ContextImpl Class Reference

This is the internal implementation of a Context. More...

#include <ContextImpl.h>

Public Member Functions
	ContextImpl (Context &owner, const System &system, Integrator &integrator, Platform *platform, const std::map< std::string, std::string > &properties)
	Create an ContextImpl for a Context;.
	~ContextImpl ()
Context &	getOwner ()
	Get the Context for which this is the implementation.
const System &	getSystem () const
	Get System being simulated in this context.
Integrator &	getIntegrator ()
	Get Integrator being used to by this context.
Platform &	getPlatform ()
	Get the Platform implementation being used for computations.
double	getTime () const
	Get the current time (in picoseconds).
void	setTime (double t)
	Set the current time (in picoseconds).
void	getPositions (std::vector< Vec3 > &positions)
	Get the positions of all particles.
void	setPositions (const std::vector< Vec3 > &positions)
	Set the positions of all particles.
void	getVelocities (std::vector< Vec3 > &velocities)
	Get the velocities of all particles.
void	setVelocities (const std::vector< Vec3 > &velocities)
	Set the velocities of all particles.
void	getForces (std::vector< Vec3 > &forces)
	Get the current forces on all particles.
const std::map< std::string, double > &	getParameters () const
	Get the set of all adjustable parameters and their values.
double	getParameter (std::string name)
	Get the value of an adjustable parameter.
void	setParameter (std::string name, double value)
	Set the value of an adjustable parameter.
void	getPeriodicBoxVectors (Vec3 &a, Vec3 &b, Vec3 &c)
	Get the vectors defining the axes of the periodic box (measured in nm).
void	setPeriodicBoxVectors (const Vec3 &a, const Vec3 &b, const Vec3 &c)
	Set the vectors defining the axes of the periodic box (measured in nm).
void	applyConstraints (double tol)
	Update the positions of particles so that all distance constraints are satisfied.
void	applyVelocityConstraints (double tol)
	Update the velocities of particles so the net velocity of each constrained distance is zero.
void	computeVirtualSites ()
	Recompute the locations of all virtual sites.
double	calcForcesAndEnergy (bool includeForces, bool includeEnergy, int groups=0xFFFFFFFF)
	Recalculate all of the forces in the system and/or the potential energy of the system (in kJ/mol).
int	getLastForceGroups () const
	Get the set of force group flags that were passed to the most recent call to calcForcesAndEnergy().
double	calcKineticEnergy ()
	Calculate the kinetic energy of the system (in kJ/mol).
void	updateContextState ()
	This should be called at the start of each time step.
const std::vector< ForceImpl * > &	getForceImpls () const
	Get the list of ForceImpls belonging to this ContextImpl.
std::vector< ForceImpl * > &	getForceImpls ()
	Get the list of ForceImpls belonging to this ContextImpl.
void *	getPlatformData ()
	Get the platform-specific data stored in this context.
const void *	getPlatformData () const
	Get the platform-specific data stored in this context.
void	setPlatformData (void *data)
	Set the platform-specific data stored in this context.
const std::vector< std::vector < int > > &	getMolecules () const
	Get a list of the particles in each molecules in the system.
void	createCheckpoint (std::ostream &stream)
	Create a checkpoint recording the current state of the Context.
void	loadCheckpoint (std::istream &stream)
	Load a checkpoint that was written by createCheckpoint().
void	integratorDeleted ()
	This is invoked by the Integrator when it is deleted.

Friends
class	Context

Detailed Description

This is the internal implementation of a Context.

Constructor & Destructor Documentation

ContextImpl	(	Context &	owner,
		const System &	system,
		Integrator &	integrator,
		Platform *	platform,
		const std::map< std::string, std::string > &	properties
	)

Create an ContextImpl for a Context;.

~ContextImpl

(

)

Member Function Documentation

void applyConstraints

(

double

tol

)

Update the positions of particles so that all distance constraints are satisfied.

This also recomputes the locations of all virtual sites.

Parameters

tol	the distance tolerance within which constraints must be satisfied.

void applyVelocityConstraints

(

double

tol

)

Update the velocities of particles so the net velocity of each constrained distance is zero.

Parameters

tol	the velocity tolerance within which constraints must be satisfied.

double calcForcesAndEnergy	(	bool	includeForces,
		bool	includeEnergy,
		int	groups = 0xFFFFFFFF
	)

Recalculate all of the forces in the system and/or the potential energy of the system (in kJ/mol).

After calling this, use getForces() to retrieve the forces that were calculated.

Parameters

includeForces	true if forces should be calculated
includeEnergy	true if the energy should be calculated
groups	a set of bit flags for which force groups to include. Group i will be included if (groups&(1<<i)) != 0. The default value includes all groups.

