Mixture of polymers and solvents. More...

#include <Mixture.h>

Inheritance diagram for Pscf::R1d::Mixture:

Public Types
typedef Propagator::WField	WField
	Monomer chemical potential field type.

typedef Propagator::CField	CField
	Monomer concentration or volume fraction field type.

Public Types inherited from Pscf::MixtureTmpl< Polymer, Solvent >
typedef Polymer	Polymer
	Polymer species solver typename.

typedef Solvent	Solvent
	Solvent species solver typename.

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
	Mixture ()
	Constructor.

	~Mixture ()
	Destructor.

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

void	setDomain (Domain const &domain)
	Create an association with the domain and allocate memory.

void	setKuhn (int monomerId, double kuhn)
	Reset statistical segment length for one monomer type.

void	compute (DArray< WField > const &wFields, DArray< CField > &cFields)
	Compute concentrations.

Public Member Functions inherited from Pscf::MixtureTmpl< Polymer, Solvent >
	MixtureTmpl ()
	Constructor.

	~MixtureTmpl ()
	Destructor.

Monomer const &	monomer (int id) const
	Get a Monomer type descriptor (const reference).

Polymer &	polymer (int id)
	Get a polymer object.

Polymer const &	polymer (int id) const
	Get a polymer object by const reference.

Solvent &	solvent (int id)
	Set a solvent solver object.

Solvent const &	solvent (int id) const
	Set a solvent solver object.

int	nMonomer () const
	Get number of monomer types.

int	nPolymer () const
	Get number of polymer species.

int	nBlock () const
	Get number of total blocks in the mixture across all polymers.

int	nSolvent () const
	Get number of solvent (point particle) species.

double	vMonomer () const
	Get monomer reference volume (set to 1.0 by default).

void	setVmonomer (double vMonomer)
	Set value of monomer reference volume.

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
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.

Protected Member Functions inherited from Pscf::MixtureTmpl< Polymer, Solvent >
Monomer &	monomer (int id)
	Get a Monomer type descriptor (non-const reference).

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.

Detailed Description

Mixture of polymers and solvents.

A Mixture contains a list of Polymer and Solvent objects. Each such object can solve the single-molecule statistical mechanics problem for an ideal gas of the associated species in a set of specified chemical potential fields, and thereby compute concentrations and single-molecule partition functions. A Mixture is thus both a chemistry descriptor and an ideal-gas solver.

A Mixture is associated with a Domain object, which models a spatial domain and a spatial discretization. Knowledge of the domain and discretization is needed to solve the ideal-gas problem.

Parameter File Format

Definition at line 42 of file r1d/solvers/Mixture.h.

Member Typedef Documentation

◆ WField

Propagator::WField Pscf::R1d::Mixture::WField

Monomer chemical potential field type.

Definition at line 52 of file r1d/solvers/Mixture.h.

◆ CField

Propagator::CField Pscf::R1d::Mixture::CField

Monomer concentration or volume fraction field type.

Definition at line 57 of file r1d/solvers/Mixture.h.

Constructor & Destructor Documentation

◆ Mixture()

Pscf::R1d::Mixture::Mixture ( )

Constructor.

Definition at line 17 of file r1d/solvers/Mixture.cpp.

References Util::ParamComposite::setClassName().

◆ ~Mixture()

Pscf::R1d::Mixture::~Mixture ( )

Destructor.

Definition at line 22 of file r1d/solvers/Mixture.cpp.

Member Function Documentation

◆ readParameters()

void Pscf::R1d::Mixture::readParameters ( std::istream & in )

virtual

Read all parameters and initialize.

This function reads in a complete description of the chemical composition and structure of all species, as well as the target contour length step size ds.

Parameters

in	input parameter stream

Reimplemented from Pscf::MixtureTmpl< Polymer, Solvent >.

Definition at line 25 of file r1d/solvers/Mixture.cpp.

References Pscf::MixtureTmpl< Polymer, Solvent >::nMonomer(), Pscf::MixtureTmpl< Polymer, Solvent >::nPolymer(), Pscf::MixtureTmpl< Polymer, Solvent >::nSolvent(), read(), Pscf::MixtureTmpl< TP, TS >::readParameters(), and UTIL_CHECK.

◆ setDomain()

void Pscf::R1d::Mixture::setDomain ( Domain const & domain )

Create an association with the domain and allocate memory.

The domain parameter must have already been initialized, e.g., by reading its parameters from a file, so that the domain dimensions are known on entry.

Parameters

domain associated Domain object (stores address).

Definition at line 37 of file r1d/solvers/Mixture.cpp.

References Pscf::MixtureTmpl< Polymer, Solvent >::nMonomer(), Pscf::MixtureTmpl< Polymer, Solvent >::nPolymer(), Pscf::MixtureTmpl< Polymer, Solvent >::nSolvent(), Pscf::MixtureTmpl< Polymer, Solvent >::polymer(), Pscf::MixtureTmpl< Polymer, Solvent >::solvent(), and UTIL_CHECK.

◆ setKuhn()

void Pscf::R1d::Mixture::setKuhn	(	int	monomerId,
		double	kuhn )

Reset statistical segment length for one monomer type.

This function resets the kuhn or statistical segment length value for a monomer type, and updates the associcated value in every block of that monomer type.

Parameters

monomerId	monomer type id
kuhn	new value for the statistical segment length

Definition at line 67 of file r1d/solvers/Mixture.cpp.

References Pscf::MixtureTmpl< Polymer, Solvent >::monomer(), Pscf::MixtureTmpl< Polymer, Solvent >::nPolymer(), Pscf::MixtureTmpl< Polymer, Solvent >::polymer(), and Pscf::Monomer::setKuhn().

◆ compute()

void Pscf::R1d::Mixture::compute	(	DArray< WField > const &	wFields,
		DArray< CField > &	cFields )

Compute concentrations.

This function calls the compute function of every molecular species, and then adds the resulting block concentration fields for blocks of each type to compute a total monomer concentration (or volume fraction) for each monomer type. Upon return, values are set for volume fraction and chemical potential (mu) members of each species, and for the concentration fields for each Block and Solvent. The total concentration for each monomer type is returned in the cFields output parameter.

The arrays wFields and cFields must each have size nMonomer(), and contain fields that are indexed by monomer type index.

Parameters

wFields	array of chemical potential fields (input)
cFields	array of monomer concentration fields (output)

Definition at line 85 of file r1d/solvers/Mixture.cpp.

References Util::Array< Data >::capacity(), Pscf::MixtureTmpl< Polymer, Solvent >::nMonomer(), Pscf::MixtureTmpl< Polymer, Solvent >::nPolymer(), Pscf::MixtureTmpl< Polymer, Solvent >::nSolvent(), Pscf::R1d::Domain::nx(), Pscf::MixtureTmpl< Polymer, Solvent >::polymer(), Pscf::MixtureTmpl< Polymer, Solvent >::solvent(), and UTIL_CHECK.

Referenced by Pscf::R1d::System::compute(), Pscf::R1d::BinaryRelaxIterator::solve(), and Pscf::R1d::NrIterator::solve().

◆ read()

template<typename Type >

ScalarParam< Type > & Util::ParamComposite::read	(	std::istream &	in,
		const char *	label,
		Type &	value )

protected

Add and read a new required ScalarParam < Type > object.

This is equivalent to ScalarParam<Type>(in, label, value, true).

Parameters

in	input stream for reading
label	Label string
value	reference to new ScalarParam< Type >

Definition at line 305 of file ParamComposite.h.

Referenced by pscfpp.command.Script::__init__(), pscfpp.field.Field::__init__(), pscfpp.output.Thermo::__init__(), pscfpp.param.Array::__init__(), pscfpp.param.Composite::__init__(), pscfpp.param.Matrix::__init__(), and readParameters().

◆ readOptional()

template<typename Type >

ScalarParam< Type > & Util::ParamComposite::readOptional	(	std::istream &	in,
		const char *	label,
		Type &	value )

inlineprotected

Add and read a new optional ScalarParam < Type > object.

This is equivalent to ScalarParam<Type>(in, label, value, false).

Parameters

in	input stream for reading
label	Label string
value	reference to new ScalarParam< Type >

Definition at line 319 of file ParamComposite.h.

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

◆ WField

◆ CField

Constructor & Destructor Documentation

◆ Mixture()

◆ ~Mixture()

Member Function Documentation

◆ readParameters()

◆ setDomain()

◆ setKuhn()

◆ compute()

◆ read()

◆ readOptional()