Switch to more standard output file format #3
Description
Currently simulation data is outputted as Numpy npy files, entire dumps as Numpy npz files and config/state data as json. I think the json files are fine, although I'd ideally like one single file that represents the entire state of the simulation. The problem with the numpy formats is they aren't as well supported by common visualisation tools. The obvious alternative is NetCDF4 which has a seemingly good python writer.