AmoebaMultipoleForce Class Reference

This class implements the Amoeba multipole interaction. More...

Inheritance diagram for AmoebaMultipoleForce:

List of all members.

Public Member Functions
def	getNumMultipoles
	getNumMultipoles(self) -> int
def	getNonbondedMethod
	getNonbondedMethod(self) -> OpenMM::AmoebaMultipoleForce::NonbondedMethod
def	setNonbondedMethod
	Set the method used for handling long-range nonbonded interactions.
def	getPolarizationType
	getPolarizationType(self) -> OpenMM::AmoebaMultipoleForce::PolarizationType
def	setPolarizationType
	Set the polarization type.
def	getCutoffDistance
	getCutoffDistance(self) -> double
def	setCutoffDistance
	Set the cutoff distance (in nm) being used for nonbonded interactions.
def	getAEwald
	getAEwald(self) -> double
def	setAEwald
	Set the Ewald alpha parameter.
def	getPmeBSplineOrder
	getPmeBSplineOrder(self) -> int
def	getPmeGridDimensions
	Get the PME grid dimensions.
def	setPmeGridDimensions
	Set the PME grid dimensions.
def	getPMEParametersInContext
	Get the parameters being used for PME in a particular Context.
def	addMultipole
	addMultipole(self, charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY, thole, dampingFactor, polarity) -> int
def	getMultipoleParameters
	Get the multipole parameters for a particle.
def	setMultipoleParameters
	Set the multipole parameters for a particle.
def	setCovalentMap
	Set the CovalentMap for an atom.
def	getCovalentMap
	Get the CovalentMap for an atom.
def	getCovalentMaps
	Get the CovalentMap for an atom.
def	getMutualInducedMaxIterations
	getMutualInducedMaxIterations(self) -> int
def	setMutualInducedMaxIterations
	Set the max number of iterations to be used in calculating the mutual induced dipoles.
def	getMutualInducedTargetEpsilon
	getMutualInducedTargetEpsilon(self) -> double
def	setMutualInducedTargetEpsilon
	Set the target epsilon to be used to test for convergence of iterative method used in calculating the mutual induced dipoles.
def	getEwaldErrorTolerance
	getEwaldErrorTolerance(self) -> double
def	setEwaldErrorTolerance
	Get the error tolerance for Ewald summation.
def	getInducedDipoles
	Get the induced dipole moments of all particles.
def	getElectrostaticPotential
	Get the electrostatic potential.
def	getSystemMultipoleMoments
	Get the system multipole moments.
def	updateParametersInContext
	Update the multipole parameters in a Context to match those stored in this Force object.
def	usesPeriodicBoundaryConditions
	usesPeriodicBoundaryConditions(self) -> bool
def	__init__
	__init__(self) -> AmoebaMultipoleForce __init__(self, other) -> AmoebaMultipoleForce
Public Attributes
	this
Static Public Attributes
	NoCutoff = _openmm.AmoebaMultipoleForce_NoCutoff
	PME = _openmm.AmoebaMultipoleForce_PME
	Mutual = _openmm.AmoebaMultipoleForce_Mutual
	Direct = _openmm.AmoebaMultipoleForce_Direct
	ZThenX = _openmm.AmoebaMultipoleForce_ZThenX
	Bisector = _openmm.AmoebaMultipoleForce_Bisector
	ZBisect = _openmm.AmoebaMultipoleForce_ZBisect
	ThreeFold = _openmm.AmoebaMultipoleForce_ThreeFold
	ZOnly = _openmm.AmoebaMultipoleForce_ZOnly
	NoAxisType = _openmm.AmoebaMultipoleForce_NoAxisType
	LastAxisTypeIndex = _openmm.AmoebaMultipoleForce_LastAxisTypeIndex
	Covalent12 = _openmm.AmoebaMultipoleForce_Covalent12
	Covalent13 = _openmm.AmoebaMultipoleForce_Covalent13
	Covalent14 = _openmm.AmoebaMultipoleForce_Covalent14
	Covalent15 = _openmm.AmoebaMultipoleForce_Covalent15
	PolarizationCovalent11 = _openmm.AmoebaMultipoleForce_PolarizationCovalent11
	PolarizationCovalent12 = _openmm.AmoebaMultipoleForce_PolarizationCovalent12
	PolarizationCovalent13 = _openmm.AmoebaMultipoleForce_PolarizationCovalent13
	PolarizationCovalent14 = _openmm.AmoebaMultipoleForce_PolarizationCovalent14
	CovalentEnd = _openmm.AmoebaMultipoleForce_CovalentEnd

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Detailed Description

This class implements the Amoeba multipole interaction.

