Spatial domain and spatial discretization for a periodic structure. More...

#include <Domain.h>

Inheritance diagram for Pscf::Rpc::Domain< D >:

Public Member Functions
	Domain ()
	Constructor.

	~Domain ()
	Destructor.

Initialization and Mutators
void	setFileMaster (FileMaster &fileMaster)
	Create association with a FileMaster, needed by FieldIo.

virtual void	readParameters (std::istream &in)
	Read body of parameter block (without opening and closing lines).

void	readRGridFieldHeader (std::istream &in, int &nMonomer)
	Read header of an r-grid field file to initialize this Domain.

void	setUnitCell (UnitCell< D > const &unitCell)
	Set unit cell.

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

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

void	makeBasis ()
	Construct basis if not done already.

Accessors (return by non-const or const reference)
UnitCell< D > &	unitCell ()
	Get UnitCell (i.e., lattice type and parameters) by reference.

UnitCell< D > const &	unitCell () const
	Get UnitCell (i.e., lattice type and parameters) by reference.

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

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

SpaceGroup< D > const &	group () const
	Get associated SpaceGroup object by const reference.

Basis< D > &	basis ()
	Get associated Basis object by reference.

Basis< D > const &	basis () const
	Get associated Basis object by const reference.

FFT< D > &	fft ()
	Get associated FFT object.

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

FieldIo< D > &	fieldIo ()
	Get associated FieldIo object.

FieldIo< D > const &	fieldIo () const
	Get associated FieldIo object by const reference.

Accessors (return by value)
UnitCell< D >::LatticeSystem	lattice () const
	Get lattice system.

std::string	groupName () const
	Get group name.

bool	hasGroup () const
	Has a space group been identified?

bool	hasBasis () const
	Has a symmetry-adapted Fourier basis been initialized?

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 ?

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

void	clearCommunicator ()
	Clear (nullify) the communicator.

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

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

Additional Inherited Members
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.

Static Public Member Functions inherited from Util::ParamComponent
static void	initStatic ()
	Initialize static echo member to false.

static void	setEcho (bool echo=true)
	Enable or disable echoing for all subclasses of ParamComponent.

static bool	echo ()
	Get echo parameter.

Protected Member Functions inherited from Util::ParamComposite
void	setClassName (const char *className)
	Set class name string.

void	setIsRequired (bool isRequired)
	Set or unset the isActive flag.

void	setIsActive (bool isActive)
	Set or unset the isActive flag.

void	setParent (ParamComponent &param, bool next=true)
	Set this to the parent of a child component.

void	addComponent (ParamComponent &param, bool isLeaf=true)
	Add a new ParamComponent object to the format array.

template<typename Type >
ScalarParam< Type > &	add (std::istream &in, const char *label, Type &value, bool isRequired=true)
	Add a new required ScalarParam < Type > object.

template<typename Type >
CArrayParam< Type > &	addCArray (std::istream &in, const char label, Type value, int n, bool isRequired=true)
	Add (but do not read) a required C array parameter.

template<typename Type >
DArrayParam< Type > &	addDArray (std::istream &in, const char *label, DArray< Type > &array, int n, bool isRequired=true)
	Add (but do not read) a DArray < Type > parameter.

template<typename Type , int N>
FArrayParam< Type, N > &	addFArray (std::istream &in, const char *label, FArray< Type, N > &array, bool isRequired=true)
	Add (but do not read) a FArray < Type, N > array parameter.

template<typename Type , int N>
FSArrayParam< Type, N > &	addFSArray (std::istream &in, const char *label, FSArray< Type, N > &array, int size, bool isRequired=true)
	Add (but do not read) a FSArray < Type, N > array parameter.

template<typename Type >
CArray2DParam< Type > &	addCArray2D (std::istream &in, const char label, Type value, int m, int n, int np, bool isRequired=true)
	Add (but do not read) a CArray2DParam < Type > 2D C-array.

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

Protected Member Functions inherited from Util::ParamComponent
	ParamComponent ()
	Constructor.

	ParamComponent (const ParamComponent &other)
	Copy constructor.

Detailed Description

template<int D>
class Pscf::Rpc::Domain< D >

Spatial domain and spatial discretization for a periodic structure.

