\(\textrm{Sr}_{2}\textrm{ScSbO}_{6}\), RT




Target

  1. Perform previous calculations, as needed

  2. Obtain the control file, .pcr, and understand it


Steps

  1. Take the structure from the paper

  2. Take the Sb to the origin

  3. Convert non-standard to standard

  4. AMPLIMODES needs the Transformation Matrix (TM)

  5. AMPLIMODES with non-standard: Transformation Matrix

  6. AMPLIMODES with standard: Transformation Matrix

  7. AMPLIMODES for FullProf with non-standard/standard

  8. Comparison of the control file (.pcr/.new) between co-ordinates and modes

  9. Comments




Take the structure from the paper




# P 1 21/n 1
014
5.6915 5.6778 8.0244 90.000000 90.03 90.000000
6
Sb	1	-	0.000000	0.500000	0.000000
Sc	1	-	0.500000	0.000000	0.000000
Sr	1	-	0.002100	0.009900	0.248700
O	1	-	0.261500	0.268000	0.028000
O	2	-	0.274000	0.262000	0.477000
O	3	-	0.949300	0.494400	0.245600



Take the Sb to the origin




  1. Copy structure

  2. Use EQUIVSTRU

Result

# P 1 21/n 1
014
5.6915 5.6778 8.0244 90.00 90.03 90.00
6
Sb	1	-	0.000000	 0.000000	0.000000
Sc	1	-	0.500000	-0.500000	0.000000
Sr	1	-	0.002100	-0.490100	0.248700
O	1	-	0.261500	-0.232000	0.028000
O	2	-	0.274000	-0.238000	0.477000
O	3	-	0.949300	-0.005600	0.245600



Convert non-standard to standard




  1. Copy structure

  2. Use SETSTRU

Result

# P 1 21/c 1
014
8.0244 5.6778 9.8355 90.00 144.64 90.00
6
Sb	1	2a	 0.000000	 0.000000	 0.000000
Sc	1	2b	-0.500000	-0.500000	-0.500000
Sr	1	4e	 0.246600	-0.490100	-0.002100
O	1	4e	-0.233500	-0.232000	-0.261500
O	2	4e	 0.203000	-0.238000	-0.274000
O	3	4e	-0.703700	-0.005600	-0.949300



AMPLIMODES needs the Transformation Matrix {TM}




Parent Phase

# F m -3 m
225
8.087481 8.087481 8.087481 90.00000 90.00000 90.00000
4
Sb	1	4a	0.000000	0.000000	0.000000
Sc	1	4b	0.500000	0.500000	0.500000
Sr	1	8c	0.250000	0.250000	0.250000
O	11	24e	0.254100	0.000000	0.000000

At least, 3 ways to obtain the Transformation Matrix:

  1. Calculate by hand: Previous Information

  2. Use PSEUDO: be careful, only admits standard settings You can obtain it also for the non-standard setting

  3. Calculate by STRUCTURE RELATIONS It is also reachable from AMPLIMODES


1. Calculate by hand: Previous Information


2. Use PSEUDO

../_images/pseudo_path_1.png

Fig. 15 irudi-oina.


../_images/pseudo_path_2.png

Fig. 16 irudi-oina.


../_images/pseudo_path_3.png

Fig. 17 irudi-oina.


Transformation Matrix (P,p): (c,1/2a+1/2b,-1/2a+1/2b-c;0,0,0)

Transformation matrix:
[     0   1/2  -1/2 ] [      0]
[     0   1/2   1/2 ] [      0]
[     1     0    -1 ] [      0]

3. Calculate by STRUCTURE RELATIONS

Transformation Matrix (P,p): (b,1/2a-1/2c,-1/2a-b-1/2c;0,0,0)

Transformation matrix:
[     0   1/2  -1/2 ] [      0]
[     1     0    -1 ] [      0]
[     0  -1/2  -1/2 ] [      0]

You can check that both matrices give the same final result…


Result, for the non-standard

Transformation Matrix (P,p): (1/2a-1/2b,1/2a+1/2b,c;0,0,0)

Result, for the standard

Transformation Matrix (P,p): (b,1/2a-1/2c,-1/2a-b-1/2c;0,0,0)

Transformation Matrix (P,p): (c,1/2a+1/2b,-1/2a+1/2b-c;0,0,0)



