AmoebaMultipoleForce¶
- class openmm.openmm.AmoebaMultipoleForce(*args)¶
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().
- __init__(self) → AmoebaMultipoleForce¶
- __init__(self, other) → AmoebaMultipoleForce
Create an AmoebaMultipoleForce.
Methods
__init__
(-> AmoebaMultipoleForce)Create an AmoebaMultipoleForce.
addMultipole
(self, charge, molecularDipole, …)Add multipole-related info for a particle
getAEwald
(self)Get the Ewald alpha parameter.
getCovalentMap
(self, index, typeId)Get the CovalentMap for an atom
getCovalentMaps
(self, index)Get the CovalentMap for an atom
getCutoffDistance
(self)Get the cutoff distance (in nm) being used for nonbonded interactions.
getElectrostaticPotential
(self, inputGrid, …)Get the electrostatic potential.
getEwaldErrorTolerance
(self)Get the error tolerance for Ewald summation.
Get the coefficients for the mu_0, mu_1, mu_2, …, mu_n terms in the extrapolation algorithm for induced dipoles.
getForceGroup
(self)Get the force group this Force belongs to.
getInducedDipoles
(self, context)Get the induced dipole moments of all particles.
getLabFramePermanentDipoles
(self, context)Get the fixed dipole moments of all particles in the global reference frame.
getMultipoleParameters
(self, index)Get the multipole parameters for a particle.
Get the max number of iterations to be used in calculating the mutual induced dipoles
Get the target epsilon to be used to test for convergence of iterative method used in calculating the mutual induced dipoles
getName
(self)Get the name of this Force.
getNonbondedMethod
(self)Get the method used for handling long-range nonbonded interactions.
getNumMultipoles
(self)Get the number of particles in the potential function
getPMEParameters
(self)Get the parameters to use for PME calculations.
getPMEParametersInContext
(self, context)Get the parameters being used for PME in a particular Context.
getPmeBSplineOrder
(self)Get the B-spline order to use for PME charge spreading
getPmeGridDimensions
(self)Get the PME grid dimensions.
getPolarizationType
(self)Get polarization type
getSystemMultipoleMoments
(self, context)Get the system multipole moments.
getTotalDipoles
(self, context)Get the total dipole moments (fixed plus induced) of all particles.
setAEwald
(self, aewald)Set the Ewald alpha parameter.
setCovalentMap
(self, index, typeId, …)Set the CovalentMap for an atom
setCutoffDistance
(self, distance)Set the cutoff distance (in nm) being used for nonbonded interactions.
setEwaldErrorTolerance
(self, tol)Get the error tolerance for Ewald summation.
setExtrapolationCoefficients
(self, coefficients)Set the coefficients for the mu_0, mu_1, mu_2, …, mu_n terms in the extrapolation algorithm for induced dipoles.
setForceGroup
(self, group)Set the force group this Force belongs to.
setMultipoleParameters
(self, index, charge, …)Set the multipole parameters for a particle.
setMutualInducedMaxIterations
(self, …)Set the max number of iterations to be used in calculating the mutual induced dipoles
setMutualInducedTargetEpsilon
(self, …)Set the target epsilon to be used to test for convergence of iterative method used in calculating the mutual induced dipoles
setName
(self, name)Set the name of this Force.
setNonbondedMethod
(self, method)Set the method used for handling long-range nonbonded interactions.
setPMEParameters
(self, alpha, nx, ny, nz)Set the parameters to use for PME calculations.
setPmeGridDimensions
(self, gridDimension)Set the PME grid dimensions.
setPolarizationType
(self, type)Set the polarization type
updateParametersInContext
(self, context)Update the multipole parameters in a Context to match those stored in this Force object.
Returns whether or not this force makes use of periodic boundary conditions.
Attributes
Bisector
Covalent12
Covalent13
Covalent14
Covalent15
CovalentEnd
Direct
Extrapolated
LastAxisTypeIndex
Mutual
NoAxisType
NoCutoff
PME
PolarizationCovalent11
PolarizationCovalent12
PolarizationCovalent13
PolarizationCovalent14
ThreeFold
ZBisect
ZOnly
ZThenX
The membership flag
- property thisown¶
The membership flag
- getNumMultipoles(self) → int¶
Get the number of particles in the potential function
- getNonbondedMethod(self) → OpenMM::AmoebaMultipoleForce::NonbondedMethod¶
Get the method used for handling long-range nonbonded interactions.
- setNonbondedMethod(self, method)¶
Set the method used for handling long-range nonbonded interactions.
