Need simplification and solution for 'Group has no unique connection' of Na5FeSi4O12.cif #74
Description
Hello developer,
First of all, I appreciate the program, and here I am new to supercell program, so I don't know fluent use of it. I am trying to simplify the cif file for the POSCAR, but as I am new to this program, I am facing some issues. it will be good if you can help me to solve.
The attached cif file is generated by using JCPDS.
#======================================================================
CRYSTAL DATA
#----------------------------------------------------------------------
data_VESTA_phase_1
_chemical_name_common 'Na5 Fe Si4 O12'
_cell_length_a 21.418(3)
_cell_length_b 21.418(3)
_cell_length_c 12.2911(18)
_cell_angle_alpha 90.000000
_cell_angle_beta 90.000000
_cell_angle_gamma 120.000000
_cell_volume 4882.915026
_space_group_name_H-M_alt 'R -3 c'
_space_group_IT_number 167
loop_
space_group_symop_operation_xyz
'x, y, z'
'-x, -y, -z'
'-y, x-y, z'
'y, -x+y, -z'
'-x+y, -x, z'
'x-y, x, -z'
'y, x, -z+1/2'
'-y, -x, z+1/2'
'x-y, -y, -z+1/2'
'-x+y, y, z+1/2'
'-x, -x+y, -z+1/2'
'x, x-y, z+1/2'
'x+2/3, y+1/3, z+1/3'
'-x+2/3, -y+1/3, -z+1/3'
'-y+2/3, x-y+1/3, z+1/3'
'y+2/3, -x+y+1/3, -z+1/3'
'-x+y+2/3, -x+1/3, z+1/3'
'x-y+2/3, x+1/3, -z+1/3'
'y+2/3, x+1/3, -z+5/6'
'-y+2/3, -x+1/3, z+5/6'
'x-y+2/3, -y+1/3, -z+5/6'
'-x+y+2/3, y+1/3, z+5/6'
'-x+2/3, -x+y+1/3, -z+5/6'
'x+2/3, x-y+1/3, z+5/6'
'x+1/3, y+2/3, z+2/3'
'-x+1/3, -y+2/3, -z+2/3'
'-y+1/3, x-y+2/3, z+2/3'
'y+1/3, -x+y+2/3, -z+2/3'
'-x+y+1/3, -x+2/3, z+2/3'
'x-y+1/3, x+2/3, -z+2/3'
'y+1/3, x+2/3, -z+1/6'
'-y+1/3, -x+2/3, z+1/6'
'x-y+1/3, -y+2/3, -z+1/6'
'-x+y+1/3, y+2/3, z+1/6'
'-x+1/3, -x+y+2/3, -z+1/6'
'x+1/3, x-y+2/3, z+1/6'
loop
_atom_type_symbol
_atom_type_oxidation_number
Fe 3
Si 4
Na 1
O -2
loop_
_atom_site_label
_atom_site_occupancy
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_adp_type
_atom_site_U_iso_or_equiv
_atom_site_type_symbol
Fe1 1.0 0.666667 0.08597(2) 0.083333 Uiso 0.005318 Fe
Si2 1.0 0.77731(3) 0.01612(3) 0.01782(5) Uiso 0.005556 Si
Si3 1.0 0.90941(3) 0.09550(3) -0.12341(5) Uiso 0.005956 Si
Na4 1.0 1.000000 0.000000 -0.250000 Uiso 0.005211 Na
Na5 1.0 1.000000 0.000000 0.000000 Uiso 0.009156 Na
Na6 1.0 0.92352(5) 0.06573(5) -0.36144(7) Uiso 0.011856 Na
Na7 1.0 0.61847(6) -0.04819(6) -0.083333 Uiso 0.014322 Na
Na8 0.6820 0.833333 0.166667 0.166667 Uiso 0.031844 Na
Na9 0.1440 0.8493(4) 0.1771(4) 0.0653(13) Uiso 0.008000 Na
Na10 0.1450 0.8512(4) 0.1796(4) 0.0211(14) Uiso 0.004000 Na
Na11 0.0170 0.840(5) 0.168(5) -0.031(11) Uiso 0.040000 Na
O12 1.0 0.95460(8) 0.05533(8) -0.13075(13) Uiso 0.012167 O
O13 1.0 0.73849(8) -0.02816(8) -0.08974(13) Uiso 0.009711 O
O14 1.0 0.85626(8) 0.07936(8) -0.22531(13) Uiso 0.009400 O
O15 1.0 0.96207(8) 0.18437(8) -0.11467(13) Uiso 0.009367 O
O16 1.0 0.86316(8) 0.07307(8) -0.00744(13) Uiso 0.011156 O
O17 1.0 0.74346(9) 0.05886(9) 0.07485(13) Uiso 0.012689 O
after using program:
Command line: supercell -i fn3279sup1.cube1.cif -s 1x1x1 -v 2 -m -q -nl10 -o BCO
Random SEED: 588557555
CIF file info:
INFO: Using symmetries from space group.
Initial system:
Chemical Formula: Fe18 Na89.292 O216 Si72
Supercell system (1x1x1):
Size a=21.418, b=21.418, c=12.2911
Current charge balance option is "try"
WARN: Total charge of the system is not zero
Total charge oxidation state (cif): -0.708
Total charge cell: -0.708
Charge balancing: no
| Atom Label | charge | mult | occup x mult
| | Ox. state | Used | (cif) |
| Fe1 | 3 | 3 | 18 | 18
| Na10 | 1 | 1 | 36 | 5.22
| Na11 | 1 | 1 | 36 | 0.612
| Na4 | 1 | 1 | 6 | 6
| Na5 | 1 | 1 | 6 | 6
| Na6 | 1 | 1 | 36 | 36
| Na7 | 1 | 1 | 18 | 18
| Na8 | 1 | 1 | 18 | 12.276
| Na9 | 1 | 1 | 36 | 5.184
| O12 | -2 | -2 | 36 | 36
| O13 | -2 | -2 | 36 | 36
| O14 | -2 | -2 | 36 | 36
| O15 | -2 | -2 | 36 | 36
| O16 | -2 | -2 | 36 | 36
| O17 | -2 | -2 | 36 | 36
| Si2 | 4 | 4 | 36 | 36
| Si3 | 4 | 4 | 36 | 36
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
ERROR: Group has no unique connection.
Create occupation groups error.