deeptime.data

The data package contains example systems.

Deterministic datasets

abc_flow([h, n_steps])

The Arnold-Beltrami-Childress flow.

bickley_jet(n_particles[, n_jobs, seed])

Simulates the Bickley jet for a number of particles.

lorenz_system([h, n_steps])

The Lorenz system.

thomas_attractor([b, h, n_steps])

The Thomas attractor.

position_based_fluids([n_burn_in, ...])

Creates a position based fluids (PBF) simulator.

Stochastic datasets

tmatrix_metropolis1d(energies[, d])

Transition matrix describing the Metropolis chain jumping between neighbors in a discrete 1D energy landscape.

birth_death_chain(q, p[, sparse])

Generates a birth and death chain simulator from annihilation and creation probabilities q and p.

ornstein_uhlenbeck([h, n_steps])

The one-dimensional Ornstein-Uhlenbeck process.

double_well_2d([h, n_steps, ...])

This dataset generates trajectories of a two-dimensional particle living in a double-well potential landscape.

double_well_discrete()

MCMC process in a symmetric double well potential, spatially discretized to 100 bins.

triple_well_1d([h, n_steps])

A simple one-dimensional triple-well potential landscape.

triple_well_2d([h, n_steps])

This dataset generates trajectories of a two-dimensional particle living in a triple-well potential landscape.

quadruple_well([h, n_steps])

This dataset generates trajectories of a two-dimensional particle living in a quadruple-well potential landscape.

quadruple_well_asymmetric([h, n_steps])

This dataset generates trajectories of a two-dimensional particle living in an asymmetric quadruple-well potential landscape.

time_dependent_quintuple_well([h, n_steps, beta])

This dataset generates trajectories of a two-dimensional particle living in a time-dependent quintuple-well potential landscape.

prinz_potential([h, n_steps, ...])

Particle diffusing in a one-dimensional quadruple well potential landscape.

ellipsoids([laziness, seed])

Example data of a two-state markov chain which can be featurized into two parallel ellipsoids and optionally rotated into higher-dimensional space.

sqrt_model(n_samples[, seed])

Sample a hidden state and an sqrt-transformed emission trajectory.

swissroll_model(n_samples[, seed])

Sample a hidden state and an swissroll-transformed emission trajectory, so that the states are not linearly separable.

drunkards_walk([grid_size, bar_location, ...])

This example dataset simulates the steps a drunkard living in a two-dimensional plane takes finding either the bar or the home as two absorbing states.

Custom systems

custom_sde(dim, rhs, sigma, h, n_steps)

This function allows the definition of custom stochastic differential equations (SDEs) of the form

custom_ode(dim, rhs, h, n_steps)

This function allows the definition of custom ordinary differential equations (ODEs) of the form

Implementations

DoubleWellDiscrete()

MCMC process in a symmetric double well potential, spatially discretized to 100 bins.

Ellipsoids([laziness, seed])

Example data of a two-state markov chain which can be featurized into two parallel ellipsoids and optionally rotated into higher-dimensional space.

PBFSimulator(domain_size, initial_positions, ...)

A position based fluids simulator for two-dimensional systems.

DrunkardsWalk(grid_size, bar_location, ...)

This example dataset simulates the steps a drunkard living in a two-dimensional plane takes finding either the bar or the home as two absorbing states.

BickleyJet(h, n_steps[, full_periodic])

Implementation of the Bickley jet.

BirthDeathChain(q, p[, sparse])

Birth and death chain.

TimeDependentSystem(system, h, n_steps[, props])

Wraps systems with a time-dependent right-hand side defined in extension code.

TimeIndependentSystem(system, h, n_steps[, ...])

Wraps systems with a time-independent right-hand side defined in extension code.

CustomSystem(system, h, n_steps[, props])

A system as yielded by custom_sde or custom_ode.