Descriptor and solver for a branched polymer species. More...

#include <Polymer.h>

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

Public Types
typedef PolymerTmpl< Block< D > >	Base
	Alias for base class.

Public Types inherited from Pscf::PolymerTmpl< Block< D > >
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	setPhi (double phi)
	Set the phi (volume fraction) for this species.

void	setMu (double mu)
	Set the mu (chemical potential) for this species.

void	setNParams (int nParams)
	Store the number of lattice parameters in the unit cell.

void	compute (DArray< RField< D > > const &wFields, double phiTot=1.0)
	Compute solution to MDE and block concentrations.

void	computeStress ()
	Compute stress from a polymer chain, needs a pointer to basis.

double	stress (int n)
	Get derivative of free energy w/ respect to a unit cell parameter.

Public Member Functions inherited from Pscf::PolymerTmpl< Block< D > >
	PolymerTmpl ()
	Constructor.

	~PolymerTmpl ()
	Destructor.

virtual void	readParameters (std::istream &in)
	Read and initialize.

virtual void	solve (double phiTot=1.0)
	Solve modified diffusion equation.

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.

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

virtual Edge &	edge (int id)
	Get a specified Edge (block descriptor) by non-const reference.

virtual Edge const &	edge (int id) const
	Get a specified Edge (block descriptor) by const reference.

Block &	block (int id)
	Get a specified Block (block solver and descriptor)

Block const &	block (int id) const
	Get a specified Block (solver and descriptor) by const reference.

Propagator &	propagator (int blockId, int directionId)
	Get the Propagator for a specific block and direction (non-const).

Propagator const &	propagator (int blockId, int directionId) const
	Get the Propagator for a specific block and direction (const).

Propagator &	propagator (int id)
	Get 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.

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.

PolymerType::Enum	type () const
	Get Polymer type (Branched or Linear)

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 ()
	Get the statistical ensemble for this species (open or 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 ?

void	setIoCommunicator (MPI::Intracomm &communicator)
	Set the communicator.

void	clearCommunicator ()
	Clear (nullify) the communicator.

bool	hasIoCommunicator () const
	Does this object have an associated MPI communicator?

MPI::Intracomm &	ioCommunicator () const
	Get the MPI communicator by reference.

Protected Member Functions
void	setClassName (const char *className)
	Set class name string.

Protected Member Functions inherited from Pscf::PolymerTmpl< Block< D > >
virtual void	allocateBlocks ()
	Allocate array of Block objects.

virtual void	readBlocks (std::istream &in)
	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.

void	isValid ()
	Check validity of graph.

Protected Member Functions inherited from Util::ParamComposite
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.

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 Attributes inherited from Pscf::Species
double	phi_
	Volume fraction, set by either setPhi or a compute function.

double	mu_
	Chemical potential, set by either setPhi or a compute function.

double	q_
	Partition function, set in subclass by a compute function.

Ensemble	ensemble_
	Statistical ensemble for this species (open or closed).

Detailed Description

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

Descriptor and solver for a branched polymer species.

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.

The phi() and mu() accessor functions, which are inherited from PolymerTmp< Block<D> >, return the value of phi (spatial average volume fraction of a species) or mu (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.

Definition at line 49 of file rpg/solvers/Polymer.h.

Member Typedef Documentation

◆ Base

template<int D>

PolymerTmpl< Block<D> > Pscf::Rpg::Polymer< D >::Base

Alias for base class.

Definition at line 57 of file rpg/solvers/Polymer.h.

Constructor & Destructor Documentation

◆ Polymer()

template<int D>

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

Constructor.

Definition at line 17 of file rpg/solvers/Polymer.tpp.

References Pscf::Rpg::Polymer< D >::setClassName().

◆ ~Polymer()

template<int D>

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

Destructor.

Definition at line 22 of file rpg/solvers/Polymer.tpp.

Member Function Documentation

◆ setPhi()

template<int D>

void Pscf::Rpg::Polymer< D >::setPhi ( double phi )

Set the phi (volume fraction) for this species.

Parameters

phi	volume fraction (input)

Definition at line 26 of file rpg/solvers/Polymer.tpp.

References UTIL_CHECK.

◆ setMu()

template<int D>

void Pscf::Rpg::Polymer< D >::setMu ( double mu )

Set the mu (chemical potential) for this species.

Parameters

mu	chemical potential (input)

Definition at line 35 of file rpg/solvers/Polymer.tpp.

References UTIL_CHECK.

◆ setNParams()

template<int D>

void Pscf::Rpg::Polymer< D >::setNParams ( int nParams )

Store the number of lattice parameters in the unit cell.

Parameters

nParams the number of lattice parameters in the unit cell

Definition at line 45 of file rpg/solvers/Polymer.tpp.

◆ compute()

template<int D>

void Pscf::Rpg::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 and then calls the base class PolymerTmpl solve function. This solves the MDE for all propagators and computes the properly scaled volume fraction fields for all blocks. After this function is called, the associated Block objects store pre-computed propagator solutions and block volume fraction fields.

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 54 of file rpg/solvers/Polymer.tpp.

◆ computeStress()

template<int D>

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

Compute stress from a polymer chain, needs a pointer to basis.

Definition at line 73 of file rpg/solvers/Polymer.tpp.

References UTIL_CHECK.

◆ stress()

template<int D>

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

Get derivative of free energy w/ respect to a unit cell parameter.

Get the contribution from this polymer species to the derivative of free energy per monomer with respect to unit cell parameter n.

Parameters

n	unit cell parameter index

Definition at line 152 of file rpg/solvers/Polymer.h.

◆ setClassName()

template<int D>

void Util::ParamComposite::setClassName ( const char * className )

protected

Set class name string.

Should be set in subclass constructor.

Definition at line 900 of file ParamComposite.cpp.

Referenced by Pscf::Rpg::Polymer< D >::Polymer().

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

Public Types

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Base

Constructor & Destructor Documentation

◆ Polymer()

◆ ~Polymer()

Member Function Documentation

◆ setPhi()

◆ setMu()

◆ setNParams()

◆ compute()

◆ computeStress()

◆ stress()

◆ setClassName()