Main class in SCFT simulation of one system. More...

#include <System.h>

Inheritance diagram for Pscf::Pspg::System< D >:

Public Member Functions
Construction and Destruction
	System ()
	Constructor. More...

	~System ()
	Destructor. More...

Lifetime (Actions)
void	setOptions (int argc, char **argv)
	Process command line options. More...

virtual void	readParam (std::istream &in)
	Read input parameters (with opening and closing lines). More...

void	readParam ()
	Read input parameters from default param file. More...

virtual void	readParameters (std::istream &in)
	Read body of parameter file (without opening, closing lines). More...

void	readCommands (std::istream &in)
	Read command script. More...

void	readCommands ()
	Read commands from default command file. More...

W Field Modifiers
void	readWBasis (const std::string &filename)
	Read chemical potential fields in symmetry adapted basis format. More...

void	readWRGrid (const std::string &filename)
	Read chemical potential fields in real space grid (r-grid) format. More...

void	setWBasis (DArray< DArray< double > > const &fields)
	Set chemical potential fields, in symmetry-adapted basis format. More...

void	setWRGrid (DArray< RDField< D > > const &fields)
	Set new w fields, in real-space (r-grid) format. More...

void	setWRGrid (DField< cudaReal > &fields)
	Set new w fields, in unfolded real-space (r-grid) format. More...

void	symmetrizeWFields ()
	Symmetrize r-grid w-fields, compute basis components. More...

void	estimateWfromC (const std::string &filename)
	Construct trial w-fields from c-fields. More...

Unit Cell Modifiers
void	setUnitCell (UnitCell< D > const &unitCell)
	Set parameters of the associated unit cell. More...

void	setUnitCell (typename UnitCell< D >::LatticeSystem lattice, FSArray< double, 6 > const &parameters)
	Set state of the associated unit cell. More...

void	setUnitCell (FSArray< double, 6 > const &parameters)
	Set parameters of the associated unit cell. More...

Primary SCFT Computations
void	compute (bool needStress=false)
	Solve the modified diffusion equation once, without iteration. More...

int	iterate (bool isContinuation=false)
	Iteratively solve a SCFT problem. More...

void	sweep ()
	Sweep in parameter space, solving an SCF problem at each point. More...

Thermodynamic Properties
void	computeFreeEnergy ()
	Compute free energy density and pressure for current fields. More...

double	fHelmholtz () const
	Get precomputed Helmoltz free energy per monomer / kT. More...

double	pressure () const
	Get precomputed pressure times monomer volume / kT. More...

Thermodynamic Data Output
void	writeParamNoSweep (std::ostream &out) const
	Write parameter file to an ostream, omitting the sweep block. More...

void	writeThermo (std::ostream &out)
	Write thermodynamic properties to a file. More...

Field Output
void	writeWBasis (const std::string &filename)
	Write chemical potential fields in symmetry adapted basis format. More...

void	writeWRGrid (const std::string &filename) const
	Write chemical potential fields in real space grid (r-grid) format. More...

void	writeCBasis (const std::string &filename)
	Write concentrations in symmetry-adapted basis format. More...

void	writeCRGrid (const std::string &filename) const
	Write concentration fields in real space grid (r-grid) format. More...

void	writeBlockCRGrid (const std::string &filename) const
	Write c fields for all blocks and solvents in r-grid format. More...

Propagator Output
void	writeQSlice (std::string const &filename, int polymerId, int blockId, int directionId, int segmentId) const
	Write specified slice of a propagator at fixed s in r-grid format. More...

void	writeQTail (std::string const &filename, int polymerId, int blockId, int directionId) const
	Write the final slice of a propagator in r-grid format. More...

void	writeQ (std::string const &filename, int polymerId, int blockId, int directionId) const
	Write one propagator for one block, in r-grid format. More...

void	writeQAll (std::string const &basename)
	Write all propagators of all blocks, each to a separate file. More...

Crystallographic Data Output
void	writeStars (const std::string &filename) const
	Output information about stars and symmetrized basis functions. More...

void	writeWaves (const std::string &filename) const
	Output information about waves. More...

void	writeGroup (std::string const &filename) const
	Output all elements of the space group. More...