Returns

the potential energy of the system, or 0 if includeEnergy is false

double calcKineticEnergy

(

)

Calculate the kinetic energy of the system (in kJ/mol).

void computeVirtualSites

(

)

Recompute the locations of all virtual sites.

There is rarely a reason to call this, since virtual sites are also updated by applyConstraints(). This is only for the rare situations when you want to enforce virtual sites but not constraints.

void createCheckpoint

(

std::ostream &

stream

)

Create a checkpoint recording the current state of the Context.

Parameters

stream

an output stream the checkpoint data should be written to

const std::vector<ForceImpl*>& getForceImpls

(

)

const

Get the list of ForceImpls belonging to this ContextImpl.

std::vector<ForceImpl*>& getForceImpls

(

)

Get the list of ForceImpls belonging to this ContextImpl.

void getForces

(

std::vector< Vec3 > &

forces

)

Get the current forces on all particles.

Parameters

forces

on exit, this contains the forces

Integrator& getIntegrator ( )

inline

Get Integrator being used to by this context.

int getLastForceGroups

(

)

const

Get the set of force group flags that were passed to the most recent call to calcForcesAndEnergy().

const std::vector<std::vector<int> >& getMolecules

(

)

const

Get a list of the particles in each molecules in the system.

Two particles are in the same molecule if they are connected by constraints or bonds.

Context& getOwner ( )

inline

Get the Context for which this is the implementation.

double getParameter

(

std::string

name

)

Get the value of an adjustable parameter.

If there is no parameter with the specified name, this throws an exception.

Parameters

name	the name of the parameter to get

const std::map<std::string, double>& getParameters

(

)

const

Get the set of all adjustable parameters and their values.

void getPeriodicBoxVectors	(	Vec3 &	a,
		Vec3 &	b,
		Vec3 &	c
	)

Get the vectors defining the axes of the periodic box (measured in nm).

They will affect any Force that uses periodic boundary conditions.

Currently, only rectangular boxes are supported. This means that a, b, and c must be aligned with the x, y, and z axes respectively. Future releases may support arbitrary triclinic boxes.

Parameters

a	the vector defining the first edge of the periodic box
b	the vector defining the second edge of the periodic box
c	the vector defining the third edge of the periodic box

Platform& getPlatform ( )

inline

Get the Platform implementation being used for computations.

void* getPlatformData

(

)

Get the platform-specific data stored in this context.

const void* getPlatformData

(

)

const

Get the platform-specific data stored in this context.

void getPositions

(

std::vector< Vec3 > &

positions

)

Get the positions of all particles.

Parameters

positions

on exit, this contains the particle positions

const System& getSystem ( ) const

inline

Get System being simulated in this context.

double getTime

(

)

const

Get the current time (in picoseconds).

void getVelocities

(

std::vector< Vec3 > &

velocities

)

Get the velocities of all particles.

Parameters

velocities

on exit, this contains the particle velocities

void integratorDeleted ( )

inline

This is invoked by the Integrator when it is deleted.

This is needed to ensure the cleanup process is done correctly, since we don't know whether the Integrator or Context will be deleted first.

void loadCheckpoint

(

std::istream &

stream

)

Load a checkpoint that was written by createCheckpoint().

Parameters

stream

an input stream the checkpoint data should be read from

void setParameter	(	std::string	name,
		double	value
	)

Set the value of an adjustable parameter.

If there is no parameter with the specified name, this throws an exception.

Parameters

name	the name of the parameter to set
value	the value of the parameter

void setPeriodicBoxVectors	(	const Vec3 &	a,
		const Vec3 &	b,
		const Vec3 &	c
	)

Set the vectors defining the axes of the periodic box (measured in nm).

They will affect any Force that uses periodic boundary conditions.

Currently, only rectangular boxes are supported. This means that a, b, and c must be aligned with the x, y, and z axes respectively. Future releases may support arbitrary triclinic boxes.

Parameters

a	the vector defining the first edge of the periodic box
b	the vector defining the second edge of the periodic box
c	the vector defining the third edge of the periodic box

void setPlatformData

(

void *

data

)

Set the platform-specific data stored in this context.

void setPositions

(

const std::vector< Vec3 > &

positions

)

Set the positions of all particles.

Parameters

positions

a vector containg the particle positions

void setTime

(

double

t

)

Set the current time (in picoseconds).

void setVelocities

(

const std::vector< Vec3 > &

velocities

)

Set the velocities of all particles.

Parameters

velocities

a vector containg the particle velocities

void updateContextState

(

)

This should be called at the start of each time step.

It calls updateContextState() on each ForceImpl in the system, allowing them to modify the values of state variables.

Friends And Related Function Documentation

friend class Context

friend

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

• ContextImpl.h