CompoundIntegrator

class simtk.openmm.openmm.CompoundIntegrator(*args)

This class allows you to use multiple integration algorithms within a single simulation, switching back and forth between them. To use it, create whatever other Integrators you need, then add all of them to a CustomIntegrator:

CompoundIntegrator compoundIntegrator;
compoundIntegrator.addIntegrator(new VerletIntegrator(0.001));
compoundIntegrator.addIntegrator(new LangevinIntegrator(300.0, 1.0, 0.001));

Next create a Context, specifying the CompoundIntegrator as the Integrator to use for the Context:

Context context(system, compoundIntegrator);

Finally, call setCurrentIntegrator() to set which Integrator is active. That one will be used for all calls to step() until the next time you change it.

compoundIntegrator.setCurrentIntegrator(0);
compoundIntegrator.step(1000); // Take 1000 steps of Verlet dynamics
compoundIntegrator.setCurrentIntegrator(1);
compoundIntegrator.step(1000); // Take 1000 steps of Langevin dynamics

When switching between integrators, it is important to make sure they are compatible with each other, and that they will interpret the positions and velocities in the same way. Remember that leapfrog style integrators assume the positions and velocities are offset from each other by half a time step. When switching between a leapfrog and non-leapfrog integrator, you must first adjust the velocities to avoid introducing error. This is also true when switching between two leapfrog integrators that use different step sizes, since they will interpret the velocities as corresponding to different times.

__init__(self) → CompoundIntegrator

__init__(self, other) -> CompoundIntegrator

Create a CompoundIntegrator.

Methods

__init__((self) -> CompoundIntegrator)	__init__(self, other) -> CompoundIntegrator
addIntegrator((self, integrator) -> int)	Add an Integrator to this CompoundIntegrator.
getConstraintTolerance((self) -> double)	Get the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
getCurrentIntegrator((self) -> int)	Get the index of the current Integrator.
getIntegrator((self, index) -> Integrator)	getIntegrator(self, index) -> Integrator
getNumIntegrators((self) -> int)	Get the number of Integrators that have been added to this CompoundIntegrator.
getStepSize((self) -> double)	Get the size of each time step, in picoseconds.
setConstraintTolerance(self, tol)	Set the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
setCurrentIntegrator(self, index)	Set the current Integrator.
setStepSize(self, size)	Set the size of each time step, in picoseconds.
step(self, steps)	Advance a simulation through time by taking a series of time steps.

getNumIntegrators(self) → int

Get the number of Integrators that have been added to this CompoundIntegrator.

addIntegrator(self, integrator) → int

Add an Integrator to this CompoundIntegrator. The Integrator object should have been created on the heap with the “new” operator. The CompoundIntegrator takes over ownership of it, and deletes it when the CompoundIntegrator itself is deleted. All Integrators must be added before the Context is created.

Parameters:integrator (Integrator *) – the Integrator to add Returns:the index of the Integrator that was added Return type:int

getIntegrator(self, index) → Integrator

getIntegrator(self, index) -> Integrator

Get a const reference to one of the Integrators that have been added to this CompoundIntegrator.

Parameters:index (int) – the index of the Integrator to get

getCurrentIntegrator(self) → int

Get the index of the current Integrator.

setCurrentIntegrator(self, index)

Set the current Integrator.

Parameters:index (int) – the index of the Integrator to use

getStepSize(self) → double

Get the size of each time step, in picoseconds. This method calls getStepSize() on whichever Integrator has been set as current.

Returns:the step size, measured in ps Return type:double

setStepSize(self, size)

Set the size of each time step, in picoseconds. This method calls setStepSize() on whichever Integrator has been set as current.

Parameters:size (double) – the step size, measured in ps

getConstraintTolerance(self) → double

Get the distance tolerance within which constraints are maintained, as a fraction of the constrained distance. This method calls getConstraintTolerance() on whichever Integrator has been set as current.

setConstraintTolerance(self, tol)

Set the distance tolerance within which constraints are maintained, as a fraction of the constrained distance. This method calls setConstraintTolerance() on whichever Integrator has been set as current.

step(self, steps)

Advance a simulation through time by taking a series of time steps. This method calls step() on whichever Integrator has been set as current.

Parameters:steps (int) – the number of time steps to take

__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__sizeof__() → int

size of object in memory, in bytes

__str__