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

#include <FieldIo.h>

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

Public Types
typedef FieldIoReal< D, RField< D >, RFieldDft< D >, FFT< D > >	Base
	Alias for base class.

Public Member Functions
bool	readFieldsRGrid (std::istream &in, DArray< RField< D > > &fields, UnitCell< D > &unitCell) const override
	Read array of RField objects (r-grid fields) from a stream.
void	readFieldsRGridData (std::istream &in, DArray< RField< D > > &fields, int nMonomer) const override
	Read data for an array of r-grid fields, with no header section.
bool	readFieldRGrid (std::istream &in, RField< D > &field, UnitCell< D > &unitCell) const override
	Read a single RField (field on an r-space grid) from a stream.
void	writeFieldsRGrid (std::ostream &out, DArray< RField< D > > const &fields, UnitCell< D > const &unitCell, bool writeHeader=true, bool isSymmetric=true, bool writeMeshSize=true) const override
	Write array of RField objects (fields on r-space grid) to a stream.
void	writeFieldRGrid (std::ostream &out, RField< D > const &field, UnitCell< D > const &unitCell, bool writeHeader=true, bool isSymmetric=true) const override
	Write a single RField (field on an r-space grid) to a stream.
void	readFieldsKGrid (std::istream &in, DArray< RFieldDft< D > > &fields, UnitCell< D > &unitCell) const override
	Read array of RFieldDft objects (k-space fields) from a stream.
void	writeFieldsKGrid (std::ostream &out, DArray< RFieldDft< D > > const &fields, UnitCell< D > const &unitCell, bool isSymmetric=true) const override
	Write array of RFieldDft objects (k-space fields) to file.
void	convertBasisToKGrid (DArray< double > const &components, RFieldDft< D > &dft) const override
	Convert a field from symmetrized basis to Fourier grid (k-grid).
void	convertKGridToBasis (RFieldDft< D > const &in, DArray< double > &out, bool checkSymmetry=true, double epsilon=1.0e-8) const override
	Convert a field from Fourier (k-grid) to symmetrized basis form.
bool	hasSymmetry (RFieldDft< D > const &in, double epsilon=1.0e-8, bool verbose=true) const override
	Check if a k-grid field has the declared space group symmetry.
void	compareFieldsRGrid (DArray< RField< D > > const &field1, DArray< RField< D > > const &field2) const override
	Compare two fields in r-grid format, output a report.
void	scaleFieldRGrid (RField< D > &field, double factor) const override
	Rescale a single r-grid field by a scalar factor.
void	expandRGridDimension (std::ostream &out, DArray< RField< D > > const &fields, UnitCell< D > const &unitCell, int d, DArray< int > const &newGridDimensions) const override
	Expand spatial dimension of an array of r-grid fields.
void	replicateUnitCell (std::ostream &out, DArray< RField< D > > const &fields, UnitCell< D > const &unitCell, IntVec< D > const &replicas) const override
	Write r-grid fields in a replicated unit cell to std::ostream.
void	associate (Mesh< D > const &mesh, FFT const &fft, typename UnitCell< D >::LatticeSystem const &lattice, bool const &hasGroup, std::string const &groupName, SpaceGroup< D > const &group, Basis< D > &basis)
	Create associations with other members of the parent Domain.
void	setFileMaster (FileMaster const &fileMaster)
	Create an association with a FileMaster.
void	readFieldsBasis (std::istream &in, DArray< DArray< double > > &fields, UnitCell< D > &unitCell) const
	Read an array of fields in basis format from an input stream.
void	readFieldsBasis (std::string filename, DArray< DArray< double > > &fields, UnitCell< D > &unitCell) const
	Read an array of fields in basis format from a named file.
void	readFieldBasis (std::istream &in, DArray< double > &field, UnitCell< D > &unitCell) const
	Read a single field in basis format from an input stream.
void	readFieldBasis (std::string filename, DArray< double > &field, UnitCell< D > &unitCell) const
	Read a single field in basis format from a named file.
void	writeFieldBasis (std::ostream &out, DArray< double > const &field, UnitCell< D > const &unitCell) const
	Write a single field in basis format to an output stream.
void	writeFieldBasis (std::string filename, DArray< double > const &field, UnitCell< D > const &unitCell) const
	Write single field in basis format to a named file.
void	writeFieldsBasis (std::ostream &out, DArray< DArray< double > > const &fields, UnitCell< D > const &unitCell) const
	Write an array of fields in basis format to an output stream.
void	writeFieldsBasis (std::string filename, DArray< DArray< double > > const &fields, UnitCell< D > const &unitCell) const
	Write an array of fields in basis format to a named file.
bool	readFieldsRGrid (std::string filename, DArray< RField< D > > &fields, UnitCell< D > &unitCell) const
	Read an array of r-grid fields from a named file.
bool	readFieldRGrid (std::string filename, RField< D > &field, UnitCell< D > &unitCell) const
	Read a single r-grid field from a named file.
