AmoebaMultipoleForce¶

class OpenMM::AmoebaMultipoleForce¶

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().

Methods

`AmoebaMultipoleForce`	Create an `AmoebaMultipoleForce`.
`getNumMultipoles`	Get the number of particles in the potential function
`getNonbondedMethod`	Get the method used for handling long-range nonbonded interactions.
`setNonbondedMethod`	Set the method used for handling long-range nonbonded interactions.
`getPolarizationType`	Get polarization type
`setPolarizationType`	Set the polarization type
`getCutoffDistance`	Get the cutoff distance (in nm) being used for nonbonded interactions.
`setCutoffDistance`	Set the cutoff distance (in nm) being used for nonbonded interactions.
`getPMEParameters`	Get the parameters to use for PME calculations.
`setPMEParameters`	Set the parameters to use for PME calculations.
`getAEwald`	Get the Ewald alpha parameter.
`setAEwald`	Set the Ewald alpha parameter.
`getPmeBSplineOrder`	Get the B-spline order to use for PME charge spreading
`getPmeGridDimensions`	Get the PME grid dimensions.
`setPmeGridDimensions`	Set the PME grid dimensions.
`getPMEParametersInContext`	Get the parameters being used for PME in a particular `Context`.
`addMultipole`	Add multipole-related info for a particle
`getMultipoleParameters`	Get the multipole parameters for a particle.
`setMultipoleParameters`	Set the multipole parameters for a particle.
`setCovalentMap`	Set the CovalentMap for an atom
`getCovalentMap`	Get the CovalentMap for an atom
`getCovalentMaps`	Get the CovalentMap for an atom
`getMutualInducedMaxIterations`	Get the max number of iterations to be used in calculating the mutual induced dipoles
`setMutualInducedMaxIterations`	Set the max number of iterations to be used in calculating the mutual induced dipoles
`getMutualInducedTargetEpsilon`	Get the target epsilon to be used to test for convergence of iterative method used in calculating the mutual induced dipoles
`setMutualInducedTargetEpsilon`	Set the target epsilon to be used to test for convergence of iterative method used in calculating the mutual induced dipoles
`setExtrapolationCoefficients`	Set the coefficients for the mu_0, mu_1, mu_2, …, mu_n terms in the extrapolation algorithm for induced dipoles.
`getExtrapolationCoefficients`	Get the coefficients for the mu_0, mu_1, mu_2, …, mu_n terms in the extrapolation algorithm for induced dipoles.
`getEwaldErrorTolerance`	Get the error tolerance for Ewald summation.
`setEwaldErrorTolerance`	Get the error tolerance for Ewald summation.
`getLabFramePermanentDipoles`	Get the fixed dipole moments of all particles in the global reference frame.
`getInducedDipoles`	Get the induced dipole moments of all particles.
`getTotalDipoles`	Get the total dipole moments (fixed plus induced) of all particles.
`getElectrostaticPotential`	Get the electrostatic potential.
`getSystemMultipoleMoments`	Get the system multipole moments.
`updateParametersInContext`	Update the multipole parameters in a `Context` to match those stored in this `Force` object.
`usesPeriodicBoundaryConditions`	Returns whether or not this force makes use of periodic boundary conditions.

Enum: NonbondedMethod

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

Mutual	Full mutually induced polarization. The dipoles are iterated until the converge to the accuracy specified by `getMutualInducedTargetEpsilon()`.
Direct	Direct polarization approximation. The induced dipoles depend only on the fixed multipoles, not on other induced dipoles.
Extrapolated	Extrapolated perturbation theory approximation. The dipoles are iterated a few times, and then an analytic approximation is used to extrapolate to the fully converged values. Call `setExtrapolationCoefficients()` to set the coefficients used for the extrapolation. The default coefficients used in this release are [-0.154, 0.017, 0.658, 0.474], but be aware that those may change in a future release.

