md_summary prints null instead of default values.

[alinelena]

  timestep: 1.0
  traj_append: false
  traj_every: 100
  traj_file: null
  restart_stem: null
  restarts_to_keep: 4
  rotate_restart: true
  seed: null
  ensemble: npt
  equil_steps: 0
  file_prefix: null

[ElliottKasoar]

My initial thought was that things like file_prefix are not readily accessible, as it's not even a simple default value, but actually we can access all of the attributes of the ensemble when we create the summary, just before we call .run, so this shouldn't be too bad to fix.

Only issue is that it depends if we consider the summary to be from the CLI perspective (it doesn't set these) or the Python perspective.

It's not possible at the moment, but if, for example, we wanted to use the summary as a new config for a different structure (so overwrite the structure only), we may want to keep file_prefix as None, rather than using the file_prefix that's been created for the first structure.