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CustomExternalForce Class Reference

This class implements an "external" force on particles. More...

Inheritance diagram for CustomExternalForce:

## Public Member Functions

def | getNumParticles
| getNumParticles(CustomExternalForce self) -> int More...
def | getNumPerParticleParameters
| getNumPerParticleParameters(CustomExternalForce self) -> int More...
def | getNumGlobalParameters
| getNumGlobalParameters(CustomExternalForce self) -> int More...
def | getEnergyFunction
| getEnergyFunction(CustomExternalForce self) -> std::string const & More...
def | setEnergyFunction
| setEnergyFunction(CustomExternalForce self, std::string const & energy) More...
def | addPerParticleParameter
| addPerParticleParameter(CustomExternalForce self, std::string const & name) -> int More...
def | getPerParticleParameterName
| getPerParticleParameterName(CustomExternalForce self, int index) -> std::string const & More...
def | setPerParticleParameterName
| setPerParticleParameterName(CustomExternalForce self, int index, std::string const & name) More...
def | addGlobalParameter
| addGlobalParameter(CustomExternalForce self, std::string const & name, double defaultValue) -> int More...
def | getGlobalParameterName
| getGlobalParameterName(CustomExternalForce self, int index) -> std::string const & More...
def | setGlobalParameterName
| setGlobalParameterName(CustomExternalForce self, int index, std::string const & name) More...
def | getGlobalParameterDefaultValue
| getGlobalParameterDefaultValue(CustomExternalForce self, int index) -> double More...
def | setGlobalParameterDefaultValue
| setGlobalParameterDefaultValue(CustomExternalForce self, int index, double defaultValue) More...
def | addParticle
| addParticle(CustomExternalForce self, int particle, vectord parameters) -> int More...
def | getParticleParameters
| getParticleParameters(CustomExternalForce self, int index) More...
def | setParticleParameters
| setParticleParameters(CustomExternalForce self, int index, int particle, vectord parameters) More...
def | updateParametersInContext
| updateParametersInContext(CustomExternalForce self, Context context) More...
def | usesPeriodicBoundaryConditions
| usesPeriodicBoundaryConditions(CustomExternalForce self) -> bool More...
def | __init__
| init(OpenMM::CustomExternalForce self, std::string const & energy) -> CustomExternalForce init(OpenMM::CustomExternalForce self, CustomExternalForce other) -> CustomExternalForce More...
def | __del__
| del(OpenMM::CustomExternalForce 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

## Detailed Description

This class implements an "external" force on particles.

The force may be applied to any subset of the particles in the System. The force on each particle is specified by an arbitrary algebraic expression, which may depend on the current position of the particle as well as on arbitrary global and per-particle parameters.

To use this class, create a CustomExternalForce object, passing an algebraic expression to the constructor that defines the potential energy of each affected particle. The expression may depend on the particle's x, y, and z coordinates, as well as on any parameters you choose. Then call addPerParticleParameter() to define per-particle parameters, and addGlobalParameter() to define global parameters. The values of per-particle parameters are specified as part of the system definition, while values of global parameters may be modified during a simulation by calling Context::setParameter(). Finally, call addParticle() once for each particle that should be affected by the force. After a particle has been added, you can modify its parameters by calling setParticleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

As an example, the following code creates a CustomExternalForce that attracts each particle to a target position (x0, y0, z0) via a harmonic potential:

`CustomExternalForce* force = new CustomExternalForce("k*((x-x0)^2+(y-y0)^2+(z-z0)^2)");`

This force depends on four parameters: the spring constant k and equilibrium coordinates x0, y0, and z0. The following code defines these parameters:

``

    force->addGlobalParameter("k", 100.0);
    force->addPerParticleParameter("x0");
    force->addPerParticleParameter("y0");
    force->addPerParticleParameter("z0");

Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select. All trigonometric functions are defined in radians, and log is the natural logarithm. step(x) = 0 if x is less than 0, 1 otherwise. delta(x) = 1 if x is 0, 0 otherwise. select(x,y,z) = z if x = 0, y otherwise.

## Constructor & Destructor Documentation

def __init__ | ( |  | self,
|  |  | args
| ) |  |

init(OpenMM::CustomExternalForce self, std::string const & energy) -> CustomExternalForce init(OpenMM::CustomExternalForce self, CustomExternalForce other) -> CustomExternalForce

Create a CustomExternalForce.

Parameters

  energy | an algebraic expression giving the potential energy of each particle as a function of its x, y, and z coordinates

References simtk.openmm.openmm.stripUnits().

def __del__ | ( |  | self | ) |

del(OpenMM::CustomExternalForce self)

References simtk.openmm.openmm.stripUnits().

## Member Function Documentation

def addGlobalParameter | ( |  | self,
|  |  | args
| ) |  |

addGlobalParameter(CustomExternalForce self, std::string const & name, double defaultValue) -> int

Add a new global parameter that the force may depend on.

Parameters

  name | the name of the parameter
  defaultValue | the default value of the parameter

References simtk.openmm.openmm.stripUnits().

def addParticle | ( |  | self,
|  |  | args
| ) |  |

addParticle(CustomExternalForce self, int particle, vectord parameters) -> int

Add a particle term to the force field.

