are many possibilitiesDo you want to put two layers? What materials do 
you want to put? Maybe you put two semiconductors, but together they are not 
semiconductors
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Re: [Wien] Need help to generate unit cell for semiconductor heterostructure

[Lawal Mohammed]

Thanks a lot Prof. Delamora for your reply.
Let me rewrite the question. We want to make a heterostructure of TiO2/ZnO, 
just two layers for now. Your response is highly appreciated.
Kind regards
Lawal 

 

On Sunday, April 28, 2019, 7:01:09 AM GMT+8, delamora  
wrote:  
 
 #yiv7308072348 P {margin-top:0;margin-bottom:0;} Dear Developers and Users,
I need your help to generate unit cell of a semiconductor structure of two 
layers of different materials. Any hint is highly 
appreciated.Your question is not clear... 
There are many possibilitiesDo you want to put two layers? What materials do 
you want to put? Maybe you put two semiconductors, but together they are not 
semiconductors
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[Wien] Need help to generate unit cell for semiconductor heterostructure

[Lawal Mohammed]

Dear Developers and Users,
I need your help to generate unit cell of a semiconductor structure of two 
layers of different materials. Any hint is highly appreciated.
Thanks a lot for your time.
With kind regards.
Lawal 

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Re: [Wien] Possible clash between different libiomp5.so library file

[Lawal Mohammed]

Thanks a lot Prof. L. Mark, I take your advice.
Actually I did nothing, because the system admin handled the issue after your 
first letter.Now, the issue of libiomp5.so is solved, I was told about an issue 
between the wien2k and intel_2015.
With kind regards.
Lawal 

 

On Thursday, January 10, 2019, 3:38:03 PM GMT+8, Laurence Marks 
 wrote:  
 
 Read the ouput from "ifort --help", or "man ifort". Learn!

_
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
On Wed, Jan 9, 2019, 23:21 Lawal Mohammed   (0x7fff3cfa7000)        libiomp5.so => 
/software/intel2015-1/composer_xe_2015.3.187/compiler/lib/intel64/libiomp5.so 
(0x2b8340b5f000)        libpthread.so.0 => /lib64/libpthread.so.0 
(0x2b8340e9f000)        libm.so.6 => /lib64/libm.so.6 (0x2b83410bf000)  
      libdl.so.2 => /lib64/libdl.so.2 (0x2b83413c7000)        libc.so.6 => 
/lib64/libc.so.6 (0x2b83415cf000)        /lib64/ld-linux-x86-64.so.2 
(0x2b8340937000)        libgcc_s.so.1 => /lib64/libgcc_s.so.1 
(0x2b8341997000)
The compilation and execution was done using composer_xe_2015.3.187, 
libiomp5.so seems to be in right directory. Please which part of compilation 
option should I edit, and I couldn't figure out what you mean by static 
compilation in this case. 
The system admin is interested, so I have already forward the link to this 
thread to him/them. 
With kind regards
Lawal



On Thursday, January 10, 2019, 10:17:23 AM GMT+8, Laurence Marks 
 wrote:

Try "ldd lapw0" to see what shared libraries are being used, then edit your 
compilation options to do static compilation. Depending upon what compiler your 
have the options will change; do "ifort --help | more" or "ifort --help > 
Fort.txt" and read (or gfortran, etc).
At least for the non-mpi you can build lapw0 & others without any shared 
libraries. I have never seen this fail, but it might.

On Wed, Jan 9, 2019, 19:58 Lawal Mohammed    lapw0  -p   (09:48:12) starting parallel lapw0 at Thu Jan 10 09:48:12 CST 
>2019 .machine0 : processorsrunning lapw0 in single mode0.022u 0.036s 
>0:00.08 62.5%     0+0k 0+56io 0pf+0werror: command   
>/software/wien2k-18.2/lapw0para lapw0.def   failed>   stop error
In the output file the error is:lapw0: relocation error: lapw0: symbol 
kmp_aligned_malloc, version VERSION not defined in file libiomp5.so with link 
time reference
grep: *scf1*: No such file or directory
grep: lapw2*.error: No such file or directory
Many thanks to Gavin for pointing out that the error was due to clash between 
other libraries with the  Intel Fortran library. However, after I reported the 
issue, system admin confirmed that the environmental variables was okay. Any 
help to rectify this issue is highly appreciated.
I will provide addition information if needed.
Thanks alot for your time.With kind regards.
Lawal


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Re: [Wien] Possible clash between different libiomp5.so library file

[Lawal Mohammed]

Thank you very much Prof. L. Mark,
"ldd lapw0" returned
linux-vdso.so.1 =>  (0x7fff3cfa7000)        libiomp5.so => 
/software/intel2015-1/composer_xe_2015.3.187/compiler/lib/intel64/libiomp5.so 
(0x2b8340b5f000)        libpthread.so.0 => /lib64/libpthread.so.0 
(0x2b8340e9f000)        libm.so.6 => /lib64/libm.so.6 (0x2b83410bf000)  
      libdl.so.2 => /lib64/libdl.so.2 (0x2b83413c7000)        libc.so.6 => 
/lib64/libc.so.6 (0x2b83415cf000)        /lib64/ld-linux-x86-64.so.2 
(0x2b8340937000)        libgcc_s.so.1 => /lib64/libgcc_s.so.1 
(0x2b8341997000)
The compilation and execution was done using composer_xe_2015.3.187, 
libiomp5.so seems to be in right directory. Please which part of compilation 
option should I edit, and I couldn't figure out what you mean by static 
compilation in this case. 
The system admin is interested, so I have already forward the link to this 
thread to him/them. 
With kind regards
Lawal 

 

On Thursday, January 10, 2019, 10:17:23 AM GMT+8, Laurence Marks 
 wrote:  
 
 Try "ldd lapw0" to see what shared libraries are being used, then edit your 
compilation options to do static compilation. Depending upon what compiler your 
have the options will change; do "ifort --help | more" or "ifort --help > 
Fort.txt" and read (or gfortran, etc).
At least for the non-mpi you can build lapw0 & others without any shared 
libraries. I have never seen this fail, but it might.

On Wed, Jan 9, 2019, 19:58 Lawal Mohammed    lapw0  -p   (09:48:12) starting parallel lapw0 at Thu Jan 10 09:48:12 CST 
>2019 .machine0 : processorsrunning lapw0 in single mode0.022u 0.036s 
>0:00.08 62.5%     0+0k 0+56io 0pf+0werror: command   
>/software/wien2k-18.2/lapw0para lapw0.def   failed>   stop error
In the output file the error is:lapw0: relocation error: lapw0: symbol 
kmp_aligned_malloc, version VERSION not defined in file libiomp5.so with link 
time reference
grep: *scf1*: No such file or directory
grep: lapw2*.error: No such file or directory
Many thanks to Gavin for pointing out that the error was due to clash between 
other libraries with the  Intel Fortran library. However, after I reported the 
issue, system admin confirmed that the environmental variables was okay. Any 
help to rectify this issue is highly appreciated.
I will provide addition information if needed.
Thanks alot for your time.With kind regards.
Lawal


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[Wien] Possible clash between different libiomp5.so library file

[Lawal Mohammed]

