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

#include <AmoebaMultipoleForce.h>

Inheritance diagram for AmoebaMultipoleForce:

Public Types
enum	NonbondedMethod { NoCutoff = 0, PME = 1 }

enum	PolarizationType { Mutual = 0, Direct = 1 }

enum	MultipoleAxisTypes { ZThenX = 0, Bisector = 1, ZBisect = 2, ThreeFold = 3, ZOnly = 4, NoAxisType = 5, LastAxisTypeIndex = 6 }

enum	CovalentType { Covalent12 = 0, Covalent13 = 1, Covalent14 = 2, Covalent15 = 3, PolarizationCovalent11 = 4, PolarizationCovalent12 = 5, PolarizationCovalent13 = 6, PolarizationCovalent14 = 7, CovalentEnd = 8 }

Public Member Functions
	AmoebaMultipoleForce ()
	Create an AmoebaMultipoleForce. More...

int	getNumMultipoles () const
	Get the number of particles in the potential function. More...

NonbondedMethod	getNonbondedMethod () const
	Get the method used for handling long-range nonbonded interactions. More...

void	setNonbondedMethod (NonbondedMethod method)
	Set the method used for handling long-range nonbonded interactions. More...

PolarizationType	getPolarizationType () const
	Get polarization type. More...

void	setPolarizationType (PolarizationType type)
	Set the polarization type. More...

double	getCutoffDistance () const
	Get the cutoff distance (in nm) being used for nonbonded interactions. More...

void	setCutoffDistance (double distance)
	Set the cutoff distance (in nm) being used for nonbonded interactions. More...

double	getAEwald () const
	Get the Ewald alpha parameter. More...

void	setAEwald (double aewald)
	Set the Ewald alpha parameter. More...

int	getPmeBSplineOrder () const
	Get the B-spline order to use for PME charge spreading. More...

void	getPmeGridDimensions (std::vector< int > &gridDimension) const
	Get the PME grid dimensions. More...

void	setPmeGridDimensions (const std::vector< int > &gridDimension)
	Set the PME grid dimensions. More...

int	addMultipole (double charge, const std::vector< double > &molecularDipole, const std::vector< double > &molecularQuadrupole, int axisType, int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity)
	Add multipole-related info for a particle. More...

void	getMultipoleParameters (int index, double &charge, std::vector< double > &molecularDipole, std::vector< double > &molecularQuadrupole, int &axisType, int &multipoleAtomZ, int &multipoleAtomX, int &multipoleAtomY, double &thole, double &dampingFactor, double &polarity) const
	Get the multipole parameters for a particle. More...

void	setMultipoleParameters (int index, double charge, const std::vector< double > &molecularDipole, const std::vector< double > &molecularQuadrupole, int axisType, int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity)
	Set the multipole parameters for a particle. More...

void	setCovalentMap (int index, CovalentType typeId, const std::vector< int > &covalentAtoms)
	Set the CovalentMap for an atom. More...

void	getCovalentMap (int index, CovalentType typeId, std::vector< int > &covalentAtoms) const
	Get the CovalentMap for an atom. More...

void	getCovalentMaps (int index, std::vector< std::vector< int > > &covalentLists) const
	Get the CovalentMap for an atom. More...

int	getMutualInducedMaxIterations (void) const
	Get the max number of iterations to be used in calculating the mutual induced dipoles. More...

void	setMutualInducedMaxIterations (int inputMutualInducedMaxIterations)
	Set the max number of iterations to be used in calculating the mutual induced dipoles. More...

double	getMutualInducedTargetEpsilon (void) const
	Get the target epsilon to be used to test for convergence of iterative method used in calculating the mutual induced dipoles. More...

void	setMutualInducedTargetEpsilon (double inputMutualInducedTargetEpsilon)
	Set the target epsilon to be used to test for convergence of iterative method used in calculating the mutual induced dipoles. More...

double	getEwaldErrorTolerance () const
	Get the error tolerance for Ewald summation. More...

void	setEwaldErrorTolerance (double tol)
	Get the error tolerance for Ewald summation. More...

void	getInducedDipoles (Context &context, std::vector< Vec3 > &dipoles)
	Get the induced dipole moments of all particles. More...

void	getElectrostaticPotential (const std::vector< Vec3 > &inputGrid, Context &context, std::vector< double > &outputElectrostaticPotential)
	Get the electrostatic potential. More...

void	getSystemMultipoleMoments (Context &context, std::vector< double > &outputMultipoleMoments)
	Get the system multipole moments. More...

void	updateParametersInContext (Context &context)
	Update the multipole parameters in a Context to match those stored in this Force object. More...

bool	usesPeriodicBoundaryConditions () const
	Returns whether or not this force makes use of periodic boundary conditions. More...

Public Member Functions inherited from Force
	Force ()

virtual	~Force ()

int	getForceGroup () const
	Get the force group this Force belongs to. More...

void	setForceGroup (int group)
	Set the force group this Force belongs to. More...

Protected Member Functions
ForceImpl *	createImpl () const
	When a Context is created, it invokes this method on each Force in the System. More...

Protected Member Functions inherited from Force
ForceImpl &	getImplInContext (Context &context)
	Get the ForceImpl corresponding to this Force in a Context. More...

ContextImpl &	getContextImpl (Context &context)
	Get the ContextImpl corresponding to a Context. More...

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().

Member Enumeration Documentation

enum CovalentType

Enumerator
Covalent12
Covalent13
Covalent14
Covalent15
PolarizationCovalent11
PolarizationCovalent12
PolarizationCovalent13
PolarizationCovalent14
CovalentEnd

enum MultipoleAxisTypes

Enumerator
ZThenX
Bisector
ZBisect
ThreeFold
ZOnly
NoAxisType
LastAxisTypeIndex

enum NonbondedMethod

Enumerator

NoCutoff

No cutoff is applied to nonbonded interactions.