Parameters

  particle | the index of the particle this term is applied to
  parameters | the list of parameters for the new force term

References simtk.openmm.openmm.stripUnits().

Referenced by NonbondedForce.addParticle_usingRVdw().

def addPerParticleParameter | ( |  | self,
|  |  | args
| ) |  |

addPerParticleParameter(CustomExternalForce self, std::string const & name) -> int

Add a new per-particle parameter that the force may depend on.

Parameters

  name | the name of the parameter

References simtk.openmm.openmm.stripUnits().

def getEnergyFunction | ( |  | self,
|  |  | args
| ) |  |

getEnergyFunction(CustomExternalForce self) -> std::string const &

Get the algebraic expression that gives the potential energy of each particle

References simtk.openmm.openmm.stripUnits().

def getGlobalParameterDefaultValue | ( |  | self,
|  |  | args
| ) |  |

getGlobalParameterDefaultValue(CustomExternalForce self, int index) -> double

Get the default value of a global parameter.

Parameters

  index | the index of the parameter for which to get the default value

References simtk.openmm.openmm.stripUnits().

def getGlobalParameterName | ( |  | self,
|  |  | args
| ) |  |

getGlobalParameterName(CustomExternalForce self, int index) -> std::string const &

Get the name of a global parameter.

Parameters

  index | the index of the parameter for which to get the name

References simtk.openmm.openmm.stripUnits().

def getNumGlobalParameters | ( |  | self,
|  |  | args
| ) |  |

getNumGlobalParameters(CustomExternalForce self) -> int

Get the number of global parameters that the force depends on.

References simtk.openmm.openmm.stripUnits().

def getNumParticles | ( |  | self,
|  |  | args
| ) |  |

getNumParticles(CustomExternalForce self) -> int

Get the number of particles for which force field parameters have been defined.

References simtk.openmm.openmm.stripUnits().

def getNumPerParticleParameters | ( |  | self,
|  |  | args
| ) |  |

getNumPerParticleParameters(CustomExternalForce self) -> int

Get the number of per-particle parameters that the force depends on

References simtk.openmm.openmm.stripUnits().

def getParticleParameters | ( |  | self,
|  |  | args
| ) |  |

getParticleParameters(CustomExternalForce self, int index)

Get the force field parameters for a force field term.

Parameters

  index | the index of the particle term for which to get parameters
  particle | the index of the particle this term is applied to
  parameters | the list of parameters for the force field term

References simtk.openmm.openmm.stripUnits().

def getPerParticleParameterName | ( |  | self,
|  |  | args
| ) |  |

getPerParticleParameterName(CustomExternalForce self, int index) -> std::string const &

Get the name of a per-particle parameter.

Parameters

  index | the index of the parameter for which to get the name

References simtk.openmm.openmm.stripUnits().

def setEnergyFunction | ( |  | self,
|  |  | args
| ) |  |

setEnergyFunction(CustomExternalForce self, std::string const & energy)

Set the algebraic expression that gives the potential energy of each particle

References simtk.openmm.openmm.stripUnits().

def setGlobalParameterDefaultValue | ( |  | self,
|  |  | args
| ) |  |

setGlobalParameterDefaultValue(CustomExternalForce self, int index, double defaultValue)

Set the default value of a global parameter.

Parameters

  index | the index of the parameter for which to set the default value
  name | the default value of the parameter

References simtk.openmm.openmm.stripUnits().

def setGlobalParameterName | ( |  | self,
|  |  | args
| ) |  |

setGlobalParameterName(CustomExternalForce self, int index, std::string const & name)

Set the name of a global parameter.

Parameters

  index | the index of the parameter for which to set the name
  name | the name of the parameter

References simtk.openmm.openmm.stripUnits().

def setParticleParameters | ( |  | self,
|  |  | args
| ) |  |

setParticleParameters(CustomExternalForce self, int index, int particle, vectord parameters)

Set the force field parameters for a force field term.

Parameters

  index | the index of the particle term for which to set parameters
  particle | the index of the particle this term is applied to
  parameters | the list of parameters for the force field term

References simtk.openmm.openmm.stripUnits().

def setPerParticleParameterName | ( |  | self,
|  |  | args
| ) |  |

setPerParticleParameterName(CustomExternalForce self, int index, std::string const & name)

Set the name of a per-particle parameter.

Parameters

  index | the index of the parameter for which to set the name
  name | the name of the parameter

References simtk.openmm.openmm.stripUnits().

def updateParametersInContext | ( |  | self,
|  |  | args
| ) |  |

updateParametersInContext(CustomExternalForce self, Context context)

Update the per-particle 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() 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 values of per-particle parameters. All other aspects of the Force (such as the energy function) are unaffected and can only be changed by reinitializing the Context. Also, this method cannot be used to add new particles, only to change the parameters of existing ones.

References simtk.openmm.openmm.stripUnits().

def usesPeriodicBoundaryConditions | ( |  | self,
|  |  | args
| ) |  |

usesPeriodicBoundaryConditions(CustomExternalForce self) -> bool

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

References simtk.openmm.openmm.stripUnits().

## Member Data Documentation

this

Referenced by System.__init__().

The documentation for this class was generated from the following file:

- openmm.py