Descriptor for a block within a block polymer. More...

#include <Edge.h>

Inheritance diagram for Pscf::Edge:

Public Member Functions
	Edge ()
	Constructor.
virtual	~Edge ()
	Destructor.
template<class Archive>
void	serialize (Archive &ar, unsigned int versionId)
	Serialize to/from archive.
Setters
void	setId (int id)
	Set the id for this block.
void	setMonomerId (int monomerId)
	Set the monomer type id.
void	setVertexIds (int vertexId0, int vertexId1)
	Set indices of associated vertices.
virtual void	setLength (double length)
	Set the length of this block (only valid for thread model).
virtual void	setNBead (int nBead)
	Set the number of beads in this block (only valid for bead model).
void	setPolymerType (PolymerType::Enum type)
	Set the type of the parent polymer (branched or linear).

Accessors (getters)
int	id () const
	Get the id of this block (unique within the polymer).
int	monomerId () const
	Get the monomer type id for this block.
const Pair< int > &	vertexIds () const
	Get the pair of associated vertex ids.
int	vertexId (int i) const
	Get the id of one associated vertex.
double	length () const
	Get the length of this block, in the thread model.
int	nBead () const
	Get the number of beads in this block, in the bead model.
PolymerType::Enum	polymerType () const
	Get the type of the parent polymer (branched or linear).
std::istream &	operator>> (std::istream &in, Edge &block)
	Input stream extractor (>>) for a Edge.
std::ostream &	operator<< (std::ostream &out, const Edge &block)
	Output stream inserter (<<) for a Edge.

Detailed Description

Descriptor for a block within a block polymer.

An Edge has:

a monomer type id
a length (thread model) or number of beads (bead model)
a block id (unique among blocks of the same polymer species)
vertex ids for the two vertices at which it terminates

Edge is a base class for the BlockTmpl class template, which is a a base class for a class named Block in each implementation-level sub-namespace of Pscf (i.e., in R1d, Rpc, or Rpg).

An Edge is a descriptor for a block within a block polymer, but does not provide functions or data structure needed to solve the modified diffusion equation (MDE). The Block class defined in each implementation-level namespace is designed to be used as an MDE solver as well as a descriptor.

An Edge can store either a value for length (the contour length of the block) when PolymerModel::isThread(), or a value for nBead (the number of beads in the block) when PolymerModel::isBead(), but not both. It is an error to get or set a value for the length when a bead model is in use or to get or set a value for nBead when a thread model is in use, because these variables are each meaningful only in the context of a specific model.

Block objects associated with a polymer are normally stored in an array that is a private member of the Pscf::PolymerTmpl class template. The block id for each Edge should be set to the element index of the associated Block within that array.

Parameter File Format

Definition at line 58 of file Edge.h.

Constructor & Destructor Documentation

◆ Edge()

Pscf::Edge::Edge ( )

Constructor.

Definition at line 16 of file Edge.cpp.

Referenced by operator<<, and operator>>.

◆ ~Edge()

Pscf::Edge::~Edge ( )

virtual

Destructor.

Definition at line 32 of file Edge.cpp.

Member Function Documentation

◆ serialize()

template<class Archive>

void Pscf::Edge::serialize	(	Archive &	ar,
		unsigned int	versionId )

Serialize to/from archive.

Parameters

ar	input or output Archive
versionId	archive format version index

Definition at line 327 of file Edge.h.

◆ setId()

void Pscf::Edge::setId ( int id )

Set the id for this block.

Parameters

id	integer index for this block

Definition at line 38 of file Edge.cpp.

References id().

Referenced by Pscf::Rpg::Block< D >::averageProductBead(), and Pscf::PolymerSpecies::readParameters().

◆ setMonomerId()

void Pscf::Edge::setMonomerId ( int monomerId )

Set the monomer type id.

Parameters

monomerId integer id of monomer type

Definition at line 44 of file Edge.cpp.

References monomerId().

Referenced by Pscf::Rpg::Block< D >::averageProductBead().

