HippoNonbondedForce¶
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class
OpenMM::
HippoNonbondedForce
¶ This class implements all nonbonded interactions in the HIPPO force field: electrostatics, induction, charge transfer, dispersion, and repulsion. Although some of these are conceptually distinct, they share parameters in common and are most efficiently computed together. For example, the same multipole definitions are used for both electrostatics and Pauli repulsion. Therefore, all of them are computed by a single
Force
object.To use it, create a
HippoNonbondedForce
object, then calladdParticle()
once for each particle. After an entry has been added, you can modify its force field parameters by callingsetParticleParameters()
. This will have no effect on Contexts that already exist unless you callupdateParametersInContext()
.You also can specify “exceptions”, particular pairs of particles whose interactions should be reduced or completely omitted. Call
addException()
to define exceptions.Methods
HippoNonbondedForce
Create a HippoNonbondedForce
.getNumParticles
Get the number of particles in the potential function. getNumExceptions
Get the number of exceptions. getNonbondedMethod
Get the method used for handling long-range nonbonded interactions. setNonbondedMethod
Set the method used for handling long-range nonbonded interactions. getCutoffDistance
Get the cutoff distance (in nm) being used for nonbonded interactions. setCutoffDistance
Set the cutoff distance (in nm) being used for nonbonded interactions. getSwitchingDistance
Get the distance at which the switching function begins to reduce the repulsion and charge transfer interactions. setSwitchingDistance
Set the distance at which the switching function begins to reduce the repulsion and charge transfer interactions. getExtrapolationCoefficients
Get the coefficients for the mu_0, mu_1, mu_2, ..., mu_n terms in the extrapolation algorithm for induced dipoles. setExtrapolationCoefficients
Set the coefficients for the mu_0, mu_1, mu_2, ..., mu_n terms in the extrapolation algorithm for induced dipoles. getPMEParameters
Get the parameters to use for PME calculations. getDPMEParameters
Get the parameters to use for dispersion PME calculations. setPMEParameters
Set the parameters to use for PME calculations. setDPMEParameters
Set the parameters to use for dispersion PME calculations. getPMEParametersInContext
Get the parameters being used for PME in a particular Context
.getDPMEParametersInContext
Get the parameters being used for dispersion PME in a particular Context
.addParticle
Add the nonbonded force parameters for a particle. getParticleParameters
Get the nonbonded force parameters for a particle. setParticleParameters
Set the nonbonded force parameters for a particle. addException
Add an interaction to the list of exceptions that should be calculated differently from other interactions. getExceptionParameters
Get the scale factors for an interaction that should be calculated differently from others. setExceptionParameters
Set the scale factors for an interaction that should be calculated differently from others. 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. updateParametersInContext
Update the particle and exception parameters in a Context
to match those stored in thisForce
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: ParticleAxisTypes
ZThenX Bisector ZBisect ThreeFold ZOnly NoAxisType -
HippoNonbondedForce
()¶ Create a
HippoNonbondedForce()
.
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int
getNumParticles
() const¶ Get the number of particles in the potential function.
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int
getNumExceptions
() const¶ Get the number of exceptions.
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NonbondedMethod
getNonbondedMethod
() const¶ Get the method used for handling long-range nonbonded interactions.
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void
setNonbondedMethod
(NonbondedMethod method)¶ Set the method used for handling long-range nonbonded interactions.
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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
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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
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double
getSwitchingDistance
() const¶ Get the distance at which the switching function begins to reduce the repulsion and charge transfer interactions. This must be less than the cutoff distance.
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void
setSwitchingDistance
(double distance)¶ Set the distance at which the switching function begins to reduce the repulsion and charge transfer interactions. This must be less than the cutoff distance.
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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.
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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.
