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
ForceImpl *	createImpl ()
	When a Context is created, it invokes this method on each Force in the System.
Protected Member Functions inherited from Force
ForceImpl &	getImplInContext (Context &context)
	Get the ForceImpl corresponding to this Force in a Context.
ContextImpl &	getContextImpl (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

numParticles	the number of particles used to define each bond
energy	an 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

particles	the indices of the particles the bond depends on
parameters	the 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

name	the name of the function as it appears in expressions
values	the 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.
min	the value of the independent variable corresponding to the first element of values
max	the 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

name	the name of the parameter
defaultValue	the 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

name	the name of the parameter

Returns

the index of the parameter that was added

ForceImpl* createImpl ( )

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

index	the index of the bond to get
particles	the indices of the particles in the bond
parameters	the 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

index	the index of the function for which to get parameters
name	the name of the function as it appears in expressions
values	the 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.
min	the value of the independent variable corresponding to the first element of values
max	the 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

index

the 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

index

the 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

index

the 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

index	the index of the bond group to set
particles	the indices of the particles in the bond
parameters	the 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

index	the index of the function for which to set parameters
name	the name of the function as it appears in expressions
values	the 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.
min	the value of the independent variable corresponding to the first element of values
max	the 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

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

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

void setPerBondParameterName	(	int	index,
		const std::string &	name
	)

Set the name of a per-bond parameter.

Parameters

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

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

• CustomCompoundBondForce.h