Dear Developers and Users,
I am facing a problem and need your help.The issue is an error when I submitted 
a job on cluster machine. The error message is:  
Calculating Bismuthtest1 in /home/username/WIEN2k/Bismuthtest1on node5 with PID 
21645using WIEN2k_18.2 (Release 17/7/2018) in /software/wien2k-18.2
    start       (Thu Jan 10 09:48:12 CST 2019) with lapw0 (100/99 to go)
    cycle 1     (Thu Jan 10 09:48:12 CST 2019)  (100/99 to go)
>   lapw0  -p   (09:48:12) starting parallel lapw0 at Thu Jan 10 09:48:12 CST 
>2019 .machine0 : processorsrunning lapw0 in single mode0.022u 0.036s 
>0:00.08 62.5%     0+0k 0+56io 0pf+0werror: command   
>/software/wien2k-18.2/lapw0para lapw0.def   failed>   stop error
In the output file the error is:lapw0: relocation error: lapw0: symbol 
kmp_aligned_malloc, version VERSION not defined in file libiomp5.so with link 
time reference
grep: *scf1*: No such file or directory
grep: lapw2*.error: No such file or directory
Many thanks to Gavin for pointing out that the error was due to clash between 
other libraries with the  Intel Fortran library. However, after I reported the 
issue, system admin confirmed that the environmental variables was okay. Any 
help to rectify this issue is highly appreciated.
I will provide addition information if needed.
Thanks alot for your time.With kind regards.
Lawal 

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Re: [Wien] STM

[Lawal Mohammed]

Dear Gavin,Thank you very much for the detail explanation. I will follow the 
suggestions.With kind regards

Lawal 

 

On Saturday, January 5, 2019, 11:47:52 PM GMT+8, Gavin Abo 
 wrote:  
 
  
Not an expert on the STM, so I could be wrong about some things, but my 
comments below.
 
 
Still on STM, I have a question regarding case.in3d, please what is the 
unit of the start and end value in the case.in3d file? For example, I have a 
test case with a vacuum of about 13 Angstrom.
 
Section 8.15.3 in the WIEN2k 18.2 usersguide has:
 
 top of file: case.in3d 
 100 100 100 # number of 3D-gridpoints in a-, b- and c-direction
 ...
 stm z 60 100 0.0001 # (optional) stmswitch, direction, start, end, density
 
 
--- bottom of file 
 
 
Looks to me that the start and end are unitless and are based on the gridpoints.
 
 What should be my start value (value above the surface atom) and end value 
(value around middle of vacuum)?
 Section 8.15.3 in the WIEN2k 18.2 usersguide has:
 
start specifies the first plane for the search of the given density (typically a
 value above the surface atom).
 
end specifies the last plane for the search of the given density (typically
 around middle of vacuum).
 
 
Sounds like something that can be found by trial and check.  If the start-end 
window is not able to capture the given density, move it or make it wider.  If 
the start-end search window is picking up an undesirable density, narrow the 
window to capture the one you want sort of thing.
 
 
 Also in the UG page 172, section 18.5 it's mentioned that "Optionally one 
can simulate a constant current STM image, where a height profile (above a 
surface slab) corresponding to a specific electron density value can be 
extracted from the case.xsf-file and written into case stm.xsf-file." Please 
the extraction of the electron density is it automatic or it should be done 
manually, and which file case.xsf or case_stm.xsf should be use for the 
plotting? 
 
 
Section 8.15 3DDENS (3D electron density plots in whole cell) in the UG has:
 
 
This program generates the charge density (or the potential) in the whole 
conventional (or primitive)
 unit cell on a three dimensional grid which can be used for plotting with an 
external program
 that can read .xsf-files (e.g., XCrysden, VESTA).
 
As the above says, the charge density case.xsf file should be generated 
automatically.
 
Section 8.15.3 in the WIEN2k 18.2 usersguide has:
 
stmswitch case_stm.xsf file is written, containing height values for the given 
density
 value.
 
As the above says, the stm image case_stm.xsf file should be generated 
automatically if the stmswitch parameter is set to "stm".
 
So if want the charge density plot, open case.xsf (in XCrySDen).  If you want 
the STM image plot, open the case_stm.xsf.
 
If you use lapw5's STM option instead of 3ddens, I'm not sure, but I'm thinking 
it outputs a case.rho file for the stm image data.  The rho file can be plotted 
with different programs 
[https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07125.html ].
 
 
You might have a look at the file SRC_lapw5/README_STM.docx.  That mentions it 
will also output a file in SEMPER format that can be read by the semper7 code.  
This is probably the semper-7.0beta image processing tool mentioned on Prof. 
Marks website [ http://www.numis.northwestern.edu/Software/Software.shtml ].

  
 
On Friday, December 7, 2018, 3:20:56 PM GMT+8, Peter Blaha 
 wrote:  
  
   STM simulations make only sense for a surface. You cannot make STM for a 
 bulk ???
 
 3ddens does not include tip vibrations, but is very fast and 
 conveniently lets you choose the best hight above the surface to 
 reproduce experimental images.
 
 Be careful with the STM mode of lapw5 in cases with angles differing 
 from 90 degrees !
 
 STM simulations are always a bit of an art, because the quality of the 
 experimental STM images changes a lot with group / time / 
 
 
 Am 07.12.2018 um 03:32 schrieb Lawal Mohammed:
 > Dear Developers and Users,
 > 
 > I need some advice on using the 3ddens program. My interest is to 
 > simulate STM image of a 3D system to compare with our experimental results.
 > My questions are:
 > 
 > Whether it's possible for 3D system.
 > What determine the size of the grid points?
 > Do I have to edit any file in my case directory before x 3ddens -XX?
 > 
 > I want to test run using TiC, what are the general tips? Any hint is 
 > highly appreciated.
 > 
 > Thanks a lot for your time.
 > 
 > With kind regards.
 > 
 > */Lawal 
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Re: [Wien] STM

[Lawal Mohammed]

Dear Prof. Peter and Users,
Still on STM, I have a question regarding case.in3d, please what is the unit of 
the start and end value in the case.in3d file? For example, I have a test case 
with a vacuum of about 13 Angstrom. What should be my start value (value above 
the surface atom) and end value (value around middle of vacuum)? Also in the UG 
page 172, section 18.5 it's mentioned that "Optionally one can simulate a 
constant current STM image, where a height profile (above a surface slab) 
corresponding to a specific electron density value can be extracted from the 
case.xsf-file and written into case stm.xsf-file." Please the extraction of the 
electron density is it automatic or it should be done manually, and which file 
case.xsf or case_stm.xsf should be use for the plotting? 

Thanks a lot for your time.
With kind regards.

Lawal 
On Friday, December 7, 2018, 3:20:56 PM GMT+8, Peter Blaha 
 wrote:  
 
 STM simulations make only sense for a surface. You cannot make STM for a 
bulk ???

3ddens does not include tip vibrations, but is very fast and 
conveniently lets you choose the best hight above the surface to 
reproduce experimental images.

Be careful with the STM mode of lapw5 in cases with angles differing 
from 90 degrees !

STM simulations are always a bit of an art, because the quality of the 
experimental STM images changes a lot with group / time / 


Am 07.12.2018 um 03:32 schrieb Lawal Mohammed:
> Dear Developers and Users,
> 
> I need some advice on using the 3ddens program. My interest is to 
> simulate STM image of a 3D system to compare with our experimental results.
> My questions are:
> 
> Whether it's possible for 3D system.
> What determine the size of the grid points?
> Do I have to edit any file in my case directory before x 3ddens -XX?
> 
> I want to test run using TiC, what are the general tips? Any hint is 
> highly appreciated.
> 
> Thanks a lot for your time.
> 
> With kind regards.
> 
> */Lawal
> /*
> 
> 
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--
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Phone: +43-1-58801-165300            FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.at    WIEN2k: http://www.wien2k.at
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Re: [Wien] STM

[Lawal Mohammed]

Dear Prof. Peter and Users,
Still on STM, I have a question regarding case.in3d, please what is the unit of 
the start and end value in the case.in3d file? For example, I have a test case 
with a vacuum of about 13 Angstrom. What should be my start value (value above 
the surface atom) and end value (value around middle of vacuum)? Also in the UG 
page 172, section 18.5 it's mentioned that "Optionally one can simulate a 
constant current STM image, where a height profile (above a surface slab) 
corresponding to a specific electron density value can be extracted from the 
case.xsf-file and written into case stm.xsf-file." extraction of the electron 
density is it automatic it should be done manually, and which file case.xsf or 
case_stm.xsf should be use the plotting? 

