Package csb :: Package statistics :: Package samplers :: Package mc :: Module propagators :: Class MDPropagator

Class MDPropagator

        object --+    
                 |    
AbstractPropagator --+
                     |
                    MDPropagator

Known Subclasses:

ThermostattedMDPropagator

Molecular Dynamics propagator. Generates a trajectory by integration of Hamiltionian equations of motion.

Nested Classes
Inherited from `AbstractPropagator`: `__metaclass__`

Instance Methods

__init__(self, gradient, timestep, mass_matrix=None, integrator=<class 'csb.numeric.integrators.FastLeapFrog'>)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

AbstractPropagationResult

generate(self, init_state, length, return_trajectory=False)
Generate a trajectory, starting from an initial state with a certain length.

source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables
	__abstractmethods__ = `frozenset([])`

Properties
	gradient
	mass_matrix
	timestep
Inherited from `object`: `__class__`

Method Details

init(self, gradient, timestep, mass_matrix=None, integrator=<class 'csb.numeric.integrators.FastLeapFrog'>)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

gradient (AbstractGradient) - Gradient of potential energy. Guides the dynamics.
timestep (float) - Timestep to be used for integration
mass_matrix (n-dimensional InvertibleMatrix with n being the dimension of the configuration space, that is, the dimension of the position / momentum vectors) - Mass matrix
integrator (type) - Subclass of AbstractIntegrator to be used to integrate Hamiltonian equations of motion

Overrides: object.__init__

(inherited documentation)

generate(self, init_state, length, return_trajectory=False)

source code

Generate a trajectory, starting from an initial state with a certain length.

Parameters:

init_state - Initial state from which to propagate
length - Length of the trajectory (in integration steps or stochastic moves)
return_trajectory - Return complete Trajectory instead of the initial and final states only (PropagationResult)

Returns: AbstractPropagationResult

Overrides: AbstractPropagator.generate

(inherited documentation)

Property Details

gradient

Get Method:: unreachable.gradient(self)
Set Method:: unreachable.gradient(self, value)

mass_matrix

Get Method:: unreachable.mass_matrix(self)
Set Method:: unreachable.mass_matrix(self, value)

timestep

Get Method:: unreachable.timestep(self)
Set Method:: unreachable.timestep(self, value)

Class MDPropagator

__init__(self, gradient, timestep, mass_matrix=None, integrator=<class 'csb.numeric.integrators.FastLeapFrog'>) (Constructor)

generate(self, init_state, length, return_trajectory=False)

gradient

mass_matrix

timestep

init(self, gradient, timestep, mass_matrix=None, integrator=<class 'csb.numeric.integrators.FastLeapFrog'>)
(Constructor)