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