Thanks a lot for your time.
With kind regards.

Lawal 

 

On Friday, December 7, 2018, 3:20:56 PM GMT+8, Peter Blaha 
 wrote:  
 
 STM simulations make only sense for a surface. You cannot make STM for a 
bulk ???

3ddens does not include tip vibrations, but is very fast and 
conveniently lets you choose the best hight above the surface to 
reproduce experimental images.

Be careful with the STM mode of lapw5 in cases with angles differing 
from 90 degrees !

STM simulations are always a bit of an art, because the quality of the 
experimental STM images changes a lot with group / time / 


Am 07.12.2018 um 03:32 schrieb Lawal Mohammed:
> Dear Developers and Users,
> 
> I need some advice on using the 3ddens program. My interest is to 
> simulate STM image of a 3D system to compare with our experimental results.
> My questions are:
> 
> Whether it's possible for 3D system.
> What determine the size of the grid points?
> Do I have to edit any file in my case directory before x 3ddens -XX?
> 
> I want to test run using TiC, what are the general tips? Any hint is 
> highly appreciated.
> 
> Thanks a lot for your time.
> 
> With kind regards.
> 
> */Lawal
> /*
> 
> 
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> SEARCH the MAILING-LIST at:  
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--
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Phone: +43-1-58801-165300            FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.at    WIEN2k: http://www.wien2k.at
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Re: [Wien] STM

[Lawal Mohammed]

Dear Prof. Laurence and Peter,
 Thank you very much for making it more clear. 

It looks like I have to copy from the UG STM mode of lapw5, because in case.in5 
from SRC_templates, the STM mode lines are missing.

With kind regards.

Lawal 

 

On Friday, December 7, 2018, 3:20:56 PM GMT+8, Peter Blaha 
 wrote:  
 
 STM simulations make only sense for a surface. You cannot make STM for a 
bulk ???

3ddens does not include tip vibrations, but is very fast and 
conveniently lets you choose the best hight above the surface to 
reproduce experimental images.

Be careful with the STM mode of lapw5 in cases with angles differing 
from 90 degrees !

STM simulations are always a bit of an art, because the quality of the 
experimental STM images changes a lot with group / time / 


Am 07.12.2018 um 03:32 schrieb Lawal Mohammed:
> Dear Developers and Users,
> 
> I need some advice on using the 3ddens program. My interest is to 
> simulate STM image of a 3D system to compare with our experimental results.
> My questions are:
> 
> Whether it's possible for 3D system.
> What determine the size of the grid points?
> Do I have to edit any file in my case directory before x 3ddens -XX?
> 
> I want to test run using TiC, what are the general tips? Any hint is 
> highly appreciated.
> 
> Thanks a lot for your time.
> 
> With kind regards.
> 
> */Lawal
> /*
> 
> 
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> SEARCH the MAILING-LIST at:  
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> 

-- 
--
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Phone: +43-1-58801-165300            FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.at    WIEN2k: http://www.wien2k.at
WWW: 
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[Wien] STM

[Lawal Mohammed]

Dear Developers and Users,
I need some advice on using the 3ddens program. My interest is to simulate STM 
image of a 3D system to compare with our experimental results. My questions 
are: 

Whether it's possible for 3D system.What determine the size of the grid 
points?Do I have to edit any file in my case directory before x 3ddens -XX?
I want to test run using TiC, what are the general tips? Any hint is highly 
appreciated.
Thanks a lot for your time.
With kind regards.

Lawal 

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Re: [Wien] character plot, crystallography related and min_lapw

[Lawal Mohammed]

Dear Prof. Peter,
Thanks a lot. I got it now.
With kind regards
Lawal 

 

On Thursday, October 11, 2018, 3:28:30 PM GMT+8, Peter Blaha 
 wrote:  
 
 > Thank you very much for your suggestion. Yes, I have tried different 
> size of heavier plotting but in vain. What I observed was, the program 
> does not read/recognise my jtype input for my case, because on w2web 
> only atom number and size are printed. However, I can plot the band 
> structure without editing the band character options.

2 possibilities:
a) your case.insp file is wrong
b) you did not run the    x lapw2 -qtl step properly.


> I am sorry for going back, in my previous mail I used *-i 150*, but the 
> scf circles terminate at 40 iterations. Why should it stops at 40 while 
> it's suppose to reach 150, because of -i 150?

For min_lapw the -i 150 switch means  150 geometry steps.
In each geometry step a  "run_lapw -i 40" is issued by default (unless 
you use -j ) and apparently in your case the 40 scf cycles do not 
give converged forces.

As was mentioned before: usually run_lapw -min  (using MSR1a) is much 
more efficient then then the old min_lapw, but of course, if you have 
enough time to wait, you can still use the old way.

> 
> Many thanks for your time.
> 
> With kind regards.
> 
> */Lawal
> /*
> 
> 
> 
> On Thursday, October 11, 2018, 9:29:38 AM GMT+8, Gavin Abo 
>  wrote:
> 
> 
>> 1) I tried to plot band character by editing case.insp as explained in 
>> the user guide, but band character for the selected orbital is not 
>> showing. I run a TiC example as test-case and it works fine, what 
>> could have been the problem?
> 
> The band character plot using the default "line switch" of 0.2 works 
> well for TiC but it does not always work well for other structures [ 
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16414.html 
> ]. Have you tried increasing the "line switch" value?
> 
> 
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--
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Phone: +43-1-58801-165300            FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.at    WIEN2k: http://www.wien2k.at
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Re: [Wien] character plot, crystallography related and min_lapw

[Lawal Mohammed]

Dear Prof. Laurence Marks,
Thank you so much for your reply.
I will check on the points that you mentioned and also try the MSR1a option. In 
the meantime I will be equally grateful if someone respond to my first question.
With kind regards.

Lawal 

 

On Wednesday, October 10, 2018, 8:03:17 PM GMT+8, Laurence Marks 
 wrote:  
 
 Concerning 2), I believe hexagonal is always the primitive cell, with the 
caveat of rhombohedral cells.
Concerning 3), it is hard (impossible) to answer without more information. It 
could be any of: a) too large RMTs, b) not enough iterations to converge the 
forces, c) inappropriate convergence parameters, d) some other incorrect 
parameters.
Note: normally MSR1a using run**_lapw -min is better than min_lapw.

_
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

On Wed, Oct 10, 2018, 6:46 AM Lawal Mohammed  wrote:

Dear Developers and Users,
I need help on these three problems.
1) I tried to plot band character by editing case.insp as explained in the user 
guide, but band character for the selected orbital is not showing. I run a TiC 
example as test-case and it works fine, what could have been the problem?

2) I run Mg(OH)2 exercise (as contained in the workshop documents) for the 
optimization of positions. I noticed that the primitive cell and the 
conventional cell of theMg(OH)2 is the same when viewed using xcrysden, is this 
always the case H lattice or there are some exceptions?
3) Please is this command min_lapw -i 150 -p-NI correct? I tried it for non 
spin polarized case, but the scf terminated at 40 circles with forces not 
converged. I already have previous scf converged for volume optimization.

Thanks for your time, looking forward for help.
With kind regards.

