Package ffx.openmm.amoeba

Class MultipoleForce

java.lang.Object

ffx.openmm.Force

ffx.openmm.amoeba.MultipoleForce

Direct Known Subclasses:

AmoebaMultipoleForce

public class MultipoleForce
extends Force

Amoeba Polarizable Multipole Force.

Field Summary

Fields inherited from class ffx.openmm.Force

pointer

Constructor Summary

Constructors

Constructor	Description
MultipoleForce()

Method Summary

Modifier and Type	Method	Description
void	addMultipole(double charge, DoubleArray dipole, DoubleArray quadrupole, int axisType, int zaxis, int xaxis, int yaxis, double thole, double pdamp, double polarizability)	Add a multipole.
void	destroy()	Destroy the force.
void	setAEwald(double aewald)	Set the Ewald coefficient for the multipole force.
void	setCovalentMap(int i, int covalentType, IntArray covalentMap)	Set the covalent map.
void	setCutoffDistance(double cutoff)	Set the cutoff distance for the multipole force.
void	setEwaldErrorTolerance(double ewaldTolerance)	Set the Ewald error tolerance for the multipole force.
void	setExtrapolationCoefficients(DoubleArray exptCoefficients)	Set extrapolation coefficients.
void	setMultipoleParameters(int index, double charge, DoubleArray dipoles, DoubleArray quadrupoles, int axisType, int zaxis, int xaxis, int yaxis, double thole, double pdamp, double polarizability)	Set the multipole parameters.
void	setMutualInducedMaxIterations(int iterations)	Set the mutual induced target maximum number of iterations.
void	setMutualInducedTargetEpsilon(double epsilon)	Set the mutual induced target epsilon.
void	setNonbondedMethod(int method)	Set the nonbonded method for the multipole force.
void	setPmeGridDimensions(IntArray gridDimensions)	Set the PME grid dimensions for the multipole force.
void	setPolarizationType(int method)	Set the polarization method.
void	updateParametersInContext(Context context)	Update the parameters in the context.

Methods inherited from class ffx.openmm.Force

getForceGroup, getForceIndex, getName, getPointer, setForceGroup, setForceIndex, setName, usesPeriodicBoundaryConditions

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

MultipoleForce

public MultipoleForce()

Method Details

setPolarizationType

public void setPolarizationType(int method)

Set the polarization method.

Parameters:

method - The polarization method.

setExtrapolationCoefficients

public void setExtrapolationCoefficients(DoubleArray exptCoefficients)

Set extrapolation coefficients.

Parameters:

exptCoefficients - The extrapolation coefficients.

addMultipole

public void addMultipole(double charge,
 DoubleArray dipole,
 DoubleArray quadrupole,
 int axisType,
 int zaxis,
 int xaxis,
 int yaxis,
 double thole,
 double pdamp,
 double polarizability)

Add a multipole.

Parameters:

charge - The charge.

dipole - The dipole.

quadrupole - The quadrupole.

axisType - The axis type.

zaxis - The z-axis.

xaxis - The x-axis.

yaxis - The y-axis.

thole - The Thole parameter.

pdamp - The damping factor.

polarizability - The polarizability.

setMultipoleParameters

public void setMultipoleParameters(int index,
 double charge,
 DoubleArray dipoles,
 DoubleArray quadrupoles,
 int axisType,
 int zaxis,
 int xaxis,
 int yaxis,
 double thole,
 double pdamp,
 double polarizability)

Set the multipole parameters.

Parameters:

index - The atom index.

charge - The charge.

dipoles - The dipole.

quadrupoles - The quadrupole.

axisType - The axis type.

zaxis - The z-axis.

xaxis - The x-axis.

yaxis - The y-axis.

thole - The Thole parameter.

pdamp - The damping factor.

polarizability - The polarizability.

setNonbondedMethod

public void setNonbondedMethod(int method)

Set the nonbonded method for the multipole force.

Parameters:

method - The nonbonded method.

setCutoffDistance

public void setCutoffDistance(double cutoff)

Set the cutoff distance for the multipole force.

Parameters:

cutoff - The cutoff distance.

setAEwald

public void setAEwald(double aewald)

Set the Ewald coefficient for the multipole force.

Parameters:

aewald - The Ewald coefficient.

setEwaldErrorTolerance

public void setEwaldErrorTolerance(double ewaldTolerance)

Set the Ewald error tolerance for the multipole force.

Parameters:

ewaldTolerance - The Ewald error tolerance.

setPmeGridDimensions

public void setPmeGridDimensions(IntArray gridDimensions)

Set the PME grid dimensions for the multipole force.

Parameters:

gridDimensions - The PME grid dimensions.

setMutualInducedMaxIterations

public void setMutualInducedMaxIterations(int iterations)

Set the mutual induced target maximum number of iterations.

Parameters:

iterations - The mutual induced max iterations.

setMutualInducedTargetEpsilon

public void setMutualInducedTargetEpsilon(double epsilon)

Set the mutual induced target epsilon.

Parameters:

epsilon - The mutual induced target epsilon.

setCovalentMap

public void setCovalentMap(int i,
 int covalentType,
 IntArray covalentMap)

Set the covalent map.

Parameters:

i - The atom index.

covalentType - The covalent type.

covalentMap - The covalent map.

updateParametersInContext

public void updateParametersInContext(Context context)

Update the parameters in the context.

Parameters:

context - The OpenMM context.

destroy

public void destroy()

Destroy the force.