csb.statistics.samplers.mc

Package mc

Abstract Monte Carlo samplers.

Submodules

csb.statistics.samplers.mc.multichain: Implements several extended-ensemble Monte Carlo sampling algorithms.
csb.statistics.samplers.mc.neqsteppropagator: Propagator class employing stepwise trajectories as used in the NCMC algorithm (Nilmeier et al., "Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation", PNAS 2011)
csb.statistics.samplers.mc.propagators: Provides various deterministic and stochastic propagators.
csb.statistics.samplers.mc.singlechain: Various Monte Carlo equilibrium sampling algorithms, which simulate only one Markov chain.

Classes

AbstractMC
Abstract Monte Carlo sampler class.

AbstractPropagationResult
Abstract class providing the interface for the result of a deterministic or stochastic propagation of a state.

MCCollection
Collection of single-chain samplers.

PropagationResult
Describes the result of a deterministic or stochastic propagation of a state.

ShortTrajectoryBuilder

Trajectory
Ordered collection of states, representing a phase-space trajectory.

TrajectoryBuilder
Allows to build a Trajectory object step by step.

Functions

State

augment_state(state, temperature=1.0, mass_matrix=None)
Augments a state with only positions given by momenta drawn from the Maxwell-Boltzmann distribution.

source code

Variables

__package__ = 'csb.statistics.samplers.mc'

Function Details

augment_state(state, temperature=1.0, mass_matrix=None)

source code

Augments a state with only positions given by momenta drawn from the Maxwell-Boltzmann distribution.

Parameters:

state (State) - State to be augmented
temperature (float) - Temperature of the desired Maxwell-Boltzmann distribution
mass_matrix (InvertibleMatrix) - Mass matrix to be used in the Maxwell-Boltzmann distribution; None defaults to a unity matrix

Returns: State

The initial state augmented with momenta