Lawal


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[Wien] character plot, crystallography related and min_lapw

[Lawal Mohammed]

Dear Developers and Users,
I need help on these three problems.
1) I tried to plot band character by editing case.insp as explained in the user 
guide, but band character for the selected orbital is not showing. I run a TiC 
example as test-case and it works fine, what could have been the problem? 

2) I run Mg(OH)2 exercise (as contained in the workshop documents) for the 
optimization of positions. I noticed that the primitive cell and the 
conventional cell of the Mg(OH)2 is the same when viewed using xcrysden, is 
this always the case H lattice or there are some exceptions?
3) Please is this command min_lapw -i 150 -p -NI correct? I tried it for non 
spin polarized case, but the scf terminated at 40 circles with forces not 
converged. I already have previous scf converged for volume optimization.

Thanks for your time, looking forward for help.
With kind regards.

Lawal 

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Re: [Wien] Problem in wien2k17 installation on remote server

[Lawal Mohammed]

Dear Gavin,
I have tried WIEN2k 18.2, but got may be similar issues in lapw0 and lapw2 
parallel compilation. This time around the errors in both SRC_lapw0/compile.msg 
and SRC_lapw2/compile.msg are:
ld: cannot find -lfftw3_mpild: cannot find -lfftw3
Please how to resolve this problem.
Thanks for your time.
Regards
Lawal 

 

On Thursday, August 23, 2018, 8:18:34 PM GMT+8, Gavin Abo 
 wrote:  
 
  
In WIEN2k 18.2, I have in siteconfig:
 
   Libraries:
  
  F  FFTW options: -DFFTW3 -I/home/username/fftw3/include
  FFTW-LIBS:   -L/home/username/fftw3/lib -lfftw3
  FFTW-PLIBS: -lfftw3_mpi
 
 In my SRC_lapw0/compile.msg, I see:
 
 -DFFTW3 -I/home/username/fftw3/include
 
 In the /home/username/fftw3/include directory my system, I have the file 
fftw3.f03.
 
 In your SRC_lapw0/compile.msg, I see:
 
-I/BIGDATA1/app/intelcompiler/14.0.2/composer_xe_2013_sp1.2.144/mkl/include  
-DFFTW3 -I/usr/lib64/include
 
 Maybe the /usr/lib64/include directory does not have file fftw3.f03.  For 
serial complication, it should be possible to use the operating system fftw3 
library installed with package manager.  However, I don't think it provided the 
fftw3 mpi library file (libfftw_mpi.a) such that parallel compilation would not 
work with it.  The fftw3 library can be download [ 
http://www.fftw.org/download.html ] and installed [Refer to "Install the 
library fftw3" 
athttp://wien2k-algerien1970.blogspot.com/2016/08/how-to-install-version-2014-of-wien2k.html
 ].
 
 Also, I cannot remember for sure, but their may have been some siteconfig 
issues with fftw when parallel compiling in 17.1.  Those problems should 
however be fixed in WIEN2k 18.2.
 
 On 8/23/2018 1:56 AM, Lawal Mohammed wrote:
  
 
  Thank you very much. 
  Errors in SRC_lapw0/compile.msg and SRC_lapw2/compile.msg are similar:  
fft_modules.F(174): error #5102: Cannot open include file 'fftw3.f03' include 
'fftw3.f03'
  . .  I attached compile.msg file for checking.  
   It seems similar issue was reported in the list here. 
  [https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09751.html]
  
  
  But, it is for wien2k13.1, should I use the same suggestion for wien2k17.1? 
And my case is fftw3.f03 not fftw3-mpi.f03  
  Thanks for your time once again.
  
 Kind regards 
 Lawal 
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Re: [Wien] Problem in wien2k17 installation on remote server

[Lawal Mohammed]

Thank you very much.
Errors in SRC_lapw0/compile.msg and SRC_lapw2/compile.msg are similar: 
fft_modules.F(174): error #5102: Cannot open include file 'fftw3.f03' include 
'fftw3.f03'
..I attached compile.msg file for checking. 
It seems similar issue was reported in the list here.
[https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09751.html]


But, it is for wien2k13.1, should I use the same suggestion for wien2k17.1?And 
my case is fftw3.f03 not fftw3-mpi.f03 
Thanks for your time once again.

Kind regards
Lawal 
 

On Thursday, August 23, 2018, 8:07:28 AM GMT+8, Gavin Abo 
 wrote:  
 
  
The SRC_lapw1/compile.msg is fine now.
 
If you don't have lapw0_mpi and lapw2_mpi, you need to check 
SRC_lapw0/compile.msg and SRC_lapw2/compile.msg, respectively, for errors.
 On 8/22/2018 8:42 AM, Lawal Mohammed wrote:
  
 
 Dear Gavin, 
  Thank you very much for your help. 
  After rerun ./siteconfig_lapw which proper compiler setting, I think it looks 
ok now. However, I attached compile.msg file for checking.  
  Moreover, these are the mpi executable (dstart_mpi  lapw1c_mpi  lapw1_mpi  
lapwso_mpi) that was generated. I think there are still more (like lapw0_mpi, 
lapw2c_mpi  lapw2_mpi nlvdw_mpi) missing as per your previous advice.   
  Thanks a lot for your time. 
  Kind regards.  
Lawal 
 
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lapw0_compile.msg
Description: Binary data


lapw2_compile.msg
Description: Binary data
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Re: [Wien] Problem in wien2k17 installation on remote server

[Lawal Mohammed]

Dear Gavin,
Thank you very much for your help.
After rerun ./siteconfig_lapw which proper compiler setting, I think it looks 
ok now. However, I attached compile.msg file for checking. 
Moreover, these are the mpi executable (dstart_mpi  lapw1c_mpi  lapw1_mpi  
lapwso_mpi) that was generated. I think there are still more (like lapw0_mpi, 
lapw2c_mpi  lapw2_mpi nlvdw_mpi) missing as per your previous advice.  
Thanks a lot for your time.
Kind regards.
Lawal 

 

On Wednesday, August 22, 2018, 12:10:59 PM GMT+8, Gavin Abo 
 wrote:  
 
  
In the SRC_lapw1/compile.msg that you sent, look at the error message:
 
ld: cannot find -lmkl_lapack
 
 
If you check the Intel mkl documentation 
[https://software.intel.com/en-us/mkl-linux-developer-guide-listing-libraries-on-a-link-line
 ], it indicates for 64 bit that the lapack library flag should be 
"-lmkl_lapack95_lp64", but the message shows it fails as "-lmkl_lapack" was 
used instead (in the compiler settings set using ./siteconfig_lapw).
 
 On 8/21/2018 7:54 AM, Lawal Mohammed wrote:
  
 
  Dear developers and users, 
  I need help, I got some problems when I tried to compile the wien2k17 
remotely on supercomputer, with some error messages during ./siteconfig_lapw.  
  I need your help to check the attached compile.msg file and advice me on way 
forward. Furthermore, fine grained parallel was selected (y), but no mpi 
executables generated.  
  I am not good in parallelization. 
  Thank you for your time. 
  Kind regards  
  Lawal 
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[Wien] Problem in wien2k17 installation on remote server

[Lawal Mohammed]

Dear developers and users,
I need help, I got some problems when I tried to compile the wien2k17 remotely 
on supercomputer, with some error messages during ./siteconfig_lapw. 
I need your help to check the attached compile.msg file and advice me on way 
forward.Furthermore, fine grained parallel was selected (y), but no mpi 
executables generated. 
I am not good in parallelization.
Thank you for your time.
Kind regards
Lawal 
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Re: [Wien] Some questions about output files

[Lawal Mohammed]

Probably the note of Prof. Stefaan Cottenier (see chapter 7) @ 
http://susi.theochem.tuwien.ac.at/reg_user/textbooks/DFT_and_LAPW_2nd.pdf will 
help you for your first question. 
Regards.
Lawal 

 

On Tuesday, May 15, 2018, 10:38:14 AM GMT+8, Gavin Abo 
 wrote:  
 
   
I'm fairly certain that the asterisk's symbol (*) corresponds to the s = -1 
column for the orbital quantum number (j) in Table 6.6 on page 107 in the 
WIEN2k 17.1 usersguide [ 
http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf ].  For 
example, p* is the 1/2. Without the asterisk, the p is the 3/2 in the s = +1 
column. 
 
 
>From what I have read, the :BAN label block in case.scf or case.scf2* shows 
>only the bands around EF 
>[https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13238.html ].
 
 On 5/14/2018 4:31 PM, Sergio Castillo Robles wrote:
  
 Hi dear Wien users,
 
 I am running the latest version of wien2k, 17.1
 
  I have a couple of questions about output files generated with wien2k, I was 
looking for answers in the UG and other sites but i couldn't find the answer.
 
  The first question is about the asterisks simbols that appears after the 
selection of the separation energy between core and valence states in lstart, I 
can see that some orbitals are tagged with an asterisk, what are the asterisk 
standing for? Maybe its an obvious answer but i can't figure  it out.
 
  The other question is about the bands showing in the scf2 file, why does it 
only shows a fraction of the total bands? (apparently the last 16 bands)  
 
  Thanks for your time and patience. Best regards.
  
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Re: [Wien] File for vacuum size

[Lawal Mohammed]

Dear Gavin,

Thank you so much for the explanation. The issue is resolved.
Please why do you used z=1 for the atom 1 position, while in the attached file 
it is z=0?

Thank you once again

Best regards

Lawal 

 

On Wednesday, May 2, 2018, 8:49:58 AM GMT+8, Gavin Abo 
<gs...@crimson.ua.edu> wrote:  
 
 This message is eligible for Automatic Cleanup! (gs...@crimson.ua.edu) Add 
cleanup rule | More info
  
I could be wrong, but as far as I know, there is currently no output file or 
program in WIEN2k to recover the vacuum thickness created by "x supercell" or 
the structeditor.
 
So, to get the vacuum thickness, you would have to look at the lattice 
parameters and atomic positions in case.struct, then calculate it by hand.
 
 
For example, if you look at the struct file at:
 
 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10104/FeCoAl31.17.struct
 
 The lattice parameters are:
 
 a = 5.414068 bohr, b = 5.414068 bohr, c = 65.769000 bohr
 
 The atomic position of atom 1 is:
 
 X=0. Y=0. Z=0. => Z=1-0. = 1
 
 The atomic position of atom 18 is:
 
 18: X=0. Y=0. Z=0.50298923 => Z=0.502989
 
 It looks like there is a vacuum between Z = 0.502989 and Z = 1.  This seems 
to be a vacuum thickness of ~33 bohr [=(1-0.502989)*c = (1-0.502989)*65.769 
bohr].
 
 If you are able to measure the distance between two atoms creating the vacuum 
region using XCrySDen [  http://www.xcrysden.org/doc/measure.html ] or VESTA 
[http://aims.pratt.duke.edu/sites/aims.pratt.duke.edu/files/HandsOnVesta.pdf 
(slide 5) , http://jp-minerals.org/vesta/en/features.html ], then maybe could 
also get the vacuum thickness that way.
 
 On 5/1/2018 7:56 AM, Lawal Mohammed wrote:
  
Dear Developers and Users,
 
 I need your help on this. It is known that, one can use x supercell or 
structeditor to create a surface or a cluster etc. 
   Please, which file to look for information on the vacuum thickness of the 
case.struct?
 
 Thanks a lot for your time.
 
 Best regards
   
Lawal 
 

 
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[Wien] File for vacuum size

[Lawal Mohammed]

Dear Developers and Users,

I need your help on this. It is known that, one can use x supercell or 
structeditor to create a surface or a cluster etc. 
Please, which file to look for information on the vacuum thickness of the 
case.struct?

Thanks a lot for your time.

Best regards

Lawal 

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Re: [Wien] AFM calculations

[Lawal Mohammed]

Thanks a lot Prof. Peter.

I run a test case with O2, I got a difference of about 0.04Ry. With sp 
calculations having the lower energy.

Regards
 
Lawal 

 

On Tuesday, April 24, 2018, 1:36:29 PM GMT+8, Peter Blaha 
<pbl...@theochem.tuwien.ac.at> wrote:  
 
 This message is eligible for Automatic Cleanup! (pbl...@theochem.tuwien.ac.at) 
Add cleanup rule | More info
 Because for cohesive energies you need the ground state energies of the 
atoms/molecules involved.

And the ground state of O2 has 2 unpaired electrons, i.e. it requeres a 
spin polarized calculation.

Test it yourself: Do a spin and non-spinpolarized calculationfor O2 (in 
2 directories) with otherwise identical parameters. Which energy is lower ?

Am 24.04.2018 um 05:19 schrieb Lawal Mohammed:
> Dear Prof. Peter,
> 
> Thanks a lot for the explanation. I have another question in this regard.
> Please why do we have to do spin-polarized calculation for O2 *(or for 
> non-closed shell elements)* as mentioned in the FAQ page under 
> *Calculations of cohesive or formation energies 
> <http://susi.theochem.tuwien.ac.at/reg_user/faq/cohesive_energies.html>*?
> 
> Thanks very much for your time.
> 
> Kind regards.
> 
> */Lawal
> /*
> 
> 
> 
> 
> 
> On Monday, April 23, 2018, 1:10:32 PM GMT+8, Peter Blaha 
> <pbl...@theochem.tuwien.ac.at> wrote:
> 
> 
> Without SO: You can either use runafm (if you can figure out the correct
> symmetry operation which transforms spin-up into spin-dn atoms) OR
> runsp_lapw (takes twice as much cpu time, but is "simpler").
> 
> With SO you must use runsp. runafm does not support spin-orbit.
> 
> 
> Am 20.04.2018 um 13:24 schrieb Lawal Mohammed:
>  > Dear respected Developers and Users,
>  >
>  > I am trying to understand how to do AFM calculations with SO. I read
>  > section 4.5.4 of the UG and check some threads in the wien list.
>  >
>  > The way I understand it, one can choose either of the two options.
>  >
>  > 1-run runsp_lapw and then do scf with SO
>  >
>  > OR
>  >
>  > 2-runafm_lapw and then do SO
>  >
>  > I may probably be wrong. I want to test run with Fe2O3.
>  >
>  > Any advice is highly appreciated.
>  >
>  > Regards
>  >
>  > */Lawal
> 
>  > /*
>  >
>  >
>  >
>  >
>  >
>  > ___
>  > Wien mailing list
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>  >
> 
> -- 
> --
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> Phone: +43-1-58801-165300            FAX: +43-1-58801-165982
> Email: bl...@theochem.tuwien.ac.at <mailto:bl...@theochem.tuwien.ac.at>  
>    WIEN2k: http://www.wien2k.at
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-- 
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Phone: +43-1-58801-165300            FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.at    WIEN2k: http://www.wien2k.at
WWW: 
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Re: [Wien] AFM calculations

[Lawal Mohammed]

Dear Prof. Peter,

Thanks a lot for the explanation. I have another question in this regard.
Please why do we have to do spin-polarized calculation for O2 (or for 
non-closed shell elements) as mentioned in the FAQ page under  Calculations of 
cohesive or formation energies?

Thanks very much for your time.

Kind regards.

Lawal 




 

On Monday, April 23, 2018, 1:10:32 PM GMT+8, Peter Blaha 
<pbl...@theochem.tuwien.ac.at> wrote:  
 
 Without SO: You can either use runafm (if you can figure out the correct 
symmetry operation which transforms spin-up into spin-dn atoms) OR 
runsp_lapw (takes twice as much cpu time, but is "simpler").

With SO you must use runsp. runafm does not support spin-orbit.


Am 20.04.2018 um 13:24 schrieb Lawal Mohammed:
> Dear respected Developers and Users,
> 
> I am trying to understand how to do AFM calculations with SO. I read 
> section 4.5.4 of the UG and check some threads in the wien list.
> 
> The way I understand it, one can choose either of the two options.
> 
> 1-run runsp_lapw and then do scf with SO
> 
> OR
> 
> 2-runafm_lapw and then do SO
> 
> I may probably be wrong. I want to test run with Fe2O3.
> 
> Any advice is highly appreciated.
> 
> Regards
> 
> */Lawal
> /*
> 
> 
> 
> 
> 
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-- 
--
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Phone: +43-1-58801-165300            FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.at    WIEN2k: http://www.wien2k.at
WWW: 
http://www.imc.tuwien.ac.at/tc_blaha-
 

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Re: [Wien] Optic

[Lawal Mohammed]

Dear Dr. Alias,
Thank you very much for the explanation.
Please what really cause these excitations since we're dealing with the ground 
state properties?
 Any comment in this regard is highly appreciated.
Lawal Mohammed
 
 From: Elias Assmann <elias.assm...@gmail.com>
 To: A Mailing list for WIEN2k users <wien@zeus.theochem.tuwien.ac.at> 
 Sent: Friday, September 18, 2015 6:56 PM
 Subject: Re: [Wien] Optic
   
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1



On 09/15/2015 08:36 PM, Lawal Mohammed wrote:
> I understand that in gga/lda the Kohn-Sham eigenstates are regarded
> as excited only when the scissors operator is non zero, is this
> correct? If yes then how valid is optical calculation when the
> scissors operator is set to zero? If no then what bring about the
> optical excitations that allow determination of some optical
> properties?

The “scissors operator” is simply a rigid shift of the unoccupied
bands in energy (where rigid means that the states themselves are not
changed).  This is done to “correct” band gaps which come out wrong
(usually too small) in DFT.  An optical excitation takes an electron
from an occupied to an unoccupied state.  This means that the scissors
operator will change the energies where these excitations are
possible, e.g. to adjust the optical gap in your calculation to the
experimental value.

HTH,

    Elias


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[Wien] Optic

[Lawal Mohammed]

Dear Developers and Users,
I need some guidance.

I understand that in gga/lda the Kohn-Sham eigenstates are regarded as excited 
only when the scissors operator is non zero, is this correct? 
If yes then how valid is optical calculation when the scissors operator is set 
to zero? If no then what bring about the optical excitations that allow 
determination of some optical properties?

Thanks in advance

With Kind regards
Lawal Mohammed


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Re: [Wien] Factroization Error in Boltztrap

[Lawal Mohammed]

http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg10656.html 
http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg10661.htmlhttp://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg10963.htmlhttp://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg08701.html
  http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg11759.html   
Lawal Mohammed
You do not really understand something until you can explain it to your 
grandmother. Albert Einstein
 


 On Saturday, June 20, 2015 6:18 AM, Abdul Jalil jalila...@gmail.com 
wrote:
   

 
Hello
I am using BoltzTraP code for the calculations of hall coefficents. 
Whats the reason of factroization error ?
Regards
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Re: [Wien] Symmetry related

[Lawal Mohammed]

Dear Dr. Víctor Luaña,
Thanks so much for the explanation.
Kind regards 
Lawal Mohammed 


 On Saturday, May 2, 2015 5:10 PM, Víctor Luaña Cabal 
vic...@fluor.quimica.uniovi.es wrote:
   

 On Sat, May 02, 2015 at 08:25:25AM +, Lawal Mohammed wrote:
 Dear Developers and Users
  Please what is wrong in having P1 symmetry? I got P1 when I
 initialized supercell calculations. In the mail archive P1 is regarded
 as less efficient. How can I improve the symmetry at the same time
 maintaining same structure? Could somebody elaborate please.

Lawal,

1) Nothing is wrong. P1 eans that there is no rotational symmetry
  available in your crystal. Rotattion, reflection, inversion, etc.

2) Unfortunately symmetry elements (other than traslation) are used
  by the codes to refuce the computationl cost so it may represent
  bad news. Traslation is also used, but that is implicit, as
  you are using solid state codes designed for crystals.

3) This computer experiment may help you to understand: Take a simple
  compund and reduce the symetry progressively. You will see how the
  computer time required for the calculation increases. The less
  symmetry operations available the higher the cpu involved.
  Bad news if your disponibility of computer resources is limited.

Best regards,
            Dr. Víctor Luaña
--
    .  .    Research is to see what everybody else has seen, and to
    / `' \  think what nobody else has thought-- Albert Szent-Gyorgi
  /(o)(o)\  
  /`. \/ .'\  Lo mediocre es peor que lo bueno, pero también es peor
 /  '`'`  \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist  prof. ! 
! Departamento de Química Física y Analítica ! 
! Universidad de Oviedo, 33006-Oviedo, Spain ! 
! e-mail:  vic...@fluor.quimica.uniovi.es  ! 
! phone: +34-985-103491  fax: +34-985-103125 ! 
++
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            (being reworked)
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[Wien] Fw: NN error during initialization

[Lawal Mohammed]

Dear All,I am forwarding this message on behalf of my colleague, who tried 
without success to get his question answered. Thank you.
Kind regards 
Lawal Mohammed

  On Thursday, March 19, 2015 6:24 PM, Auwalu Musa 
auwalu_m...@yahoo.co.uk wrote:
   

 

  On Monday, 16 March 2015, 15:18, Auwalu Musa auwalu_m...@yahoo.co.uk 
wrote:
   

 Dear Developers and Users
I am a new user of the wien2k, I have got an error when I try to run x nn.My 
aim is to calculate the optical properties of oligoacene starting from benzene. 
Following the instruction in the UG. I construct the struct file, set RMT for 
Carbon and Hydrogen (1.0 and 0.6). Then I got this errorspecify nn-bondlength 
factor: (usually=2) [and optionally dlimit, dstmax (about
  1.d-5, 20)]
 DSTMAX:   20.275371000 
 iix,iiy,iiz   2   2   3   28.194726000 
   36.5322039.877017000 

   ERROR !!!
 RMT(  1)=1.0 AND RMT(  4)=1.0
 SUMS TO 2.0 GT NNN-DIST= 0.0
FATAL ERROR, Atoms   1 and   4 sit at identical positions
NN-ERROR: identical positions

Please I need your help. Thank you.

Musa   



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[Wien] structeditor

[Lawal Mohammed]

Dear Developers and Users;
I have some problems and I need your help.
(1) I am trying to make a replacement on interstitial sites of a given crystal 
system. But, it looks like the atomic ID in xcrysden doesn't represent the 
atomic index (ind) in the readme.txt of the structeditor. If I am right then, 
is there any package that can be used for that purpose?
 (2) How can I use vacuum in three directions using the structeditor?
Your help is highly welcome.
Regards
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Re: [Wien] triclinic optimization

[Lawal Mohammed]

Dear Peter Blaha Sir,

Thank you for your reply.
Actually as you have mentioned that

    for a triclinic case a 6D search by E-tot only is hardly possible. 
somewhere here 
http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg01914.html

I thought there is a way around it. 

With kind regards
Lawal Mohammed


On Sunday, April 13, 2014 11:01 PM, Peter Blaha pbl...@theochem.tuwien.ac.at 
wrote:
 
You cannot optimize all 6 lattice parameters (a,b,c,,alpha,beta,gamma)
with wien2k (in a reasonable time).


