Detailed Description

template<class Interaction>
class McMd::AnglePotentialImpl< Interaction >

Implementation template for an AnglePotential.

Definition at line 34 of file mcMd/potentials/angle/AnglePotentialImpl.h.

#include <AnglePotentialImpl.h>

Inheritance diagram for McMd::AnglePotentialImpl< Interaction >:

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

	AnglePotentialImpl (AnglePotentialImpl< Interaction > &other)
	Copy constructor. More...

virtual	~AnglePotentialImpl ()
	Destructor. More...

virtual void	readParameters (std::istream &in)
	Read angle potential parameters. 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...

Interactions Interface
double	energy (double cosTheta, int type) const
	Returns potential energy for one angle. More...

void	force (const Vector &R1, const Vector &R2, Vector &F1, Vector &F2, int type) const
	Returns forces along two bonds at the angle, for use in MD and stress calculation. More...

virtual double	randomAngle (Random *random, double beta, int type) const
	Returns a random bond Angle. More...

virtual double	randomCosineAngle (Random *random, double beta, int type) const
	Returns Cosine a random bond Angle. More...

void	set (std::string name, int type, double value)
	Modify a parameter, identified by a string. More...

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

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

Interaction &	interaction ()
	Return angle interaction by reference. More...

const Interaction &	interaction () const
	Return angle interaction by const reference. More...

System Energy and Force Calculators
virtual double	atomEnergy (const Atom &atom) const
	Calculate the angle energy for one Atom. More...

virtual void	addForces ()
	Calculate the angle energy for one Atom. More...

virtual void	computeEnergy ()
	Calculate and store total angle energy. More...

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

Public Member Functions inherited from McMd::AnglePotential
	AnglePotential ()
	Constructor. More...

virtual	~AnglePotential ()
	Destructor (does nothing) 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::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...

Constructor & Destructor Documentation

template<class Interaction >

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

Constructor.

Definition at line 226 of file mcMd/potentials/angle/AnglePotentialImpl.h.

template<class Interaction >

McMd::AnglePotentialImpl< Interaction >::AnglePotentialImpl ( AnglePotentialImpl< Interaction > & other )

Copy constructor.

Definition at line 237 of file mcMd/potentials/angle/AnglePotentialImpl.h.

template<class Interaction >

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

virtual

Destructor.

Definition at line 249 of file mcMd/potentials/angle/AnglePotentialImpl.h.

Member Function Documentation

template<class Interaction >

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

virtual

Read angle potential parameters.

This method reads the angle potential Interaction parameter block. Before calling Interaction::readParameters(), it passes simulation().nAngleType() to Interaction::setNAngleType().

Parameters

in	input parameter stream.

Reimplemented from Util::ParamComposite.

Definition at line 261 of file mcMd/potentials/angle/AnglePotentialImpl.h.

References Util::ParamComposite::addParamComposite(), McMd::AnglePotentialImpl< Interaction >::interaction(), and McMd::SystemInterface::simulation().

template<class Interaction >

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

virtual

Load internal state from an archive.

Parameters

ar	input/loading archive

Reimplemented from Util::ParamComposite.

Definition at line 276 of file mcMd/potentials/angle/AnglePotentialImpl.h.

References Util::ParamComposite::addParamComposite(), McMd::AnglePotentialImpl< Interaction >::interaction(), and McMd::SystemInterface::simulation().

template<class Interaction >

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

virtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from Util::ParamComposite.

Definition at line 291 of file mcMd/potentials/angle/AnglePotentialImpl.h.

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

template<class Interaction >

double McMd::AnglePotentialImpl< Interaction >::energy	(	double	cosTheta,
		int	type
	)		const

virtual

Returns potential energy for one angle.

Parameters

cosTheta	cosine of the bend angle.
type	integer angle type index

Implements McMd::AnglePotential.

Definition at line 303 of file mcMd/potentials/angle/AnglePotentialImpl.h.

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

template<class Interaction >

void McMd::AnglePotentialImpl< Interaction >::force	(	const Vector &	R1,
		const Vector &	R2,
		Vector &	F1,
		Vector &	F2,
		int	type
	)		const

virtual

Returns forces along two bonds at the angle, for use in MD and stress calculation.

Parameters

R1	bond vector from atom 1 to 2.
R2	bond vector from atom 2 to 3.
F1	return force along R1 direction.
F2	return force along R2 direction.
type	integer angle type index