Re: Making an unit cell with all sites occupied by multiple atoms in FullProf

[Kotaro SAITO]

Dear Leopoldo and all,

Thank you for the comment. I’m relieved that I didn’t do wrong about this.

> If you don´t have a site with full occupation or just two atoms in such a 
> site to put first in your atoms list then you will need to apply your trick, 
> as far as I know, to have a correct cif output.

This is another interesting point.
Strangely, I’ve just found that the pcr files with and without a “transparent” 
dummy atom give **exactly same intensities**, although the two pcr files give 
different site occupancies in cif files.
There are also some differences in .out files for both cases as shown below.

===with a dummy atom==
 => Initial parameters ==>
 AtomNtyp  X Y Z B occ. 
in  fin  Spc  Mult
 B11   B22   B33   B12   B13   
B23
 Dummy  DM 0.25000   0.25000   0.25000   0.5   0.08333  
 0008
 Codes:0.0   0.0   0.0   0.0   0.0
 Co CO 0.0   0.0   0.0   0.5   0.01041  
 0002
 Codes:0.0   0.0   0.0   0.0   0.0
 Fe Fe 0.0   0.0   0.0   0.5   0.00521  
 0002
 Codes:0.0   0.0   0.0   0.0   0.0
 Si Si 0.0   0.0   0.0   0.5   0.00521  
 0002
 Codes:0.0   0.0   0.0   0.0   0.0

 => IT IS ASSUMED THAT THE FIRST GIVEN SITE IS FULLY OCCUPIED 
OR THE FIRST AND SECOND ATOMS ARE IN THE SAME SITE WITH TOTAL FULL 
OCCUPATION
  (If this is not the case, change the order of atoms to obtain correct values 
for the content of the unit cell)
The phase contains sites partially occupied
  -> Atom: DM  ,  Chemical element: DM  Atomic Mass: 0.
  -> Atom: CO  ,  Chemical element: CO  Atomic Mass:58.9332
  -> Atom: Fe  ,  Chemical element: FE  Atomic Mass:55.8470
  -> Atom: Si  ,  Chemical element: SI  Atomic Mass:28.0860
 => The suggested value of ATZ is100.87
This value will be used for quantitative analysis and ouput to the PCR/NEW 
file
 => The chemical content of the unit cell is: 
   8. DM   +   0.9994 CO   +   0.5002 Fe   +   0.5002 Si 
 => The normalized site occupation numbers in % are: 
 100. Dummy  :   49.9700 Co :   25.0090 Fe :   
25.0090 Si   
 => The density (volumic mass) of the compound is:6.592 g/cm3


===without a dummy atom==
 => Initial parameters ==>
 AtomNtyp  X Y Z B occ. 
in  fin  Spc  Mult
 B11   B22   B33   B12   B13   
B23
 Co CO 0.0   0.0   0.0   0.5   0.01041  
 0002
 Codes:0.0   0.0   0.0   0.0   0.0
 Fe Fe 0.0   0.0   0.0   0.5   0.00521  
 0002
 Codes:0.0   0.0   0.0   0.0   0.0
 Si Si 0.0   0.0   0.0   0.5   0.00521  
 0002
 Codes:0.0   0.0   0.0   0.0   0.0

 => IT IS ASSUMED THAT THE FIRST GIVEN SITE IS FULLY OCCUPIED 
OR THE FIRST AND SECOND ATOMS ARE IN THE SAME SITE WITH TOTAL FULL 
OCCUPATION
  (If this is not the case, change the order of atoms to obtain correct values 
for the content of the unit cell)
The phase contains sites partially occupied
  -> Atom: CO  ,  Chemical element: CO  Atomic Mass:58.9332
  -> Atom: Fe  ,  Chemical element: FE  Atomic Mass:55.8470
  -> Atom: Si  ,  Chemical element: SI  Atomic Mass:28.0860
 => The suggested value of ATZ is 75.63
This value will be used for quantitative analysis and ouput to the PCR/NEW 
file
 => The chemical content of the unit cell is: 
   1.3329 CO   +   0.6671 Fe   +   0.6671 Si 
 => The normalized site occupation numbers in % are: 
  66.6453 Co :   33.3547 Fe :   33.3547 Si   
 => The density (volumic mass) of the compound is:8.792 g/cm3


Site occupation in cif files seems to reflect “The normalized site occupation 
numbers in %”.

So my understanding of this situation is following.
- FullProf uses occupancy values in pcr files to calculate intensities, and the 
assumption written in .out file with capital letters is not applied in the 
calculation.
- FullProf calculates “the normalized site occupation numbers” under the 
capitalized assumption and put the calculated values in a cif file.

Is it correct?
If correct, I’m curious about the reason why FullProf 

Re: Making an unit cell with all sites occupied by multiple atoms in FullProf

[Leopoldo Suescun]

Dear Kotaro,
If you keep a physically sensible structure, any trick is valid when trying
to deal with software limitations.
If you don´t have a site with full occupation or just two atoms in such a
site to put first in your atoms list then you will need to apply your
trick, as far as I know, to have a correct cif output. Unless you keep that
in mind and correct your output by hand when you finish your refinement.
Best luck,
Leo


2016-10-03 5:41 GMT-03:00 Kotaro SAITO :