Enum: MultipoleAxisTypes

ZThenX
Bisector
ZBisect
ThreeFold
ZOnly
NoAxisType
LastAxisTypeIndex

Enum: CovalentType

Covalent12
Covalent13
Covalent14
Covalent15
PolarizationCovalent11
PolarizationCovalent12
PolarizationCovalent13
PolarizationCovalent14
CovalentEnd

AmoebaMultipoleForce()¶: Create an AmoebaMultipoleForce().

int getNumMultipoles() const¶: Get the number of particles in the potential function

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

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

PolarizationType getPolarizationType() const¶: Get polarization type

void setPolarizationType(PolarizationType type)¶: Set the polarization type

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 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 getPMEParameters(double &alpha, int &nx, int &ny, int &nz) const¶

Get the parameters to use for PME calculations. If alpha is 0 (the default), these parameters are ignored and instead their values are chosen based on the Ewald error tolerance.

Parameters

alpha – [out] the separation parameter
nx – [out] the number of grid points along the X axis
ny – [out] the number of grid points along the Y axis
nz – [out] the number of grid points along the Z axis

void setPMEParameters(double alpha, int nx, int ny, int nz)¶

Set the parameters to use for PME calculations. If alpha is 0 (the default), these parameters are ignored and instead their values are chosen based on the Ewald error tolerance.

Parameters

alpha – the separation parameter
nx – the number of grid points along the X axis
ny – the number of grid points along the Y axis
nz – the number of grid points along the Z axis

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

Deprecated

This method exists only for backward compatibility. Use getPMEParameters() instead.

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

aewald – alpha parameter

Deprecated

This method exists only for backward compatibility. Use setPMEParameters() instead.

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

Deprecated

This method exists only for backward compatibility. Use getPMEParameters() instead.

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

gridDimension – the PME grid dimensions

Deprecated

This method exists only for backward compatibility. Use setPMEParameters() instead.

void getPMEParametersInContext(const Context &context, double &alpha, int &nx, int &ny, int &nz) const¶

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 – the Context for which to get the parameters
alpha – [out] the separation parameter
nx – [out] the number of grid points along the X axis
ny – [out] the number of grid points along the Y axis
nz – [out] the number of grid points along the Z axis

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

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

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
thole – thole parameter
dampingFactor – damping factor parameter
polarity – polarity 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 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 – [out] 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 – [out] output vector of covalent lists of atoms

int getMutualInducedMaxIterations(void) const¶

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

Returns: max number of iterations

void setMutualInducedMaxIterations(int inputMutualInducedMaxIterations)¶

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

Parameters

inputMutualInducedMaxIterations – 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

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

inputMutualInducedTargetEpsilon – target epsilon

void setExtrapolationCoefficients(const std::vector<double> &coefficients)¶

Set the coefficients for the mu_0, mu_1, mu_2, …, mu_n terms in the extrapolation algorithm for induced dipoles.

Parameters

coefficients – a vector whose mth entry specifies the coefficient for mu_m. The length of this vector determines how many iterations are performed.

const std::vector<double> &getExtrapolationCoefficients() const¶: Get the coefficients for the mu_0, mu_1, mu_2, …, mu_n terms in the extrapolation algorithm for induced dipoles. In this release, the default values for the coefficients are [-0.154, 0.017, 0.658, 0.474], but be aware that those may change in a future release.

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 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 getLabFramePermanentDipoles(Context &context, std::vector<Vec3> &dipoles)¶

Get the fixed dipole moments of all particles in the global reference frame.

Parameters

context – the Context for which to get the fixed dipoles
dipoles – [out] the fixed dipole moment of particle i is stored into the i’th element

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 – [out] the induced dipole moment of particle i is stored into the i’th element

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

Get the total dipole moments (fixed plus induced) of all particles.

Parameters

context – the Context for which to get the total dipoles
dipoles – [out] the total dipole moment of particle i is stored into the i’th element

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 – [out] output potential

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

Parameters

context – context
outputMultipoleMoments – [out] (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 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¶

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

Returns: true if nonbondedMethod uses PBC and false otherwise