Field File Operations
void	basisToRGrid (const std::string &inFileName, const std::string &outFileName)
	Convert a field from symmetry-adapted basis to r-grid format. More...

void	rGridToBasis (const std::string &inFileName, const std::string &outFileName)
	Convert a field from real-space grid to symmetrized basis format. More...

void	kGridToRGrid (const std::string &inFileName, const std::string &outFileName)
	Convert fields from Fourier (k-grid) to real-space (r-grid) format. More...

void	rGridToKGrid (const std::string &inFileName, const std::string &outFileName)
	Convert fields from real-space (r-grid) to Fourier (k-grid) format. More...

void	kGridToBasis (const std::string &inFileName, const std::string &outFileName)
	Convert fields from Fourier (k-grid) to symmetrized basis format. More...

void	basisToKGrid (const std::string &inFileName, const std::string &outFileName)
	Convert fields from symmetrized basis to Fourier (k-grid) format. More...

Member Object Accessors
WFieldContainer< D > const &	w () const
	Get container of chemical potential fields. More...

CFieldContainer< D > const &	c () const
	Get container of monomer concentration / volume fration fields. More...

Mixture< D > &	mixture ()
	Get Mixture by reference. More...

Interaction &	interaction ()
	Get interaction (i.e., excess free energy model) by reference. More...

Interaction const &	interaction () const
	Get interaction (i.e., excess free energy model) by const ref. More...

Domain< D > const &	domain () const
	Get Domain by const reference. More...

Iterator< D > &	iterator ()
	Get the iterator by reference. More...

UnitCell< D > const &	unitCell () const
	Get crystal UnitCell by const reference. More...

Mesh< D > const &	mesh () const
	Get spatial discretization Mesh by const reference. More...

Basis< D > const &	basis () const
	Get the Basis by reference. More...

FieldIo< D > const &	fieldIo () const
	Get the FieldIo by const reference. More...

FFT< D > const &	fft () const
	Get the FFT object by reference. More...

Homogeneous::Mixture &	homogeneous ()
	Get homogeneous mixture (for reference calculations). More...

FileMaster &	fileMaster ()
	Get FileMaster by reference. More...

Queries
bool	hasCFields () const
	Have monomer concentration fields (c fields) been computed? More...

bool	hasSweep () const
	Does this system have an associated Sweep object? 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	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...

Additional Inherited Members
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...

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...

Detailed Description

template<int D>
class Pscf::Pspg::System< D >

Main class in SCFT simulation of one system.

A System has (among other components):

a Mixture (a container for polymer and solvent solvers)
an Interaction (list of chi parameters)
a Domain (a description of the unit cell and discretization)
a container of monomer chemical potential fields (w fields)
a container of monomer concentration fields (c fields)

A System may also optionally contain Iterator and Sweep objects.

A minimal main program that uses this class template to implement a program for 3-dimensional structures (D=3) looks something like this:

int main(int argc, char **argv) {
   Pscf::Pspg::System<3> system;
   system.setOptions(argc, argv);
   system.readParam();
   system.readCommands();
}

This main program is given for D=1, 2, and 3 dimensional structures in the files pscf_pg1.cpp, pscf_pg2.cpp, and pscf_pg3.cpp

Definition at line 70 of file pspg/System.h.

Constructor & Destructor Documentation

◆ System()

template<int D>

Pscf::Pspg::System< D >::System

Constructor.

Definition at line 43 of file pspg/System.tpp.

References Pscf::Pspg::ThreadGrid::init(), Util::BracketPolicy::set(), and Util::ParamComposite::setClassName().

◆ ~System()

template<int D>

Pscf::Pspg::System< D >::~System

Destructor.

Definition at line 80 of file pspg/System.tpp.

Member Function Documentation

◆ setOptions()

template<int D>

void Pscf::Pspg::System< D >::setOptions	(	int	argc,
		char **	argv
	)

Process command line options.

This function takes the same arguments as any C/C++ main program function. The arguments of the main function should d be passed to this function unaltered, to allow this function to process the command line options.

Parameters

argc	number of command line arguments
argv	array of pointers to command line arguments

Definition at line 103 of file pspg/System.tpp.

References Util::Log::file(), Util::ParamComponent::setEcho(), Pscf::Pspg::ThreadGrid::setThreadsPerBlock(), and UTIL_THROW.

