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OpenMM
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OpenMM
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This class implements forces that are specific to Drude oscillators. More...
Inheritance diagram for DrudeForce:Public Member Functions | |
| def | getNumParticles |
| getNumParticles(DrudeForce self) -> int More... | |
| def | getNumScreenedPairs |
| getNumScreenedPairs(DrudeForce self) -> int More... | |
| def | addParticle |
| addParticle(DrudeForce self, int particle, int particle1, int particle2, int particle3, int particle4, double charge, double polarizability, double aniso12, double aniso34) -> int More... | |
| def | getParticleParameters |
| getParticleParameters(DrudeForce self, int index) More... | |
| def | setParticleParameters |
| setParticleParameters(DrudeForce self, int index, int particle, int particle1, int particle2, int particle3, int particle4, double charge, double polarizability, double aniso12, double aniso34) More... | |
| def | addScreenedPair |
| addScreenedPair(DrudeForce self, int particle1, int particle2, double thole) -> int More... | |
| def | getScreenedPairParameters |
| getScreenedPairParameters(DrudeForce self, int index) More... | |
| def | setScreenedPairParameters |
| setScreenedPairParameters(DrudeForce self, int index, int particle1, int particle2, double thole) More... | |
| def | updateParametersInContext |
| updateParametersInContext(DrudeForce self, Context context) More... | |
| def | usesPeriodicBoundaryConditions |
| usesPeriodicBoundaryConditions(DrudeForce self) -> bool More... | |
| def | __init__ |
| init(OpenMM::DrudeForce self) -> DrudeForce init(OpenMM::DrudeForce self, DrudeForce other) -> DrudeForce More... | |
| def | __del__ |
| del(OpenMM::DrudeForce self) More... | |
| Public Member Functions inherited from Force | |
| def | __init__ |
| def | __del__ |
| del(OpenMM::Force self) More... | |
| def | getForceGroup |
| getForceGroup(Force self) -> int More... | |
| def | setForceGroup |
| setForceGroup(Force self, int group) More... | |
| def | usesPeriodicBoundaryConditions |
| usesPeriodicBoundaryConditions(Force self) -> bool More... | |
| def | __copy__ |
| def | __deepcopy__ |
Public Attributes | |
| this | |
This class implements forces that are specific to Drude oscillators.
There are two distinct forces it applies: an anisotropic harmonic force connecting each Drude particle to its parent particle; and a screened Coulomb interaction between specific pairs of dipoles. The latter is typically used between closely bonded particles whose Coulomb interaction would otherwise be fully excluded.
To use this class, create a DrudeForce object, then call addParticle() once for each Drude particle in the System to define its parameters. After a particle has been added, you can modify its force field parameters by calling setParticleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext(). Likewise, call addScreenedPair() for each pair of dipoles (each dipole consisting of a Drude particle and its parent) that should be computed.
| def __init__ | ( | self, | |
| args | |||
| ) |
init(OpenMM::DrudeForce self) -> DrudeForce init(OpenMM::DrudeForce self, DrudeForce other) -> DrudeForce
Create a DrudeForce.
References simtk.openmm.openmm.stripUnits().
| def __del__ | ( | self | ) |
del(OpenMM::DrudeForce self)
References simtk.openmm.openmm.stripUnits().
| def addParticle | ( | self, | |
| args | |||
| ) |
addParticle(DrudeForce self, int particle, int particle1, int particle2, int particle3, int particle4, double charge, double polarizability, double aniso12, double aniso34) -> int
Add a Drude particle to which forces should be applied.
| particle | the index within the System of the Drude particle |
| particle1 | the index within the System of the particle to which the Drude particle is attached |
| particle2 | the index within the System of the second particle used for defining anisotropic polarizability. This may be set to -1, in which case aniso12 will be ignored. |
| particle3 | the index within the System of the third particle used for defining anisotropic polarizability. This may be set to -1, in which case aniso34 will be ignored. |
| particle4 | the index within the System of the fourth particle used for defining anisotropic polarizability. This may be set to -1, in which case aniso34 will be ignored. |
| charge | The charge on the Drude particle |
| polarizability | The isotropic polarizability |
| aniso12 | The scale factor for the polarizability along the direction defined by particle1 and particle2 |
| aniso34 | The scale factor for the polarizability along the direction defined by particle3 and particle4 |
References simtk.openmm.openmm.stripUnits().