◆ setVertexIds()

void Pscf::Edge::setVertexIds	(	int	vertexId0,
		int	vertexId1 )

Set indices of associated vertices.

Parameters

vertexId0	integer id of vertex 0
vertexId1	integer id of vertex 1

Definition at line 50 of file Edge.cpp.

Referenced by Pscf::Rpg::Block< D >::averageProductBead(), and Pscf::PolymerSpecies::readParameters().

◆ setLength()

void Pscf::Edge::setLength ( double length )

virtual

Set the length of this block (only valid for thread model).

In the continuous thread model, the length of a block is given by the ratio of block steric volume / monomer reference volume.

Precondition: PolymerModel::isThread()

Parameters

length block length (thread model).

Reimplemented in Pscf::R1d::Block, Pscf::Rpc::Block< D >, and Pscf::Rpg::Block< D >.

Definition at line 68 of file Edge.cpp.

References Pscf::PolymerModel::isThread(), length(), and UTIL_CHECK.

Referenced by Pscf::Rpg::Block< D >::averageProductBead(), Pscf::R1d::Block::setLength(), Pscf::Rpc::Block< D >::setLength(), and Pscf::Rpg::Block< D >::setLength().

◆ setNBead()

void Pscf::Edge::setNBead ( int nBead )

virtual

Set the number of beads in this block (only valid for bead model).

Precondition: PolymerModel::isBead()

Parameters

nBead number of beads (bead model)

Definition at line 59 of file Edge.cpp.

References Pscf::PolymerModel::isBead(), nBead(), and UTIL_CHECK.

◆ setPolymerType()

void Pscf::Edge::setPolymerType ( PolymerType::Enum type )

Set the type of the parent polymer (branched or linear).

By convention, if the polymer type is PolymerType::Linear, then vertexId(0) = id and vertexId(1) = id + 1 for block number id. By using this convention, the stream insertion and extraction operators for an Edge can thus use a shorter string representation for linear polymers in which vertex ids are omitted.

Parameters

type	type of polymer (branched or linear)

Definition at line 77 of file Edge.cpp.

Referenced by Pscf::PolymerSpecies::readParameters().

◆ id()

int Pscf::Edge::id ( ) const

inline

Get the id of this block (unique within the polymer).

Definition at line 278 of file Edge.h.

Referenced by Pscf::Vertex::addEdge(), Pscf::Rpg::Block< D >::averageProductBead(), and setId().

◆ monomerId()

int Pscf::Edge::monomerId ( ) const

inline

Get the monomer type id for this block.

Definition at line 284 of file Edge.h.

Referenced by Pscf::Rpg::Block< D >::averageProductBead(), Pscf::Rpc::IntraCorrelation< D >::computeIntraCorrelations(), Pscf::Rpg::IntraCorrelation< D >::computeIntraCorrelations(), Pscf::FloryHuggins::Mixture::initialize(), and setMonomerId().

◆ vertexIds()

const Pair< int > & Pscf::Edge::vertexIds ( ) const

inline

Get the pair of associated vertex ids.

Definition at line 290 of file Edge.h.

Referenced by Pscf::Rpg::Block< D >::averageProductBead().

◆ vertexId()

int Pscf::Edge::vertexId ( int i ) const

inline

Get the id of one associated vertex.

Parameters

i	index of vertex (0 or 1)

Definition at line 296 of file Edge.h.

Referenced by Pscf::Vertex::addEdge(), Pscf::Rpg::Block< D >::averageProductBead(), Pscf::PolymerSpecies::makePaths(), Pscf::PolymerSpecies::makePlan(), Pscf::EdgeIterator::operator++(), Pscf::VertexIterator::operator++(), and Pscf::PolymerSpecies::readParameters().

◆ length()

double Pscf::Edge::length ( ) const

inline

Get the length of this block, in the thread model.

Precondition: PolymerModel::isThread()

Definition at line 311 of file Edge.h.

References Pscf::PolymerModel::isThread(), and UTIL_CHECK.

Referenced by Pscf::Rpg::Block< D >::averageProductBead(), Pscf::Rpc::IntraCorrelation< D >::computeIntraCorrelations(), Pscf::Rpg::IntraCorrelation< D >::computeIntraCorrelations(), Pscf::FloryHuggins::Mixture::initialize(), Pscf::PolymerSpecies::length(), Pscf::R1d::Block::setDiscretization(), setLength(), Pscf::R1d::Block::setLength(), and Pscf::R1d::Block::setupSolver().

◆ nBead()

int Pscf::Edge::nBead ( ) const

inline

Get the number of beads in this block, in the bead model.

Precondition: PolymerModel::isBead()

Definition at line 302 of file Edge.h.

References Pscf::PolymerModel::isBead(), and UTIL_CHECK.

Referenced by Pscf::Rpg::Block< D >::averageProductBead(), Pscf::Rpc::IntraCorrelation< D >::computeIntraCorrelations(), Pscf::Rpg::IntraCorrelation< D >::computeIntraCorrelations(), Pscf::PolymerSpecies::nBead(), and setNBead().

◆ polymerType()

PolymerType::Enum Pscf::Edge::polymerType ( ) const

inline

Get the type of the parent polymer (branched or linear).

Definition at line 320 of file Edge.h.

◆ operator>>

std::istream & operator>>	(	std::istream &	in,
		Edge &	block )

friend

Input stream extractor (>>) for a Edge.

The polymerType must be set before an Edge can be read from a stream. The block id must be set explicitly by calling setId, and are not read from an istream. Vertex id values for blocks in a linear polymer must be set explicitly by calling setVertexIds with consecutive values, as done in the function Pscf::PolymerTmpl::readParameters.

Different text representations are used for bead and thread models, and for linear and branched polymers:

Thread model:

In the thread model, if PolymerModel::isThread(), the text representation of an Edge for a branched polymer is:

monomerId length vertexId(0) vertexid(1)

Pscf::Edge::monomerId

int monomerId() const

Get the monomer type id for this block.

Definition Edge.h:284

Pscf::Edge::vertexId

int vertexId(int i) const

Get the id of one associated vertex.

Definition Edge.h:296

Pscf::Edge::length

double length() const

Get the length of this block, in the thread model.

Definition Edge.h:311

Here, length is a floating point number. For a linear polymer in the thread model, the vertex ids are omitted, because the vertex ids for block id of linear polymer must be equal to id and id + 1.

Bead model:

In the bead model, if PolymerModel::isBead(), the text representation for a branched polymer is:

monomerId nBead vertexId(0) vertexid(1)

Pscf::Edge::nBead

int nBead() const

Get the number of beads in this block, in the bead model.

Definition Edge.h:302

where nBead is the integer number of beads in the chain. The corresponding text representation for a bead-spring linear chain omits the vertex ids, as for the thread model.

Parameters

in	input stream
block	Edge to be read from stream

Returns: modified input stream

Definition at line 83 of file Edge.cpp.

References Edge().

◆ operator<<

std::ostream & operator<<	(	std::ostream &	out,
		const Edge &	block )

friend

Output stream inserter (<<) for a Edge.

Different text representations are used for linear and branched polymers, as discussed in documentation for the stream extractor (>>) operator. Vertex ids are output only for blocks of branched polymers.

Parameters

out	output stream
block	Edge to be written to stream

Returns: modified output stream

Definition at line 108 of file Edge.cpp.

References Edge(), Pscf::PolymerModel::isBead(), and Pscf::PolymerModel::isThread().

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

Public Member Functions

Accessors (getters)

Detailed Description

Constructor & Destructor Documentation

◆ Edge()

◆ ~Edge()

Member Function Documentation

◆ serialize()

◆ setId()

◆ setMonomerId()

◆ setVertexIds()

◆ setLength()

◆ setNBead()

◆ setPolymerType()

◆ id()

◆ monomerId()

◆ vertexIds()

◆ vertexId()

◆ length()

◆ nBead()

◆ polymerType()

Friends And Related Symbol Documentation

◆ operator>>

◆ operator<<