PSCF v1.3
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Mixture of polymers and solvents. More...
#include <Mixture.h>
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. | |
PolymerT & | polymer (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. | |
SolventT & | solvent (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. | |
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 | |
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 | |
Monomer & | monomer (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 ¶m, bool next=true) |
Set this to the parent of a child component. | |
void | addComponent (ParamComponent ¶m, 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< Monomer > | monomers_ |
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). |
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.
Definition at line 42 of file r1d/solvers/Mixture.h.
Field type.
Definition at line 52 of file r1d/solvers/Mixture.h.
Pscf::R1d::Mixture::Mixture | ( | ) |
Constructor.
Definition at line 17 of file r1d/solvers/Mixture.cpp.
References Util::ParamComposite::setClassName().
Pscf::R1d::Mixture::~Mixture | ( | ) |
Destructor.
Definition at line 22 of file r1d/solvers/Mixture.cpp.
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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.
in | input 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.
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.
domain | associated 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.
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.
monomerId | monomer type id |
kuhn | new 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 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.
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::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().
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protected |
Add and read a new required ScalarParam < Type > object.
This is equivalent to ScalarParam<Type>(in, label, value, true).
in | input stream for reading |
label | Label string |
value | reference to new ScalarParam< Type > |
Definition at line 305 of file ParamComposite.h.
Referenced by readParameters().
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inlineprotected |
Add and read a new optional ScalarParam < Type > object.
This is equivalent to ScalarParam<Type>(in, label, value, false).
in | input stream for reading |
label | Label string |
value | reference to new ScalarParam< Type > |
Definition at line 319 of file ParamComposite.h.