`test/utils/rpdf_ref.py` uses old `rpdf` API

[elcorto]

The line

crys.rpdf(coords, rmax=5.0, cell=cell, ...)

uses and older API that is no longer supported. It needs to be converted to using a Structure as input, where we build the latter using coords, cell and symbols.

This is not critical since the generated data is part of the repo in test/files/rpdf/, just has to be fixed if new data is to be generated.