Thermostat for Brownian dynamics. More...

#include <thermostat.hpp>

Inheritance diagram for BrownianThermostat:

Collaboration diagram for BrownianThermostat:

Public Member Functions
void	recalc_prefactors (double kT)
	Recalculate prefactors.

Public Member Functions inherited from BaseThermostat
void	rng_initialize (uint32_t const seed)
	Initialize or re-initialize the RNG counter with a seed.

void	rng_increment ()
	Increment the RNG counter.

uint64_t	rng_counter () const
	Get current value of the RNG.

void	set_rng_counter (uint64_t value)

bool	is_seed_required () const
	Is the RNG seed required.

uint32_t	rng_seed () const

Static Public Member Functions
static GammaType	sigma (double kT, GammaType const &gamma)
	Calculate the noise prefactor.

static double	sigma (double kT)
	Calculate the noise prefactor.

Public Attributes
Parameters
GammaType	gamma = Thermostat::gamma_sentinel
	Translational friction coefficient \( \gamma_{\text{trans}} \).

GammaType	gamma_rotation = Thermostat::gamma_sentinel
	Rotational friction coefficient \( \gamma_{\text{rot}} \).

Prefactors
GammaType	sigma_pos = Thermostat::gamma_sentinel
	Translational noise standard deviation.

GammaType	sigma_pos_rotation = Thermostat::gamma_sentinel
	Rotational noise standard deviation.

double	sigma_vel = 0.
	Translational velocity noise standard deviation.

double	sigma_vel_rotation = 0.
	Angular velocity noise standard deviation.

Detailed Description

Thermostat for Brownian dynamics.

Default particle mass is assumed to be unitary in these global parameters.

Definition at line 193 of file core/thermostat.hpp.

Member Function Documentation

◆ recalc_prefactors()

void BrownianThermostat::recalc_prefactors ( double kT )

inline

Recalculate prefactors.

Needs to be called every time the parameters are changed.

The heat velocity dispersion corresponds to the Gaussian noise only, which is only valid for the BD. Just a square root of kT, see (10.2.17) and comments in 2 paragraphs afterwards, [37].

The random walk position dispersion is defined by the second eq. (14.38) of [40]. Its time interval factor will be added in the Brownian Dynamics functions. Its square root is the standard deviation.

Note: the BD thermostat assigns the brownian viscous parameters as well. They correspond to the friction tensor Z from the eq. (14.31) of [40].

Definition at line 201 of file core/thermostat.hpp.

References gamma, gamma_rotation, sigma(), sigma_pos, sigma_pos_rotation, sigma_vel, and sigma_vel_rotation.

◆ sigma() [1/2]

static double BrownianThermostat::sigma ( double kT )

inlinestatic

Calculate the noise prefactor.

Evaluates the quantity \( \sqrt{k_B T} / \sigma_\eta \) with \( \sigma_\eta \) the standard deviation of the random gaussian process \( \eta(t) \).

Definition at line 235 of file core/thermostat.hpp.

References stream.

◆ sigma() [2/2]

static GammaType BrownianThermostat::sigma	(	double	kT,
		GammaType const &	gamma
	)

inlinestatic

Calculate the noise prefactor.

Evaluates the quantity \( \sqrt{2 k_B T / \gamma} / \sigma_\eta \) with \( \sigma_\eta \) the standard deviation of the random gaussian process \( \eta(t) \).

Definition at line 226 of file core/thermostat.hpp.

References gamma, Utils::hadamard_division(), and stream.

Referenced by bd_random_walk(), bd_random_walk_rot(), and recalc_prefactors().