One-dimensional spatial domain and discretization grid. More...

#include <Domain.h>

Inheritance diagram for Pscf::Fd1d::Domain:

Public Types
typedef DArray< double >	Field
	Generic field type (base class) More...

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

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

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

	~Domain ()
	Destructor. More...

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

void	setPlanarParameters (double xMin, double xMax, int nx)
	Set grid parameters for a planar domain. More...

void	setShellParameters (GeometryMode mode, double xMin, double xMax, int nx)
	Set grid parameters for a cylindrical or spherical shell. More...

void	setCylinderParameters (double xMax, int nx)
	Set grid parameters for a cylinder. More...

void	setSphereParameters (double xMax, int nx)
	Set grid parameters for a sphere. More...

Accessors
double	xMin () const
	Get minimum spatial coordinate. More...

double	xMax () const
	Get maximum spatial coordinate. More...

double	volume () const
	Get generalized volume of domain. More...

double	dx () const
	Get spatial grid step size. More...

int	nx () const
	Get number of spatial grid points, including both endpoints. More...

GeometryMode const &	mode () const
	Get coordinate system flag (Planar, Cylindrical or Spherical). More...

bool	isShell () const
	Is this a cylindrical or spherical shell? More...

Spatial integrals
double	spatialAverage (Field const &f) const
	Compute spatial average of a field. More...

double	innerProduct (Field const &f, Field const &g) const
	Compute inner product of two real fields. More...

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

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

	ParamComposite (int capacity)
	Constructor. More...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

template<typename Type >
DArrayParam< Type > &	readDArray (std::istream &in, const char *label, DArray< Type > &array, int n)
	Add and read a required DArray < Type > parameter. More...

template<typename Type >
DArrayParam< Type > &	readOptionalDArray (std::istream &in, const char *label, DArray< Type > &array, int n)
	Add and read an optional DArray < Type > parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	readFArray (std::istream &in, const char *label, FArray< Type, N > &array)
	Add and read a required FArray < Type, N > array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	readOptionalFArray (std::istream &in, const char *label, FArray< Type, N > &array)
	Add and read an optional FArray < Type, N > array parameter. More...

template<typename Type , int N>
FSArrayParam< Type, N > &	readFSArray (std::istream &in, const char *label, FSArray< Type, N > &array, int size)
	Add and read a required FSArray < Type, N > array parameter. More...

template<typename Type , int N>
FSArrayParam< Type, N > &	readOptionalFSArray (std::istream &in, const char *label, FSArray< Type, N > &array, int size)
	Add and read an optional FSArray < Type, N > array parameter. More...

template<typename Type >
CArray2DParam< Type > &	readCArray2D (std::istream &in, const char label, Type value, int m, int n, int np)
	Add and read a required CArray2DParam < Type > 2D C-array. More...

template<typename Type >
CArray2DParam< Type > &	readOptionalCArray2D (std::istream &in, const char label, Type value, int m, int n, int np)
	Add and read an optional CArray2DParam < Type > 2D C-array parameter. More...

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

template<typename Type >
DMatrixParam< Type > &	readOptionalDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and read an optional DMatrix < Type > matrix parameter. More...

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

template<typename Type >
DSymmMatrixParam< Type > &	readOptionalDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
	Add and read an optional DMatrix matrix parameter. More...

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

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

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

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

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

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

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

template<typename Type >
CArrayParam< Type > &	loadCArray (Serializable::IArchive &ar, const char label, Type value, int n, bool isRequired)
	Add a C array parameter and load its elements. More...

template<typename Type >
CArrayParam< Type > &	loadCArray (Serializable::IArchive &ar, const char label, Type value, int n)
	Add and load a required CArrayParam< Type > array parameter. More...

template<typename Type >
DArrayParam< Type > &	loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n, bool isRequired)
	Add an load a DArray < Type > array parameter. More...

template<typename Type >
DArrayParam< Type > &	loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n)
	Add and load a required DArray< Type > array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array, bool isRequired)
	Add and load an FArray < Type, N > fixed-size array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array)
	Add and load a required FArray < Type > array parameter. More...

template<typename Type , int N>
FSArrayParam< Type, N > &	loadFSArray (Serializable::IArchive &ar, const char *label, FSArray< Type, N > &array, int size, bool isRequired)
	Add and load an FSArray < Type, N > array parameter. More...