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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
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void
getDPMEParameters
(double &alpha, int &nx, int &ny, int &nz) const¶ Get the parameters to use for dispersion 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 dispersion grid points along the X axis
- ny – [out] the number of dispersion grid points along the Y axis
- nz – [out] the number of dispersion grid points along the Z axis
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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
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void
setDPMEParameters
(double alpha, int nx, int ny, int nz)¶ Set the parameters to use for dispersion 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
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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
- context – the
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void
getDPMEParametersInContext
(const Context &context, double &alpha, int &nx, int &ny, int &nz) const¶ Get the parameters being used for dispersion 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 withsetPMEParameters()
, 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
- context – the
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int
addParticle
(double charge, const std::vector<double> &dipole, const std::vector<double> &quadrupole, double coreCharge, double alpha, double epsilon, double damping, double c6, double pauliK, double pauliQ, double pauliAlpha, double polarizability, int axisType, int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY)¶ Add the nonbonded force parameters for a particle. This should be called once for each particle in the
System
. When it is called for the i’th time, it specifies the parameters for the i’th particle.Parameters: - charge – the particle’s charge
- dipole – the particle’s molecular dipole (vector of size 3)
- quadrupole – the particle’s molecular quadrupole (vector of size 9)
- coreCharge – the charge of the atomic core
- alpha – controls the width of the particle’s electron density
- epsilon – sets the magnitude of charge transfer
- damping – sets the length scale for charge transfer
- c6 – the coefficient of the dispersion interaction
- pauliK – the coefficient of the Pauli repulsion interaction
- pauliQ – the charge used in computing the Pauli repulsion interaction
- pauliAlpha – the width of the particle’s electron density for computing the Pauli repulsion interaction
- polarizability – atomic polarizability
- axisType – the particle’s axis type
- multipoleAtomZ – index of first atom used in defining the local coordinate system for multipoles
- multipoleAtomX – index of second atom used in defining the local coordinate system for multipoles
- multipoleAtomY – index of third atom used in defining the local coordinate system for multipoles
Returns: the index of the particle that was added
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void
getParticleParameters
(int index, double &charge, std::vector<double> &dipole, std::vector<double> &quadrupole, double &coreCharge, double &alpha, double &epsilon, double &damping, double &c6, double &pauliK, double &pauliQ, double &pauliAlpha, double &polarizability, int &axisType, int &multipoleAtomZ, int &multipoleAtomX, int &multipoleAtomY) const¶ Get the nonbonded force parameters for a particle.
Parameters: - index – the index of the particle for which to get parameters
- charge – the particle’s charge
- dipole – the particle’s molecular dipole (vector of size 3)
- quadrupole – the particle’s molecular quadrupole (vector of size 9)
- coreCharge – the charge of the atomic core
- alpha – controls the width of the particle’s electron density
- epsilon – sets the magnitude of charge transfer
- damping – sets the length scale for charge transfer
- c6 – the coefficient of the dispersion interaction
- pauliK – the coefficient of the Pauli repulsion interaction
- pauliQ – the charge used in computing the Pauli repulsion interaction
- pauliAlpha – the width of the particle’s electron density for computing the Pauli repulsion interaction
- polarizability – atomic polarizability
- axisType – the particle’s axis type
- multipoleAtomZ – index of first atom used in defining the local coordinate system for multipoles
- multipoleAtomX – index of second atom used in defining the local coordinate system for multipoles
- multipoleAtomY – index of third atom used in defining the local coordinate system for multipoles
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void
setParticleParameters
(int index, double charge, const std::vector<double> &dipole, const std::vector<double> &quadrupole, double coreCharge, double alpha, double epsilon, double damping, double c6, double pauliK, double pauliQ, double pauliAlpha, double polarizability, int axisType, int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY)¶ Set the nonbonded force parameters for a particle.
Parameters: - index – the index of the particle for which to set parameters
- charge – the particle’s charge
- dipole – the particle’s molecular dipole (vector of size 3)
- quadrupole – the particle’s molecular quadrupole (vector of size 9)
- coreCharge – the charge of the atomic core
- alpha – controls the width of the particle’s electron density
- epsilon – sets the magnitude of charge transfer
- damping – sets the length scale for charge transfer
- c6 – the coefficient of the dispersion interaction
- pauliK – the coefficient of the Pauli repulsion interaction
- pauliQ – the charge used in computing the Pauli repulsion interaction
- pauliAlpha – the width of the particle’s electron density for computing the Pauli repulsion interaction
- polarizability – atomic polarizability
- axisType – the particle’s axis type
- multipoleAtomZ – index of first atom used in defining the local coordinate system for multipoles
- multipoleAtomX – index of second atom used in defining the local coordinate system for multipoles
- multipoleAtomY – index of third atom used in defining the local coordinate system for multipoles
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int
addException
(int particle1, int particle2, double multipoleMultipoleScale, double dipoleMultipoleScale, double dipoleDipoleScale, double dispersionScale, double repulsionScale, double chargeTransferScale, bool replace = false)¶ Add an interaction to the list of exceptions that should be calculated differently from other interactions. If all scale factors are set to 0, this will cause the interaction to be completely omitted from force and energy calculations.
