Re: [Wien] File for vacuum size

[Gavin Abo]

I believe it is the nonequivalent (0,0,0) atomic position that is 
creating the equivalent position at (0,0,1).


You might also think about the (0,0,0) being (0,0,-0), such that +1 can 
be added to the -0 [ 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12202.html 
].


In addition, there may be periodically an atom at (0,0,n) with n = ..., 
-2, -1, 0, 1, 2, ... because of the periodic boundary conditions [ 
http://susi.theochem.tuwien.ac.at/reg_user/textbooks/WIEN2k_lecture-notes_2011/Schwarz_introduction.pdf 
(slide 4)] that WIEN2k uses.


However, the simplest explanation may be that when I have a look at 
FeCoAl31.17.struct in XCrySDen, I see an atom at (0,0,1).


On 5/2/2018 11:47 PM, Lawal Mohammed wrote:

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 
 wrote:



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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 [Â 
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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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 
 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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Re: [Wien] File for vacuum size

[Gavin Abo]

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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