[WIP] Add I/O interface with Metalwalls

[chiang-yuan]

MetalWalls (MW) is a molecular dynamics code dedicated to the modelling of electrochemical systems. Its main originality is the inclusion of a series of methods allowing to apply a constant potential within the electrode materials.

This is the same PR but without dirty commit from other branch. The input classes are mostly finished.

• [ ] Need to add string representation for classes and file export method to print out runtime.inpt file
• [ ] Data input class. Should be convenient to convert Structure to metalwalls data.inpt format
• [ ] Output classes for post-processing
• [ ] Add tests

Detailed implementation

Input

Top level parameter keywords

• [x] num_steps
• [x] timestep
• [x] temperature
• [x] num_pbc

Top level block keywords

• [x] thermostat

• [x] barostat

• [x] velocity

• [x] species

  • [x] species_type
  • [x] dipoles_minimization
  • [ ] preconditioner
  • [x] radius_minimization

• [x] molecules

  • [x] constraint
  • [x] harmonic_bond
  • [x] harmonic_angle
  • [x] dihedral
  • [x] improper

• [x] electrodes

  • [x] electrode_type
  • [x] electrode_charges
  • [x] preconditioner
  • [x] charge_neutrality
  • [x] compute_force

• [x] dipoles_and_electrodes

  • [x] algorithm
  • [x] preconditioner
  • [x] charge_neutrality

• [x] interactions

  • [x] coulomb
  • [x] lennard-jones
  • [x] fumi-tosi
  • [x] xft
  • [x] daim
  • [x] damping
  • [x] steele

• [ ] external_field

• [x] plumed

• [x] output

Data

• [ ] header
• [ ] box
• [ ] coordinates
• [ ] velocities
• [ ] forces
• [ ] dipole
• [ ] radius
• [ ] charges
• [ ] potential_shift
• [ ] piston_velocity
• [ ] thermostat
• [ ] barostat
• [ ] polarization

Output

None

Checklist

• [ ] Google format doc strings added. Check with ruff.
• [ ] Type annotations included. Check with mypy.
• [ ] Tests added for new features/fixes.
• [ ] If applicable, new classes/functions/modules have duecredit @due.dcite decorators to reference relevant papers by DOI (example)