◆ readParam() [1/2]

template<int D>

void Pscf::Pspg::System< D >::readParam ( std::istream & in )

virtual

Read input parameters (with opening and closing lines).

Parameters

in	input parameter stream

Reimplemented from Util::ParamComposite.

Definition at line 187 of file pspg/System.tpp.

◆ readParam() [2/2]

template<int D>

void Pscf::Pspg::System< D >::readParam

Read input parameters from default param file.

This function reads the parameter file set by the -p command line option.

Definition at line 198 of file pspg/System.tpp.

◆ readParameters()

template<int D>

void Pscf::Pspg::System< D >::readParameters ( std::istream & in )

virtual

Read body of parameter file (without opening, closing lines).

Parameters

in	input parameter stream

Reimplemented from Util::ParamComposite.

Definition at line 204 of file pspg/System.tpp.

References Util::Log::file(), UTIL_CHECK, and UTIL_THROW.

◆ readCommands() [1/2]

template<int D>

void Pscf::Pspg::System< D >::readCommands ( std::istream & in )

Read command script.

Parameters

in	command script file.

Definition at line 285 of file pspg/System.tpp.

References Util::Log::file(), and UTIL_CHECK.

◆ readCommands() [2/2]

template<int D>

void Pscf::Pspg::System< D >::readCommands

Read commands from default command file.

This function reads the parameter file set by the -c command line option.

Definition at line 479 of file pspg/System.tpp.

References UTIL_THROW.

◆ readWBasis()

template<int D>

void Pscf::Pspg::System< D >::readWBasis ( const std::string & filename )

Read chemical potential fields in symmetry adapted basis format.

This function opens and reads the file with the name given by the "filename" string, which must contain chemical potential fields in symmetry-adapted basis format. The function copies these fields to set new values for the system w fields in basis format, and also computes and resets the system w fields in r-space format. On exit, both w().basis() and w().rgrid() have been reset, w().hasData and w().isSymmetric() are true, and hasCFields() is false.

Parameters

filename name of input w-field basis file

Definition at line 493 of file pspg/System.tpp.

◆ readWRGrid()

template<int D>

void Pscf::Pspg::System< D >::readWRGrid ( const std::string & filename )

Read chemical potential fields in real space grid (r-grid) format.

This function opens and reads the file with the name given by the "filename" string, which must contains chemical potential fields in real space grid (r-grid) format. The function sets values for system w fields in r-grid format. It does not set attempt to set field values in symmetry-adapted basis format, because it cannot be known whether the r-grid field exhibits the declared space group symmetry. On exit, w().rgrid() is reset and w().hasData() is true, while w().isSymmetric() and hasCFields() are false.

Parameters

filename name of input w-field basis file

Definition at line 511 of file pspg/System.tpp.

◆ setWBasis()

template<int D>

void Pscf::Pspg::System< D >::setWBasis ( DArray< DArray< double > > const & fields )

Set chemical potential fields, in symmetry-adapted basis format.

This function sets values for w fields in both symmetry adapted and r-grid format. On exit, values of both w().basis() and w().rgrid() are reset, w().hasData() and w().isSymmetric() are true, and hasCFields() is false.

Parameters

fields array of new w (chemical potential) fields

Definition at line 531 of file pspg/System.tpp.

◆ setWRGrid() [1/2]

template<int D>

void Pscf::Pspg::System< D >::setWRGrid ( DArray< RDField< D > > const & fields )

Set new w fields, in real-space (r-grid) format.

This function set values for w fields in r-grid format, but does not set components the symmetry-adapted basis format. On exit, w.rgrid() is reset, w().hasData() is true, hasCFields() is false and w().isSymmetric() is false.

Parameters

fields array of new w (chemical potential) fields

Definition at line 541 of file pspg/System.tpp.

◆ setWRGrid() [2/2]

template<int D>

void Pscf::Pspg::System< D >::setWRGrid ( DField< cudaReal > & fields )

Set new w fields, in unfolded real-space (r-grid) format.

The function parameter "fields" is an unfolded array containing r-grid fields for all monomer types in a single array, with the field for monomer 0 first, followed by the field for monomer 1, etc. This function sets w().rgrid() but does not set w().basis(). On exit, w().hasData is true, while w().isSymmetric() and hasCFields() are both false.

Parameters

fields unfolded array of new chemical potential fields

Definition at line 551 of file pspg/System.tpp.

