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

Inherits _object.

Public Member Functions
def	__del__
	del(OpenMM::Context self) More...

def	getSystem
	getSystem(Context self) -> System More...

def	getIntegrator
	getIntegrator(Context self) -> Integrator getIntegrator(Context self) -> Integrator More...

def	getPlatform
	getPlatform(Context self) -> Platform getPlatform(Context self) -> Platform More...

def	setTime
	setTime(Context self, double time) More...

def	setPositions
	setPositions(self, positions) More...

def	setVelocities
	setVelocities(self, velocities) More...

def	setVelocitiesToTemperature
	setVelocitiesToTemperature(Context self, double temperature, int randomSeed=osrngseed()) setVelocitiesToTemperature(Context self, double temperature) More...

def	getParameter
	getParameter(Context self, std::string const & name) -> double More...

def	setParameter
	setParameter(Context self, std::string const & name, double value) More...

def	setPeriodicBoxVectors
	setPeriodicBoxVectors(Context self, Vec3 const & a, Vec3 const & b, Vec3 const & c) More...

def	applyConstraints
	applyConstraints(Context self, double tol) More...

def	applyVelocityConstraints
	applyVelocityConstraints(Context self, double tol) More...

def	computeVirtualSites
	computeVirtualSites(Context self) More...

def	reinitialize
	reinitialize(Context self) More...

def	getMolecules
	getMolecules(Context self) -> vectorii More...

def	getState
	getState(self, getPositions = False, getVelocities = False, getForces = False, getEnergy = False, getParameters = False, enforcePeriodicBox = False, groups = -1) -> State More...

def	setState
	setState(Context self, State state) More...

def	createCheckpoint
	createCheckpoint(Context self) -> std::string More...

def	loadCheckpoint
	loadCheckpoint(Context self, std::string checkpoint) More...

def	__init__
	init(OpenMM::Context self, System system, Integrator integrator) -> Context init(OpenMM::Context self, System system, Integrator integrator, Platform platform) -> Context init(OpenMM::Context self, System system, Integrator integrator, Platform platform, mapstringstring properties) -> Context init(OpenMM::Context self, Context other) -> Context More...

Public Attributes
	this

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

def __del__ ( self )

del(OpenMM::Context self)

References simtk.openmm.openmm.stripUnits().

def __init__	(	self,
		args
	)

init(OpenMM::Context self, System system, Integrator integrator) -> Context init(OpenMM::Context self, System system, Integrator integrator, Platform platform) -> Context init(OpenMM::Context self, System system, Integrator integrator, Platform platform, mapstringstring properties) -> Context init(OpenMM::Context self, Context other) -> Context

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.

References simtk.openmm.openmm.stripUnits().

Member Function Documentation

def applyConstraints	(	self,
		args
	)

applyConstraints(Context self, 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.

References simtk.openmm.openmm.stripUnits().

def applyVelocityConstraints	(	self,
		args
	)

applyVelocityConstraints(Context self, 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.

References simtk.openmm.openmm.stripUnits().

def computeVirtualSites ( self )

computeVirtualSites(Context self)

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.

References simtk.openmm.openmm.stripUnits().

def createCheckpoint ( self )

createCheckpoint(Context self) -> std::string

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.

Returns: a string containing the checkpoint data

def getIntegrator	(	self,
		args
	)

getIntegrator(Context self) -> Integrator getIntegrator(Context self) -> Integrator

Get Integrator being used to by this context.

References simtk.openmm.openmm.stripUnits().

def getMolecules ( self )

getMolecules(Context self) -> vectorii

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.

References Context.getState(), and simtk.openmm.openmm.stripUnits().

def getParameter	(	self,
		args
	)

getParameter(Context self, std::string const & name) -> double

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

Parameters

name	the name of the parameter to get

References simtk.openmm.openmm.stripUnits().

def getPlatform	(	self,
		args
	)

getPlatform(Context self) -> Platform getPlatform(Context self) -> Platform

Get the Platform being used for calculations.

References simtk.openmm.openmm.stripUnits().

def getState	(	self,
		getPositions = `False`,
		getVelocities = `False`,
		getForces = `False`,
		getEnergy = `False`,
		getParameters = `False`,
		enforcePeriodicBox = `False`,
		groups = `-1`
	)

getState(self, getPositions = False, getVelocities = False, getForces = False, getEnergy = False, getParameters = False, enforcePeriodicBox = False, groups = -1) -> State

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

Parameters

getPositions	(bool=False) whether to store particle positions in the State
getVelocities	(bool=False) whether to store particle velocities in the State
getForces	(bool=False) whether to store the forces acting on particles in the State
getEnergy	(bool=False) whether to store potential and kinetic energy in the State
getParameter	(bool=False) whether to store context parameters in the State
enforcePeriodicBox	(bool=False) 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	(int=-1) 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.

References RPMDIntegrator._getStateAsLists(), and Context._getStateAsLists().

Referenced by Context.getMolecules().

def getSystem ( self )

getSystem(Context self) -> System

Get System being simulated in this context.

References simtk.openmm.openmm.stripUnits().

def loadCheckpoint	(	self,
		args
	)

loadCheckpoint(Context self, std::string checkpoint)

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

checkpoint (string) the checkpoint data to load

def reinitialize ( self )

reinitialize(Context self)

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.

References simtk.openmm.openmm.stripUnits().

def setParameter	(	self,
		args
	)

setParameter(Context self, std::string const & 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

References simtk.openmm.openmm.stripUnits().

Referenced by Context.setState().

def setPeriodicBoxVectors	(	self,
		args
	)

setPeriodicBoxVectors(Context self, Vec3 const & a, Vec3 const & b, Vec3 const & 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

References simtk.openmm.openmm.stripUnits().

Referenced by Context.setState().

def setPositions	(	self,
		args
	)

setPositions(self, 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.

References simtk.openmm.openmm.stripUnits().

Referenced by Context.setState().

def setState	(	self,
		state
	)

setState(Context self, 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.

References Context.setParameter(), Context.setPeriodicBoxVectors(), RPMDIntegrator.setPositions(), Context.setPositions(), Context.setTime(), RPMDIntegrator.setVelocities(), and Context.setVelocities().

def setTime	(	self,
		args
	)

setTime(Context self, double time)

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

References simtk.openmm.openmm.stripUnits().

Referenced by Context.setState().

def setVelocities	(	self,
		args
	)

setVelocities(self, 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.

References simtk.openmm.openmm.stripUnits().

Referenced by Context.setState().

def setVelocitiesToTemperature	(	self,
		args
	)

setVelocitiesToTemperature(Context self, double temperature, int randomSeed=osrngseed()) setVelocitiesToTemperature(Context self, double temperature)

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

References simtk.openmm.openmm.stripUnits().

Member Data Documentation

this

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

openmm.py

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation