Descriptor and solver for one polymer species. More...

#include <Polymer.h>

Inheritance diagram for Pscf::Rpc::Polymer< D >:

Public Types
using	Base = PolymerTmpl< Block<D> >
	Base class, partial template specialization.
using	BlockT = Block<D>
	Block type, for a block within a block polymer.
using	PropagatorT = typename BlockT::PropagatorT
	Propagator type, for one direction within a block.
Public Types inherited from Pscf::PolymerTmpl< Block< D > >
using	BlockT
	Block of a block polymer.
using	PropagatorT
	Modified diffusion equation solver for one block, in one direction.
Public Types inherited from Pscf::Species
enum	Ensemble
	Statistical ensemble for number of molecules. More...
Public Types inherited from Util::Serializable
typedef BinaryFileOArchive	OArchive
	Type of output archive used by save method.
typedef BinaryFileIArchive	IArchive
	Type of input archive used by load method.

Public Member Functions
	Polymer ()
	Constructor.
	~Polymer ()
	Destructor.
void	setNParams (int nParam)
	Set the number of unit cell parameters.
void	clearUnitCellData ()
	Clear all data that depends on unit cell parameters.
void	compute (DArray< RField< D > > const &wFields, double phiTot=1.0)
	Compute solution to MDE and block concentrations.
void	computeStress ()
	Compute SCFT stress contribution from this polymer species.
double	stress (int n) const
	Get precomputed contribution to stress from this species.
Edge &	edge (int id) final
	Get a specified Edge (block descriptor) by non-const reference.
Edge const &	edge (int id) const final
	Get a specified Edge (block descriptor) by const reference.
Block< D > &	block (int id)
	Get a specified Block (solver and descriptor).
Block< D > const &	block (int id) const
	Get a specified Block (solver and descriptor) by const reference.
PropagatorT &	propagator (int blockId, int directionId)
	Get the propagator for a specific block and direction (non-const).
PropagatorT const &	propagator (int blockId, int directionId) const
	Get the propagator for a specific block and direction (const).
PropagatorT &	propagator (int id)
	Get a propagator indexed in order of computation (non-const).
const Vertex &	vertex (int id) const
	Get a specified Vertex by const reference.
Pair< int > const &	propagatorId (int id) const
	Get a propagator identifier, indexed by order of computation.
Pair< int > const &	path (int is, int it) const
	Get an id for a propagator from one vertex towards a target.
int	nBlock () const
	Number of blocks.
int	nVertex () const
	Number of vertices (junctions and chain ends).
int	nPropagator () const
	Number of propagators (2*nBlock).
double	length () const
	Sum of the lengths of all blocks in the polymer (thread model).
int	nBead () const
	Total number of beads in the polymer (bead model).
PolymerType::Enum	type () const
	Get Polymer type (Branched or Linear)
double	phi () const
	Get the overall volume fraction for this species.
double	mu () const
	Get the chemical potential for this species (units kT=1).
double	q () const
	Get the molecular partition function for this species.
Ensemble	ensemble () const
	Get the statistical ensemble for this species (open or closed).
void	setPhi (double phi)
	Set value of phi (volume fraction), if ensemble is closed.
void	setMu (double mu)
	Set value of mu (chemical potential), if ensemble is closed.
Public Member Functions inherited from Pscf::PolymerTmpl< Block< D > >
	PolymerTmpl ()
	Constructor.
	~PolymerTmpl ()
	Destructor.
virtual void	readParameters (std::istream &in)
	Read and initialize.
Block< D > &	block (int id)
	Get a specified Block (solver and descriptor).
Block< D > const &	block (int id) const
	Get a specified Block (solver and descriptor) by const reference.
PropagatorT &	propagator (int blockId, int directionId)
	Get the propagator for a specific block and direction (non-const).
PropagatorT const &	propagator (int blockId, int directionId) const
	Get the propagator for a specific block and direction (const).
PropagatorT &	propagator (int id)
	Get a propagator indexed in order of computation (non-const).
Public Member Functions inherited from Pscf::PolymerSpecies
	PolymerSpecies ()
	Constructor.
	~PolymerSpecies ()
	Destructor.
const Vertex &	vertex (int id) const
	Get a specified Vertex by const reference.
int	nBlock () const
	Number of blocks.
int	nVertex () const
	Number of vertices (junctions and chain ends).
int	nPropagator () const
	Number of propagators (2*nBlock).
double	length () const
	Sum of the lengths of all blocks in the polymer (thread model).
int	nBead () const
	Total number of beads in the polymer (bead model).
PolymerType::Enum	type () const
	Get Polymer type (Branched or Linear)
Pair< int > const &	propagatorId (int id) const
	Get a propagator identifier, indexed by order of computation.
Pair< int > const &	path (int is, int it) const
	Get an id for a propagator from one vertex towards a target.
Public Member Functions inherited from Pscf::Species
	Species ()
	Default constructor.
double	phi () const
	Get the overall volume fraction for this species.
double	mu () const
	Get the chemical potential for this species (units kT=1).
double	q () const
	Get the molecular partition function for this species.
Ensemble	ensemble () const
	Get the statistical ensemble for this species (open or closed).
void	setPhi (double phi)
	Set value of phi (volume fraction), if ensemble is closed.
void	setMu (double mu)
	Set value of mu (chemical potential), if ensemble is closed.
Public Member Functions inherited from Util::ParamComposite
	ParamComposite ()
	Constructor.
	ParamComposite (const ParamComposite &other)
	Copy constructor.
	ParamComposite (int capacity)
	Constructor.
virtual	~ParamComposite ()
	Virtual destructor.
void	resetParam ()
	Resets ParamComposite to its empty state.
virtual void	readParam (std::istream &in)
