1) The first step is to create a molpro input deck that controls how the CASSCF electronic structure calculations are performed. AIMS requires a fairly complicated structure to the molpro deck and it is highly recommended that you use the ethylene CASSCF example as a starting point (section 30.5). Control.dat should then be modified for your system and desired simulation parameters (section 30.2.2).
2) Next, the initial conditions should be defined. This involves providing an initial geometry in Geometry.dat (section 30.2.3) and normal-mode frequencies and displacements in FrequenciesMP.dat (section 30.2.4), which will be used to generate a phase-space distribution that the initial conditions sample. Alternatively, one can also provide momenta in Geometry.dat and set InitialCond='NoSample' in Control.dat, and directly specify the initial conditions.
3) The AIMS calculation is then initiated by running molpro on the input deck, in the usual fashion. In order to sample different initial conditions, multiple AIMS simulations should be run with different values of the random number seed IRndSeed (or different Geometry.dat files) - each of these should be run in a unique directory.