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ASE Manual, Release 3.6.1.2828 7.9.5 Surfaces Common surfaces A number of utility functions are provided to set up the most common surfaces, to add vacuum layers, and to add adsorbates to a surface. In general, all surfaces can be set up with the modules described in the section General crystal structures and surfaces, but these utility functions make common tasks easier. Example To setup an Al(111) surface with a hydrogen atom adsorbed in an on-top position: from ase.lattice.surface import * slab = fcc111(’Al’, size=(2,2,3), vacuum=10.0) This will produce a slab 2x2x3 times the minimal possible size, with a (111) surface in the z direction. A 10 Å vacuum layer is added on each side. To set up the same surface with with a hydrogen atom adsorbed in an on-top position 1.5 Å above the top layer: from ase.lattice.surface import * slab = fcc111(’Al’, size=(2,2,3)) add_adsorbate(slab, ’H’, 1.5, ’ontop’) slab.center(vacuum=10.0, axis=2) Note that in this case is is probably not meaningful to use the vacuum keyword to fcc111, as we want to leave 10 Å of vacuum after the adsorbate has been added. Instead, the center() method of the Atoms is used to add the vacuum and center the system. The atoms in the slab will have tags set to the layer number: First layer atoms will have tag=1, second layer atoms will have tag=2, and so on. Addsorbates get tag=0: >>> print atoms.get_tags() [3 3 3 3 2 2 2 2 1 1 1 1 0] This can be useful for setting up constraints (see Diffusion of gold atom on Al(100) surface (NEB)). Utility functions for setting up surfaces All the functions setting up surfaces take the same arguments. symbol: The chemical symbol of the element to use. size: A tuple giving the system size in units of the minimal unit cell. a: (optional) The lattice constant. If specified, it overrides the expermental lattice constant of the element. Must be specified if setting up a crystal structure different from the one found in nature. c: (optional) Extra HCP lattice constant. If specified, it overrides the expermental lattice constant of the element. Can be specified if setting up a crystal structure different from the one found in nature and an ideal c/a ratio is not wanted (c/a = (8/3) 1/3 ). vacuum: The thickness of the vacuum layer. The specified amount of vacuum appears on both sides of the slab. Default value is None, meaning not to add any vacuum. In that case a “vacuum” layer equal to the interlayer spacing will be present on the upper surface of the slab. Specify vacuum=0.0 to remove it. orthogonal: (optional, not supported by all functions). If specified and true, forces the creation of a unit cell with orthogonal basis vectors. If the default is such a unit cell, this argument is not supported. Each function defines a number of standard adsorbtion sites that can later be used when adding an adsorbate with lattice.surface.add_adsorbate(). 86 Chapter 7. Documentation for modules in ASE
The following functions are provided ase.lattice.surface.fcc100(symbol, size, a=None, vacuum=0.0) ase.lattice.surface.fcc110(symbol, size, a=None, vacuum=0.0) ase.lattice.surface.bcc100(symbol, size, a=None, vacuum=0.0) ase.lattice.surface.hcp10m10(symbol, size, a=None, c=None, vacuum=0.0) ase.lattice.surface.diamond100(symbol, size, a=None, vacuum=0.0) These allways give orthorhombic cells: ASE Manual, Release 3.6.1.2828 7.9. Creating atomic structures 87
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