class CustomSystem

class deeptime.data.CustomSystem(system, h: float, n_steps: int, props=None)

A system as yielded by custom_sde or custom_ode.

Attributes

dimension	The dimension of the system's state.
f	The right-hand side of the system as callable function.
h	The integration step size.
has_potential_function	Whether the system defines a potential.
integrator	The type of integrator.
n_steps	The number of integration steps between each evaluation of the state.
time_dependent	Whether the potential (if available) and the right-hand side depend on time.
vectorized_f	Yields whether the right-hand side function is vectorized.

Methods

potential(points)	Evaluates the system's potential function at given points in state space.
trajectory(x0, length[, seed])	Simulates one or multiple trajectories.

__call__(test_points, seed=-1, **kw)

Evolves the provided tests points under the dynamic for n_steps and returns.

Parameters:

• test_points (array_like) – The test points.

• seed (int, optional, default=-1) – The seed for reproducibility. In case it is set to seed >= 0 the number of jobs needs to be fixed to n_jobs=1.

• n_jobs (int, optional, default=None) – Specify number of jobs according to deeptime.util.parallel.handle_n_jobs().

Returns:

points – The evolved test points.

Return type:

np.ndarray

potential(points)

Evaluates the system’s potential function at given points in state space.

Parameters:

points (array_like) – The points.

Returns:

energy – The energy for each of these points.

Return type:

np.ndarray

Raises:

AssertionError – If the system does not have a potential function defined.

trajectory(x0, length, seed=-1, **kw)

Simulates one or multiple trajectories.

Parameters:

• x0 (array_like) – The initial condition. Must be compatible in shape to a (n_test_points, dimension)-array.

• length (int) – The length of the trajectory that is to be generated.

• seed (int, optional, default=-1) – The random seed. In case it is specified to be something else than -1, n_jobs must be set to n_jobs=1.

• n_jobs (int, optional, default=None) – Specify number of jobs according to deeptime.util.parallel.handle_n_jobs().

Returns:

trajectory – The trajectory of shape (n_initial_conditions, n_evaluations, dimension). In case of just one initial condition the shape is squeezed to (n_evaluations, dimension).

Return type:

np.ndarray

property dimension: int

The dimension of the system’s state.

Type:

int

property f: Callable[[float, ndarray], ndarray]

The right-hand side of the system as callable function. In case of SDEs, this only evaluates the deterministic part of the function definition.

Some of these definitions are vectorized.

Returns:

right_hand_side – The right-hand side.

Return type:

Callable[[float, ndarray], ndarray]

property h: float

The integration step size.

property has_potential_function: bool

Whether the system defines a potential. This means that the deterministic part of the right-hand side is the negative gradient of that potential.

property integrator: str

The type of integrator.

Type:

str

property n_steps: int

The number of integration steps between each evaluation of the state.

property time_dependent: bool

Whether the potential (if available) and the right-hand side depend on time.

Type:

bool

property vectorized_f: bool

Yields whether the right-hand side function is vectorized.

Type:

bool