CustomNonbondedForce Class Reference

This class implements nonbonded interactions between particles. More...

#include <CustomNonbondedForce.h>

Inheritance diagram for CustomNonbondedForce:

List of all members.

Classes
class	ExclusionInfo
	This is an internal class used to record information about an exclusion.
class	FunctionInfo
	This is an internal class used to record information about a tabulated function.
class	GlobalParameterInfo
	This is an internal class used to record information about a global parameter.
class	ParticleInfo
	This is an internal class used to record information about a particle.
class	PerParticleParameterInfo
	This is an internal class used to record information about a per-particle parameter.
Public Types
enum	NonbondedMethod { NoCutoff = 0, CutoffNonPeriodic = 1, CutoffPeriodic = 2 }
	This is an enumeration of the different methods that may be used for handling long range nonbonded forces. More...
Public Member Functions
	CustomNonbondedForce (const std::string &energy)
	Create a CustomNonbondedForce.
int	getNumParticles () const
	Get the number of particles for which force field parameters have been defined.
int	getNumExclusions () const
	Get the number of particle pairs whose interactions should be excluded.
int	getNumPerParticleParameters () const
	Get the number of per-particle 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 between two particles.
void	setEnergyFunction (const std::string &energy)
	Set the algebraic expression that gives the interaction energy between two particles.
NonbondedMethod	getNonbondedMethod () const
	Get the method used for handling long range nonbonded interactions.
void	setNonbondedMethod (NonbondedMethod method)
	Set the method used for handling long range nonbonded interactions.
double	getCutoffDistance () const
	Get the cutoff distance (in nm) being used for nonbonded interactions.
void	setCutoffDistance (double distance)
	Set the cutoff distance (in nm) being used for nonbonded interactions.
int	addPerParticleParameter (const std::string &name)
	Add a new per-particle parameter that the interaction may depend on.
const std::string &	getPerParticleParameterName (int index) const
	Get the name of a per-particle parameter.
void	setPerParticleParameterName (int index, const std::string &name)
	Set the name of a per-particle 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	addParticle (const std::vector< double > &parameters)
	Add the nonbonded force parameters for a particle.
void	getParticleParameters (int index, std::vector< double > &parameters) const
	Get the nonbonded force parameters for a particle.
void	setParticleParameters (int index, const std::vector< double > &parameters)
	Set the nonbonded force parameters for a particle.
int	addExclusion (int particle1, int particle2)
	Add a particle pair to the list of interactions that should be excluded.
void	getExclusionParticles (int index, int &particle1, int &particle2) const
	Get the particles in a pair whose interaction should be excluded.
void	setExclusionParticles (int index, int particle1, int particle2)
	Set the particles in a pair whose interaction should be excluded.
int	addFunction (const std::string &name, const std::vector< double > &values, double min, double max, bool interpolating)
	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, bool &interpolating) 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, bool interpolating)
	Set the parameters for a tabulated function that may appear in algebraic expressions.
Protected Member Functions
ForceImpl *	createImpl ()
	When a Context is created, it invokes this method on each Force in the System.

---

Detailed Description

This class implements nonbonded interactions between particles.

Unlike NonbondedForce, the functional form of the interaction is completely customizable, and may involve arbitrary algebraic expressions and tabulated functions. It may depend on the distance between particles, as well as on arbitrary global and per-particle parameters. It also optionally supports periodic boundary conditions and cutoffs for long range interactions.

To use this class, create a CustomNonbondedForce object, passing an algebraic expression to the constructor that defines the interaction energy between each pair of particles. The expression may depend on r, the distance between the particles, 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().

Next, call addParticle() once for each particle in the System to set the values of its per-particle parameters. The number of particles for which you set parameters must be exactly equal to the number of particles in the System, or else an exception will be thrown when you try to create a Context. After a particle has been added, you can modify its parameters by calling setParticleParameters().

CustomNonbondedForce also lets you specify "exclusions", particular pairs of particles whose interactions should be omitted from force and energy calculations. This is most often used for particles that are bonded to each other.

As an example, the following code creates a CustomNonbondedForce that implements a 12-6 Lennard-Jones potential:

CustomNonbondedForce* force = new CustomNonbondedForce("4*epsilon*((sigma/r)^12-(sigma/r)^6); sigma=0.5*(sigma1*sigma2); epsilon=sqrt(epsilon1*epsilon2)");

This force depends on two parameters: sigma and epsilon. The following code defines these parameters, and specifies combining rules for them which correspond to the standard Lorentz-Bertelot combining rules:

 force->addPerParticleParameter("sigma");
 force->addPerParticleParameter("epsilon");
 

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, step. All trigonometric functions are defined in radians, and log is the natural logarithm. step(x) = 0 if x is less than 0, 1 otherwise. The names of per-particle parameters have the suffix "1" or "2" appended to them to indicate the values for the two interacting particles. As seen in the above example, the expression may also involve intermediate quantities that are defined following the main expression, using ";" as a separator.

