File input/output operations and format conversions for fields. More...

#include <FieldIo.h>

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

	~FieldIo ()
	Destructor. More...

void	associate (Mesh< D > const &mesh, FFT< D > const &fft, typename UnitCell< D >::LatticeSystem &lattice, std::string &groupName, SpaceGroup< D > &group, Basis< D > &basis, FileMaster const &fileMaster)
	Get and store addresses of associated objects. More...

Field File IO - Symmetry Adapted Basis Format
void	readFieldBasis (std::istream &in, DArray< double > &field, UnitCell< D > &unitCell) const
	Read single concentration or chemical potential field from file. More...

void	readFieldBasis (std::string filename, DArray< double > &field, UnitCell< D > &unitCell) const
	Read single concentration or chemical potential field from file. More...

void	writeFieldBasis (std::ostream &out, DArray< double > const &field, UnitCell< D > const &unitCell) const
	Write single concentration or chemical potential field to output stream out. More...

void	writeFieldBasis (std::string filename, DArray< double > const &field, UnitCell< D > const &unitCell) const
	Write single concentration or chemical potential field to file. More...

void	readFieldsBasis (std::istream &in, DArray< DArray< double > > &fields, UnitCell< D > &unitCell) const
	Read concentration or chemical potential field components from file. More...

void	readFieldsBasis (std::string filename, DArray< DArray< double > > &fields, UnitCell< D > &unitCell) const
	Read concentration or chemical potential field components from file. More...

void	writeFieldsBasis (std::ostream &out, DArray< DArray< double > > const &fields, UnitCell< D > const &unitCell) const
	Write concentration or chemical potential field components to file. More...

void	writeFieldsBasis (std::string filename, DArray< DArray< double > > const &fields, UnitCell< D > const &unitCell) const
	Write concentration or chemical potential field components to file. More...

Field File IO - Real Space Grid Format
void	readFieldRGrid (std::istream &in, RField< D > &field, UnitCell< D > &unitCell) const
	Read single RField (field on an r-space grid) from istream. More...

void	readFieldRGrid (std::string filename, RField< D > &field, UnitCell< D > &unitCell) const
	Read single RField (field on an r-space grid) from named file. More...

void	readFieldsRGrid (std::istream &in, DArray< RField< D > > &fields, UnitCell< D > &unitCell) const
	Read array of RField objects (fields on r-space grid) from istream. More...

void	readFieldsRGrid (std::string filename, DArray< RField< D > > &fields, UnitCell< D > &unitCell) const
	Read array of RField objects (fields on an r-space grid) from file. More...

void	writeFieldRGrid (std::ostream &out, RField< D > const &field, UnitCell< D > const &unitCell, bool writeHeader=true) const
	Write a single RField (field on an r-space grid) to ostream. More...

void	writeFieldRGrid (std::string filename, RField< D > const &field, UnitCell< D > const &unitCell) const
	Write a single RField (fields on an r-space grid) to a file. More...

void	writeFieldsRGrid (std::ostream &out, DArray< RField< D > > const &fields, UnitCell< D > const &unitCell) const
	Write array of RField objects (fields on r-space grid) to ostream. More...

void	writeFieldsRGrid (std::string filename, DArray< RField< D > > const &fields, UnitCell< D > const &unitCell) const
	Write array of RField objects (fields on an r-space grid) to file. More...

Field File IO - Fourier Space (K-Space) Grid Format
void	readFieldsKGrid (std::istream &in, DArray< RFieldDft< D > > &fields, UnitCell< D > &unitCell) const
	Read array of RFieldDft objects (k-space fields) from file. More...

void	readFieldsKGrid (std::string filename, DArray< RFieldDft< D > > &fields, UnitCell< D > &unitCell) const
	Read array of RFieldDft objects (k-space fields) from file. More...

void	writeFieldsKGrid (std::ostream &out, DArray< RFieldDft< D > > const &fields, UnitCell< D > const &unitCell) const
	Write array of RFieldDft objects (k-space fields) to file. More...

void	writeFieldsKGrid (std::string filename, DArray< RFieldDft< D > > const &fields, UnitCell< D > const &unitCell) const
	Write array of RFieldDft objects (k-space fields) to a file. More...

File IO Utilities
void	readFieldHeader (std::istream &in, int &nMonomer, UnitCell< D > &unitCell) const
	Reader header of field file (fortran pscf format) More...

void	writeFieldHeader (std::ostream &out, int nMonomer, UnitCell< D > const &unitCell) const
	Write header for field file (fortran pscf format) More...

Field Format Conversion
void	convertBasisToKGrid (DArray< double > const &components, RFieldDft< D > &dft) const
	Convert a field from symmetrized basis to Fourier transform (k-grid). More...

void	convertBasisToKGrid (DArray< DArray< double > > const &in, DArray< RFieldDft< D > > &out) const
	Convert fields from symmetrized basis to Fourier transform (k-grid). More...

void	convertKGridToBasis (RFieldDft< D > const &in, DArray< double > &out, bool checkSymmetry=true, double epsilon=1.0e-8) const
	Convert a field from Fourier transform (kgrid) to symmetrized basis. More...

void	convertKGridToBasis (DArray< RFieldDft< D > > const &in, DArray< DArray< double > > &out, bool checkSymmetry=true, double epsilon=1.0e-8) const
	Convert fields from Fourier transform (k-grid) to symmetrized basis. More...

void	convertBasisToRGrid (DArray< double > const &in, RField< D > &out) const
	Convert a field from symmetrized basis to spatial grid (r-grid). More...

void	convertBasisToRGrid (DArray< DArray< double > > const &in, DArray< RField< D > > &out) const
	Convert fields from symmetrized basis to spatial grid (r-grid). More...

void	convertRGridToBasis (RField< D > const &in, DArray< double > &out, bool checkSymmetry=true, double epsilon=1.0e-8) const
	Convert a field from spatial grid (r-grid) to symmetrized basis. More...

void	convertRGridToBasis (DArray< RField< D > > const &in, DArray< DArray< double > > &out, bool checkSymmetry=true, double epsilon=1.0e-8) const
	Convert fields from spatial grid (r-grid) to symmetrized basis. More...

void	convertKGridToRGrid (DArray< RFieldDft< D > > &in, DArray< RField< D > > &out) const
	Convert fields from k-grid (DFT) to real space (r-grid) format. More...

void	convertKGridToRGrid (RFieldDft< D > &in, RField< D > &out) const
	Convert a field from k-grid (DFT) to real space (r-grid) format. More...

void	convertRGridToKGrid (DArray< RField< D > > const &in, DArray< RFieldDft< D > > &out) const
	Convert fields from spatial grid (r-grid) to k-grid format. More...

void	convertRGridToKGrid (RField< D > const &in, RFieldDft< D > &out) const
	Convert a field from spatial grid (r-grid) to k-grid format. More...

Test Space Group Symmetry
bool	hasSymmetry (RField< D > const &in, double epsilon=1.0e-8, bool verbose=true) const
	Check if an r-grid field has the declared space group symmetry. More...

bool	hasSymmetry (RFieldDft< D > const &in, double epsilon=1.0e-8, bool verbose=true) const
	Check if a k-grid field has declared space group symmetry. More...

Detailed Description

template<int D>
class Pscf::Pspc::FieldIo< D >

File input/output operations and format conversions for fields.

This class provides functions to read and write arrays that contain fields in any of three representations (symmetry-adapted basis, r-space grid, or Fourier k-space grid), and to convert among these representations. The functions that implement IO operations define file formats for these field representations.

Definition at line 42 of file pspc/field/FieldIo.h.

Constructor & Destructor Documentation

◆ FieldIo()

template<int D>

Pscf::Pspc::FieldIo< D >::FieldIo

Constructor.

Definition at line 35 of file pspc/field/FieldIo.tpp.

◆ ~FieldIo()

template<int D>

Pscf::Pspc::FieldIo< D >::~FieldIo

Destructor.

Definition at line 48 of file pspc/field/FieldIo.tpp.

Member Function Documentation

◆ associate()

template<int D>

void Pscf::Pspc::FieldIo< D >::associate	(	Mesh< D > const &	mesh,
		FFT< D > const &	fft,
		typename UnitCell< D >::LatticeSystem &	lattice,
		std::string &	groupName,
		SpaceGroup< D > &	group,
		Basis< D > &	basis,
		FileMaster const &	fileMaster
	)

Get and store addresses of associated objects.

Parameters

mesh	associated spatial discretization Mesh<D>
fft	associated FFT object for fast transforms
lattice	lattice system type (enumeration value)
groupName	space group name string
group	associated SpaceGroup object
basis	associated Basis object
fileMaster	associated FileMaster (for file paths)

Definition at line 56 of file pspc/field/FieldIo.tpp.

◆ readFieldBasis() [1/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::readFieldBasis	(	std::istream &	in,
		DArray< double > &	field,
		UnitCell< D > &	unitCell
	)		const

Read single concentration or chemical potential field from file.

