Detailed Description

Mix-in class for mutable subclasses of Species.

A mutable species is a class that is derived from both Species and SpeciesMutator. A mutable species models a species in which each molecule can be in any of an enumerable number of internal states. This may be used to represent, for example, homopolymers that can change type within a semi-grand canonical simulation, or polymers that can grow or shrink within some extended ensemble simulations. Changes in internal states may change the types of atoms and bonds, and may temporarily erase, or deactivate, certain atoms and bonds.

Each molecule in a mutable species is assigned an integer state id, to specify its internal state. Each state is assigned a floating point statistical weight. The statistical weights are unnormalized, i.e., they need not add to unity. The SpeciesMutator class provides arrays that store these state variables and statistical weights, and methods to access them.

Definition at line 41 of file SpeciesMutator.h.

#include <SpeciesMutator.h>

Inheritance diagram for McMd::SpeciesMutator:

Public Member Functions
	SpeciesMutator ()
	Constructor. More...

virtual	~SpeciesMutator ()
	Destructor. More...

Mutators
virtual void	readMoleculeState (std::istream &in, Molecule &molecule)
	Read the state id for one molecule from a configuration file stream. More...

virtual void	writeMoleculeState (std::ostream &out, const Molecule &molecule) const
	Write the state id for one molecule to a configuration file stream. More...

virtual void	setMoleculeState (Molecule &molecule, int stateId)=0
	Change the state of a specific molecule. More...

void	setWeight (int stateId, double weight)
	Set the statistical weight associated with a specific state. More...

int	moleculeStateId (const Molecule &molecule) const
	Get the state id for a specific molecule. More...

int	nState () const
	Get the number of possible molecule states. More...

int	stateOccupancy (int stateId) const
	Get the number of molecules with a specified state. More...

double	stateWeight (int stateId) const
	Get the statistical weight for a specfic molecular state. More...

Static Public Attributes
static const int	NullStateId = -1
	Null value for a state index. More...

Protected Member Functions
void	allocateSpeciesMutator (int nMolecule, int nState)
	Allocate arrays of molecule state ids and statistical weights. More...

void	setMoleculeStateId (const Molecule &molecule, int stateId)
	Set the state id of a specific molecule. More...

Constructor & Destructor Documentation

McMd::SpeciesMutator::SpeciesMutator ( )

Constructor.

The constructor sets Species::isSpeciesMutator_ to true.

Definition at line 19 of file SpeciesMutator.cpp.

McMd::SpeciesMutator::~SpeciesMutator ( )

virtual

Destructor.

Definition at line 27 of file SpeciesMutator.cpp.

Member Function Documentation

void McMd::SpeciesMutator::readMoleculeState	(	std::istream &	in,
		Molecule &	molecule
	)

virtual

Read the state id for one molecule from a configuration file stream.

Parameters

in	input stream
molecule	molecule of interest

Definition at line 84 of file SpeciesMutator.cpp.

References setMoleculeState().

Referenced by McMd::McMdConfigIo::read().

void McMd::SpeciesMutator::writeMoleculeState	(	std::ostream &	out,
		const Molecule &	molecule
	)		const

virtual

Write the state id for one molecule to a configuration file stream.

Parameters

out	output stream
molecule	molecule of interest

Definition at line 75 of file SpeciesMutator.cpp.

References moleculeStateId().

Referenced by McMd::McMdConfigIo::write().

virtual void McMd::SpeciesMutator::setMoleculeState	(	Molecule &	molecule,
		int	stateId
	)

pure virtual

Change the state of a specific molecule.

The method should be used to implement MC moves that change the internal state of a molecule, after the previous stateId and bead positions are known. The method can use knowledge of the previous stateId and previous bead positions to implement transitions between a specific pairs of states.

Parameters