Fragments

Unlike the ADF program BAND is not based on fragments. Quite fundamentally the building blocks are the atoms. A fragment feature is available albeit rather primitive. 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 and obtain the fragment orbitals with the option

PREPAREFRAGMENTS

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 you need the result file of this calculation, therefore specify

RUNKF name

somewhere in the input, where 'name' is the name of the result file.

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 over-layer with the substrate. There are two restrictions: the atoms of the fragment - the hydrogens in the example - should be the first atoms on the input list and they should not be of the same type. You can force atoms of the same chemical element to be of a different type, by putting them in a different ATOMS block.

You make a second ATOMS block for the second hydrogen. Of course, you have to add also a second DIRAC, BASISFUNCTIONS and FITFUNCTIONS block. Tell the program that the two hydrogens constitute a fragment by

NATOMSASFRAGMENT 2

Finally, you add to the input the FRG key block where you give the name of the fragment file, and the key SIMPLEFRAG, which toggles the molecular fragment option. The basis will be transformed accordingly, and also the partitioning of basis functions is affected. The new basis and partitioning are reflected in the Mulliken gross and overlap populations. It is allowed to have more than one fragment. The key FRAGLABELS gives you the possibility to introduce labels for the fragment orbitals.

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 use of fragments is a valuable analysis tool. A previous fragment option in ADF-BAND could only be used for restart purposes. The new fragment option provides the possibility to use molecular fragments in

a subsequest periodic calculation. The provided example is a slab calculation of Cu with an CO molecule adsorbed. A DOS analysis is performed in terms of the Cu atomic orbitals and the CO molecular orbitals.

The new SIMPLEFRAG option (key) uses a molecular fragment that is created in the first part of this sample run. Note the key PREPAREFRAGMENTS and 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 has been saved as t21.CO, and is input for the second step of this example. The basis is transformed according to the eigenvectors of the CO fragment. Orbital labels are adapted by specifying FRAGLABELS.

The Density-of-States output are computed in the adapted basis.

The results can be interpreted in terms of the molecular solutions of CO, making the analysis easier.

FRAGLABELS (block-type)

The program will generate labels for the fragment orbitals automatically by default. With this option you can assign your own label to each fragment orbital.

Example:

FRAGLABELS

Sigma

Sigma*

Pi_x

Pi_y

Pi_x*

Pi_y*

**

In this example the first four fragment orbitals will be labeled as stated in the body of this key. The remaining orbitals are labeled by the default labeling system (e.g. 1/FO/5, etc.). The labels are used in combination with options like PRINT EIGENSYSTEM and PRINT ORBPOP. (See also PRINT ORBLABELS).

This key can be given once for each fragment.

SIMPLEFRAG

Triggers the fragment option that uses a molecular fragment from a previous calculation. Other keys that should be present also:

NATOMSASFRAGMENT, to specify the number of atoms per fragment, and

FRG, a block-type key that contains the name of the fragment file as well as the mapping from the atoms in the fragment to the atoms in the actual system (see keys NATOMSASFRAGMENT and FRG).

A calculation that uses SIMPLEFRAG should be preceded by a calculation that creates an appropriate fragment file, i.e. a quasi-molecular calculation (large lattice constants, KSPACE 1).