Rework meta file format

[ashenoy463]

Reworks needed for xarray:

• Execution dates need to be extracted (through #5)
• Current nested format is not supported by xarray

[ashenoy463]

Current file format is:

Metadata:
  # Global ID for this sim (ideally 1 word)
  sim_id: "prelim"
  # Readable description
  sim_desc: "Preliminary run of 1 nanosecond at 300 K — test bed for refactoring and further processing code"
  # Dates yyyymmdd of chunk run start
  exec_date: [202401220710,202401241139,202401260443,202401270056]
  partition:
    # stepsize in real units
    step_fs: 0.5     
    # steps in a chunk
    chunk_size: 500000
    # number of chunks
    n_chunks: 40
  box:
    # number of atoms
    n_atoms: 49026

# real simtime = step_fs*chunk_size*n_chunks

[ashenoy463]

Needs to include:

• Semantic info of atom types
• Fixed experimental parameters (eg. thermo/barostat values)
• Output granularities (sub. for all types)
• Output parameters (eg. BO cutoff for species)

Nested structure can then be flattened for inclusion in dataset through a form_xarr_attrs() private function of mdx.io.scribe()

• Flatten separator "_"
• Flatten and reconstitute with helper functions

[ashenoy463]

Perhaps experimental metadata and output parameters should be left entirely to the user.. Either way, #14