Thermostat Struct Reference

Represents a Nose-Hoover thermostat for molecular dynamics simulations. More...

Collaboration diagram for Thermostat:

Public Member Functions
	Thermostat ()
	Default constructor for the Thermostat struct.
	Thermostat (double temperature, std::size_t thermostatChainLength, std::size_t numberOfYoshidaSuzukiSteps, double deltaT, std::size_t translationalDegreesOfFreedom, std::size_t rotationalDgreesOfFreedom)
	Constructs a Thermostat with specified parameters.
void	initialize (RandomNumber &random)
	Initializes the thermostat with random velocities.
std::pair< double, double >	NoseHooverNVT (double UKineticTranslation, double UKineticRotation)
	Performs a Nose-Hoover NVT integration step.
double	getEnergy ()
	Computes the total energy of the thermostat.

Public Attributes
std::uint64_t	versionNumber {1}
	Version number for serialization.
double	temperature
	The target temperature for the thermostat.
std::size_t	thermostatChainLength
	The length of the thermostat chain.
double	timeScaleParameterThermostat {0.15}
	Time scale parameter for the thermostat.
std::size_t	numberOfRespaSteps {5}
	Number of RESPA steps.
std::size_t	numberOfYoshidaSuzukiSteps {5}
	Number of Yoshida-Suzuki steps for integration.
double	deltaT {}
	The simulation time step.
std::size_t	translationalCenterOfMassConstraint {}
	Constraint on translational center of mass degrees of freedom.
std::size_t	translationalDegreesOfFreedom
	Number of translational degrees of freedom.
std::size_t	rotationalDgreesOfFreedom
	Number of rotational degrees of freedom.
std::vector< double >	thermostatDegreesOfFreedomTranslation
	Degrees of freedom for the translational thermostat chain.
std::vector< double >	thermostatForceTranslation
	Forces for the translational thermostat chain.
std::vector< double >	thermostatVelocityTranslation
	Velocities for the translational thermostat chain.
std::vector< double >	thermostatPositionTranslation
	Positions for the translational thermostat chain.
std::vector< double >	thermostatMassTranslation
	Masses for the translational thermostat chain.
std::vector< double >	thermostatDegreesOfFreedomRotation
	Degrees of freedom for the rotational thermostat chain.
std::vector< double >	thermostatForceRotation
	Forces for the rotational thermostat chain.
std::vector< double >	thermostatVelocityRotation
	Velocities for the rotational thermostat chain.
std::vector< double >	thermostatPositionRotation
	Positions for the rotational thermostat chain.
std::vector< double >	thermostatMassRotation
	Masses for the rotational thermostat chain.
std::vector< double >	w
	Weights for Yoshida-Suzuki integration steps.

Friends
Archive< std::ofstream > &	operator<< (Archive< std::ofstream > &archive, const Thermostat &s)
Archive< std::ifstream > &	operator>> (Archive< std::ifstream > &archive, Thermostat &s)

Detailed Description

Represents a Nose-Hoover thermostat for molecular dynamics simulations.

The Thermostat struct encapsulates the properties and methods required to implement a Nose-Hoover thermostat for temperature control in molecular dynamics simulations. It includes parameters for temperature, thermostat chain length, Yoshida-Suzuki steps, and degrees of freedom. The struct provides methods to initialize the thermostat, perform Nose-Hoover NVT integration steps, and compute the thermostat's energy contribution.

Constructor & Destructor Documentation

Thermostat() [1/2]

Thermostat::Thermostat ( )

inline

Default constructor for the Thermostat struct.

Initializes a Thermostat object with default values.

Thermostat() [2/2]

Thermostat::Thermostat	(	double	temperature,
		std::size_t	thermostatChainLength,
		std::size_t	numberOfYoshidaSuzukiSteps,
		double	deltaT,
		std::size_t	translationalDegreesOfFreedom,
		std::size_t	rotationalDgreesOfFreedom
	)

Constructs a Thermostat with specified parameters.

Initializes a Thermostat with the provided temperature, thermostat chain length, number of Yoshida-Suzuki steps, time step deltaT, and degrees of freedom for translation and rotation.

Parameters

temperature	The target temperature for the thermostat.
thermostatChainLength	The length of the thermostat chain.
numberOfYoshidaSuzukiSteps	The number of Yoshida-Suzuki steps for integration.
deltaT	The simulation time step.
translationalDegreesOfFreedom	The number of translational degrees of freedom.
rotationalDgreesOfFreedom	The number of rotational degrees of freedom.

Member Function Documentation

getEnergy()

double Thermostat::getEnergy

(

)

Computes the total energy of the thermostat.

Calculates the energy contribution from both translational and rotational thermostat chains.

Returns

The total energy of the thermostat.

initialize()

void Thermostat::initialize

(

RandomNumber &

random

)

Initializes the thermostat with random velocities.

Sets up the thermostat chain by initializing velocities using a random number generator.

Parameters

random

A reference to a RandomNumber generator.

NoseHooverNVT()

std::pair< double, double > Thermostat::NoseHooverNVT	(	double	UKineticTranslation,
		double	UKineticRotation
	)

Performs a Nose-Hoover NVT integration step.

Updates the thermostat variables and computes scaling factors for translational and rotational degrees of freedom based on the provided kinetic energies.

Parameters

UKineticTranslation	The kinetic energy of translation.
UKineticRotation	The kinetic energy of rotation.

Returns

A pair of scaling factors for translation and rotation.

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

• src/raspakit/thermostat.ixx