Description

Implements the Nose-Hoover temperature coupling.

Public Member Functions
real	integral (int temperatureGroup, real numDegreesOfFreedom, real referenceTemperature)
	Calculate the current value of the temperature coupling integral.

real	apply (Step gmx_unused step, int temperatureGroup, real currentKineticEnergy, real currentTemperature, const TemperatureCouplingData &thermostatData) override
	Apply the Nose-Hoover temperature control.

real	applyLeapFrog (Step gmx_unused step, int temperatureGroup, real currentKineticEnergy, real currentTemperature, const TemperatureCouplingData &thermostatData)
	Apply for leap-frog. More...

void	connectWithPropagator (const PropagatorConnection &connectionData, int numTemperatureGroups) override
	Connect with propagator - Nose-Hoover scales start and end step velocities.

	NoseHooverTemperatureCoupling (int numTemperatureGroups, ArrayRef< const real > referenceTemperature, ArrayRef< const real > couplingTime)
	Constructor.

template<CheckpointDataOperation operation>
void	doCheckpointData (CheckpointData< operation > *checkpointData)
	Helper function to read from / write to CheckpointData.

void	writeCheckpoint (std::optional< WriteCheckpointData > checkpointData, const t_commrec *cr) override
	Write thermostat dof to checkpoint.

void	readCheckpoint (std::optional< ReadCheckpointData > checkpointData, const t_commrec *cr) override
	Read thermostat dof from checkpoint.

real	updateReferenceTemperatureAndIntegral (int temperatureGroup, real gmx_unused newTemperature, ReferenceTemperatureChangeAlgorithm gmx_unused algorithm, const TemperatureCouplingData &temperatureCouplingData) override
	Adapt masses.

Public Member Functions inherited from gmx::ITemperatureCouplingImpl
virtual real	apply (Step step, int temperatureGroup, real currentKineticEnergy, real currentTemperature, const TemperatureCouplingData &temperatureCouplingData)=0
	Make a temperature control step. More...

virtual real	updateReferenceTemperatureAndIntegral (int temperatureGroup, real newTemperature, ReferenceTemperatureChangeAlgorithm algorithm, const TemperatureCouplingData &temperatureCouplingData)=0
	Update the reference temperature and update and return the temperature coupling integral.

virtual	~ITemperatureCouplingImpl ()=default
	Standard virtual destructor.

Member Function Documentation

real gmx::NoseHooverTemperatureCoupling::applyLeapFrog	(	Step gmx_unused	step,
		int	temperatureGroup,
		real	currentKineticEnergy,
		real	currentTemperature,
		const TemperatureCouplingData &	thermostatData
	)

inline

Apply for leap-frog.

This is called after the force calculation, before coordinate update

We expect system to be at x(t), v(t-dt/2), f(t), T(t-dt/2) Internal variables are at xi(t-dt), v_xi(t-dt) Force on xi is calculated at time of system temperature After calling this, we will have xi(t), v_xi(t) The thermostat integral returned is a function of xi and v_xi, and hence at time t.

This performs an update of the thermostat variables calculated as a_xi(t-dt/2) = (T_sys(t-dt/2) - T_ref) / mass_xi; v_xi(t) = v_xi(t-dt) + dt_xi * a_xi(t-dt/2); xi(t) = xi(t-dt) + dt_xi * (v_xi(t-dt) + v_xi(t))/2;

This will be followed by leap-frog integration of coordinates, calculated as v(t-dt/2) *= - 0.5 * dt * v_xi(t); // scale previous velocities v(t+dt/2) = update_leapfrog_v(v(t-dt/2), f(t)); // do whatever LF does v(t+dt/2) *= 1 / (1 + 0.5 * dt * v_xi(t)) // scale new velocities x(t+dt) = update_leapfrog_x(x(t), v(t+dt/2)); // do whatever LF does

The documentation for this class was generated from the following file:

src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp

Description

Public Member Functions

Member Function Documentation