	Read the parameter file block.
virtual void	readParamOptional (std::istream &in)
	Read optional parameter file block.
virtual void	writeParam (std::ostream &out) const
	Write all parameters to an output stream.
virtual void	load (Serializable::IArchive &ar)
	Load all parameters from an input archive.
virtual void	loadOptional (Serializable::IArchive &ar)
	Load an optional ParamComposite.
virtual void	loadParameters (Serializable::IArchive &ar)
	Load state from archive, without adding Begin and End lines.
virtual void	save (Serializable::OArchive &ar)
	Saves all parameters to an archive.
void	saveOptional (Serializable::OArchive &ar)
	Saves isActive flag, and then calls save() iff isActive is true.
void	readParamComposite (std::istream &in, ParamComposite &child, bool next=true)
	Add and read a required child ParamComposite.
void	readParamCompositeOptional (std::istream &in, ParamComposite &child, bool next=true)
	Add and attempt to read an optional child ParamComposite.
template<typename Type>
ScalarParam< Type > &	read (std::istream &in, const char *label, Type &value)
	Add and read a new required ScalarParam < Type > object.
template<typename Type>
ScalarParam< Type > &	readOptional (std::istream &in, const char *label, Type &value)
	Add and read a new optional ScalarParam < Type > object.
template<typename Type>
CArrayParam< Type > &	readCArray (std::istream &in, const char label, Type value, int n)
	Add and read a required C array parameter.
template<typename Type>
CArrayParam< Type > &	readOptionalCArray (std::istream &in, const char label, Type value, int n)
	Add and read an optional C array parameter.
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.
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.
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.
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.
template<typename Type, int N>
FSArrayParam< Type, N > &	readFSArray (std::istream &in, const char *label, FSArray< Type, N > &array, int size)
	Add and read a required FSArray < Type, N > array parameter.
template<typename Type, int N>
FSArrayParam< Type, N > &	readOptionalFSArray (std::istream &in, const char *label, FSArray< Type, N > &array, int size)
	Add and read an optional FSArray < Type, N > array parameter.
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.
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.
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.
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.
template<typename Type>
DSymmMatrixParam< Type > &	readDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
	Add and read a required symmetrix DMatrix.
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.
Begin &	readBegin (std::istream &in, const char *label, bool isRequired=true)
	Add and read a class label and opening bracket.
End &	readEnd (std::istream &in)
	Add and read the closing bracket.
Blank &	readBlank (std::istream &in)
	Add and read a new Blank object, representing a blank line.
void	loadParamComposite (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load a required child ParamComposite.
void	loadParamCompositeOptional (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load an optional child ParamComposite if isActive.
template<typename Type>
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value, bool isRequired)
	Add and load a new ScalarParam < Type > object.
template<typename Type>
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value)
	Add and load new required ScalarParam < Type > object.
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.
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.
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.
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.
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.
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.
template<typename Type, int N>
FSArrayParam< Type, N > &	loadFSArray (Serializable::IArchive &ar, const char *label, FSArray< Type, N > &array, int size, bool isRequired)
	Add and load an FSArray < Type, N > array parameter.
template<typename Type, int N>
FSArrayParam< Type, N > &	loadFSArray (Serializable::IArchive &ar, const char *label, FSArray< Type, N > &array, int size)
	Add and load a required FSArray < Type > array parameter.
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.
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.
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.
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.
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.
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.
void	addParamComposite (ParamComposite &child, bool next=true)
	Add a child ParamComposite object to the format array.
Begin &	addBegin (const char *label)
	Add a Begin object representing a class name and bracket.
End &	addEnd ()
	Add a closing bracket.
Blank &	addBlank ()
	Create and add a new Blank object, representing a blank line.
std::string	className () const
	Get class name string.
bool	isRequired () const
	Is this ParamComposite required in the input file?
bool	isActive () const
	Is this parameter active?
Public Member Functions inherited from Util::ParamComponent
virtual	~ParamComponent ()
	Destructor.
void	setIndent (const ParamComponent &parent, bool next=true)
	Set indent level.
std::string	indent () const
	Return indent string for this object (string of spaces).
template<class Archive>
void	serialize (Archive &ar, const unsigned int version)
	Serialize this ParamComponent as a string.
Public Member Functions inherited from Util::Serializable
virtual	~Serializable ()
	Destructor.
Public Member Functions inherited from Util::MpiFileIo
	MpiFileIo ()
	Constructor.
	MpiFileIo (const MpiFileIo &other)
	Copy constructor.
bool	isIoProcessor () const
	Can this processor do file I/O ?

