Package csb :: Package statistics :: Package samplers :: Package mc :: Module propagators :: Class ThermostattedMDPropagator |
[frames] | no frames]

# Class ThermostattedMDPropagator

source code

            object --+
                     |
    AbstractPropagator --+
                         |
              MDPropagator --+
                             |
                            ThermostattedMDPropagator

Thermostatted Molecular Dynamics propagator. Employs the Andersen thermostat which simulates collision with particles of a heat bath at a given temperature.

Nested Classes
Inherited from `AbstractPropagator`: `__metaclass__`

Instance Methods
__init__(self, gradient, timestep, mass_matrix=None, temperature=<function <lambda> at 0x03807F70>, collision_probability=0.1, update_interval=1, integrator=<class 'csb.numeric.integrators.VelocityVerlet'>) 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
Inherited from `MDPropagator`: `__abstractmethods__`

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

Method Details

### __init__(self, gradient, timestep, mass_matrix=None, temperature=<function <lambda> at 0x03807F70>, collision_probability=0.1, update_interval=1, integrator=<class 'csb.numeric.integrators.VelocityVerlet'>) (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 `temperature` (Real-valued function) - Time-dependent temperature `collision_probability` (float) - collision probability within duration of one timestep `update_interval` (int) - Interval with which momenta are redrawn `integrator` (type) - Subclass of AbstractIntegrator to be used to perform integration steps between momentum updates 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)