OpenMM

This is an error contolled, variable time step Integrator that simulates a System using the leapfrog Verlet algorithm. More...
#include <VariableVerletIntegrator.h>
Public Member Functions  
VariableVerletIntegrator (double errorTol)  
Create a VariableVerletIntegrator. More...  
double  getErrorTolerance () const 
Get the error tolerance. More...  
void  setErrorTolerance (double tol) 
Set the error tolerance. More...  
void  step (int steps) 
Advance a simulation through time by taking a series of time steps. More...  
void  stepTo (double time) 
Advance a simulation through time by taking a series of steps until a specified time is reached. More...  
Public Member Functions inherited from Integrator  
Integrator ()  
virtual  ~Integrator () 
double  getStepSize () const 
Get the size of each time step, in picoseconds. More...  
void  setStepSize (double size) 
Set the size of each time step, in picoseconds. More...  
double  getConstraintTolerance () const 
Get the distance tolerance within which constraints are maintained, as a fraction of the constrained distance. More...  
void  setConstraintTolerance (double tol) 
Set the distance tolerance within which constraints are maintained, as a fraction of the constrained distance. More...  
Protected Member Functions  
void  initialize (ContextImpl &context) 
This will be called by the Context when it is created. More...  
void  cleanup () 
This will be called by the Context when it is destroyed to let the Integrator do any necessary cleanup. More...  
std::vector< std::string >  getKernelNames () 
Get the names of all Kernels used by this Integrator. More...  
double  computeKineticEnergy () 
Compute the kinetic energy of the system at the current time. More...  
Protected Member Functions inherited from Integrator  
virtual void  stateChanged (State::DataType changed) 
This will be called by the Context when the user modifies aspects of the context state, such as positions, velocities, or parameters. More...  
Additional Inherited Members  
Protected Attributes inherited from Integrator  
ContextImpl *  context 
Context *  owner 
This is an error contolled, variable time step Integrator that simulates a System using the leapfrog Verlet algorithm.
It compares the result of the Verlet integrator to that of an explicit Euler integrator, takes the difference between the two as a measure of the integration error in each time step, and continuously adjusts the step size to keep the error below a specified tolerance. This both improves the stability of the integrator and allows it to take larger steps on average, while still maintaining comparable accuracy to a fixed step size integrator.
It is best not to think of the error tolerance as having any absolute meaning. It is just an adjustable parameter that affects the step size and integration accuracy. You should try different values to find the largest one that produces a trajectory sufficiently accurate for your purposes. 0.001 is often a good starting point.
Unlike a fixed step size Verlet integrator, variable step size Verlet is not symplectic. This means that at a given accuracy level, energy is not as precisely conserved over long time periods. This makes it most appropriate for constant temperate simulations. In constant energy simulations where precise energy conservation over long time periods is important, a fixed step size Verlet integrator may be more appropriate.

explicit 
Create a VariableVerletIntegrator.
errorTol  the error tolerance 

protectedvirtual 
This will be called by the Context when it is destroyed to let the Integrator do any necessary cleanup.
It will also get called again if the application calls reinitialize() on the Context.
Reimplemented from Integrator.

protectedvirtual 
Compute the kinetic energy of the system at the current time.
Implements Integrator.

inline 
Get the error tolerance.

protectedvirtual 
Get the names of all Kernels used by this Integrator.
Implements Integrator.

protectedvirtual 
This will be called by the Context when it is created.
It informs the Integrator of what context it will be integrating, and gives it a chance to do any necessary initialization. It will also get called again if the application calls reinitialize() on the Context.
Implements Integrator.

inline 
Set the error tolerance.

virtual 
Advance a simulation through time by taking a series of time steps.
steps  the number of time steps to take 
Implements Integrator.
void stepTo  (  double  time  ) 
Advance a simulation through time by taking a series of steps until a specified time is reached.
When this method returns, the simulation time will exactly equal the time which was specified. If you call this method and specify a time that is earlier than the current time, it will return without doing anything.
time  the time to which the simulation should be advanced 