Additional Inherited Members
Static Public Member Functions inherited from Util::ParamComponent
static void	initStatic ()
	Initialize static echo member to false.
static void	setEcho (bool echo=true)
	Enable or disable echoing for all subclasses of ParamComponent.
static bool	echo ()
	Get echo parameter.
Protected Member Functions inherited from Pscf::PolymerTmpl< Block< D > >
void	allocateBlocks () final
	Allocate array of Block objects.
void	readBlocks (std::istream &in) final
	Read array of data for blocks from parameter file.
Protected Member Functions inherited from Pscf::PolymerSpecies
virtual void	makePlan ()
	Make a plan for order in which propagators should be computed.
void	makePaths ()
	Create a matrix of vertex-to-vertex path signposts.
Protected Member Functions inherited from Pscf::Species
void	setQ (double q)
	Set q and compute phi or mu (depending on the ensemble).
void	setClassName (const char *className)
	Set class name string.
void	setIsRequired (bool isRequired)
	Set or unset the isActive flag.
void	setIsActive (bool isActive)
	Set or unset the isActive flag.
void	setParent (ParamComponent &param, bool next=true)
	Set this to the parent of a child component.
void	addComponent (ParamComponent &param, bool isLeaf=true)
	Add a new ParamComponent object to the format array.
template<typename Type>
ScalarParam< Type > &	add (std::istream &in, const char *label, Type &value, bool isRequired=true)
	Add a new required ScalarParam < Type > object.
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.
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.
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.
template<typename Type, int N>
FSArrayParam< Type, N > &	addFSArray (std::istream &in, const char *label, FSArray< Type, N > &array, int size, bool isRequired=true)
	Add (but do not read) a FSArray < Type, N > array parameter.
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.
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.
Protected Member Functions inherited from Util::ParamComponent
	ParamComponent ()
	Constructor.
	ParamComponent (const ParamComponent &other)
	Copy constructor.

Detailed Description

template<int D>
class Pscf::Rpc::Polymer< D >

Descriptor and solver for one polymer species.

The phi() and mu() accessor functions, which are inherited from PolymerSpecies, return the value of phi (spatial average volume fraction of a species) or mu (species chemical potential) computed in the last call of the compute() function. If the ensemble for this species is closed, phi is read from the parameter file and mu is computed. If the ensemble is open, mu is read from the parameter file and phi is computed.

The block concentrations stored in the constituent Block<D> objects contain the block concentrations (i.e., volume fractions) computed in the most recent call of the compute function. These can be accessed using the Block<D>::cField() function.

Manual Page

Definition at line 54 of file rpc/solvers/Polymer.h.

