Fragments

A fragment feature is available albeit rather primitive. It allows for the analysis of the DOS in a fragment basis and for the calculation of the deformation density with respect to fragment densities. A typical application is the periodical adsorption of one or more molecules on a surface. For instance, consider periodic adsorption of hydrogen molecules over a surface. First you calculate the free molecule in the same orientation as when adsorbed to the substrate. Since you would like to use a molecular fragment, it makes sense to put the molecules far apart (large lattice spacing) and force dispersion to be neglected (KSPACE 1). To use the fragment in the next run you need to rename the result file ("RUNKF"), to something like "frag.runkf", see the example script discussed below.

Specifying

PRINT EIGENS

for this calculation produces output concerning the eigen states, thereby providing a means to identify the eigen states (e.g. to be sigma, pi, et cetera).

Next, prepare the input for the overlayer with the substrate. With one or more Fragment keys you specify which fragment file(s) to use and to which atoms they should be mapped. It is allowed to have more than one fragment. The sub key Labels of a Fragment gives you the possibility to introduce labels for the fragment orbitals. Finally you can specify which fragments to use in the DOS analysis, via the DosBas key.

An example of using the fragments feature in BAND is provided in one of the sample runs (CO on a Cu surface) in the directory $ADFHOME/examples/band/e_Frags_COCu, see the Examples document. The provided example is a slab calculation of Cu with a CO molecule adsorbed. A DOS analysis is performed in terms of the Cu atomic orbitals and the CO molecular orbitals. Note in the first step the use of KSPACE 1, together with a large lattice spacing. In this way a 'molecular' solution is obtained, which can be used as a fragment. This fragment is saved as CO.runkf, and is input for the second step of this example. Some of the orbital labels are adapted by specifying Labels. In the remaining steps this example demonstrates how to obtain the deformation density with respect to the sum of fragments (CO molecule + bare Cu slab) densities.