Surface Setup

This section is related to the geometry optimization section. To run a geometry optimization calculation, the slab needs to be defined in the script. Some examples of defining metal and metal oxide surfaces are given here.

This first example is a complete geometry optimization script. To set up a different slab, the part defining the slab (line 14) should be modified.

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#!/usr/bin/python

from ase import Atoms
from ase.calculators.vasp import Vasp
from ase.constraints import FixAtoms
from ase.optimize import QuasiNewton
from ase.lattice.surface import hcp0001
from ase.io import write,read

#A simple Ru(0001) surface. Surface element, size and 
#vacuum are specified in the parentheses

#define slab
slab = hcp0001('Ru', size=(3,3,2), vacuum=10)
#define adsorbate
molecule = Atoms('CO', [(0., 0., 0.), (0., 0., 1.16)])
#add adsorbate to the surface
add_adsorbate(slab, molecule, 1.7, ‘hcp’)

#read in the input file 
fName = 'input.xyz'
slab = read(fName)
#set slab coordinates from input file
slab.set_positions(slab.get_positions())

#set up calculator
calc = Vasp(xc='PBE',lreal='Auto',kpts=[2,2,1],
       ismear=1,sigma=0.2,algo='fast',istart=0,npar=8)
slab.set_calculator(calc)

#freeze all layers below top layer
mask = [atom.tag > 1 for atom in slab]
slab.set_constraint(FixAtoms(mask=mask))

#run optimization
dyn = QuasiNewton(slab, trajectory='CO-Ru.traj')
dyn.run(fmax=0.05) #(eV/A)

#write output
write('outPut.xyz', slab)


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#CeO2(111) surface

#Lattice constant
a = 5.46745036711

#Coordinates of the unit-cell atoms in fractional 
#coordinates (the fractional coordinates can be 
#found in the link given in external link section)
CeO2 = Atoms([
              Atom('Ce', (0., 0., 0.)),
              Atom('Ce', (0., 0.5, 0.5)),
              Atom('Ce', (0.5, 0., 0.5)),
              Atom('Ce', (0.5, 0.5, 0.)),
              Atom('O', (0.75, 0.25, 0.25)),
              Atom('O', (0.25, 0.75, 0.75)),
              Atom('O', (0.75, 0.75, 0.75)),
              Atom('O', (0.25, 0.25, 0.25)),
              Atom('O', (0.25, 0.25, 0.75)),
              Atom('O', (0.75, 0.75, 0.25)),
              Atom('O', (0.25, 0.75, 0.25)),
              Atom('O', (0.75, 0.25, 0.75))
                                           ])

#Defining lattice size in a, b and c directions. 
#In this case, they are all equal.
cell = [(a, 0., 0.),
        (0., a, 0.),
        (0., 0., a)]

#Scales the atomic positions with the unit cell
CeO2.set_cell(cell, scale_atoms=True)
#(1,1,1) is the slab type. There are 2 unit cells along 
#z direction
slab = surface(CeO2, (1, 1, 1), 2)

#Repeating the slab 2 unit cells in x and 1 unit cell 
#in y directions
slab = slab.repeat((2,1,1))
slab.center(vacuum=10, axis=2)


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#Building a gold surface with one of the atoms replaced 
#by Pd

slab = fcc111('Au', size=(3,3,4), vacuum=10)
slab.set_chemical_symbols('AuAuAuAuAuAuAuAuAuAuAuAuAuAuAuAuAuAuAuAuAuAuAuAuAuAuAuAuAuAuAuPdAuAuAuAu')