Member Typedef Documentation

◆ Base

template<int D>

using Pscf::Rpc::Polymer< D >::Base = PolymerTmpl< Block<D> >

Base class, partial template specialization.

Definition at line 62 of file rpc/solvers/Polymer.h.

◆ BlockT

template<int D>

using Pscf::Rpc::Polymer< D >::BlockT = Block<D>

Block type, for a block within a block polymer.

Definition at line 65 of file rpc/solvers/Polymer.h.

◆ PropagatorT

template<int D>

using Pscf::Rpc::Polymer< D >::PropagatorT = typename BlockT::PropagatorT

Propagator type, for one direction within a block.

Definition at line 68 of file rpc/solvers/Polymer.h.

Constructor & Destructor Documentation

◆ Polymer()

template<int D>

Pscf::Rpc::Polymer< D >::Polymer ( )

Constructor.

Definition at line 18 of file rpc/solvers/Polymer.tpp.

References Util::ParamComposite::setClassName().

◆ ~Polymer()

template<int D>

Pscf::Rpc::Polymer< D >::~Polymer ( )

Destructor.

Definition at line 24 of file rpc/solvers/Polymer.tpp.

Member Function Documentation

◆ setNParams()

template<int D>

void Pscf::Rpc::Polymer< D >::setNParams ( int nParam )

Set the number of unit cell parameters.

Parameters

nParam the number of unit cell parameters

Definition at line 31 of file rpc/solvers/Polymer.tpp.

◆ clearUnitCellData()

template<int D>

void Pscf::Rpc::Polymer< D >::clearUnitCellData ( )

Clear all data that depends on unit cell parameters.

This function should be called after each change in the unit cell. It calls Block<D>::clearUnitCellData() for all blocks in this polymer.

Definition at line 38 of file rpc/solvers/Polymer.tpp.

References block(), and nBlock().

◆ compute()

template<int D>

void Pscf::Rpc::Polymer< D >::compute	(	DArray< RField< D > > const &	wFields,
		double	phiTot = 1.0 )

Compute solution to MDE and block concentrations.

This function sets up w-fields in the MDE solvers for all blocks, calls the base class PolymerTmpl solve function to solve the MDE for all blocks, and then computes concentrations associated with all blocks. On return, the associated Block objects all contain propagator solutions and block volume fraction fields, while q and phi or mu are set to new values.

The parameter phiTot is only relevant to problems such as thin films in which the material is excluded from part of the unit cell by imposing an inhogeneous constraint on the sum of the monomer concentrations (i.e., a "Mask").

Parameters

wFields	array of chemical potential fields.
phiTot	volume fraction of unit cell occupied by material

Definition at line 50 of file rpc/solvers/Polymer.tpp.

References block(), Pscf::PolymerModel::isBead(), Pscf::PolymerModel::isThread(), length(), nBead(), nBlock(), phi(), and q().

◆ computeStress()

template<int D>

void Pscf::Rpc::Polymer< D >::computeStress ( )

Compute SCFT stress contribution from this polymer species.

This function computes contributions from this species to the derivatives of SCFT free energy per monomer with respect to unit cell parameters and stores the values. It requires that the MDE has been solved for all blocks prior to entry, and so must be called after the compute function.

Definition at line 85 of file rpc/solvers/Polymer.tpp.

References block(), Pscf::PolymerModel::isThread(), length(), nBead(), nBlock(), phi(), and q().

◆ stress()

template<int D>

double Pscf::Rpc::Polymer< D >::stress ( int n ) const

inline

Get precomputed contribution to stress from this species.

Get stress component n.

Get the contribution from this polymer species to the deritative of free energy per monomer with respect to unit cell parameter n, as computed by the most recent call to computeStress().

Parameters

n	index of unit cell parameter

Definition at line 178 of file rpc/solvers/Polymer.h.

◆ edge() [1/2]

template<int D>

Edge & Pscf::PolymerTmpl< Block< D > >::edge ( int id )

finalvirtual

Get a specified Edge (block descriptor) by non-const reference.

The edge member functions implements pure virtual functions defined by the PolymerSpecies base class, and provide access to each Block as a reference to an Edge (a block descriptor).

Parameters

id	block index, 0 <= id < nBlock

Reimplemented from Pscf::PolymerTmpl< Block< D > >.

