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Package csb :: Package statistics :: Package samplers :: Package mc :: Module propagators :: Class ThermostattedMDPropagator
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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 0x7fe107ba27d0>, 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 0x7fe107ba27d0>, 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)

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