Simp::CosineSqAngle Class Reference

Detailed Description

A three body angle potential, as a function of angle cosine.

This class implements an angle potential: kappa (cos[theta0] - cos[theta])^2.

See also

parameter file format

Definition at line 34 of file CosineSqAngle.h.

#include <CosineSqAngle.h>

Inheritance diagram for Simp::CosineSqAngle:

Public Member Functions
	CosineSqAngle ()
	Default constructor. More...
	CosineSqAngle (const CosineSqAngle &other)
	Copy constructor. More...
CosineSqAngle &	operator= (const CosineSqAngle &other)
	Assignment. More...
void	setNAngleType (int nAngleType)
	Set the number of angle types. More...
void	readParameters (std::istream &in)
	Read angle interaction parameters from input stream. 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...
void	set (std::string name, int type, double value)
	Modify a parameter, identified by a string. More...
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
	Compute angle forces. More...
double	randomAngle (Random *random, double beta, int type) const
	Return bond angle chosen from equilibrium distribution. More...
double	randomCosineAngle (Random *random, double beta, int type) const
	Return bond angle cosine chosen from equilibrium distribution. More...
double	get (std::string name, int type) const
	Get a parameter value, identified by a string. More...
std::string	className () const
	Return name string "CosineSqAngle" for this evaluator class. 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...

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...

Constructor & Destructor Documentation

Simp::CosineSqAngle::CosineSqAngle

(

)

Default constructor.

Definition at line 23 of file CosineSqAngle.cpp.

References Util::ParamComposite::setClassName().

Simp::CosineSqAngle::CosineSqAngle

(

const CosineSqAngle &

other

)

Copy constructor.

Definition at line 37 of file CosineSqAngle.cpp.

Member Function Documentation

CosineSqAngle & Simp::CosineSqAngle::operator=

(

const CosineSqAngle &

other

)

Assignment.

Definition at line 50 of file CosineSqAngle.cpp.

void Simp::CosineSqAngle::setNAngleType

(

int

nAngleType

)

Set the number of angle types.

Parameters

nAngleType

number of angle types

Definition at line 64 of file CosineSqAngle.cpp.

References UTIL_THROW.

void Simp::CosineSqAngle::readParameters ( std::istream &  in )

virtual

Read angle interaction parameters from input stream.

Format: kappa CArray<double>

Precondition

nAngleType must be set, by calling setNAngleType().

Parameters

in	input stream

Reimplemented from Util::ParamComposite.

Definition at line 75 of file CosineSqAngle.cpp.

References Util::Constants::Pi, and UTIL_CHECK.

void Simp::CosineSqAngle::loadParameters ( Serializable::IArchive &  ar )

virtual

Load internal state from an archive.

Parameters

ar	input/loading archive

Reimplemented from Util::ParamComposite.

Definition at line 93 of file CosineSqAngle.cpp.

References UTIL_CHECK.

void Simp::CosineSqAngle::save ( Serializable::OArchive &  ar )

virtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from Util::ParamComposite.

Definition at line 109 of file CosineSqAngle.cpp.

References Util::BinaryFileOArchive::pack(), and UTIL_CHECK.

void Simp::CosineSqAngle::set	(	std::string	name,
		int	type,
		double	value
	)

Modify a parameter, identified by a string.

Parameters

name	parameter name
type	angle type index
value	new value of parameter

Definition at line 172 of file CosineSqAngle.cpp.

References UTIL_THROW.

double Simp::CosineSqAngle::energy ( double  cosTheta, int  type  ) const

inline

Returns potential energy for one angle.

Parameters

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

Definition at line 184 of file CosineSqAngle.h.

Referenced by randomAngle(), and randomCosineAngle().

void Simp::CosineSqAngle::force ( const Vector &  R1, const Vector &  R2, Vector &  F1, Vector &  F2, int  type  ) const

inline

Compute angle forces.

Computes forces F1 and F2 along the two bonds in the angle.

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	type of angle.

Definition at line 198 of file CosineSqAngle.h.

References Util::Vector::abs(), Util::Vector::dot(), and Util::Vector::multiply().

double Simp::CosineSqAngle::randomAngle	(	Random *	random,
		double	beta,
		int	type
	)		const

Return bond angle chosen from equilibrium distribution.

This function returns a bond angle chosen from the Boltzmann distribution of angle for bonds of random orientation. The distribution P(theta) of values of the angle theta is proportional to sin(theta)*exp[-beta*phi(theta) ], where phi(theta) is the bond energy.

Parameters

random	pointer to random number generator object.
beta	inverse temperature
type	bond type

Returns

random bond length chosen from equilibrium distribution.

Definition at line 123 of file CosineSqAngle.cpp.

References energy(), Util::Constants::Pi, and Util::Random::uniform().

double Simp::CosineSqAngle::randomCosineAngle	(	Random *	random,
		double	beta,
		int	type
	)		const

Return bond angle cosine chosen from equilibrium distribution.

This function returns a bond angle chosen from the Boltzmann distribution of angle for bonds of random orientation. The distribution P(theta) of values of the angle theta is proportional to sin(theta)*exp[-beta*phi(theta) ], where phi(theta) is the bond energy.

Parameters

random	pointer to random number generator object.
beta	inverse temperature
type	bond type

Returns

random bond length chosen from equilibrium distribution.

Definition at line 149 of file CosineSqAngle.cpp.

References energy(), and Util::Random::uniform().

double Simp::CosineSqAngle::get	(	std::string	name,
		int	type
	)		const

Get a parameter value, identified by a string.

Parameters

name	parameter name
type	angle type index

Returns

parameter value

Definition at line 187 of file CosineSqAngle.cpp.

References UTIL_THROW.

std::string Simp::CosineSqAngle::className

(

)

const

Return name string "CosineSqAngle" for this evaluator class.

Definition at line 204 of file CosineSqAngle.cpp.

---

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

• CosineSqAngle.h
• CosineSqAngle.cpp