A Context stores the complete state of a simulation. More...
#include <Context.h>
Public Member Functions | |
| Context (System &system, Integrator &integrator) | |
| Construct a new Context in which to run a simulation. | |
| Context (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. | |
| Context (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. | |
| ~Context () | |
| const System & | getSystem () const |
| Get System being simulated in this context. | |
| System & | getSystem () |
| Get System being simulated in this context. | |
| const Integrator & | getIntegrator () const |
| Get Integrator being used to by this context. | |
| Integrator & | getIntegrator () |
| Get Integrator being used to by this context. | |
| 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. | |
| void | setTime (double time) |
| Set the current time of the simulation (in picoseconds). | |
| void | setPositions (const std::vector< Vec3 > &positions) |
| Set the positions of all particles in the System (measured in nm). | |
| void | setVelocities (const std::vector< Vec3 > &velocities) |
| Set the velocities of all particles in the System (measured in nm/picosecond). | |
| double | getParameter (const std::string &name) |
| Get the value of an adjustable parameter defined by a Force object in the System. | |
| void | setParameter (const std::string &name, double value) |
| Set the value of an adjustable parameter defined by a Force object in the System. | |
| 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 | computeVirtualSites () |
| Recompute the locations of all virtual sites. | |
| void | reinitialize () |
| When a Context is created, it may cache information about the System being simulated and the Force objects contained in it. | |
Friends | |
| class | Platform |
A Context stores the complete state of a simulation.
More specifically, it includes:
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.
| Context | ( | System & | system, | |
| Integrator & | integrator | |||
| ) |
Construct a new Context in which to run a simulation.
| system | the System which will be simulated | |
| integrator | the Integrator which will be used to simulate the System |
| Context | ( | System & | system, | |
| Integrator & | integrator, | |||
| Platform & | platform | |||
| ) |
| Context | ( | 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.
| 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 | ( | ) |
| 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.
| tol | the distance 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.
| Integrator& getIntegrator | ( | ) |
Get Integrator being used to by this context.
| const Integrator& getIntegrator | ( | ) | const |
Get Integrator being used to by this context.
| double getParameter | ( | const std::string & | name | ) |
| State getState | ( | int | types, | |
| bool | enforcePeriodicBox = false, |
|||
| int | groups = 0xFFFFFFFF | |||
| ) | const |
Get a State object recording the current state information stored in this context.
| 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. |
| 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 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.
| 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.
| 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 setTime | ( | double | time | ) |
Set the current time of the simulation (in picoseconds).
| void setVelocities | ( | const std::vector< Vec3 > & | velocities | ) |
friend class Platform [friend] |
1.6.2