This class supports a wide variety of nonbonded N-particle interactions, where N is user specified. More...

#include <CustomManyParticleForce.h>

Inheritance diagram for CustomManyParticleForce:

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...

enum	PermutationMode { SinglePermutation = 0, UniqueCentralParticle = 1 }
	This is an enumeration of the different modes for selecting which permutations of a set of particles to evaluate the interaction for. More...

Public Member Functions
	CustomManyParticleForce (int particlesPerSet, const std::string &energy)
	Create a CustomManyParticleForce. More...

	~CustomManyParticleForce ()

int	getNumParticlesPerSet () const
	Get the number of particles in each set for which the energy is evaluated. More...

int	getNumParticles () const
	Get the number of particles for which force field parameters have been defined. More...

int	getNumExclusions () const
	Get the number of particle pairs whose interactions should be excluded. More...

int	getNumPerParticleParameters () const
	Get the number of per-particle parameters that the interaction depends on. More...

int	getNumGlobalParameters () const
	Get the number of global parameters that the interaction depends on. More...

int	getNumTabulatedFunctions () const
	Get the number of tabulated functions that have been defined. More...

const std::string &	getEnergyFunction () const
	Get the algebraic expression that gives the interaction energy of each bond. More...

void	setEnergyFunction (const std::string &energy)
	Set the algebraic expression that gives the interaction energy of each bond. More...

NonbondedMethod	getNonbondedMethod () const
	Get the method used for handling long range nonbonded interactions. More...

void	setNonbondedMethod (NonbondedMethod method)
	Set the method used for handling long range nonbonded interactions. More...

PermutationMode	getPermutationMode () const
	Get the mode that selects which permutations of a set of particles to evaluate the interaction for. More...

void	setPermutationMode (PermutationMode mode)
	Set the mode that selects which permutations of a set of particles to evaluate the interaction for. More...

double	getCutoffDistance () const
	Get the cutoff distance (in nm) being used for nonbonded interactions. More...

void	setCutoffDistance (double distance)
	Set the cutoff distance (in nm) being used for nonbonded interactions. More...

int	addPerParticleParameter (const std::string &name)
	Add a new per-particle parameter that the interaction may depend on. More...

const std::string &	getPerParticleParameterName (int index) const
	Get the name of a per-particle parameter. More...

void	setPerParticleParameterName (int index, const std::string &name)
	Set the name of a per-particle parameter. More...

int	addGlobalParameter (const std::string &name, double defaultValue)
	Add a new global parameter that the interaction may depend on. More...

const std::string &	getGlobalParameterName (int index) const
	Get the name of a global parameter. More...

void	setGlobalParameterName (int index, const std::string &name)
	Set the name of a global parameter. More...

double	getGlobalParameterDefaultValue (int index) const
	Get the default value of a global parameter. More...

void	setGlobalParameterDefaultValue (int index, double defaultValue)
	Set the default value of a global parameter. More...

int	addParticle (const std::vector< double > &parameters, int type=0)
	Add the nonbonded force parameters for a particle. More...

void	getParticleParameters (int index, std::vector< double > &parameters, int &type) const
	Get the nonbonded force parameters for a particle. More...

void	setParticleParameters (int index, const std::vector< double > &parameters, int type)
	Set the nonbonded force parameters for a particle. More...

int	addExclusion (int particle1, int particle2)
	Add a particle pair to the list of interactions that should be excluded. More...

void	getExclusionParticles (int index, int &particle1, int &particle2) const
	Get the particles in a pair whose interaction should be excluded. More...

void	setExclusionParticles (int index, int particle1, int particle2)
	Set the particles in a pair whose interaction should be excluded. More...

void	createExclusionsFromBonds (const std::vector< std::pair< int, int > > &bonds, int bondCutoff)
	Identify exclusions based on the molecular topology. More...

void	getTypeFilter (int index, std::set< int > &types) const
	Get the allowed particle types for one of the particles involved in the interaction. More...

void	setTypeFilter (int index, const std::set< int > &types)
	Set the allowed particle types for one of the particles involved in the interaction. More...

int	addTabulatedFunction (const std::string &name, TabulatedFunction *function)
	Add a tabulated function that may appear in the energy expression. More...

const TabulatedFunction &	getTabulatedFunction (int index) const
	Get a const reference to a tabulated function that may appear in the energy expression. More...

TabulatedFunction &	getTabulatedFunction (int index)
	Get a reference to a tabulated function that may appear in the energy expression. More...

const std::string &	getTabulatedFunctionName (int index) const
	Get the name of a tabulated function that may appear in the energy expression. More...

void	updateParametersInContext (Context &context)
	Update the per-particle parameters in a Context to match those stored in this Force object. More...

Public Member Functions inherited from Force
	Force ()

virtual	~Force ()

int	getForceGroup () const
	Get the force group this Force belongs to. More...

void	setForceGroup (int group)
	Set the force group this Force belongs to. More...

Protected Member Functions
ForceImpl *	createImpl () const
	When a Context is created, it invokes this method on each Force in the System. More...

Protected Member Functions inherited from Force
ForceImpl &	getImplInContext (Context &context)
	Get the ForceImpl corresponding to this Force in a Context. More...

ContextImpl &	getContextImpl (Context &context)
	Get the ContextImpl corresponding to a Context. More...

Detailed Description

This class supports a wide variety of nonbonded N-particle interactions, where N is user specified.

The interaction energy is determined by an arbitrary, user specified algebraic expression that is evaluated for every possible set of N particles in the system. It may depend on the positions of the 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.

Be aware that the cost of evaluating an N-particle interaction increases very rapidly with N. Values larger than N=3 are rarely used.

We refer to a set of particles for which the energy is being evaluated as p1, p2, p3, etc. The energy 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.
arbitrary global and per-particle parameters that you define.

To use this class, create a CustomManyParticleForce object, passing an algebraic expression to the constructor that defines the interaction energy of each set of particles. 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(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

Multi-particle interactions can be very expensive to evaluate, so they are usually used with a cutoff distance. The exact interpretation of the cutoff depends on the permutation mode, as discussed below.

CustomManyParticleForce 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. If you specify a pair of particles as an exclusion, all sets that include those two particles will be omitted.

As an example, the following code creates a CustomManyParticleForce that implements an Axilrod-Teller potential. This is an interaction between three particles that depends on all three distances and angles formed by the particles.


CustomManyParticleForce* force = new CustomManyParticleForce(3,
    "C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
    "theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
    "r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
force->setPermutationMode(CustomManyParticleForce::SinglePermutation);

This force depends on one parameter, C. The following code defines it as a global parameter:


force->addGlobalParameter("C", 1.0);

Notice that the expression is symmetric with respect to the particles. It only depends on the products cos(theta1)*cos(theta2)*cos(theta3) and r12*r13*r23, both of which are unchanged if the labels p1, p2, and p3 are permuted. This is required because we specified SinglePermutation as the permutation mode. (This is the default, so we did not really need to set it, but doing so makes the example clearer.) In this mode, the expression is only evaluated once for each set of particles. No guarantee is made about which particle will be identified as p1, p2, etc. Therefore, the energy must be symmetric with respect to exchange of particles. Otherwise, the results would be undefined because permuting the labels would change the energy.

Not all many-particle interactions work this way. Another common pattern is for the expression to describe an interaction between one central particle and other nearby particles. An example of this is the 3-particle piece of the Stillinger-Weber potential:


CustomManyParticleForce* force = new CustomManyParticleForce(3,
    "L*eps*(cos(theta1)+1/3)^2*exp(sigma*gamma/(r12-a*sigma))*exp(sigma*gamma/(r13-a*sigma));"
    "r12 = distance(p1,p2); r13 = distance(p1,p3); theta1 = angle(p3,p1,p2)");
force->setPermutationMode(CustomManyParticleForce::UniqueCentralParticle);

When the permutation mode is set to UniqueCentralParticle, particle p1 is treated as the central particle. For a set of N particles, the expression is evaluated N times, once with each particle as p1. The expression can therefore treat p1 differently from the other particles. Notice that it is still symmetric with respect to p2 and p3, however. There is no guarantee about how those labels will be assigned to particles.

Distance cutoffs are applied in different ways depending on the permutation mode. In SinglePermutation mode, every particle in the set must be within the cutoff distance of every other particle. If any two particles are further apart than the cutoff distance, the interaction is skipped. In UniqueCentralParticle mode, each particle must be within the cutoff distance of the central particle, but not necessarily of all the other particles. The cutoff may therefore exclude a subset of the permutations of a set of particles.

Another common situation is that some particles are fundamentally different from others, causing the expression to be inherently non-symmetric. An example would be a water model that involves three particles, two of which must be hydrogen and one of which must be oxygen. Cases like this can be implemented using particle types.

A particle type is an integer that you specify when you call addParticle(). (If you omit the argument, it defaults to 0.) For the water model, you could specify 0 for all oxygen atoms and 1 for all hydrogen atoms. You can then call setTypeFilter() to specify the list of allowed types for each of the N particles involved in an interaction:


set<int> oxygenTypes, hydrogenTypes;
oxygenTypes.insert(0);
hydrogenTypes.insert(1);
force->setTypeFilter(0, oxygenTypes);
force->setTypeFilter(1, hydrogenTypes);
force->setTypeFilter(2, hydrogenTypes);

This specifies that of the three particles in an interaction, p1 must be oxygen while p2 and p3 must be hydrogen. The energy expression will only be evaluated for triplets of particles that satisfy those requirements. It will still only be evaluated once for each triplet, so it must still be symmetric with respect to p2 and p3.

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. The names of per-particle parameters have the suffix "1", "2", etc. appended to them to indicate the values for the multiple interacting particles. For example, if you define a per-particle parameter called "charge", then the variable "charge2" is the charge of particle p2. As seen above, the expression may also involve intermediate quantities that are defined following the main expression, using ";" as a separator.

In addition, you can call addTabulatedFunction() to define a new function based on tabulated values. You specify the function by creating a TabulatedFunction object. 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 interactions is computed exactly. This necessarily means that periodic boundary conditions cannot be used. This is the default.