A Domain has (among other components):

a Pscf::Mesh spatial discretization mesh
a Prdc::UnitCell crystallographic unit cell
a Prdc::SpaceGroup crystallographic space group
a Prdc::Basis symmetry-adapated Fourier basis
a Prdc::Cpu::FFT Fast Fourier Transform
a Rpc::FieldIo object for field IO and conversion operations
a lattice system enum (type Prdc::UnitCell<D>::LatticeSystem)
a groupName string

Note: Class names Pscf::Mesh, Prdc::UnitCell, etc. mentioned above are actually all class templates with a template parameter D. Actual class names are Mesh <D>, Prdc::UnitCell <D>, etc. with D=1, 2, or 3.

See also: Manual Page

Definition at line 55 of file rpc/field/Domain.h.

Constructor & Destructor Documentation

◆ Domain()

template<int D>

Pscf::Rpc::Domain< D >::Domain ( )

Constructor.

Definition at line 26 of file rpc/field/Domain.tpp.

References Util::ParamComposite::setClassName().

◆ ~Domain()

template<int D>

Pscf::Rpc::Domain< D >::~Domain ( )

Destructor.

Definition at line 49 of file rpc/field/Domain.tpp.

Member Function Documentation

◆ setFileMaster()

template<int D>

void Pscf::Rpc::Domain< D >::setFileMaster ( FileMaster & fileMaster )

Create association with a FileMaster, needed by FieldIo.

Parameters

fileMaster associated FileMaster object.

Definition at line 53 of file rpc/field/Domain.tpp.

◆ readParameters()

template<int D>

void Pscf::Rpc::Domain< D >::readParameters ( std::istream & in )

virtual

Read body of parameter block (without opening and closing lines).

Parameters

in	input parameter stream

Reimplemented from Util::ParamComposite.

Definition at line 63 of file rpc/field/Domain.tpp.

References UTIL_CHECK.

◆ readRGridFieldHeader()

template<int D>

void Pscf::Rpc::Domain< D >::readRGridFieldHeader	(	std::istream &	in,
		int &	nMonomer )

Read header of an r-grid field file to initialize this Domain.

Useful for unit testing.

Parameters

in	input parameter stream
nMonomer	number of monomers in field file (output)

Definition at line 102 of file rpc/field/Domain.tpp.

References Pscf::Prdc::readFieldHeader(), UTIL_CHECK, and UTIL_THROW.

◆ setUnitCell() [1/3]

template<int D>

void Pscf::Rpc::Domain< D >::setUnitCell ( UnitCell< D > const & unitCell )

Set unit cell.

The lattice system in the unitCell must match any value that was read from the parameter file. This function initializes the basis if a space group exists and the basis was not initialized previously.

Parameters

unitCell new unit cell

Definition at line 154 of file rpc/field/Domain.tpp.

References UTIL_CHECK.

◆ setUnitCell() [2/3]

template<int D>

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

Set unit cell state.

The "lattice" lattice system enumeration match any non-null value that was read from the parameter file. This function initializes the basis if a space group exists and the basis was not initialized previously.

Parameters

lattice	lattice system
parameters	array of unit cell parameters

Definition at line 173 of file rpc/field/Domain.tpp.

References UTIL_CHECK.

◆ setUnitCell() [3/3]

template<int D>

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

Set unit cell parameters.

The lattice system must already be set to non-null value on entry. This function initializes the basis if a space group exists and the basis was not initialized previously.

Parameters

parameters array of unit cell parameters

Definition at line 193 of file rpc/field/Domain.tpp.

References Util::FSArray< T, N >::size(), and UTIL_CHECK.

◆ makeBasis()

template<int D>

void Pscf::Rpc::Domain< D >::makeBasis ( )

Construct basis if not done already.

Definition at line 206 of file rpc/field/Domain.tpp.

References UTIL_CHECK.

◆ unitCell() [1/2]

template<int D>

UnitCell< D > & Pscf::Rpc::Domain< D >::unitCell ( )

inline

Get UnitCell (i.e., lattice type and parameters) by reference.

Definition at line 292 of file rpc/field/Domain.h.

Referenced by Pscf::Rpc::Simulator< D >::computeHamiltonian(), Pscf::Rpc::ConcentrationWriter< D >::writeFrame(), Pscf::Rpc::TrajectoryWriter< D >::writeFrame(), Pscf::Rpc::ConcentrationWriter< D >::writeHeader(), and Pscf::Rpc::TrajectoryWriter< D >::writeHeader().

