Add Correlator CLI

[harveydevereux]

Still a work in progress.

todo:

• documentation
• defaults (and in python interface)
• example
• more robust test
• StressShear and StressHydrostatic
• the names blocks, points, and averaging could be more descriptive perhaps, they control coarsening in time.

Currently this is example functionality

janus md \
--ensemble nve --struct tests/data/NaCl.cif \
--steps 10 --correlation-kwargs \
"{'vaf1': {'a': 'velocity', 'points': 10}, 'vaf_x': {'a': 'velocity', 'update_frequency': 2, 'points': 10, 'a_kwargs': {'components': ['x']}, 'b_kwargs': '.'}}"

Syntax

• If one of 'a' and 'b' is omitted it is duplicated.
• The special "ditto" kwarg value "." indicates copying the kwargs.
• 'blocks', 'points' etc have defaults which are not thought out yet.

it results in

cat NaCl-nve-T300.0-cor.dat
vaf1:
  lags: [0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0]
  value: [0.0005823628861742493, 0.0005829660336725057, 0.0005832862278350698, 0.0005833234400626741,
    0.0005830778925578795, 0.0005825500577781349, 0.0005817406577431897, 0.0005806506631988626,
    0.0005792812926375899, 0.0005776340111746314]
vaf_x:
  lags: [0.0, 1.0, 2.0, 3.0, 4.0, 5.0]
  value: [0.0005445815119304412, 0.0005449602181734653, 0.0005449448511073212, 0.0005445360209632227,
    0.0005437350402279519, 0.0005425439175493092]

[ElliottKasoar]

Did we not want getattr here to get anything defined in janus_core.processing.observables, rather than manually listing them?