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

The line

```py
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.