◆ symmetrizeWFields()

template<int D>

void Pscf::Pspg::System< D >::symmetrizeWFields

Symmetrize r-grid w-fields, compute basis components.

On exit, w().hasData() and w().isSymmetric() are true, while hasCFields() is false.

Definition at line 611 of file pspg/System.tpp.

◆ estimateWfromC()

template<int D>

void Pscf::Pspg::System< D >::estimateWfromC ( const std::string & filename )

Construct trial w-fields from c-fields.

This function reads concentration fields in symmetrized basis format and constructs an initial guess for corresponding chemical potential fields by setting the Lagrange multiplier field xi to zero. The result is stored in the system w field container.

Upon return, w().hasData() and w().isSymmetric() are true, while hasCFields() is false.

Parameters

filename name of input c-field file (basis format)

Definition at line 563 of file pspg/System.tpp.

References Util::DArray< Data >::allocate(), and UTIL_CHECK.

◆ setUnitCell() [1/3]

template<int D>

void Pscf::Pspg::System< D >::setUnitCell ( UnitCell< D > const & unitCell )

Set parameters of the associated unit cell.

The lattice system declared within the input unitCell must agree with Domain::lattice() on input if Domain::lattice() is not null.

Parameters

unitCell new UnitCell<D> (i.e., new parameters)

Definition at line 620 of file pspg/System.tpp.

◆ setUnitCell() [2/3]

template<int D>

void Pscf::Pspg::System< D >::setUnitCell	(	typename UnitCell< D >::LatticeSystem< D >	lattice,
		FSArray< double, 6 > const &	parameters
	)

Set state of the associated unit cell.

The lattice argument must agree with Domain::lattice() on input if Domain::lattice() is not null, and the size of the parameters array must agree with the expected number of lattice parameters.

Parameters

lattice	lattice system
parameters	array of new unit cell parameters.

Definition at line 634 of file pspg/System.tpp.

◆ setUnitCell() [3/3]

template<int D>

void Pscf::Pspg::System< D >::setUnitCell ( FSArray< double, 6 > const & parameters )

Set parameters of the associated unit cell.

The size of the FSArray<double, 6> parameters must agree with the expected number of parameters for the current lattice type.

Parameters

parameters array of new unit cell parameters.

Definition at line 648 of file pspg/System.tpp.

◆ compute()

template<int D>

void Pscf::Pspg::System< D >::compute ( bool needStress = false )

Solve the modified diffusion equation once, without iteration.

This function calls the Mixture::compute() function to solve the statistical mechanics problem for a non-interacting system subjected to the currrent chemical potential fields (wFields and wFieldRGrid). This requires solution of the modified diffusion equation for all polymers, computation of Boltzmann weights for all solvents, computation of molecular partition functions for all species, and computation of concentration fields for blocks and solvents, and computation of overall concentrations for all monomer types. This function does not compute the canonical (Helmholtz) free energy or grand-canonical free energy (i.e., pressure). Upon return, the flag hasCFields is set true.

Precondition: The boolean w().hasData() must be true on entry

Postcondition: hasCFields is true on exit

If argument needStress == true, then this function also calls Mixture<D>::computeStress() to compute the stress.

Parameters

needStress true if stress is needed, false otherwise

Definition at line 663 of file pspg/System.tpp.

References UTIL_CHECK.

◆ iterate()

template<int D>

int Pscf::Pspg::System< D >::iterate ( bool isContinuation = false )

Iteratively solve a SCFT problem.

This function calls the iterator to attempt to solve the SCFT problem for the current mixture and system parameters, using the current chemical potential fields (wFields and wFieldRGrid) and current unit cell parameter values as initial guesses. Upon exist, hasCFields is set true whether or not convergence is obtained to within the desired tolerance. The Helmholtz free energy and pressure are computed if and only if convergence is obtained.

Precondition: The w().hasData() flag must be true on entry, to confirm that chemical potential fields have been set.; The w().isSymmetric() flag must be set true if the chosen iterator uses a basis representation, and thus requires this.

Parameters

isContinuation true iff continuation within a sweep

Returns: returns 0 for successful convergence, 1 for failure

Definition at line 685 of file pspg/System.tpp.

References Util::Log::file(), and UTIL_CHECK.

