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CustomTorsionForce Class Reference

This class implements interactions between sets of four particles that depend on the torsion angle between them. More...

#include <CustomTorsionForce.h>

+ Inheritance diagram for CustomTorsionForce:

Public Member Functions

 CustomTorsionForce (const std::string &energy)
 Create a CustomTorsionForce.
 
int getNumTorsions () const
 Get the number of torsions for which force field parameters have been defined.
 
int getNumPerTorsionParameters () const
 Get the number of per-torsion parameters that the interaction depends on.
 
int getNumGlobalParameters () const
 Get the number of global parameters that the interaction depends on.
 
const std::string & getEnergyFunction () const
 Get the algebraic expression that gives the interaction energy for each torsion.
 
void setEnergyFunction (const std::string &energy)
 Set the algebraic expression that gives the interaction energy for each torsion.
 
int addPerTorsionParameter (const std::string &name)
 Add a new per-torsion parameter that the interaction may depend on.
 
const std::string & getPerTorsionParameterName (int index) const
 Get the name of a per-torsion parameter.
 
void setPerTorsionParameterName (int index, const std::string &name)
 Set the name of a per-torsion parameter.
 
int addGlobalParameter (const std::string &name, double defaultValue)
 Add a new global parameter that the interaction may depend on.
 
const std::string & getGlobalParameterName (int index) const
 Get the name of a global parameter.
 
void setGlobalParameterName (int index, const std::string &name)
 Set the name of a global parameter.
 
double getGlobalParameterDefaultValue (int index) const
 Get the default value of a global parameter.
 
void setGlobalParameterDefaultValue (int index, double defaultValue)
 Set the default value of a global parameter.
 
int addTorsion (int particle1, int particle2, int particle3, int particle4, const std::vector< double > &parameters)
 Add a torsion term to the force field.
 
void getTorsionParameters (int index, int &particle1, int &particle2, int &particle3, int &particle4, std::vector< double > &parameters) const
 Get the force field parameters for a torsion term.
 
void setTorsionParameters (int index, int particle1, int particle2, int particle3, int particle4, const std::vector< double > &parameters)
 Set the force field parameters for a torsion term.
 
void updateParametersInContext (Context &context)
 Update the per-torsion parameters in a Context to match those stored in this Force object.
 
- Public Member Functions inherited from Force
 Force ()
 
virtual ~Force ()
 
int getForceGroup () const
 Get the force group this Force belongs to.
 
void setForceGroup (int group)
 Set the force group this Force belongs to.
 

Protected Member Functions

ForceImplcreateImpl () const
 When a Context is created, it invokes this method on each Force in the System.
 
- Protected Member Functions inherited from Force
ForceImplgetImplInContext (Context &context)
 Get the ForceImpl corresponding to this Force in a Context.
 
ContextImplgetContextImpl (Context &context)
 Get the ContextImpl corresponding to a Context.
 

Detailed Description

This class implements interactions between sets of four particles that depend on the torsion angle between them.

Unlike PeriodicTorsionForce, 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-torsion parameters.

To use this class, create a CustomTorsionForce 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 torsion angle formed by the particles, as well as on any parameters you choose. Then call addPerTorsionParameter() to define per-torsion parameters, and addGlobalParameter() to define global parameters. The values of per-torsion 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 addTorsion() once for each torsion. After an torsion has been added, you can modify its parameters by calling setTorsionParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

As an example, the following code creates a CustomTorsionForce that implements a harmonic potential:

CustomTorsionForce* force = new CustomTorsionForce("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->addPerTorsionParameter("k");
force->addPerTorsionParameter("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, 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.

Constructor & Destructor Documentation

CustomTorsionForce ( const std::string &  energy)
explicit

Create a CustomTorsionForce.

Parameters
energyan algebraic expression giving the interaction energy between three particles as a function of theta, the torsion angle between them

Member Function Documentation

int addGlobalParameter ( const std::string &  name,
double  defaultValue 
)

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

Parameters
namethe name of the parameter
defaultValuethe default value of the parameter
Returns
the index of the parameter that was added
int addPerTorsionParameter ( const std::string &  name)

Add a new per-torsion parameter that the interaction may depend on.

Parameters
namethe name of the parameter
Returns
the index of the parameter that was added
int addTorsion ( int  particle1,
int  particle2,
int  particle3,
int  particle4,
const std::vector< double > &  parameters 
)

Add a torsion term to the force field.

Parameters
particle1the index of the first particle connected by the torsion
particle2the index of the second particle connected by the torsion
particle3the index of the third particle connected by the torsion
particle4the index of the fourth particle connected by the torsion
parametersthe list of parameters for the new torsion
Returns
the index of the torsion that was added
ForceImpl* createImpl ( ) const
protectedvirtual

When a Context is created, it invokes this method on each Force in the System.

It should create a new ForceImpl object which can be used by the context for calculating forces. The ForceImpl will be deleted automatically when the Context is deleted.

Implements Force.

const std::string& getEnergyFunction ( ) const

Get the algebraic expression that gives the interaction energy for each torsion.

double getGlobalParameterDefaultValue ( int  index) const

Get the default value of a global parameter.

Parameters
indexthe index of the parameter for which to get the default value
Returns
the parameter default value
const std::string& getGlobalParameterName ( int  index) const

Get the name of a global parameter.

Parameters
indexthe index of the parameter for which to get the name
Returns
the parameter name
int getNumGlobalParameters ( ) const
inline

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

int getNumPerTorsionParameters ( ) const
inline

Get the number of per-torsion parameters that the interaction depends on.

int getNumTorsions ( ) const
inline

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

const std::string& getPerTorsionParameterName ( int  index) const

Get the name of a per-torsion parameter.

Parameters
indexthe index of the parameter for which to get the name
Returns
the parameter name
void getTorsionParameters ( int  index,
int &  particle1,
int &  particle2,
int &  particle3,
int &  particle4,
std::vector< double > &  parameters 
) const

Get the force field parameters for a torsion term.

Parameters
indexthe index of the torsion for which to get parameters
particle1the index of the first particle connected by the torsion
particle2the index of the second particle connected by the torsion
particle3the index of the third particle connected by the torsion
particle4the index of the fourth particle connected by the torsion
parametersthe list of parameters for the torsion
void setEnergyFunction ( const std::string &  energy)

Set the algebraic expression that gives the interaction energy for each torsion.

void setGlobalParameterDefaultValue ( int  index,
double  defaultValue 
)

Set the default value of a global parameter.

Parameters
indexthe index of the parameter for which to set the default value
namethe default value of the parameter
void setGlobalParameterName ( int  index,
const std::string &  name 
)

Set the name of a global parameter.

Parameters
indexthe index of the parameter for which to set the name
namethe name of the parameter
void setPerTorsionParameterName ( int  index,
const std::string &  name 
)

Set the name of a per-torsion parameter.

Parameters
indexthe index of the parameter for which to set the name
namethe name of the parameter
void setTorsionParameters ( int  index,
int  particle1,
int  particle2,
int  particle3,
int  particle4,
const std::vector< double > &  parameters 
)

Set the force field parameters for a torsion term.

Parameters
indexthe index of the torsion for which to set parameters
particle1the index of the first particle connected by the torsion
particle2the index of the second particle connected by the torsion
particle3the index of the third particle connected by the torsion
particle4the index of the fourth particle connected by the torsion
parametersthe list of parameters for the torsion
void updateParametersInContext ( Context context)

Update the per-torsion 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 setTorsionParameters() 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-torsion parameters. All other aspects of the Force (such as the energy function) are unaffected and can only be changed by reinitializing the Context. The set of particles involved in a torsion cannot be changed, nor can new torsions be added.


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