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PSCF v1.4.0
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Descriptor and MDE solver for a block polymer. More...
#include <PolymerTmpl.h>
Public Types | |
| using | BlockT = BT |
| Block of a block polymer. | |
| using | PropagatorT = PT |
| Modified diffusion equation solution (propagator). | |
| 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 | |
| void | readParameters (std::istream &in) override |
| Read and initialize. | |
| virtual void | solve (double phiTot=1.0) |
| Solve modified diffusion equation for all propagators. | |
Accessors (objects, by reference) | |
| Edge & | edge (int id) final |
| Get a specified Edge (block descriptor) by non-const reference. | |
| Edge const & | edge (int id) const final |
| Get a specified Edge (block descriptor) by const reference. | |
| BT & | block (int id) |
| Get a specified Block (solver and descriptor). | |
| BT const & | block (int id) const |
| Get a specified Block (solver and descriptor) by const reference. | |
| PT & | propagator (int blockId, int directionId) |
| Get the propagator for a specific block and direction (non-const). | |
| PT const & | propagator (int blockId, int directionId) const |
| Get the propagator for a specific block and direction (const). | |
| PT & | propagator (int id) |
| Get a propagator indexed in order of computation (non-const). | |
| Public Member Functions inherited from Pscf::PolymerSpecies< double > | |
| PolymerSpecies () | |
| Constructor. | |
| virtual | ~PolymerSpecies ()=default |
| Destructor. | |
| const Vertex & | vertex (int id) const |
| Get a specified Vertex by const reference. | |
| int | nBlock () const |
| Number of blocks. | |
| int | nVertex () const |
| Number of vertices (junctions and chain ends). | |
| int | nPropagator () const |
| Number of propagators (2*nBlock). | |
| double | length () const |
| Sum of the lengths of all blocks in the polymer (thread model). | |
| int | nBead () const |
| Total number of beads in the polymer (bead model). | |
| PolymerType::Enum | type () const |
| Get Polymer type (Branched or Linear) | |
| Pair< int > const & | propagatorId (int id) const |
| Get a propagator identifier, indexed by order of computation. | |
| Pair< int > const & | path (int is, int it) const |
| Get an id for a propagator from one vertex towards a target. | |
| Public Member Functions inherited from Pscf::Species< double > | |
| Species () | |
| Constructor. | |
| virtual | ~Species ()=default |
| Destructor. | |
| 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 () const |
| Get the statistical ensemble for this species (open or closed). | |
| void | setPhi (double phi) |
| Set value of phi (volume fraction), if ensemble is closed. | |
| void | setMu (double mu) |
| Set value of mu (chemical potential), if ensemble is 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 ? | |
Protected Types | |
| using | SpeciesT = Species<WT> |
| Indirect (grandparent) base class. | |
| using | PolymerSpeciesT = PolymerSpecies<WT> |
| Direct (parent) base class. | |
Protected Member Functions | |
| PolymerTmpl () | |
| Constructor. | |
| ~PolymerTmpl () override=default | |
| Destructor. | |
| void | allocateBlocks () final |
| Allocate array of Block objects. | |
| void | readBlocks (std::istream &in) final |
| Read array of data for blocks from parameter file. | |
| Protected Member Functions inherited from Pscf::PolymerSpecies< double > | |
| virtual void | makePlan () |
| Make a plan for order in which propagators should be computed. | |
| void | makePaths () |
| Create a matrix of vertex-to-vertex path signposts. | |
| Protected Member Functions inherited from Pscf::Species< double > | |
| void | setQ (double q) |
| Set q and compute phi or mu (depending on the ensemble). | |
| 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. | |
Descriptor and MDE solver for a block polymer.
Specializations of this template are used as base classes for classes named "Polymer" that are defined in each program-level namespace. Each such program-level Polymer class is both a subclass of PolymerSpecies, which provides a description of polymer structure, and a modified diffusion equation solver. The PolymerTmpl template provides templates for several data structures and algorithms that are needed by all such Polymer classes. Specializations of this template should only be used within instances of derived classes, The constructor and destructor are protected to document this intent.
Class template argument BT is an alias for a class that represents a block of a block polymer. By convention, this is a class named Block defined in each program-level sub-namespace of Pscf.
Class template PT is an alias for the class that represents a propagator, which holds the solution of the modified diffusion equation for one block, in one direction. By convention, this is a class named Propagator defined in each program-level sub-namespace of Pscf.
Class template WT is an alias for the data type of the value of a chemical potential field defined at a grid point, which can be either a real (e.g., double) or complex data type. This type is also the type used to store several thermodynamic properties stored as members of the Species<WT> base class.
A PolymerTmpl<Block, Propagator, WT> object has an array of Block objects, as well as an array of Vertex objects inherited from the PolymerSpecies<WT> base class. Each Block owns two Propagator objects associated with the two directions along each block.
The solve() member function solves the modified diffusion equation (MDE) for all propagators in the molecule (i.e., all blocks, in both directions) in a pre-defined order.
Definition at line 62 of file PolymerTmpl.h.
| using Pscf::PolymerTmpl< BT, PT, WT >::BlockT = BT |
Block of a block polymer.
Definition at line 187 of file PolymerTmpl.h.
| using Pscf::PolymerTmpl< BT, PT, WT >::PropagatorT = PT |
Modified diffusion equation solution (propagator).
Definition at line 192 of file PolymerTmpl.h.
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protected |
Indirect (grandparent) base class.
Definition at line 223 of file PolymerTmpl.h.
