Gromacs
2024.4
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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. | |
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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