Provides information about all the normal modes for a periodic system. The periodicity is
described by a set of wave vectors, which are provided via a WaveVectorFactory. For
each wave vector there is a set of coupled degrees of freedom (e.g., xyz motions) that have been
further decomposed into normal modes with corresponding frequencies and eigenvectors.
In most cases these frequencies/vectors are determined via a simulation and recorded to file; the
implmentation of this class then reads the data and provides it via the interface methods.
Returns a factory that provides the wave vectors and coefficients for
the periodic system.
Returns an array giving the frequencies (squared) corresponding to the normal-mode
motions. First index indicates the wave vector, and second index indicates the
eigenvector. Length of second index is coordinateDim.
First index corresponds to the wave vector; second index gives the eigenvector, and
third index gives the elements of the vector. Length of 2nd and 3rd dimensions is
void setHarmonicFudge(double newHarmonicFudge)
Set the fudge factor applied to frequencies. The squared-frequencies returned
by getOmegaSquared will be the nominal values divided by the given
fudge factor. Thus a smaller value of this fudge factor will make for "tighter"
harmonic springs, corresponding to to smaller deviation from the lattice sites.
void setTemperature(double newTemperature)
Set the temperature used for calculating omega-squared. Omega-squared