Dynamics input documentation

Specify molecular dynamics parameters.

Used to initialize class qimpy.geometry.Dynamics.

YAML template:

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:

Thermostat

Parameters:

n-steps

Type: int

Number of MD steps.

thermostat

Type: Thermostat, Default: null

Thermostat/barostat method. Specify name of thermostat eg. ‘nose-hoover’ if using default options for that thermostat method, and dictionary of parameters if not.

seed

Type: int, Default: 1234

Random seed for initial velocities.

T0

Type: Unit or float, Default: 298.000 K

Initial temperature / temperature set point.

P0

Type: Unit or float, Default: 1.000 bar

Pressure set point for NPT, if lattice.movable is yes. Note that this is overridden by stress0, if that is specified.

stress0

Type: <class ‘numpy.ndarray’> or <class ‘torch.Tensor’> or null, Default: null

Stress set point for N-stress-T, if lattice.movable is yes. If specified and lattice.movable, strain tensor will fluctuate during dynamics, instead of only volume in NPT mode. (Set to null and specify P0 instead for NPT mode.)

t-damp-T

Type: Unit or float, Default: 50.000 fs

Thermostat damping time.

t-damp-P

Type: Unit or float, Default: 100.000 fs

Barostat damping time.

drag-wavefunctions

Type: bool, Default: yes

Whether to drag atomic components of wavefunctions.

save-history