sisl.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 theAtom
object, only a list index.- Parameters
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)
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 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 atomsremove
(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 atomatom
(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
Array of atomic numbers
List of unique atoms in this group of atoms
First orbital of the corresponding atom in the consecutive list of orbitals
Last orbital of the corresponding atom in the consecutive list of orbitals
Array of masses of the contained objects
Total number of orbitals in this list of atoms
Number of different species
Array of orbitals of the contained objects
Initial charge per atom
List of atomic species
- property Z¶
Array of atomic numbers
- add(other)¶
Append other to this list of atoms and return the appended version
- property atom¶
List of unique atoms in this group of atoms
- equal(other, R=True)[source]¶
True if the contained atoms are the same in the two lists (also checks indices)
- Parameters
See also
hassame
only check whether the two atoms are contained in both
- property firsto¶
First orbital of the corresponding atom in the consecutive list of orbitals
- group_atom_data(data, axis=0)[source]¶
Group data for each atom based on number of orbitals
This is useful for grouping data that is orbitally resolved. This will return a list of length
len(self)
and with each item having the sub-slice of the data corresponding to the orbitals on the given atom.Examples
>>> atoms = Atoms([Atom(4, [0.1, 0.2]), Atom(6, [0.2, 0.3, 0.5])]) >>> orb_data = np.arange(10).reshape(2, 5) >>> atoms.group_data(orb_data, axis=1) [ [[0, 1], [2, 3]], [[4, 5, 6], [7, 8, 9]] ]
- Parameters
data (numpy.ndarray) – data to be grouped
axis (int, optional) – along which axis one should split the data
- hassame(other, R=True)[source]¶
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
See also
equal
explicit check of the indices and the contained atoms
- iter(species=False)[source]¶
Loop on all atoms
This iterator may be used in two contexts:
species is
False
, this is the slowest method and will yield theAtom
per contained atom.species is
True
, which yields a tuple of (Atom, list) wherelist
contains all indices of atoms that has theAtom
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¶
Last orbital of the corresponding atom in the consecutive list of orbitals
- property mass¶
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).
- property no¶
Total number of orbitals in this list of atoms
- property nspecie¶
Number of different species
- property orbitals¶
Array of orbitals of the contained objects
- property q0¶
Initial charge per atom
- reorder(in_place=False)[source]¶
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
- replace(index, atom)[source]¶
Replace all atomic indices
index
with the atomatom
(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 toreplace_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
: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)[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
- property specie¶
List of atomic species