Question on equal atoms

Hi everyone,
I am a new leaner on GULP try to use it to fit buckingham potential parameter between Al-F. However, when I use the data of AlF3 from material project (mp-468: AlF3 (trigonal, R-3c, 167)) including xyz coordinates and cell parameters, warning like “The irreducible atom 2 is equivalent to atom 2” shows and I don’t understand why. My input and output files are listed below and hope you could provide some help if convenient.

Input files:

opti prop conp simul
cell
5.112 5.112 5.112 58.996 58.996 58.996
frac
Al 0 0 0
Al 0.5 0.5 0.5
F 0.1858 0.3142 0.75
F 0.25 0.8142 0.6858
F 0.3142 0.75 0.1858
F 0.6858 0.25 0.8142
F 0.75 0.1858 0.3142
F 0.8142 0.6858 0.25
space
167
species
Al 1.8
F -0.6
buckingham
Al Al 0 1 0 0.0 10.0 0 0 0
Al F 47181.82 5.48 22.75 0.0 10.0 0 1 0
F F 24300.26 5.04 6.56 0.0 12.0 0 1 0
Note: The potential and the species (partial charge model is used) are quoted from other references.

Output files:

> Job Started  at 06:08.47 21st May        2021                              
>   Number of CPUs =     1
>   Total number of configurations input =      1
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !! WARNING : The irreducible atom 2    is equivalent to atom 2
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !! WARNING : The irreducible atom 4    is equivalent to atom 7
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !! WARNING : The irreducible atom 5    is equivalent to atom 5
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !! WARNING : The irreducible atom 6    is equivalent to atom 8
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !! WARNING : The irreducible atom 7    is equivalent to atom 4
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !! WARNING : The irreducible atom 8    is equivalent to atom 6
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> ********************************************************************************
> *  Input for Configuration =   1                                               *
> ********************************************************************************
>   Formula = Al2F6                                                      
>   Number of irreducible atoms/shells =       8
>   Total number atoms/shells =       8
>   Dimensionality = 3               :  Bulk  
>   Symmetry :
>   Crystal family                   :  Hexagonal  
>   Crystal class  (Groth - 1921)    :  Ditrigonal Scalenohedral            
>   Space group (centrosymmetric)    :  R -3 C          
>   Patterson group                  :  R -3 m  
>   Cartesian lattice vectors (Angstroms) :
>         2.517114    1.453256    4.205321
>        -2.517114    1.453256    4.205321
>         0.000000   -2.906513    4.205321
>   Cell parameters (Angstroms/Degrees):
>   a =       5.1120    alpha =  58.9960
>   b =       5.1120    beta  =  58.9960
>   c =       5.1120    gamma =  58.9960
>   Initial cell volume =          92.298693 Angs**3
>   Temperature of configuration =   0.00     K
>   Pressure of configuration =         0.000 GPa
>   Fractional coordinates of asymmetric unit :
> --------------------------------------------------------------------------------
>    No.  Atomic       x           y          z         Charge      Occupancy
>         Label      (Frac)      (Frac)     (Frac)        (e)         (Frac)  
> --------------------------------------------------------------------------------
>       1 Al    c    0.000000    0.000000    0.000000     1.80000    1.000000    
>       2 Al    c    0.185800    0.314200    0.750000     1.80000    1.000000    
>       3 F     c    0.185800 *  0.314200    0.750000    -0.60000    1.000000    
>       4 F     c    0.935800 *  0.878400    0.435800 *  -0.60000    1.000000    
>       5 F     c    0.935800    0.878400 *  0.435800    -0.60000    1.000000    
>       6 F     c    0.935800    0.878400    0.435800    -0.60000    1.000000    
>       7 F     c    0.935800    0.878400    0.435800    -0.60000    1.000000    
>       8 F     c    0.935800    0.878400    0.435800    -0.60000    1.000000    
> --------------------------------------------------------------------------------
>   Constraints :
> --------------------------------------------------------------------------------
>   Constraint no.      Unconstrained     Constrained    Coefficient    Offset
>                          Variable         Variable
> --------------------------------------------------------------------------------
>            1              Strain 1        Strain 2       1.00000      0.0000
>            2                 4 x             5 x         1.00000      0.0000
>            3                 4 z             5 z         1.00000      0.0000
>            4                 4 x             6 x         1.00000      0.0000
>            5                 4 z             6 z         1.00000      0.0000
>            6                 5 y             6 y         1.00000      0.0000
>            7                 4 x             7 x         1.00000      0.0000
>            8                 4 z             7 z         1.00000      0.0000
>            9                 5 y             7 y         1.00000      0.0000
>           10                 4 x             8 x         1.00000      0.0000
>           11                 4 z             8 z         1.00000      0.0000
>           12                 5 y             8 y         1.00000      0.0000
> --------------------------------------------------------------------------------
> ********************************************************************************
