SCM: ADF User's Guide

Fragment mode

In Fragment mode more input is required than in Create mode: you have to specify at least: (1) the atomic positions and (2) how the total system is built up from fragments. We recommended to specify also (3) the point group symmetry.

Example of an input file for the C2H4 molecule:

ATOMS
 C  0    0  .6685
 C  0    0 -.6685
 H  .927 0 -1.203
 H -.927 0 -1.203
 H  .927 0  1.203
 H -.927 0  1.203
end

fragments
 C TAPE21c.dzp
 H TAPE21h.dzp
end

symmetry D(2h)
end input

Three keys are used: atoms, fragments and symmetry. The first two are block keys.

atoms

defines the atomic positions: each record in the data block contains the chemical symbol of an atom followed by its Cartesian coordinates in Angstroms.
Z-matrix type input of atomic positions is also possible. This will be explained in a later section.

fragments

lists the fragment files each record contains a fragment type followed by the corresponding fragment file. In the example the files are local files. Files in other directories are addressed by giving the complete file path.
Note: if a parallel calculation is performed, be sure that each 'kid' finds the specified fragment files. This will usually require that the files are not local to the job, but first be moved to some shared volume, and that the references to the fragment files in the input contain the full path. An alternative is to ensure that the (local) files in the parent directory are copied first to the 'kid' directories before the parallel calculation starts.

symmetry

specifies the point group symmetry by a Schönfliess type symbol. Appendix 3 contains a complete list of all Schönfliess symbols that are recognized by adf. If no symmetry is specified adf will take the true symmetry of the nuclear frame as the user-specified symmetry. If (electric) fields are used, see later, the computed symmetry will take this into account. Note that the computed symmetry may not occur in the list of allowed symmetries (see Appendix 3), in which case you have to explicitly specify the (lower) point group symmetry you wish to apply.

The atomic coordinates must conform to the point group symmetry; the program will check this and abort if the atomic system does not have the specified symmetry. It is allowed, however, to specify a lower symmetry than what is actually present in the set of atomic positions. The specified symmetry determines how results are analyzed and how irreducible representations and subspecies are labeled. It also determines various algorithmic aspects: the program runs more efficiently with the highest possible symmetry.

The spatial orientation of the molecular coordinate system is not arbitrary. ADF requires for each pointgroup symmetry a specific standard orientation. In axial groups for instance, the main rotation axis must be the z-axis. This implies a restriction on how you can define the atomic coordinates under atoms. The orientation requirements for all point groups are listed in Appendix 3. If the specified symmetry equals the true symmetry of the nuclear frame adf will adjust the input orientation of the molecule to the requirements (if necessary). If you have specified a subgroup of the true nuclear symmetry, no such orientation adjustment is carried out and the user has to make sure that his input data yield the correct orientation, lest an error will occur.

Restrictions apply to the symmetry (as specified) of the molecule, related to the symmetries of the fragments as they were stipulated in the preceding fragment calculations. All symmetry operators of the molecule that internally rotate or reflect a fragment but leave it at the same position in the molecule, must also be operators of the symmetry group in which the fragment has been computed. Furthermore, two fragments must not be symmetry-equivalent in the molecule only by an improper rotation. The implied internal reflection of the fragment must be one of the symmetry operators in the point group symmetry that is used in the fragment calculation and the molecular symmetry group must also contain a proper rotation that maps the two fragments onto each other.

The example of Fig.1 implicitly assumes that all fragments are single atom fragments. When the fragments are larger the data records in the atoms key have to be extended: you must specify which atoms belong together in one fragment.

SYMMETRY T(D)
Atoms
 Ni 0     0     0 
 C -1.06 -1.06  1.06 f=CO/1
 C -1.06  1.06 -1.06 f=CO/2
 C -1.06  1.06 -1.06 f=CO/3
 C  1.06 -1.06 -1.06 f=CO/4
 O  1.71  1.71  1.71 f=CO/1
 O -1.71 -1.71  1.71 f=CO/2
 O -1.71  1.71 -1.71 f=CO/3
 O  1.71 -1.71 -1.71 f=CO/4
End
Fragments
 CO TAPE21co.yesterday
 Ni t 21ni.dzp
End
End Input

Another sample input file; using a single atom ni fragment and four molecular CO fragments. The keys symmetry and fragments operate as before. Again we have two types of fragments (here: Ni and CO); for each of them, the fragment file is specified.

Under the key atoms the chemical symbols and the nuclear coordinates are listed. Added is the f=...-part; f stands here for fragment and tells the program that the carbon and oxygen atoms belong to CO fragments. The last part /n enumerates the individual CO fragments: here you define which C and O belong together in one CO fragment.

The record for Ni contains no f= part, implying the default for this atom: it is a fragment on its own. In the C2H4 example before the default applied to all atoms.

There are more possibilities with the keys atoms and fragments. This is worked out later. The purpose of this section was to provide a quick and easy start.

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