To use it, create an AmoebaMultipoleForce object then call addMultipole() once for each atom. After an entry has been added, you can modify its force field parameters by calling setMultipoleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

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Constructor & Destructor Documentation

def __init__	(		self,
			args
	)

__init__(self) -> AmoebaMultipoleForce __init__(self, other) -> AmoebaMultipoleForce

Create an AmoebaMultipoleForce.

---

Member Function Documentation

def addMultipole	(		self,
			charge,
			molecularDipole,
			molecularQuadrupole,
			axisType,
			multipoleAtomZ,
			multipoleAtomX,
			multipoleAtomY,
			thole,
			dampingFactor,
			polarity
	)

addMultipole(self, charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY, thole, dampingFactor, polarity) -> int

Add multipole-related info for a particle

Parameters:

charge	(double) the particle's charge
molecularDipole	(vector< double >) the particle's molecular dipole (vector of size 3)
molecularQuadrupole	(vector< double >) the particle's molecular quadrupole (vector of size 9)
axisType	(int) the particle's axis type
multipoleAtomZ	(int) index of first atom used in constructing lab<->molecular frames
multipoleAtomX	(int) index of second atom used in constructing lab<->molecular frames
multipoleAtomY	(int) index of second atom used in constructing lab<->molecular frames
thole	(double) Thole parameter
dampingFactor	(double) dampingFactor parameter
polarity	(double) polarity parameter

Returns:

(int) the index of the particle that was added

def getAEwald

(

self

)

getAEwald(self) -> double

Get the Ewald alpha parameter. If this is 0 (the default), a value is chosen automatically based on the Ewald error tolerance.

Returns:

(double) the Ewald alpha parameter

def getCovalentMap	(		self,
			index,
			typeId
	)

Get the CovalentMap for an atom.

Parameters:

index	(int) the index of the atom for which to set parameters
typeId	(CovalentType) CovalentTypes type

Returns:

(vector< int >) output vector of covalent atoms associated w/ the specfied CovalentType

def getCovalentMaps	(		self,
			index
	)

Get the CovalentMap for an atom.

Parameters:

index

(int) the index of the atom for which to set parameters

Returns:

(vector< std::vector< int > >) output vector of covalent lists of atoms

def getCutoffDistance

(

self

)

getCutoffDistance(self) -> double

Get the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use is NoCutoff, this value will have no effect.

Returns:

(double) the cutoff distance, measured in nm

def getElectrostaticPotential	(		self,
			inputGrid,
			context
	)

Get the electrostatic potential.

Parameters:

inputGrid	(vector< Vec3 >) input grid points over which the potential is to be evaluated
context	(Context) context

Returns:

(vector< double >) output potential

def getEwaldErrorTolerance

(

self

)

getEwaldErrorTolerance(self) -> double

Get the error tolerance for Ewald summation. This corresponds to the fractional error in the forces which is acceptable. This value is used to select the grid dimensions and separation (alpha) parameter so that the average error level will be less than the tolerance. There is not a rigorous guarantee that all forces on all atoms will be less than the tolerance, however.

This can be overridden by explicitly setting an alpha parameter and grid dimensions to use.

def getInducedDipoles	(		self,
			context
	)

Get the induced dipole moments of all particles.

Parameters:

context

(Context) the Context for which to get the induced dipoles

Returns:

(vector< Vec3 >) the induced dipole moment of particle i is stored into the i'th element

def getMultipoleParameters	(		self,
			index
	)

Get the multipole parameters for a particle.

Parameters:

index

(int) the index of the atom for which to get parameters

Returns:

(double) the particle's charge

(vector< double >) the particle's molecular dipole (vector of size 3)

(vector< double >) the particle's molecular quadrupole (vector of size 9)

(int) the particle's axis type

(int) index of first atom used in constructing lab<->molecular frames

(int) index of second atom used in constructing lab<->molecular frames

(int) index of second atom used in constructing lab<->molecular frames

(double) Thole parameter

(double) dampingFactor parameter

(double) polarity parameter

def getMutualInducedMaxIterations

(

self

)

getMutualInducedMaxIterations(self) -> int

Get the max number of iterations to be used in calculating the mutual induced dipoles

Returns:

(int) max number of iterations

def getMutualInducedTargetEpsilon

(

self

)

getMutualInducedTargetEpsilon(self) -> double

Get the target epsilon to be used to test for convergence of iterative method used in calculating the mutual induced dipoles

Returns:

(double) target epsilon

def getNonbondedMethod

(

self

)

getNonbondedMethod(self) -> OpenMM::AmoebaMultipoleForce::NonbondedMethod

Get the method used for handling long-range nonbonded interactions.

def getNumMultipoles

(

self

)

getNumMultipoles(self) -> int

Get the number of particles in the potential function

def getPmeBSplineOrder

(

self

)

getPmeBSplineOrder(self) -> int

Get the B-spline order to use for PME charge spreading

Returns:

(int) the B-spline order

def getPmeGridDimensions

(

self

)

Get the PME grid dimensions.

If Ewald alpha is 0 (the default), this is ignored and grid dimensions are chosen automatically based on the Ewald error tolerance.

Returns:

(void) the PME grid dimensions

def getPMEParametersInContext	(		self,
			context
	)

Get the parameters being used for PME in a particular Context.

Because some platforms have restrictions on the allowed grid sizes, the values that are actually used may be slightly different from those specified with setPmeGridDimensions(), or the standard values calculated based on the Ewald error tolerance. See the manual for details.

Parameters:

context

(Context) the Context for which to get the parameters

Returns:

(double) the separation parameter

(int) the number of grid points along the X axis

(int) the number of grid points along the Y axis

(int) the number of grid points along the Z axis

def getPolarizationType

(

self

)

getPolarizationType(self) -> OpenMM::AmoebaMultipoleForce::PolarizationType

Get polarization type

def getSystemMultipoleMoments	(		self,
			context
	)

Get the system multipole moments.

This method is most useful for non-periodic systems. When called for a periodic system, only the lowest nonvanishing moment has a well defined value. This means that if the system has a net nonzero charge, the dipole and quadrupole moments are not well defined and should be ignored. If the net charge is zero, the dipole moment is well defined (and really represents a dipole density), but the quadrupole moment is still undefined and should be ignored.

Parameters:

context

(Context) context

Returns:

(vector< double >) (charge, dipole_x, dipole_y, dipole_z, quadrupole_xx, quadrupole_xy, quadrupole_xz, quadrupole_yx, quadrupole_yy, quadrupole_yz, quadrupole_zx, quadrupole_zy, quadrupole_zz)

def setAEwald	(		self,
			aewald
	)

Set the Ewald alpha parameter.

If this is 0 (the default), a value is chosen automatically based on the Ewald error tolerance.

Parameters:

aewald

(double) alpha parameter

def setCovalentMap	(		self,
			index,
			typeId,
			covalentAtoms
	)

Set the CovalentMap for an atom.

Parameters:

index	(int) the index of the atom for which to set parameters
typeId	(CovalentType) CovalentTypes type
covalentAtoms	(vector< int >) vector of covalent atoms associated w/ the specfied CovalentType

def setCutoffDistance	(		self,
			distance
	)

Set the cutoff distance (in nm) being used for nonbonded interactions.

If the NonbondedMethod in use is NoCutoff, this value will have no effect.

Parameters:

distance

(double) the cutoff distance, measured in nm

def setEwaldErrorTolerance	(		self,
			tol
	)

Get the error tolerance for Ewald summation.

This corresponds to the fractional error in the forces which is acceptable. This value is used to select the grid dimensions and separation (alpha) parameter so that the average error level will be less than the tolerance. There is not a rigorous guarantee that all forces on all atoms will be less than the tolerance, however.

This can be overridden by explicitly setting an alpha parameter and grid dimensions to use.

def setMultipoleParameters	(		self,
			index,
			charge,
			molecularDipole,
			molecularQuadrupole,
			axisType,
			multipoleAtomZ,
			multipoleAtomX,
			multipoleAtomY,
			thole,
			dampingFactor,
			polarity
	)

Set the multipole parameters for a particle.