AMPLIMODES with non-standard: Transformation Matrix




# F m -3 m
225
8.087481 8.087481 8.087481 90.00000 90.00000 90.00000
4
Sb	1	4a	0.000000	0.000000	0.000000
Sc	1	4b	0.500000	0.500000	0.500000
Sr	1	8c	0.250000	0.250000	0.250000
O	11	24e	0.254100	0.000000	0.000000

# P 1 21/n 1
014
8.0244 5.6778 9.8355 90.00 144.64 90.00
6
Sb	1	2a	 0.000000	 0.000000	 0.000000
Sc	1	2b	-0.500000	-0.500000	-0.500000
Sr	1	4e	 0.246600	-0.490100	-0.002100
O	1	4e	-0.233500	-0.232000	-0.261500
O	2	4e	 0.203000	-0.238000	-0.274000
O	3	4e	-0.703700	-0.005600	-0.949300

Transformation matrix:

[     0   1/2  -1/2 ] [      0]
[     1     0    -1 ] [      0]
[     0  -1/2  -1/2 ] [      0]
b,1/2a-1/2c,-1/2a-b-1/2c; 0 0 0



AMPLIMODES with standard: Transformation Matrix




# F m -3 m
225
8.087481 8.087481 8.087481 90.00000 90.00000 90.00000
4
Sb	1	4a	0.000000	0.000000	0.000000
Sc	1	4b	0.500000	0.500000	0.500000
Sr	1	8c	0.250000	0.250000	0.250000
O	11	24e	0.254100	0.000000	0.000000

# P 1 21/n 1
014
5.6915 5.6778 8.0244 90.00 90.03 90.00
6
Sb	1	-	0.000000	 0.000000	0.000000
Sc	1	-	0.500000	-0.500000	0.000000
Sr	1	-	0.002100	-0.490100	0.248700
O	1	-	0.261500	-0.232000	0.028000
O	2	-	0.274000	-0.238000	0.477000
O	3	-	0.949300	-0.005600	0.245600

Transformation matrix:

[   1/2   1/2     0 ] [      0]
[  -1/2   1/2     0 ] [      0]
[     0     0     1 ] [      0]
1/2a+1/2b,1/2a-1/2b,c; 0 0 0



AMPLIMODES for FullProf with non-standard/standard




# F m -3 m
225
8.087481 8.087481 8.087481 90.00000 90.00000 90.00000
4
Sb	1	4a	0.000000	0.000000	0.000000
Sc	1	4b	0.500000	0.500000	0.500000
Sr	1	8c	0.250000	0.250000	0.250000
O	11	24e	0.254100	0.000000	0.000000

# P 1 21/n 1
014
5.6915 5.6778 8.0244 90.00 90.03 90.00
6
Sb	1	-	0.000000	 0.000000	0.000000
Sc	1	-	0.500000	-0.500000	0.000000
Sr	1	-	0.002100	-0.490100	0.248700
O	1	-	0.261500	-0.232000	0.028000
O	2	-	0.274000	-0.238000	0.477000
O	3	-	0.949300	-0.005600	0.245600

Transformation matrix:

[   1/2   1/2     0 ] [      0]
[  -1/2   1/2     0 ] [      0]
[     0     0     1 ] [      0]
1/2a-1/2b,1/2a+1/2b,c; 0 0 0



Comparison of the control file (.pcr/.new) between co-ordinates and modes




!Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth       ATZ    Nvk Npr More
   6   0   0 1.0 0.0 0.0   0   0   0   0   0        875.885   0   7   1
!
!Jvi Jdi Hel Sol Mom Ter  Brind   RMua    RMub    RMuc   Jtyp  Nsp_Ref Ph_Shift N_Domains
   0   3   0   0   0   0  1.0000  0.0000  0.0000  0.0000    1      0      0      0
!
! Max_dst(dist) (angles)  Bond-Valence Calc.
      3.2000      3.2000        BVS
!  N_cations   N_anions     Tolerance(%) / Name or cations/ and Anions
       3           1                0.00
SR+2 SC+3 SB+5
O-2
!
!
P 1 21/N 1               <--Space group symbol
!Atom   Typ       X        Y        Z     Biso       Occ     In Fin N_t Spc /Codes
Sb     SB      0.00000  0.50000  0.00000  0.14020   0.50000   0   0   0    1  
                  0.00     0.00     0.00   271.00      0.00
Sc     SC      0.50000  0.00000  0.00000  0.14020   0.50000   0   0   0    2  
                  0.00     0.00     0.00   271.00      0.00
Sr     SR      0.00023  0.00977  0.25025  0.32583   1.00000   0   0   0    3  
                131.00   141.00   151.00   261.00      0.00
O1     O       0.25933  0.27162  0.02536  0.49182   1.00000   0   0   0    4  
                161.00   171.00   181.00   251.00      0.00
O2     O       0.27538  0.26338  0.47468  0.49182   1.00000   0   0   0    4  
                191.00   201.00   211.00   251.00      0.00
O3     O       0.94813  0.49532  0.24404  0.49182   1.00000   0   0   0    4  
                221.00   231.00   241.00   251.00      0.00

!Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth       ATZ    Nvk Npr More
   6   0   0 1.0 0.0 0.0   6   0   0   0  12        875.885   0   7   1
!
!Jvi Jdi Hel Sol Mom Ter  Brind   RMua    RMub    RMuc   Jtyp  Nsp_Ref Ph_Shift N_Domains
   0   3   0   0   0   0  1.0000  0.0000  0.0000  0.0000    1      0      0      0
!
! Max_dst(dist) (angles)  Bond-Valence Calc.
      3.2000      3.2000        BVS
!  N_cations   N_anions     Tolerance(%) / Name or cations/ and Anions
       3           1                0.00
SR+2 SC+3 SB+5
O-2
!
!
P 1 21/n 1               <--Space group symbol
!Atom   Typ       X         Y         Z     Biso      Occ     In Fin N_t Spc /Codes
Sb1    SB      0.000000  0.000000  0.000000 0.500000 0.500000  0   0   0    1
                   0.00      0.00      0.00     0.00     0.00
Sc1    SC      0.500000  0.000000  0.000000 0.500000 0.500000  0   0   0    1
                   0.00      0.00      0.00     0.00     0.00
Sr1    SR      0.750000  0.000000  0.500000 0.500000 1.000000  0   0   0    1
                   0.00      0.00      0.00     0.00     0.00
O11    O       0.745900  0.254100  0.745900 0.500000 1.000000  0   0   0    1
                   0.00      0.00      0.00     0.00     0.00
O11_2  O       0.254100  0.500000  0.500000 0.500000 1.000000  0   0   0    1
                   0.00      0.00      0.00     0.00     0.00
O11_3  O       0.745900  0.754100  0.245900 0.500000 1.000000  0   0   0    1
                   0.00      0.00      0.00     0.00     0.00
! Polarisation Vectors of Symmetry Modes for each atom
V_MODES   30
! Nm Atm     Irrep      Vx        Vy        Vz         Coeff
  1 O11    GM1+   -0.035694  0.035694 -0.035694 1.00
  1 O11_2  GM1+    0.035694  0.000000  0.000000 1.00
  1 O11_3  GM1+   -0.035694  0.035694 -0.035694 1.00
  2 O11    GM3+   -0.025240  0.025240 -0.025240 1.00
  2 O11_2  GM3+   -0.050479  0.000000  0.000000 1.00
  2 O11_3  GM3+   -0.025240  0.025240 -0.025240 1.00
  3 O11    GM4+   -0.030912  0.000000  0.000000 1.00
  3 O11_2  GM4+   -0.061824  0.000000 -0.061824 1.00
  3 O11_3  GM4+   -0.030912  0.000000  0.000000 1.00
  4 Sr1    GM5+    0.061824  0.000000  0.000000 1.00
  5 Sr1    GM5+   -0.087432  0.000000 -0.087432 1.00
  6 O11    GM5+    0.030912  0.000000  0.000000 1.00
  6 O11_2  GM5+   -0.061824  0.000000 -0.061824 1.00
  6 O11_3  GM5+    0.030912  0.000000  0.000000 1.00
  7 O11    GM5+   -0.043716 -0.043716 -0.043716 1.00
  7 O11_2  GM5+    0.000000  0.000000  0.000000 1.00
  7 O11_3  GM5+   -0.043716 -0.043716 -0.043716 1.00
  8 O11    X2+    -0.043716  0.043716 -0.043716 1.00
  8 O11_2  X2+     0.000000  0.000000  0.000000 1.00
  8 O11_3  X2+     0.043716 -0.043716  0.043716 1.00
  9 O11    X3+     0.043716  0.043716  0.043716 1.00
  9 O11_2  X3+     0.000000  0.000000  0.000000 1.00
  9 O11_3  X3+    -0.043716 -0.043716 -0.043716 1.00
 10 Sr1    X5+     0.000000 -0.087432  0.000000 1.00
 11 O11    X5+    -0.043716  0.000000  0.000000 1.00
 11 O11_2  X5+     0.000000  0.000000  0.000000 1.00
 11 O11_3  X5+     0.043716  0.000000  0.000000 1.00
 12 O11    X5+     0.000000  0.000000  0.000000 1.00
 12 O11_2  X5+     0.000000  0.087432  0.000000 1.00
 12 O11_3  X5+     0.000000  0.000000  0.000000 1.00
!Amplitudes of Symmetry Modes
A_MODES    12   2
Max_Amplitude   2.0
    A1_GM1+   -0.242338     1.00
    A2_GM3+   -0.002972     1.00
    A3_GM4+   -0.822497     1.00
    A4_GM5+    0.021028     1.00
    A5_GM5+   -0.024019     1.00
    A6_GM5+    0.002426     1.00
    A7_GM5+   -0.037172     1.00
    A8_X2+    -0.031453     1.00
    A9_X3+     0.374577     1.00
    A10_X5+   -0.113230     1.00
    A11_X5+    0.057188     1.00
    A12_X5+    0.064050     1.00