◆ unitCell() [2/2]

template<int D>

UnitCell< D > const & Pscf::Rpc::Domain< D >::unitCell ( ) const

inline

Get UnitCell (i.e., lattice type and parameters) by reference.

Definition at line 297 of file rpc/field/Domain.h.

◆ mesh() [1/2]

template<int D>

Mesh< D > & Pscf::Rpc::Domain< D >::mesh ( )

inline

Get spatial discretization mesh by reference.

Definition at line 302 of file rpc/field/Domain.h.

Referenced by Pscf::Rpc::Simulator< D >::computeHamiltonian().

◆ mesh() [2/2]

template<int D>

Mesh< D > const & Pscf::Rpc::Domain< D >::mesh ( ) const

inline

Get spatial discretization mesh by const reference.

Definition at line 307 of file rpc/field/Domain.h.

◆ group()

template<int D>

SpaceGroup< D > const & Pscf::Rpc::Domain< D >::group ( ) const

inline

Get associated SpaceGroup object by const reference.

Definition at line 312 of file rpc/field/Domain.h.

◆ basis() [1/2]

template<int D>

Basis< D > & Pscf::Rpc::Domain< D >::basis ( )

inline

Get associated Basis object by reference.

Definition at line 317 of file rpc/field/Domain.h.

◆ basis() [2/2]

template<int D>

Basis< D > const & Pscf::Rpc::Domain< D >::basis ( ) const

inline

Get associated Basis object by const reference.

Definition at line 322 of file rpc/field/Domain.h.

◆ fft() [1/2]

template<int D>

FFT< D > & Pscf::Rpc::Domain< D >::fft ( )

inline

Get associated FFT object.

Definition at line 327 of file rpc/field/Domain.h.

◆ fft() [2/2]

template<int D>

FFT< D > const & Pscf::Rpc::Domain< D >::fft ( ) const

inline

Get associated FFT object by const reference.

Definition at line 332 of file rpc/field/Domain.h.

◆ fieldIo() [1/2]

template<int D>

FieldIo< D > & Pscf::Rpc::Domain< D >::fieldIo ( )

inline

Get associated FieldIo object.

Definition at line 337 of file rpc/field/Domain.h.

Referenced by Pscf::Rpc::ConcentrationWriter< D >::writeFrame(), Pscf::Rpc::TrajectoryWriter< D >::writeFrame(), Pscf::Rpc::ConcentrationWriter< D >::writeHeader(), and Pscf::Rpc::TrajectoryWriter< D >::writeHeader().

◆ fieldIo() [2/2]

template<int D>

FieldIo< D > const & Pscf::Rpc::Domain< D >::fieldIo ( ) const

inline

Get associated FieldIo object by const reference.

Definition at line 342 of file rpc/field/Domain.h.

◆ lattice()

template<int D>

UnitCell< D >::LatticeSystem Pscf::Rpc::Domain< D >::lattice ( ) const

inline

Get lattice system.

Definition at line 348 of file rpc/field/Domain.h.

◆ groupName()

template<int D>

std::string Pscf::Rpc::Domain< D >::groupName ( ) const

inline

Get group name.

Definition at line 354 of file rpc/field/Domain.h.

◆ hasGroup()

template<int D>

bool Pscf::Rpc::Domain< D >::hasGroup ( ) const

inline

Has a space group been identified?

Definition at line 359 of file rpc/field/Domain.h.

◆ hasBasis()

template<int D>

bool Pscf::Rpc::Domain< D >::hasBasis ( ) const

inline

Has a symmetry-adapted Fourier basis been initialized?

Definition at line 364 of file rpc/field/Domain.h.

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

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Domain()

◆ ~Domain()

Member Function Documentation

◆ setFileMaster()

◆ readParameters()

◆ readRGridFieldHeader()

◆ setUnitCell() [1/3]

◆ setUnitCell() [2/3]

◆ setUnitCell() [3/3]

◆ makeBasis()

◆ unitCell() [1/2]

◆ unitCell() [2/2]

◆ mesh() [1/2]

◆ mesh() [2/2]

◆ group()

◆ basis() [1/2]

◆ basis() [2/2]

◆ fft() [1/2]

◆ fft() [2/2]

◆ fieldIo() [1/2]

◆ fieldIo() [2/2]

◆ lattice()

◆ groupName()

◆ hasGroup()

◆ hasBasis()