CompoundIntegrator

class 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__(-> CompoundIntegrator)	Create a CompoundIntegrator.
addIntegrator(self, integrator)	Add an Integrator to this CompoundIntegrator.
getConstraintTolerance(self)	Get the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
getCurrentIntegrator(self)	Get the index of the current Integrator.
getIntegrationForceGroups(self)	Get which force groups to use for integration.
getIntegrator(-> Integrator)	Get a const reference to one of the Integrators that have been added to this CompoundIntegrator.
getNumIntegrators(self)	Get the number of Integrators that have been added to this CompoundIntegrator.
getStepSize(self)	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.
setIntegrationForceGroups(groups)	Set which force groups to use for integration.
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.

Attributes

thisown

The membership flag

property thisown

The membership flag

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

getIntegrationForceGroups(self) → int

Get which force groups to use for integration. By default, all force groups are included. This is interpreted as a set of bit flags: the forces from group i will be included if (groups&(1<<i)) != 0.

setIntegrationForceGroups(groups)

Set which force groups to use for integration. By default, all force groups are included.

Parameters

groups (set or int) – a set of indices for which force groups to include when integrating the equations of motion. Alternatively, the groups can be passed as a single unsigned integer interpreted as a bitmask, in which case group i will be included if (groups&(1<<i)) != 0.