Detailed Description

Molecule rebridging move for a Ring species.

The exchange of positions of two closely approaching atoms is attempted. Each atom is bonded to two other atoms. The move requires that the 6 atoms form an octahedron in which the edge lengths satisfying certain distance criterions, before the exchange is attempted.

Definition at line 32 of file RingOctaRebridgeMove.h.

#include <RingOctaRebridgeMove.h>

Inheritance diagram for McMd::RingOctaRebridgeMove:

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

virtual void	readParameters (std::istream &in)
	Read species to which displacement is applied. More...

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

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

virtual bool	move ()
	Generate and accept or reject configuration bias move. More...

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

virtual	~GroupRebridgeBase ()
	Destructor. More...

void	tetraEnergy (Atom aPtr, Atom bPtr, Atom cPtr, Atom dPtr, int bondType, double &energy)
	Calculate the energy cost for rebriding a tetra group. More...

double	angleEnergy (const Atom &a, const Atom &b, const Atom &c, int type)
	Calculate the angle energy for a bead triple. More...

void	octaEnergy (Atom aPtr, Atom bPtr, Atom cPtr, Atom dPtr, Atom mPtr, Atom nPtr, int bondType, double &energy)
	Calculate the energy cost for rebriding an octa group. 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 void	setup ()
	Setup before the beginning of each simulation run. 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
bool	scanBridge (Molecule *molPtr, int mId, int &molId2, int &nId)
	Scan potential rebridging sites. More...

int	modId (int id, int n)
	Shift Atom index along a Ring. 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
int	speciesId_
	Integer index for molecular species. More...

double	upperBridge_
	Upper bounds for trial length of a bridge. More...

double	lowerBridge_
	Lower bounds for trial length of a bridge. More...

CellList::NeighborArray	neighbors_
	Neighbor list around test 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...

Constructor & Destructor Documentation

McMd::RingOctaRebridgeMove::RingOctaRebridgeMove ( McSystem & system )

Constructor.

Definition at line 30 of file RingOctaRebridgeMove.cpp.

References Util::ParamComposite::setClassName().

Member Function Documentation

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

virtual

Read species to which displacement is applied.

Reimplemented from McMd::McMove.

Definition at line 40 of file RingOctaRebridgeMove.cpp.

References lowerBridge_, McMd::McMove::readProbability(), McMd::McMove::simulation(), McMd::Simulation::species(), speciesId_, upperBridge_, and UTIL_THROW.

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

virtual

Load state from an archive.

Parameters

ar	loading (input) archive.

Reimplemented from McMd::McMove.

Definition at line 59 of file RingOctaRebridgeMove.cpp.

References McMd::McMove::loadParameters(), lowerBridge_, McMd::McMove::simulation(), McMd::Simulation::species(), speciesId_, upperBridge_, and UTIL_THROW.

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

virtual

Save state to an archive.

Parameters

ar	saving (output) archive.

Reimplemented from McMd::McMove.

Definition at line 77 of file RingOctaRebridgeMove.cpp.

References lowerBridge_, McMd::McMove::save(), speciesId_, and upperBridge_.

bool McMd::RingOctaRebridgeMove::move ( )

virtual

Generate and accept or reject configuration bias move.

Reimplemented from McMd::McMove.

Definition at line 95 of file RingOctaRebridgeMove.cpp.

References McMd::Molecule::atom(), McMd::McSystem::atomPotentialEnergy(), McMd::SystemMove::boltzmann(), McMd::McMove::incrementNAccept(), McMd::McMove::incrementNAttempt(), Util::Random::metropolis(), McMd::System::molecule(), McMd::Molecule::nAtom(), McMd::McSystem::pairPotential(), McMd::Atom::position(), McMd::McMove::random(), McMd::System::randomMolecule(), scanBridge(), speciesId_, McMd::SystemMove::system(), Util::Random::uniformInt(), and McMd::McPairPotential::updateAtomCell().

bool McMd::RingOctaRebridgeMove::scanBridge	(	Molecule *	molPtr,
		int	mId,
		int &	molId2,
		int &	nId
	)

protected

Scan potential rebridging sites.

Parameters

molPtr	Pointer to the first molecule.
mId	The middle atom Id on the first molecule.
molId2	The index of the second molecule.
nId	The middle atom Id on the second molecule.

Definition at line 176 of file RingOctaRebridgeMove.cpp.

References McMd::Molecule::atom(), McMd::SystemMove::boundary(), McMd::McPairPotential::cellList(), Simp::OrthorhombicBoundary::distanceSq(), McMd::CellList::getNeighbors(), McMd::Molecule::id(), Simp::Species::id(), McMd::Atom::indexInMolecule(), lowerBridge_, modId(), McMd::Atom::molecule(), McMd::System::molecule(), McMd::Molecule::nAtom(), neighbors_, McMd::McSystem::pairPotential(), McMd::Atom::position(), McMd::McMove::random(), Util::FSArray< Data, Capacity >::size(), McMd::Molecule::species(), speciesId_, McMd::SystemMove::system(), Util::Random::uniformInt(), and upperBridge_.

Referenced by move().

int McMd::RingOctaRebridgeMove::modId	(	int	id,
		int	n
	)

inlineprotected

Shift Atom index along a Ring.

Parameters

id	Atom id to be regulated, which can be negative.
n	Number of atoms in the Ring.

Definition at line 102 of file RingOctaRebridgeMove.h.

Referenced by scanBridge().

Member Data Documentation

int McMd::RingOctaRebridgeMove::speciesId_

protected

Integer index for molecular species.

Definition at line 69 of file RingOctaRebridgeMove.h.

Referenced by loadParameters(), move(), readParameters(), save(), and scanBridge().

double McMd::RingOctaRebridgeMove::upperBridge_

protected

Upper bounds for trial length of a bridge.

Definition at line 72 of file RingOctaRebridgeMove.h.

Referenced by loadParameters(), readParameters(), save(), and scanBridge().

double McMd::RingOctaRebridgeMove::lowerBridge_

protected

Lower bounds for trial length of a bridge.

Definition at line 75 of file RingOctaRebridgeMove.h.

Referenced by loadParameters(), readParameters(), save(), and scanBridge().

CellList::NeighborArray McMd::RingOctaRebridgeMove::neighbors_

protected

Neighbor list around test atom.

Definition at line 78 of file RingOctaRebridgeMove.h.

Referenced by scanBridge().

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

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation