[ase-users] systematic construction of surface unit cells

[John Kitchin]

I am trying to develop some tutorials for surface unit cell making in
ase. The simple unit cells like fcc111-MxN are easy with the
ase.lattice.surface helper functions. I am having much more difficulty
figuring out how to construct surface unit cells for the
root3xroot3-R30 (111) unit cell or the (211) or (643) surfaces of fcc
lattices.

I thought I could use the lattice factories for this purpose, someting
like this for root3xroot3-R30 (111) surface:

atoms = FaceCenteredCubic(directions=[d1,d2,d3],
                          miller=(None,None,(1,1,1)),
                          symbol='Pd')

where d3 would be [1,1,1] (normal vector to the (1,1,1) plane that
isthe surface I want. d1 and d2 would be calculated as the
cross-product of a vector in the plane of the surface and d3 to get
the normal direction to the plane defining that side of the unit cell.
The specification of miller is to add a double check that I have the
surface I wanted.

This worked for making a simple 1x1 cell, but not for root3xroot3-R30
(111) surface (at least, I did not recognize the unit cell it made as
what I wanted!). There are three atoms per layer as i would have
expected, but the unit cell shape is not what I expected. Here is the
script that i thought would make a root3xroot3-r30 surface:

from ase.lattice.cubic import *
from ase import *

d3 = np.array([1.,1.,1.]) #normal to the surface we want

#fcc lattice vectors
p1 = np.array([0.5, 0.5, 0.])
p2 = np.array([0., 0.5, 0.5])

a1 = 2.*p1 - p2
a2 = p1 + p2

d1 = np.cross(a1,d3)
d2 = np.cross(a2,d3)

atoms = FaceCenteredCubic(directions=[d1,d2,d3],
                          miller=(None,None,(1,1,1)),
                          symbol='Pd',
                          debug=2)

uc = atoms.get_cell()
# add 10 angstroms of vacuum
uc[2] += [0,0,10]
atoms.set_cell(uc,scale_atoms=False)
view(atoms)

Is this the right way to think about using this module?  thanks,

j



-----------------------------------
John Kitchin
Assistant Professor
NETL-IAES Resident Institute Fellow
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu