qimpy.dft.geometry.Dynamics

class Dynamics(*, comm, dt, n_steps, thermostat=None, seed=1234, T0=298.0 K, P0=1.0 bar, stress0=None, t_damp_T=50.0 fs, t_damp_P=100.0 fs, drag_wavefunctions=True, save_history=True, report_callback=None, checkpoint_in=(None, ''))

Bases: TreeNode

Molecular dynamics of ions and/or lattice. Whether lattice changes is controlled by lattice.movable.

Parameters:

comm (Comm) –
dt (float) –
n_steps (int) –
thermostat (Thermostat) –
seed (int) –
T0 (float) –
P0 (UnitOrFloat) –
stress0 (Tensor) –
t_damp_T (float) –
t_damp_P (float) –
drag_wavefunctions (bool) –
save_history (bool) –
report_callback (Callable[[Dynamics, int], None] | None) –
checkpoint_in (CheckpointPath) –

__init__(*, comm, dt, n_steps, thermostat=None, seed=1234, T0=298.0 K, P0=1.0 bar, stress0=None, t_damp_T=50.0 fs, t_damp_P=100.0 fs, drag_wavefunctions=True, save_history=True, report_callback=None, checkpoint_in=(None, ''))

Specify molecular dynamics parameters.

Parameters:

dt (float) – [Input file] Time step.
n_steps (int) – [Input file] Number of MD steps.
thermostat (Thermostat | dict | str | None) – [Input file] 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 (int) – [Input file] Random seed for initial velocities.
T0 (Unit | float) – [Input file] Initial temperature / temperature set point.
P0 (Unit | float) – [Input file] Pressure set point for NPT, if lattice.movable is True. Note that this is overridden by stress0, if that is specified.
stress0 (ndarray | Tensor | None) – [Input file] Stress set point for N-stress-T, if lattice.movable is True. If specified and lattice.movable, strain tensor will fluctuate during dynamics, instead of only volume in NPT mode. (Set to None and specify P0 instead for NPT mode.)
t_damp_T (Unit | float) – [Input file] Thermostat damping time.
t_damp_P (Unit | float) – [Input file] Barostat damping time.
drag_wavefunctions (bool) – [Input file] Whether to drag atomic components of wavefunctions.
save_history (bool) – [Input file] Whether to save history along the trajectory. Saved quantities include positions, forces, velocities, temperature, pressure, potential and total stress (if available), and lattice (if movable).
report_callback (Callable[[Dynamics, int], None] | None) – Optional function to call at each step during report. Use this to perform additional reporting / data collection. The functional will be called as report_callback(dynamics, i_iter).
comm (Comm) –
checkpoint_in (CheckpointPath) –

Return type:

None

Methods

`__init__`	Specify molecular dynamics parameters.
`add_child`	Construct child object self.`attr_name` of type cls.
`add_child_one_of`	Invoke add_child on one of several child options in args.
`create_gradient`	Create gradient from ionic part, initializing optional parts correctly.
`get_KE`	Compute kinetic energy from ion velocity.
`get_T`	Compute temperature from kinetic energy KE.
`get_acceleration`	Acceleration due to ionic forces.
`get_masses`	Collect the masses of all ions as an n_ions x 1 tensor.
`get_pressure`
`get_stress`	Compute total stress tensor including ion velocity contributions.
`report`
`run`
`save_checkpoint`	Save self and all children in hierarchy to cp_path.
`thermal_velocities`	Thermal velocity distribution at T, randomized with seed.

Attributes

`nDOF`	Number of degrees of freedom in the dynamics.
`system`	System being optimized currently
`masses`	n_ions x 1 for bcast)
`stepper`
`comm`	Communictaor over which forces consistent
`dt`	Time step
`n_steps`	Number of MD steps
`thermostat`	Thermostat/barostat method
`seed`	Random seed for initial velocities
`T0`	Initial temperature / temperature set point
`stress0`	Stress set point (used only if lattice.movable)
`isotropic`	Whether lattice change is isotropic (NPT, vs.
`t_damp_T`	Thermostat damping time
`t_damp_P`	Barostat damping time
`B0`	Characteristic bulk modulus for Berendsen barostat
`langevin_gamma`	Damping rate for Langevin thermostat
`drag_wavefunctions`	Whether to drag atomic components of wavefunctions
`P`	Current pressure (available if lattice.compute_stress)
`T`	Current temperature
`KE`	Current kinetic energy
`stress`	Current stress including kinetic contributions
`history`	Utility to save trajectory data
`report_callback`	Callback from report
`i_iter_start`	Starting iteration number (when continuing from checkpoint)
`child_names`	Names of attributes with child objects.

create_gradient(ions)

Create gradient from ionic part, initializing optional parts correctly.

Parameters:: ions (Tensor) –
Return type:: Gradient

get_KE(velocity)

Compute kinetic energy from ion velocity.

Parameters:: velocity (Tensor) –
Return type:: float

get_T(KE)

Compute temperature from kinetic energy KE.

Parameters:: KE (float) –
Return type:: float

get_acceleration()

Acceleration due to ionic forces.

Return type:: Gradient

static get_masses(ions)

Collect the masses of all ions as an n_ions x 1 tensor.

Parameters:: ions (Ions) –
Return type:: Tensor

get_stress(velocity)

Compute total stress tensor including ion velocity contributions.

Parameters:: velocity (Tensor) –
Return type:: Tensor | None

thermal_velocities(T, seed)

Thermal velocity distribution at T, randomized with seed.

Parameters:

T (float) –
seed (int) –

Return type:

Tensor

B0: float: Characteristic bulk modulus for Berendsen barostat

KE: float: Current kinetic energy

P: float | None: Current pressure (available if lattice.compute_stress)

T: float: Current temperature

T0: float: Initial temperature / temperature set point

comm: Comm: Communictaor over which forces consistent

drag_wavefunctions: bool: Whether to drag atomic components of wavefunctions

dt: float: Time step

history: History | None: Utility to save trajectory data

i_iter_start: int: Starting iteration number (when continuing from checkpoint)

isotropic: bool: Whether lattice change is isotropic (NPT, vs. N-stress-T mode)

langevin_gamma: float: Damping rate for Langevin thermostat

masses: Tensor

n_ions x 1 for bcast)

Type:: Mass of each ion in system (Dim

property nDOF: int: Number of degrees of freedom in the dynamics.

n_steps: int: Number of MD steps

report_callback: Callable[[Dynamics, int], None] | None: Callback from report

seed: int: Random seed for initial velocities

stress: Tensor | None: Current stress including kinetic contributions

stress0: Tensor: Stress set point (used only if lattice.movable)

system: System: System being optimized currently

t_damp_P: float: Barostat damping time

t_damp_T: float: Thermostat damping time

thermostat: Thermostat: Thermostat/barostat method