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

#include <Polymer.h>

Inheritance diagram for Pscf::Rp::Polymer< D, T >:

Public Types
using	BlockT = typename T::Block
	Block type, for a block within a block polymer.
using	PropagatorT = typename T::Propagator
	Propagator type, for one direction within a block.
using	PolymerTmplT = PolymerTmpl<BlockT, PropagatorT, double>
	Direct base class, specialization of PolymerTmpl class template.
Public Types inherited from Pscf::PolymerTmpl< T::Block, T::Propagator, double >
using	BlockT
	Block of a block polymer.
using	PropagatorT
	Modified diffusion equation solution (propagator).
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
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< typename T::RField > const &wFields, double phiTot=1.0)
	Compute MDE solutions and block concentrations.
void	computeStress ()
	Compute SCFT stress contribution from this polymer species.
double	stress (int n) const
	Get the 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.
BlockT &	block (int id)
	Get a specified Block (solver and descriptor).
BlockT 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::PolymerTmpl< T::Block, T::Propagator, double >
void	readParameters (std::istream &in) override
	Read and initialize.
T::Block &	block (int id)
	Get a specified Block (solver and descriptor).
T::Propagator &	propagator (int blockId, int directionId)
	Get the propagator for a specific block and direction (non-const).
Public Member Functions inherited from Pscf::PolymerSpecies< double >
	PolymerSpecies ()
	Constructor.
virtual	~PolymerSpecies ()=default
	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< double >
	Species ()
	Constructor.
virtual	~Species ()=default
	Destructor.
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 ?

Protected Member Functions
	Polymer ()
	Constructor.
	~Polymer ()
	Destructor.
Protected Member Functions inherited from Pscf::PolymerTmpl< T::Block, T::Propagator, double >
	PolymerTmpl ()
	Constructor.
	~PolymerTmpl () override=default
	Destructor.
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< double >
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< double >
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.

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 Types inherited from Pscf::PolymerTmpl< T::Block, T::Propagator, double >
using	SpeciesT
	Indirect (grandparent) base class.
using	PolymerSpeciesT
	Direct (parent) base class.

Detailed Description

template<int D, class T>
class Pscf::Rp::Polymer< D, T >

Descriptor and MDE solver for one polymer species.

Manual Page

This template adds functions required for periodic systems to an appropriate specialization of the Pscf::PolymerTmpl base class template.

Specializations of this class template are used as base classes for two closely analogous class templates, also named Polymer, that are defined in the Rpc and Rpg program-level name spaces for use in the pscf_rpc and pscf_rpg programs, respectively.

Template parameters :

D dimension of space
T class with aliases for use in a program-level namespace.

Definition at line 46 of file rp/solvers/Polymer.h.

Member Typedef Documentation

◆ BlockT

template<int D, class T>

using Pscf::Rp::Polymer< D, T >::BlockT = typename T::Block

Block type, for a block within a block polymer.

Definition at line 55 of file rp/solvers/Polymer.h.

◆ PropagatorT

template<int D, class T>

using Pscf::Rp::Polymer< D, T >::PropagatorT = typename T::Propagator

Propagator type, for one direction within a block.

Definition at line 58 of file rp/solvers/Polymer.h.

◆ PolymerTmplT

template<int D, class T>

using Pscf::Rp::Polymer< D, T >::PolymerTmplT = PolymerTmpl<BlockT, PropagatorT, double>

Direct base class, specialization of PolymerTmpl class template.

Definition at line 61 of file rp/solvers/Polymer.h.

Constructor & Destructor Documentation

◆ Polymer()

template<int D, class T>

Pscf::Rp::Polymer< D, T >::Polymer ( )

protected

Constructor.

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

References Util::ParamComposite::setClassName().

◆ ~Polymer()

template<int D, class T>

Pscf::Rp::Polymer< D, T >::~Polymer ( )

protected

Destructor.

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

Member Function Documentation

◆ setNParams()

template<int D, class T>

void Pscf::Rp::Polymer< D, T >::setNParams ( int nParam )

Set the number of unit cell parameters.

Parameters

nParam the number of unit cell parameters

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

◆ clearUnitCellData()

template<int D, class T>

void Pscf::Rp::Polymer< D, T >::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::clearUnitCellData() for all blocks in this polymer.

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

References block(), and Pscf::PolymerSpecies< double >::nBlock().

◆ compute()

template<int D, class T>

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

Compute MDE solutions 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 57 of file rp/solvers/Polymer.tpp.

References block(), Pscf::PolymerModel::isThread(), Pscf::PolymerSpecies< double >::length(), Pscf::PolymerSpecies< double >::nBlock(), Pscf::Species< double >::phi(), and Pscf::Species< double >::q().

◆ computeStress()

template<int D, class T>

void Pscf::Rp::Polymer< D, T >::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 91 of file rp/solvers/Polymer.tpp.

References block(), Pscf::PolymerModel::isThread(), Pscf::PolymerSpecies< double >::length(), Pscf::PolymerSpecies< double >::nBead(), Pscf::PolymerSpecies< double >::nBlock(), Pscf::Species< double >::phi(), Pscf::Species< double >::q(), and UTIL_CHECK.

◆ stress()

template<int D, class T>

double Pscf::Rp::Polymer< D, T >::stress ( int n ) const

inline

Get the precomputed contribution to stress from this species.

Get stress component n.

Get the contribution from this polymer species to 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	unit cell parameter index

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

◆ edge() [1/2]

template<int D, class T>

Edge & Pscf::PolymerTmpl< BlockT, PropagatorT, double >::edge ( int id )

finalvirtual

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

The edge member function implements a pure virtual function defined by the PolymerSpecies base class, and provides access to a specific Block as a reference to an Edge (a block descriptor), which is a base class of the Block (BT) class.

Parameters

id	block index, 0 <= id < nBlock

Reimplemented from Pscf::PolymerTmpl< T::Block, T::Propagator, double >.

◆ edge() [2/2]

template<int D, class T>

Edge const & Pscf::PolymerTmpl< BlockT, PropagatorT, double >::edge ( int id ) const

finalvirtual

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

Parameters

id	block index, 0 <= id < nBlock

Implements Pscf::PolymerSpecies< double >.

◆ block() [1/2]

template<int D, class T>

BlockT & Pscf::PolymerTmpl< BlockT, PropagatorT, double >::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, class T>

BlockT const & Pscf::PolymerTmpl< BlockT, PropagatorT, double >::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, class T>

PropagatorT & Pscf::PolymerTmpl< BlockT, PropagatorT, double >::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, class T>

PropagatorT const & Pscf::PolymerTmpl< BlockT, PropagatorT, double >::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, class T>

PropagatorT & Pscf::PolymerTmpl< BlockT, PropagatorT, double >::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

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

◆ BlockT

◆ PropagatorT

◆ PolymerTmplT

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]