Atoms

class sisl.Atoms(atom=None, na=None)[source]

A list-like object to contain a list of different atoms with minimum data duplication.

This holds multiple Atom objects which are indexed via a species index. This is convenient when having geometries with millions of atoms because it will not duplicate the Atom object, only a list index.

Parameters:
atom : list of Atom

atoms to be contained in this list of atoms

na : int or None

total number of atoms, if len(atom) is smaller than na it will be repeated to match na.
Attributes:
atom : list of Atom

Return the unique atoms list

specie : (na, )

Return the specie list

no : int

Return the total number of orbitals in this list of atoms

q0 : (no, )

Initial charge per atom

mass : (na, )

Return an array of masses of the contained objects

firsto : (no + 1,)

The first orbital of the corresponding atom in the consecutive list of orbitals

lasto : (no, )

The lasto orbital of the corresponding atom in the consecutive list of orbitals

Attributes

Z Return an array of atomic numbers
atom Return the unique atoms list
firsto The first orbital of the corresponding atom in the consecutive list of orbitals
lasto The lasto orbital of the corresponding atom in the consecutive list of orbitals
mass Return an array of masses of the contained objects
no Return the total number of orbitals in this list of atoms
orbitals Return an array of orbitals of the contained objects
q0 Initial charge per atom
specie Return the specie list

Methods

__init__([atom, na]) Initialize self.
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)
hassame(other[, R]) True if the contained atoms are the same in the two lists
index(atom) Return the species index 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([in_place]) Returns a new Atoms object by removing non-used atoms
remove(atom) Remove a set of atoms
reorder([in_place]) Reorders the atoms and species index so that they are ascending (starting with a specie 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([atom]) Returns a reversed geometry
scale(scale) Scale the atomic radii and return an equivalent atom.
sub(atom) Return a subset of the list
swap(a, b) Swaps atoms
tile(reps) Tile this atom object
Z

Return an array of atomic numbers

add(other)

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

Parameters:
other : Atoms or Atom

new atoms to be added
Returns:
Atoms : a merging of this objects atoms and the other objects atoms.
append(other)[source]

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

Parameters:
other : Atoms or Atom

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

Return the unique atoms list

copy()[source]

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

See also

hassame
only check whether the two atoms are contained in both
firsto

The first orbital of the corresponding atom in the consecutive list of orbitals

hassame(other, R=True)[source]

True if the contained atoms are the same in the two lists

Parameters:
other : Atoms

the list of atoms to check against

R : bool, optional

if True also checks that the orbital radius are the same

See also

equal
explicit check of the indices and the contained atoms

Notes

This does not necessarily mean that the order, nor the number of atoms are the same.

index(atom)[source]

Return the species index of the atom object

insert(index, other)[source]

Insert other atoms into the list of atoms at index

iter(species=False)[source]

Loop on all atoms

This iterator may be used in two contexts:

  1. species is False, this is the slowest method and will yield the Atom per contained atom.
  2. species is True, which yields a tuple of (Atom, list) where list contains all indices of atoms that has the Atom specie. This is much faster than the first option.
Parameters:
species : bool, optional

If True loops only on different species and yields a tuple of (Atom, list) Else yields the atom for the equivalent index.
lasto

The lasto orbital of the corresponding atom in the consecutive list of orbitals

mass

Return an array of masses of the contained objects

maxR(all=False)[source]

The maximum radius of the atoms

Parameters:
all : bool

determine the returned maximum radii. If True is passed an array of all atoms maximum radii is returned (array). Else, if False the maximum of all atoms maximum radii is returned (scalar).
no

Return the total number of orbitals in this list of atoms

orbital(io)[source]

Return an array of orbital of the contained objects

orbitals

Return an array of orbitals of the contained objects

prepend(other)[source]
q0

Initial charge per atom

reduce(in_place=False)[source]

Returns a new Atoms object by removing non-used atoms

remove(atom)[source]

Remove a set of atoms

reorder(in_place=False)[source]

Reorders the atoms and species index so that they are ascending (starting with a specie that exists

repeat(reps)[source]

Repeat this atom object

replace(index, atom)[source]

Replace all atomic indices index with the atom atom (in-place)

This is the preferred way of replacing atoms in geometries.

Parameters:
index : list of int or Atom

the indices of the atoms that should be replaced by the new atom. If an Atom is passed, this routine defers its call to replace_atom.

atom : Atom

the replacement atom.
replace_atom(atom_from, atom_to)[source]

Replace all atoms equivalent to atom_from with atom_to (in-place)

I.e. this is the preferred way of adapting all atoms of a specific type with another one.

If the two atoms does not have the same number of orbitals a warning will be raised.

Parameters:
atom_from : Atom

the atom that should be replaced, if not found in the current list of atoms, nothing will happen.

atom_to : Atom

the replacement atom.
Raises:
UserWarning : if the atoms does not have the same number of orbitals.
reverse(atom=None)[source]

Returns a reversed geometry

Also enables reversing a subset of the atoms.

scale(scale)[source]

Scale the atomic radii and return an equivalent atom.

Parameters:
scale : float

the scale factor for the atomic radii
specie

Return the specie list

sub(atom)[source]

Return a subset of the list

swap(a, b)[source]

Swaps atoms

tile(reps)[source]

Tile this atom object