Parameters:

index	(int) the index of the atom for which to set parameters
charge	(double) the particle's charge
molecularDipole	(vector< double >) the particle's molecular dipole (vector of size 3)
molecularQuadrupole	(vector< double >) the particle's molecular quadrupole (vector of size 9)
axisType	(int) the particle's axis type
multipoleAtomZ	(int) index of first atom used in constructing lab<->molecular frames
multipoleAtomX	(int) index of second atom used in constructing lab<->molecular frames
multipoleAtomY	(int) index of second atom used in constructing lab<->molecular frames
thole	(double) thole parameter
dampingFactor	(double) damping factor parameter
polarity	(double) polarity parameter

def setMutualInducedMaxIterations	(		self,
			inputMutualInducedMaxIterations
	)

Set the max number of iterations to be used in calculating the mutual induced dipoles.

Parameters:

inputMutualInducedMaxIterations

(int) number of iterations

def setMutualInducedTargetEpsilon	(		self,
			inputMutualInducedTargetEpsilon
	)

Set the target epsilon to be used to test for convergence of iterative method used in calculating the mutual induced dipoles.

Parameters:

inputMutualInducedTargetEpsilon

(double) target epsilon

def setNonbondedMethod	(		self,
			method
	)

Set the method used for handling long-range nonbonded interactions.

def setPmeGridDimensions	(		self,
			gridDimension
	)

Set the PME grid dimensions.

If Ewald alpha is 0 (the default), this is ignored and grid dimensions are chosen automatically based on the Ewald error tolerance.

Parameters:

gridDimension

(vector< int >) the PME grid dimensions

def setPolarizationType	(		self,
			type
	)

Set the polarization type.

def updateParametersInContext	(		self,
			context
	)

Update the multipole parameters in a Context to match those stored in this Force object.

This method provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it. Simply call setMultipoleParameters() to modify this object's parameters, then call updateParametersInContext() to copy them over to the Context.

This method has several limitations. The only information it updates is the parameters of multipoles. All other aspects of the Force (the nonbonded method, the cutoff distance, etc.) are unaffected and can only be changed by reinitializing the Context. Furthermore, this method cannot be used to add new multipoles, only to change the parameters of existing ones.

def usesPeriodicBoundaryConditions

(

self

)

usesPeriodicBoundaryConditions(self) -> bool

Returns whether or not this force makes use of periodic boundary conditions.

Returns:

(bool) true if nonbondedMethod uses PBC and false otherwise

Reimplemented from Force.

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Member Data Documentation

Bisector = _openmm.AmoebaMultipoleForce_Bisector [static]

Covalent12 = _openmm.AmoebaMultipoleForce_Covalent12 [static]

Covalent13 = _openmm.AmoebaMultipoleForce_Covalent13 [static]

Covalent14 = _openmm.AmoebaMultipoleForce_Covalent14 [static]

Covalent15 = _openmm.AmoebaMultipoleForce_Covalent15 [static]

CovalentEnd = _openmm.AmoebaMultipoleForce_CovalentEnd [static]

Direct = _openmm.AmoebaMultipoleForce_Direct [static]

LastAxisTypeIndex = _openmm.AmoebaMultipoleForce_LastAxisTypeIndex [static]

Mutual = _openmm.AmoebaMultipoleForce_Mutual [static]

NoAxisType = _openmm.AmoebaMultipoleForce_NoAxisType [static]

NoCutoff = _openmm.AmoebaMultipoleForce_NoCutoff [static]

PME = _openmm.AmoebaMultipoleForce_PME [static]

PolarizationCovalent11 = _openmm.AmoebaMultipoleForce_PolarizationCovalent11 [static]

PolarizationCovalent12 = _openmm.AmoebaMultipoleForce_PolarizationCovalent12 [static]

PolarizationCovalent13 = _openmm.AmoebaMultipoleForce_PolarizationCovalent13 [static]

PolarizationCovalent14 = _openmm.AmoebaMultipoleForce_PolarizationCovalent14 [static]

this

Reimplemented from Force.

ThreeFold = _openmm.AmoebaMultipoleForce_ThreeFold [static]

ZBisect = _openmm.AmoebaMultipoleForce_ZBisect [static]

ZOnly = _openmm.AmoebaMultipoleForce_ZOnly [static]

ZThenX = _openmm.AmoebaMultipoleForce_ZThenX [static]

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

• openmm.py