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CustomCompoundBondForce Class Reference

This class supports a wide variety of bonded interactions. More...

#include <CustomCompoundBondForce.h>

+ Inheritance diagram for CustomCompoundBondForce:

Public Member Functions

 CustomCompoundBondForce (int numParticles, const std::string &energy)
 Create a CustomCompoundBondForce.
 
int getNumParticlesPerBond () const
 Get the number of particles used to define each bond.
 
int getNumBonds () const
 Get the number of bonds for which force field parameters have been defined.
 
int getNumPerBondParameters () const
 Get the number of per-bond parameters that the interaction depends on.
 
int getNumGlobalParameters () const
 Get the number of global parameters that the interaction depends on.
 
int getNumFunctions () const
 Get the number of tabulated functions that have been defined.
 
const std::string & getEnergyFunction () const
 Get the algebraic expression that gives the interaction energy of each bond.
 
void setEnergyFunction (const std::string &energy)
 Set the algebraic expression that gives the interaction energy of each bond.
 
int addPerBondParameter (const std::string &name)
 Add a new per-bond parameter that the interaction may depend on.
 
const std::string & getPerBondParameterName (int index) const
 Get the name of a per-bond parameter.
 
void setPerBondParameterName (int index, const std::string &name)
 Set the name of a per-bond 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 addBond (const std::vector< int > &particles, const std::vector< double > &parameters)
 Add a bond to the force.
 
void getBondParameters (int index, std::vector< int > &particles, std::vector< double > &parameters) const
 Get the properties of a bond.
 
void setBondParameters (int index, const std::vector< int > &particles, const std::vector< double > &parameters)
 Set the properties of a bond.
 
int addFunction (const std::string &name, const std::vector< double > &values, double min, double max)
 Add a tabulated function that may appear in the energy expression.
 
void getFunctionParameters (int index, std::string &name, std::vector< double > &values, double &min, double &max) const
 Get the parameters for a tabulated function that may appear in the energy expression.
 
void setFunctionParameters (int index, const std::string &name, const std::vector< double > &values, double min, double max)
 Set the parameters for a tabulated function that may appear in algebraic expressions.
 
void updateParametersInContext (Context &context)
 Update the per-bond 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 supports a wide variety of bonded interactions.

It defines a "bond" as a single energy term that depends on the positions of a fixed set of particles. The number of particles involved in a bond, and how the energy depends on their positions, is configurable. It may depend on the positions of individual particles, the distances between pairs of particles, the angles formed by sets of three particles, and the dihedral angles formed by sets of four particles.

We refer to the particles in a bond as p1, p2, p3, etc. For each bond, CustomCompoundBondForce evaluates a user supplied algebraic expression to determine the interaction energy. The expression may depend on the following variables and functions:

  • x1, y1, z1, x2, y2, z2, etc.: The x, y, and z coordinates of the particle positions. For example, x1 is the x coordinate of particle p1, and y3 is the y coordinate of particle p3.
  • distance(p1, p2): the distance between particles p1 and p2 (where "p1" and "p2" may be replaced by the names of whichever particles you want to calculate the distance between).
  • angle(p1, p2, p3): the angle formed by the three specified particles.
  • dihedral(p1, p2, p3, p4): the dihedral angle formed by the four specified particles.

The expression also may involve tabulated functions, and may depend on arbitrary global and per-bond parameters.

To use this class, create a CustomCompoundBondForce object, passing an algebraic expression to the constructor that defines the interaction energy of each bond. Then call addPerBondParameter() to define per-bond parameters and addGlobalParameter() to define global parameters. The values of per-bond parameters are specified as part of the system definition, while values of global parameters may be modified during a simulation by calling Context::setParameter().

Next, call addBond() to define bonds and specify their parameter values. After a bond has been added, you can modify its parameters by calling setBondParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

As an example, the following code creates a CustomCompoundBondForce that implements a Urey-Bradley potential. This is an interaction between three particles that depends on the angle formed by p1-p2-p3, and on the distance between p1 and p3.

CustomCompoundBondForce* force = new CustomCompoundBondForce(3, "0.5*(kangle*(angle(p1,p2,p3)-theta0)^2+kbond*(distance(p1,p3)-r0)^2)");

This force depends on four parameters: kangle, kbond, theta0, and r0. The following code defines these as per-bond parameters:

force->addPerBondParameter("kangle");
force->addPerBondParameter("kbond");
force->addPerBondParameter("theta0");
force->addPerBondParameter("r0");

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.

In addition, you can call addFunction() to define a new function based on tabulated values. You specify a vector of values, and a natural spline is created from them. That function can then appear in the expression.

Constructor & Destructor Documentation

CustomCompoundBondForce ( int  numParticles,
const std::string &  energy 
)
explicit

Create a CustomCompoundBondForce.

Parameters
numParticlesthe number of particles used to define each bond
energyan algebraic expression giving the interaction energy of each bond as a function of particle positions, inter-particle distances, angles, and dihedrals, and any global and per-bond parameters

Member Function Documentation

int addBond ( const std::vector< int > &  particles,
const std::vector< double > &  parameters 
)

Add a bond to the force.

Parameters
particlesthe indices of the particles the bond depends on
parametersthe list of per-bond parameter values for the new bond
Returns
the index of the bond that was added
int addFunction ( const std::string &  name,
const std::vector< double > &  values,
double  min,
double  max 
)

Add a tabulated function that may appear in the energy expression.

Parameters
namethe name of the function as it appears in expressions
valuesthe tabulated values of the function f(x) at uniformly spaced values of x between min and max. The function is assumed to be zero for x < min or x > max.
minthe value of the independent variable corresponding to the first element of values
maxthe value of the independent variable corresponding to the last element of values
Returns
the index of the function that was added
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 addPerBondParameter ( const std::string &  name)

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

Parameters
namethe name of the parameter
Returns
the index of the parameter 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.

void getBondParameters ( int  index,
std::vector< int > &  particles,
std::vector< double > &  parameters 
) const

Get the properties of a bond.

Parameters
indexthe index of the bond to get
particlesthe indices of the particles in the bond
parametersthe list of per-bond parameter values for the bond
const std::string& getEnergyFunction ( ) const

Get the algebraic expression that gives the interaction energy of each bond.

void getFunctionParameters ( int  index,
std::string &  name,
std::vector< double > &  values,
double &  min,
double &  max 
) const

Get the parameters for a tabulated function that may appear in the energy expression.

Parameters
indexthe index of the function for which to get parameters
namethe name of the function as it appears in expressions
valuesthe tabulated values of the function f(x) at uniformly spaced values of x between min and max. The function is assumed to be zero for x < min or x > max.
minthe value of the independent variable corresponding to the first element of values
maxthe value of the independent variable corresponding to the last element of values
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 getNumBonds ( ) const
inline

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

int getNumFunctions ( ) const
inline

Get the number of tabulated functions that have been defined.

int getNumGlobalParameters ( ) const
inline

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

int getNumParticlesPerBond ( ) const
inline

Get the number of particles used to define each bond.

int getNumPerBondParameters ( ) const
inline

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

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

Get the name of a per-bond parameter.

Parameters
indexthe index of the parameter for which to get the name
Returns
the parameter name
void setBondParameters ( int  index,
const std::vector< int > &  particles,
const std::vector< double > &  parameters 
)

Set the properties of a bond.

Parameters
indexthe index of the bond group to set
particlesthe indices of the particles in the bond
parametersthe list of per-bond parameter values for the bond
void setEnergyFunction ( const std::string &  energy)

Set the algebraic expression that gives the interaction energy of each bond.

void setFunctionParameters ( int  index,
const std::string &  name,
const std::vector< double > &  values,
double  min,
double  max 
)

Set the parameters for a tabulated function that may appear in algebraic expressions.

Parameters
indexthe index of the function for which to set parameters
namethe name of the function as it appears in expressions
valuesthe tabulated values of the function f(x) at uniformly spaced values of x between min and max. The function is assumed to be zero for x < min or x > max.
minthe value of the independent variable corresponding to the first element of values
maxthe value of the independent variable corresponding to the last element of values
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 setPerBondParameterName ( int  index,
const std::string &  name 
)

Set the name of a per-bond parameter.

Parameters
indexthe index of the parameter for which to set the name
namethe name of the parameter
void updateParametersInContext ( Context context)

Update the per-bond 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 setBondParameters() 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-bond 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 bond cannot be changed, nor can new bonds be added.


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