◆ sweep()

template<int D>

void Pscf::Pspg::System< D >::sweep

Sweep in parameter space, solving an SCF problem at each point.

This function uses a Sweep object that was initialized in the parameter file to solve the SCF problem at a sequence of points along a line in parameter space. The nature of this sequence is determined by implementation of a subclass of Sweep and the parameters passed to the sweep object in the parameter file.

Precondition: The w().hasData() flag must be true on entry.; A sweep object must have been created in the parameter file.

Definition at line 716 of file pspg/System.tpp.

References Util::Log::file(), and UTIL_CHECK.

Referenced by pscfpp.output.Sweep::__getitem__(), pscfpp.output.Sweep::__init__(), pscfpp.output.Sweep::__len__(), pscfpp.output.Sweep::summary(), and pscfpp.output.Sweep::summaryString().

◆ computeFreeEnergy()

template<int D>

void Pscf::Pspg::System< D >::computeFreeEnergy

Compute free energy density and pressure for current fields.

This function should be called after a successful call of iterator().solve(). Resulting values are returned by the freeEnergy() and pressure() accessor functions.

Precondition: w().hasData must be true.; hasCFields must be true.

Definition at line 735 of file pspg/System.tpp.

References Pscf::PolymerTmpl< Block >::length(), Pscf::Species::mu(), Pscf::Species::phi(), Pscf::Pspg::ThreadGrid::setThreadsLogical(), Pscf::SolventDescriptor::size(), and UTIL_CHECK.

◆ fHelmholtz()

template<int D>

double Pscf::Pspg::System< D >::fHelmholtz

inline

Get precomputed Helmoltz free energy per monomer / kT.

The value retrieved by this function is pre-computed by the computeFreeEnergy() function.

Definition at line 983 of file pspg/System.h.

Referenced by pscfpp.output.Thermo::__init__(), and pscfpp.output.Thermo::read().

◆ pressure()

template<int D>

double Pscf::Pspg::System< D >::pressure

inline

Get precomputed pressure times monomer volume / kT.

The value retrieved by this function is pre-computed by the computeFreeEnergy() function.

Definition at line 988 of file pspg/System.h.

Referenced by pscfpp.output.Thermo::__init__(), and pscfpp.output.Thermo::read().

◆ writeParamNoSweep()

template<int D>

void Pscf::Pspg::System< D >::writeParamNoSweep ( std::ostream & out ) const

Write parameter file to an ostream, omitting the sweep block.

This function omits the Sweep block of the parameter file, if any, in order to allow the output produced during a sweep to refer only to parameters relevant to a single state point, and to be rerunnable as a parameter file for a single SCFT calculation.

Definition at line 852 of file pspg/System.tpp.

◆ writeThermo()

template<int D>

void Pscf::Pspg::System< D >::writeThermo ( std::ostream & out )

Write thermodynamic properties to a file.

This function outputs Helmholtz free energy per monomer, pressure (in units of kT per monomer volume), the volume fraction and chemical potential of each species, and unit cell parameters.

If parameter "out" is a file that already exists, this function will append this information to the end of the file, rather than overwriting that file. Calling writeParamNoSweep and writeThermo in succession with the same file will thus produce a single file containing both input parameters and resulting thermodynanic properties.

Parameters

out	output stream

Definition at line 865 of file pspg/System.tpp.

◆ writeWBasis()

template<int D>

void Pscf::Pspg::System< D >::writeWBasis ( const std::string & filename )

Write chemical potential fields in symmetry adapted basis format.

Parameters

filename name of output file

Definition at line 922 of file pspg/System.tpp.

References UTIL_CHECK.

◆ writeWRGrid()

template<int D>

void Pscf::Pspg::System< D >::writeWRGrid ( const std::string & filename ) const

Write chemical potential fields in real space grid (r-grid) format.

Parameters

filename name of output file

Definition at line 933 of file pspg/System.tpp.

References UTIL_CHECK.

◆ writeCBasis()

template<int D>

void Pscf::Pspg::System< D >::writeCBasis ( const std::string & filename )

Write concentrations in symmetry-adapted basis format.

Parameters

filename name of output file

Definition at line 943 of file pspg/System.tpp.

References UTIL_CHECK.

