Detailed Description

template<class Interaction>
class McMd::McPairPotentialImpl< Interaction >

Implementation template for an McPairPotential.

Definition at line 33 of file McPairPotentialImpl.h.

#include <McPairPotentialImpl.h>

Inheritance diagram for McMd::McPairPotentialImpl< Interaction >:

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

virtual	~McPairPotentialImpl ()
	Destructor. More...

virtual void	readParameters (std::istream &in)
	Reads the pair potential Interaction blocks. 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...

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

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

virtual double	maxPairCutoff () const
	Return maximum cutoff. More...

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

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

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

Interaction &	interaction ()
	Return reference to underlying pair interaction. More...

const Interaction &	interaction () const
	Return reference to underlying pair interaction. More...

Energy and stress calculators
double	atomEnergy (const Atom &atom) const
	Calculate the nonbonded pair energy for one Atom. More...

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

virtual void	computeEnergy ()
	Compute and store nonbonded pair energy of this System. More...

virtual void	computeStress ()
	Compute and store total short-range pair stress. More...

Public Member Functions inherited from McMd::McPairPotential
	McPairPotential (System &system)
	Constructor. More...

virtual	~McPairPotential ()
	Destructor. More...

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	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...

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

Public Member Functions inherited from McMd::EnergyCalculator
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	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...

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...

Protected Attributes inherited from McMd::McPairPotential
CellList::NeighborArray	neighbors_
	Array to hold neighbors returned by a CellList. More...

CellList	cellList_
	Cell list for atom positions. More...

Constructor & Destructor Documentation

template<class Interaction >

McMd::McPairPotentialImpl< Interaction >::McPairPotentialImpl ( System & system )

Constructor.

Definition at line 207 of file McPairPotentialImpl.h.

template<class Interaction >

McMd::McPairPotentialImpl< Interaction >::~McPairPotentialImpl ( )

virtual

Destructor.

Definition at line 215 of file McPairPotentialImpl.h.

Member Function Documentation

template<class Interaction >

void McMd::McPairPotentialImpl< Interaction >::readParameters ( std::istream & in )

virtual

Reads the pair potential Interaction blocks.

This method reads the Interaction parameter blocks, and initializes an internal CellList. It passes the value simulation().nAtomType() to the Interaction::setNAtomType() function before calling Interaction::readParameters().

Reimplemented from Util::ParamComposite.

Definition at line 222 of file McPairPotentialImpl.h.

References Util::ParamComposite::addParamComposite(), McMd::McPairPotential::cellList_, McMd::McPairPotentialImpl< Interaction >::interaction(), McMd::CellList::setAtomCapacity(), and McMd::SystemInterface::simulation().

template<class Interaction >

void McMd::McPairPotentialImpl< Interaction >::loadParameters ( Serializable::IArchive & ar )

virtual

Load internal state from an archive.

Parameters

ar	input/loading archive

Reimplemented from Util::ParamComposite.

Definition at line 240 of file McPairPotentialImpl.h.

References Util::ParamComposite::addParamComposite(), McMd::McPairPotential::cellList_, McMd::McPairPotentialImpl< Interaction >::interaction(), McMd::CellList::setAtomCapacity(), and McMd::SystemInterface::simulation().

template<class Interaction >

void McMd::McPairPotentialImpl< Interaction >::save ( Serializable::OArchive & ar )

virtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from Util::ParamComposite.

Definition at line 257 of file McPairPotentialImpl.h.

References McMd::McPairPotentialImpl< Interaction >::interaction().

template<class Interaction >

double McMd::McPairPotentialImpl< Interaction >::energy	(	double	rsq,
		int	iAtomType,
		int	jAtomType
	)		const

virtual

Return pair energy for a single pair.

Implements McMd::PairPotential.

Definition at line 267 of file McPairPotentialImpl.h.

References McMd::McPairPotentialImpl< Interaction >::interaction().

template<class Interaction >

double McMd::McPairPotentialImpl< Interaction >::forceOverR	(	double	rsq,
		int	iAtomType,
		int	jAtomType
	)		const

virtual

Return force / separation for a single pair.

Implements McMd::PairPotential.

Definition at line 276 of file McPairPotentialImpl.h.

References McMd::McPairPotentialImpl< Interaction >::interaction().

template<class Interaction >

double McMd::McPairPotentialImpl< Interaction >::maxPairCutoff ( ) const

virtual

Return maximum cutoff.

Implements McMd::PairPotential.

Definition at line 290 of file McPairPotentialImpl.h.

References McMd::McPairPotentialImpl< Interaction >::interaction().

template<class Interaction>

void McMd::McPairPotentialImpl< Interaction >::set	(	std::string	name,
		int	i,
		int	j,
		double	value
	)

inlinevirtual

Get a parameter value, identified by a string.

Parameters

name	parameter name
i	type index of first atom
j	type index of first atom
value	parameter value

Implements McMd::PairPotential.

Definition at line 98 of file McPairPotentialImpl.h.

template<class Interaction>

double McMd::McPairPotentialImpl< Interaction >::get	(	std::string	name,
		int	i,
		int	j
	)		const

inlinevirtual

Get a parameter value, identified by a string.

Parameters

name	parameter name
i	type index of first atom
j	type index of first atom

Implements McMd::PairPotential.

Definition at line 108 of file McPairPotentialImpl.h.

template<class Interaction >

std::string McMd::McPairPotentialImpl< Interaction >::interactionClassName ( ) const

virtual

Return pair interaction class name (e.g., "LJPair").

Implements McMd::PairPotential.

Definition at line 520 of file McPairPotentialImpl.h.

References McMd::McPairPotentialImpl< Interaction >::interaction().

template<class Interaction >

Interaction & McMd::McPairPotentialImpl< Interaction >::interaction ( )

inline

Return reference to underlying pair interaction.

Definition at line 506 of file McPairPotentialImpl.h.

template<class Interaction >

const Interaction & McMd::McPairPotentialImpl< Interaction >::interaction ( ) const

inline

Return reference to underlying pair interaction.

Definition at line 513 of file McPairPotentialImpl.h.

template<class Interaction >

double McMd::McPairPotentialImpl< Interaction >::atomEnergy ( const Atom & atom ) const

virtual

Calculate the nonbonded pair energy for one Atom.

Parameters

atom	Atom object of interest

Returns: nonbonded pair potential energy of atom

Implements McMd::McPairPotential.

Definition at line 297 of file McPairPotentialImpl.h.

References McMd::SystemInterface::boundary(), McMd::McPairPotential::cellList_, McMd::EnergyCalculator::energy(), McMd::CellList::getNeighbors(), McMd::Atom::id(), McMd::McPairPotentialImpl< Interaction >::interaction(), McMd::Mask::isMasked(), McMd::Atom::mask(), McMd::McPairPotential::neighbors_, McMd::Atom::position(), Util::FSArray< Data, Capacity >::size(), and McMd::Atom::typeId().

template<class Interaction >

double McMd::McPairPotentialImpl< Interaction >::moleculeEnergy ( const Molecule & molecule ) const

virtual

Calculate the nonbonded pair energy for an entire Molecule.

Parameters

molecule Molecule object of interest

Returns: nonbonded pair potential energy of atom

Implements McMd::McPairPotential.

Definition at line 334 of file McPairPotentialImpl.h.

References McMd::Molecule::atom(), McMd::SystemInterface::boundary(), McMd::McPairPotential::cellList_, Simp::OrthorhombicBoundary::distanceSq(), McMd::EnergyCalculator::energy(), McMd::CellList::getNeighbors(), McMd::Atom::id(), McMd::McPairPotentialImpl< Interaction >::interaction(), McMd::Mask::isMasked(), McMd::Atom::mask(), McMd::Atom::molecule(), McMd::Molecule::nAtom(), McMd::McPairPotential::neighbors_, McMd::Atom::position(), Util::FSArray< Data, Capacity >::size(), and McMd::Atom::typeId().

template<class Interaction >

void McMd::McPairPotentialImpl< Interaction >::computeEnergy ( )

virtual

Compute and store nonbonded pair energy of this System.

If energy is already known (set), this function does nothing.

Implements McMd::EnergyCalculator.

Definition at line 380 of file McPairPotentialImpl.h.

References McMd::SystemInterface::boundary(), McMd::McPairPotential::cellList_, Simp::OrthorhombicBoundary::distanceSq(), McMd::EnergyCalculator::energy(), McMd::CellList::getCellNeighbors(), McMd::Atom::id(), McMd::McPairPotentialImpl< Interaction >::interaction(), McMd::Mask::isMasked(), McMd::Atom::mask(), McMd::McPairPotential::neighbors_, McMd::Atom::position(), Util::Setable< T >::set(), Util::setToZero(), Util::FSArray< Data, Capacity >::size(), McMd::CellList::totCells(), McMd::Atom::typeId(), and Simp::OrthorhombicBoundary::volume().

template<class Interaction >

void McMd::McPairPotentialImpl< Interaction >::computeStress ( )

virtual

Compute and store total short-range pair stress.

If stress is already known (set), this function does nothing.

Reimplemented from McMd::StressCalculator.

Definition at line 494 of file McPairPotentialImpl.h.

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

McPairPotentialImpl.h

Detailed Description

template<class Interaction> class McMd::McPairPotentialImpl< Interaction >

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

template<class Interaction>
class McMd::McPairPotentialImpl< Interaction >