Atoms

class sisl.Atoms(atoms=None, na=None)

Bases: object

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

• atoms (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.

atom

a list of unique atoms in this object

Type

list of Atom

specie

a list of unique specie indices

Type

(na, )

no

total number of orbitals

Type

int

q0

initial charge on each orbital

Type

(no, )

mass

mass for each atom

Type

(na, )

firsto

a list of orbital indices for each atom, this corresponds to the first orbital on each of the atoms. The last element is the total number of orbitals and is equivalent to no.

Type

(no + 1,)

lasto

a list of orbital indices for each atom, this corresponds to the last orbital on each of the atoms.

Type

(no, )

Attributes

Z	Return an array of atomic numbers (integers)
__doc__
__hash__
__module__
__slots__
_atom
_firsto
_specie
atom	List of unique atoms in this group of atoms
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
nspecie	Number of different species
orbitals	Return an array of orbitals of the contained objects
q0	Initial charge per atom
specie	Atomic specie list

Methods

__contains__(key)	Determine whether the key is in the unique atoms list
__delattr__	Implement delattr(self, name).
__dir__	Default dir() implementation.
__eq__(b)	Returns true if the contained atoms are the same
__format__	Default object formatter.
__ge__	Return self>=value.
__getattribute__	Return getattr(self, name).
__getitem__(key)	Return an Atom object corresponding to the key(s)
__getstate__()	Return the state of this object
__gt__	Return self>value.
__init__([atoms, na])	Initialize self.
__init_subclass__	This method is called when a class is subclassed.
__iter__()	Loop on all atoms with the same specie in order of atoms
__le__	Return self<=value.
__len__()	Return number of atoms in the object
__lt__	Return self<value.
__ne__	Return self!=value.
__new__	Create and return a new object.
__reduce__	Helper for pickle.
__reduce_ex__	Helper for pickle.
__repr__()	Return repr(self).
__setattr__	Implement setattr(self, name, value).
__setitem__(key, value)	Overwrite an Atom object corresponding to the key(s)
__setstate__(d)	Re-create the state of this object
__sizeof__	Size of object in memory, in bytes.
__str__()	Return the Atoms in str
__subclasshook__	Abstract classes can override this to customize issubclass().
_update_orbitals()	Internal routine for updating the firsto attribute
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(atoms)	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([atoms])	Returns a reversed geometry
scale(scale)	Scale the atomic radii and return an equivalent atom.
sub(atoms)	Return a subset of the list
swap(a, b)	Swaps all atoms
swap_atom(a, b)	Swap specie index positions
tile(reps)	Tile this atom object

property Z

Return an array of atomic numbers (integers)

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

merging of this objects atoms and the other objects atoms.

Return type

Atoms

append(other)

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

Parameters

other (Atoms or Atom) – new atoms to be added

Returns

merging of this objects atoms and the other objects atoms.

Return type

Atoms

property atom

List of unique atoms in this group of atoms

copy()

Return a copy of this atom

equal(other, R=True)

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

property firsto

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

hassame(other, R=True)

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

Notes

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

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

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=False)

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.

property lasto

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

property mass

Return an array of masses of the contained objects

maxR(all=False)

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).

property no

Return the total number of orbitals in this list of atoms

property nspecie

Number of different species

orbital(io)

Return an array of orbital of the contained objects

property orbitals

Return an array of orbitals of the contained objects

prepend(other)

property q0

Initial charge per atom

reduce(in_place=False)

Returns a new Atoms object by removing non-used atoms

remove(atoms)

Remove a set of atoms

reorder(in_place=False)

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

Parameters

in_place (bool, optional) – whether the re-order is done in-place

repeat(reps)

Repeat this atom object

replace(index, atom)

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)

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 KeyError : if atom_from does not exist in the list of atoms: :raises UserWarning : if the atoms does not have the same number of orbitals.:

reverse(atoms=None)

Returns a reversed geometry

Also enables reversing a subset of the atoms.

scale(scale)

Scale the atomic radii and return an equivalent atom.

Parameters

scale (float) – the scale factor for the atomic radii

property specie

Atomic specie list

sub(atoms)

Return a subset of the list

swap(a, b)

Swaps all atoms

swap_atom(a, b)

Swap specie index positions

tile(reps)

Tile this atom object