- getPolarizationType(self) → OpenMM::AmoebaMultipoleForce::PolarizationType¶
Get polarization type
- setPolarizationType(self, type)¶
Set the polarization type
- getCutoffDistance(self) → double¶
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
- Return type
double
- setCutoffDistance(self, 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 (double) – the cutoff distance, measured in nm
- getPMEParameters(self)¶
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.
- Returns
alpha (double) – the separation parameter
nx (int) – the number of grid points along the X axis
ny (int) – the number of grid points along the Y axis
nz (int) – the number of grid points along the Z axis
- setPMEParameters(self, alpha, nx, ny, 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 (double) – the separation parameter
nx (int) – the number of grid points along the X axis
ny (int) – the number of grid points along the Y axis
nz (int) – the number of grid points along the Z axis
- getAEwald(self) → double¶
Get the Ewald alpha parameter. If this is 0 (the default), a value is chosen automatically based on the Ewald error tolerance.
Deprecated
This method exists only for backward compatibility. Use getPMEParameters() instead.
- Returns
the Ewald alpha parameter
- Return type
double
- setAEwald(self, aewald)¶
Set the Ewald alpha parameter. If this is 0 (the default), a value is chosen automatically based on the Ewald error tolerance.
Deprecated
This method exists only for backward compatibility. Use setPMEParameters() instead.
- Parameters
aewald (double) – alpha parameter
- getPmeBSplineOrder(self) → int¶
Get the B-spline order to use for PME charge spreading
- Returns
the B-spline order
- Return type
int
- getPmeGridDimensions(self)¶
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.
Deprecated
This method exists only for backward compatibility. Use getPMEParameters() instead.
- Returns
the PME grid dimensions
- Return type
void
- setPmeGridDimensions(self, 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.
Deprecated
This method exists only for backward compatibility. Use setPMEParameters() instead.
- Parameters
gridDimension (vector< int >) – the PME grid dimensions
- getPMEParametersInContext(self, context)¶
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 (Context) – the Context for which to get the parameters
- Returns
alpha (double) – the separation parameter
nx (int) – the number of grid points along the X axis
ny (int) – the number of grid points along the Y axis
nz (int) – the number of grid points along the Z axis
- addMultipole(self, charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY, thole, dampingFactor, polarity) → int¶
Add multipole-related info for a particle
- Parameters
charge (double) – the particle’s charge
molecularDipole (vector< double >) – the particle’s molecular dipole (vector of size 3)
molecularQuadrupole (vector< double >) – the particle’s molecular quadrupole (vector of size 9)
axisType (int) – the particle’s axis type
multipoleAtomZ (int) – index of first atom used in constructing lab<->molecular frames
multipoleAtomX (int) – index of second atom used in constructing lab<->molecular frames
multipoleAtomY (int) – index of second atom used in constructing lab<->molecular frames
thole (double) – Thole parameter
dampingFactor (double) – dampingFactor parameter
polarity (double) – polarity parameter
- Returns
the index of the particle that was added
- Return type
int
- getMultipoleParameters(self, index)¶
Get the multipole parameters for a particle.
- Parameters
index (int) – the index of the atom for which to get parameters
- Returns
charge (double) – the particle’s charge
molecularDipole (vector< double >) – the particle’s molecular dipole (vector of size 3)
molecularQuadrupole (vector< double >) – the particle’s molecular quadrupole (vector of size 9)
axisType (int) – the particle’s axis type
multipoleAtomZ (int) – index of first atom used in constructing lab<->molecular frames
multipoleAtomX (int) – index of second atom used in constructing lab<->molecular frames
multipoleAtomY (int) – index of second atom used in constructing lab<->molecular frames
thole (double) – Thole parameter
dampingFactor (double) – dampingFactor parameter
polarity (double) – polarity parameter
- setMultipoleParameters(self, index, charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY, thole, dampingFactor, polarity)¶
Set the multipole parameters for a particle.