◆ writeCRGrid()

template<int D>

void Pscf::Pspg::System< D >::writeCRGrid ( const std::string & filename ) const

Write concentration fields in real space grid (r-grid) format.

Parameters

filename name of output file

Definition at line 954 of file pspg/System.tpp.

References UTIL_CHECK.

◆ writeBlockCRGrid()

template<int D>

void Pscf::Pspg::System< D >::writeBlockCRGrid ( const std::string & filename ) const

Write c fields for all blocks and solvents in r-grid format.

Writes concentrations for all blocks of all polymers and all solvent species in r-grid format. Columns associated with blocks appear ordered by polymer id and then by block id, followed by solvent species ordered by solvent id.

Parameters

filename name of output file

Definition at line 965 of file pspg/System.tpp.

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

◆ writeQSlice()

template<int D>

void Pscf::Pspg::System< D >::writeQSlice	(	std::string const &	filename,
		int	polymerId,
		int	blockId,
		int	directionId,
		int	segmentId
	)		const

Write specified slice of a propagator at fixed s in r-grid format.

Parameters

filename	name of output file
polymerId	integer id of the polymer
blockId	integer id of the block within the polymer
directionId	integer id of the direction (0 or 1)
segmentId	integer integration step index

Definition at line 986 of file pspg/System.tpp.

References Pscf::Pspg::RDField< D >::allocate(), Pscf::Pspg::DField< Data >::cDField(), Pscf::PolymerTmpl< Block >::nBlock(), Pscf::PolymerTmpl< Block >::propagator(), Pscf::Pspg::Propagator< D >::q(), and UTIL_CHECK.

◆ writeQTail()

template<int D>

void Pscf::Pspg::System< D >::writeQTail	(	std::string const &	filename,
		int	polymerId,
		int	blockId,
		int	directionId
	)		const

Write the final slice of a propagator in r-grid format.

Parameters

filename	name of output file
polymerId	integer id of the polymer
blockId	integer id of the block within the polymer
directionId	integer id of the direction (0 or 1)

Definition at line 1011 of file pspg/System.tpp.

References Pscf::Pspg::RDField< D >::allocate(), Pscf::Pspg::DField< Data >::cDField(), Pscf::PolymerTmpl< Block >::nBlock(), Pscf::PolymerTmpl< Block >::propagator(), Pscf::Pspg::Propagator< D >::tail(), and UTIL_CHECK.

◆ writeQ()

template<int D>

void Pscf::Pspg::System< D >::writeQ	(	std::string const &	filename,
		int	polymerId,
		int	blockId,
		int	directionId
	)		const

Write one propagator for one block, in r-grid format.

Parameters

filename	name of output file
polymerId	integer id of the polymer
blockId	integer id of the block within the polymer
directionId	integer id of the direction (0 or 1)

Definition at line 1036 of file pspg/System.tpp.

References Pscf::Pspg::RDField< D >::allocate(), Pscf::Pspg::DField< Data >::cDField(), Pscf::PolymerTmpl< Block >::nBlock(), Pscf::Pspg::Propagator< D >::ns(), Pscf::PolymerTmpl< Block >::propagator(), Pscf::Pspg::Propagator< D >::q(), and UTIL_CHECK.

◆ writeQAll()

template<int D>

void Pscf::Pspg::System< D >::writeQAll ( std::string const & basename )

Write all propagators of all blocks, each to a separate file.

Write all propagators for both directions for all blocks of all polymers, with each propagator in a separate file. The function writeQ is called internally for each propagator, and is passed an automatically generated file name. The file name for each propagator is given by a string of the form (basename)_(ip)_(ib)_(id), where (basename) denotes the value of the std::string function parameter basename, and where (ip), (ib), and (id) denote the string representations of a polymer indiex ip, a block index ib, and direction index id, with id = 0 or 1. For example, if basename == "out/q", then the file name of the propagator for direction 1 of block 2 of polymer 0 would be "out/q_0_2_1".

Parameters

basename common prefix for output file names

Definition at line 1079 of file pspg/System.tpp.

References Util::toString().

◆ writeStars()

template<int D>

void Pscf::Pspg::System< D >::writeStars ( const std::string & filename ) const

Output information about stars and symmetrized basis functions.

This function opens a file with the specified filename and then calls Basis::outputStars.

