I did phonon dispersion by using Phonopy codes. I got some small imaginary frequency for my system.How could I analysis the eigenvectors of the soft modes and relax the structure accordingly to get all positive modes?
(1) Small imaginary might not be the real soft modes. Where is the soft modes? Around \Gamma point? Is force sufficiently converged?
(2) If it is confirmed to be a soft mode. You can choose to print the eigenvector in Phonopy. The eigenvector obtained from diagonalizing dynamical matrix is a normalized vector contains 3*natom elements. It should be divided by the atomic mass and then used to move the atoms along the vector. You can explicitly plot the displacement vs energy curve.