void	writeFieldsRGrid (std::string filename, DArray< RField< D > > const &fields, UnitCell< D > const &unitCell, bool isSymmetric=true) const
	Write an array of r-grid fields to a named file.
void	writeFieldRGrid (std::string filename, RField< D > const &field, UnitCell< D > const &unitCell, bool isSymmetric=true) const
	Write a single r-grid field to a named file.
void	readFieldsKGrid (std::string filename, DArray< RFieldDft< D > > &fields, UnitCell< D > &unitCell) const
	Read an array of k-grid fields from a named file.
void	writeFieldsKGrid (std::string filename, DArray< RFieldDft< D > > const &fields, UnitCell< D > const &unitCell, bool isSymmetric=true) const
	Write an array of k-grid fields to a named file.
void	convertBasisToKGrid (DArray< DArray< double > > const &in, DArray< RFieldDft< D > > &out) const
	Convert an array of fields from basis to Fourier (k-grid) form.
void	convertBasisToKGrid (std::string const &inFileName, std::string const &outFileName) const
	Convert a field file from basis to Fourier (k-grid) format.
void	convertKGridToBasis (DArray< RFieldDft< D > > const &in, DArray< DArray< double > > &out, bool checkSymmetry=true, double epsilon=1.0e-8) const
	Convert an array of fields from Fourier (k-grid) to basis form.
void	convertKGridToBasis (std::string const &inFileName, std::string const &outFileName) const
	Convert a field file from Fourier (k-grid) to basis format.
void	convertBasisToRGrid (DArray< double > const &in, RField< D > &out) const
	Convert a single field from basis to r-grid format.
void	convertBasisToRGrid (DArray< DArray< double > > const &in, DArray< RField< D > > &out) const
	Convert an array of fields from basis to r-grid format.
void	convertBasisToRGrid (std::string const &inFileName, std::string const &outFileName) const
	Convert a field file from basis format to r-grid format.
void	convertRGridToBasis (RField< D > const &in, DArray< double > &out, bool checkSymmetry=true, double epsilon=1.0e-8) const
	Convert a single field from r-grid to basis form.
void	convertRGridToBasis (DArray< RField< D > > const &in, DArray< DArray< double > > &out, bool checkSymmetry=true, double epsilon=1.0e-8) const
	Convert an array of fields from r-grid to basis format.
void	convertRGridToBasis (std::string const &inFileName, std::string const &outFileName) const
	Convert a field file from r-grid to basis format.
void	convertKGridToRGrid (DArray< RFieldDft< D > > const &in, DArray< RField< D > > &out) const
	Convert an array of field from k-grid to r-grid format.
void	convertKGridToRGrid (RFieldDft< D > const &in, RField< D > &out) const
	Convert a single field from k-grid to r-grid format.
void	convertKGridToRGrid (std::string const &inFileName, std::string const &outFileName) const
	Convert a field file from Fourier (k-grid) to r-grid format.
void	convertRGridToKGrid (DArray< RField< D > > const &in, DArray< RFieldDft< D > > &out) const
	Convert an array of fields from r-grid to k-grid (Fourier) format.
void	convertRGridToKGrid (RField< D > const &in, RFieldDft< D > &out) const
	Convert a field from r-grid to k-grid (Fourier) format.
void	convertRGridToKGrid (std::string const &inFileName, std::string const &outFileName) const
	Convert a field file from r-grid to Fourier (k-grid) format.
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.
bool	hasSymmetry (std::string const &inFileName, double epsilon=1.0E-8) const
	Check if an r-grid field file has declared space group symmetry.
void	compareFieldsBasis (DArray< DArray< double > > const &field1, DArray< DArray< double > > const &field2) const
	Compare array of fields in basis form, write a report to Log file.
void	compareFieldsBasis (std::string const &filename1, std::string const &filename2) const
	Compare two r-grid field files, write a report to Log file.
void	compareFieldsRGrid (std::string const &filename1, std::string const &filename2) const
	Compare two r-grid field files, write a report to Log file.
void	scaleFieldsBasis (DArray< DArray< double > > &fields, double factor) const
	Multiply an array of fields in basis format by a real scalar.
void	scaleFieldsBasis (std::string const &inFileName, std::string const &outFileName, double factor) const
	Multiply all fields in a basis field file by a scalar.
void	scaleFieldsRGrid (DArray< RField< D > > &fields, double factor) const
	Scale an array of r-grid fields by a scalar.
void	scaleFieldsRGrid (std::string const &inFileName, const std::string &outFileName, double factor) const
	Multiply all fields in an r-grid field file by a scalar.
void	estimateWBasis (DMatrix< double > const &chi, DArray< DArray< double > > &fields) const
	Convert c fields to estimated w fields, in basis format.
void	estimateWBasis (std::string const &inFileName, std::string const &outFileName, DMatrix< double > const &chi) const
	Convert a file of c fields to estimated w fields, in basis format.
void	replicateUnitCell (std::string filename, DArray< RField< D > > const &fields, UnitCell< D > const &unitCell, IntVec< D > const &replicas) const
