How to use

Quick use

shry STRUCTURE_CIF

You can prepare CIFs with partial occupations by one of the ways below

Editing CIF file

The important part is the _atom_site_occupancy and _atom_site_label, which are typically grouped together in a loop

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
_atom_site_U_iso_or_equiv
Sm1 Sm 0.000 0.00 0.00 1.000 0.0
Fe1 Fe 0.250 0.25 0.25 1.000 0.0
Fe2 Fe 0.278 0.50 0.00 1.000 0.0

Suppose that here we want to replace Fe1 to a 40/60 mix together with Nb. Copy and edit the Fe1 line, adjusting the labels and occupations.

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
_atom_site_U_iso_or_equiv
Sm1 Sm 0.000 0.00 0.00 1.000 0.0
Fe1 Fe 0.250 0.25 0.25 0.400 0.0
Nb1 Nb 0.250 0.25 0.25 0.600 0.0
Fe2 Fe 0.278 0.50 0.00 1.000 0.0

SHRY will automatically stop if the total occupancy of a site is either less or more than 1.0. To simulate vacancies, create a pseudatom with species X.

Using SHRY option to create partial occupation

The below example achieves the same modification. You can also choose to above by the below options.

shry [-f/--from-species] Fe1 [-t/--to-species] Fe0.4Nb0.6 STRUCTURE_CIF

Note that SHRY targets either _atom_site_label or _atom_site_label. If instead Fe is used in the first argument, all iron sites including Fe2 will be replaced by `Fe0.4Nb0.6.

Check total symmetry-inequivalent structures

shry --count-only STRUCTURE_CIF

This operation is based on Polya enumeration and takes much less time than a proper generation.

More command line options

Creating supercell

Sometimes a supercell is required to fit in finer concentrations. SHRY accepts either 3-digit (diagonal) or 9-digit (non-diagonal) format to specify the supercell’s scaling matrix. For example a 2x2x1 supercell can be specified by either

shry -s 2 2 1 ...

or

shry -s 2 0 0 0 2 0 0 0 1 ...

Disorder only

If you just want to modify the CIF, without making the unique structures, you can add

shry --mod-only ...

Other options

Other options can be found in the help menu

shry -h