The NumForce script provides with the option -frznuclei a possibility to do a vibrational analysis with fixed atoms. The atoms for which the cartesian coordinates should frozen have to be marked in $coord with a "f" behind the atom type. The frozen coordinates will be skipped during the numerical evaluation of the force constant matrix; instead all off-diagonal elements of the force constant matrix which refer to one or two frozen coordinates will be set to zero, while the diagonale elements for the frozen coordinates will be set to an arbitrarly chosen large value.
This feature is mainly intended to allow for a vibrational analysis in embbeded cluster calculations e.g. for defects in ionic crystals. The vibrational analysis uses a kind of ``frozen phonon'' approximation which corresponds to setting the masses of the fixed atoms to infinity, i.e. decoupling the fixed atoms mechanically from the ``mechanically active'' subsystem. The resulting vibrational frequencies will thus only provide good approximations to the true (harmonic) frequencies for such modes for which the mechanical coupling to the embedding environment is negligible. In particular the frequencies of stretch modes which involve bonds between the ``mechanically active'' subsystem and atoms with frozen coordinates will be strongly affected by this approximation.