> *  General input information                                                   *
> ********************************************************************************
>   Species output for all configurations :
> --------------------------------------------------------------------------------
>   Species    Type    Atomic    Atomic    Charge       Radii (Angs)     Library
>                      Number     Mass       (e)     Cova   Ionic  VDW   Symbol
> --------------------------------------------------------------------------------
>     Al       Core       13      26.98   1.800000   1.350  0.000  2.050          
>     F        Core        9      19.00  -0.600000   0.710  0.000  1.300          
> --------------------------------------------------------------------------------
>   Lattice summation method               =    Ewald          (3-D)
>                                          =    Parry          (2-D)
>                                          =    Saunders et al (1-D)
>   Accuracy factor for lattice sums       =   12.000
>   Analytic derivatives to be used
>   Time limit = Infinity
>   Maximum range for interatomic potentials =    100000.000000 Angstroms
>   General interatomic potentials :
> --------------------------------------------------------------------------------
> Atom  Types   Potential      Parameter       Value         Units   Cutoffs(Ang)
>   1     2                                                            Min /  Max
> --------------------------------------------------------------------------------
> Al   c Al   c Buckingham    Buckingham A     0.0000000    eV        0.000 10.000
>                             Buckingham rho   1.0000000    Ang      
>                             Buckingham C     0.0000000    eV*Ang^6  
> --------------------------------------------------------------------------------
> F    c Al   c Buckingham    Buckingham A     47181.820    eV        0.000 10.000
>                             Buckingham rho   5.4800000    Ang      
>                             Buckingham C     22.750000    eV*Ang^6  
> --------------------------------------------------------------------------------
> F    c F    c Buckingham    Buckingham A     24300.260    eV        0.000 12.000
>                             Buckingham rho   5.0400000    Ang      
>                             Buckingham C     6.5600000    eV*Ang^6  
> --------------------------------------------------------------------------------
> ********************************************************************************
> *  Output for configuration   1                                                *
> ********************************************************************************
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !! WARNING : The irreducible atom 2    is equivalent to atom 2
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !! WARNING : The irreducible atom 4    is equivalent to atom 7
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !! WARNING : The irreducible atom 6    is equivalent to atom 9
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !! WARNING : The irreducible atom 7    is equivalent to atom 9
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !! WARNING : The irreducible atom 8    is equivalent to atom 9
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>   Configuration number =   1
>   **** Unit cell is not charge neutral    ****
>   **** Sum of charges =   -3.6000000000   ****
>   **** Check that a special position atom ****
>   **** coordinate has not been varied     ****
>   Current coordinates :
> --------------------------------------------------------------------------------
>      No.  Atomic         x            y            z          Charge  Occupancy
>           Number       (frac)       (frac)       (frac)         (e)  
> --------------------------------------------------------------------------------
>       1  Al    c      0.000000     0.000000     0.000000      1.800000  1.0000
>       2  Al    c      0.500000     0.500000     0.500000      1.800000  1.0000
>       3  F     c      0.185800     0.314200     0.750000     -0.600000  1.0000
>       4  F     c      0.750000     0.185800     0.314200     -0.600000  1.0000
>       5  F     c      0.314200     0.750000     0.185800     -0.600000  1.0000
>       6  F     c      0.814200     0.685800     0.250000     -0.600000  1.0000
>       7  F     c      0.250000     0.814200     0.685800     -0.600000  1.0000
>       8  F     c      0.685800     0.250000     0.814200     -0.600000  1.0000
>       9  F     c      0.250000     0.147533     0.352467     -0.600000  1.0000
>      10  F     c      0.352467     0.250000     0.147533     -0.600000  1.0000
>      11  F     c      0.147533     0.352467     0.250000     -0.600000  1.0000
>      12  F     c      0.750000     0.852467     0.647533     -0.600000  1.0000
>      13  F     c      0.647533     0.750000     0.852467     -0.600000  1.0000
>      14  F     c      0.852467     0.647533     0.750000     -0.600000  1.0000
> --------------------------------------------------------------------------------
>  Program terminated by processor     0 in                setup

Any guidance you provide would be greatly appreciated.
Sincerely,
Ji Yao

Hi Ji Yao,
When you specify the space group for a material you only need to give the atoms in asymmetric unit. The warnings you are getting are because you’ve specified all the atoms in the unit cell and the space group. You can either delete the space group or better only input the symmetry unique atoms.
Regards, Julian

Thanks Julian, It helps!
Regards, Ji Yao