Partial occupancy groups get fixed by themselves

[gagarofalo]

Hi,

I'm trying to generate some disordered cells, but with all the .cif files I use the occupancy gets fixed. I tried to do some tests with different percentages and it seems it chooses 1 for the atom with the highest percentage, even if it's 51. This is one of the .cif files, with just one partial occupied site:

_symmetry_space_group_name_H-M 'P 1' _cell_length_a 5.60256400 _cell_length_b 5.60256400 _cell_length_c 5.60256400 _cell_angle_alpha 90.00000000 _cell_angle_beta 90.00000000 _cell_angle_gamma 90.00000000 _symmetry_Int_Tables_number 1 _chemical_formula_structural Fe3Si _chemical_formula_sum 'Fe12 Si4' _cell_volume 175.85733158 _cell_formula_unitsZ 4 loop _symmetry_equiv_pos_site_id _symmetry_equiv_pos_asxyz 1 'x, y, z' loop _atom_site_type_symbol _atom_site_label _atom_site_symmetry_multiplicity _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_occupancy Fe Fe0 1 0.25000000 0.25000000 0.75000000 0.5 Si Si0 1 0.25000000 0.25000000 0.75000000 0.5 Fe Fe1 1 0.00000000 0.00000000 0.00000000 1 Fe Fe2 1 0.25000000 0.75000000 0.75000000 1 Fe Fe3 1 0.25000000 0.75000000 0.25000000 1 Fe Fe4 1 0.00000000 0.50000000 0.50000000 1 Fe Fe5 1 0.25000000 0.25000000 0.25000000 1 Fe Fe6 1 0.75000000 0.25000000 0.25000000 1 Fe Fe7 1 0.50000000 0.00000000 0.50000000 1 Fe Fe8 1 0.75000000 0.75000000 0.25000000 1 Fe Fe9 1 0.75000000 0.75000000 0.75000000 1 Fe Fe10 1 0.50000000 0.50000000 0.00000000 1 Fe Fe11 1 0.75000000 0.25000000 0.75000000 1 Si Si12 1 0.50000000 0.00000000 0.00000000 1 Si Si13 1 0.50000000 0.50000000 0.50000000 1 Si Si14 1 0.00000000 0.00000000 0.50000000 1 Si Si15 1 0.00000000 0.50000000 0.00000000 1

and here is the output I got after executing supercell -d -i <input>.cif -m:

The other groups are fixed, as they should be. What am I doing wrong?

[orex]

In the example you wrote, there is only one site for the disordered atom. So, it is occupied either by 1 Fe or 1 Si atom. Please increase the cell size to get the result. For example,

supercell -d -i <input>.cif -m -s 2x2x2

[gagarofalo]

But in the Ca2Al2SiO7 example the disordered site is distributed even in the 1x1x1 run. I would like to avoid increasing the cell size because, in the end, I'd like to do just one 1x1x1 big cluster (100s of atoms big) randomly assigning the site species. Is that possible?

[orex]

Again. You have ONE site with multiplicity 1 in you cell. When you have only physical 1 place where you can put your atom, it is not possible to distribute several atoms around one site (see output).

...
Group 1 (1 atomic position in supercell):
...

For Ca2Al2SiO7 example:

....
 Group 2 (4 atomic positions in supercell):
  * Site #1: AlT2 (occ. 0.5) -> distributed over 2 positions out of 4 (actual occ.: 0.500).
  * Site #2: SiT2 (occ. 0.5) -> distributed over 2 positions out of 4 (actual occ.: 0.500).
  Number of combinations for the group is 6
...

[gagarofalo]

Ok thanks I see.