[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

• num_steps
• timestep
• temperature
• num_pbc

Top level block keywords

• thermostat

• barostat

• velocity

• species

  • species_type
  • dipoles_minimization
  • preconditioner
  • radius_minimization

• molecules

  • constraint
  • harmonic_bond
  • harmonic_angle
  • dihedral
  • improper

• electrodes

  • electrode_type
  • electrode_charges
  • preconditioner
  • charge_neutrality
  • compute_force

• dipoles_and_electrodes

  • algorithm
  • preconditioner
  • charge_neutrality

• interactions

  • coulomb
  • lennard-jones
  • fumi-tosi
  • xft
  • daim
  • damping
  • steele

• external_field

• plumed

• 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)

[janosh]

I think better to be explicit here and write out the name: pymatgen/io/metalwalls/__init__.py

[chiang-yuan]

Thanks @janosh! Will change that when I get back to this. It has been put off in my TODOs and is going to stale for a while.

[shyuep]

Thanks for your contribution. However, we have moved this to pymatgen-core. Please resubmit a PR there when ready.