Detailed Description

template<class Interaction>
class McMd::MdPairPotentialImpl< Interaction >

Implementation template for an MdPairPotential.

Definition at line 36 of file MdPairPotentialImpl.h.

#include <MdPairPotentialImpl.h>

Inheritance diagram for McMd::MdPairPotentialImpl< Interaction >:

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

	MdPairPotentialImpl (McPairPotentialImpl< Interaction > &other)
	Constructor (copied from McPairPotentialImpl) More...

virtual	~MdPairPotentialImpl ()
	Destructor. More...

virtual void	readParameters (std::istream &in)
	Read pair potential interaction and pair list 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...

Pair 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)
	Modify an interaction parameter, identified by a string. More...

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

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

Global force and energy calculators
virtual void	addForces ()
	Calculate non-bonded pair forces for all atoms in this System. More...

virtual void	computeEnergy ()
	Calculate and store pair energy for this System. More...

virtual void	computeStress ()
	Compute and store the total nonbonded pressure. More...

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

virtual	~MdPairPotential ()
	Destructor. More...

void	buildPairList ()
	Build the internal PairList. More...

bool	isPairListCurrent ()
	Return true if PairList is current, false if obsolete. More...

void	clearPairListStatistics ()
	Clear all statistical accumulators stored in PairList. More...

const PairList &	pairList () const
	Return a const reference to the internal PairList. 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...

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...

	SystemInterface (System &parent)
	Constructor. More...

virtual	~SystemInterface ()
	Destructor. More...

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

Protected Attributes inherited from McMd::MdPairPotential
PairList	pairList_
	Verlet neighbor pair list for nonbonded interactions. More...

Constructor & Destructor Documentation

template<class Interaction >

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

Constructor.

Parameters

system parent System object.

Definition at line 220 of file MdPairPotentialImpl.h.

template<class Interaction >

McMd::MdPairPotentialImpl< Interaction >::MdPairPotentialImpl ( McPairPotentialImpl< Interaction > & other )

Constructor (copied from McPairPotentialImpl)

This constructor is intended to construct an MdPairPotential for use in a hybrid MC/MD simulation, in which it is owned by an MdSystem that is created by the hybrid MC move to perform short MD simulations. This constructor creates an instance of MdPairPotentialImpl<Interaction> with a pointer to the Interaction object owned by the parent McPairPotentialImpl.

Parameters

other parent Monte-Carlo pair potential object

Definition at line 230 of file MdPairPotentialImpl.h.

template<class Interaction >

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

virtual

Destructor.

Definition at line 241 of file MdPairPotentialImpl.h.

Member Function Documentation

template<class Interaction >

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

virtual

Read pair potential interaction and pair list blocks.

This method reads the pair potential Interaction parameter and PairList blocks, and initializes an internal PairList. Before calling the Interaction::readParameters method, it passes nAtomType to Interaction::setNAtomType().

Parameters

in	input parameter stream.

Reimplemented from Util::ParamComposite.

Definition at line 250 of file MdPairPotentialImpl.h.

References Util::ParamComposite::addParamComposite(), McMd::PairList::initialize(), McMd::MdPairPotential::pairList_, Util::ParamComposite::readParamComposite(), and McMd::SystemInterface::simulation().

template<class Interaction >

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

virtual

Load internal state from an archive.

Parameters

ar	input/loading archive

Reimplemented from Util::ParamComposite.

Definition at line 271 of file MdPairPotentialImpl.h.

References Util::ParamComposite::addParamComposite(), Util::ParamComposite::loadParamComposite(), McMd::MdPairPotential::pairList_, and McMd::SystemInterface::simulation().

template<class Interaction >

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

virtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from Util::ParamComposite.

Definition at line 287 of file MdPairPotentialImpl.h.

References McMd::MdPairPotential::pairList_, and McMd::PairList::save().

template<class Interaction >

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

virtual

Return pair energy for a single pair.

Parameters

rsq	square distance between atoms in pair
iAtomType	atom type index of 1st atom
jAtomType	atom type index of 2nd atom

Returns: energy of pair

Implements McMd::PairPotential.

Definition at line 300 of file MdPairPotentialImpl.h.

template<class Interaction >

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

virtual

Return force / separation for a single pair.

Parameters

rsq	square distance between atoms in pair
iAtomType	atom type index of 1st atom
jAtomType	atom type index of 2nd atom

Returns: ratio of pair force (> 0 if repulsive) to distance

Implements McMd::PairPotential.

Definition at line 308 of file MdPairPotentialImpl.h.

template<class Interaction >

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

virtual

Return maximum cutoff.

Implements McMd::PairPotential.

Definition at line 322 of file MdPairPotentialImpl.h.

template<class Interaction>

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

inlinevirtual

Modify an interaction parameter, identified by a string.

Parameters

name	parameter name
i	type index of first atom
j	type index of first atom
value	new value of parameter (input)

Implements McMd::PairPotential.

Definition at line 131 of file MdPairPotentialImpl.h.

template<class Interaction>

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

inlinevirtual

Get an interaction parameter value, identified by a string.

Parameters

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

Returns: parameter value

Implements McMd::PairPotential.

Definition at line 142 of file MdPairPotentialImpl.h.

template<class Interaction >

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

virtual

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

Implements McMd::PairPotential.

Definition at line 329 of file MdPairPotentialImpl.h.

template<class Interaction >

void McMd::MdPairPotentialImpl< Interaction >::addForces ( )

virtual

Calculate non-bonded pair forces for all atoms in this System.

Adds non-bonded pair forces to the current values of the forces for all atoms in this system. Before calculating forces, the method checks if the pair list is current, and rebuilds it if necessary.

Implements McMd::MdPairPotential.

Definition at line 336 of file MdPairPotentialImpl.h.

References McMd::PairList::begin(), McMd::SystemInterface::boundary(), McMd::MdPairPotential::buildPairList(), McMd::Atom::force(), McMd::PairIterator::getPair(), McMd::MdPairPotential::isPairListCurrent(), McMd::PairIterator::notEnd(), McMd::MdPairPotential::pairList_, McMd::Atom::position(), and McMd::Atom::typeId().