Descriptor for a solvent species. More...

#include <SolventSpecies.h>

Inheritance diagram for Pscf::SolventSpecies:

Public Member Functions
	SolventSpecies ()
	Constructor.

	~SolventSpecies ()
	Constructor.

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

Setters (set member data)
void	setPhi (double phi)
	Set input value of phi (volume fraction), if ensemble is closed.

void	setMu (double mu)
	Set input value of mu (chemical potential), if ensemble is open.

void	setMonomerId (int monomerId)
	Set the monomer id for this solvent.

void	setSize (double size)
	Set the molecular volume of this solvent species.

Accessors (getters)
int	monomerId () const
	Get the monomer type id.

double	size () const
	Get the size (number of monomers) in this solvent.

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 Attributes
int	monomerId_
	Identifier for the associated monomer type.

double	size_
	Size of this block = volume / monomer reference volume.

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).

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 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.

Detailed Description

Descriptor for a solvent species.

A SolventSpecies has values for monomer type index (monomerId) and steric volume per molecule of a solvent species (size), in addition to properties phi, mu, q, and ensemble inherited from the Species base class. The size parameter is defined to be the ratio of solvent molecule volume to the monomer reference volume.

Definition at line 29 of file SolventSpecies.h.

Constructor & Destructor Documentation

◆ SolventSpecies()

Pscf::SolventSpecies::SolventSpecies ( )

Constructor.

Definition at line 15 of file SolventSpecies.cpp.

References Util::ParamComposite::setClassName().

◆ ~SolventSpecies()

Pscf::SolventSpecies::~SolventSpecies ( )

Constructor.

Definition at line 24 of file SolventSpecies.cpp.

Member Function Documentation

◆ readParameters()

void Pscf::SolventSpecies::readParameters ( std::istream & in )

virtual

Read and initialize.

Parameters

in	input parameter stream

Reimplemented from Util::ParamComposite.

Definition at line 30 of file SolventSpecies.cpp.

References Pscf::Species::ensemble_, monomerId_, Pscf::Species::mu_, Pscf::Species::phi_, Util::ParamComposite::read(), Util::ParamComposite::readOptional(), and size_.

◆ setPhi()

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

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

This function may be used to modify phi during a sweep, after initialization. An Exception is thrown if this function is called when the ensemble is open on entry.

Parameters

phi	desired volume fraction for this species

Definition at line 48 of file SolventSpecies.cpp.

References Pscf::Species::ensemble(), Pscf::Species::phi(), Pscf::Species::phi_, and UTIL_CHECK.

◆ setMu()

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

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

This function may be used to modify mu during a sweep, after initialization. An Exception is thrown if this function is called when the ensemble is closed on entry.

Parameters

mu	desired chemical potential for this species

Definition at line 59 of file SolventSpecies.cpp.

References Pscf::Species::ensemble(), Pscf::Species::mu(), Pscf::Species::mu_, and UTIL_CHECK.

◆ setMonomerId()

void Pscf::SolventSpecies::setMonomerId ( int monomerId )

Set the monomer id for this solvent.

Parameters

monomerId integer id of monomer type, in [0,nMonomer-1]

Definition at line 68 of file SolventSpecies.cpp.

References monomerId(), and monomerId_.

◆ setSize()

void Pscf::SolventSpecies::setSize ( double size )

Set the molecular volume of this solvent species.

The ``size" is the ratio (solvent molecule volume) / vMonomer, where vMonomer is the monomer reference volume, i.e., the volume per monomer (or unit contour length) of any polymer.

Parameters

size	volume of solvent

Definition at line 74 of file SolventSpecies.cpp.

References size(), and size_.

◆ monomerId()

int Pscf::SolventSpecies::monomerId ( ) const

inline

Get the monomer type id.

Definition at line 137 of file SolventSpecies.h.

References monomerId_.

Referenced by setMonomerId().

◆ size()

double Pscf::SolventSpecies::size ( ) const

inline

Get the size (number of monomers) in this solvent.

Definition at line 143 of file SolventSpecies.h.

References size_.

Referenced by pscfpp.file.File::__eq__(), pscfpp.file.File::__init__(), pscfpp.text.Record::__init__(), pscfpp.file.File::__repr__(), pscfpp.text.Record::__str__(), Pscf::R1d::Solvent::compute(), Pscf::R1d::System::computeFreeEnergy(), Pscf::Rpc::System< D >::computeFreeEnergy(), Pscf::Rpg::System< D >::computeFreeEnergy(), Pscf::Rpc::Simulator< D >::computeHamiltonian(), Pscf::Rpg::Simulator< D >::computeHamiltonian(), and setSize().

Member Data Documentation

◆ monomerId_

int Pscf::SolventSpecies::monomerId_

protected

Identifier for the associated monomer type.

Definition at line 125 of file SolventSpecies.h.

Referenced by monomerId(), readParameters(), and setMonomerId().

◆ size_

double Pscf::SolventSpecies::size_

protected

Size of this block = volume / monomer reference volume.

Definition at line 128 of file SolventSpecies.h.

Referenced by readParameters(), setSize(), and size().

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

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SolventSpecies()

◆ ~SolventSpecies()

Member Function Documentation

◆ readParameters()

◆ setPhi()

◆ setMu()

◆ setMonomerId()

◆ setSize()

◆ monomerId()

◆ size()

Member Data Documentation

◆ monomerId_

◆ size_