Detailed Description

Base class configuration bias moves internal segment regrowth moves.

Base class for configuration bias Monte Carlo moves that erase and regrow internal segments of linear polymer chains, with fixed endpoints.

Definition at line 31 of file CfbRebridgeBase.h.

#include <CfbRebridgeBase.h>

Inheritance diagram for McMd::CfbRebridgeBase:

Public Member Functions
	CfbRebridgeBase (McSystem &system)
	Constructor. More...

virtual	~CfbRebridgeBase ()
	Destructor. More...

virtual void	readParameters (std::istream &in)
	Read species type, nTrial, and parameters needed to evaluate the orientation bias. More...

virtual void	loadParameters (Serializable::IArchive &ar)
	Load internal state from an archive. More...

virtual void	save (Serializable::OArchive &ar)
	Save internal state to an archive. More...

virtual void	setup ()
	Initialize the arrays for preferential angle, effective spring constant and normalization factor. More...

Public Member Functions inherited from McMd::CfbEndBase
	CfbEndBase (McSystem &system)
	Constructor. More...

virtual	~CfbEndBase ()
	Destructor. More...

void	deleteEndAtom (Atom endPtr, Atom pvtPtr, int bondType, double &rosenbluth, double &energy)
	CFB algorithm for deleting an end atom from a flexible chain. More...

void	addEndAtom (Atom endPtr, Atom pvtPtr, int bondType, double &rosenbluth, double &energy)
	Configuration bias algorithm for adding an atom to a chain end. More...

Public Member Functions inherited from McMd::SystemMove
	SystemMove (McSystem &system)
	Constructor. More...

virtual	~SystemMove ()
	Destructor. More...

Public Member Functions inherited from McMd::McMove
	McMove (Simulation &simulation)
	Constructor. More...

virtual	~McMove ()
	Destructor. More...

void	setProbability (double probability)
	Set the probability for this McMove. More...

virtual bool	move ()
	Generate, attempt, and accept or reject a Monte Carlo move. More...

double	probability () const
	Return probability for this McMove. More...

long	nAttempt () const
	Return number of moves that have been attempted. More...

long	nAccept () const
	Return number of moves that have been accepted. More...

virtual void	output ()
	Output statistics for this move (called at the end of the simulation) More...

Public Member Functions inherited from Util::ParamComposite
	ParamComposite ()
	Constructor. More...

	ParamComposite (const ParamComposite &other)
	Copy constructor. More...

	ParamComposite (int capacity)
	Constructor. More...

virtual	~ParamComposite ()
	Virtual destructor. More...

void	resetParam ()
	Resets ParamComposite to its empty state. More...

virtual void	readParam (std::istream &in)
	Read the parameter file block. More...

virtual void	readParamOptional (std::istream &in)
	Read optional parameter file block. More...

virtual void	writeParam (std::ostream &out)
	Write all parameters to an output stream. More...

virtual void	load (Serializable::IArchive &ar)
	Load all parameters from an input archive. More...

virtual void	loadOptional (Serializable::IArchive &ar)
	Load an optional ParamComposite. More...

void	saveOptional (Serializable::OArchive &ar)
	Saves isActive flag, and then calls save() iff isActive is true. More...

void	readParamComposite (std::istream &in, ParamComposite &child, bool next=true)
	Add and read a required child ParamComposite. More...

void	readParamCompositeOptional (std::istream &in, ParamComposite &child, bool next=true)
	Add and attempt to read an optional child ParamComposite. More...

template<typename Type >
ScalarParam< Type > &	read (std::istream &in, const char *label, Type &value)
	Add and read a new required ScalarParam < Type > object. More...

template<typename Type >
ScalarParam< Type > &	readOptional (std::istream &in, const char *label, Type &value)
	Add and read a new optional ScalarParam < Type > object. More...

template<typename Type >
CArrayParam< Type > &	readCArray (std::istream &in, const char label, Type value, int n)
	Add and read a required C array parameter. More...

template<typename Type >
CArrayParam< Type > &	readOptionalCArray (std::istream &in, const char label, Type value, int n)
	Add and read an optional C array parameter. More...

template<typename Type >
DArrayParam< Type > &	readDArray (std::istream &in, const char *label, DArray< Type > &array, int n)
	Add and read a required DArray < Type > parameter. More...

template<typename Type >
DArrayParam< Type > &	readOptionalDArray (std::istream &in, const char *label, DArray< Type > &array, int n)
	Add and read an optional DArray < Type > parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	readFArray (std::istream &in, const char *label, FArray< Type, N > &array)
	Add and read a required FArray < Type, N > array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	readOptionalFArray (std::istream &in, const char *label, FArray< Type, N > &array)
	Add and read an optional FArray < Type, N > array parameter. More...

template<typename Type >
CArray2DParam< Type > &	readCArray2D (std::istream &in, const char label, Type value, int m, int n, int np)
	Add and read a required CArray2DParam < Type > 2D C-array. More...

template<typename Type >
CArray2DParam< Type > &	readOptionalCArray2D (std::istream &in, const char label, Type value, int m, int n, int np)
	Add and read an optional CArray2DParam < Type > 2D C-array parameter. More...

template<typename Type >
DMatrixParam< Type > &	readDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and read a required DMatrix < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	readOptionalDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and read an optional DMatrix < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	readDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
	Add and read a required symmetrix DMatrix. More...

template<typename Type >
DSymmMatrixParam< Type > &	readOptionalDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
	Add and read an optional DMatrix matrix parameter. More...

Begin &	readBegin (std::istream &in, const char *label, bool isRequired=true)
	Add and read a class label and opening bracket. More...

End &	readEnd (std::istream &in)
	Add and read the closing bracket. More...

Blank &	readBlank (std::istream &in)
	Add and read a new Blank object, representing a blank line. More...

void	loadParamComposite (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load a required child ParamComposite. More...

void	loadParamCompositeOptional (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load an optional child ParamComposite if isActive. More...

template<typename Type >
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value, bool isRequired)
	Add and load a new ScalarParam < Type > object. More...

template<typename Type >
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value)
	Add and load new required ScalarParam < Type > object. More...

template<typename Type >
CArrayParam< Type > &	loadCArray (Serializable::IArchive &ar, const char label, Type value, int n, bool isRequired)
	Add a C array parameter and load its elements. More...

template<typename Type >
CArrayParam< Type > &	loadCArray (Serializable::IArchive &ar, const char label, Type value, int n)
	Add and load a required CArrayParam< Type > array parameter. More...

template<typename Type >
DArrayParam< Type > &	loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n, bool isRequired)
	Add an load a DArray < Type > array parameter. More...

template<typename Type >
DArrayParam< Type > &	loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n)
	Add and load a required DArray< Type > array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array, bool isRequired)
	Add and load an FArray < Type, N > fixed-size array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array)
	Add and load a required FArray < Type > array parameter. More...

template<typename Type >
CArray2DParam< Type > &	loadCArray2D (Serializable::IArchive &ar, const char label, Type value, int m, int n, int np, bool isRequired)
	Add and load a CArray2DParam < Type > C 2D array parameter. More...

template<typename Type >
CArray2DParam< Type > &	loadCArray2D (Serializable::IArchive &ar, const char label, Type value, int m, int n, int np)
	Add and load a required < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired)
	Add and load a DMatrixParam < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and load a required DMatrixParam < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n, bool isRequired)
	Add and load a symmetric DSymmMatrixParam < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n)
	Add and load a required DSymmMatrixParam < Type > matrix parameter. More...

void	addParamComposite (ParamComposite &child, bool next=true)
	Add a child ParamComposite object to the format array. More...

Begin &	addBegin (const char *label)
	Add a Begin object representing a class name and bracket. More...

End &	addEnd ()
	Add a closing bracket. More...

Blank &	addBlank ()
	Create and add a new Blank object, representing a blank line. More...

std::string	className () const
	Get class name string. More...

bool	isRequired () const
	Is this ParamComposite required in the input file? More...

bool	isActive () const
	Is this parameter active? More...

Public Member Functions inherited from Util::ParamComponent
virtual	~ParamComponent ()
	Destructor. More...

void	setIndent (const ParamComponent &parent, bool next=true)
	Set indent level. More...

std::string	indent () const
	Return indent string for this object (string of spaces). More...

template<class Archive >
void	serialize (Archive &ar, const unsigned int version)
	Serialize this ParamComponent as a string. More...

Public Member Functions inherited from Util::Serializable
virtual	~Serializable ()
	Destructor. More...

Public Member Functions inherited from Util::MpiFileIo
	MpiFileIo ()
	Constructor. More...

	MpiFileIo (const MpiFileIo &other)
	Copy constructor. More...

bool	isIoProcessor () const
	Can this processor do file I/O ? More...

void	setIoCommunicator (MPI::Intracomm &communicator)
	Set the communicator. More...

void	clearCommunicator ()
	Clear (nullify) the communicator. More...

bool	hasIoCommunicator () const
	Does this object have an associated MPI communicator? More...

MPI::Intracomm &	ioCommunicator () const
	Get the MPI communicator by reference. More...

Protected Member Functions
void	deleteMiddleAtom (Atom partPtr, Atom prevPtr, Atom *nextPtr, int prevBType, int nextBType, double &rosenbluth, double &energy)
	Configuration bias algorithm for deleting a particle between two monomers and compute the corresponding Rosenbluth factor. More...

void	addMiddleAtom (Atom partPtr, Atom prevPtr, Atom *nextPtr, int prevBType, int nextBType, double &rosenbluth, double &energy)
	Configuration bias algorithm for adding the last particle with special bias in favor of closing the bridge. More...

void	deleteSequence (int nActive, int sign, Atom endPtr, int bonds, double &rosenbluth, double &energy)
	Configuration bias algorithm for deleting a consequtive sequence of atoms. More...

void	addSequence (int nActive, int sign, Atom beginPtr, int bonds, double &rosenbluth, double &energy)
	Configuration bias algorithm for adding a consequtive sequence of atoms. More...

Protected Member Functions inherited from McMd::SystemMove
McSystem &	system ()
	Get parent McSystem. More...

Boundary &	boundary ()
	Get Boundary object of parent McSystem. More...

EnergyEnsemble &	energyEnsemble ()
	Get EnergyEnsemble object of parent McSystem. More...

double	boltzmann (double energy)
	Boltzmann weight associated with an energy difference. More...

Protected Member Functions inherited from McMd::McMove
void	incrementNAttempt ()
	Increment the number of attempted moves. More...

void	incrementNAccept ()
	Increment the number of accepted moves. More...

Simulation &	simulation ()
	Get parent Simulation object. More...

Random &	random ()
	Get Random number generator of parent Simulation. More...

void	readProbability (std::istream &in)
	Read the probability from file. More...

Protected Member Functions inherited from Util::ParamComposite
void	setClassName (const char *className)
	Set class name string. More...

void	setIsRequired (bool isRequired)
	Set or unset the isActive flag. More...

void	setIsActive (bool isActive)
	Set or unset the isActive flag. More...

void	setParent (ParamComponent &param, bool next=true)
	Set this to the parent of a child component. More...

void	addComponent (ParamComponent &param, bool isLeaf=true)
	Add a new ParamComponent object to the format array. More...

template<typename Type >
ScalarParam< Type > &	add (std::istream &in, const char *label, Type &value, bool isRequired=true)
	Add a new required ScalarParam < Type > object. More...

template<typename Type >
CArrayParam< Type > &	addCArray (std::istream &in, const char label, Type value, int n, bool isRequired=true)
	Add (but do not read) a required C array parameter. More...

template<typename Type >
DArrayParam< Type > &	addDArray (std::istream &in, const char *label, DArray< Type > &array, int n, bool isRequired=true)
	Add (but do not read) a DArray < Type > parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	addFArray (std::istream &in, const char *label, FArray< Type, N > &array, bool isRequired=true)
	Add (but do not read) a FArray < Type, N > array parameter. More...

template<typename Type >
CArray2DParam< Type > &	addCArray2D (std::istream &in, const char label, Type value, int m, int n, int np, bool isRequired=true)
	Add (but do not read) a CArray2DParam < Type > 2D C-array. More...

template<typename Type >
DMatrixParam< Type > &	addDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired=true)
	Add and read a required DMatrix < Type > matrix parameter. More...

Protected Member Functions inherited from Util::ParamComponent
	ParamComponent ()
	Constructor. More...

	ParamComponent (const ParamComponent &other)
	Copy constructor. More...

Protected Attributes
double	length21_
	Equilibrium bond lengths (2-1 bond). More...

double	length10_
	Equilibrium bond lengths (1-0 bonds). More...

double	kappa10_
	Spring constant (1-0 bond). More...

Protected Attributes inherited from McMd::CfbEndBase
int	nTrial_
	Actual number of trial positions for each regrown atom. More...

Additional Inherited Members
Public Types inherited from Util::Serializable
typedef BinaryFileOArchive	OArchive
	Type of output archive used by save method. More...

typedef BinaryFileIArchive	IArchive
	Type of input archive used by load method. More...

Static Public Member Functions inherited from Util::ParamComponent
static void	initStatic ()
	Initialize static echo member to false. More...

static void	setEcho (bool echo=true)
	Enable or disable echoing for all subclasses of ParamComponent. More...

static bool	echo ()
	Get echo parameter. More...

Static Protected Attributes inherited from McMd::CfbEndBase
static const int	MaxTrial_ = 20
	Maximum allowed number of trial positions for a regrown atom. More...

Constructor & Destructor Documentation

McMd::CfbRebridgeBase::CfbRebridgeBase ( McSystem & system )

Constructor.

Definition at line 23 of file CfbRebridgeBase.cpp.

References McMd::McSystem::hasDihedralPotential(), and UTIL_THROW.

McMd::CfbRebridgeBase::~CfbRebridgeBase ( )

virtual

Destructor.

Definition at line 42 of file CfbRebridgeBase.cpp.

Member Function Documentation

void McMd::CfbRebridgeBase::readParameters ( std::istream & in )

virtual

Read species type, nTrial, and parameters needed to evaluate the orientation bias.

Reimplemented from McMd::CfbEndBase.

Reimplemented in McMd::CfbRingRebridgeMove, McMd::CfbRebridgeMove, and McMd::CfbDoubleRebridgeMove.

Definition at line 48 of file CfbRebridgeBase.cpp.

References kappa10_, length10_, length21_, McMd::CfbEndBase::MaxTrial_, McMd::CfbEndBase::nTrial_, and UTIL_THROW.

Referenced by McMd::CfbDoubleRebridgeMove::readParameters(), McMd::CfbRebridgeMove::readParameters(), and McMd::CfbRingRebridgeMove::readParameters().

void McMd::CfbRebridgeBase::loadParameters ( Serializable::IArchive & ar )

virtual

Load internal state from an archive.

Parameters

ar	input/loading archive

Reimplemented from McMd::McMove.

Reimplemented in McMd::CfbRingRebridgeMove, McMd::CfbRebridgeMove, and McMd::CfbDoubleRebridgeMove.

Definition at line 65 of file CfbRebridgeBase.cpp.

References kappa10_, length10_, length21_, McMd::CfbEndBase::MaxTrial_, McMd::CfbEndBase::nTrial_, and UTIL_THROW.

Referenced by McMd::CfbDoubleRebridgeMove::loadParameters(), McMd::CfbRebridgeMove::loadParameters(), and McMd::CfbRingRebridgeMove::loadParameters().

void McMd::CfbRebridgeBase::save ( Serializable::OArchive & ar )

virtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from McMd::McMove.

Reimplemented in McMd::CfbRingRebridgeMove, McMd::CfbRebridgeMove, and McMd::CfbDoubleRebridgeMove.

Definition at line 81 of file CfbRebridgeBase.cpp.

References kappa10_, length10_, length21_, and McMd::CfbEndBase::nTrial_.

Referenced by McMd::CfbDoubleRebridgeMove::save(), McMd::CfbRebridgeMove::save(), and McMd::CfbRingRebridgeMove::save().

void McMd::CfbRebridgeBase::setup ( )

virtual

Initialize the arrays for preferential angle, effective spring constant and normalization factor.

Reimplemented from McMd::McMove.

Definition at line 92 of file CfbRebridgeBase.cpp.

References kappa10_, length10_, and length21_.

Referenced by McMd::CfbDoubleRebridgeMove::loadParameters(), McMd::CfbRebridgeMove::loadParameters(), McMd::CfbRingRebridgeMove::loadParameters(), McMd::CfbDoubleRebridgeMove::readParameters(), McMd::CfbRebridgeMove::readParameters(), and McMd::CfbRingRebridgeMove::readParameters().

void McMd::CfbRebridgeBase::deleteMiddleAtom	(	Atom *	partPtr,
		Atom *	prevPtr,
		Atom *	nextPtr,
		int	prevBType,
		int	nextBType,
		double &	rosenbluth,
		double &	energy
	)

protected

Configuration bias algorithm for deleting a particle between two monomers and compute the corresponding Rosenbluth factor.

Definition at line 151 of file CfbRebridgeBase.cpp.

References Util::Vector::add(), McMd::McSystem::anglePotential(), McMd::McPairPotential::atomEnergy(), McMd::ExternalPotential::atomEnergy(), McMd::AnglePotential::atomEnergy(), McMd::SystemMove::boltzmann(), McMd::McSystem::bondPotential(), McMd::SystemMove::boundary(), Simp::OrthorhombicBoundary::distanceSq(), McMd::BondPotential::energy(), McMd::McSystem::externalPotential(), McMd::CfbEndBase::nTrial_, McMd::McSystem::pairPotential(), McMd::Atom::position(), McMd::McMove::random(), Simp::OrthorhombicBoundary::shift(), McMd::SystemMove::system(), and Util::Random::unitVector().

Referenced by deleteSequence(), and McMd::CfbRingRebridgeMove::move().

void McMd::CfbRebridgeBase::addMiddleAtom	(	Atom *	partPtr,
		Atom *	prevPtr,
		Atom *	nextPtr,
		int	prevBType,
		int	nextBType,
		double &	rosenbluth,
		double &	energy
	)