	Write r-grid fields in a replicated unit cell to a named file.
void	replicateUnitCell (std::string const &inFileName, std::string const &outFileName, IntVec< D > const &replicas) const
	Write replicated fields read from one file to another.
void	expandRGridDimension (std::string filename, DArray< RField< D > > const &fields, UnitCell< D > const &unitCell, int d, DArray< int > newGridDimensions) const
	Increase D for an array of r-grid fields, write to a named file.
void	expandRGridDimension (std::string const &inFileName, std::string const &outFileName, int d, DArray< int > newGridDimensions) const
	Increase D for an r-grid field file.
void	readFieldHeader (std::istream &in, int &nMonomer, UnitCell< D > &unitCell, bool &isSymmetric) const
	Reader header of field file (fortran PSCF format)
void	writeFieldHeader (std::ostream &out, int nMonomer, UnitCell< D > const &unitCell, bool isSymmetric=true) const
	Write header for field file (fortran pscf format).
Mesh< D > const &	mesh () const
	Get spatial discretization mesh by const reference.
Basis< D > const &	basis () const
	Get the associated Basis by const reference.
FileMaster const &	fileMaster () const
	Get associated FileMaster by const reference.
Public Member Functions inherited from Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT< D > >
	FieldIoReal ()
	Constructor.
virtual	~FieldIoReal ()
	Destructor.
void	associate (Mesh< D > const &mesh, FFT const &fft, typename UnitCell< D >::LatticeSystem const &lattice, bool const &hasGroup, std::string const &groupName, SpaceGroup< D > const &group, Basis< D > &basis)
	Create associations with other members of the parent Domain.
void	setFileMaster (FileMaster const &fileMaster)
	Create an association with a FileMaster.
void	setNMonomer (int nMonomer)
	Set the number of monomer types.
void	readFieldsBasis (std::istream &in, DArray< DArray< double > > &fields, UnitCell< D > &unitCell) const
	Read an array of fields in basis format from an input stream.
void	readFieldsBasis (std::string filename, DArray< DArray< double > > &fields, UnitCell< D > &unitCell) const
	Read an array of fields in basis format from a named file.
void	readFieldBasis (std::istream &in, DArray< double > &field, UnitCell< D > &unitCell) const
	Read a single field in basis format from an input stream.
void	readFieldBasis (std::string filename, DArray< double > &field, UnitCell< D > &unitCell) const
	Read a single field in basis format from a named file.
void	writeFieldsBasis (std::ostream &out, DArray< DArray< double > > const &fields, UnitCell< D > const &unitCell) const
	Write an array of fields in basis format to an output stream.
void	writeFieldsBasis (std::string filename, DArray< DArray< double > > const &fields, UnitCell< D > const &unitCell) const
	Write an array of fields in basis format to a named file.
void	writeFieldBasis (std::ostream &out, DArray< double > const &field, UnitCell< D > const &unitCell) const
	Write a single field in basis format to an output stream.
void	writeFieldBasis (std::string filename, DArray< double > const &field, UnitCell< D > const &unitCell) const
	Write single field in basis format to a named file.
bool	readFieldsRGrid (std::string filename, DArray< RField< D > > &fields, UnitCell< D > &unitCell) const
	Read an array of r-grid fields from a named file.
bool	readFieldRGrid (std::string filename, RField< D > &field, UnitCell< D > &unitCell) const
	Read a single r-grid field from a named file.
void	writeFieldsRGrid (std::string filename, DArray< RField< D > > const &fields, UnitCell< D > const &unitCell, bool isSymmetric=true) const
	Write an array of r-grid fields to a named file.
void	writeFieldRGrid (std::string filename, RField< D > const &field, UnitCell< D > const &unitCell, bool isSymmetric=true) const
	Write a single r-grid field to a named file.
void	readFieldsKGrid (std::string filename, DArray< RFieldDft< D > > &fields, UnitCell< D > &unitCell) const
	Read an array of k-grid fields from a named file.
void	writeFieldsKGrid (std::string filename, DArray< RFieldDft< D > > const &fields, UnitCell< D > const &unitCell, bool isSymmetric=true) const
	Write an array of k-grid fields to a named file.
void	convertBasisToKGrid (DArray< DArray< double > > const &in, DArray< RFieldDft< D > > &out) const
	Convert an array of fields from basis to Fourier (k-grid) form.
void	convertKGridToBasis (DArray< RFieldDft< D > > const &in, DArray< DArray< double > > &out, bool checkSymmetry=true, double epsilon=1.0e-8) const
	Convert an array of fields from Fourier (k-grid) to basis form.
void	convertBasisToRGrid (DArray< double > const &in, RField< D > &out) const
	Convert a single field from basis to r-grid format.
void	convertBasisToRGrid (DArray< DArray< double > > const &in, DArray< RField< D > > &out) const
	Convert an array of fields from basis to r-grid format.
