Fix checkpointing in HDF5Writer

Fix for issue #358 

 - rename default data file
 - new default name for checkpoint files
 - create both data and checkpoint if triggered for the same timestep

Tested with 2 GPUs with
`--checkpoints 256` and `--restart --restart-step 256` (creates only checkpoints) and
`--checkpoints 256 --hdf5.period 256` (creates both checkpoints and data)