◆ edge() [2/2]

template<int D>

Edge const & Pscf::PolymerTmpl< Block< D > >::edge ( int id ) const

finalvirtual

Get a specified Edge (block descriptor) by const reference.

Parameters

id	block index, 0 <= id < nBlock

Reimplemented from Pscf::PolymerTmpl< Block< D > >.

◆ block() [1/2]

template<int D>

Block< D > & Pscf::PolymerTmpl< Block< D > >::block ( int id )

Get a specified Block (solver and descriptor).

Parameters

id	block index, 0 <= id < nBlock

Referenced by clearUnitCellData(), compute(), and computeStress().

◆ block() [2/2]

template<int D>

Block< D > const & Pscf::PolymerTmpl< Block< D > >::block ( int id ) const

Get a specified Block (solver and descriptor) by const reference.

Parameters

id	block index, 0 <= id < nBlock

◆ propagator() [1/3]

template<int D>

PropagatorT & Pscf::PolymerTmpl< Block< D > >::propagator	(	int	blockId,
		int	directionId )

Get the propagator for a specific block and direction (non-const).

For an edge that terminates at vertices with vertex indices given by the return values of Edge::vertexId(0) and Edge::vertexId(1):

direction 0 propagates from vertexId(0) to vertexId(1)
direction 1 propagates from vertexId(1) to vertexId(0)

Parameters

blockId	integer index of associated block
directionId	integer index for direction (0 or 1)

◆ propagator() [2/3]

template<int D>

PropagatorT const & Pscf::PolymerTmpl< Block< D > >::propagator	(	int	blockId,
		int	directionId ) const

Get the propagator for a specific block and direction (const).

Parameters

blockId	integer index of associated block
directionId	integer index for direction (0 or 1)

◆ propagator() [3/3]

template<int D>

PropagatorT & Pscf::PolymerTmpl< Block< D > >::propagator ( int id )

Get a propagator indexed in order of computation (non-const).

The propagator index argument must satisfy 0 <= id < 2*nBlock.

Parameters

id	propagator index, in order of computation plan

◆ vertex()

template<int D>

Vertex const & Pscf::PolymerSpecies::vertex ( int id ) const

inline

Get a specified Vertex by const reference.

Chain ends and block junctions are all vertices.

Parameters

id	vertex index, 0 <= id < nVertex

Definition at line 124 of file PolymerSpecies.h.

◆ propagatorId()

template<int D>

Pair< int > const & Pscf::PolymerSpecies::propagatorId ( int id ) const

inline

Get a propagator identifier, indexed by order of computation.

The return value is a pair of integers that identifies a directed edge, or a propagator. The first integer is a block index between 0 and nBlock - 1, and the second is a propagator direction id, which must be 0 or 1. By convention, direction 0 of Edge i propagates from vertex edge(i).vertexId(0) to vertex edge(i).vertexId(1), while direction 1 propagates in the other direction, from edge(i).vertexId(1) to edge(i).vertexId(0).

The propagators are indexed in an order that is computed by the protected function PolymerSpecies::makePlan. The indexing is chosen such that, if MDEs for different propagators are solved in sequential order by propagator index, then information required to construct the initial condition for the MDE within each propagator (the source slice) is guaranteed to be available from the solution of previous calculations.

Parameters

id	propagator index, in order of computation plan

Definition at line 192 of file PolymerSpecies.h.

◆ path()

template<int D>

Pair< int > const & Pscf::PolymerSpecies::path	(	int	is,
		int	it ) const

inline

Get an id for a propagator from one vertex towards a target.

For is != it, the return value is an identifier for an outgoing propagator that begins at the source vertex (vertex index is) and is the first edge of the directed path that leads from the source vertex to the target vertex (vertex id it). The return value is a pair of integers analogous to that returned by the propagatorId(int) member function, for which the first element is a block index and the second element is a direction id (0 or 1) for the propagator direction for that block that is outgoing from from the source vertex along the unique path leading to the target vertex. The requirement that the propagator be outgoing from vertex is implies that if path(is, it) == [ib, id], then edge(ib).vertexId(id) == is.

Parameters

is	index of the source vertex
it	index of the target vertex

Definition at line 212 of file PolymerSpecies.h.

◆ nBlock()

template<int D>

int Pscf::PolymerSpecies::nBlock ( ) const

inline

Number of blocks.

Definition at line 133 of file PolymerSpecies.h.

Referenced by clearUnitCellData(), compute(), and computeStress().

◆ nVertex()

template<int D>

int Pscf::PolymerSpecies::nVertex ( ) const

inline

Number of vertices (junctions and chain ends).

A theorem of graph theory tells us that, for any linear or acyclic branched polymer, nVertex = nBlock + 1.

Definition at line 141 of file PolymerSpecies.h.

◆ nPropagator()

template<int D>

int Pscf::PolymerSpecies::nPropagator ( ) const

inline

Number of propagators (2*nBlock).

Definition at line 146 of file PolymerSpecies.h.

◆ length()

template<int D>

double Pscf::PolymerSpecies::length ( ) const

Sum of the lengths of all blocks in the polymer (thread model).

Precondition: PolymerModel::isThread()

Definition at line 153 of file PolymerSpecies.cpp.

Referenced by compute(), Pscf::Rpc::Simulator< D >::computeHamiltonian(), and computeStress().

◆ nBead()

template<int D>

int Pscf::PolymerSpecies::nBead ( ) const

Total number of beads in the polymer (bead model).

Precondition: PolymerModel::isBead()

Definition at line 160 of file PolymerSpecies.cpp.

Referenced by compute(), Pscf::Rpc::Simulator< D >::computeHamiltonian(), and computeStress().

◆ type()

template<int D>

PolymerType::Enum Pscf::PolymerSpecies::type ( ) const

inline

Get Polymer type (Branched or Linear)

Definition at line 165 of file PolymerSpecies.h.

◆ phi()

template<int D>

double Pscf::Species::phi ( ) const

inline

Get the overall volume fraction for this species.

Definition at line 62 of file Species.h.

Referenced by compute(), Pscf::Rpc::Simulator< D >::computeHamiltonian(), and computeStress().

◆ mu()

template<int D>

double Pscf::Species::mu ( ) const

inline

Get the chemical potential for this species (units kT=1).

Definition at line 67 of file Species.h.

Referenced by Pscf::Rpc::Simulator< D >::computeHamiltonian().

◆ q()

template<int D>

double Pscf::Species::q ( ) const

inline

Get the molecular partition function for this species.

Definition at line 72 of file Species.h.

Referenced by compute(), and computeStress().

◆ ensemble()

template<int D>

Species::Ensemble Pscf::Species::ensemble ( ) const

inline

Get the statistical ensemble for this species (open or closed).

Definition at line 77 of file Species.h.

◆ setPhi()

template<int D>

void Pscf::Species::setPhi ( double phi )

Set value of phi (volume fraction), if ensemble is closed.

An initial value for phi or mu is normally read from a parameter file. This function is provided for use by a sweep or other procedure in which phi for a species with a closed enesmble is modified after initialization. It is an error to call setPhi for a polymer species with an open ensemble.

Exceptions

Exception if ensemble is open

Parameters

phi	new volume fraction value for this species

Definition at line 91 of file Species.cpp.

◆ setMu()

template<int D>

void Pscf::Species::setMu ( double mu )

Set value of mu (chemical potential), if ensemble is closed.

An initial value for phi or mu is normally read from a parameter file. This function is provided for use in a sweep or other procedure in which mu for a species with an open enesmble is modified after initialization. It is an error to call setMu for a polymer species with a closed ensemble.

Exceptions

Exception if ensemble is closed

Parameters

mu	new chemical potential value for this species

Definition at line 105 of file Species.cpp.

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

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Base

◆ BlockT

◆ PropagatorT

Constructor & Destructor Documentation

◆ Polymer()

◆ ~Polymer()

Member Function Documentation

◆ setNParams()

◆ clearUnitCellData()

◆ compute()

◆ computeStress()

◆ stress()

◆ edge() [1/2]

◆ edge() [2/2]

◆ block() [1/2]

◆ block() [2/2]

◆ propagator() [1/3]

◆ propagator() [2/3]

◆ propagator() [3/3]

◆ vertex()

◆ propagatorId()

◆ path()

◆ nBlock()

◆ nVertex()

◆ nPropagator()

◆ length()

◆ nBead()

◆ type()

◆ phi()

◆ mu()

◆ q()

◆ ensemble()

◆ setPhi()

◆ setMu()