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OpenMM
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OpenMM
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A Context stores the complete state of a simulation. More...
Inherits _object.
Public Member Functions | |
| def | getSystem |
| getSystem(self) -> System | |
| def | getIntegrator |
| getIntegrator(self) -> Integrator getIntegrator(self) -> Integrator | |
| def | getPlatform |
| getPlatform(self) -> Platform getPlatform(self) -> Platform | |
| def | setTime |
| Set the current time of the simulation (in picoseconds). | |
| def | setPositions |
| Set the positions of all particles in the System (measured in nm). | |
| def | setVelocities |
| Set the velocities of all particles in the System (measured in nm/picosecond). | |
| def | setVelocitiesToTemperature |
| Set the velocities of all particles in the System to random values chosen from a Boltzmann distribution at a given temperature. | |
| def | getParameters |
| getParameters(self) -> mapstringdouble | |
| def | getParameter |
| getParameter(self, name) -> double | |
| def | setParameter |
| Set the value of an adjustable parameter defined by a Force object in the System. | |
| def | setPeriodicBoxVectors |
| Set the vectors defining the axes of the periodic box (measured in nm). | |
| def | applyConstraints |
| Update the positions of particles so that all distance constraints are satisfied. | |
| def | applyVelocityConstraints |
| Update the velocities of particles so the net velocity of each constrained distance is zero. | |
| def | computeVirtualSites |
| Recompute the locations of all virtual sites. | |
| def | reinitialize |
| When a Context is created, it may cache information about the System being simulated and the Force objects contained in it. | |
| def | getMolecules |
| getMolecules(self) -> vectorii | |
| def | getState |
| Get a State object recording the current state information stored in this context. | |
| def | setState |
| Copy information from a State object into this Context. | |
| def | createCheckpoint |
| createCheckpoint(self) -> std::string | |
| def | loadCheckpoint |
| Load a checkpoint that was written by createCheckpoint(). | |
| def | __init__ |
| __init__(self, system, integrator) -> Context __init__(self, system, integrator, platform) -> Context __init__(self, system, integrator, platform, properties) -> Context __init__(self, other) -> Context | |
Public Attributes | |
| this | |
Static Public Attributes | |
| tuple | groups_mask = int(groups) |
| tuple | state |
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.
| def __init__ | ( | self, | |
| args | |||
| ) |
__init__(self, system, integrator) -> Context __init__(self, system, integrator, platform) -> Context __init__(self, system, integrator, platform, properties) -> Context __init__(self, 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.
| system | (System) the System which will be simulated |
| integrator | (Integrator) the Integrator which will be used to simulate the System |
| platform | (Platform) the Platform to use for calculations |
| properties | (map< std::string, std::string >) a set of values for platform-specific properties. Keys are the property names. |
| def applyConstraints | ( | self, | |
| tol | |||
| ) |
Update the positions of particles so that all distance constraints are satisfied.
This also recomputes the locations of all virtual sites.
| tol | (double) the distance tolerance within which constraints must be satisfied. |
| def applyVelocityConstraints | ( | self, | |
| tol | |||
| ) |
Update the velocities of particles so the net velocity of each constrained distance is zero.
| tol | (double) the velocity tolerance within which constraints must be satisfied. |
| def computeVirtualSites | ( | 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.
| def createCheckpoint | ( | self | ) |
createCheckpoint(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(self) -> Integrator getIntegrator(self) -> Integrator
Get Integrator being used to by this context.
| def getMolecules | ( | self | ) |
getMolecules(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.
| def getParameter | ( | self, | |
| name | |||
| ) |
| def getParameters | ( | self | ) |
| def getPlatform | ( | self, | |
| args | |||
| ) |
| def getState | ( | self, | |
getPositions = False, |
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getVelocities = False, |
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getForces = False, |
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getEnergy = False, |
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getParameters = False, |
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enforcePeriodicBox = False, |
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groups = -1 |
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| ) |
Get a State object recording the current state information stored in this context.
| 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 | (set={0,1,2,...,31}) a set of indices for which force groups to include when computing forces and energies. The default value includes all groups. groups can also be passed as an unsigned integer interpreted as a bitmask, in which case group i will be included if (groups&(1<<i)) != 0. |
| def loadCheckpoint | ( | self, | |
| 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:
| def reinitialize | ( | 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.
| def setParameter | ( | self, | |
| name, | |||
| value | |||
| ) |
| def setPeriodicBoxVectors | ( | self, | |
| a, | |||
| b, | |||
| 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.
| a | (Vec3) the vector defining the first edge of the periodic box |
| b | (Vec3) the vector defining the second edge of the periodic box |
| c | (Vec3) the vector defining the third edge of the periodic box |
| def 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.
| positions | (vector< Vec3 >) a vector whose length equals the number of particles in the System. The i'th element contains the position of the i'th particle. |
| def setState | ( | self, | |
| 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.
| def setTime | ( | self, | |
| time | |||
| ) |
Set the current time of the simulation (in picoseconds).
| def setVelocities | ( | self, | |
| velocities | |||
| ) |
| def setVelocitiesToTemperature | ( | self, | |
| args | |||
| ) |
Set the velocities of all particles in the System to random values chosen from a Boltzmann distribution at a given temperature.
| temperature | (double) the temperature for which to select the velocities (measured in Kelvin) |
| randomSeed | (int) the random number seed to use when selecting velocities |
tuple groups_mask = int(groups) [static] |
tuple state [static] |
State(simTime=simTime,
energy=energy,
coordList=coordList,
velList=velList,
forceList=forceList,
periodicBoxVectorsList=periodicBoxVectorsList,
paramMap=paramMap)
1.7.6.1