AMDIntegrator Class Reference

AMDIntegrator implements the aMD integration algorithm. More...

Inheritance diagram for AMDIntegrator:

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

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).

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

References CustomIntegrator.addComputePerDof(), CustomIntegrator.addConstrainPositions(), CustomIntegrator.addGlobalVariable(), CustomIntegrator.addPerDofVariable(), and CustomIntegrator.addUpdateContextState().

Member Function Documentation

def getAlpha

(

self

)

Get the value of alpha for the integrator.

References CustomIntegrator.getGlobalVariable().

Referenced by AMDIntegrator.getEffectiveEnergy().

def getE

(

self

)

Get the energy threshold E for the integrator.

References CustomIntegrator.getGlobalVariable().

Referenced by AMDIntegrator.getEffectiveEnergy().

def getEffectiveEnergy	(		self,
			energy
	)

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

References AMDIntegrator.getAlpha(), and AMDIntegrator.getE().

def setAlpha	(		self,
			alpha
	)

Set the value of alpha for the integrator.

References CustomIntegrator.setGlobalVariable().

def setE	(		self,
			E
	)

Set the energy threshold E for the integrator.

References CustomIntegrator.setGlobalVariable().

---

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

• amd.py