Simp::FeneBond Class Reference

Detailed Description

A finitely-extensible nonlinear element (FENE) bond potential.

Finitely extensible nonlinear element (FENE) bond potential V(r) = -0.5*kappa*r0^2 log( 1 - (r^2/r0^2)) with a spring constant kappa and maximum bond length r0.

This implementation uses the FENE potential for distances less than a cutoff rl at which the FENE potentail reaches a parameter energyCutoff, and a linear potential for all r > rl.

See also

Parameter file format

Bond Interaction Class Interface

Definition at line 39 of file FeneBond.h.

#include <FeneBond.h>

Inheritance diagram for Simp::FeneBond:

Public Member Functions
	FeneBond ()
	Default constructor. More...
	FeneBond (const FeneBond &other)
	Copy constructor. More...
FeneBond &	operator= (const FeneBond &other)
	Assignment. More...
void	setNBondType (int nBondType)
	Set the number of bond types. More...
void	readParameters (std::istream &in)
	Read bond 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 rSq, int type) const
	Returns potential energy for one bond. More...
double	forceOverR (double rSq, int type) const
	Returns force/distance for one bond, for use in MD. More...
double	randomBondLength (Random *random, double beta, int type) const
	Return bond length chosen from equilibrium distribution. More...
double	get (std::string name, int type) const
	Get a parameter value, identified by a string. 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::FeneBond::FeneBond

(

)

Default constructor.

Definition at line 20 of file FeneBond.cpp.

References Util::ParamComposite::setClassName().

Simp::FeneBond::FeneBond

(

const FeneBond &

other

)

Copy constructor.

Definition at line 39 of file FeneBond.cpp.

Member Function Documentation

FeneBond & Simp::FeneBond::operator=

(

const FeneBond &

other

)

Assignment.

Definition at line 57 of file FeneBond.cpp.

void Simp::FeneBond::setNBondType

(

int

nBondType

)

Set the number of bond types.

Parameters

nBondType

number of bond types

Definition at line 77 of file FeneBond.cpp.

References UTIL_CHECK.

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

virtual

Read bond interaction parameters from input stream.

Format: kappa CArray<double> length CArray<double> energyCutoff double

Precondition

nBondType must be set, by calling setNBondType().

Parameters

in	input stream

Reimplemented from Util::ParamComposite.

Definition at line 86 of file FeneBond.cpp.

References UTIL_CHECK.

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

virtual

Load internal state from an archive.

Parameters

ar	input/loading archive

Reimplemented from Util::ParamComposite.

Definition at line 112 of file FeneBond.cpp.

References UTIL_CHECK.

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

virtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from Util::ParamComposite.

Definition at line 139 of file FeneBond.cpp.

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

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

Modify a parameter, identified by a string.

Parameters

name	parameter name
type	bond type index
value	new value of parameter

Definition at line 192 of file FeneBond.cpp.

References UTIL_THROW.

double Simp::FeneBond::energy ( double  rSq, int  type  ) const

inline

Returns potential energy for one bond.

Parameters

rSq	square of distance between bonded particles.
type	type of bond.

Definition at line 192 of file FeneBond.h.

Referenced by randomBondLength().

double Simp::FeneBond::forceOverR ( double  rSq, int  type  ) const

inline

Returns force/distance for one bond, for use in MD.

A positive return value represents a repulsive radial force.

Parameters

rSq	square of distance between bonded particles.
type	type of bond.

Returns

scalar repulsive force divided by distance.

Definition at line 207 of file FeneBond.h.

double Simp::FeneBond::randomBondLength	(	Random *	random,
		double	beta,
		int	type
	)		const

Return bond length chosen from equilibrium distribution.

This function returns a bond length chosen from the Boltzmann distribution of lengths for bonds of random orientation. The distribution P(l) of values of the length l is proportional to l*l*exp[-beta*phi(l) ], where phi(l) 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 166 of file FeneBond.cpp.

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

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

Get a parameter value, identified by a string.

Parameters

name	parameter name
type	bond type index

Definition at line 215 of file FeneBond.cpp.

References UTIL_THROW.

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

• FeneBond.h
• FeneBond.cpp