All Classes Namespaces Functions Variables Typedefs Enumerations Enumerator Friends Pages
Context Class Reference

A Context stores the complete state of a simulation. More...

`#include <Context.h>`

## Public Member Functions

| Context (const System &system, Integrator &integrator)
| Construct a new Context in which to run a simulation. More...
| Context (const System &system, Integrator &integrator, Platform &platform)
| Construct a new Context in which to run a simulation, explicitly specifying what Platform should be used to perform calculations. More...
| Context (const System &system, Integrator &integrator, Platform &platform, const std::map< std::string, std::string > &properties)
| Construct a new Context in which to run a simulation, explicitly specifying what Platform should be used to perform calculations and the values of platform-specific properties. More...
| ~Context ()
const System & | getSystem () const
| Get System being simulated in this context. More...
const Integrator & | getIntegrator () const
| Get Integrator being used to by this context. More...
Integrator & | getIntegrator ()
| Get Integrator being used to by this context. More...
const Platform & | getPlatform () const
| Get the Platform being used for calculations. More...
Platform & | getPlatform ()
| Get the Platform being used for calculations. More...
State | getState (int types, bool enforcePeriodicBox=false, int groups=0xFFFFFFFF) const
| Get a State object recording the current state information stored in this context. More...
void | setState (const State &state)
| Copy information from a State object into this Context. More...
void | setTime (double time)
| Set the current time of the simulation (in picoseconds). More...
void | setPositions (const std::vector< Vec3 > &positions)
| Set the positions of all particles in the System (measured in nm). More...
void | setVelocities (const std::vector< Vec3 > &velocities)
| Set the velocities of all particles in the System (measured in nm/picosecond). More...
void | setVelocitiesToTemperature (double temperature, int randomSeed=osrngseed())
| Set the velocities of all particles in the System to random values chosen from a Boltzmann distribution at a given temperature. More...
double | getParameter (const std::string &name) const
| Get the value of an adjustable parameter defined by a Force object in the System. More...
void | setParameter (const std::string &name, double value)
| Set the value of an adjustable parameter defined by a Force object in the System. More...
void | setPeriodicBoxVectors (const Vec3 &a, const Vec3 &b, const Vec3 &c)
| Set the vectors defining the axes of the periodic box (measured in nm). More...
void | applyConstraints (double tol)
| Update the positions of particles so that all distance constraints are satisfied. More...
void | applyVelocityConstraints (double tol)
| Update the velocities of particles so the net velocity of each constrained distance is zero. More...
void | computeVirtualSites ()
| Recompute the locations of all virtual sites. More...
void | reinitialize ()
| When a Context is created, it may cache information about the System being simulated and the Force objects contained in it. More...
void | createCheckpoint (std::ostream &stream)
| Create a checkpoint recording the current state of the Context. More...
void | loadCheckpoint (std::istream &stream)
| Load a checkpoint that was written by createCheckpoint(). More...
const std::vector< std::vector < int > > & | getMolecules () const
| Get a description of how the particles in the system are grouped into molecules. More...

## Friends

class | Force
class | Platform

## Detailed Description

A Context stores the complete state of a simulation.

More specifically, it includes:

- The current time
- The position of each particle
- The velocity of each particle
- The values of configurable parameters defined by Force objects in the System

You can retrieve a snapshot of the current state at any time by calling getState(). This allows you to record the state of the simulation at various points, either for analysis or for checkpointing. getState() can also be used to retrieve the current forces on each particle and the current energy of the System.

## Constructor & Destructor Documentation

Context | ( | const System & | system,
|  | Integrator & | integrator
| ) |  |

Construct a new Context in which to run a simulation.

Parameters

  system | the System which will be simulated
  integrator | the Integrator which will be used to simulate the System

Context | ( | const System & | system,
|  | Integrator & | integrator,
|  | Platform & | platform
| ) |  |

Construct a new Context in which to run a simulation, explicitly specifying what Platform should be used to perform calculations.

Parameters

  system | the System which will be simulated
  integrator | the Integrator which will be used to simulate the System
  platform | the Platform to use for calculations

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

Construct a new Context in which to run a simulation, explicitly specifying what Platform should be used to perform calculations and the values of platform-specific properties.

Parameters

  system | the System which will be simulated
  integrator | the Integrator which will be used to simulate the System
  platform | the Platform to use for calculations
  properties | a set of values for platform-specific properties. Keys are the property names.

~Context | ( |  | ) |

## 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.

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.

This should be treated as an opaque block of binary data. See loadCheckpoint() for more details.

Parameters

  stream | an output stream the checkpoint data should be written to

const Integrator& getIntegrator | ( |  | ) | const

Get Integrator being used to by this context.

Integrator& getIntegrator | ( |  | ) |

Get Integrator being used to by this context.

const std::vector<std::vector<int> >& getMolecules | ( |  | ) | const

Get a description of how the particles in the system are grouped into molecules.

Two particles are in the same molecule if they are connected by constraints or bonds, where every Force object can define bonds in whatever way are appropriate to that force.

Each element lists the indices of all particles in a single molecule. Every particle is guaranteed to belong to exactly one molecule.

double getParameter | ( | const std::string & | name | ) | const

Get the value of an adjustable parameter defined by a Force object in the System.

Parameters

  name | the name of the parameter to get

const Platform& getPlatform | ( |  | ) | const

Get the Platform being used for calculations.

Platform& getPlatform | ( |  | ) |

Get the Platform being used for calculations.

State getState | ( | int | types,
|  | bool | enforcePeriodicBox = `false`,
|  | int | groups = `0xFFFFFFFF`
| ) |  | const

Get a State object recording the current state information stored in this context.

Parameters

  types | the set of data types which should be stored in the State object. This should be a union of DataType values, e.g. (State::Positions | State::Velocities).
  enforcePeriodicBox | if false, the position of each particle will be whatever position is stored in the Context, regardless of periodic boundary conditions. If true, particle positions will be translated so the center of every molecule lies in the same periodic box.
  groups | a set of bit flags for which force groups to include when computing forces and energies. Group i will be included if (groups&(1<<i)) != 0. The default value includes all groups.

const System& getSystem | ( |  | ) | const

Get System being simulated in this context.

void loadCheckpoint | ( | std::istream & | stream | ) |

Load a checkpoint that was written by createCheckpoint().

A checkpoint contains not only publicly visible data such as the particle positions and velocities, but also internal data such as the states of random number generators. Ideally, loading a checkpoint should restore the Context to an identical state to when it was written, such that continuing the simulation will produce an identical trajectory. This is not strictly guaranteed to be true, however, and should not be relied on. For most purposes, however, the internal state should be close enough to be reasonably considered equivalent.

A checkpoint contains data that is highly specific to the Context from which it was created. It depends on the details of the System, the Platform being used, and the hardware and software of the computer it was created on. If you try to load it on a computer with different hardware, or for a System that is different in any way, loading is likely to fail. Checkpoints created with different versions of OpenMM are also often incompatible. If a checkpoint cannot be loaded, that is signaled by throwing an exception.

Parameters

  stream | an input stream the checkpoint data should be read from

void reinitialize | ( |  | ) |

When a Context is created, it may cache information about the System being simulated and the Force objects contained in it.

This means that, if the System or Forces are then modified, the Context might not see all of the changes. Call reinitialize() to force the Context to rebuild its internal representation of the System and pick up any changes that have been made.

This is an expensive operation, so you should try to avoid calling it too frequently.

void setParameter | ( | const std::string & | name,
|  | double | value
| ) |  |

Set the value of an adjustable parameter defined by a Force object in the System.

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.

Triclinic boxes are supported, but the vectors must satisfy certain requirements. In particular, a must point in the x direction, b must point "mostly" in the y direction, and c must point "mostly" in the z direction. See the documentation for details.

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 setPositions | ( | const std::vector< Vec3 > & | positions | ) |

Set the positions of all particles in the System (measured in nm).

This method simply sets the positions without checking to see whether they satisfy distance constraints. If you want constraints to be enforced, call applyConstraints() after setting the positions.

Parameters

  positions | a vector whose length equals the number of particles in the System. The i'th element contains the position of the i'th particle.

void setState | ( | const State & | state | ) |

Copy information from a State object into this Context.

This restores the Context to approximately the same state it was in when the State was created. If the State does not include a piece of information (e.g. positions or velocities), that aspect of the Context is left unchanged.

Even when all possible information is included in the State, the effect of calling this method is still less complete than loadCheckpoint(). For example, it does not restore the internal states of random number generators. On the other hand, it has the advantage of not being hardware specific.

void setTime | ( | double | time | ) |

Set the current time of the simulation (in picoseconds).

void setVelocities | ( | const std::vector< Vec3 > & | velocities | ) |

Set the velocities of all particles in the System (measured in nm/picosecond).

Parameters

  velocities | a vector whose length equals the number of particles in the System. The i'th element contains the velocity of the i'th particle.

void setVelocitiesToTemperature | ( | double | temperature,
|  | int | randomSeed = `osrngseed()`
| ) |  |

Set the velocities of all particles in the System to random values chosen from a Boltzmann distribution at a given temperature.

Parameters

  temperature | the temperature for which to select the velocities (measured in Kelvin)
  randomSeed | the random number seed to use when selecting velocities

## Friends And Related Function Documentation

friend class Force

friend

friend class Platform

friend

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

- Context.h