Descriptor and MDE solver for an acyclic block polymer. More...

#include <PolymerTmpl.h>

Inheritance diagram for Pscf::PolymerTmpl< Block >:

Public Member Functions
	PolymerTmpl ()
	Constructor.

	~PolymerTmpl ()
	Destructor.

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

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

Accessors (objects, by reference)
Block &	block (int id)
	Get a specified Block.

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

const Vertex &	vertex (int id) const
	Get a specified Vertex by const reference.

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

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

Propagator &	propagator (int id)
	Get propagator indexed in order of computation.

const Pair< int > &	propagatorId (int id) const
	Get propagator identifier, indexed by order of computation.

Accessors (by value)
int	nBlock () const
	Number of blocks.

int	nVertex () const
	Number of vertices (junctions and chain ends).

int	nPropagator () const
	Number of propagators (nBlock*2).

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
virtual void	makePlan ()
	Make a plan for order in which propagators should be computed.

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
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.

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<class Block>
class Pscf::PolymerTmpl< Block >

Descriptor and MDE solver for an acyclic block polymer.

A PolymerTmpl<Block> object has arrays of Block and Vertex objects. Each Block has two propagator MDE solver objects. The solve() member function solves the modified diffusion equation (MDE) for the entire molecule and computes monomer concentration fields for all blocks.

Definition at line 41 of file PolymerTmpl.h.

Constructor & Destructor Documentation

◆ PolymerTmpl()

template<class Block >

Pscf::PolymerTmpl< Block >::PolymerTmpl ( )

Constructor.

Definition at line 345 of file PolymerTmpl.h.

References Util::ParamComposite::setClassName().

◆ ~PolymerTmpl()

template<class Block >

Pscf::PolymerTmpl< Block >::~PolymerTmpl ( )

Destructor.

Definition at line 359 of file PolymerTmpl.h.

Member Function Documentation

◆ readParameters()

template<class Block >

void Pscf::PolymerTmpl< Block >::readParameters ( std::istream & in )

virtual

Read and initialize.

Parameters

in	input parameter stream

Reimplemented from Util::ParamComposite.

Definition at line 363 of file PolymerTmpl.h.

References Pscf::Vertex::inPropagatorId(), Pscf::Vertex::size(), and UTIL_CHECK.

◆ solve()

template<class Block >

void Pscf::PolymerTmpl< Block >::solve ( double phiTot = 1.0 )

virtual

Solve modified diffusion equation.

Upon return, propagators for all blocks, molecular partition function q, phi and mu, and the block concentration fields for all blocks are set.

This function should be called within a member function named "compute" of each concrete subclass. This compute function must take an array of chemical potential fields (w-fields) as an argument. Before calling the solve() function declared here, the compute() function of each such subclass must store information required to solve the MDE within each block within a set of implementation dependent private members of the class class that represents a block of a block polymer. The implementation of PolymerTmpl::solve() the calls the solve() function for all propagators in the molecule in a predeternined order.

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

Parameters

phiTot fraction of volume occupied by material

Definition at line 534 of file PolymerTmpl.h.

References UTIL_CHECK.

Referenced by Pscf::R1d::Polymer::compute().

◆ block() [1/2]

template<class Block >

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

inline

Get a specified Block.

Parameters

id	block index, 0 <= id < nBlock

Definition at line 281 of file PolymerTmpl.h.

Referenced by Pscf::R1d::Polymer::compute().

◆ block() [2/2]

template<class Block >

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

inline

Get a specified Block by const reference.

Parameters

id	block index, 0 <= id < nBlock

Definition at line 288 of file PolymerTmpl.h.

◆ vertex()

template<class Block >

const Vertex & Pscf::PolymerTmpl< Block >::vertex ( int id ) const

inline

Get a specified Vertex by const reference.

Both chain ends and junctions are vertices.

Parameters

id	vertex index, 0 <= id < nVertex

Definition at line 274 of file PolymerTmpl.h.

Referenced by Pscf::R1d::FieldIo::writeVertexQ().

◆ propagator() [1/3]

template<class Block >

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

inline

Get propagator for a specific block and direction.

Parameters

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

Definition at line 309 of file PolymerTmpl.h.

Referenced by Pscf::R1d::System::writeQ(), Pscf::Rpc::System< D >::writeQ(), Pscf::Rpg::System< D >::writeQ(), Pscf::R1d::System::writeQSlice(), Pscf::Rpc::System< D >::writeQSlice(), Pscf::Rpg::System< D >::writeQSlice(), Pscf::R1d::System::writeQTail(), Pscf::Rpc::System< D >::writeQTail(), Pscf::Rpg::System< D >::writeQTail(), and Pscf::R1d::FieldIo::writeVertexQ().

◆ propagator() [2/3]

template<class Block >

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

inline

Get a const propagator for a specific block and direction.

Parameters

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

Definition at line 318 of file PolymerTmpl.h.

◆ propagator() [3/3]

template<class Block >

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

inline

Get propagator indexed in order of computation.

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

Parameters

id	propagator index, in order of computation plan

Definition at line 326 of file PolymerTmpl.h.

◆ propagatorId()

template<class Block >

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

inline

Get propagator identifier, indexed by order of computation.

The return value is a pair of integers. 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.

Parameters

id	propagator index, in order of computation plan

Definition at line 296 of file PolymerTmpl.h.

References UTIL_CHECK.

◆ nBlock()

template<class Block >

int Pscf::PolymerTmpl< Block >::nBlock ( ) const

inline

Number of blocks.

Definition at line 246 of file PolymerTmpl.h.

Referenced by Pscf::R1d::Polymer::compute(), Pscf::Rpc::IntraCorrelation< D >::computeIntraCorrelation(), Pscf::Rpg::IntraCorrelation< D >::computeIntraCorrelation(), Pscf::R1d::System::writeQ(), Pscf::Rpc::System< D >::writeQ(), Pscf::Rpg::System< D >::writeQ(), Pscf::R1d::System::writeQSlice(), Pscf::Rpc::System< D >::writeQSlice(), Pscf::Rpg::System< D >::writeQSlice(), Pscf::R1d::System::writeQTail(), Pscf::Rpc::System< D >::writeQTail(), Pscf::Rpg::System< D >::writeQTail(), and Pscf::R1d::FieldIo::writeVertexQ().

◆ nVertex()

template<class Block >

int Pscf::PolymerTmpl< Block >::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 239 of file PolymerTmpl.h.

◆ nPropagator()

template<class Block >

int Pscf::PolymerTmpl< Block >::nPropagator ( ) const

inline

Number of propagators (nBlock*2).

Definition at line 253 of file PolymerTmpl.h.

◆ length()

template<class Block >

double Pscf::PolymerTmpl< Block >::length ( ) const

inline

Sum of the lengths of all blocks in the polymer.

Definition at line 260 of file PolymerTmpl.h.

Referenced by Pscf::R1d::System::computeFreeEnergy(), Pscf::Rpc::System< D >::computeFreeEnergy(), Pscf::Rpg::System< D >::computeFreeEnergy(), Pscf::Rpc::Simulator< D >::computeHamiltonian(), Pscf::Rpg::Simulator< D >::computeHamiltonian(), Pscf::Rpc::IntraCorrelation< D >::computeIntraCorrelation(), and Pscf::Rpg::IntraCorrelation< D >::computeIntraCorrelation().

◆ type()

template<class Block >

PolymerType::Enum Pscf::PolymerTmpl< Block >::type ( ) const

inline

Get Polymer type (Branched or Linear)

Definition at line 336 of file PolymerTmpl.h.

Referenced by pscfpp.field.Field::__init__(), pscfpp.field.Field::__str__(), Pscf::Rpc::IntraCorrelation< D >::computeIntraCorrelation(), Pscf::Rpg::IntraCorrelation< D >::computeIntraCorrelation(), and pscfpp.field.Field::read().

◆ makePlan()

template<class Block >

void Pscf::PolymerTmpl< Block >::makePlan ( )

protectedvirtual

Make a plan for order in which propagators should be computed.

The algorithm creates a plan for computing propagators in an that guarantees that the inital conditions required for each propagator are known before it is processed. The algorithm is works for any acyclic branched block copolymer. This function is called in the default implementation of readParameters, and must be called the readParameters method of any subclass.

Definition at line 482 of file PolymerTmpl.h.

References Util::DMatrix< Data >::allocate(), Pscf::Vertex::inPropagatorId(), Pscf::Vertex::size(), and UTIL_THROW.

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

PolymerTmpl.h

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PolymerTmpl()

◆ ~PolymerTmpl()

Member Function Documentation

◆ readParameters()

◆ solve()

◆ block() [1/2]

◆ block() [2/2]

◆ vertex()

◆ propagator() [1/3]

◆ propagator() [2/3]

◆ propagator() [3/3]

◆ propagatorId()

◆ nBlock()

◆ nVertex()

◆ nPropagator()

◆ length()

◆ type()

◆ makePlan()