Pscf::Rpc::Polymer< D > Class Template Reference

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

#include <Polymer.h>

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

Public Types
typedef PolymerTmpl< Block< D > >	Base
	Base class typedef (PolymerTmpl instance)
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 ()
	Default constructor.
	~Polymer ()
	Destructor.
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.
void	setNParams (int nParam)
	Store 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 stress contribution from this species.
double	stress (int n) const
	Get precomputed contribution to stress from this species.
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::Rpc::Polymer< D >

Descriptor and solver for one polymer species.

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 (species chemical potential) computed in the most recent 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 42 of file rpc/solvers/Polymer.h.

Member Typedef Documentation

Base

template<int D>

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

Base class typedef (PolymerTmpl instance)

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

Constructor & Destructor Documentation

Polymer()

template<int D>

Pscf::Rpc::Polymer< D >::Polymer

(

)

Default constructor.

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

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

~Polymer()

template<int D>

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

(

)

Destructor.

Definition at line 23 of file rpc/solvers/Polymer.tpp.

Member Function Documentation

setPhi()

template<int D>

void Pscf::Rpc::Polymer< D >::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 27 of file rpc/solvers/Polymer.tpp.

References UTIL_CHECK.

setMu()

template<int D>

void Pscf::Rpc::Polymer< D >::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 36 of file rpc/solvers/Polymer.tpp.

References UTIL_CHECK.

setNParams()

template<int D>

void Pscf::Rpc::Polymer< D >::setNParams

(

int

nParam

)

Store the number of unit cell parameters.

Parameters

nParam

the number of unit cell parameters

Definition at line 46 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 53 of file rpc/solvers/Polymer.tpp.

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 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 64 of file rpc/solvers/Polymer.tpp.

computeStress()

template<int D>

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

(

)

Compute stress contribution from this species.

This function computes contributions from this species to the derivatives of free energy per monomer with respect to unit cell parameters and stores the values.

Definition at line 82 of file rpc/solvers/Polymer.tpp.

stress()

template<int D>

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

inline

Get precomputed contribution to stress from this species.

Get stress with respect to unit cell parameter n.

This function gets the precomputed value of the derivative 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 172 of file rpc/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::Rpc::Polymer< D >::Polymer().

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

• rpc/solvers/Polymer.h
• rpc/solvers/Polymer.tpp