Detailed Description

McMove is an abstract base class for Monte Carlo moves.

The virtual move() method must generate a trial move, decide whether to accept or reject it, and update the associated System or Systems if it is accepted.

Definition at line 31 of file McMove.h.

#include <McMove.h>

Inheritance diagram for McMd::McMove:

Public Member Functions
	McMove (Simulation &simulation)
	Constructor. More...

virtual	~McMove ()
	Destructor. More...

virtual void	readParameters (std::istream &in)
	Read required parameters from file. 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...

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

virtual void	setup ()
	Setup before the beginning of each simulation run. 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	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...

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...

Constructor & Destructor Documentation

McMd::McMove::McMove ( Simulation & simulation )

Constructor.

Parameters

simulation parent Simulation object.

Definition at line 20 of file McMove.cpp.

McMd::McMove::~McMove ( )

virtual

Destructor.

Empty default implementation.

Definition at line 30 of file McMove.cpp.

Member Function Documentation

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

virtual

Read required parameters from file.

Empty default implementation.

Reimplemented from Util::ParamComposite.

Reimplemented in McMd::MdMove, McMd::CfbLinear, McMd::DpdMove, McMd::HybridNphMdMove, McMd::CfbEndBase, McMd::HybridMdMove, McMd::CfbRebridgeBase, McMd::CfbReptateMove, McMd::EndSwapMove, McMd::CfbRingRebridgeMove, McMd::CfbReptationMove, McMd::CfbRebridgeMove, McMd::CfbLinearEndMove, McMd::RingTetraRebridgeMove, McMd::RigidDisplaceMove, McMd::CfbEndMove, McMd::RingOctaRebridgeMove, McMd::CfbDoubleRebridgeMove, McMd::AtomDisplaceMove, McMd::HomopolymerSemiGrandMove, McMd::GcSliplinkMove, McMd::Sliplinker, McMd::SliplinkerAll, McMd::SliplinkerEnd, and McMd::SliplinkMove.

Definition at line 36 of file McMove.cpp.

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

virtual

Load internal state from an archive.

Parameters

ar	input/loading archive

Reimplemented from Util::ParamComposite.

Reimplemented in McMd::MdMove, McMd::CfbLinear, McMd::DpdMove, McMd::HybridNphMdMove, McMd::HybridMdMove, McMd::RingTetraRebridgeMove, McMd::CfbRebridgeBase, McMd::CfbReptateMove, McMd::EndSwapMove, McMd::CfbRingRebridgeMove, McMd::CfbReptationMove, McMd::CfbRebridgeMove, McMd::CfbLinearEndMove, McMd::RigidDisplaceMove, McMd::CfbEndMove, McMd::RingOctaRebridgeMove, McMd::CfbDoubleRebridgeMove, McMd::AtomDisplaceMove, and McMd::HomopolymerSemiGrandMove.

Definition at line 48 of file McMove.cpp.

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

virtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from Util::ParamComposite.

Reimplemented in McMd::MdMove, McMd::CfbLinear, McMd::DpdMove, McMd::HybridNphMdMove, McMd::HybridMdMove, McMd::RingTetraRebridgeMove, McMd::CfbRebridgeBase, McMd::CfbReptateMove, McMd::EndSwapMove, McMd::CfbRingRebridgeMove, McMd::CfbReptationMove, McMd::CfbRebridgeMove, McMd::CfbLinearEndMove, McMd::RigidDisplaceMove, McMd::CfbEndMove, McMd::RingOctaRebridgeMove, McMd::CfbDoubleRebridgeMove, McMd::AtomDisplaceMove, and McMd::HomopolymerSemiGrandMove.

Definition at line 58 of file McMove.cpp.

Referenced by McMd::HomopolymerSemiGrandMove::save(), McMd::AtomDisplaceMove::save(), McMd::CfbDoubleRebridgeMove::save(), McMd::RingOctaRebridgeMove::save(), McMd::CfbEndMove::save(), McMd::RigidDisplaceMove::save(), McMd::CfbLinearEndMove::save(), McMd::CfbRebridgeMove::save(), McMd::CfbReptationMove::save(), McMd::CfbRingRebridgeMove::save(), McMd::EndSwapMove::save(), McMd::CfbReptateMove::save(), McMd::RingTetraRebridgeMove::save(), McMd::HybridMdMove::save(), McMd::HybridNphMdMove::save(), McMd::DpdMove::save(), and McMd::MdMove::save().

void McMd::McMove::setProbability ( double probability )

inline

Set the probability for this McMove.

