PSCF v1.3
Pscf::R1d::Mixture Class Reference

Mixture of polymers and solvents. More...

#include <Mixture.h>

Inheritance diagram for Pscf::R1d::Mixture:
Pscf::MixtureTmpl< Polymer, Solvent > Pscf::MixtureBase Util::ParamComposite Util::ParamComponent Util::Serializable Util::MpiFileIo

Public Types

typedef Propagator::FieldT FieldT
 Field type.
Public Types inherited from Pscf::MixtureTmpl< Polymer, Solvent >
using SolventT
 Solvent species solver type.
using PolymerT
 Polymer species solver type.
using BlockT
 Block polymer block type.
using PropagatorT
 Polymer block propagator type.
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< FieldT > const &wFields, DArray< FieldT > &cFields)
 Compute concentrations.
Public Member Functions inherited from Pscf::MixtureTmpl< Polymer, Solvent >
 MixtureTmpl ()
 Constructor.
 ~MixtureTmpl ()
 Destructor.
PolymerTpolymer (int id)
 Get a polymer solver object by non-const reference.
PolymerSpecies const & polymerSpecies (int id) const final
 Get a PolymerSpecies descriptor by const reference.
SolventTsolvent (int id)
 Get a solvent solver object.
SolventSpecies const & solventSpecies (int id) const final
 Set a SolventSpecies descriptor object by const reference.
Public Member Functions inherited from Pscf::MixtureBase
 MixtureBase ()
 Constructor.
 ~MixtureBase ()
 Destructor.
void setVmonomer (double vMonomer)
 Set new vMonomer value.
int nMonomer () const
 Get number of monomer types.
int nPolymer () const
 Get number of polymer species.
int nSolvent () const
 Get number of solvent (point particle) species.
int nBlock () const
 Get total number blocks among all polymer species.
double vMonomer () const
 Get monomer reference volume (set to 1.0 by default).
bool isCanonical () const
 Is this mixture being treated in canonical ensemble?
Monomer const & monomer (int id) const
 Get a Monomer type descriptor by const reference.
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.
BeginreadBegin (std::istream &in, const char *label, bool isRequired=true)
 Add and read a class label and opening bracket.
EndreadEnd (std::istream &in)
 Add and read the closing bracket.
BlankreadBlank (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.
BeginaddBegin (const char *label)
 Add a Begin object representing a class name and bracket.
EndaddEnd ()
 Add a closing bracket.
BlankaddBlank ()
 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

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::MixtureBase
Monomermonomer (int id)
 Get a Monomer type descriptor (non-const reference).
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 Attributes inherited from Pscf::MixtureBase
DArray< Monomermonomers_
 Array of monomer type descriptors.
int nMonomer_
 Number of monomer types.
int nPolymer_
 Number of polymer species.
int nSolvent_
 Number of solvent species.
int nBlock_
 Number of blocks total, across all polymers.
double vMonomer_
 Monomer reference volume (set to 1.0 by default).

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

◆ FieldT

Field type.

Definition at line 52 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
ininput parameter stream

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

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

References Pscf::MixtureBase::nMonomer(), Pscf::MixtureBase::nPolymer(), Pscf::MixtureBase::nSolvent(), read(), Pscf::MixtureTmpl< PT, ST >::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
domainassociated Domain object (stores address).

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

References Pscf::MixtureBase::nMonomer(), Pscf::MixtureBase::nPolymer(), Pscf::MixtureBase::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
monomerIdmonomer type id
kuhnnew value for the statistical segment length

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

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

◆ compute()

void Pscf::R1d::Mixture::compute ( DArray< FieldT > const & wFields,
DArray< FieldT > & 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
wFieldsarray of chemical potential fields (input)
cFieldsarray of monomer concentration fields (output)

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

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

Referenced by 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
ininput stream for reading
labelLabel string
valuereference to new ScalarParam< Type >

Definition at line 305 of file ParamComposite.h.

Referenced by 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
ininput stream for reading
labelLabel string
valuereference to new ScalarParam< Type >

Definition at line 319 of file ParamComposite.h.


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