This function reads the field in symmetry adapted basis format from input stream in.

Parameters

in	input stream (i.e., input file)
field	array to store the field (basis format)
unitCell	associated crystallographic unit cell

Definition at line 74 of file pspc/field/FieldIo.tpp.

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

◆ readFieldBasis() [2/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::readFieldBasis	(	std::string	filename,
		DArray< double > &	field,
		UnitCell< D > &	unitCell
	)		const

Read single concentration or chemical potential field from file.

This function opens an input file with the specified filename, reads field in symmetry adapted basis format from that file, and closes the file.

Parameters

filename	name of input file
field	array to store the field (basis format)
unitCell	associated crystallographic unit cell

Definition at line 90 of file pspc/field/FieldIo.tpp.

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

◆ writeFieldBasis() [1/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::writeFieldBasis	(	std::ostream &	out,
		DArray< double > const &	field,
		UnitCell< D > const &	unitCell
	)		const

Write single concentration or chemical potential field to output stream out.

This function writes the field in symmetry adapted basis format.

Parameters

out	output stream (i.e., output file)
field	field to be written (symmetry adapted basis format)
unitCell	associated crystallographic unit cell

Definition at line 106 of file pspc/field/FieldIo.tpp.

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

◆ writeFieldBasis() [2/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::writeFieldBasis	(	std::string	filename,
		DArray< double > const &	field,
		UnitCell< D > const &	unitCell
	)		const

Write single concentration or chemical potential field to file.

This function opens an output file with the specified filename, writes the field in symmetry adapted basis format to that file, and closes the file.

Parameters

filename	name of output file
field	field to be written (symmetry adapted basis format)
unitCell	associated crystallographic unit cell

Definition at line 119 of file pspc/field/FieldIo.tpp.

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

◆ readFieldsBasis() [1/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::readFieldsBasis	(	std::istream &	in,
		DArray< DArray< double > > &	fields,
		UnitCell< D > &	unitCell
	)		const

Read concentration or chemical potential field components from file.

This function reads fields in a symmetry adapted basis from input stream in.

The capacity of DArray fields is equal to nMonomer, and element fields[i] is a DArray containing components of the field associated with monomer type i.

Parameters

in	input stream (i.e., input file)
fields	array of fields (symmetry adapted basis components)
unitCell	associated crystallographic unit cell

Definition at line 132 of file pspc/field/FieldIo.tpp.

References Util::DArray< Data >::allocate(), Pscf::Basis< D >::Star::basisId, Pscf::Basis< D >::Star::beginId, Pscf::Basis< D >::Star::cancel, Util::Log::file(), Pscf::Basis< D >::Star::invertFlag, Pscf::Vec< D, T >::negate(), Pscf::Pspc::FieldIo< D >::readFieldHeader(), Pscf::Basis< D >::Star::size, UTIL_CHECK, UTIL_THROW, and Pscf::Basis< D >::Star::waveBz.

◆ readFieldsBasis() [2/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::readFieldsBasis	(	std::string	filename,
		DArray< DArray< double > > &	fields,
		UnitCell< D > &	unitCell
	)		const

Read concentration or chemical potential field components from file.

This function opens an input file with the specified filename, reads components in symmetry-adapted form from that file, and closes the file.

Parameters

filename	name of input file
fields	array of fields (symmetry adapted basis components)
unitCell	associated crystallographic unit cell

Definition at line 416 of file pspc/field/FieldIo.tpp.

◆ writeFieldsBasis() [1/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::writeFieldsBasis	(	std::ostream &	out,
		DArray< DArray< double > > const &	fields,
		UnitCell< D > const &	unitCell
	)		const

Write concentration or chemical potential field components to file.

This function writes components in a symmetry adapted basis.

Parameters

out	output stream (i.e., output file)
fields	array of fields (symmetry adapted basis components)
unitCell	associated crystallographic unit cell

Definition at line 430 of file pspc/field/FieldIo.tpp.

References UTIL_CHECK.

◆ writeFieldsBasis() [2/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::writeFieldsBasis	(	std::string	filename,
		DArray< DArray< double > > const &	fields,
		UnitCell< D > const &	unitCell
	)		const

Write concentration or chemical potential field components to file.

This function opens an output file with the specified filename, writes components in symmetry-adapted form to that file, and then closes the file.

Parameters

filename	name of input file
fields	array of fields (symmetry adapted basis components)
unitCell	associated crystallographic unit cell

Definition at line 466 of file pspc/field/FieldIo.tpp.

◆ readFieldRGrid() [1/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::readFieldRGrid	(	std::istream &	in,
		RField< D > &	field,
		UnitCell< D > &	unitCell
	)		const

Read single RField (field on an r-space grid) from istream.

Parameters

in	input stream (i.e., input file)
field	fields defined on r-space grid
unitCell	associated crystallographic unit cell

Definition at line 715 of file pspc/field/FieldIo.tpp.

References Pscf::Pspc::RField< D >::allocate(), Pscf::MeshIterator< D >::atEnd(), Pscf::MeshIterator< D >::begin(), Util::Log::file(), Util::DArray< Data >::isAllocated(), Pscf::Pspc::RField< D >::meshDimensions(), Pscf::MeshIterator< D >::rank(), Pscf::Pspc::FieldIo< D >::readFieldHeader(), UTIL_CHECK, and UTIL_THROW.

◆ readFieldRGrid() [2/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::readFieldRGrid	(	std::string	filename,
		RField< D > &	field,
		UnitCell< D > &	unitCell
	)		const

Read single RField (field on an r-space grid) from named file.

This function opens an input file with the specified filename, reads a field in RField<D> real-space grid format, and closes the file.

Parameters

filename	name of input file
field	fields defined on r-space grid
unitCell	associated crystallographic unit cell

Definition at line 820 of file pspc/field/FieldIo.tpp.

◆ readFieldsRGrid() [1/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::readFieldsRGrid	(	std::istream &	in,
		DArray< RField< D > > &	fields,
		UnitCell< D > &	unitCell
	)		const

Read array of RField objects (fields on r-space grid) from istream.

The capacity of array fields is equal to nMonomer, and element fields[i] is the RField<D> associated with monomer type i.

Parameters

in	input stream (i.e., input file)
fields	array of RField fields (r-space grid)
unitCell	associated crystallographic unit cell

Definition at line 478 of file pspc/field/FieldIo.tpp.

References Util::DArray< Data >::allocate(), Pscf::MeshIterator< D >::atEnd(), Pscf::MeshIterator< D >::begin(), Util::Log::file(), Pscf::MeshIterator< D >::rank(), Pscf::Pspc::FieldIo< D >::readFieldHeader(), UTIL_CHECK, and UTIL_THROW.

◆ readFieldsRGrid() [2/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::readFieldsRGrid	(	std::string	filename,
		DArray< RField< D > > &	fields,
		UnitCell< D > &	unitCell
	)		const

Read array of RField objects (fields on an r-space grid) from file.

The capacity of array fields is equal to nMonomer, and element fields[i] is the RField<D> associated with monomer type i.

This function opens an input file with the specified filename, reads fields in RField<D> real-space grid format from that file, and then closes the file.

Parameters

filename	name of input file
fields	array of RField fields (r-space grid)
unitCell	associated crystallographic unit cell

Definition at line 602 of file pspc/field/FieldIo.tpp.

◆ writeFieldRGrid() [1/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::writeFieldRGrid	(	std::ostream &	out,
		RField< D > const &	field,
		UnitCell< D > const &	unitCell,
		bool	writeHeader = `true`
	)		const

Write a single RField (field on an r-space grid) to ostream.

Parameters

out	output stream
field	field defined on r-space grid
unitCell	associated crystallographic unit cell
writeHeader	should a file header be written?

Definition at line 832 of file pspc/field/FieldIo.tpp.

References Pscf::Pspc::RField< D >::allocate(), Pscf::MeshIterator< D >::atEnd(), Pscf::MeshIterator< D >::begin(), Util::Log::file(), and Pscf::MeshIterator< D >::rank().

◆ writeFieldRGrid() [2/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::writeFieldRGrid	(	std::string	filename,
		RField< D > const &	field,
		UnitCell< D > const &	unitCell
	)		const

Write a single RField (fields on an r-space grid) to a file.

This function opens an output file with the specified filename, write a field in RField<D> real-space grid format to that file, and then closes the file.

Parameters

filename	name of output file
field	field defined on r-space grid
unitCell	associated crystallographic unit cell

Definition at line 909 of file pspc/field/FieldIo.tpp.

◆ writeFieldsRGrid() [1/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::writeFieldsRGrid	(	std::ostream &	out,
		DArray< RField< D > > const &	fields,
		UnitCell< D > const &	unitCell
	)		const

Write array of RField objects (fields on r-space grid) to ostream.

Parameters

out	output stream (i.e., output file)
fields	array of RField fields (r-space grid)
unitCell	associated crystallographic unit cell

Definition at line 614 of file pspc/field/FieldIo.tpp.

References Util::DArray< Data >::allocate(), Pscf::MeshIterator< D >::atEnd(), Pscf::MeshIterator< D >::begin(), Util::Log::file(), Pscf::MeshIterator< D >::rank(), and UTIL_CHECK.

◆ writeFieldsRGrid() [2/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::writeFieldsRGrid	(	std::string	filename,
		DArray< RField< D > > const &	fields,
		UnitCell< D > const &	unitCell
	)		const

Write array of RField objects (fields on an r-space grid) to file.

This function opens an output file with the specified filename, writes fields in RField<D> real-space grid format to that file, and then closes the file.

Parameters

filename	name of output file
fields	array of RField fields (r-space grid)
unitCell	associated crystallographic unit cell

Definition at line 703 of file pspc/field/FieldIo.tpp.

◆ readFieldsKGrid() [1/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::readFieldsKGrid	(	std::istream &	in,
		DArray< RFieldDft< D > > &	fields,
		UnitCell< D > &	unitCell
	)		const

Read array of RFieldDft objects (k-space fields) from file.

The capacity of the array is equal to nMonomer, and element fields[i] is the discrete Fourier transform of the field for monomer type i.

Parameters

in	input stream (i.e., input file)
fields	array of RFieldDft fields (k-space grid)
unitCell	associated crystallographic unit cell

Definition at line 921 of file pspc/field/FieldIo.tpp.

References Pscf::MeshIterator< D >::atEnd(), Pscf::MeshIterator< D >::begin(), Pscf::MeshIterator< D >::rank(), Pscf::Pspc::FieldIo< D >::readFieldHeader(), UTIL_CHECK, and UTIL_THROW.

◆ readFieldsKGrid() [2/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::readFieldsKGrid	(	std::string	filename,
		DArray< RFieldDft< D > > &	fields,
		UnitCell< D > &	unitCell
	)		const

Read array of RFieldDft objects (k-space fields) from file.

This function opens a file with name filename, reads discrete Fourier components (Dft) of fields from that file, and closes the file.

The capacity of the array is equal to nMonomer, and element fields[i] is the discrete Fourier transform of the field for monomer type i.

Parameters

filename	name of input file
fields	array of RFieldDft fields (k-space grid)
unitCell	associated crystallographic unit cell

Definition at line 985 of file pspc/field/FieldIo.tpp.

◆ writeFieldsKGrid() [1/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::writeFieldsKGrid	(	std::ostream &	out,
		DArray< RFieldDft< D > > const &	fields,
		UnitCell< D > const &	unitCell
	)		const

Write array of RFieldDft objects (k-space fields) to file.

The capacity of the array fields is equal to nMonomer. Element fields[i] is the discrete Fourier transform of the field for monomer type i.

Parameters

out	output stream (i.e., output file)
fields	array of RFieldDft fields
unitCell	associated crystallographic unit cell

Definition at line 997 of file pspc/field/FieldIo.tpp.

References Pscf::MeshIterator< D >::atEnd(), Pscf::MeshIterator< D >::begin(), Pscf::MeshIterator< D >::rank(), and UTIL_CHECK.

◆ writeFieldsKGrid() [2/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::writeFieldsKGrid	(	std::string	filename,
		DArray< RFieldDft< D > > const &	fields,
		UnitCell< D > const &	unitCell
	)		const

Write array of RFieldDft objects (k-space fields) to a file.

This function opens a file with name filename, writes discrete Fourier transform components (DFT) components of fields to that file, and closes the file.

Parameters

filename	name of output file.
fields	array of RFieldDft fields (k-space grid)
unitCell	associated crystallographic unit cell

Definition at line 1031 of file pspc/field/FieldIo.tpp.

◆ readFieldHeader()

template<int D>

void Pscf::Pspc::FieldIo< D >::readFieldHeader	(	std::istream &	in,
		int &	nMonomer,
		UnitCell< D > &	unitCell
	)		const

Reader header of field file (fortran pscf format)

This reads the common part of the header for all field file formats. This contains the dimension of space, the unit cell, the group name and the the number of monomers. The unit cell data is read into the associated UnitCell<D>, which is thus updated.

If the associated basis is not initialized, this function will attempt to initialize it using the unit cell read from file and the associated group (if available) or group name.

This function throws an exception if the values of "dim" read from file do not match the FieldIo template parameter D.

The function does not impose any requirements on the value of the input parameter nMonomer; it is overwritten and will contain the value of "N_monomer" from the field file header at termination of the function.

If the UnitCell object passed to this function already contains unit cell data, the function will check to ensure that the crystal system and space group in the field file header match the data already stored. A warning will also be printed if the lattice parameters do not match. If, instead, the function is passed an empty UnitCell object, we assume that the UnitCell data is unknown or that the field file header does not need to be cross-checked with existing data. In this case, the field file header data is stored directly in the UnitCell object that was passed in.

Parameters

in	input stream (i.e., input file)
nMonomer	number of fields contained in the field file
unitCell	associated crystallographic unit cell

Definition at line 1047 of file pspc/field/FieldIo.tpp.

References Util::Log::file(), Pscf::UnitCellBase< D >::isInitialized(), Pscf::UnitCellBase< D >::nParameter(), UTIL_CHECK, and UTIL_THROW.

Referenced by Pscf::Pspc::FieldIo< D >::readFieldRGrid(), Pscf::Pspc::FieldIo< D >::readFieldsBasis(), Pscf::Pspc::FieldIo< D >::readFieldsKGrid(), and Pscf::Pspc::FieldIo< D >::readFieldsRGrid().

◆ writeFieldHeader()

template<int D>

void Pscf::Pspc::FieldIo< D >::writeFieldHeader	(	std::ostream &	out,
		int	nMonomer,
		UnitCell< D > const &	unitCell
	)		const

Write header for field file (fortran pscf format)

Parameters

out	output stream (i.e., output file)
nMonomer	number of monomer types or fields
unitCell	associated crystallographic unit cell

Definition at line 1126 of file pspc/field/FieldIo.tpp.

◆ convertBasisToKGrid() [1/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::convertBasisToKGrid	(	DArray< double > const &	components,
		RFieldDft< D > &	dft
	)		const

Convert a field from symmetrized basis to Fourier transform (k-grid).

Parameters

components	coefficients of symmetry-adapted basis functions
dft	discrete Fourier transform of a real field

Definition at line 1137 of file pspc/field/FieldIo.tpp.

References Pscf::Basis< D >::Star::basisId, Pscf::Basis< D >::Star::beginId, Pscf::Basis< D >::Star::cancel, Pscf::Basis< D >::Wave::coeff, Pscf::Pspc::RFieldDft< D >::dftDimensions(), Pscf::Basis< D >::Wave::implicit, Pscf::Basis< D >::Wave::indicesDft, Pscf::Basis< D >::Star::invertFlag, Pscf::Mesh< D >::rank(), Pscf::Mesh< D >::size(), UTIL_CHECK, and UTIL_THROW.

◆ convertBasisToKGrid() [2/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::convertBasisToKGrid	(	DArray< DArray< double > > const &	in,
		DArray< RFieldDft< D > > &	out
	)		const

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

The in and out parameters are arrays of fields, in which element number i is the field associated with monomer type i.

Parameters

in	fields expanded in symmetry-adapted Fourier basis
out	fields defined as discrete Fourier transforms (k-grid)

Definition at line 1359 of file pspc/field/FieldIo.tpp.

References UTIL_ASSERT.

◆ convertKGridToBasis() [1/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::convertKGridToBasis	(	RFieldDft< D > const &	in,
		DArray< double > &	out,
		bool	checkSymmetry = `true`,
		double	epsilon = `1.0e-8`
	)		const

Convert a field from Fourier transform (kgrid) to symmetrized basis.

If the checkSymmetry parameter is true, this function checks if the input field satisfies the space group symmetry to within a tolerance given by the epsilon parameter, and prints a warning to Log::file() if it does not.

Parameters

in	discrete Fourier transform (k-grid) of a field
out	components of field in asymmetry-adapted Fourier basis
checkSymmetry	flag indicating whether to check symmetry
epsilon	error tolerance for symmetry test (if any)

Definition at line 1240 of file pspc/field/FieldIo.tpp.

References Pscf::Basis< D >::Star::basisId, Pscf::Basis< D >::Star::beginId, Pscf::Basis< D >::Star::cancel, Pscf::Basis< D >::Wave::coeff, Pscf::Pspc::RFieldDft< D >::dftDimensions(), Pscf::Basis< D >::Star::endId, Util::Log::file(), Pscf::Basis< D >::Wave::implicit, Pscf::Basis< D >::Wave::indicesDft, Pscf::Basis< D >::Star::invertFlag, Pscf::Mesh< D >::rank(), Pscf::Basis< D >::Wave::starId, UTIL_CHECK, and UTIL_THROW.

◆ convertKGridToBasis() [2/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::convertKGridToBasis	(	DArray< RFieldDft< D > > const &	in,
		DArray< DArray< double > > &	out,
		bool	checkSymmetry = `true`,
		double	epsilon = `1.0e-8`
	)		const

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

The in and out parameters are each an array of fields, in which element i is the field associated with monomer type i.

If the checkSymmetry parameter is true, this function checks if the input fields all satisfies the space group symmetry to within a tolerance given by the parameter epsilon, and prints a warning to Log::file() if one or more fields do not.

Parameters

in	fields defined as discrete Fourier transforms (k-grid)
out	components of fields in symmetry adapted basis
checkSymmetry	flag indicate whether to check symmetry
epsilon	error tolerance for symmetry test (if any)

Definition at line 1370 of file pspc/field/FieldIo.tpp.

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

◆ convertBasisToRGrid() [1/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::convertBasisToRGrid	(	DArray< double > const &	in,
		RField< D > &	out
	)		const

Convert a field from symmetrized basis to spatial grid (r-grid).

Parameters

in	field in symmetry adapted basis form
out	field defined on real-space grid

Definition at line 1403 of file pspc/field/FieldIo.tpp.

◆ convertBasisToRGrid() [2/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::convertBasisToRGrid	(	DArray< DArray< double > > const &	in,
		DArray< RField< D > > &	out
	)		const

Convert fields from symmetrized basis to spatial grid (r-grid).

Parameters

in	fields in symmetry adapted basis form
out	fields defined on real-space grid

Definition at line 1413 of file pspc/field/FieldIo.tpp.

References UTIL_ASSERT.

◆ convertRGridToBasis() [1/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::convertRGridToBasis	(	RField< D > const &	in,
		DArray< double > &	out,
		bool	checkSymmetry = `true`,
		double	epsilon = `1.0e-8`
	)		const

Convert a field from spatial grid (r-grid) to symmetrized basis.

Parameters

in	field defined on real-space grid
out	field in symmetry adapted basis form
checkSymmetry	boolean indicating whether to check that the symmetry of the input field matches the space group symmetry. If input does not have correct symmetry, prints warning to Log::file()
epsilon	if checkSymmetry = true, epsilon is the error threshold used when comparing the k-grid and symmetry-adapted formats to determine whether field has the declared space group symmetry

Definition at line 1428 of file pspc/field/FieldIo.tpp.

◆ convertRGridToBasis() [2/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::convertRGridToBasis	(	DArray< RField< D > > const &	in,
		DArray< DArray< double > > &	out,
		bool	checkSymmetry = `true`,
		double	epsilon = `1.0e-8`
	)		const

Convert fields from spatial grid (r-grid) to symmetrized basis.

Parameters

in	fields defined on real-space grid
out	fields in symmetry adapted basis form
checkSymmetry	boolean indicating whether to check that the symmetry of the input field matches the space group symmetry. If input does not have correct symmetry, prints warning to Log::file()
epsilon	if checkSymmetry = true, epsilon is the error threshold used when comparing the k-grid and symmetry-adapted formats to determine whether field has the declared space group symmetry

Definition at line 1440 of file pspc/field/FieldIo.tpp.

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

◆ convertKGridToRGrid() [1/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::convertKGridToRGrid	(	DArray< RFieldDft< D > > &	in,
		DArray< RField< D > > &	out
	)		const

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

This function simply calls the inverse FFT for an array of fields. The inverse FFT provided by the underlying FFTW library overwrites its input, which is why argument "in" not a const reference.

Parameters

in	fields in discrete Fourier format (k-grid)
out	fields defined on real-space grid (r-grid)

Definition at line 1480 of file pspc/field/FieldIo.tpp.

References UTIL_ASSERT.

◆ convertKGridToRGrid() [2/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::convertKGridToRGrid	(	RFieldDft< D > &	in,
		RField< D > &	out
	)		const

Convert a field from k-grid (DFT) to real space (r-grid) format.

This function simply calls the inverse FFT for a single field. The inverse FFT provided by the underlying FFTW library overwrites its input, which is why argument "in" not a const reference.

Parameters

in	field in discrete Fourier format (k-grid)
out	field defined on real-space grid (r-grid)

Definition at line 1495 of file pspc/field/FieldIo.tpp.

◆ convertRGridToKGrid() [1/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::convertRGridToKGrid	(	DArray< RField< D > > const &	in,
		DArray< RFieldDft< D > > &	out
	)		const

Convert fields from spatial grid (r-grid) to k-grid format.

Parameters

in	fields defined on real-space grid (r-grid)
out	fields in discrete Fourier format (k-grid)

Definition at line 1505 of file pspc/field/FieldIo.tpp.

References UTIL_ASSERT.

◆ convertRGridToKGrid() [2/2]

template<int D>

void Pscf::Pspc::FieldIo< D >::convertRGridToKGrid	(	RField< D > const &	in,
		RFieldDft< D > &	out
	)		const

Convert a field from spatial grid (r-grid) to k-grid format.

Parameters

in	field defined on real-space grid (r-grid)
out	field in discrete Fourier format (k-grid)

Definition at line 1520 of file pspc/field/FieldIo.tpp.

◆ hasSymmetry() [1/2]

template<int D>

bool Pscf::Pspc::FieldIo< D >::hasSymmetry	(	RField< D > const &	in,
		double	epsilon = `1.0e-8`,
		bool	verbose = `true`
	)		const

Check if an r-grid field has the declared space group symmetry.

Parameters

in	field in real space grid (r-grid) format
epsilon	error threshold used when comparing the k-grid and symmetry-adapted formats to determine whether field has the declared space group symmetry.
verbose	if field does not have symmetry and verbose = true, function will write error values to Log::file().

Returns: true if the field is symmetric, false otherwise

Definition at line 1532 of file pspc/field/FieldIo.tpp.

◆ hasSymmetry() [2/2]

template<int D>

bool Pscf::Pspc::FieldIo< D >::hasSymmetry	(	RFieldDft< D > const &	in,
		double	epsilon = `1.0e-8`,
		bool	verbose = `true`
	)		const

Check if a k-grid field has declared space group symmetry.

Parameters

in	field in real space grid (r-grid) format
epsilon	error threshold used when comparing the k-grid and symmetry-adapted formats to determine whether field has the declared space group symmetry.
verbose	if field does not have symmetry and verbose = true, function will write error values to Log::file().

Returns: true if the field is symmetric, false otherwise

Definition at line 1546 of file pspc/field/FieldIo.tpp.

References Pscf::Basis< D >::Star::beginId, Pscf::Basis< D >::Star::cancel, Pscf::Basis< D >::Wave::coeff, Pscf::Pspc::RFieldDft< D >::dftDimensions(), Pscf::Basis< D >::Star::endId, Util::Log::file(), Pscf::Basis< D >::Wave::implicit, Pscf::Basis< D >::Wave::indicesDft, Pscf::Mesh< D >::rank(), and UTIL_CHECK.

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

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ FieldIo()

◆ ~FieldIo()

Member Function Documentation

◆ associate()

◆ readFieldBasis() [1/2]

◆ readFieldBasis() [2/2]

◆ writeFieldBasis() [1/2]

◆ writeFieldBasis() [2/2]

◆ readFieldsBasis() [1/2]

◆ readFieldsBasis() [2/2]

◆ writeFieldsBasis() [1/2]

◆ writeFieldsBasis() [2/2]

◆ readFieldRGrid() [1/2]

◆ readFieldRGrid() [2/2]

◆ readFieldsRGrid() [1/2]

◆ readFieldsRGrid() [2/2]

◆ writeFieldRGrid() [1/2]

◆ writeFieldRGrid() [2/2]

◆ writeFieldsRGrid() [1/2]

◆ writeFieldsRGrid() [2/2]

◆ readFieldsKGrid() [1/2]

◆ readFieldsKGrid() [2/2]

◆ writeFieldsKGrid() [1/2]

◆ writeFieldsKGrid() [2/2]

◆ readFieldHeader()

◆ writeFieldHeader()

◆ convertBasisToKGrid() [1/2]

◆ convertBasisToKGrid() [2/2]

◆ convertKGridToBasis() [1/2]

◆ convertKGridToBasis() [2/2]

◆ convertBasisToRGrid() [1/2]

◆ convertBasisToRGrid() [2/2]

◆ convertRGridToBasis() [1/2]

◆ convertRGridToBasis() [2/2]

◆ convertKGridToRGrid() [1/2]

◆ convertKGridToRGrid() [2/2]

◆ convertRGridToKGrid() [1/2]

◆ convertRGridToKGrid() [2/2]

◆ hasSymmetry() [1/2]

◆ hasSymmetry() [2/2]