Parameters: - particle1 – the index of the first particle involved in the interaction
- particle2 – the index of the second particle involved in the interaction
- multipoleMultipoleScale – the factor by which to scale the Coulomb interaction between fixed multipoles
- dipoleMultipoleScale – the factor by which to scale the Coulomb interaction between an induced dipole and a fixed multipole
- dipoleDipoleScale – the factor by which to scale the Coulomb interaction between induced dipoles
- dispersionScale – the factor by which to scale the dispersion interaction
- repulsionScale – the factor by which to scale the Pauli repulsion
- chargeTransferScale – the factor by which to scale the charge transfer interaction
- replace – determines the behavior if there is already an exception for the same two particles. If true, the existing one is replaced. If false, an exception is thrown.
Returns: the index of the exception that was added
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void
getExceptionParameters
(int index, int &particle1, int &particle2, double &multipoleMultipoleScale, double &dipoleMultipoleScale, double &dipoleDipoleScale, double &dispersionScale, double &repulsionScale, double &chargeTransferScale) const¶ Get the scale factors for an interaction that should be calculated differently from others.
Parameters: - index – the index of the interaction for which to get parameters
- particle1 – the index of the first particle involved in the interaction
- particle2 – the index of the second particle involved in the interaction
- multipoleMultipoleScale – the factor by which to scale the Coulomb interaction between fixed multipoles
- dipoleMultipoleScale – the factor by which to scale the Coulomb interaction between an induced dipole and a fixed multipole
- dipoleDipoleScale – the factor by which to scale the Coulomb interaction between induced dipoles
- dispersionScale – the factor by which to scale the dispersion interaction
- repulsionScale – the factor by which to scale the Pauli repulsion
- chargeTransferScale – the factor by which to scale the charge transfer interaction
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void
setExceptionParameters
(int index, int particle1, int particle2, double multipoleMultipoleScale, double dipoleMultipoleScale, double dipoleDipoleScale, double dispersionScale, double repulsionScale, double chargeTransferScale)¶ Set the scale factors for an interaction that should be calculated differently from others. If all scale factors are set to 0, this will cause the interaction to be completely omitted from force and energy calculations.
Parameters: - index – the index of the interaction for which to set parameters
- particle1 – the index of the first particle involved in the interaction
- particle2 – the index of the second particle involved in the interaction
- multipoleMultipoleScale – the factor by which to scale the Coulomb interaction between fixed multipoles
- dipoleMultipoleScale – the factor by which to scale the Coulomb interaction between an induced dipole and a fixed multipole
- dipoleDipoleScale – the factor by which to scale the Coulomb interaction between induced dipoles
- dispersionScale – the factor by which to scale the dispersion interaction
- repulsionScale – the factor by which to scale the Pauli repulsion
- chargeTransferScale – the factor by which to scale the charge transfer interaction
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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.
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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.
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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
- context – the
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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
- context – the
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void
updateParametersInContext
(Context &context)¶ Update the particle and exception parameters in a
Context
to match those stored in thisForce
object. This method provides an efficient method to update certain parameters in an existingContext
without needing to reinitialize it. Simply callsetParticleParameters()
to modify this object’s parameters, then callupdateParametersInContext()
to copy them over to theContext
.This method has several limitations. The only information it updates is the parameters of particles and exceptions. All other aspects of the
Force
(the nonbonded method, the cutoff distance, etc.) are unaffected and can only be changed by reinitializing theContext
. Furthermore, only the scale factors for an exception can be changed; the pair of particles involved in the exception cannot change. Finally, this method cannot be used to add new particles or exceptions, only to change the parameters of existing ones.
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bool
usesPeriodicBoundaryConditions
() const¶ Returns whether or not this force makes use of periodic boundary conditions.
Returns: true if nonbondedMethod uses PBC and false otherwise
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