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

---

Member Enumeration Documentation

enum NonbondedMethod

This is an enumeration of the different methods that may be used for handling long range nonbonded forces.

Enumerator:

NoCutoff	No cutoff is applied to nonbonded interactions. The full set of N^2 interactions is computed exactly. This necessarily means that periodic boundary conditions cannot be used. This is the default.
CutoffNonPeriodic	Interactions beyond the cutoff distance are ignored.
CutoffPeriodic	Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic copy of each other particle. Interactions beyond the cutoff distance are ignored.

---

Constructor & Destructor Documentation

CustomNonbondedForce

(

const std::string &

energy

)

Create a CustomNonbondedForce.

Parameters:

energy

an algebraic expression giving the interaction energy between two particles as a function of r, the distance between them, as well as any global and per-particle parameters

---

Member Function Documentation

int addExclusion	(	int	particle1,
		int	particle2
	)

Add a particle pair to the list of interactions that should be excluded.

Parameters:

	particle1	the index of the first particle in the pair
	particle2	the index of the second particle in the pair

Returns:

the index of the exclusion that was added

int addFunction	(	const std::string &	name,
		const std::vector< double > &	values,
		double	min,
		double	max,
		bool	interpolating
	)

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
	interpolating	if true, an interpolating (Catmull-Rom) spline will be used to represent the function. If false, an approximating spline (B-spline) will be used.

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 addParticle

(

const std::vector< double > &

parameters

)

Add the nonbonded force parameters for a particle.

This should be called once for each particle in the System. When it is called for the i'th time, it specifies the parameters for the i'th particle.

Parameters:

parameters

the list of parameters for the new particle

Returns:

the index of the particle that was added

int addPerParticleParameter

(

const std::string &

name

)

Add a new per-particle 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

(

)

[protected, virtual]

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.

double getCutoffDistance

(

)

const

Get the cutoff distance (in nm) being used for nonbonded interactions.

If the NonbondedMethod in use is NoCutoff, this value will have no effect.

Returns:

the cutoff distance, measured in nm

const std::string& getEnergyFunction

(

)

const

Get the algebraic expression that gives the interaction energy between two particles.

void getExclusionParticles	(	int	index,
		int &	particle1,
		int &	particle2
	)			const

Get the particles in a pair whose interaction should be excluded.

Parameters:

	index	the index of the exclusion for which to get particle indices
	particle1	the index of the first particle in the pair
	particle2	the index of the second particle in the pair

void getFunctionParameters	(	int	index,
		std::string &	name,
		std::vector< double > &	values,
		double &	min,
		double &	max,
		bool &	interpolating
	)			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
	interpolating	if true, an interpolating (Catmull-Rom) spline will be used to represent the function. If false, an approximating spline (B-spline) will be used.

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

NonbondedMethod getNonbondedMethod

(

)

const

Get the method used for handling long range nonbonded interactions.

int getNumExclusions

(

)

const [inline]

Get the number of particle pairs whose interactions should be excluded.

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 getNumParticles

(

)

const [inline]

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

int getNumPerParticleParameters

(

)

const [inline]

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

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

Get the nonbonded force parameters for a particle.

Parameters:

	index	the index of the particle for which to get parameters
	parameters	the list of parameters for the specified particle

const std::string& getPerParticleParameterName

(

int

index

)

const

Get the name of a per-particle parameter.

Parameters:

index

the index of the parameter for which to get the name

Returns:

the parameter name

void setCutoffDistance

(

double

distance

)

Set the cutoff distance (in nm) being used for nonbonded interactions.

If the NonbondedMethod in use is NoCutoff, this value will have no effect.

Parameters:

distance

the cutoff distance, measured in nm

void setEnergyFunction

(

const std::string &

energy

)

Set the algebraic expression that gives the interaction energy between two particles.

void setExclusionParticles	(	int	index,
		int	particle1,
		int	particle2
	)

Set the particles in a pair whose interaction should be excluded.

Parameters:

	index	the index of the exclusion for which to set particle indices
	particle1	the index of the first particle in the pair
	particle2	the index of the second particle in the pair

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

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
	interpolating	if true, an interpolating (Catmull-Rom) spline will be used to represent the function. If false, an approximating spline (B-spline) will be used.

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 setNonbondedMethod

(

NonbondedMethod

method

)

Set the method used for handling long range nonbonded interactions.

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

Set the nonbonded force parameters for a particle.

Parameters:

	index	the index of the particle for which to set parameters
	parameters	the list of parameters for the specified particle

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

Set the name of a per-particle parameter.

Parameters:

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

---

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

• CustomNonbondedForce.h