quantity.observables

Molecular dynamics observable functions acting on trajectories rather than single snapshots.

Builds on the TrajectoryState object defined in traj_util.py.

This module contains methods to compute ensemble quantities given a trajectory of instantaneous quantities.

Ensemble Averages

Ensemble averages of instantaneous quantities, optionally via a reweighting approach.

init_traj_mean_fn(quantity_key)	Initialize the computation of a (perturbed) ensemble average.
init_linear_traj_mean_fn(quantity_key)	Initializes the linear approximation of an observable average.

Fluctuation Quantities

init_heat_capacity_nvt(kT, dof, **kwargs)	Returns the specific heat capacity of a system in the NPT ensemble via
init_heat_capacity_npt(kT, dof, pressure, ...)	Initializes the isobaric heat capacity of a system in the NPT ensemble.
init_born_stiffness_tensor(reference_box, ...)	Computes the elastic stiffness tensor via the stress fluctuation method in the NVT ensemble.
stiffness_tensor_components_cubic_crystal(...)	Computes the 3 independent elastic stiffness components of a cubic crystal from the whole stiffness tensor.
stiffness_tensor_components_hexagonal_crystal(...)	Computes 5 independent elastic stiff components of a hexagonal crystal from the whole stiffness tensor

State-Space Quantities

Quantities which are no ensemble averages.

init_relative_entropy_traj_fn(kT[, ...])

Initializes the computation of the relative entropy difference between the current canonical distribution and reference distribution.

Utility

init_identity_fn(quantity_key)	Initialize a wrapper that returns the snapshots unchanged.
dynamic_statepoint([keys_with_defaults])	Initializes a decorator enabeling a dynamically provided statepoint definition.