ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
We now add an adatom. Since the supercell is now declared as the unit cell for our atoms we can either add the
atom using its cartesian coordinates in Angstrom or rescale the unit cell and use scaled coordinates. We try the
latter:
>>> from numpy import identity
>>> from ase import Atom
>>> xyzcell = identity(3) # The 3x3 unit matrix
>>> atoms.set_cell(xyzcell, scale_atoms=True) # Set the unit cell and rescale
>>> atoms.append(Atom(’Ni’, (1/6., 1/6., .1)))
>>> atoms.set_cell(cell, scale_atoms=True) # Set the unit cell and scale back
The structure now looks like this:
>>> view(atoms)
6.2.3 Using the spacegroup subpackage
The most evident usage of the spacegroup subpackage is to set up an initial unit of a bulk structure. For this you
only need to supply the unique atoms and their scaled positions, space group and lattice parameters.
Examples of setting up bulk structures
We start by showing some examples of how to set up some common or interesting bulk structures using
ase.lattice.spacegroup.crystal(). This function takes a lot of arguments, of which the most important are:
symbols [string | sequence of strings] Either a string formula or sequence of element symbols. E.g.
‘NaCl’ and (‘Na’, ‘Cl’) are equivalent.
basis [list of scaled coordinates] Coordinates of the non-equivalent sites in units of the lattice vectors.
spacegroup [int | string | Spacegroup instance] Space group given either as its number in International
Tables or as its Hermann-Mauguin (or international) symbol.
setting [1 | 2] Space group setting.
6.2. ASE 23