template<typename Type , int N>
FSArrayParam< Type, N > &	loadFSArray (Serializable::IArchive &ar, const char *label, FSArray< Type, N > &array, int size)
	Add and load a required FSArray < Type > array parameter. More...

template<typename Type >
CArray2DParam< Type > &	loadCArray2D (Serializable::IArchive &ar, const char label, Type value, int m, int n, int np, bool isRequired)
	Add and load a CArray2DParam < Type > C 2D array parameter. More...

template<typename Type >
CArray2DParam< Type > &	loadCArray2D (Serializable::IArchive &ar, const char label, Type value, int m, int n, int np)
	Add and load a required < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired)
	Add and load a DMatrixParam < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and load a required DMatrixParam < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n, bool isRequired)
	Add and load a symmetric DSymmMatrixParam < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n)
	Add and load a required DSymmMatrixParam < Type > matrix parameter. More...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Additional Inherited Members
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

One-dimensional spatial domain and discretization grid.

Parameter File Format

Definition at line 26 of file fd1d/domain/Domain.h.

Member Typedef Documentation

◆ Field

typedef DArray<double> Pscf::Fd1d::Domain::Field

Generic field type (base class)

Definition at line 34 of file fd1d/domain/Domain.h.

Constructor & Destructor Documentation

◆ Domain()

Pscf::Fd1d::Domain::Domain ( )

Constructor.

Definition at line 15 of file fd1d/domain/Domain.cpp.

References Util::ParamComposite::setClassName().

◆ ~Domain()

Pscf::Fd1d::Domain::~Domain ( )

Destructor.

Definition at line 25 of file fd1d/domain/Domain.cpp.

Member Function Documentation

◆ readParameters()

void Pscf::Fd1d::Domain::readParameters ( std::istream & in )

virtual

Read all parameters and initialize.

Reimplemented from Util::ParamComposite.

Definition at line 28 of file fd1d/domain/Domain.cpp.

References Util::ParamComposite::read(), Util::ParamComposite::readOptional(), and UTIL_CHECK.

◆ setPlanarParameters()

void Pscf::Fd1d::Domain::setPlanarParameters	(	double	xMin,
		double	xMax,
		int	nx
	)

Set grid parameters for a planar domain.

Parameters

xMin	minimum normal coordinate value
xMax	maximum normal coordinate value
nx	number of grid points, including endpoints

Definition at line 48 of file fd1d/domain/Domain.cpp.

References nx(), xMax(), and xMin().

◆ setShellParameters()

void Pscf::Fd1d::Domain::setShellParameters	(	GeometryMode	mode,
		double	xMin,
		double	xMax,
		int	nx
	)

Set grid parameters for a cylindrical or spherical shell.

Parameters

mode	enumeration (Llamellar, Cylindrical or Spherical)
xMin	minimum radius
xMax	maximum radius
nx	number of grid points, including endpoints

Definition at line 59 of file fd1d/domain/Domain.cpp.

References mode(), nx(), xMax(), and xMin().

◆ setCylinderParameters()

void Pscf::Fd1d::Domain::setCylinderParameters	(	double	xMax,
		int	nx
	)

Set grid parameters for a cylinder.

Parameters

xMax	maximum radius
nx	number of grid points, including endpoints

Definition at line 71 of file fd1d/domain/Domain.cpp.

References nx(), and xMax().

◆ setSphereParameters()

void Pscf::Fd1d::Domain::setSphereParameters	(	double	xMax,
		int	nx
	)

Set grid parameters for a sphere.

Parameters

xMax	maximum radius
nx	number of grid points, including endpoints

Definition at line 82 of file fd1d/domain/Domain.cpp.

References nx(), and xMax().

◆ xMin()

double Pscf::Fd1d::Domain::xMin ( ) const

inline

Get minimum spatial coordinate.

Definition at line 219 of file fd1d/domain/Domain.h.

Referenced by Pscf::Fd1d::FieldIo::remesh(), setPlanarParameters(), setShellParameters(), and Pscf::Fd1d::Block::setupSolver().

◆ xMax()

double Pscf::Fd1d::Domain::xMax ( ) const

inline

Get maximum spatial coordinate.

Definition at line 222 of file fd1d/domain/Domain.h.