void	convertRGridToBasis (RField< D > const &in, DArray< double > &out, bool checkSymmetry=true, double epsilon=1.0e-8) const
	Convert a single field from r-grid to basis form.
void	convertRGridToBasis (DArray< RField< D > > const &in, DArray< DArray< double > > &out, bool checkSymmetry=true, double epsilon=1.0e-8) const
	Convert an array of fields from r-grid to basis format.
void	convertKGridToRGrid (DArray< RFieldDft< D > > const &in, DArray< RField< D > > &out) const
	Convert an array of field from k-grid to r-grid format.
void	convertKGridToRGrid (RFieldDft< D > const &in, RField< D > &out) const
	Convert a single field from k-grid to r-grid format.
void	convertRGridToKGrid (DArray< RField< D > > const &in, DArray< RFieldDft< D > > &out) const
	Convert an array of fields from r-grid to k-grid (Fourier) format.
void	convertRGridToKGrid (RField< D > const &in, RFieldDft< D > &out) const
	Convert a field from r-grid to k-grid (Fourier) format.
void	convertBasisToRGrid (std::string const &inFileName, std::string const &outFileName) const
	Convert a field file from basis format to r-grid format.
void	convertRGridToBasis (std::string const &inFileName, std::string const &outFileName) const
	Convert a field file from r-grid to basis format.
void	convertKGridToRGrid (std::string const &inFileName, std::string const &outFileName) const
	Convert a field file from Fourier (k-grid) to r-grid format.
void	convertRGridToKGrid (std::string const &inFileName, std::string const &outFileName) const
	Convert a field file from r-grid to Fourier (k-grid) format.
void	convertKGridToBasis (std::string const &inFileName, std::string const &outFileName) const
	Convert a field file from Fourier (k-grid) to basis format.
void	convertBasisToKGrid (std::string const &inFileName, std::string const &outFileName) const
	Convert a field file from basis to Fourier (k-grid) format.
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.
bool	hasSymmetry (std::string const &inFileName, double epsilon=1.0E-8) const
	Check if an r-grid field file has declared space group symmetry.
void	compareFieldsBasis (DArray< DArray< double > > const &field1, DArray< DArray< double > > const &field2) const
	Compare array of fields in basis form, write a report to Log file.
void	compareFieldsBasis (std::string const &filename1, std::string const &filename2) const
	Compare two r-grid field files, write a report to Log file.
void	compareFieldsRGrid (std::string const &filename1, std::string const &filename2) const
	Compare two r-grid field files, write a report to Log file.
virtual void	scaleFieldBasis (DArray< double > &field, double factor) const
	Multiply a single field in basis form by a real scalar.
void	scaleFieldsBasis (DArray< DArray< double > > &fields, double factor) const
	Multiply an array of fields in basis format by a real scalar.
void	scaleFieldsBasis (std::string const &inFileName, std::string const &outFileName, double factor) const
	Multiply all fields in a basis field file by a scalar.
void	scaleFieldsRGrid (DArray< RField< D > > &fields, double factor) const
	Scale an array of r-grid fields by a scalar.
void	scaleFieldsRGrid (std::string const &inFileName, const std::string &outFileName, double factor) const
	Multiply all fields in an r-grid field file by a scalar.
void	estimateWBasis (DMatrix< double > const &chi, DArray< DArray< double > > &fields) const
	Convert c fields to estimated w fields, in basis format.
void	estimateWBasis (std::string const &inFileName, std::string const &outFileName, DMatrix< double > const &chi) const
	Convert a file of c fields to estimated w fields, in basis format.
void	replicateUnitCell (std::string filename, DArray< RField< D > > const &fields, UnitCell< D > const &unitCell, IntVec< D > const &replicas) const
	Write r-grid fields in a replicated unit cell to a named file.
void	replicateUnitCell (std::string const &inFileName, std::string const &outFileName, IntVec< D > const &replicas) const
	Write replicated fields read from one file to another.
void	expandRGridDimension (std::string filename, DArray< RField< D > > const &fields, UnitCell< D > const &unitCell, int d, DArray< int > newGridDimensions) const
	Increase D for an array of r-grid fields, write to a named file.
void	expandRGridDimension (std::string const &inFileName, std::string const &outFileName, int d, DArray< int > newGridDimensions) const
	Increase D for an r-grid field file.
void	readFieldHeader (std::istream &in, int &nMonomer, UnitCell< D > &unitCell, bool &isSymmetric) const
	Reader header of field file (fortran PSCF format)
void	writeFieldHeader (std::ostream &out, int nMonomer, UnitCell< D > const &unitCell, bool isSymmetric=true) const
	Write header for field file (fortran pscf format).
Mesh< D > const &	mesh () const
	Get spatial discretization mesh by const reference.
Basis< D > const &	basis () const
	Get the associated Basis by const reference.
FileMaster const &	fileMaster () const
	Get associated FileMaster by const reference.