Comments




  1. \(\#\) degrees of freedom

  2. The structure is fixed: you refine the amplitude values The structure is the parent phase Result form AMPLIMODES:

    Transformed high symmetry structure in the subgroup basis Reference Structure

    Symmetry mode analysis
    
    High symmetry structure
    
    225
    8.087481 8.087481 8.087481 90.00000 90.00000 90.00000
    4
    Sb	1	4a	0.000000	0.000000	0.000000
    Sc	1	4b	0.500000	0.500000	0.500000
    Sr	1	8c	0.250000	0.250000	0.250000
    O	11	24e	0.254100	0.000000	0.000000
    
    Transformation matrix
    
    [     0   1/2  -1/2 ] [      0]
    [     1     0    -1 ] [      0]
    [     0  -1/2  -1/2 ] [      0]
    
    Transformed high symmetry structure in the subgroup basis   
    Reference Structure
    
    014
    8.087481 5.718712 9.905101 90.000000 144.735611 90.000000
    6
    Sb	1	2a	0.000000	0.000000	0.000000
    Sc	1	2b	0.500000	0.000000	0.000000
    Sr	1	4e	0.750000	0.000000	0.500000
    O	11	4e	0.745900	0.254100	0.745900
    O	11_2	4e	0.254100	0.500000	0.500000
    O	11_3	4e	0.745900	0.754100	0.245900
    

    From AMPLIMODES for FullProf:


    P 1 21/n 1               <--Space group symbol
    !Atom   Typ       X         Y         Z     Biso      Occ     In Fin N_t Spc /Codes
    Sb1    SB      0.000000  0.000000  0.000000 0.500000 0.500000  0   0   0    1
                       0.00      0.00      0.00     0.00     0.00
    Sc1    SC      0.500000  0.000000  0.000000 0.500000 0.500000  0   0   0    1
                       0.00      0.00      0.00     0.00     0.00
    Sr1    SR      0.750000  0.000000  0.500000 0.500000 1.000000  0   0   0    1
                       0.00      0.00      0.00     0.00     0.00
    O11    O       0.745900  0.254100  0.745900 0.500000 1.000000  0   0   0    1
                       0.00      0.00      0.00     0.00     0.00
    O11_2  O       0.254100  0.500000  0.500000 0.500000 1.000000  0   0   0    1
                       0.00      0.00      0.00     0.00     0.00
    O11_3  O       0.745900  0.754100  0.245900 0.500000 1.000000  0   0   0    1
                       0.00      0.00      0.00     0.00     0.00
    
  3. Differences:

    1. Jbt=6 \(\quad\) Furth=12 (depending on the case!)

    2. vector polarization list: you could generate it by hand you have to go to the Detailed Information, and further…