CustomAngleForce¶
-
class
OpenMM::
CustomAngleForce
¶ This class implements interactions between sets of three particles that depend on the angle between them. Unlike
HarmonicAngleForce
, the functional form of the interaction is completely customizable, and may involve arbitrary algebraic expressions. In addition to the angle formed by the particles, it may depend on arbitrary global and per-angle parameters.To use this class, create a
CustomAngleForce()
object, passing an algebraic expression to the constructor that defines the interaction energy between each set of particles. The expression may depend on theta, the angle formed by the particles, as well as on any parameters you choose. Then calladdPerAngleParameter()
to define per-angle parameters, andaddGlobalParameter()
to define global parameters. The values of per-angle parameters are specified as part of the system definition, while values of global parameters may be modified during a simulation by callingContext::setParameter()
. Finally, calladdAngle()
once for each angle. After an angle has been added, you can modify its parameters by callingsetAngleParameters()
. This will have no effect on Contexts that already exist unless you callupdateParametersInContext()
.As an example, the following code creates a
CustomAngleForce()
that implements a harmonic potential:CustomAngleForce* force = new CustomAngleForce("0.5*k*(theta-theta0)^2");
This force depends on two parameters: the spring constant k and equilibrium angle theta0. The following code defines these parameters:
force->addPerAngleParameter("k"); force->addPerAngleParameter("theta0");
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.
Methods
CustomAngleForce()
Create a CustomAngleForce()
.getNumAngles()
Get the number of angles for which force field parameters have been defined. getNumPerAngleParameters()
Get the number of per-angle parameters that the interaction depends on. getNumGlobalParameters()
Get the number of global parameters that the interaction depends on. getEnergyFunction()
Get the algebraic expression that gives the interaction energy for each angle setEnergyFunction()
Set the algebraic expression that gives the interaction energy for each angle addPerAngleParameter()
Add a new per-angle parameter that the interaction may depend on. getPerAngleParameterName()
Get the name of a per-angle parameter. setPerAngleParameterName()
Set the name of a per-angle parameter. addGlobalParameter()
Add a new global parameter that the interaction may depend on. getGlobalParameterName()
Get the name of a global parameter. setGlobalParameterName()
Set the name of a global parameter. getGlobalParameterDefaultValue()
Get the default value of a global parameter. setGlobalParameterDefaultValue()
Set the default value of a global parameter. addAngle()
Add an angle term to the force field. getAngleParameters()
Get the force field parameters for an angle term. setAngleParameters()
Set the force field parameters for an angle term. updateParametersInContext()
Update the per-angle parameters in a Context
to match those stored in thisForce
object.usesPeriodicBoundaryConditions()
Returns whether or not this force makes use of periodic boundary conditions. -
CustomAngleForce
(const std::string &energy)¶ Create a
CustomAngleForce()
.Parameters: - energy – an algebraic expression giving the interaction energy between three particles as a function of theta, the angle between them
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int
getNumAngles
() const¶ Get the number of angles for which force field parameters have been defined.
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int
getNumPerAngleParameters
() const¶ Get the number of per-angle parameters that the interaction depends on.
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int
getNumGlobalParameters
() const¶ Get the number of global parameters that the interaction depends on.
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const std::string &
getEnergyFunction
() const¶ Get the algebraic expression that gives the interaction energy for each angle
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void
setEnergyFunction
(const std::string &energy)¶ Set the algebraic expression that gives the interaction energy for each angle
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int
addPerAngleParameter
(const std::string &name)¶ Add a new per-angle parameter that the interaction may depend on.
Parameters: - name – the name of the parameter
Returns: the index of the parameter that was added
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const std::string &
getPerAngleParameterName
(int index) const¶ Get the name of a per-angle parameter.
Parameters: - index – the index of the parameter for which to get the name
Returns: the parameter name
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void
setPerAngleParameterName
(int index, const std::string &name)¶ Set the name of a per-angle parameter.
Parameters: - index – the index of the parameter for which to set the name
- name – the name of the parameter
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int
addGlobalParameter
(const std::string &name, double defaultValue)¶ Add a new global parameter that the interaction may depend on.
Parameters: - name – the name of the parameter
- defaultValue – the default value of the parameter
Returns: the index of the parameter that was added
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const std::string &
getGlobalParameterName
(int index) const¶ Get the name of a global parameter.
Parameters: - index – the index of the parameter for which to get the name
Returns: the parameter name
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void
setGlobalParameterName
(int index, const std::string &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
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double
getGlobalParameterDefaultValue
(int index) const¶ Get the default value of a global parameter.
Parameters: - index – the index of the parameter for which to get the default value
Returns: the parameter default value
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void
setGlobalParameterDefaultValue
(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
- defaultValue – the default value of the parameter
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int
addAngle
(int particle1, int particle2, int particle3, const std::vector<double> ¶meters = std::vector< double >())¶ Add an angle term to the force field.
Parameters: - particle1 – the index of the first particle connected by the angle
- particle2 – the index of the second particle connected by the angle
- particle3 – the index of the third particle connected by the angle
- parameters – the list of parameters for the new angle
Returns: the index of the angle that was added
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void
getAngleParameters
(int index, int &particle1, int &particle2, int &particle3, std::vector<double> ¶meters) const¶ Get the force field parameters for an angle term.
Parameters: - index – the index of the angle for which to get parameters
- particle1 – [out] the index of the first particle connected by the angle
- particle2 – [out] the index of the second particle connected by the angle
- particle3 – [out] the index of the third particle connected by the angle
- parameters – [out] the list of parameters for the angle
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void
setAngleParameters
(int index, int particle1, int particle2, int particle3, const std::vector<double> ¶meters = std::vector< double >())¶ Set the force field parameters for an angle term.
Parameters: - index – the index of the angle for which to set parameters
- particle1 – the index of the first particle connected by the angle
- particle2 – the index of the second particle connected by the angle
- particle3 – the index of the third particle connected by the angle
- parameters – the list of parameters for the angle
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void
updateParametersInContext
(Context &context)¶ Update the per-angle 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 callsetAngleParameters()
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 values of per-angle parameters. All other aspects of the
Force
(such as the energy function) are unaffected and can only be changed by reinitializing theContext
. The set of particles involved in a angle cannot be changed, nor can new angles be added.
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bool
usesPeriodicBoundaryConditions
() const¶ Returns whether or not this force makes use of periodic boundary conditions.
Returns: false
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