- Parameters
index (int) – the index of the atom for which to set parameters
charge (double) – the particle’s charge
molecularDipole (vector< double >) – the particle’s molecular dipole (vector of size 3)
molecularQuadrupole (vector< double >) – the particle’s molecular quadrupole (vector of size 9)
axisType (int) – the particle’s axis type
multipoleAtomZ (int) – index of first atom used in constructing lab<->molecular frames
multipoleAtomX (int) – index of second atom used in constructing lab<->molecular frames
multipoleAtomY (int) – index of second atom used in constructing lab<->molecular frames
thole (double) – thole parameter
dampingFactor (double) – damping factor parameter
polarity (double) – polarity parameter
- setCovalentMap(self, index, typeId, covalentAtoms)¶
Set the CovalentMap for an atom
- Parameters
index (int) – the index of the atom for which to set parameters
typeId (CovalentType) – CovalentTypes type
covalentAtoms (vector< int >) – vector of covalent atoms associated w/ the specfied CovalentType
- getCovalentMap(self, index, typeId)¶
Get the CovalentMap for an atom
- Parameters
index (int) – the index of the atom for which to set parameters
typeId (CovalentType) – CovalentTypes type
- Returns
covalentAtoms – output vector of covalent atoms associated w/ the specfied CovalentType
- Return type
vector< int >
- getCovalentMaps(self, index)¶
Get the CovalentMap for an atom
- Parameters
index (int) – the index of the atom for which to set parameters
- Returns
covalentLists – output vector of covalent lists of atoms
- Return type
vector< std::vector< int > >
- getMutualInducedMaxIterations(self) → int¶
Get the max number of iterations to be used in calculating the mutual induced dipoles
- Returns
max number of iterations
- Return type
int
- setMutualInducedMaxIterations(self, inputMutualInducedMaxIterations)¶
Set the max number of iterations to be used in calculating the mutual induced dipoles
- Parameters
inputMutualInducedMaxIterations (int) – number of iterations
- getMutualInducedTargetEpsilon(self) → double¶
Get the target epsilon to be used to test for convergence of iterative method used in calculating the mutual induced dipoles
- Returns
target epsilon
- Return type
double
- setMutualInducedTargetEpsilon(self, inputMutualInducedTargetEpsilon)¶
Set the target epsilon to be used to test for convergence of iterative method used in calculating the mutual induced dipoles
- Parameters
inputMutualInducedTargetEpsilon (double) – target epsilon
- setExtrapolationCoefficients(self, coefficients)¶
Set the coefficients for the mu_0, mu_1, mu_2, …, mu_n terms in the extrapolation algorithm for induced dipoles.
- Parameters
coefficients (vector< double >) – a vector whose mth entry specifies the coefficient for mu_m. The length of this vector determines how many iterations are performed.
- getExtrapolationCoefficients(self) → vectord¶
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.
- getEwaldErrorTolerance(self) → double¶
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.
- setEwaldErrorTolerance(self, 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.
- getLabFramePermanentDipoles(self, context)¶
Get the fixed dipole moments of all particles in the global reference frame.
- Parameters
context (Context) – the Context for which to get the fixed dipoles
- Returns
dipoles – the fixed dipole moment of particle i is stored into the i’th element
- Return type
vector< Vec3 >
- getInducedDipoles(self, context)¶
Get the induced dipole moments of all particles.
- Parameters
context (Context) – the Context for which to get the induced dipoles
- Returns
dipoles – the induced dipole moment of particle i is stored into the i’th element
- Return type
vector< Vec3 >
- getTotalDipoles(self, context)¶
Get the total dipole moments (fixed plus induced) of all particles.
- Parameters
context (Context) – the Context for which to get the total dipoles
- Returns
dipoles – the total dipole moment of particle i is stored into the i’th element
- Return type
vector< Vec3 >
- getElectrostaticPotential(self, inputGrid, context)¶
Get the electrostatic potential.
- Parameters
inputGrid (vector< Vec3 >) – input grid points over which the potential is to be evaluated
context (Context) – context
- Returns
outputElectrostaticPotential – output potential
- Return type
vector< double >
- getSystemMultipoleMoments(self, context)¶
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) – context
- Returns
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)
- Return type
vector< double >
- updateParametersInContext(self, 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.
- usesPeriodicBoundaryConditions(self) → bool¶
Returns whether or not this force makes use of periodic boundary conditions.
- Returns
true if nonbondedMethod uses PBC and false otherwise
- Return type
bool
- getForceGroup(self) → int¶
Get the force group this Force belongs to.
- getName(self) → std::string const &¶
Get the name of this Force. This is an arbitrary, user modifiable identifier. By default it equals the class name, but you can change it to anything useful.
- setForceGroup(self, group)¶
Set the force group this Force belongs to.
- Parameters
group (int) – the group index. Legal values are between 0 and 31 (inclusive).
- setName(self, name)¶
Set the name of this Force. This is an arbitrary, user modifiable identifier. By default it equals the class name, but you can change it to anything useful.