CutoffNonPeriodic

Interactions are ignored if any two particles are further apart than the cutoff distance.

CutoffPeriodic

Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic copy of each other particle.

Interactions are ignored if any two particles are further apart than the cutoff distance.

enum PermutationMode

This is an enumeration of the different modes for selecting which permutations of a set of particles to evaluate the interaction for.

Enumerator

SinglePermutation

For any set of particles, the interaction is evaluated only once for a single permutation of the particles.

There is no guarantee about which permutation will be used (aside from the requirement to satisfy type filters), so the expression must be symmetric. If cutoffs are used, then every particle in the set must be within the cutoff distance of every other particle.

UniqueCentralParticle

The interaction is treated as an interaction between one central particle (p1) and various other nearby particles (p2, p3, ...).

For a set of N particles it will be evaluated N times, once with each particle as p1. The expression must be symmetric with respect to the other particles, but may treat p1 differently. If cutoffs are used, then every particle must be within the cutoff distance of p1.

Constructor & Destructor Documentation

CustomManyParticleForce	(	int	particlesPerSet,
		const std::string &	energy
	)

explicit

Create a CustomManyParticleForce.

Parameters

particlesPerSet	the number of particles in each set for which the energy is evaluated
energy	an algebraic expression giving the interaction energy of each triplet as a function of particle positions, inter-particle distances, angles, and any global and per-particle parameters

~CustomManyParticleForce ( )

Member Function Documentation

int addExclusion	(	int	particle1,
		int	particle2
	)

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

In many cases, you can use createExclusionsFromBonds() rather than adding each exclusion explicitly.

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 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,
		int	type = `0`
	)

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
type	the type of 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

int addTabulatedFunction	(	const std::string &	name,
		TabulatedFunction *	function
	)

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

Parameters

name	the name of the function as it appears in expressions
function	a TabulatedFunction object defining the function. The TabulatedFunction should have been created on the heap with the "new" operator. The Force takes over ownership of it, and deletes it when the Force itself is deleted.

Returns: the index of the function that was added

void createExclusionsFromBonds	(	const std::vector< std::pair< int, int > > &	bonds,
		int	bondCutoff
	)

Identify exclusions based on the molecular topology.

Particles which are separated by up to a specified number of bonds are added as exclusions.

Parameters

bonds	the set of bonds based on which to construct exclusions. Each element specifies the indices of two particles that are bonded to each other.
bondCutoff	pairs of particles that are separated by this many bonds or fewer are added to the list of exclusions

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.

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 of each bond.

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

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 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 getNumParticlesPerSet ( ) const

inline

Get the number of particles in each set for which the energy is evaluated.

int getNumPerParticleParameters ( ) const

inline

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

int getNumTabulatedFunctions ( ) const

inline

Get the number of tabulated functions that have been defined.

void getParticleParameters	(	int	index,
		std::vector< double > &	parameters,
		int &	type
	)		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
type	the type of the specified particle

PermutationMode getPermutationMode ( ) const

Get the mode that selects which permutations of a set of particles to evaluate the interaction for.

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

const TabulatedFunction& getTabulatedFunction ( int index ) const

Get a const reference to a tabulated function that may appear in the energy expression.

Parameters

index the index of the function to get

Returns: the TabulatedFunction object defining the function

TabulatedFunction& getTabulatedFunction ( int index )

Get a reference to a tabulated function that may appear in the energy expression.

Parameters

index the index of the function to get

Returns: the TabulatedFunction object defining the function

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

Get the name of a tabulated function that may appear in the energy expression.

Parameters

index the index of the function to get

Returns: the name of the function as it appears in expressions

void getTypeFilter	(	int	index,
		std::set< int > &	types
	)		const

Get the allowed particle types for one of the particles involved in the interaction.

If this an empty set (the default), no filter is applied and all interactions are evaluated regardless of the type of the specified particle.

Parameters

index	the index of the particle within the interaction (between 0 and getNumParticlesPerSet())
types	the allowed types for the specified particle

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 of each bond.

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 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,
		int	type
	)

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
type	the type of the specified particle

void setPermutationMode ( PermutationMode mode )

Set the mode that selects which permutations of a set of particles to evaluate the interaction for.

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

void setTypeFilter	(	int	index,
		const std::set< int > &	types
	)

Set the allowed particle types for one of the particles involved in the interaction.

If this an empty set (the default), no filter is applied and all interactions are evaluated regardless of the type of the specified particle.

Parameters

index	the index of the particle within the interaction (between 0 and getNumParticlesPerSet())
types	the allowed types for the specified particle

void updateParametersInContext ( Context & context )

Update the per-particle 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 setParticleParameters() to modify this object's parameters, then call updateParametersInContext() to copy them over to the Context.

This method has several limitations. The only information it updates is the values of per-particle parameters. All other aspects of the Force (the energy function, nonbonded method, cutoff distance, etc.) are unaffected and can only be changed by reinitializing the Context. Also, this method cannot be used to add new particles, only to change the parameters of existing ones.

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

CustomManyParticleForce.h

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation