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