Protected Member Functions
UnitCell< D >::LatticeSystem const &	lattice () const
	Get the lattice type enum value by const reference.
bool	hasGroup () const
	Has a space group been declared externally ?
std::string const &	groupName () const
	Get an associated group name string by const reference.
SpaceGroup< D > const &	group () const
	Get an associated SpaceGroup<D> by const reference.
FFT const &	fft () const
	Get FFT object by const reference.
Protected Member Functions inherited from Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT< D > >
UnitCell< D >::LatticeSystem const &	lattice () const
	Get the lattice type enum value by const reference.
bool	hasGroup () const
	Has a space group been declared externally ?
std::string const &	groupName () const
	Get an associated group name string by const reference.
SpaceGroup< D > const &	group () const
	Get an associated SpaceGroup<D> by const reference.
FFT const &	fft () const
	Get FFT object by const reference.
void	checkAllocateRGrid () const
	Check if r-grid workspace is allocated, allocate if necessary.
void	checkAllocateKGrid () const
	Check if k-grid workspace is allocated, allocate if necessary.
void	checkAllocateBasis (std::string const &inFileName) const
	Check if basis workspace is allocated, allocate if necessary.

Detailed Description

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

File input/output operations and format conversions for fields.

Please refer to the documentation of the base class template Prdc::FieldIoReal for complete API documentation. The public interface of this class is identical to that of the base class.

This class template is derived from a partial specialization of the template Prdc::FieldIoReal<D, RFT, KFT, FFT> using classes RFT = RField<D>, KFT = RFieldDft<D>, and FFT = FFT<D> that are all defined in the Prdc::Cpu subspace, and that all use conventional CPU hardware. An analogous class template named Rpg::FieldIo that is defined in the Pscf::Rpg namespace instead uses a GPU.

The member functions defined in this class are all implementations of pure virtual functions declared in the base class, Prdc::FieldIoReal. These are all functions for which different implementations are required for the CPU and GPU variants, usually because the GPU implementation requires data transfer between host and device.

Definition at line 57 of file rpc/field/FieldIo.h.

Member Typedef Documentation

◆ Base

template<int D>

typedef FieldIoReal<D, RField<D>, RFieldDft<D>, FFT<D> > Pscf::Rpc::FieldIo< D >::Base

Alias for base class.

Definition at line 276 of file rpc/field/FieldIo.h.

Member Function Documentation

◆ readFieldsRGrid() [1/2]

template<int D>

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

overridevirtual

Read array of RField objects (r-grid fields) from a stream.

See documentation of analogous function in Prdc::FieldIoReal.

Parameters

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

Returns: true iff the header contains a space group (isSymmetric)

Implements Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT< D > >.

Definition at line 37 of file rpc/field/FieldIo.tpp.

References Pscf::Prdc::checkAllocateFields(), mesh(), Pscf::Prdc::readFieldHeader(), Pscf::Prdc::readMeshDimensions(), and Pscf::Prdc::readRGridData().

Referenced by Pscf::Rpc::EinsteinCrystalPerturbation< D >::setup().

◆ readFieldsRGridData()

template<int D>

void Pscf::Rpc::FieldIo< D >::readFieldsRGridData	(	std::istream &	in,
		DArray< RField< D > > &	fields,
		int	nMonomer ) const

overridevirtual

Read data for an array of r-grid fields, with no header section.

See documentation of analogous function in Prdc::FieldIoReal.

Parameters

in	input file stream
fields	array of RField fields (r-space grid)
nMonomer	number of monomer types

Implements Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT< D > >.

Definition at line 61 of file rpc/field/FieldIo.tpp.

References Pscf::Prdc::checkAllocateFields(), mesh(), and Pscf::Prdc::readRGridData().

Referenced by Pscf::Rpc::RGridTrajectoryReader< D >::readFrame().

◆ readFieldRGrid() [1/2]

template<int D>

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

overridevirtual

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

See documentation of analogous function in Prdc::FieldIoReal.

Parameters

in	input file stream
field	fields defined on r-space grid
unitCell	associated crystallographic unit cell

Returns: true iff the header contains a space group (isSymmetric)

Implements Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT< D > >.

Definition at line 76 of file rpc/field/FieldIo.tpp.

References Pscf::Prdc::checkAllocateField(), mesh(), Pscf::Prdc::readFieldHeader(), Pscf::Prdc::readMeshDimensions(), Pscf::Prdc::readRGridData(), and UTIL_CHECK.

◆ writeFieldsRGrid() [1/2]

template<int D>

void Pscf::Rpc::FieldIo< D >::writeFieldsRGrid	(	std::ostream &	out,
		DArray< RField< D > > const &	fields,
		UnitCell< D > const &	unitCell,
		bool	writeHeader = true,
		bool	isSymmetric = true,
		bool	writeMeshSize = true ) const

overridevirtual

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

See documentation of analogous function in Prdc::FieldIoReal.

Parameters

out	output stream (i.e., output file)
fields	array of RField objects (fields on r-space grid)
unitCell	associated crystallographic unit cell
writeHeader	flag to write file header if true
isSymmetric	Do fields have a space group symmetry ?
writeMeshSize	Should mesh size be written in header?

Implements Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT< D > >.

Definition at line 101 of file rpc/field/FieldIo.tpp.

References Pscf::Prdc::inspectFields(), Pscf::Prdc::writeFieldHeader(), Pscf::Prdc::writeMeshDimensions(), and Pscf::Prdc::writeRGridData().

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

◆ writeFieldRGrid() [1/2]

template<int D>

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

overridevirtual

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

See documentation of analogous function in Prdc::FieldIoReal.

Parameters

out	output stream
field	field defined on r-space grid
unitCell	associated crystallographic unit cell
writeHeader	Should a file header be written?
isSymmetric	Does the field have a space group symmetry?

Implements Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT< D > >.

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

References Pscf::Prdc::Cpu::RField< D >::meshDimensions(), Pscf::Prdc::writeFieldHeader(), Pscf::Prdc::writeMeshDimensions(), and Pscf::Prdc::writeRGridData().

◆ readFieldsKGrid() [1/2]

template<int D>

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

overridevirtual

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

See documentation of analogous function in Prdc::FieldIoReal.

Parameters

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

Implements Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT< D > >.

Definition at line 157 of file rpc/field/FieldIo.tpp.

References Pscf::Prdc::checkAllocateFields(), mesh(), Pscf::Prdc::readFieldHeader(), Pscf::Prdc::readKGridData(), and Pscf::Prdc::readMeshDimensions().

◆ writeFieldsKGrid() [1/2]

template<int D>

void Pscf::Rpc::FieldIo< D >::writeFieldsKGrid	(	std::ostream &	out,
		DArray< RFieldDft< D > > const &	fields,
		UnitCell< D > const &	unitCell,
		bool	isSymmetric = true ) const

overridevirtual

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

See documentation of analogous function in Prdc::FieldIoReal.

Parameters

out	output stream (i.e., output file)
fields	array of RFieldDft fields
unitCell	associated crystallographic unit cell
isSymmetric	Does this field have space group symmetry?

Implements Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT< D > >.

Definition at line 181 of file rpc/field/FieldIo.tpp.

References Pscf::Prdc::inspectFields(), Pscf::Prdc::writeFieldHeader(), Pscf::Prdc::writeKGridData(), and Pscf::Prdc::writeMeshDimensions().

◆ convertBasisToKGrid() [1/3]

template<int D>

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

overridevirtual

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

See documentation of analogous function in Prdc::FieldIoReal.

Parameters

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

Implements Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT< D > >.

Definition at line 207 of file rpc/field/FieldIo.tpp.

References basis(), Pscf::Prdc::convertBasisToKGrid(), and Pscf::Prdc::Cpu::RFieldDft< D >::dftDimensions().

Referenced by Pscf::Rpc::System< D >::readCommands().

◆ convertKGridToBasis() [1/3]

template<int D>

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

overridevirtual

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

See documentation of analogous function in Prdc::FieldIoReal.

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)

Implements Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT< D > >.

Definition at line 220 of file rpc/field/FieldIo.tpp.

References basis(), Pscf::Prdc::convertKGridToBasis(), and Pscf::Prdc::Cpu::RFieldDft< D >::dftDimensions().

Referenced by Pscf::Rpc::System< D >::readCommands().

◆ hasSymmetry() [1/3]

template<int D>

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

overridevirtual

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

See documentation of analogous function in Prdc::FieldIoReal.

Parameters

in	field in real space grid (r-grid) format
epsilon	error threshold used to test for symmetry
verbose	if true, write error to Log::file()

Returns: true iff the field is symmetric to within tolerance

Implements Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT< D > >.

Definition at line 236 of file rpc/field/FieldIo.tpp.

References basis(), Pscf::Prdc::Cpu::RFieldDft< D >::dftDimensions(), and Pscf::Prdc::hasSymmetry().

Referenced by Pscf::Rpc::System< D >::readCommands().

◆ compareFieldsRGrid() [1/2]

template<int D>

void Pscf::Rpc::FieldIo< D >::compareFieldsRGrid	(	DArray< RField< D > > const &	field1,
		DArray< RField< D > > const &	field2 ) const

overridevirtual

Compare two fields in r-grid format, output a report.

Outputs maximum and root-mean-squared differences to the standard Log file.

Parameters

field1	first array of fields (r-grid format)
field2	second array of fields (r-grid format)

Implements Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT< D > >.

Definition at line 251 of file rpc/field/FieldIo.tpp.

References Pscf::FieldComparison< FT >::compare(), Util::Log::file(), Pscf::FieldComparison< FT >::maxDiff(), and Pscf::FieldComparison< FT >::rmsDiff().

Referenced by Pscf::Rpc::System< D >::readCommands().

◆ scaleFieldRGrid()

template<int D>

void Pscf::Rpc::FieldIo< D >::scaleFieldRGrid	(	RField< D > &	field,
		double	factor ) const

overridevirtual

Rescale a single r-grid field by a scalar factor.

See documentation of analogous function in Prdc::FieldIoReal. Multiplication is done in-place, and so modifies the input.

Parameters

field	real space (r-grid) field (in-out)
factor	real scalar by which to multiply all elements

Implements Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT< D > >.

Definition at line 270 of file rpc/field/FieldIo.tpp.

References Util::Array< Data >::capacity().

◆ expandRGridDimension() [1/3]

template<int D>

void Pscf::Rpc::FieldIo< D >::expandRGridDimension	(	std::ostream &	out,
		DArray< RField< D > > const &	fields,
		UnitCell< D > const &	unitCell,
		int	d,
		DArray< int > const &	newGridDimensions ) const

overridevirtual

Expand spatial dimension of an array of r-grid fields.

See documentation of analogous function in Prdc::FieldIoReal.

Parameters

out	output file stream
fields	input array of D-dimensional r-grid fields
unitCell	original D-dimensional unit cell
d	expanded spatial dimension (d > D)
newGridDimensions	number of grid points in added dimensions

Implements Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT< D > >.

Definition at line 306 of file rpc/field/FieldIo.tpp.

References Pscf::Prdc::expandRGridDimension().

Referenced by Pscf::Rpc::System< D >::readCommands().

