Detailed Description

Base class for configuration bias (CFB) end regrowth moves.

This class provides functions that use Rosenbluth sampling to delete or add a single atom to a specified end of a Linear molecule. These are the building blocks of configuration bias regrowth and reptation algorithms for linear chains.

Limitations: The current implementation works with model with external and angle potentials, but does not yet work with dihedral potentials. The treatment of angle potentials does not use the angle potential to bias the choice of trial bond orientations, and so is not efficient for strong angle potentials.

Definition at line 39 of file CfbLinear.h.

#include <CfbLinear.h>

Inheritance diagram for McMd::CfbLinear:

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

virtual	~CfbLinear ()
	Destructor. More...

virtual void	readParameters (std::istream &in)
	Read and validate speciesId and nTrial. More...

virtual void	loadParameters (Serializable::IArchive &ar)
	Load and validate speciesId and nTrial. More...

virtual void	save (Serializable::OArchive &ar)
	Save speciesId and nTrial. More...

void	deleteAtom (Molecule &molecule, int atomId, int sign, double &rosenbluth, double &energy)
	CFB algorithm for deleting an end atom from a Linear molecule. More...

void	addAtom (Molecule &molecule, Atom &atom0, Atom &atom1, int atomId, int sign, double &rosenbluth, double &energy)
	Configuration bias algorithm for adding an atom to a Linear molecule. 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...

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
int	nTrial () const
	Get nTrial. More...

int	speciesId () const
	Get speciesId. 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...

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::CfbLinear::CfbLinear ( McSystem & system )

Constructor.

Definition at line 32 of file CfbLinear.cpp.

References UTIL_THROW.

McMd::CfbLinear::~CfbLinear ( )

virtual

Destructor.

Definition at line 45 of file CfbLinear.cpp.

References McMd::McSystem::hasAnglePotential(), McMd::McSystem::hasDihedralPotential(), McMd::McSystem::hasExternalPotential(), Simp::Species::nAngle(), Simp::Species::nDihedral(), McMd::McMove::simulation(), McMd::Simulation::species(), McMd::SystemMove::system(), and UTIL_THROW.

Member Function Documentation

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

virtual

Read and validate speciesId and nTrial.

Reimplemented from McMd::McMove.

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

Definition at line 92 of file CfbLinear.cpp.

Referenced by McMd::CfbLinearEndMove::readParameters(), and McMd::CfbReptateMove::readParameters().

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

virtual

Load and validate speciesId and nTrial.

Parameters

ar	input (loading) archive

Reimplemented from McMd::McMove.

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

Definition at line 102 of file CfbLinear.cpp.

Referenced by McMd::CfbLinearEndMove::loadParameters(), and McMd::CfbReptateMove::loadParameters().

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

virtual

Save speciesId and nTrial.

Parameters

ar	output (loading) archive

Reimplemented from McMd::McMove.

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

Definition at line 112 of file CfbLinear.cpp.

Referenced by McMd::CfbLinearEndMove::save(), and McMd::CfbReptateMove::save().

void McMd::CfbLinear::deleteAtom	(	Molecule &	molecule,
		int	atomId,
		int	sign,
		double &	rosenbluth,
		double &	energy
	)

CFB algorithm for deleting an end atom from a Linear molecule.

This function computes the energy of an end atom and a Rosenbluth factor for removing it. It does not remove the end atom from the system cell list.

Upon return:

rosenbluth is the nonbonded Rosenblush factor for the deleted atom, i.e., the sum of Boltzmann factors from nonbonded pair interactions for the initial position and nTrial_ - 1 trials.
energy is the total energy (bonded + nonbonded) of the end atom before it was deleted.

Parameters

molecule	molecule
atomId	id of atom to be deleted
sign	end from which deletion is occuring (= +-1)
rosenbluth	nonbonded Rosenbluth factor of deleted atom (out)
energy	total potential energy of deleted atom (out)

Definition at line 122 of file CfbLinear.cpp.

References McMd::McSystem::anglePotential(), McMd::Molecule::atom(), McMd::McPairPotential::atomEnergy(), McMd::ExternalPotential::atomEnergy(), McMd::SystemMove::boltzmann(), McMd::Molecule::bond(), McMd::McSystem::bondPotential(), McMd::SystemMove::boundary(), Simp::OrthorhombicBoundary::distanceSq(), Util::Vector::dot(), McMd::BondPotential::energy(), McMd::AnglePotential::energy(), McMd::McSystem::externalPotential(), McMd::Molecule::nAtom(), McMd::McSystem::pairPotential(), McMd::Atom::position(), McMd::McMove::random(), Simp::OrthorhombicBoundary::shift(), Util::Vector::subtract(), McMd::SystemMove::system(), McMd::Group< NAtom >::typeId(), and Util::Random::unitVector().

Referenced by McMd::CfbLinearEndMove::move(), and McMd::CfbReptateMove::move().

void McMd::CfbLinear::addAtom	(	Molecule &	molecule,
		Atom &	atom0,
		Atom &	atom1,
		int	atomId,
		int	sign,
		double &	rosenbluth,
		double &	energy
	)

Configuration bias algorithm for adding an atom to a Linear molecule.

This function generates and computes Rosenbluth factors for nTrial trial positions, chooses one, updates the atomic position. It does not add the end atom to the system cell list.

The function signature requires references to atom0 (the atom to be added) and atom1 (the one to which it is bonded) in order to allow this to be used in a reptation algorithm in which atoms are not added in place: In the reptation algorithm, a trial removal is made at the tail end of the molecule, and then the removed atom is used to store the position of trial addition at the head end. The atom positions are then shifted to restore the proper order in memory only if the move is accepted.

Upon return:

rosenbluth is assigned the nonbonded Rosenblush factor for the added atom, i.e., the sum of Boltzmann factors for all nTrial_ trial positions.
energy is assigned the total energy (bonded + nonbonded) of the new atom in the selected new position.

Parameters

molecule	molecule
atom0	atom to be added
atom1	atom to which atom0 is bonded (pivot atom)
atomId	local id of atom0 (0 <= id < molecule.nAtom())
sign	end from which deletion is occuring (=+-1)
rosenbluth	Rosenbluth factor of added atom (out)
energy	potential energy of deleted atom (out)