Two programs need to be run in order to set initial conditions. If the model you are interested in do not have massive neutrinos, the programs are PMmodels and PMstartCDM. For models with massive neutrinos, the corresponding programs are PMmodelCHDM and PMstartCHDM. Additionally, if you wish to run the PM code for a model for which the initial power spectrum is not included in the package, it is possible for you (with a bit more work) to specify whatever power spectrum you want.