The full set of N^2 interactions is computed exactly. This necessarily means that periodic boundary conditions cannot be used. This is the default.

PME

Periodic boundary conditions are used, and Particle-Mesh Ewald (PME) summation is used to compute the interaction of each particle with all periodic copies of every other particle.

enum PolarizationType

Enumerator
Mutual	Mutual polarization.
Direct	Direct polarization.

Constructor & Destructor Documentation

AmoebaMultipoleForce ( )

Create an AmoebaMultipoleForce.

Member Function Documentation

int addMultipole	(	double	charge,
		const std::vector< double > &	molecularDipole,
		const std::vector< double > &	molecularQuadrupole,
		int	axisType,
		int	multipoleAtomZ,
		int	multipoleAtomX,
		int	multipoleAtomY,
		double	thole,
		double	dampingFactor,
		double	polarity
	)

Add multipole-related info for a particle.

Parameters

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

Returns: the index of the particle that was added

ForceImpl* createImpl ( ) const

protectedvirtual

When a Context is created, it invokes this method on each Force in the System.

It should create a new ForceImpl object which can be used by the context for calculating forces. The ForceImpl will be deleted automatically when the Context is deleted.

Implements Force.

double getAEwald ( ) const

Get the Ewald alpha parameter.

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

Returns: the Ewald alpha parameter

void getCovalentMap	(	int	index,
		CovalentType	typeId,
		std::vector< int > &	covalentAtoms
	)		const

Get the CovalentMap for an atom.

Parameters

index	the index of the atom for which to set parameters
typeId	CovalentTypes type
covalentAtoms	output vector of covalent atoms associated w/ the specfied CovalentType

void getCovalentMaps	(	int	index,
		std::vector< std::vector< int > > &	covalentLists
	)		const

Get the CovalentMap for an atom.

Parameters

index	the index of the atom for which to set parameters
covalentLists	output vector of covalent lists of atoms

double getCutoffDistance ( ) const

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: the cutoff distance, measured in nm

void getElectrostaticPotential	(	const std::vector< Vec3 > &	inputGrid,
		Context &	context,
		std::vector< double > &	outputElectrostaticPotential
	)

Get the electrostatic potential.

Parameters

inputGrid	input grid points over which the potential is to be evaluated
context	context
outputElectrostaticPotential	output potential

double getEwaldErrorTolerance ( ) const

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.

void getInducedDipoles	(	Context &	context,
		std::vector< Vec3 > &	dipoles
	)

Get the induced dipole moments of all particles.

Parameters

context	the Context for which to get the induced dipoles
dipoles	the induced dipole moment of particle i is stored into the i'th element

void getMultipoleParameters	(	int	index,
		double &	charge,
		std::vector< double > &	molecularDipole,
		std::vector< double > &	molecularQuadrupole,
		int &	axisType,
		int &	multipoleAtomZ,
		int &	multipoleAtomX,
		int &	multipoleAtomY,
		double &	thole,
		double &	dampingFactor,
		double &	polarity
	)		const

Get the multipole parameters for a particle.

Parameters

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

int getMutualInducedMaxIterations ( void ) const

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

Returns: max number of iterations

double getMutualInducedTargetEpsilon ( void ) const

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

Returns: target epsilon

NonbondedMethod getNonbondedMethod ( ) const

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

int getNumMultipoles ( ) const

inline

Get the number of particles in the potential function.

int getPmeBSplineOrder ( ) const

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

Returns: the B-spline order

void getPmeGridDimensions ( std::vector< int > & gridDimension ) const

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: the PME grid dimensions

PolarizationType getPolarizationType ( ) const

Get polarization type.

void getSystemMultipoleMoments	(	Context &	context,
		std::vector< double > &	outputMultipoleMoments
	)

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
outputMultipoleMoments	(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)

void setAEwald ( double aewald )

Set the Ewald alpha parameter.

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

Parameters

Ewald alpha parameter

void setCovalentMap	(	int	index,
		CovalentType	typeId,
		const std::vector< int > &	covalentAtoms
	)

Set the CovalentMap for an atom.

Parameters

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

void setCutoffDistance ( double 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 the cutoff distance, measured in nm

void setEwaldErrorTolerance ( double 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.

void setMultipoleParameters	(	int	index,
		double	charge,
		const std::vector< double > &	molecularDipole,
		const std::vector< double > &	molecularQuadrupole,
		int	axisType,
		int	multipoleAtomZ,
		int	multipoleAtomX,
		int	multipoleAtomY,
		double	thole,
		double	dampingFactor,
		double	polarity
	)

Set the multipole parameters for a particle.

Parameters

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

void setMutualInducedMaxIterations ( int inputMutualInducedMaxIterations )

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

Parameters

max	number of iterations

void setMutualInducedTargetEpsilon ( double inputMutualInducedTargetEpsilon )

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

Parameters

target epsilon

void setNonbondedMethod ( NonbondedMethod method )

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

void setPmeGridDimensions ( const std::vector< int > & 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

the	PME grid dimensions

void setPolarizationType ( PolarizationType type )

Set the polarization type.

void updateParametersInContext ( Context & 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.

bool usesPeriodicBoundaryConditions ( ) const

inlinevirtual

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

Returns: true if nonbondedMethod uses PBC and false otherwise

Reimplemented from Force.

References AmoebaMultipoleForce::PME.

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

AmoebaMultipoleForce.h

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation