Make HyMD output valid HyMD input

[mortele]

The extra step of converting it with the external script is getting tedious. I think we should allow output from the code to be used directly as input.

This would involve storing bonds in the output. Bond information is already stored in the output in the /parameters/vmd_structure/bond_from and /parameters/vmd_structure/bond_to datasets, but I am not writing a built-in parser back to the format we use internally (if someone else wants to, feel free). I would much rather just store an extra array of integers.

[mortele]

There are some minor design decisions involved in this, such as: Do we make a new keyword in config to specify which frame to use as the starting point for the new simulation? I think in any case that it should default to the last frame.

[Lun4m]

I think we should """just""" rework the parser so that it only reads the H5MD format, without having to switch formats inside the code. But this will probably require a lot a work and might break stuff/create bugs.

[samiransen23]

Are you still using h5md2input.py to extract the last(/specific) frame to convert it into an input.h5 to restart a simulation from there or have you already improved the method? @mortele