wulfric.crystal.populate_atom_species#

wulfric.crystal.populate_atom_species(atoms, raise_on_fail=False) → None[source]#

Populate atom species, based on their names. If atom species are already present in the atoms, then they will be overwritten.

Parameters:
atomsdict

Dictionary with atoms. Must have a names with the value of list of N str.

raise_on_failbool, default False

Whether to raise an error if the atom type can not be deduced based on its name.

Raises:
FailedToDeduceAtomSpecies

If raise_on_fail = True and automatic species deduction fails.

Warning

If raise_on_fail = True and automatic species deduction fails, then RuntimeWarning is issued, and atom species is set to "X".

Examples

>>> import wulfric as wulf
>>> atoms = {"names" : ["Cr1", "cr2", "Br3", "S4", "fe5", "Fe6"]}
>>> atoms
{'names': ['Cr1', 'cr2', 'Br3', 'S4', 'fe5', 'Fe6']}
>>> wulf.crystal.populate_atom_species(atoms)
>>> atoms
{'names': ['Cr1', 'cr2', 'Br3', 'S4', 'fe5', 'Fe6'], 'species': ['Cr', 'Cr', 'Br', 'S', 'Fe', 'Fe']}