Referenced by NonbondedForce.addParticle_usingRVdw().
| def addScreenedPair | ( | self, | |
| args | |||
| ) |
addScreenedPair(DrudeForce self, int particle1, int particle2, double thole) -> int
Add an interaction to the list of screened pairs.
| particle1 | the index within this Force of the first particle involved in the interaction |
| particle2 | the index within this Force of the second particle involved in the interaction |
| thole | the Thole screening factor |
References simtk.openmm.openmm.stripUnits().
| def getNumParticles | ( | self, | |
| args | |||
| ) |
getNumParticles(DrudeForce self) -> int
Get the number of particles for which force field parameters have been defined.
References simtk.openmm.openmm.stripUnits().
| def getNumScreenedPairs | ( | self, | |
| args | |||
| ) |
getNumScreenedPairs(DrudeForce self) -> int
Get the number of special interactions that should be calculated differently from other interactions.
References simtk.openmm.openmm.stripUnits().
| def getParticleParameters | ( | self, | |
| args | |||
| ) |
getParticleParameters(DrudeForce self, int index)
Get the parameters for a Drude particle.
| index | the index of the Drude particle for which to get parameters |
| particle | the index within the System of the Drude particle |
| particle1 | the index within the System of the particle to which the Drude particle is attached |
| particle2 | the index within the System of the second particle used for defining anisotropic polarizability. This may be set to -1, in which case aniso12 will be ignored. |
| particle3 | the index within the System of the third particle used for defining anisotropic polarizability. This may be set to -1, in which case aniso34 will be ignored. |
| particle4 | the index within the System of the fourth particle used for defining anisotropic polarizability. This may be set to -1, in which case aniso34 will be ignored. |
| charge | The charge on the Drude particle |
| polarizability | The isotropic polarizability |
| aniso12 | The scale factor for the polarizability along the direction defined by particle1 and particle2 |
| aniso34 | The scale factor for the polarizability along the direction defined by particle3 and particle4 |
References simtk.openmm.openmm.stripUnits().
| def getScreenedPairParameters | ( | self, | |
| args | |||
| ) |
getScreenedPairParameters(DrudeForce self, int index)
Get the force field parameters for screened pair.
| index | the index of the pair for which to get parameters |
| particle1 | the index within this Force of the first particle involved in the interaction |
| particle2 | the index within this Force of the second particle involved in the interaction |
| thole | the Thole screening factor |
References simtk.openmm.openmm.stripUnits().
| def setParticleParameters | ( | self, | |
| args | |||
| ) |
setParticleParameters(DrudeForce self, int index, int particle, int particle1, int particle2, int particle3, int particle4, double charge, double polarizability, double aniso12, double aniso34)
Set the parameters for a Drude particle.
| index | the index of the Drude particle for which to set parameters |
| particle | the index within the System of the Drude particle |
| particle1 | the index within the System of the particle to which the Drude particle is attached |
| particle2 | the index within the System of the second particle used for defining anisotropic polarizability. This may be set to -1, in which case aniso12 will be ignored. |
| particle3 | the index within the System of the third particle used for defining anisotropic polarizability. This may be set to -1, in which case aniso34 will be ignored. |
| particle4 | the index within the System of the fourth particle used for defining anisotropic polarizability. This may be set to -1, in which case aniso34 will be ignored. |
| charge | The charge on the Drude particle |
| polarizability | The isotropic polarizability |
| aniso12 | The scale factor for the polarizability along the direction defined by particle1 and particle2 |
| aniso34 | The scale factor for the polarizability along the direction defined by particle3 and particle4 |
References simtk.openmm.openmm.stripUnits().
| def setScreenedPairParameters | ( | self, | |
| args | |||
| ) |
setScreenedPairParameters(DrudeForce self, int index, int particle1, int particle2, double thole)
Set the force field parameters for screened pair.
| index | the index of the pair for which to get parameters |
| particle1 | the index within this Force of the first particle involved in the interaction |
| particle2 | the index within this Force of the second particle involved in the interaction |
| thole | the Thole screening factor |
References simtk.openmm.openmm.stripUnits().
| def updateParametersInContext | ( | self, | |
| args | |||
| ) |
updateParametersInContext(DrudeForce self, Context context)
Update the particle and screened pair 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 setParticleParameters() and setScreenedPairParameters() to modify this object's parameters, then call updateParametersInContext() to copy them over to the Context.
This method has several limitations. It can be used to modify the numeric parameters associated with a particle or screened pair (polarizability, thole, etc.), but not the identities of the particles they involve. It also cannot be used to add new particles or screenedPairs, only to change the parameters of existing ones.
References simtk.openmm.openmm.stripUnits().
| def usesPeriodicBoundaryConditions | ( | self, | |
| args | |||
| ) |
usesPeriodicBoundaryConditions(DrudeForce self) -> bool
Returns whether or not this force makes use of periodic boundary conditions.
References simtk.openmm.openmm.stripUnits().
| this |
Referenced by System.__init__().
1.8.8 
