Generate equivalent positions like it appears in vesta

pymatgen
1

So I am generating supercells to deal with partial occupations the cif file looks like this:
loop_
space_group_symop_operation_xyz
x,y,z
loop
_atom_type_symbol
atom_type_oxidation_number
Fe1 +3
Li1 +1
O1 -2
loop
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Li1 Li 0.00000 0.00000 0.00000 1.000
Li1 Li 0.00000 0.25000 0.50000 1.000
Li1 Li 0.25000 0.00000 0.50000 1.000
Li1 Li 0.25000 0.25000 0.00000 1.000
Li1 Li 0.00000 0.50000 0.00000 1.000
Li1 Li 0.00000 0.75000 0.50000 1.000
Li1 Li 0.25000 0.50000 0.50000 1.000
Fe1 Fe 0.25000 0.75000 0.00000 1.000
Li1 Li 0.50000 0.00000 0.00000 1.000
Fe1 Fe 0.50000 0.25000 0.50000 1.000
Fe1 Fe 0.75000 0.00000 0.50000 1.000
Fe1 Fe 0.75000 0.25000 0.00000 1.000
Fe1 Fe 0.50000 0.50000 0.00000 1.000
Fe1 Fe 0.50000 0.75000 0.50000 1.000
Fe1 Fe 0.75000 0.50000 0.50000 1.000
Fe1 Fe 0.75000 0.75000 0.00000 1.000
O1 O 0.00000 0.00000 0.50000 1.000
O1 O 0.25000 0.00000 0.00000 1.000
O1 O 0.00000 0.25000 0.00000 1.000
O1 O 0.25000 0.25000 0.50000 1.000
O1 O 0.00000 0.50000 0.50000 1.000
O1 O 0.25000 0.50000 0.00000 1.000
O1 O 0.00000 0.75000 0.00000 1.000
O1 O 0.25000 0.75000 0.50000 1.000
O1 O 0.50000 0.00000 0.50000 1.000
O1 O 0.75000 0.00000 0.00000 1.000
O1 O 0.50000 0.25000 0.00000 1.000
O1 O 0.75000 0.25000 0.50000 1.000
O1 O 0.50000 0.50000 0.50000 1.000
O1 O 0.75000 0.50000 0.00000 1.000
O1 O 0.50000 0.75000 0.00000 1.000
O1 O 0.75000 0.75000 0.50000 1.000
However when I open it in Vesta it shows much more lithium atoms than here displayed, what I want is to produce a cif file withou the sym operations that show the same number of Li atoms has vesta.
Thanks in advance

2

Hey @Joao_Fonseca, it would probably help if you posted a complete CIF to help with this. I tried completing your CIF and visualizing in VESTA - I get the same number of atoms and same stoichiometry in pymatgen and VESTA (32 atoms, Li8Fe8O16) once I change the cell boundary in VESTA to (0, 0.99) for a, b, and c

That boundary choice just hides periodic images of the cell represented by the CIF

FWIW, here’s the CIF I used:

example matsci cif
data_example-matsci-cif
_chemical_formula_structural 'Fe Li O'

_cell_length_a 15.0
_cell_length_b 15.0
_cell_length_c 15.0
_cell_angle_alpha 90.
_cell_angle_beta 90.
_cell_angle_gamma 90.

loop_
_space_group_symop_operation_xyz
'x, y, z'
loop_
_atom_type_symbol
_atom_type_oxidation_number
Fe1 +3
Li1 +1
O1 -2
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Li1 Li 0.00000 0.00000 0.00000 1.000
Li1 Li 0.00000 0.25000 0.50000 1.000
Li1 Li 0.25000 0.00000 0.50000 1.000
Li1 Li 0.25000 0.25000 0.00000 1.000
Li1 Li 0.00000 0.50000 0.00000 1.000
Li1 Li 0.00000 0.75000 0.50000 1.000
Li1 Li 0.25000 0.50000 0.50000 1.000
Fe1 Fe 0.25000 0.75000 0.00000 1.000
Li1 Li 0.50000 0.00000 0.00000 1.000
Fe1 Fe 0.50000 0.25000 0.50000 1.000
Fe1 Fe 0.75000 0.00000 0.50000 1.000
Fe1 Fe 0.75000 0.25000 0.00000 1.000
Fe1 Fe 0.50000 0.50000 0.00000 1.000
Fe1 Fe 0.50000 0.75000 0.50000 1.000
Fe1 Fe 0.75000 0.50000 0.50000 1.000
Fe1 Fe 0.75000 0.75000 0.00000 1.000
O1 O 0.00000 0.00000 0.50000 1.000
O1 O 0.25000 0.00000 0.00000 1.000
O1 O 0.00000 0.25000 0.00000 1.000
O1 O 0.25000 0.25000 0.50000 1.000
O1 O 0.00000 0.50000 0.50000 1.000
O1 O 0.25000 0.50000 0.00000 1.000
O1 O 0.00000 0.75000 0.00000 1.000
O1 O 0.25000 0.75000 0.50000 1.000
O1 O 0.50000 0.00000 0.50000 1.000
O1 O 0.75000 0.00000 0.00000 1.000
O1 O 0.50000 0.25000 0.00000 1.000
O1 O 0.75000 0.25000 0.50000 1.000
O1 O 0.50000 0.50000 0.50000 1.000
O1 O 0.75000 0.50000 0.00000 1.000
O1 O 0.50000 0.75000 0.00000 1.000
O1 O 0.75000 0.75000 0.50000 1.000