Am 13.04.2014 09:25, schrieb Lawal Mohammed:
 Dear Developers and Users,

 I am trying to optimize lattice parameters for a triclinic crystal system, 
 but there is no option for triclinic in the optimizer.
 Any hint in this regard is appreciated.

 Kind regards
 Lawal Mohammed


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Fax: +43-1-5880115698
email: pbl...@theochem.tuwien.ac.at
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[Wien] triclinic optimization

[Lawal Mohammed]

Dear Developers and Users,

I am trying to optimize lattice parameters for a triclinic crystal system, but 
there is no option for triclinic in the optimizer.
Any hint in this regard is appreciated.

Kind regards
Lawal Mohammed
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[Wien] structeditor

[Lawal Mohammed]

Dear Developers and Users,
 
I understand that STRUCTEDITOR need octave environment, which is working on my 
system. The question is I don't know how to install the structeditor and I need 
your help to do that. 

In the readme.txt (/SRC_structeditor/doc), it says 

*Compile fortran sources (SRC_*) and copy binaries to bin.
 To do this adjust options in make.inc file and run install script.
*Make sure that octave will find the bin directory, e.g. update
 octave enviroment variables:  OCTAVE_EXEC_PATH, OCTAVE_PATH 

In my bashrc I have      
export STRUCTEDIT_PATH=$WIENROOT/SRC_structeditor/bin
export OCTAVE_EXEC_PATH=${PATH}::
export OCTAVE_PATH=${STRUCTEDIT_PATH}::
So, I assume that my  octave environment variables are updated.

However, I don't know how to adjust options in make.inc file and run install 
script?

Always appreciating your help.

Kind regards
Lawal Mohammed
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Re: [Wien] structeditor

[Lawal Mohammed]

Dear Robert, Sir,

 Thank you for your help.


Yes it works, I will start practising the examples. 

Kind regards
Lawal Mohammed





On Friday, March 28, 2014 3:34 PM, Robert Laskowski rol...@ihpc.a-star.edu.sg 
wrote:
 
Hi,
 
I think the install script did it for you. Go to any of your case directories, 
start octave, and try to load the struct file,
type s=loadstruct(yourcase.struct), if this works then you have it.
 
regards
 
Robert
 
 
On 28 March 2014 AM 12:25:07 Lawal Mohammed wrote:

Dear Developers and Users,
 
I understand that STRUCTEDITOR need octave environment, which is working on my 
system. The question is I don't know how to install the structeditor and I need 
your help to do that. 

In the readme.txt (/SRC_structeditor/doc), it says 

*Compile fortran sources (SRC_*) and copy binaries to bin.
 To do this adjust options in make.inc file and run install script.
*Make sure that octave will find the bin directory, e.g. update
 octave enviroment variables:  OCTAVE_EXEC_PATH, OCTAVE_PATH 

In my bashrc I have      
export STRUCTEDIT_PATH=$WIENROOT/SRC_structeditor/bin
export OCTAVE_EXEC_PATH=${PATH}::
export OCTAVE_PATH=${STRUCTEDIT_PATH}::
So, I assume that my  octave environment variables are updated.

However, I don't know how to adjust options in make.inc file and run install 
script?

Always appreciating your help.

Kind regards
Lawal Mohammed



-- 
==
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Institute of High Performance Computing, A*STAR
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Tel(Off): +65. 64191493 Fax: +65. 64632536
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[Wien] Error in lapw2 during DOS

[Lawal Mohammed]

Dear Developers and Users,

We are trying to improve our calculation by using MBJ potential. Electron 
charge density finished successfully,as we run x lapw2 -qtl for DOS this error 
appears.

forrtl: severe (24): end-of-file during read, unit 10, file 
/root/WIEN2k/mbj/./mbj.vector
Image  PCRoutineLineSource  
   
lapw2  0053BE1A  Unknown   Unknown  Unknown
lapw2  0053A995  Unknown   Unknown  Unknown
lapw2  004DF6B6  Unknown   Unknown  Unknown
lapw2  0049C476  Unknown   Unknown  Unknown
lapw2  0049BBE9  Unknown   Unknown  Unknown
lapw2  004B7DD4  Unknown   Unknown  Unknown
lapw2  0045E0D5  l2main_   618  
l2main_tmp_.F
lapw2  00474CAC  MAIN__564  lapw2_tmp_.F
lapw2  00403CEC  Unknown   Unknown  Unknown
libc.so.6  00346442169D  Unknown   Unknown  Unknown
lapw2  00403BE9  Unknown   Unknown  Unknown
0.441u 0.025s 0:00.46 100.0%0+0k 0+3424io 0pf+0w
error: command   /home/mohammed/WIEN2K/lapw2 lapw2.def   failed 
We need help from you to overcome this problem.

With best regards
Lawal Mohammed
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Re: [Wien] find minimum

[Lawal Mohammed]

Dear Gavin Abo, Sir,

In line with the discussion above, I got when I plot E vs c/a the following

Fit of:  E = a1 + a2*x + a3*x^2 + a4*x^3 + a5*x^4
a1                    1.000
a2                 0.000    1.000
a3                    -0.761   -0.000    1.000
a4                    -0.000   -0.930    0.000    1.000
a5                 0.642    0.000    -0.972   -0.000    1.000   

In this case what should be the value for a2, a3, a4, and a5? 

Thank you in advance for your response.
With kind regards
Mohammed Lawal 





On Friday, January 24, 2014 7:08 AM, Gavin Abo gs...@crimson.ua.edu wrote:
 
Below is a summary of previous posts that should help.

To plot energy vs b/a:

(a) You should be able to rename the scf files and then plot with
  the energy vs c/a option of eplot
[http://zeus.theochem.tuwien.ac.at/pipermail/wien/2009-January/012053.html].
(b) You could also plot energy vs b/a in another program like
  Origin
[http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08841.html].

To get the optimized c/a (or b/a) value,  you can calculate it
  from the curve fit equation
[http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05826.html].

An example calculation is given below.

When you plot E vs. c/a with eplot, you should get something like:

Fit of:  E = a1 + a2*x + a3*x^2 + a4*x^3 + a5*x^4
a1  = -2201.24
a2  = 0.00233422
a3  = 0.000188276
a4  = 1.33462e-05
a5  = 9.76521e-07

From dE/dx = 0, we get the equation:

a2 + 2*a3*x+3*a4*x^2+4*a5*x^3 = 0

Solving this equation for x, x = -7.7555, which is the optimized
  c/a ratio in %.  I got x with Octave, but there are other software
  programs that you can find on the internet to solve the polynomial
  equation.

Octave input:

dEdx = [4*9.76521e-07,3*1.33462e-05,2*0.000188276,0.00233422]
roots(dEdx)

Octave output:

  -1.2474 + 8.6889i
  -1.2474 - 8.6889i
  -7.7555 + 0.i  = This polynomial root is chosen as x,
  because the imaginary part is zero and it appears in the energy vs
  c/a plot.

If you also want the minimum E, just plug the x value back into
  the curve fit equation and solve for E (= -2201.2495).

On 1/22/2014 7:22 AM, MAHDI SALMANI HIRMAND wrote:

Dear Prof. Blaha,
Please let me know why there is not a program for finding minimum of c/a or 
b/a ratio with Wien2k Package when we optimize c/a or b/a.
eplot program can show curve of Energy Vs. c/a but it doesn't find minimum of 
c/a.
Please guide me
With best
Mahdi

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[Wien] pseudo convergence

[Lawal Mohammed]

Dear Developers and Users,

Please, how can I know that the mBJ cycle stops at fake convergence?
Any response is appreciated.

