Element names

The way TensErLEED works leads to a distinction in what an “element” is. Two (sometimes overlapping) categories exist:

• Elements as defined in the POSCAR file (here often referred to as “POSCAR elements”): These do not need to be chemical elements, but can in principle have arbitrary names.[1]

• Chemical elements, as they appear in the periodic table: Each of the POSCAR elements that does not already have names of chemical elements must be specified by either the ELEMENT_MIX or the ELEMENT_RENAME parameters.

The main reason why this distinction is necessary is mixed occupation of sites. It is possible for specific atomic positions (as specified in the POSCAR file) to contain mixtures of two or more elements. This split should be specified by ELEMENT_MIX. In these cases, it is strongly recommended to rename the elements in the POSCAR file such that the POSCAR elements and chemical elements don’t overlap. For example, if your POSCAR contains atoms labeled La but your material contains some mixture of La and Sr in those sites, you could rename La to A in the POSCAR, then use ELEMENT_MIX A = La Sr to specify that these atoms are actually either La or Sr. If you do not do this, but simply use ELEMENT_MIX La = La Sr, you produce an element-name collision. This means that in your later input (e.g., in the VIBROCC and DISPLACEMENTS files) viperleed.calc has no clear way to distinguish whether you wanted to refer to the POSCAR element (i.e., all chemical species in that position) or to one specific chemical element.

Note that element names are not case sensitive. This means that, for example, Pb, PB and pb are considered equal. Thus, having a POSCAR element PB defined as ELEMENT_MIX PB = P B and the chemical element Pb in the same calculation will lead to a name collision.

As mentioned above, the recommended approach is to avoid name collisions by renaming the POSCAR elements where necessary. However, name collisions do not normally cause the program to stop, although they will produce a warning. If you insist to work with a name collision, you must make sure that your later input is interpreted correctly. Generally, the program’s approach is to interpret element names as POSCAR elements, that is, to assign your input to all atoms in the given site, wherever this makes sense. Chemical elements only take precedence where interpreting as POSCAR elements would be nonsensical, that is on the right-hand side of input in the VIBROCC file, and in OCC_DELTA blocks in the DISPLACEMENTS file.

Footnotes

[1]

Mind the fact that the POSCAR-file specification only considers the first two characters of each element name. This is also reflected in VESTA, which reads only the first two characters. This means that Atom1 and Atom2 will both appear as species At both in VESTA [12] and in a DFT calculation with VASP [20]. ViPErLEED will instead read the full name.