Solver for a mixture of polymers and solvents. More...

#include <Mixture.h>

Inheritance diagram for Pscf::Pspc::Mixture< D >:

Public Member Functions
	Mixture ()
	Constructor. More...

	~Mixture ()
	Destructor. More...

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

void	setMesh (Mesh< D > const &mesh)
	Create an association with the mesh and allocate memory. More...

void	setupUnitCell (const UnitCell< D > &unitCell)
	Set unit cell parameters used in solver. More...

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

void	compute (DArray< RField< D > > const &wFields, DArray< RField< D > > &cFields, double phiTot=1.0)
	Compute partition functions and concentrations. More...

void	computeStress ()
	Compute derivatives of free energy w/ respect to cell parameters. More...

void	createBlockCRGrid (DArray< RField< D > > &blockCFields) const
	Combine cFields for each block/solvent into one DArray, which is used in System.tpp to print a more detailed r-grid file using the command WRITE_C_BLOCK_RGRID. More...

double	stress (int n) const
	Get derivative of free energy w/ respect to a unit cell parameter. More...

bool	isCanonical ()
	Is this mixture being treated in canonical ensemble? More...

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

	~MixtureTmpl ()
	Destructor. More...

virtual void	readParameters (std::istream &in)
	Read parameters from file and initialize. More...

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

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

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

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

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

int	nMonomer () const
	Get number of monomer types. More...

int	nPolymer () const
	Get number of polymer species. More...

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

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

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

Public Member Functions inherited from Util::ParamComposite
	ParamComposite ()
	Constructor. More...

	ParamComposite (const ParamComposite &other)
	Copy constructor. More...

	ParamComposite (int capacity)
	Constructor. More...

virtual	~ParamComposite ()
	Virtual destructor. More...

void	resetParam ()
	Resets ParamComposite to its empty state. More...

virtual void	readParam (std::istream &in)
	Read the parameter file block. More...

virtual void	readParamOptional (std::istream &in)
	Read optional parameter file block. More...

virtual void	writeParam (std::ostream &out) const
	Write all parameters to an output stream. More...

virtual void	load (Serializable::IArchive &ar)
	Load all parameters from an input archive. More...

virtual void	loadOptional (Serializable::IArchive &ar)
	Load an optional ParamComposite. More...

virtual void	loadParameters (Serializable::IArchive &ar)
	Load state from archive, without adding Begin and End lines. More...

virtual void	save (Serializable::OArchive &ar)
	Saves all parameters to an archive. More...

void	saveOptional (Serializable::OArchive &ar)
	Saves isActive flag, and then calls save() iff isActive is true. More...

void	readParamComposite (std::istream &in, ParamComposite &child, bool next=true)
	Add and read a required child ParamComposite. More...

void	readParamCompositeOptional (std::istream &in, ParamComposite &child, bool next=true)
	Add and attempt to read an optional child ParamComposite. More...

template<typename Type >
ScalarParam< Type > &	read (std::istream &in, const char *label, Type &value)
	Add and read a new required ScalarParam < Type > object. More...

template<typename Type >
ScalarParam< Type > &	readOptional (std::istream &in, const char *label, Type &value)
	Add and read a new optional ScalarParam < Type > object. More...

template<typename Type >
CArrayParam< Type > &	readCArray (std::istream &in, const char label, Type value, int n)
	Add and read a required C array parameter. More...

template<typename Type >
CArrayParam< Type > &	readOptionalCArray (std::istream &in, const char label, Type value, int n)
	Add and read an optional C array parameter. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

template<typename Type >
DSymmMatrixParam< Type > &	readDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
	Add and read a required symmetrix DMatrix. More...

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. More...

Begin &	readBegin (std::istream &in, const char *label, bool isRequired=true)
	Add and read a class label and opening bracket. More...

End &	readEnd (std::istream &in)
	Add and read the closing bracket. More...

Blank &	readBlank (std::istream &in)
	Add and read a new Blank object, representing a blank line. More...

void	loadParamComposite (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load a required child ParamComposite. More...

void	loadParamCompositeOptional (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load an optional child ParamComposite if isActive. More...

template<typename Type >
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value, bool isRequired)
	Add and load a new ScalarParam < Type > object. More...

template<typename Type >
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value)
	Add and load new required ScalarParam < Type > object. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

void	addParamComposite (ParamComposite &child, bool next=true)
	Add a child ParamComposite object to the format array. More...

Begin &	addBegin (const char *label)
	Add a Begin object representing a class name and bracket. More...

End &	addEnd ()
	Add a closing bracket. More...

Blank &	addBlank ()
	Create and add a new Blank object, representing a blank line. More...

std::string	className () const
	Get class name string. More...

bool	isRequired () const
	Is this ParamComposite required in the input file? More...

bool	isActive () const
	Is this parameter active? More...

Public Member Functions inherited from Util::ParamComponent
virtual	~ParamComponent ()
	Destructor. More...

virtual void	readParam (std::istream &in)=0
	Read parameter(s) from file. More...

virtual void	writeParam (std::ostream &out) const =0
	Read parameter(s) to file. More...

virtual void	load (Serializable::IArchive &ar)
	Load internal state from an archive. More...

virtual void	save (Serializable::OArchive &ar)
	Save internal state to an archive. More...

virtual void	resetParam ()
	Nontrivial implementation provided by ParamComposite subclass. More...

void	setIndent (const ParamComponent &parent, bool next=true)
	Set indent level. More...

std::string	indent () const
	Return indent string for this object (string of spaces). More...

template<class Archive >
void	serialize (Archive &ar, const unsigned int version)
	Serialize this ParamComponent as a string. More...

Public Member Functions inherited from Util::Serializable
virtual	~Serializable ()
	Destructor. More...

virtual void	save (OArchive &ar)=0
	Save to an archive. More...

virtual void	load (IArchive &ar)=0
	Load from an archive. More...

Public Member Functions inherited from Util::MpiFileIo
	MpiFileIo ()
	Constructor. More...

	MpiFileIo (const MpiFileIo &other)
	Copy constructor. More...

bool	isIoProcessor () const
	Can this processor do file I/O ? More...

void	setIoCommunicator (MPI::Intracomm &communicator)
	Set the communicator. More...

void	clearCommunicator ()
	Clear (nullify) the communicator. More...

bool	hasIoCommunicator () const
	Does this object have an associated MPI communicator? More...

MPI::Intracomm &	ioCommunicator () const
	Get the MPI communicator by reference. More...

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. More...

template<typename Type >
ScalarParam< Type > &	readOptional (std::istream &in, const char *label, Type &value)
	Add and read a new optional ScalarParam < Type > object. More...

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

Protected Member Functions inherited from Util::ParamComposite
void	setClassName (const char *className)
	Set class name string. More...

void	setIsRequired (bool isRequired)
	Set or unset the isActive flag. More...

void	setIsActive (bool isActive)
	Set or unset the isActive flag. More...

void	setParent (ParamComponent &param, bool next=true)
	Set this to the parent of a child component. More...

void	addComponent (ParamComponent &param, bool isLeaf=true)
	Add a new ParamComponent object to the format array. More...

template<typename Type >
ScalarParam< Type > &	add (std::istream &in, const char *label, Type &value, bool isRequired=true)
	Add a new required ScalarParam < Type > object. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

Protected Member Functions inherited from Util::ParamComponent
	ParamComponent ()
	Constructor. More...

	ParamComponent (const ParamComponent &other)
	Copy constructor. More...

Additional Inherited Members
Public Types inherited from Pscf::MixtureTmpl< Polymer< D >, Solvent< D > >
typedef Polymer< D >	Polymer
	Polymer species solver typename. More...

typedef Solvent< D >	Solvent
	Solvent species solver typename. More...

Public Types inherited from Util::Serializable
typedef BinaryFileOArchive	OArchive
	Type of output archive used by save method. More...

typedef BinaryFileIArchive	IArchive
	Type of input archive used by load method. More...

Static Public Member Functions inherited from Util::ParamComponent
static void	initStatic ()
	Initialize static echo member to false. More...

static void	setEcho (bool echo=true)
	Enable or disable echoing for all subclasses of ParamComponent. More...

static bool	echo ()
	Get echo parameter. More...

Detailed Description

template<int D>
class Pscf::Pspc::Mixture< D >

Solver for a 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 and single-molecule partition functions. A Mixture is thus both a a chemistry descriptor and an ideal-gas solver.

The single-molecule partition functions and concentrations for a non-interacting mixture of polymer and solvent species are computed by invoking the Mixture::compute function. The Mixture::compute function takes an arrays of monomer chemical potential fields (w fields) as an input argument and an array of monomer concentration fields (c fields) as an output. The objects that store these fields are owned by the parent System.

A Mixture is associated with a Mesh<D> object, which models a spatial discretization mesh, and a UnitCell<D> object, which describes the the periodic unit cell. The Mixture::setupUnitCell function sets up all parameters that depend on the unit cell, and must be called once once after every time the unit cell is initialized or modified, before the next call to Mixture::compute.

Parameter File Format

Definition at line 58 of file pspc/solvers/Mixture.h.

Constructor & Destructor Documentation

◆ Mixture()

template<int D>

Pscf::Pspc::Mixture< D >::Mixture

Constructor.

Definition at line 21 of file pspc/solvers/Mixture.tpp.

References Util::ParamComposite::setClassName().

◆ ~Mixture()

template<int D>

Pscf::Pspc::Mixture< D >::~Mixture

Destructor.

Definition at line 29 of file pspc/solvers/Mixture.tpp.

Member Function Documentation

◆ readParameters()

template<int D>

void Pscf::Pspc::Mixture< D >::readParameters ( std::istream & in )

virtual

Read all parameters and initialize.

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

Parameters

in	input parameter stream

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

Definition at line 33 of file pspc/solvers/Mixture.tpp.

References UTIL_CHECK.

◆ setMesh()

template<int D>

void Pscf::Pspc::Mixture< D >::setMesh ( Mesh< D > const & mesh )

Create an association with the mesh and allocate memory.

The Mesh<D> object must have already been initialized, e.g., by reading its parameters from a file, so that the mesh dimensions are known on entry.

Parameters

mesh	associated Mesh<D> object (stores address).

Definition at line 44 of file pspc/solvers/Mixture.tpp.

References UTIL_CHECK.

◆ setupUnitCell()

template<int D>

void Pscf::Pspc::Mixture< D >::setupUnitCell ( const UnitCell< D > & unitCell )

Set unit cell parameters used in solver.

This function resets unit cell information in the solvers for every species in the system. It should be called once after every change in the unit cell.

Parameters

unitCell UnitCell<D> object that contains Bravais lattice.

Definition at line 73 of file pspc/solvers/Mixture.tpp.

◆ setKuhn()

template<int D>

void Pscf::Pspc::Mixture< D >::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 94 of file pspc/solvers/Mixture.tpp.

◆ compute()

template<int D>

void Pscf::Pspc::Mixture< D >::compute	(	DArray< RField< D > > const &	wFields,
		DArray< RField< D > > &	cFields,
		double	phiTot = `1.0`
	)

Compute partition functions and concentrations.

This function calls the compute function of every molecular species, and then adds the resulting block concentration fields for blocks of the same monomer 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. Monomer "concentrations" are returned in units of inverse steric volume per monomer in an incompressible mixture, and are thus also volume fractions.

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

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 imposing an inhomogeneous constrain on the sum of mononer concentrations, (i.e., a "mask").

Parameters

wFields	array of chemical potential fields (input)
cFields	array of monomer concentration fields (output)
phiTot	volume fraction of unit cell occupied by material

Definition at line 114 of file pspc/solvers/Mixture.tpp.

References Util::Array< Data >::capacity(), and UTIL_CHECK.

◆ computeStress()

template<int D>

void Pscf::Pspc::Mixture< D >::computeStress

Compute derivatives of free energy w/ respect to cell parameters.

Definition at line 187 of file pspc/solvers/Mixture.tpp.

◆ createBlockCRGrid()

template<int D>

void Pscf::Pspc::Mixture< D >::createBlockCRGrid ( DArray< RField< D > > & blockCFields ) const

Combine cFields for each block/solvent into one DArray, which is used in System.tpp to print a more detailed r-grid file using the command WRITE_C_BLOCK_RGRID.

Parameters

blockCFields empty but allocated DArray to store fields

Definition at line 242 of file pspc/solvers/Mixture.tpp.

References UTIL_CHECK.

◆ stress()

template<int D>

double Pscf::Pspc::Mixture< D >::stress ( int n ) const

inline

Get derivative of free energy w/ respect to a unit cell parameter.

Get the pre-computed derivative with respect to unit cell parameter number n of the free energy per monomer (i.e., of the product of the free energy density and the monomer reference volume). The returned value is precomputed by the computeStress() function.

Parameters

n	index of unit cell parameter

Definition at line 227 of file pspc/solvers/Mixture.h.

References UTIL_CHECK.

◆ isCanonical()

template<int D>

bool Pscf::Pspc::Mixture< D >::isCanonical

Is this mixture being treated in canonical ensemble?

Returns true iff an closed ensemble is used for every polymer and solve species, by specifying a volume fraction phi rather than a chemical potential mu for every species.

Definition at line 219 of file pspc/solvers/Mixture.tpp.

◆ read()

template<int D>

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

◆ readOptional()

template<int D>

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 Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Mixture()

◆ ~Mixture()

Member Function Documentation

◆ readParameters()

◆ setMesh()

◆ setupUnitCell()

◆ setKuhn()

◆ compute()

◆ computeStress()

◆ createBlockCRGrid()

◆ stress()

◆ isCanonical()

◆ read()

◆ readOptional()