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AMDForceGroupIntegrator Class Reference

AMDForceGroupIntegrator implements a single boost aMD integration algorithm. More...

+ Inheritance diagram for AMDForceGroupIntegrator:

Public Member Functions

def __init__
 Create a AMDForceGroupIntegrator. More...
 
def getAlphaGroup
 Get the value of alpha for the boosted force group. More...
 
def setAlphaGroup
 Set the value of alpha for the boosted force group. More...
 
def getEGroup
 Get the energy threshold E for the boosted force group. More...
 
def setEGroup
 Set the energy threshold E for the boosted force group. More...
 
def getEffectiveEnergy
 Given the actual group energy of the system, return the value of the effective potential. More...
 

Detailed Description

AMDForceGroupIntegrator implements a single boost aMD integration algorithm.

This is similar to AMDIntegrator, but is applied based on the energy of a single force group (typically representing torsions).

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

Constructor & Destructor Documentation

def __init__ (   self,
  dt,
  group,
  alphaGroup,
  EGroup 
)

Create a AMDForceGroupIntegrator.

Parameters
dt(time) The integration time step to use
group(int) The force group to apply the boost to
alphaGroup(energy) The alpha parameter to use for the boosted force group
EGroup(energy) The energy cutoff to use for the boosted force group

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

Member Function Documentation

def getAlphaGroup (   self)

Get the value of alpha for the boosted force group.

References CustomIntegrator.getGlobalVariable().

Referenced by AMDForceGroupIntegrator.getEffectiveEnergy(), and DualAMDIntegrator.getEffectiveEnergy().

def getEffectiveEnergy (   self,
  groupEnergy 
)

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

Parameters
groupEnergy(energy): the actual potential energy of the boosted force group
Returns
the value of the effective potential

References AMDForceGroupIntegrator.getAlphaGroup(), and AMDForceGroupIntegrator.getEGroup().

def getEGroup (   self)

Get the energy threshold E for the boosted force group.

References CustomIntegrator.getGlobalVariable().

Referenced by AMDForceGroupIntegrator.getEffectiveEnergy(), and DualAMDIntegrator.getEffectiveEnergy().

def setAlphaGroup (   self,
  alpha 
)

Set the value of alpha for the boosted force group.

References CustomIntegrator.setGlobalVariable().

def setEGroup (   self,
  E 
)

Set the energy threshold E for the boosted force group.

References CustomIntegrator.setGlobalVariable().


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