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protected |
Direct (parent) base class.
Definition at line 228 of file PolymerTmpl.h.
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protected |
Constructor.
Definition at line 24 of file PolymerTmpl.tpp.
References Util::ParamComposite::setClassName().
Referenced by edge().
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overrideprotecteddefault |
Destructor.
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overridevirtual |
Read and initialize.
| in | input parameter stream |
Reimplemented from Pscf::PolymerSpecies< double >.
Definition at line 50 of file PolymerTmpl.tpp.
References block(), Pscf::PolymerSpecies< double >::nBlock(), Pscf::PolymerSpecies< WT >::nBlock(), and Pscf::PolymerSpecies< WT >::readParameters().
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virtual |
Solve modified diffusion equation for all propagators.
Upon return, solutions are stored for both propagators of all blocks, and values are set for the molecular partition function q, and phi or mu. This function calls the solve() function for all propagators in the molecule in a predeternined order, then computes q, and finally computes mu from phi or phi from mu, depending on the ensemble (open or closed) for this polymer species. The order in which propgator solutions are computed is determined by a plan that is defined by the PolymerSpecies base class. This function does not compute monomer concentration fields.
Each program-level namespace defines a class or class template named Polymer that is derived from a specialization of PolymerTmpl. Each such program-level Polymer class defines a member function named "compute" that takes an array of chemical fields (w-fields) as an argument, and that calls PolymerTmpl<BT,PT,WT>::solve internally. Before calling the PolymerTmpl::solve() function, the Polymer::compute() function must also pass the w-fields and any other required mutable data to all Block objects in order to set up the MDE solver for each block. After calling this solve() function, the Polymer::compute function must also compute monomer concentrations for all blocks, each of which is stored in a field container owned by the associated Block.
The optional parameter phiTot is only relevant to problems involving a Mask that excludes material from part of the unit cell, as done to define thin film problems. In problems that do not use such a mask, the default parameter value of phiTot = 1.0 should be used.
| phiTot | fraction of unit cell volume occupied by material |
Definition at line 157 of file PolymerTmpl.tpp.
References Pscf::PolymerSpecies< double >::nPropagator(), and Pscf::PolymerSpecies< WT >::nPropagator().
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inlinefinalvirtual |
Get a specified Edge (block descriptor) by non-const reference.
The edge member function implements a pure virtual function defined by the PolymerSpecies base class, and provides access to a specific Block as a reference to an Edge (a block descriptor), which is a base class of the Block (BT) class.
| id | block index, 0 <= id < nBlock |
Implements Pscf::PolymerSpecies< double >.
Reimplemented in Pscf::Rp::Polymer< D, T >, and Pscf::Rp::Polymer< D, Types< D > >.
Definition at line 250 of file PolymerTmpl.h.
References edge(), and PolymerTmpl().
Referenced by edge().
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inlinefinalvirtual |
Get a specified Edge (block descriptor) by const reference.
| id | block index, 0 <= id < nBlock |
Implements Pscf::PolymerSpecies< double >.
Reimplemented in Pscf::Rp::Polymer< D, Types< D > >.
Definition at line 257 of file PolymerTmpl.h.
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inline |
Get a specified Block (solver and descriptor).
| id | block index, 0 <= id < nBlock |
Definition at line 264 of file PolymerTmpl.h.
Referenced by propagator(), and readParameters().
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inline |
Get a specified Block (solver and descriptor) by const reference.
| id | block index, 0 <= id < nBlock |
Definition at line 271 of file PolymerTmpl.h.
| PT & Pscf::PolymerTmpl< BT, PT, WT >::propagator | ( | int | blockId, |
| int | directionId ) |
Get the propagator for a specific block and direction (non-const).
For an edge that terminates at vertices with vertex indices given by the return values of Edge::vertexId(0) and Edge::vertexId(1):
| blockId | integer index of associated block |
| directionId | integer index for direction (0 or 1) |
Definition at line 190 of file PolymerTmpl.tpp.
References block().
Referenced by propagator(), Pscf::R1d::System::writeQ(), Pscf::R1d::System::writeQSlice(), Pscf::R1d::System::writeQTail(), and Pscf::R1d::FieldIo::writeVertexQ().
| PT const & Pscf::PolymerTmpl< BT, PT, WT >::propagator | ( | int | blockId, |
| int | directionId ) const |
Get the propagator for a specific block and direction (const).
| blockId | integer index of associated block |
| directionId | integer index for direction (0 or 1) |
Definition at line 198 of file PolymerTmpl.tpp.
| PT & Pscf::PolymerTmpl< BT, PT, WT >::propagator | ( | int | id | ) |
Get a propagator indexed in order of computation (non-const).
The propagator index argument must satisfy 0 <= id < 2*nBlock.
| id | propagator index, in order of computation plan |
Definition at line 205 of file PolymerTmpl.tpp.
References propagator(), and Pscf::PolymerSpecies< WT >::propagatorId().
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finalprotectedvirtual |
Allocate array of Block objects.
Implements Pscf::PolymerSpecies< double >.
Definition at line 33 of file PolymerTmpl.tpp.
References Pscf::PolymerSpecies< WT >::nBlock().
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finalprotectedvirtual |
Read array of data for blocks from parameter file.
| in | parameter input stream |
Implements Pscf::PolymerSpecies< double >.
Definition at line 40 of file PolymerTmpl.tpp.
References Pscf::PolymerSpecies< double >::nBlock(), Pscf::PolymerSpecies< WT >::nBlock(), and Util::ParamComposite::readDArray().