With regards
Mohammed Lawal
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Re: [Wien] Need help

[Lawal Mohammed]

Dear Dr. H.A.Rahnamaye Aliabad,

Thank you for your help. I did that, but still I am having issues. I was 
prompted to 

give x and y-offset scaling factors (in units of d12)

The question is that I don't know what x and y-offset scaling factors are. If 
you can explain further I will be grateful.
With regards
Lawal







On Wednesday, January 8, 2014 2:58 PM, hossien rahnama h_rahna...@yahoo.com 
wrote:
 
Dear Lawal,
You have to run in Terminal as a separate command.
Yours,
Rahnama
 
Dr. H.A.Rahnamaye Aliabad,
Assistant Professor,
Department of physics,Hakim Sabzevari University,
Sabzevar,Iran
Tel:+98-571-4003155
Fax:+98-571-4411161
Academic email:rahn...@hsu.ac.ir



On Wednesday, January 8, 2014 8:46 AM, Lawal Mohammed 
mohammedlawa...@yahoo.com wrote:
 
Dear Developers and users,
I have got a problem. I am using wien2k 11 version. I don't know where to 
locate rhomb_in5 program in w2web. Can someone please help on how to use the 
program?  
Regards
Lawal

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[Wien] Need help

[Lawal Mohammed]

Dear Developers and users,
I have got a problem. I am using wien2k 11 version. I don't know where to 
locate rhomb_in5 program in w2web. Can someone please help on how to use the 
program?  
Regards
Lawal
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[Wien] installation issues

[Lawal Mohammed]

Dear users and developers 


We are having problems with two of our systems, and couldn't figure out what is 
wrong. Even after checking the mailing list.
 1- We couldn't plot our output using rhoplot, For example, when we try 
 electron density plots for TiC, there was no visual. However, it works 
in some of our systems under the same condition.
 2- When I try to copy/upload the original case struct file into a new 
directory for supercell calculations I got this msg

 Can't locate CGI.pm in @INC (@INC contains: /usr/local/lib64/perl5 
/usr/local/share/perl5 /usr/lib64/perl5/vendor_perl 
/usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at 
/home/mohammed/WIEN2K/SRC_w2web/htdocs/util/upload2.pl line 3. BEGIN 
failed--compilation aborted at 
/home/mohammed/WIEN2K/SRC_w2web/htdocs/util/upload2.pl line 3.


However, it works on one of our system. If there are any info that anybody may 
need to assist we will be grateful to provide.

With best regards

Mohammed lawal
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Re: [Wien] installation issues

[Lawal Mohammed]

Thank you so much Prof. Peter Blaha, Abo Gavin, ...
The link you provided help. The issues are now resolved using two commands
1) yum install gnutplot gnuplot-x11   
2) yum install perl-CGI
in fedora 16 and18.

Another issue, in this regard, I got this error 

/home/mohammed/WIEN2K/lapw0: error while loading shared libraries: 
libmkl_intel_lp64.so: cannot open shared object file: No such file or directory 
   stop error
while running scf, Chakrabarti Shamik suggested that it is because the path for 
the file (libmkl_intel_lp64.so) is not properly given during compilation of 
wien2k (during userconfig_lapw). If that is the case, can anybody please tell 
me how to set the path for that file properly.

Thanking you all in advance for your response.

Best regards.








On Friday, October 18, 2013 3:30 PM, Gavin Abo gs...@crimson.ua.edu wrote:
 
1- Is gnuplot installed on the non-working systems? Of note, it could be 
installed with sudo apt-get install gnuplot on older Ubuntu versions.  
However, I believe you have to use now sudo apt-get install gnuplot 
gnuplot-x11 on recent Ubuntu versions, since it seems that they decided to 
remove gnuplot-x11 as a dependency of gnuplot.

2- You likely need to install a missing Perl module.  For example,
  for Fedora:

https://ask.fedoraproject.org/question/8330/where-is-perl-module-cgipm-installed/

Since we don't know what operating systems you are using, you can
  search the Internet or your OS support (manual, forum, etc) on how
  to install these for your systems.

On 10/18/2013 12:27 AM, Lawal Mohammed wrote:

Dear users and developers 



We are having problems with two of our systems, and couldn't figure out what 
is wrong. Even after checking the mailing list.
 1- We couldn't plot our output using rhoplot, For example,
  when we try  electron density plots for TiC, there was no
  visual. However, it works in some of our systems under the
  same condition.
 2- When I try to copy/upload the original case struct file
  into a new directory for supercell calculations I got this msg

 Can't locate CGI.pm in @INC (@INC contains:
  /usr/local/lib64/perl5 /usr/local/share/perl5
  /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl
  /usr/lib64/perl5 /usr/share/perl5 .) at
  /home/mohammed/WIEN2K/SRC_w2web/htdocs/util/upload2.pl line 3.
  BEGIN failed--compilation aborted at
  /home/mohammed/WIEN2K/SRC_w2web/htdocs/util/upload2.pl line 3.



However, it works on one of our system. If there are any info that anybody may 
need to assist we will be grateful to provide.

With best regards

Mohammed lawal
universiti Technologi Malaysia



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Re: [Wien] (no subject)

[Lawal Mohammed]

Thank you Sir,
I have attached my struct file for you. For RMT I used 2.5 for Sb and 2.0 for 
S,  but when I set automatically RMT and cont.. editing the RMT of the two 
different atoms become same, i.e. 1.43. Also as you have said I lower the 
core-separation energy to -8.0 Ry and -10.0 Ry, and I got the same leakage 
(0.074 for Sb and 0.021 for S).




On Monday, October 14, 2013 3:19 PM, Peter Blaha pbl...@theochem.tuwien.ac.at 
wrote:
 
First guess:   Is your struct file correct ???

Sb is a fairly big atom and usually has large distances to its neighbors.
What is your RMT of Sb.

If you are forced to use a small RMT for real reasons, lower the 
core-separation energy to -8.0 Ry.   Still core leakage (must be 
terrible small spheres ???)

When using .lcore, your error information is completely unspecific. 
Nobody can help, but I
 doubt very much that it has to do with 
core-leakage, but the problem might be too large basis set due to 
unphysically small spheres,.


On 10/14/2013 06:57 AM, Lawal Mohammed wrote:
 Dear users and developers,

 I am a new user trying to initialize calculation for a (20 atoms) in
 unit cell (a sulfide material) with a Pnma (No.62) spacegroup. My
 problem is  I got this warning.
 WARNING: 0.254 Sb CORE electrons leak out of MT-sphere 
 I checked the WIEN2k.outputst for which atom/states the core-leakage
 occurs and rerun lstart with lower core-seperation energy. But still the
 warning appears, then I try to increase RMT, again the
 problem persist.
 And when I neglect the core-leakage error thinking that the .lcore will
 created and directs the scf-cycle to peform a superposition of core
 densities, as mentioned in UG. The SCF hangs-up (still hangs-up).
 Furthermore, I got this (Error in LAPW2) in the the case.output file.
 HELP PLEASE!
 Thanks in advance for your response.
 MOHAMMED Lawal
 Universiti Technologi Malaysia




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--
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Phone: +43-1-58801-165300             FAX: +43-1-58801-165982
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_root_WIEN2k_0021_0021.struct
Description: Binary data
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[Wien] Need assistance

[Lawal Mohammed]

Dear Wien2k Community,
I am a new user of Wien2k code. I want to know if it is possible to do 
simulation study of quantum dots using Wien2k. Actually, I am about to start a 
research on quantum dots based materials for intermediate band solar cells. 
Therefore, I really need to know the potential of Wien2k package. Could you 
please help me?
With kind regards
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