Phonon calculation is presently a two-step process. First, you have to find the ground-state atomic and electronic configuration; Second, you can calculate phonons using Density-Functional Perturbation Theory. Further processing to calculate Interatomic Force Constants, to add macroscopic electric field and impose Acoustic Sum Rules at = 0 may be needed. In the following, we will indicate by the phonon wavevectors, while will indicate Bloch vectors used for summing over the Brillouin Zone.
The main code ph.x can be used whenever PWscf can be used, with the exceptions of hybrid and meta-GGA functionals, external electric fields, constraints on magnetization, nonperiodic boundary conditions. USPP and PAW are not implemented for higher-order response calculations. See the header of file PHonon/PH/phonon.f90 for a complete and updated list of what PHonon can and cannot do.
Since version 4.0 it is possible to safely stop execution of ph.x code using the same mechanism of the pw.x code, i.e. by creating a file prefix.EXIT in the working directory. Execution can be resumed by setting recover=.true. in the subsequent input data. Moreover the execution can be (cleanly) stopped after a given time is elapsed, using variable max_seconds. See example/Recover_example/.