ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

translate(displacement)
Translate atomic positions.
ASE Manual, Release 3.6.1.2828
The displacement argument can be a float an xyz vector or an nx3 array (where n is the number of
atoms).
write(filename, format=None, **kwargs)
Write yourself to a file.
7.2 The Atom object
ASE defines a python class called Atom to setup and handle atoms in electronic structure and molecular simulations.
From a python script, atoms can be created like this:
>>> from ase import Atom
>>> a1 = Atom(’Si’, (0, 0, 0))
>>> a2 = Atom(’H’, (1.3, 0, 0), mass=2)
>>> a3 = Atom(position=(0, 0, 0), Z=14) # same is a1
class ase.atom.Atom(symbol=’X’, position=(0, 0, 0), tag=None, momentum=None, mass=None, magmom=None,
charge=None, atoms=None, index=None)
Class for representing a single atom.
Parameters:
symbol: str or int Can be a chemical symbol (str) or an atomic number (int).
position: sequence of 3 floats Atomi position.
tag: int Special purpose tag.
momentum: sequence of 3 floats Momentum for atom.
mass: float Atomic mass in atomic units.
magmom: float or 3 floats Magnetic moment.
charge: float Atomic charge.
The first argument to the constructor of an Atom object is the chemical symbol, and the second argument is the
position in Å units (see units). The position can be any numerical sequence of length three. The properties of
an atom can also be set using keywords like it is done in the a2 and a3 examples above.
More examples:
>>> a = Atom(’O’, charge=-2)
>>> b = Atom(8, charge=-2)
>>> c = Atom(’H’, (1, 2, 3), magmom=1)
>>> print a.charge, a.position
-2 [ 0. 0. 0.]
>>> c.x = 0.0
>>> c.position
array([ 0., 2., 3.])
>>> b.symbol
’O’
>>> c.tag = 42
>>> c.number
1
>>> c.symbol = ’Li’
>>> c.number
3
If the atom object belongs to an Atoms object, then assigning values to the atom attributes will change the corresponding
arrays of the atoms object:
7.2. The Atom object 65