Parameters

filename name of output file

Definition at line 1108 of file pspg/System.tpp.

References UTIL_CHECK.

◆ writeWaves()

template<int D>

void Pscf::Pspg::System< D >::writeWaves ( const std::string & filename ) const

Output information about waves.

This function opens a file with the specified filename and then calls Basis::outputWaves.

Parameters

filename name of output file

Definition at line 1122 of file pspg/System.tpp.

References UTIL_CHECK.

◆ writeGroup()

template<int D>

void Pscf::Pspg::System< D >::writeGroup ( std::string const & filename ) const

Output all elements of the space group.

Parameters

filename name of output file

Definition at line 1136 of file pspg/System.tpp.

◆ basisToRGrid()

template<int D>

void Pscf::Pspg::System< D >::basisToRGrid	(	const std::string &	inFileName,
		const std::string &	outFileName
	)

Convert a field from symmetry-adapted basis to r-grid format.

This and other field conversion functions do not change the w or c fields stored by this System - all required calculations are performed using temporary or mutable memory.

Parameters

inFileName	name of input file
outFileName	name of output file

Definition at line 1147 of file pspg/System.tpp.

◆ rGridToBasis()

template<int D>

void Pscf::Pspg::System< D >::rGridToBasis	(	const std::string &	inFileName,
		const std::string &	outFileName
	)

Convert a field from real-space grid to symmetrized basis format.

This function checks if the input fields have the declared space group symmetry, and prints a warning if it detects deviations that exceed some small threshhold, but proceeds to attempt the conversion even if such an error is detected. Converting a field that does not have the declared space group symmetry to basis format is a destructive operation that modifies the fields.

Parameters

inFileName	name of input file
outFileName	name of output file

Definition at line 1169 of file pspg/System.tpp.

◆ kGridToRGrid()

template<int D>

void Pscf::Pspg::System< D >::kGridToRGrid	(	const std::string &	inFileName,
		const std::string &	outFileName
	)

Convert fields from Fourier (k-grid) to real-space (r-grid) format.

Parameters

inFileName	name of input file
outFileName	name of output file

Definition at line 1191 of file pspg/System.tpp.

◆ rGridToKGrid()

template<int D>

void Pscf::Pspg::System< D >::rGridToKGrid	(	const std::string &	inFileName,
		const std::string &	outFileName
	)

Convert fields from real-space (r-grid) to Fourier (k-grid) format.

Parameters

inFileName	name of input file
outFileName	name of output file

Definition at line 1215 of file pspg/System.tpp.

◆ kGridToBasis()

template<int D>

void Pscf::Pspg::System< D >::kGridToBasis	(	const std::string &	inFileName,
		const std::string &	outFileName
	)

Convert fields from Fourier (k-grid) to symmetrized basis format.

This function checks if the input fields have the declared space group symmetry, and prints a warning if it detects deviations that exceed some small threshhold, but proceeds to attempt the conversion even if such an error is detected. Converting a field that does not have the declared space group symmetry to basis format is a destructive operation that modifies the fields.

Parameters

inFileName	name of input file
outFileName	name of output file

Definition at line 1240 of file pspg/System.tpp.

◆ basisToKGrid()

template<int D>

void Pscf::Pspg::System< D >::basisToKGrid	(	const std::string &	inFileName,
		const std::string &	outFileName
	)

Convert fields from symmetrized basis to Fourier (k-grid) format.

Parameters

inFileName	name of input file (basis format)
outFileName	name of output file (k-grid format)

Definition at line 1262 of file pspg/System.tpp.

◆ w()

template<int D>

WFieldContainer< D > const & Pscf::Pspg::System< D >::w

inline

Get container of chemical potential fields.

Definition at line 972 of file pspg/System.h.

◆ c()

template<int D>

CFieldContainer< D > const & Pscf::Pspg::System< D >::c

inline

Get container of monomer concentration / volume fration fields.

Definition at line 978 of file pspg/System.h.

◆ mixture()

template<int D>

Mixture< D > & Pscf::Pspg::System< D >::mixture

inline

Get Mixture by reference.

Definition at line 903 of file pspg/System.h.

◆ interaction() [1/2]

template<int D>

Interaction & Pscf::Pspg::System< D >::interaction

inline

Get interaction (i.e., excess free energy model) by reference.

