A Collection with a "solvent", using the Langevin equation. More...

#include <collection.hpp>

Inheritance diagram for CollectionSol:

Public Member Functions
	CollectionSol (sptr< Box > box, sptr< AtomGroup > atoms, const flt dt, const flt damping, const flt desired_temperature, vector< sptr< Interaction > > interactions=vector< sptr< Interaction > >(), vector< sptr< StateTracker > > trackers=vector< sptr< StateTracker > >(), vector< sptr< Constraint > > constraints=vector< sptr< Constraint > >())

void	change_temperature (const flt damp, const flt desired_temperature)
	Change the desired damping coefficient \(\xi\) or temperature \(T\). More...

void	change_force (const flt damp, const flt fmag, const flt desired_temperature)

void	set_dt (const flt newdt)

void	timestep ()
	Take one step forward in time. More...

Public Member Functions inherited from Collection
	Collection (sptr< Box > box, sptr< AtomGroup > atoms, vector< sptr< Interaction > > interactions=vector< sptr< Interaction > >(), vector< sptr< StateTracker > > trackers=vector< sptr< StateTracker > >(), vector< sptr< Constraint > > constraints=vector< sptr< Constraint > >(), bool should_initialize=true)

virtual void	initialize ()

virtual void	set_forces (bool constraints_and_a=true)
	Set forces. More...

flt	degrees_of_freedom ()
	Total degrees of freedom. More...

flt	potential_energy ()

flt	energy ()
	Total energy, including both potential and kinetic_energy. More...

virtual flt	temp (bool minuscomv=true)

virtual flt	kinetic_energy ()

virtual flt	virial ()

virtual flt	pressure ()
	Returns (1/d V) Σ ri dot fi where d is number of dimensions note that Interaction->pressure just returns Σ ri dot fi. More...

sptr< Box >	get_box ()

Vec	com ()

Vec	com_velocity ()

Vec	angular_momentum (const Vec &loc)
	Shortcut to `AtomGroup` method of the same name. More...

Vec	angular_momentum ()
	Shortcut to `AtomGroup` method of the same name. More...

flt	gyradius ()

virtual	~Collection ()

void	reset_com_velocity ()
	Shortcut to `AtomGroup` method of the same name. More...

void	reset_L ()
	Shortcut to `AtomGroup` method of the same name. More...

void	scale_velocities (flt scaleby)
	Scale all velocities by a factor. More...

void	scale_velocities_to_temp (flt T, bool minuscomv=true)
	Scale all velocities to get to a specific temperature. More...

void	scale_velocities_to_energy (flt E)
	Scale all velocities to get to a specific total energy. More...

void	add_interaction (sptr< Interaction > inter)

void	add_tracker (sptr< StateTracker > track)

void	add_constraint (sptr< Constraint > c)

void	add (sptr< Interaction > a)

void	add (sptr< StateTracker > a)

void	add (sptr< Constraint > a)

vector< sptr< Interaction > >	get_interactions ()

Protected Member Functions
void	set_constants ()
	Set c0, c1, c2, sigmar, sigmav, corr from desT, dt, and damping. More...

Protected Member Functions inherited from Collection
void	update_trackers ()
	To be called immediately after setting particle positions and velocities; lets `StateTracker` instances stay updated automatically. More...

void	update_constraint_positions ()
	To be called approximately after forces have been set. More...

void	update_constraint_velocities ()

void	update_constraint_forces ()

virtual flt	set_forces_get_pressure (bool constraints_and_a=true)

Protected Attributes
BivariateGauss	gauss
	The random number generator. More...

flt	dt

flt	damping
	Damping coefficient, \(\xi\). More...

flt	force_mag

flt	desT
	desired temperature More...

flt	sigmar
	note that this is sigmar/sqrt(T/m), same for sigmav corr is unitless, and correct More...

flt	sigmav

flt	corr

flt	c0

flt	c1

flt	c2

Protected Attributes inherited from Collection
sptr< Box >	box

sptr< AtomGroup >	atoms

vector< sptr< Interaction > >	interactions

vector< sptr< StateTracker > >	trackers

vector< sptr< Constraint > >	constraints

Detailed Description

A Collection with a "solvent", using the Langevin equation.

