sisl.Atoms

class sisl.Atoms(atoms: AtomsLike = 'H', na: int | None = None)

Bases: object

Efficient collection of Atom objects

A container object for Atom objects in a specific order. No two Atom objects will be duplicated and indices will be used to determine which Atom any indexable atom corresponds to. This is convenient when having geometries with millions of atoms because it will not duplicate the Atom object, only a list index.

Parameters:

atoms – atoms to be contained in this list of atoms If a str, or a single Atom it will be the only atom in the resulting class repeated na times. If a list, it will create all unique atoms and retain these, each item in the list may a single argument passed to the Atom or a dictionary that is passed to Atom, see examples.
na – total number of atoms, if len(atoms) is smaller than na it will be repeated to match na.

Examples

Creating an atoms object consisting of 5 atoms, all the same.

>>> atoms = Atoms("H", na=5)

Creating a set of 4 atoms, 2 Hydrogen, 2 Helium, in an alternate ordere

>>> Z = [1, 2, 1, 2]
>>> atoms = Atoms(Z)
>>> atoms = Atoms([1, 2], na=4) # equivalent

Creating individual atoms using dictionary entries, two Hydrogen atoms, one with a tag H_ghost.

>>> Atoms([dict(Z=1, tag="H_ghost"), 1])

Methods

`add`(other)	Append other to this list of atoms and return the appended version
`append`(other)	Append other to this list of atoms and return the appended version
`copy`()	Return a copy of this atom
`equal`(other[, R])	True if the contained atoms are the same in the two lists (also checks indices)
`formula`([system])	Return the chemical formula for the species in this object
`group_atom_data`(data[, axis])	Group data for each atom based on number of orbitals
`hassame`(other[, R])	True if the contained atoms are the same in the two lists
`index`(atom)	Return the indices of the atom object
`insert`(index, other)	Insert other atoms into the list of atoms at index
`iter`([species])	Loop on all atoms
`maxR`([all])	The maximum radius of the atoms
`orbital`(io)	Return an array of orbital of the contained objects
`prepend`(other)
`reduce`([inplace])	Returns a new `Atoms` object by removing non-used atoms
`remove`(atoms)	Remove a set of atoms
`reorder`([inplace])	Reorders the atoms and species index so that they are ascending (starting with a species that exists)
`repeat`(reps)	Repeat this atom object
`replace`(index, atom)	Replace all atomic indices `index` with the atom `atom` (in-place)
`replace_atom`(atom_from, atom_to)	Replace all atoms equivalent to atom_from with atom_to (in-place)
`reverse`([atoms])	Returns a reversed geometry
`scale`(scale)	Scale the atomic radii and return an equivalent atom.
`specie_index`(atom)	Return the species index of the atom object
`species_index`(atom)	Return the species index of the atom object
`sub`(atoms)	Return a subset of the list
`swap`(atoms1, atoms2)	Swaps atoms by index
`swap_atom`(a, b)	Swap species index positions
`tile`(reps)	Tile this atom object

Attributes

`Z`	Array of atomic numbers
`atom`	List of unique atoms in this group of atoms
`firsto`	First orbital of the corresponding atom in the consecutive list of orbitals
`lasto`	Last orbital of the corresponding atom in the consecutive list of orbitals
`mass`	Array of masses of the contained objects
`no`	Total number of orbitals in this list of atoms
`nspecie`	Number of different species
`nspecies`	Number of different species
`orbitals`	Array of orbitals of the contained objects
`q0`	Initial charge per atom
`specie`	List of atomic species
`species`	List of atomic species

add(other: Atom | Atoms) → Atoms

Append other to this list of atoms and return the appended version

Parameters:: other – new atoms to be added
Returns:: Atoms – merging of this objects atoms and the other objects atoms.

append(other: Atom | Atoms) → Atoms

Append other to this list of atoms and return the appended version

Parameters:: other – new atoms to be added
Returns:: Atoms – merging of this objects atoms and the other objects atoms.

copy() → Atoms: Return a copy of this atom

equal(other, R=True)[source]

True if the contained atoms are the same in the two lists (also checks indices)

Parameters:

other (Atoms) – the list of atoms to check against
R (bool, optional) – if True also checks that the orbital radius are the same