Referenced by Pscf::Fd1d::FieldIo::remesh(), setCylinderParameters(), setPlanarParameters(), setShellParameters(), setSphereParameters(), and Pscf::Fd1d::Block::setupSolver().

◆ volume()

double Pscf::Fd1d::Domain::volume ( ) const

inline

Get generalized volume of domain.

Returns volume of spherical domain, area of cylindrical domain, or a length of a planar domain.

Definition at line 225 of file fd1d/domain/Domain.h.

Referenced by Pscf::Fd1d::HomogeneousComparison::output(), and Pscf::Fd1d::Sweep::outputSummary().

◆ dx()

double Pscf::Fd1d::Domain::dx ( ) const

inline

Get spatial grid step size.

Definition at line 216 of file fd1d/domain/Domain.h.

Referenced by Pscf::Fd1d::FieldIo::remesh(), and Pscf::Fd1d::Block::setupSolver().

◆ nx()

int Pscf::Fd1d::Domain::nx ( ) const

inline

Get number of spatial grid points, including both endpoints.

Definition at line 213 of file fd1d/domain/Domain.h.

Referenced by Pscf::Fd1d::Sweep::checkAllocation(), Pscf::Fd1d::Mixture::compute(), Pscf::Fd1d::HomogeneousComparison::compute(), Pscf::Fd1d::Solvent::compute(), Pscf::Fd1d::Block::computeConcentration(), Pscf::Fd1d::System::computeFreeEnergy(), Pscf::Fd1d::Sweep::extrapolate(), Pscf::Fd1d::FieldIo::remesh(), setCylinderParameters(), Pscf::Fd1d::Solvent::setDiscretization(), Pscf::Fd1d::Block::setDiscretization(), setPlanarParameters(), setShellParameters(), setSphereParameters(), Pscf::Fd1d::Block::setupSolver(), Pscf::Fd1d::BinaryRelaxIterator::solve(), Pscf::Fd1d::NrIterator::solve(), Pscf::Fd1d::Block::step(), Pscf::Fd1d::FieldIo::writeBlockCFields(), Pscf::Fd1d::System::writeQ(), and Pscf::Fd1d::FieldIo::writeVertexQ().

◆ mode()

GeometryMode const & Pscf::Fd1d::Domain::mode ( ) const

inline

Get coordinate system flag (Planar, Cylindrical or Spherical).

Definition at line 228 of file fd1d/domain/Domain.h.

Referenced by setShellParameters(), and Pscf::Fd1d::Block::setupSolver().

◆ isShell()

bool Pscf::Fd1d::Domain::isShell ( ) const

inline

Is this a cylindrical or spherical shell?

This value is relevant only if the geometry mode is spherical or cylindrical. If so, isShell is set true if the optional parameter xMin is present and assigned a positive value in the parameter file. If geometryMode is planar or xMin is absent, then isShell is false.

Definition at line 231 of file fd1d/domain/Domain.h.

Referenced by Pscf::Fd1d::Block::setupSolver().

◆ spatialAverage()

double Pscf::Fd1d::Domain::spatialAverage ( Field const & f ) const

Compute spatial average of a field.

Parameters

f	a field that depends on one spatial coordinate

Returns: spatial average of field f

Definition at line 119 of file fd1d/domain/Domain.cpp.

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

Referenced by Pscf::Fd1d::Solvent::compute(), Pscf::Fd1d::System::computeFreeEnergy(), and innerProduct().

◆ innerProduct()

double Pscf::Fd1d::Domain::innerProduct	(	Field const &	f,
		Field const &	g
	)		const

Compute inner product of two real fields.

Parameters

f	first field
g	second field

Returns: spatial average of product of two fields.

Definition at line 201 of file fd1d/domain/Domain.cpp.

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

Referenced by Pscf::Fd1d::System::computeFreeEnergy(), and Pscf::Fd1d::Propagator::computeQ().

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

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Field

Constructor & Destructor Documentation

◆ Domain()

◆ ~Domain()

Member Function Documentation

◆ readParameters()

◆ setPlanarParameters()

◆ setShellParameters()

◆ setCylinderParameters()

◆ setSphereParameters()

◆ xMin()

◆ xMax()

◆ volume()

◆ dx()

◆ nx()

◆ mode()

◆ isShell()

◆ spatialAverage()

◆ innerProduct()