Geometry input documentation

Specify one of the supported geometry actions. Defaults to Fixed if none specified.

Used to initialize class qimpy.geometry.Geometry.

YAML template:

fixed:                     # Electronic optimization only at a fixed geometry:

relax:                     # Geometry relaxation of ions, and optionally, also the lattice:
  n-iterations: 20         # Maximum number of iterations.
  energy-threshold: 5e-05  # Convergence threshold on energy change in Eh.
  fmax-threshold: 0.0005   # Convergence threshold on maximum force in Eh/a0.
  stress-threshold: 1e-05  # Convergence threshold on |stress| (stress tensor norm) in Eh/a0^3.
  n-consecutive: 1         # Number of consecutive iterations each threshold must be satisfied.
  method: l-bfgs           # Relaxation algorithm: L-BFGS, CG or Gradient.
  cg-type: polak-ribiere   # CG variant: Polak-Ribiere, Fletcher-Reeves or Hestenes-Stiefel.
  line-minimize: auto      # Line minimization scheme: Auto, Constant, Quadratic, Wolfe.
  n-history: 15            # Maximum history size (only used for L-BFGS).
  converge-on: all         # Converge on 'any', 'all' or a specific number of thresholds.
  drag-wavefunctions: yes  # Whether to drag atomic components of wavefunctions.
  save-history: yes        # Whether to save history along the trajectory.

dynamics:                  # Molecular dynamics of ions, and optionally, also the lattice:
  dt: [float]              # Time step.
  n-steps: [int]           # Number of MD steps.
  thermostat:              # Thermostat/barostat method:
    nve:                   # No thermostat (or barostat), i.e. NVE ensemble:

    nose-hoover:           # Nose-Hoover thermostat and/or barostat:
      chain-length-T: 3    # Nose-Hoover chain length for thermostat.
      chain-length-P: 3    # Nose-Hoover chain length for barostat.

    berendsen:             # Berendsen velocity-rescaling thermostat and/or barostat:
      B0: 2.200 GPa        # Characteristic bulk modulus for Berendsen barostat.

    langevin:              # Langevin stochastic thermostat and/or barostat:

  seed: 1234               # Random seed for initial velocities.
  T0: 298.000 K            # Initial temperature / temperature set point.
  P0: 1.000 bar            # Pressure set point for NPT, if lattice.movable is True.
  stress0: null            # Stress set point for N-stress-T, if lattice.movable is True.
  t-damp-T: 50.000 fs      # Thermostat damping time.
  t-damp-P: 100.000 fs     # Barostat damping time.
  drag-wavefunctions: yes  # Whether to drag atomic components of wavefunctions.
  save-history: yes        # Whether to save history along the trajectory.

Component classes:

• Fixed
• Relax
• Dynamics

Parameters:

fixed

Type: Fixed, Default: null

Electronic optimization only at a fixed geometry.

relax

Type: Relax, Default: null

Geometry relaxation of ions, and optionally, also the lattice.

dynamics

Type: Dynamics, Default: null

Molecular dynamics of ions, and optionally, also the lattice.