◆ replicateUnitCell() [1/3]

template<int D>

void Pscf::Rpc::FieldIo< D >::replicateUnitCell	(	std::ostream &	out,
		DArray< RField< D > > const &	fields,
		UnitCell< D > const &	unitCell,
		IntVec< D > const &	replicas ) const

overridevirtual

Write r-grid fields in a replicated unit cell to std::ostream.

See documentation of analogous function in Prdc::FieldIoReal.

Parameters

out	output file stream
fields	array of RField (r-space) fields to be replicated
unitCell	original crystallographic unit cell
replicas	number of unit cell replicas in each direction

Implements Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT< D > >.

Definition at line 284 of file rpc/field/FieldIo.tpp.

References Pscf::Prdc::inspectFields(), and Pscf::Prdc::replicateUnitCell().

Referenced by Pscf::Rpc::System< D >::readCommands().

◆ associate()

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::associate	(	Mesh< D > const &	mesh,
		FFT const &	fft,
		typename UnitCell< D >::LatticeSystem const &	lattice,
		bool const &	hasGroup,
		std::string const &	groupName,
		SpaceGroup< D > const &	group,
		Basis< D > &	basis )

Create associations with other members of the parent Domain.

This function may be called within the constructor of the Domain object, since addresses of other members of the Domain are known at this point.

Parameters

mesh	associated spatial discretization Mesh<D>
fft	associated FFT object for fast transforms
lattice	lattice system type (enumeration value)
hasGroup	true iff a space group has been declared
groupName	space group name string
group	associated SpaceGroup object
basis	associated Basis object

◆ setFileMaster()

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::setFileMaster ( FileMaster const & fileMaster )

Create an association with a FileMaster.

The FileMaster is used to open and close files in all member functions that take file name arguments and that open and close files. This allows prefixes for input and output files (if any) to be automatically prepended to file names.

Parameters

fileMaster associated FileMaster (for file paths)

◆ readFieldsBasis() [1/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::readFieldsBasis	(	std::istream &	in,
		DArray< DArray< double > > &	fields,
		UnitCell< D > &	unitCell ) const

Read an array of fields in basis format from an input stream.

This function reads fields in a symmetry adapted basis format from input stream in. The header of the field file must declare a group name, and this name must agree with that declared in the parameter file. Upon successful return, element fields[i] of the fields container is a DArray<double> containing the components of the field associated with monomer type i, defined as coefficients of symmetry-adapted basis functions defined by the current basis. If a basis has not been constructed before entry, it will be constructed within this function.

On entry, the fields container must either be allocated with a capacity equal to the number of monomer types in the field file, and a capacity for each field equal to the number of basis functions in the basis, or it may be unallocated. If the fields container is not allocated, it will allocated within this function with these dimensions. The number of monomer types does not need to be equal to the value set by the setNMonomer(int) function.

Parameters

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

Referenced by Pscf::Rpc::BasisFieldState< D >::read().

◆ readFieldsBasis() [2/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::readFieldsBasis	(	std::string	filename,
		DArray< DArray< double > > &	fields,
		UnitCell< D > &	unitCell ) const

Read an array of fields in basis format from a named file.

This function opens an input file with the specified filename, reads an array of fields in symmetry-adapted form from that file, and then closes the file. The overloaded readFieldsBasis member function that takes a std::istream& argument is called internally to read the file.

Parameters

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

◆ readFieldBasis() [1/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::readFieldBasis	(	std::istream &	in,
		DArray< double > &	field,
		UnitCell< D > &	unitCell ) const

Read a single field in basis format from an input stream.

This function reads a single field in symmetry adapted basis format from an input stream. Upon successful return, the field array contains the components of a single field, defined as coefficients of symmetry-adapted basis functions. On entry, the field array must either be allocated with a capacity equal to the number of basis functions in the associated basis, or unallocated. If field is unallocated, it will be allocated by this function.

Parameters

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

◆ readFieldBasis() [2/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::readFieldBasis	(	std::string	filename,
		DArray< double > &	field,
		UnitCell< D > &	unitCell ) const

Read a single field in basis format from a named file.

This function opens an input file with the specified filename, reads a single field in symmetry adapted basis format from that file, and and then closes the file. The overloaded member function readFieldBasis that takes an std::istream& argument is called internally to read the file.

Parameters

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

◆ writeFieldBasis() [1/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::writeFieldBasis	(	std::ostream &	out,
		DArray< double > const &	field,
		UnitCell< D > const &	unitCell ) const

Write a single field in basis format to an output stream.

This function writes one field in symmetry adapted basis format. On entry, the field array must be allocated with a capacity equal to the number of basis functions in the basis.

Parameters

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

◆ writeFieldBasis() [2/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::writeFieldBasis	(	std::string	filename,
		DArray< double > const &	field,
		UnitCell< D > const &	unitCell ) const

Write single field in basis format to a named 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. The overloaded writeFieldBasis that takes a std::ostream& argument is called to write the file.

Parameters

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

◆ writeFieldsBasis() [1/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::writeFieldsBasis	(	std::ostream &	out,
		DArray< DArray< double > > const &	fields,
		UnitCell< D > const &	unitCell ) const

Write an array of fields in basis format to an output stream.

