This is a Monte Carlo barostat designed specifically for membrane simulations. More...

#include <MonteCarloMembraneBarostat.h>

Inheritance diagram for MonteCarloMembraneBarostat:

Public Types
enum	XYMode { XYIsotropic = 0, XYAnisotropic = 1 }
	This is an enumeration of the different behaviors for the X and Y axes. More...

enum	ZMode { ZFree = 0, ZFixed = 1, ConstantVolume = 2 }
	This is an enumeration of the different behaviors for Z axis. More...

Public Member Functions
	MonteCarloMembraneBarostat (double defaultPressure, double defaultSurfaceTension, double temperature, XYMode xymode, ZMode zmode, int frequency=25)
	Create a MonteCarloMembraneBarostat. More...

double	getDefaultPressure () const
	Get the default pressure acting on the system (in bar). More...

void	setDefaultPressure (double pressure)
	Set the default pressure acting on the system. More...

double	getDefaultSurfaceTension () const
	Get the default surface tension acting on the system (in bar*nm). More...

void	setDefaultSurfaceTension (double surfaceTension)
	Set the default surface tension acting on the system. More...

int	getFrequency () const
	Get the frequency (in time steps) at which Monte Carlo volume changes should be attempted. More...

void	setFrequency (int freq)
	Set the frequency (in time steps) at which Monte Carlo volume changes should be attempted. More...

double	getTemperature () const
	Get the temperature at which the system is being maintained, measured in Kelvin. More...

void	setTemperature (double temp)
	Set the temperature at which the system is being maintained. More...

XYMode	getXYMode () const
	Get the mode specifying the behavior of the X and Y axes. More...

void	setXYMode (XYMode mode)
	Set the mode specifying the behavior of the X and Y axes. More...

ZMode	getZMode () const
	Get the mode specifying the behavior of the Z axis. More...

void	setZMode (ZMode mode)
	Set the mode specifying the behavior of the Z axis. More...

int	getRandomNumberSeed () const
	Get the random number seed. More...

void	setRandomNumberSeed (int seed)
	Set the random number seed. More...

bool	usesPeriodicBoundaryConditions () const
	Returns whether or not this force makes use of periodic boundary conditions. More...

Public Member Functions inherited from Force
	Force ()

virtual	~Force ()

int	getForceGroup () const
	Get the force group this Force belongs to. More...

void	setForceGroup (int group)
	Set the force group this Force belongs to. More...

Static Public Member Functions
static const std::string &	Pressure ()
	This is the name of the parameter which stores the current pressure acting on the system (in bar). More...

static const std::string &	SurfaceTension ()
	This is the name of the parameter which stores the current surface tension acting on the system (in bar*nm). More...

Protected Member Functions
ForceImpl *	createImpl () const
	When a Context is created, it invokes this method on each Force in the System. More...

Protected Member Functions inherited from Force
ForceImpl &	getImplInContext (Context &context)
	Get the ForceImpl corresponding to this Force in a Context. More...

ContextImpl &	getContextImpl (Context &context)
	Get the ContextImpl corresponding to a Context. More...

Detailed Description

This is a Monte Carlo barostat designed specifically for membrane simulations.

It assumes the membrane lies in the XY plane. The Monte Carlo acceptance criterion includes a term to model isotropic pressure, which depends on the volume of the periodic box, and a second term to model surface tension, which depends on the cross sectional area of the box in the XY plane. Note that pressure and surface tension are defined with opposite senses: a larger pressure tends to make the box smaller, but a larger surface tension tends to make the box larger.

There are options for configuring exactly how the various box dimensions are allowed to change:

The X and Y axes may be treated isotropically, in which case they always scale by the same amount and remain in proportion to each other; or they may be treated anisotropically, in which case they can vary independently of each other.
The Z axis can be allowed to vary independently of the other axes; or held fixed; or constrained to vary in inverse proportion to the other two axes, so that the total box volume remains fixed.

This class assumes the simulation is also being run at constant temperature, and requires you to specify the system temperature (since it affects the acceptance probability for Monte Carlo moves). It does not actually perform temperature regulation, however. You must use another mechanism along with it to maintain the temperature, such as LangevinIntegrator or AndersenThermostat.

Member Enumeration Documentation

enum XYMode

This is an enumeration of the different behaviors for the X and Y axes.

Enumerator
XYIsotropic	The X and Y axes are always scaled by the same amount, so the ratio of their lengths remains constant.
XYAnisotropic	The X and Y axes are allowed to vary independently of each other.

enum ZMode

This is an enumeration of the different behaviors for Z axis.

Enumerator

ZFree

The Z axis is allowed to vary freely, independent of the other two axes.

ZFixed

The Z axis is held fixed and does not change.

ConstantVolume

The Z axis is always scaled in inverse proportion to the other two axes so the box volume remains fixed.

Note that in this mode pressure has no effect on the system, only surface tension.

Constructor & Destructor Documentation

MonteCarloMembraneBarostat	(	double	defaultPressure,
		double	defaultSurfaceTension,
		double	temperature,
		XYMode	xymode,
		ZMode	zmode,
		int	frequency = `25`
	)

Create a MonteCarloMembraneBarostat.

Parameters

defaultPressure	the default pressure acting on the system (in bar)
defaultSurfaceTension	the default surface tension acting on the system (in bar*nm)
temperature	the temperature at which the system is being maintained (in Kelvin)
xymode	the mode specifying the behavior of the X and Y axes
zmode	the mode specifying the behavior of the Z axis
frequency	the frequency at which Monte Carlo volume changes should be attempted (in time steps)

Member Function Documentation

ForceImpl* createImpl ( ) const

protectedvirtual

When a Context is created, it invokes this method on each Force in the System.

It should create a new ForceImpl object which can be used by the context for calculating forces. The ForceImpl will be deleted automatically when the Context is deleted.

Implements Force.

double getDefaultPressure ( ) const

inline

Get the default pressure acting on the system (in bar).

Returns: the default pressure acting on the system, measured in bar.

double getDefaultSurfaceTension ( ) const

inline

Get the default surface tension acting on the system (in bar*nm).

Returns: the default surface tension acting on the system, measured in bar*nm.

int getFrequency ( ) const

inline

Get the frequency (in time steps) at which Monte Carlo volume changes should be attempted.

If this is set to 0, the barostat is disabled.

int getRandomNumberSeed ( ) const

inline

Get the random number seed.

See setRandomNumberSeed() for details.

double getTemperature ( ) const

inline

Get the temperature at which the system is being maintained, measured in Kelvin.

XYMode getXYMode ( ) const

inline

Get the mode specifying the behavior of the X and Y axes.

ZMode getZMode ( ) const

inline

Get the mode specifying the behavior of the Z axis.

static const std::string& Pressure ( )

inlinestatic

This is the name of the parameter which stores the current pressure acting on the system (in bar).

void setDefaultPressure ( double pressure )

inline

Set the default pressure acting on the system.

This will affect any new Contexts you create, but not ones that already exist.

Parameters

pressure the default pressure acting on the system, measured in bar.

void setDefaultSurfaceTension ( double surfaceTension )

inline

Set the default surface tension acting on the system.

This will affect any new Contexts you create, but not ones that already exist.

Parameters

surfaceTension the default surface tension acting on the system, measured in bar.

void setFrequency ( int freq )

inline

Set the frequency (in time steps) at which Monte Carlo volume changes should be attempted.

If this is set to 0, the barostat is disabled.

void setRandomNumberSeed ( int seed )

inline

Set the random number seed.

It is guaranteed that if two simulations are run with different random number seeds, the sequence of Monte Carlo steps will be different. On the other hand, no guarantees are made about the behavior of simulations that use the same seed. In particular, Platforms are permitted to use non-deterministic algorithms which produce different results on successive runs, even if those runs were initialized identically.

If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context is created from this Force. This is done to ensure that each Context receives unique random seeds without you needing to set them explicitly.

void setTemperature ( double temp )

inline

Set the temperature at which the system is being maintained.

Parameters

temp	the system temperature, measured in Kelvin.

void setXYMode ( XYMode mode )

inline

Set the mode specifying the behavior of the X and Y axes.

void setZMode ( ZMode mode )

inline

Set the mode specifying the behavior of the Z axis.

static const std::string& SurfaceTension ( )

inlinestatic

This is the name of the parameter which stores the current surface tension acting on the system (in bar*nm).

bool usesPeriodicBoundaryConditions ( ) const

inlinevirtual

Returns whether or not this force makes use of periodic boundary conditions.

Returns: true if force uses PBC and false otherwise

Reimplemented from Force.

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

MonteCarloMembraneBarostat.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation