MonteCarloAnisotropicBarostat Class Reference

This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure. More...

Inheritance diagram for MonteCarloAnisotropicBarostat:

Public Member Functions
def	PressureX
	PressureX() -> std::string const &.
def	PressureY
	PressureY() -> std::string const &.
def	PressureZ
	PressureZ() -> std::string const &.
def	getDefaultPressure
	getDefaultPressure(MonteCarloAnisotropicBarostat self) -> Vec3 const &
def	getScaleX
	getScaleX(MonteCarloAnisotropicBarostat self) -> bool
def	getScaleY
	getScaleY(MonteCarloAnisotropicBarostat self) -> bool
def	getScaleZ
	getScaleZ(MonteCarloAnisotropicBarostat self) -> bool
def	getFrequency
	getFrequency(MonteCarloAnisotropicBarostat self) -> int
def	setFrequency
	setFrequency(MonteCarloAnisotropicBarostat self, int freq)
def	getTemperature
	getTemperature(MonteCarloAnisotropicBarostat self) -> double
def	setTemperature
	setTemperature(MonteCarloAnisotropicBarostat self, double temp)
def	getRandomNumberSeed
	getRandomNumberSeed(MonteCarloAnisotropicBarostat self) -> int
def	setRandomNumberSeed
	setRandomNumberSeed(MonteCarloAnisotropicBarostat self, int seed)
def	__init__
	init(OpenMM::MonteCarloAnisotropicBarostat self, Vec3 const & defaultPressure, double temperature, bool scaleX=True, bool scaleY=True, bool scaleZ=True, int frequency=25) -> MonteCarloAnisotropicBarostat init(OpenMM::MonteCarloAnisotropicBarostat self, Vec3 const & defaultPressure, double temperature, bool scaleX=True, bool scaleY=True, bool scaleZ=True) -> MonteCarloAnisotropicBarostat init(OpenMM::MonteCarloAnisotropicBarostat self, Vec3 const & defaultPressure, double temperature, bool scaleX=True, bool scaleY=True) -> MonteCarloAnisotropicBarostat init(OpenMM::MonteCarloAnisotropicBarostat self, Vec3 const & defaultPressure, double temperature, bool scaleX=True) -> MonteCarloAnisotropicBarostat init(OpenMM::MonteCarloAnisotropicBarostat self, Vec3 const & defaultPressure, double temperature) -> MonteCarloAnisotropicBarostat init(OpenMM::MonteCarloAnisotropicBarostat self, MonteCarloAnisotropicBarostat other) -> MonteCarloAnisotropicBarostat
def	__del__
	del(OpenMM::MonteCarloAnisotropicBarostat self)
Public Member Functions inherited from Force
def	__init__
def	__del__
	del(OpenMM::Force self)
def	getForceGroup
	getForceGroup(Force self) -> int
def	setForceGroup
	setForceGroup(Force self, int group)
def	__copy__
def	__deepcopy__

Public Attributes
	this

Detailed Description

This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure.

This class is similar to MonteCarloBarostat, but each Monte Carlo move is applied to only one axis of the periodic box (unlike MonteCarloBarostat, which scales the entire box isotropically). This means that the box may change shape as well as size over the course of the simulation. It also allows you to specify a different pressure for each axis of the box, or to keep the box size fixed along certain axes while still allowing it to change along others.

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.

Constructor & Destructor Documentation

def __init__	(		self,
			args
	)

init(OpenMM::MonteCarloAnisotropicBarostat self, Vec3 const & defaultPressure, double temperature, bool scaleX=True, bool scaleY=True, bool scaleZ=True, int frequency=25) -> MonteCarloAnisotropicBarostat init(OpenMM::MonteCarloAnisotropicBarostat self, Vec3 const & defaultPressure, double temperature, bool scaleX=True, bool scaleY=True, bool scaleZ=True) -> MonteCarloAnisotropicBarostat init(OpenMM::MonteCarloAnisotropicBarostat self, Vec3 const & defaultPressure, double temperature, bool scaleX=True, bool scaleY=True) -> MonteCarloAnisotropicBarostat init(OpenMM::MonteCarloAnisotropicBarostat self, Vec3 const & defaultPressure, double temperature, bool scaleX=True) -> MonteCarloAnisotropicBarostat init(OpenMM::MonteCarloAnisotropicBarostat self, Vec3 const & defaultPressure, double temperature) -> MonteCarloAnisotropicBarostat init(OpenMM::MonteCarloAnisotropicBarostat self, MonteCarloAnisotropicBarostat other) -> MonteCarloAnisotropicBarostat

Create a MonteCarloAnisotropicBarostat.

Parameters

defaultPressure	The default pressure acting on each axis (in bar)
temperature	the temperature at which the system is being maintained (in Kelvin)
scaleX	whether to allow the X dimension of the periodic box to change size
scaleY	whether to allow the Y dimension of the periodic box to change size
scaleZ	whether to allow the Z dimension of the periodic box to change size
frequency	the frequency at which Monte Carlo pressure changes should be attempted (in time steps)

def __del__

(

self

)

del(OpenMM::MonteCarloAnisotropicBarostat self)

Member Function Documentation

def getDefaultPressure

(

self

)

getDefaultPressure(MonteCarloAnisotropicBarostat self) -> Vec3 const &

Get the default pressure (in bar).

def getFrequency

(

self

)

getFrequency(MonteCarloAnisotropicBarostat self) -> int

Get the frequency (in time steps) at which Monte Carlo pressure changes should be attempted. If this is set to 0, the barostat is disabled.

def getRandomNumberSeed

(

self

)

getRandomNumberSeed(MonteCarloAnisotropicBarostat self) -> int

Get the random number seed. See setRandomNumberSeed() for details.

def getScaleX

(

self

)

getScaleX(MonteCarloAnisotropicBarostat self) -> bool

Get whether to allow the X dimension of the periodic box to change size.

def getScaleY

(

self

)

getScaleY(MonteCarloAnisotropicBarostat self) -> bool

Get whether to allow the Y dimension of the periodic box to change size.

def getScaleZ

(

self

)

getScaleZ(MonteCarloAnisotropicBarostat self) -> bool

Get whether to allow the Z dimension of the periodic box to change size.

def getTemperature

(

self

)

getTemperature(MonteCarloAnisotropicBarostat self) -> double

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

def PressureX

(

)

PressureX() -> std::string const &.

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

def PressureY

(

)

PressureY() -> std::string const &.

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

def PressureZ

(

)

PressureZ() -> std::string const &.

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

def setFrequency	(		self,
			args
	)

setFrequency(MonteCarloAnisotropicBarostat self, int freq)

Set the frequency (in time steps) at which Monte Carlo pressure changes should be attempted. If this is set to 0, the barostat is disabled.

def setRandomNumberSeed	(		self,
			args
	)

setRandomNumberSeed(MonteCarloAnisotropicBarostat self, int seed)

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.

def setTemperature	(		self,
			args
	)

setTemperature(MonteCarloAnisotropicBarostat self, double temp)

Set the temperature at which the system is being maintained.

Parameters

temp	the system temperature, measured in Kelvin.

Member Data Documentation

this

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

• openmm.py