Parameters

probability Probability of this move being chosen.

Definition at line 221 of file McMove.h.

void McMd::McMove::setup ( )

virtual

Setup before the beginning of each simulation run.

This method zeros the statistical accumulators nAttempt and nAccept. Derived class implementations should complete any other initialization that is required at the beginning of each simulation run within a sequence of several such runs.

Reimplemented in McMd::DpdMove, and McMd::CfbRebridgeBase.

Definition at line 68 of file McMove.cpp.

bool McMd::McMove::move ( )

virtual

Generate, attempt, and accept or reject a Monte Carlo move.

Implementations of this by subclasses should:

Generate a move (e.g., choose new atomic positions)
Decide to accept or reject (use random::metropolis)
Implement the move if accepted

Trivial default implemention always returns false.

Returns: true if accepted, false if rejected

Reimplemented in McMd::DpdMove, McMd::MdMove, McMd::HybridNphMdMove, McMd::RigidDisplaceMove, McMd::HybridMdMove, McMd::CfbReptateMove, McMd::EndSwapMove, McMd::CfbRingRebridgeMove, McMd::CfbReptationMove, McMd::HomopolymerSemiGrandMove, McMd::CfbRebridgeMove, McMd::CfbLinearEndMove, McMd::CfbEndMove, McMd::RingOctaRebridgeMove, McMd::CfbDoubleRebridgeMove, McMd::AtomDisplaceMove, McMd::RingTetraRebridgeMove, McMd::GcSliplinkMove, McMd::Sliplinker, McMd::SliplinkerAll, McMd::SliplinkerEnd, and McMd::SliplinkMove.

Definition at line 77 of file McMove.cpp.

Referenced by McMd::McSimulation::simulate().

double McMd::McMove::probability ( ) const

inline

Return probability for this McMove.

Definition at line 215 of file McMove.h.

long McMd::McMove::nAttempt ( ) const

inline

Return number of moves that have been attempted.

Definition at line 177 of file McMove.h.

long McMd::McMove::nAccept ( ) const

inline

Return number of moves that have been accepted.

Definition at line 183 of file McMove.h.

void McMd::McMove::output ( )

virtual

Output statistics for this move (called at the end of the simulation)

Reimplemented in McMd::CfbReptateMove, and McMd::CfbReptationMove.

Definition at line 86 of file McMove.cpp.

void McMd::McMove::incrementNAttempt ( )

inlineprotected

void McMd::McMove::incrementNAccept ( )

inlineprotected

Simulation & McMd::McMove::simulation ( )

inlineprotected

Get parent Simulation object.

Definition at line 203 of file McMove.h.

Random & McMd::McMove::random ( )

inlineprotected

Get Random number generator of parent Simulation.

Definition at line 209 of file McMove.h.

Referenced by McMd::CfbLinear::addAtom(), McMd::CfbEndBase::addEndAtom(), McMd::CfbRebridgeBase::addMiddleAtom(), McMd::CfbLinear::deleteAtom(), McMd::CfbEndBase::deleteEndAtom(), McMd::CfbRebridgeBase::deleteMiddleAtom(), McMd::GcSliplinkMove::move(), McMd::SliplinkerEnd::move(), McMd::Sliplinker::move(), McMd::SliplinkerAll::move(), McMd::SliplinkMove::move(), McMd::RingTetraRebridgeMove::move(), McMd::AtomDisplaceMove::move(), McMd::CfbDoubleRebridgeMove::move(), McMd::CfbEndMove::move(), McMd::RingOctaRebridgeMove::move(), McMd::CfbLinearEndMove::move(), McMd::CfbRebridgeMove::move(), McMd::HomopolymerSemiGrandMove::move(), McMd::CfbReptationMove::move(), McMd::EndSwapMove::move(), McMd::CfbRingRebridgeMove::move(), McMd::CfbReptateMove::move(), McMd::HybridMdMove::move(), McMd::HybridNphMdMove::move(), McMd::RigidDisplaceMove::move(), McMd::RingOctaRebridgeMove::scanBridge(), and McMd::RingTetraRebridgeMove::scanBridge().

void McMd::McMove::readProbability ( std::istream & in )

protected

Read the probability from file.

Definition at line 42 of file McMove.cpp.

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

Detailed Description

Public Member Functions

Protected Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation