SITE_DEF

SITE_DEF defines the different types of sites for a given element. Different sites can have different occupancies and vibrational amplitudes.

Default: all atoms have site name def.

Syntax:

SITE_DEF Fe = tet 1 2, oct 4-10 12, surf top(2)
SITE_DEF O = surf top(2)

The first argument is the element name in the POSCAR file for sites that are being defined. After the “=” sign, comma-delimited groups should contain names of the sites and the atom numbers to be assigned (number of atom in the POSCAR list / same as progressional numbers in VESTA’s Edit>Data>Structure parameters, not the VESTA number per type, i.e., not the number in ‘Fe2’, ‘O16’ etc.). The top(N) function selects the N topmost atoms of the given POSCAR element. 4-10 or 4:10 will select atoms 4 to 10, including 4 and 10. In the example, atoms 1 and 2 will get site type ‘tet’, atoms 4 through 10 and atom 12 will get site type ‘oct’, and the two topmost Fe atoms will get site type ‘surf’. The two topmost O atoms will get site type ‘surf’. For atoms identified by number, the element label must match the element label specified in the POSCAR. Otherwise an error will be raised asking the user to check the input.

If site types for multiple elements are being assigned, have multiple lines, each starting with SITE_DEF and the respective elements left of the ‘=’ sign, as in the example.

Only atoms that need special treatment need to be listed. All others will get site type 'def’, which can be accessed normally. For most simple cases, a simple assignment of the topmost (undercoordinated) atoms as special sites should be sufficient. The following example is for Fe2O3(012), where the topmost layer has two Fe and two O atoms per unit cell:

SITE_DEF Fe = atTop top(2)
SITE_DEF O = atTop top(2)