Atomic displacements and eigenvectors are defined using Cartesian coordinates in this code, and therefore only apply to periodic systems that don't experience rotational degrees of freedom.
To generalize for systems with rotational and other degrees of freedom, we need to transform Cartesian coordinates to "internal" coordinates (bonds, angles, dihedrals, etc.). This feature is not yet implemented, but will be useful for molecules like proteins.
Atomic displacements and eigenvectors are defined using Cartesian coordinates in this code, and therefore only apply to periodic systems that don't experience rotational degrees of freedom.
To generalize for systems with rotational and other degrees of freedom, we need to transform Cartesian coordinates to "internal" coordinates (bonds, angles, dihedrals, etc.). This feature is not yet implemented, but will be useful for molecules like proteins.