Fragments

Except in Create mode, where a basic atom is constructed, the system is built up from fragments and the corresponding fragment files are attached to the run. The program reads from the files the fragment MOs and these are used as (compound) basis functions for the molecular calculation. The fragment MOs are called Fragment Orbitals (FO).

FOs belong of course to one of the symmetry representations of the fragment, but not necessarily to a symmetry representation of the new molecule. The FOs are therefore combined into symmetry-adapted combinations, SFOs, to serve as a symmetry-adapted basis in the molecule. These combinations may involve one or more FOs from the same fragment and/or from different fragments. In the latter case the fragments must be symmetry related by one of the operators of the molecule. Symmetry related fragments must of course be identical, apart from their spatial location: they must be of the same fragment type.

FOs are naturally orthogonal to the Core Orbitals of their own fragment, but not necessarily to COs of other fragments. By a suitable combination of the SFOs with all CFs in the molecule we obtain the core-orthogonalized symmetry-adapted CSFOs.

The CSFOs can be transformed to an orthonormal basis by a Lowdin transformation. The resulting basis is called low, as above.