Detailed Description

A PairPotential for MC simulations (abstract).

Definition at line 30 of file McPairPotential.h.

#include <McPairPotential.h>

Inheritance diagram for McMd::McPairPotential:

Public Member Functions
	McPairPotential (System &system)
	Constructor. More...

virtual	~McPairPotential ()
	Destructor. More...

Energy Evaluators (pure virtual)
virtual double	atomEnergy (const Atom &atom) const =0
	Calculate the nonbonded pair energy for one Atom. More...

virtual double	moleculeEnergy (const Molecule &molecule) const =0
	Calculate the nonbonded pair energy for an entire Molecule. More...

Cell List Management
void	buildCellList ()
	Build the CellList with current configuration. More...

void	addAtom (Atom &atom)
	Add an Atom to the CellList. More...

void	deleteAtom (Atom &atom)
	Remove an Atom from the CellList. More...

void	updateAtomCell (Atom &atom)
	Update the cell list to reflect a new position. More...

void	moveAtom (Atom &atom, const Vector &position)
	Move an Atom position, and update the CellList. More...

const CellList &	cellList () const
	Get the cellList by const reference. 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	readParameters (std::istream &in)
	Read the body of parameter block, without begin and end lines. 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...

virtual void	loadParameters (Serializable::IArchive &ar)
	Load state from archive, without adding Begin and End lines. More...

virtual void	save (Serializable::OArchive &ar)
	Saves all parameters to an archive. 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...

Public Member Functions inherited from McMd::PairPotential
virtual	~PairPotential ()
	Destructor (does nothing) More...

virtual double	energy (double rsq, int iAtomType, int jAtomType) const =0
	Return pair energy for a single pair. More...

virtual double	forceOverR (double rsq, int iAtomType, int jAtomType) const =0
	Return force / separation for a single pair. More...

virtual void	set (std::string name, int i, int j, double value)=0
	Modify a parameter, identified by a string. More...

virtual double	get (std::string name, int i, int j) const =0
	Get a parameter value, identified by a string. More...

virtual double	maxPairCutoff () const =0
	Return maximum cutoff distance. More...

virtual std::string	interactionClassName () const =0
	Return name of pair interaction class (e.g., "LJPair"). More...

Public Member Functions inherited from McMd::EnergyCalculator
virtual void	computeEnergy ()=0
	Calculate the total nonBonded pair energy for the associated System. More...

virtual void	unsetEnergy ()
	Mark the energy as unknown. More...

double	energy ()
	Return the energy contribution, compute if necessary. More...

Public Member Functions inherited from McMd::StressCalculator
virtual void	computeStress ()
	Compute and store the stress tensor. More...

virtual void	unsetStress ()
	Mark the stress as unknown. More...

void	computeStress (Tensor &stress)
	Get pair stress tensor. More...

void	computeStress (Vector &pressures)
	Get the xx, yy, zz non-Coulomb pair pressures. More...

void	computeStress (double &pressure)
	Get the scalar pressure. More...

bool	createsStress () const
	Return false if subclass does not generate stress. More...

Public Member Functions inherited from McMd::SystemInterface
	SystemInterface (System &parent)
	Constructor. More...

virtual	~SystemInterface ()
	Destructor. More...

System &	system () const
	Get the parent System by reference. More...

Protected Attributes
CellList::NeighborArray	neighbors_
	Array to hold neighbors returned by a CellList. More...

CellList	cellList_
	Cell list for atom positions. 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...

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 Member Functions inherited from McMd::StressCalculator
	StressCalculator (bool createsStress=true)
	Constructor (protected to prevent direct instantiation). More...

Protected Member Functions inherited from McMd::SystemInterface
Boundary &	boundary () const
	Get the Boundary by reference. More...

Simulation &	simulation () const
	Get the parent Simulation by reference. More...

int	nMolecule (int speciesId) const
	Get the number of molecules of one Species in this SystemInterface. More...

int	nAtom () const
	Return the total number of atoms in this SystemInterface. More...

bool	isEmpty () const
	Is this an empty SystemInterface (i.e., one with no molecules) ? More...

void	begin (int speciesId, System::MoleculeIterator &iterator)
	Initialize an iterator for molecules of one species in this SystemInterface. More...

void	begin (int speciesId, System::ConstMoleculeIterator &iterator) const
	Initialize a const iterator for molecules of one species in this SystemInterface. More...

bool	hasBonds () const
	Does a bond potential exist? More...

bool	hasAngles () const
	Does an angle potential exist? More...

bool	hasDihedrals () const
	Does a dihedral potential exist? More...

bool	hasLinks () const
	Does a link potential exist? More...

bool	hasExternal () const
	Does an external potential exist? More...

Constructor & Destructor Documentation

McMd::McPairPotential::McPairPotential ( System & system )

Constructor.

Definition at line 27 of file McPairPotential.cpp.

References Util::ParamComposite::setClassName().

McMd::McPairPotential::~McPairPotential ( )

virtual

Destructor.

Definition at line 35 of file McPairPotential.cpp.

Member Function Documentation

virtual double McMd::McPairPotential::atomEnergy ( const Atom & atom ) const

pure virtual

Calculate the nonbonded pair energy for one Atom.

Parameters

atom	Atom object of interest

Returns: nonbonded pair potential energy of atom

Implemented in McMd::McPairPotentialImpl< Interaction >.

Referenced by McMd::CfbLinear::addAtom(), McMd::CfbEndBase::addEndAtom(), McMd::CfbRebridgeBase::addMiddleAtom(), McMd::McSystem::atomPotentialEnergy(), McMd::CfbLinear::deleteAtom(), McMd::CfbEndBase::deleteEndAtom(), McMd::CfbRebridgeBase::deleteMiddleAtom(), McMd::McNVTChemicalPotential::load(), McMd::CfbReptationMove::move(), McMd::CfbReptateMove::move(), McMd::RigidDisplaceMove::move(), and McMd::McNVTChemicalPotential::sample().

virtual double McMd::McPairPotential::moleculeEnergy ( const Molecule & molecule ) const

pure virtual

Calculate the nonbonded pair energy for an entire Molecule.

The return value is the change in total pair potential upon inserting or removing a molecule. This is the sum of all inter-molecular pair interactions involving atoms of this molecule, plus an intramolecular contribution in which each pair is counted only once.

Parameters

molecule Molecule object of interest

Returns: nonbonded pair potential energy of molecule

Implemented in McMd::McPairPotentialImpl< Interaction >.

Referenced by McMd::HomopolymerSemiGrandMove::move(), and McMd::EndSwapMove::move().

void McMd::McPairPotential::buildCellList ( )

Build the CellList with current configuration.

Calls CellList::clear() to clear the CellList, then adds every Atom in this System. Each Atom position is shifted into the primary box by Boundary::shift() before being added.

Definition at line 41 of file McPairPotential.cpp.

References McMd::CellList::addAtom(), McMd::SystemInterface::begin(), McMd::SystemInterface::boundary(), cellList_, McMd::PairPotential::maxPairCutoff(), Util::ArrayIterator< Data >::notEnd(), Util::PArrayIterator< Data >::notEnd(), McMd::Simulation::nSpecies(), McMd::CellList::setup(), Simp::OrthorhombicBoundary::shift(), and McMd::SystemInterface::simulation().

Referenced by McMd::McSimulation::analyzeConfigs(), McMd::McSimulation::analyzeTrajectory(), McMd::McSystem::generateMolecules(), McMd::McSystem::loadConfig(), McMd::HybridMdMove::move(), McMd::HybridNphMdMove::move(), McMd::MdMove::move(), McMd::DpdMove::move(), McMd::McSystem::readConfig(), McMd::McCommandManager::readStandardCommand(), McMd::McDeformCommand::reneighbor(), and McMd::McSimulation::simulate().

void McMd::McPairPotential::addAtom ( Atom & atom )

inline

Add an Atom to the CellList.

Parameters

atom	Atom object of interest.

Definition at line 141 of file McPairPotential.h.

Referenced by McMd::CfbRebridgeBase::addSequence(), McMd::CfbEndMove::move(), McMd::CfbLinearEndMove::move(), McMd::CfbReptationMove::move(), McMd::CfbRingRebridgeMove::move(), McMd::CfbReptateMove::move(), and McMd::McNVTChemicalPotential::sample().

void McMd::McPairPotential::deleteAtom ( Atom & atom )

inline

Remove an Atom from the CellList.

Parameters

atom	Atom object of interest

Definition at line 145 of file McPairPotential.h.

Referenced by McMd::CfbRebridgeBase::deleteSequence(), McMd::CfbEndMove::move(), McMd::CfbLinearEndMove::move(), McMd::CfbReptationMove::move(), McMd::CfbRingRebridgeMove::move(), McMd::CfbReptateMove::move(), and McMd::McNVTChemicalPotential::sample().

void McMd::McPairPotential::updateAtomCell ( Atom & atom )

inline

Update the cell list to reflect a new position.

Use this to update the cell list after an Atom position has already been assigned a new value.

Parameters

atom	Atom object whose position has been modified.

Definition at line 149 of file McPairPotential.h.

References McMd::Atom::position().

Referenced by McMd::RingTetraRebridgeMove::move(), McMd::AtomDisplaceMove::move(), McMd::CfbDoubleRebridgeMove::move(), McMd::RingOctaRebridgeMove::move(), McMd::CfbEndMove::move(), McMd::CfbLinearEndMove::move(), McMd::CfbRebridgeMove::move(), McMd::CfbReptationMove::move(), McMd::EndSwapMove::move(), McMd::CfbRingRebridgeMove::move(), McMd::CfbReptateMove::move(), and McMd::RigidDisplaceMove::move().

void McMd::McPairPotential::moveAtom	(	Atom &	atom,
		const Vector &	position
	)

inline

Move an Atom position, and update the CellList.

On output, atom.position() is reset to to position, and the new position is recorded in the CellList. This is equivalent to atom.position() = position and then updateAtomCell(atom).

Parameters