The Langevin Equation ((modified with \(\vec{f}\)):

\(\dot{\vec{p}} = - \xi \vec{p} + \vec{f} + \overset{\circ}{\vec{p}}\)

Where \(- \xi \vec{p}\) is a drag term, \(\overset{\circ}{\vec{p}}\) is a "random force" term, and \(\vec{f}\) is the standard force term. When \(\vec{f} = \vec{0}\), particles undergo Brownian motion, with \(\xi = \frac{k_B T}{m D}\).

This particular algorithm is from Allen and Tildesley, p. 263:

\( \begin{align*} \vec{r}\left(t+\delta t\right)) & =\vec{r}\left(t\right)+c_{1}\delta t\vec{v}\left(t\right)+c_{2}\delta t^{2}\vec{a}\left(t\right)+\delta r^{G}\\ \vec{v}\left(t+\delta t\right) & =c_{0}v\left(t\right)+\left(c_{1}-c_{2}\right)\delta t\vec{a}\left(t\right)+c_{2}\delta t\vec{a}\left(t+\delta t\right)+\delta v^{G} \end{align*} \)

where

\( \begin{align*} c_0 & = e^{- \xi \delta t} & c_1 & = \frac{1 - c_0}{\xi \delta t} & c_2 & = \frac{1 - c_1}{\xi \delta t} \end{align*} \)

There are expansions for all 3; see Allen and Tildesley page 261.

\(\delta r^G\) and \(\delta v^G\) are drawn from correlated Gaussian distributions, with

\( \begin{align*} \sigma_{r}^{2} & =\left(\xi dt\right)^{-1}\left[2-\left(\xi dt\right)^{-1}\left(3-4e^{-\xi dt}+e^{-2\xi dt}\right)\right]\\ \sigma_{v}^{2} & =1-e^{-2\xi dt}\\ c_{rv} & =\frac{\left(1-e^{-\xi dt}\right)^{2}}{\xi dt\sigma_{r}\sigma_{v}} \end{align*} \)

Those are the unitless versions, multiply by \(\frac{\delta t^2 k_B T}{m}\), \(\frac{k_B T}{m}\), and \(\frac{\delta t k_B T}{m}\) respectively to get the unit-full versions in the book

Constructor & Destructor Documentation

CollectionSol::CollectionSol	(	sptr< Box >	box,
		sptr< AtomGroup >	atoms,
		const flt	dt,
		const flt	damping,
		const flt	desired_temperature,
		vector< sptr< Interaction > >	interactions = `vector<sptr<Interaction> >()`,
		vector< sptr< StateTracker > >	trackers = `vector<sptr<StateTracker> >()`,
		vector< sptr< Constraint > >	constraints = `vector<sptr<Constraint> >()`
	)

Parameters

box	Box for the atoms
atoms	The atoms
dt	The timestep \(\delta t\)
damping	Damping coefficient, \(\xi\)
desired_temperature	The desired temperature \(T\)
interactions	The interactions, other than brownian motion. These provide \(\vec{f}\).
trackers	Trackers, such as a NeighborList
constraints	Constraints

Member Function Documentation

void CollectionSol::change_force	(	const flt	damp,
		const flt	fmag,
		const flt	desired_temperature
	)

inline

Change the timestep \(\delta t\).

void CollectionSol::change_temperature	(	const flt	damp,
		const flt	desired_temperature
	)

inline

Change the desired damping coefficient \(\xi\) or temperature \(T\).

void CollectionSol::set_constants ( )

protected

Set c0, c1, c2, sigmar, sigmav, corr from desT, dt, and damping.

void CollectionSol::set_dt ( const flt newdt )

inline

void CollectionSol::timestep ( )

virtual

Take one step forward in time.

Implements Collection.

Member Data Documentation

flt CollectionSol::c0

protected

flt CollectionSol::c1

protected

flt CollectionSol::c2

protected

flt CollectionSol::corr

protected

flt CollectionSol::damping

protected

Damping coefficient, \(\xi\).

flt CollectionSol::desT

protected

desired temperature

flt CollectionSol::dt

protected

flt CollectionSol::force_mag

protected

BivariateGauss CollectionSol::gauss

protected

The random number generator.

flt CollectionSol::sigmar

protected

note that this is sigmar/sqrt(T/m), same for sigmav corr is unitless, and correct

flt CollectionSol::sigmav

protected

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

src/collection.hpp
src/collection.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation