Molecule Types Vibrational Structure Vibrational Energy Levels and Franck-Condon Factors <Prev Next>

Vibrating Molecule

These are the settings for a molecule as a whole, i.e. those common to all states (but perhaps different for different isotopologues).


nNuclei Number of atoms. Only required if the l matrix is not being used to calculate Franck-Condon factors, otherwise can be left at zero.
Jmin Not used
Jmax For linear point groups, this is taken as the maximum vibrational angular momentum to include when simulating spectra.
Colour Colour - set to "None" to take value from elsewhere.
JAdjustSym Currently ignored for this molecule type.
BlockMatrix Set to force check of Hamiltonian matrix for factorization into blocks before diagonalization. If blocks are found, these are diagonalized separately, ensuring states that have no connecting matrix elements are not accidentally mixed if the eigenvalues happen to be very close. In principle, if full use is made of symmetry and states are separated into separate manifolds as appropriate, this should not be necessary but can easily happen if selected terms in the Hamiltonian are zero or interactions between states are omitted.
AbsoluteE True if energies have not been offset. This is not the default for compatibility with previous versions, though perhaps should be for new calculations. Setting this false (the default) allows transitions with negative frequencies, which can occasionally be convenient for simulations involving a small spread of frequencies around a large central frequency where a large offset is applied to the upper state origin. This can give erroneous negative frequencies; while there is logic to detect common cases where this might arise, some calculations (typically involving near degenerate manifolds) require this to be set to true for correct operation.
PointGroup Point group of molecule. Currently C1, Ci, C2, Cs, D2, C2v, C2h, D2h, Cinfinityv and Dinfinityh are implemented.
nModes Number of vibrational modes to include in the calculation.
Set false to hide vibrational quantum numbers with vmin = vmax = 0 in all states. This is essential for large molecules with many modes.


Abundance Abundance of this isotope; default is 1
AssumedOrigin Can normally be left at the default value; see the generic Molecule entry for more information
SmallCoefficient Threshold for discarding values. This threshold is used to discard low frequency modes (translations and rotations) and also values smaller than this are set to zero in certain contexts to avoid spurious mixing of modes or rotation of axis systems.