# ContextImpl Class Reference

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

`#include <ContextImpl.h>`

List of all members.

## 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.
## Static Public Member Functions
static std::vector < std::vector< int > > | findMolecules (int numParticles, std::vector< std::vector< int > > &particleBonds)
| This is the routine that actually computes the list of molecules returned by getMolecules().
## 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

static std::vector<std::vector<int> > findMolecules | ( | int | numParticles,
|  | std::vector< std::vector< int > > & | particleBonds |
| ) |  |  | `[static]`

This is the routine that actually computes the list of molecules returned by getMolecules().

Normally you should never call it. It is exposed here because the same logic is useful to other classes too.

std::vector<ForceImpl*>& getForceImpls | ( |  | ) |

Get the list of ForceImpls belonging to this ContextImpl.

const std::vector<ForceImpl*>& getForceImpls | ( |  | ) | const

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.

const void* getPlatformData | ( |  | ) | const

Get the platform-specific data stored in this context.

void* getPlatformData | ( |  | ) |

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]`

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

- ContextImpl.h