Definition at line 908 of file pspg/System.h.

References UTIL_ASSERT.

◆ interaction() [2/2]

template<int D>

Interaction const & Pscf::Pspg::System< D >::interaction

inline

Get interaction (i.e., excess free energy model) by const ref.

Definition at line 916 of file pspg/System.h.

References UTIL_ASSERT.

◆ domain()

template<int D>

Domain< D > const & Pscf::Pspg::System< D >::domain

inline

Get Domain by const reference.

Definition at line 923 of file pspg/System.h.

◆ iterator()

template<int D>

Iterator< D > & Pscf::Pspg::System< D >::iterator

inline

Get the iterator by reference.

Definition at line 952 of file pspg/System.h.

References UTIL_ASSERT.

◆ unitCell()

template<int D>

UnitCell< D > const & Pscf::Pspg::System< D >::unitCell

inline

Get crystal UnitCell by const reference.

Definition at line 927 of file pspg/System.h.

◆ mesh()

template<int D>

Mesh< D > const & Pscf::Pspg::System< D >::mesh

inline

Get spatial discretization Mesh by const reference.

Definition at line 932 of file pspg/System.h.

◆ basis()

template<int D>

Basis< D > const & Pscf::Pspg::System< D >::basis

inline

Get the Basis by reference.

Definition at line 937 of file pspg/System.h.

◆ fieldIo()

template<int D>

FieldIo< D > const & Pscf::Pspg::System< D >::fieldIo

inline

Get the FieldIo by const reference.

Definition at line 947 of file pspg/System.h.

◆ fft()

template<int D>

FFT< D > const & Pscf::Pspg::System< D >::fft

inline

Get the FFT object by reference.

Definition at line 942 of file pspg/System.h.

◆ homogeneous()

template<int D>

Homogeneous::Mixture & Pscf::Pspg::System< D >::homogeneous

inline

Get homogeneous mixture (for reference calculations).

Definition at line 966 of file pspg/System.h.

◆ fileMaster()

template<int D>

FileMaster & Pscf::Pspg::System< D >::fileMaster

inline

Get FileMaster by reference.

Definition at line 960 of file pspg/System.h.

◆ hasCFields()

template<int D>

bool Pscf::Pspg::System< D >::hasCFields

inline

Have monomer concentration fields (c fields) been computed?

Returns true if and only if monomer concentration fields have been computed by solving the modified diffusion equation for the current w fields.

Definition at line 993 of file pspg/System.h.

◆ hasSweep()

template<int D>

bool Pscf::Pspg::System< D >::hasSweep

inline

Does this system have an associated Sweep object?

Definition at line 998 of file pspg/System.h.

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

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ System()

◆ ~System()

Member Function Documentation

◆ setOptions()

◆ readParam() [1/2]

◆ readParam() [2/2]

◆ readParameters()

◆ readCommands() [1/2]

◆ readCommands() [2/2]

◆ readWBasis()

◆ readWRGrid()

◆ setWBasis()

◆ setWRGrid() [1/2]

◆ setWRGrid() [2/2]

◆ symmetrizeWFields()

◆ estimateWfromC()

◆ setUnitCell() [1/3]

◆ setUnitCell() [2/3]

◆ setUnitCell() [3/3]

◆ compute()

◆ iterate()

◆ sweep()

◆ computeFreeEnergy()

◆ fHelmholtz()

◆ pressure()

◆ writeParamNoSweep()

◆ writeThermo()

◆ writeWBasis()

◆ writeWRGrid()

◆ writeCBasis()

◆ writeCRGrid()

◆ writeBlockCRGrid()

◆ writeQSlice()

◆ writeQTail()

◆ writeQ()

◆ writeQAll()

◆ writeStars()

◆ writeWaves()

◆ writeGroup()

◆ basisToRGrid()

◆ rGridToBasis()

◆ kGridToRGrid()

◆ rGridToKGrid()

◆ kGridToBasis()

◆ basisToKGrid()

◆ w()

◆ c()

◆ mixture()

◆ interaction() [1/2]

◆ interaction() [2/2]

◆ domain()

◆ iterator()

◆ unitCell()

◆ mesh()

◆ basis()

◆ fieldIo()

◆ fft()

◆ homogeneous()

◆ fileMaster()

◆ hasCFields()

◆ hasSweep()