=============== Tips and tricks =============== In order to get the most out out the tips below (and ASE in general), it is a good idea to get to know the Python language and the NumPy library well. See: * https://www.python.org/ * https://docs.scipy.org/doc/numpy/ .. contents:: Atoms objects ============= Species ------- >>> from ase import Atoms >>> atoms = Atoms('CH4') >>> len(set(atoms.numbers)) # number of species 2 >>> set(atoms.get_chemical_symbols()) # set of species {'C', 'H'} Indexing -------- >>> atoms Atoms(symbols='CH4', pbc=False) >>> [atom.index for atom in atoms if atom.symbol == 'H'] [1, 2, 3, 4] >>> atoms[[atom.index for atom in atoms if atom.symbol == 'H']] Atoms(symbols='H4', pbc=False) Indexing with lists of booleans: >>> atoms.numbers == 1 array([False, True, True, True, True], dtype=bool) >>> atoms[atoms.numbers == 1] Atoms(symbols='H4', pbc=False) Three equivalent ways to delete carbon atoms: >>> del atoms[atoms.numbers == 6] >>> del atoms[[atom.index for atom in atoms if atom.symbol == 'C']] >>> del atoms[[atom.symbol == 'C' for atom in atoms]] Swap the positions of two atoms with index 3 and 4: >>> atoms.positions[[3, 4]] = atoms.positions[[4, 3]] Trajectories ============ Append one trajectory to the end of another ------------------------------------------- .. testsetup:: from ase.io import write from ase import Atoms write('t1.traj', Atoms('H')) write('t2.traj', Atoms('H')) write('abc.traj', Atoms('H')) >>> from ase.io import Trajectory >>> t1 = Trajectory('t1.traj', 'a') >>> t2 = Trajectory('t2.traj') >>> for atoms in t2: ... t1.write(atoms) >>> t1.close() Input/output ============ Convert from one format to another ---------------------------------- >>> from ase.io import read, write >>> write('abc.xyz', read('abc.traj'))