> Dear FullProf users,
>
> I would like to make a pcr file for a Heusler alloy with so-called A2
> structure, in which three atoms are completely disordered.
> (See Fig.1 in http://dx.doi.org/10.1088/0022-3727/48/16/164011
> or this direct link http://cdn.iopscience.com/
> images/0022-3727/48/16/164011/Full/jphysd500490f01_online.jpg)
>
> For example, a straightforward description of A2 Heusler alloy Co2FeSi
> would be like this.
>   I m -3 m   <--Space group symbol
>   !Atom   Typ   XYZ Biso   Occ In Fin N_t
> Spc /Codes
>   Co Co  0.0  0.0  0.0  0.5   0.01041   0   0   0
>   0
> 0.00 0.00 0.00 0.00  0.00
>   Fe FE  0.0  0.0  0.0  0.5   0.00521   0   0   0
>   0
> 0.00 0.00 0.00 0.00  0.00
>   Si  SI  0.0  0.0  0.0  0.5   0.00521   0   0
>  00
> 0.00 0.00 0.00 0.00  0.00
> (general multiplicity = 96, multiplicity of (0,0,0) is 2, so Occ=0.02083
> when fully occupied by one atom)
>
> But, as many of you know, FullProf assumes that "THE FIRST GIVEN SITE IS
> FULLY OCCUPIED OR THE FIRST AND SECOND ATOMS ARE IN THE SAME SITE WITH
> TOTAL FULL OCCUPATION (If this is not the case, change the order of atoms
> to obtain correct values for the content of the unit cell)” (quoted from a
> output file).
> Accordingly, a cif file generated after running of a pcr with the atomic
> position above shows unintended values as below.
>   loop_
> _atom_site_label
> _atom_site_fract_x
> _atom_site_fract_y
> _atom_site_fract_z
> _atom_site_U_iso_or_equiv
> _atom_site_occupancy
> _atom_site_adp_type  # Not in version 2.0.1
> _atom_site_type_symbol
>
>   Co  0.0  0.0  0.0  0.00633  0.66645 Uiso Co
>   Fe  0.0  0.0  0.0  0.00633  0.33355 Uiso Fe
>   Si  0.0  0.0  0.0  0.00633  0.33355 Uiso Si
> This rule seems tricky if one wants to make an unit cell consisting of
> sites occupied by multiple atoms like A2-type Heusler alloys.
>
> Actually, I came up with an idea to place a “transparent” dummy atom using
> Nsc option at the top of the atomic position list to bypass the rule, and
> it seems to work.
> But I’m not sure this is the best way. Does anyone have other or better
> ideas?
> Thanks in advance.
>
> Kotaro
>
> //////
>   Kotaro SAITO
>   High Energy Accelerator Research Organization
>   Institute of Materials Structure Science
>   1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
> //////
>
>
> ++
> Please do NOT attach files to the whole list  >
> Send commands to  eg: HELP as the subject with no body
> text
> The Rietveld_L list archive is on http://www.mail-archive.com/
> rietveld_l@ill.fr/
> ++
>
>
>


-- 
Dr. Leopoldo Suescun
Prof. Agr (Assoc. Prof.) de Física  Tel: (+598) 29290705/29249859
Cryssmat-Lab./Cátedra de Fisica/DETEMA  Fax: (+598) 29241906*
Facultad de Quimica, Universidad de la Republica. Montevideo, Uruguay

Ahora la cristalografía importa más (www.iucr.org) Crystallography Matters
more.
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Making an unit cell with all sites occupied by multiple atoms in FullProf

[Kotaro SAITO]

Dear FullProf users,

I would like to make a pcr file for a Heusler alloy with so-called A2 
structure, in which three atoms are completely disordered.
(See Fig.1 in http://dx.doi.org/10.1088/0022-3727/48/16/164011
or this direct link 
http://cdn.iopscience.com/images/0022-3727/48/16/164011/Full/jphysd500490f01_online.jpg)

For example, a straightforward description of A2 Heusler alloy Co2FeSi would be 
like this.
  I m -3 m   <--Space group symbol
  !Atom   Typ   XYZ Biso   Occ In Fin N_t Spc 
/Codes
  Co Co  0.0  0.0  0.0  0.5   0.01041   0   0   00
0.00 0.00 0.00 0.00  0.00
  Fe FE  0.0  0.0  0.0  0.5   0.00521   0   0   00
0.00 0.00 0.00 0.00  0.00
  Si  SI  0.0  0.0  0.0  0.5   0.00521   0   0   00
0.00 0.00 0.00 0.00  0.00
(general multiplicity = 96, multiplicity of (0,0,0) is 2, so Occ=0.02083 when 
fully occupied by one atom)

But, as many of you know, FullProf assumes that "THE FIRST GIVEN SITE IS FULLY 
OCCUPIED OR THE FIRST AND SECOND ATOMS ARE IN THE SAME SITE WITH TOTAL FULL 
OCCUPATION (If this is not the case, change the order of atoms to obtain 
correct values for the content of the unit cell)” (quoted from a output file).
Accordingly, a cif file generated after running of a pcr with the atomic 
position above shows unintended values as below.
  loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_occupancy
_atom_site_adp_type  # Not in version 2.0.1
_atom_site_type_symbol

  Co  0.0  0.0  0.0  0.00633  0.66645 Uiso Co  
  Fe  0.0  0.0  0.0  0.00633  0.33355 Uiso Fe  
  Si  0.0  0.0  0.0  0.00633  0.33355 Uiso Si  
This rule seems tricky if one wants to make an unit cell consisting of sites 
occupied by multiple atoms like A2-type Heusler alloys.

Actually, I came up with an idea to place a “transparent” dummy atom using Nsc 
option at the top of the atomic position list to bypass the rule, and it seems 
to work.
But I’m not sure this is the best way. Does anyone have other or better ideas?
Thanks in advance.

Kotaro

//////
  Kotaro SAITO
  High Energy Accelerator Research Organization
  Institute of Materials Structure Science
  1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
//////

++
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Send commands to  eg: HELP as the subject with no body text
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++