> I am trying to calculate the vibration mode of H2 molecure. I put H2 > into a unit cell of a lattice, and then make the lattice constant equal > to 10 Ang ( I think this will prevent the interaction of different H2 > molecure in different unit cell). However, after following the way ( > using fcbuild to make FC.fdf and using siesta to calculate FC constant > and then analyze using vibrator), I get 6 vibration mode, while 3 are > trivial, but the other three are not). As H2 is a linear molecure, I > think the number of vibration mode should be 1. I am not sure what's > wrong with my calculation.
Probably nothing, but Siesta doesn't know about the symmetry and produces always 3N frequencies. Of which three must correspond to uniform translations and be more or less zero, either for crystal or molecule, and moreover, in general for a molecule, three rotations, whose frequencies should also be nearly zero. In case of diatomic molecule however, one rotation (along the molecule axis) leaves the molecule invariant, so it should not be counted among these "trivial" modes, and you stay instead with one "genuine" vibration mode. It is relatively easy to get zero frequency of three translation modes (setting MeshCutoff high enough); the rotational modes are more tricky - I think, it is simply more numerically demanding. Probably you got them not close enough to zero, due to unsufficient isotropy of "Siesta space" (mesh, basis etc.). Best regards Andrei Postnikov
