The standalone code of the 3GPP 3D model in one of the earliest versions of the code which needs a launcher file in order to be executed.
To get the channel matrix you mention, I recommend to use our LTE-A System Level simulator v1.9 Q2-2016. In sim_main_launcher_files, use LTE_sim_main_launcher_3D_model.m to start simulations.
If you are referring to the paper F. Ademaj et al. ‘Evaluating the Spatial Resolution of 2D Antenna Arrays for Massive MIMO Transmissions’, EUSIPCO 2016, you can consider a single user in a single eNodeB scenario, by just modifying input parameters in the launcher file.