DrudeNoseHooverIntegrator

class DrudeNoseHooverIntegrator : public OpenMM::NoseHooverIntegrator

This Integrator simulates systems that include Drude particles. It applies two different Nose-Hoover chain thermostats to the different parts of the system. The first is applied to ordinary particles (ones that are not part of a Drude particle pair), as well as to the center of mass of each Drude particle pair. A second thermostat, typically with a much lower temperature, is applied to the relative internal displacement of each pair.

This integrator can optionally set an upper limit on how far any Drude particle is ever allowed to get from its parent particle. This can sometimes help to improve stability. The limit is enforced with a hard wall constraint. By default the limit is set to 0.02 nm.

This Integrator requires the System to include a DrudeForce, which it uses to identify the Drude particles.

Public Functions

DrudeNoseHooverIntegrator(double temperature, double collisionFrequency, double drudeTemperature, double drudeCollisionFrequency, double stepSize, int chainLength = 3, int numMTS = 3, int numYoshidaSuzuki = 7)

Create a DrudeNoseHooverIntegrator.

Parameters

  • temperature – the target temperature for the system (in Kelvin).

  • collisionFrequency – the frequency of the system’s interaction with the heat bath (in inverse picoseconds).

  • drudeTemperature – the target temperature for the Drude particles, relative to their parent atom (in Kelvin).

  • drudeCollisionFrequency – the frequency of the drude particles’ interaction with the heat bath (in inverse picoseconds).

  • stepSize – the step size with which to integrator the system (in picoseconds)

  • chainLength – the number of beads in the Nose-Hoover chain.

  • numMTS – the number of step in the multiple time step chain propagation algorithm.

  • numYoshidaSuzuki – the number of terms in the Yoshida-Suzuki multi time step decomposition used in the chain propagation algorithm (must be 1, 3, or 5).

virtual void initialize(ContextImpl &context) override

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.

double getMaxDrudeDistance() const

Get the maximum distance a Drude particle can ever move from its parent particle, measured in nm. This is implemented with a hard wall constraint. If this distance is set to 0 (the default), the hard wall constraint is omitted.

void setMaxDrudeDistance(double distance)

Set the maximum distance a Drude particle can ever move from its parent particle, measured in nm. This is implemented with a hard wall constraint. If this distance is set to 0 (the default), the hard wall constraint is omitted.

double computeDrudeKineticEnergy()

Compute the kinetic energy of the drude particles at the current time.

double computeTotalKineticEnergy()

Compute the kinetic energy of all (real and drude) particles at the current time.

double computeSystemTemperature()

Compute the instantaneous temperature of the System, measured in Kelvin. This is calculated based on the kinetic energy of the ordinary particles (ones not attached to a Drude particle), as well as the center of mass motion of the Drude particle pairs. It does not include the internal motion of the pairs. On average, this should be approximately equal to the value returned by getTemperature().

double computeDrudeTemperature()

Compute the instantaneous temperature of the Drude system, measured in Kelvin. This is calculated based on the kinetic energy of the internal motion of Drude pairs and should remain close to the prescribed Drude temperature.