ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

e_slab = slab.get_potential_energy()
molecule = Atoms(’2N’, positions=[(0., 0., 0.), (0., 0., d)])
molecule.set_calculator(EMT())
e_N2 = molecule.get_potential_energy()
add_adsorbate(slab, molecule, h, ’ontop’)
constraint = FixAtoms(mask=[a.symbol != ’N’ for a in slab])
slab.set_constraint(constraint)
dyn = QuasiNewton(slab, trajectory=’N2Cu.traj’)
dyn.run(fmax=0.05)
ASE Manual, Release 3.6.1.2828
print ’Adsorption energy:’, e_slab + e_N2 - slab.get_potential_energy()
#view(slab)
Assuming you have ASE setup correctly (Installation requirements) run the script:
python N2Cu.py
Please read below what the script does.
Atoms
The Atoms object is a collection of atoms. Here is how to define a N2 molecule by directly specifying the position
of two nitrogen atoms:
from ase import Atoms
d = 1.10
molecule = Atoms(’2N’, positions=[(0., 0., 0.), (0., 0., d)])
You can also build crystals using, for example, the lattice module which returns Atoms objects corresponding to
common crystal structures. Let us make a Cu (111) surface:
from ase.lattice.surface import fcc111
slab = fcc111(’Cu’, size=(4,4,2), vacuum=10.0)
Calculators
Many calculators can be used with ASE, including emt, Asap, Dacapo, GPAW, Abinit, Vasp. See the ASE
home page for the full list.
In this overview we use the effective medium theory (EMT) calculator, as it is very fast and hence useful for
getting started.
We can attach a calculator to the previously created Atoms objects:
from ase import EMT
slab.set_calculator(EMT())
molecule.set_calculator(EMT())
and use it to calculate the total energies for the systems by using the get_potential_energy() method
from the Atoms class:
e_slab = slab.get_potential_energy()
e_N2 = molecule.get_potential_energy()
Structure relaxation
Let’s use the QuasiNewton minimizer to optimize the structure of the N2 molecule adsorbed on the Cu surface.
First add the adsorbate to the Cu slab, for example in the on-top position:
6.2. ASE 19