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OpenMM
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OpenMM
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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 | __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 | __copy__ |
| def | __deepcopy__ |
Public Attributes | |
| this | |
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, step, delta. 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.
| def __init__ | ( | self, | |
| args | |||
| ) |
init(OpenMM::CustomExternalForce self, std::string const & energy) -> CustomExternalForce init(OpenMM::CustomExternalForce self, CustomExternalForce other) -> CustomExternalForce
Create a CustomExternalForce.
| 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().
| 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.
| 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.
| 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().
| def addPerParticleParameter | ( | self, | |
| args | |||
| ) |
addPerParticleParameter(CustomExternalForce self, std::string const & name) -> int
Add a new per-particle parameter that the force may depend on.
| name | the name of the parameter |
References simtk.openmm.openmm.stripUnits().
| def getEnergyFunction | ( | self | ) |
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.
| 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.
| index | the index of the parameter for which to get the name |
References simtk.openmm.openmm.stripUnits().
| def getNumGlobalParameters | ( | self | ) |
getNumGlobalParameters(CustomExternalForce self) -> int
Get the number of global parameters that the force depends on.
References simtk.openmm.openmm.stripUnits().
| def getNumParticles | ( | self | ) |
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 | ) |
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.
| 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.
| 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.
| 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.
| 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.
| 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.
| 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 updateParametersInState() 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().
| this |
Referenced by System.__init__().
1.8.6