AMDIntegrator Class Reference

AMDIntegrator implements the aMD integration algorithm. More...

Inherits CustomIntegrator.

List of all members.

Public Member Functions
def	__init__
	Create an AMDIntegrator.
def	getAlpha
	Get the value of alpha for the integrator.
def	setAlpha
	Set the value of alpha for the integrator.
def	getE
	Get the energy threshold E for the integrator.
def	setE
	Set the energy threshold E for the integrator.
def	getEffectiveEnergy
	Given the actual potential energy of the system, return the value of the effective potential.

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Detailed Description

AMDIntegrator implements the aMD integration algorithm.

The system is integrated based on a modified potential. Whenever the energy V(r) is less than a cutoff value E, the following effective potential is used:

V*(r) = V(r) + (E-V(r))^2 / (alpha+E-V(r))

For details, see Hamelberg et al., J. Chem. Phys. 127, 155102 (2007).

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Constructor & Destructor Documentation

def __init__	(		self,
			dt,
			alpha,
			E
	)

Create an AMDIntegrator.

Parameters:

dt	(time) The integration time step to use
alpha	(energy) The alpha parameter to use
E	(energy) The energy cutoff to use

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Member Function Documentation

def getAlpha

(

self

)

Get the value of alpha for the integrator.

def getE

(

self

)

Get the energy threshold E for the integrator.

def getEffectiveEnergy	(		self,
			energy
	)

Given the actual potential energy of the system, return the value of the effective potential.

def setAlpha	(		self,
			alpha
	)

Set the value of alpha for the integrator.

def setE	(		self,
			E
	)

Set the energy threshold E for the integrator.

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The documentation for this class was generated from the following file:

• amd.py