By default SLAPAF optimizes in force-constant weighted normal coordinates that are determined automatically. However, the user can define his own coordinates. The definition of internal coordinates, similar to constraints, is based on primitive coordinates. The input is:
INTERNAL,[[NAME=]name],[[FACTOR=]fac],prim,[[FACTOR=]fac],prim,...;
FIX, [[NAME=]name],[[FACTOR=]fac],prim,[[FACTOR=]fac],prim,...;
Internal coordinates that are specified using INTERNAL are varied and those using FIX are fixed to their initial values.
An important point for the definition of internal coordinates is that their total number must be equal to the number of degrees of freedom of the molecule . Otherwise an error message is generated. Only symmetry independent coordinates need to be given.