This function writes field components in a symmetry adapted basis to an output stream. On entry, the fields array must be allocated, and the capacity of each field must be equal the number of basis functions in the basis.

Parameters

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

Referenced by Pscf::Rpc::BasisFieldState< D >::write().

◆ writeFieldsBasis() [2/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::writeFieldsBasis	(	std::string	filename,
		DArray< DArray< double > > const &	fields,
		UnitCell< D > const &	unitCell ) const

Write an array of fields in basis format to a named 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. The overloaded writeFieldsBasis member function that takes a std::ostream& argument is called to write the file.

Parameters

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

◆ readFieldsRGrid() [2/2]

template<int D>

bool Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::readFieldsRGrid	(	std::string	filename,
		DArray< RField< D > > &	fields,
		UnitCell< D > &	unitCell ) const

Read an array of r-grid fields from a named file.

This function opens an input file with the specified filename, reads fields in real-space grid format from that file, and then closes the file. The overloaded readFieldsRGrid member function that takes a std::istream& argument is called to read the file.

Parameters

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

Returns: true iff header declares a space group

◆ readFieldRGrid() [2/2]

template<int D>

bool Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::readFieldRGrid	(	std::string	filename,
		RField< D > &	field,
		UnitCell< D > &	unitCell ) const

Read a single r-grid field from a named file.

This function opens an input file with the specified filename, reads a field in real-space grid format from that file, and then closes the file. The overloaded readFieldRGrid member function that takes a std::istream& argument is called to read the file.

Parameters

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

Returns: true iff header has a space group (isSymmetric flag)

◆ writeFieldsRGrid() [2/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::writeFieldsRGrid	(	std::string	filename,
		DArray< RField< D > > const &	fields,
		UnitCell< D > const &	unitCell,
		bool	isSymmetric = true ) const

Write an array of r-grid fields to a named file.

This function opens a file, writes field file header and data to the file, and closes the file. The overloaded writeFieldsGrid member function that takes a std::ostream& argument is called internally with writeHeader == true to write the data.

Parameters

filename	name of output file
fields	array of RFT objects (fields on r-space grid)
unitCell	associated crystallographic unit cell
isSymmetric	iff true, write space group name

◆ writeFieldRGrid() [2/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::writeFieldRGrid	(	std::string	filename,
		RField< D > const &	field,
		UnitCell< D > const &	unitCell,
		bool	isSymmetric = true ) const

Write a single r-grid field to a named file.

This function opens a file, writes the header and data for a single field to the file, and closes that file. The overloaded writeFieldGrid member function that takes a std::ostream& argument is called internally with writeHeader == true to write the file.

Parameters

filename	name of output file
field	field defined on r-space grid
unitCell	associated crystallographic unit cell
isSymmetric	iff true, write space group name

◆ readFieldsKGrid() [2/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::readFieldsKGrid	(	std::string	filename,
		DArray< RFieldDft< D > > &	fields,
		UnitCell< D > &	unitCell ) const

Read an array of k-grid fields from a named file.

This function opens a file with name filename, reads discrete Fourier components (Dft) of fields from that file, and closes the file. The overloaded readFieldsKGrid member function that takes a std::istream& argument is called to read the file.

Parameters

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

◆ writeFieldsKGrid() [2/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::writeFieldsKGrid	(	std::string	filename,
		DArray< RFieldDft< D > > const &	fields,
		UnitCell< D > const &	unitCell,
		bool	isSymmetric = true ) const

Write an array of k-grid fields to a named 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 Fourier-grid fields (instances of KFT)
unitCell	associated crystallographic unit cell
isSymmetric	iff true, write space group name

◆ convertBasisToKGrid() [2/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::convertBasisToKGrid	(	DArray< DArray< double > > const &	in,
		DArray< RFieldDft< D > > &	out ) const

Convert an array of fields from basis to Fourier (k-grid) form.

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)

◆ convertBasisToKGrid() [3/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::convertBasisToKGrid	(	std::string const &	inFileName,
		std::string const &	outFileName ) const

Convert a field file from basis to Fourier (k-grid) format.

The number of monomers in the input file must equal the number set by the setNMonomer(int) member function.

Parameters

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

◆ convertKGridToBasis() [2/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::convertKGridToBasis	(	DArray< RFieldDft< D > > const &	in,
		DArray< DArray< double > > &	out,
		bool	checkSymmetry = true,
		double	epsilon = 1.0e-8 ) const

Convert an array of fields from Fourier (k-grid) to basis form.

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() for each field that does 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)

◆ convertKGridToBasis() [3/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::convertKGridToBasis	(	std::string const &	inFileName,
		std::string const &	outFileName ) const

Convert a field file from Fourier (k-grid) to basis format.

The number of monomers in the input file must equal the number set by the setNMonomer(int) member function.

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 field in unpredictable ways.

Parameters

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

◆ convertBasisToRGrid() [1/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::convertBasisToRGrid	(	DArray< double > const &	in,
		RField< D > &	out ) const

Convert a single field from basis to r-grid format.

Parameters

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

Referenced by Pscf::Rpc::System< D >::readCommands().

◆ convertBasisToRGrid() [2/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::convertBasisToRGrid	(	DArray< DArray< double > > const &	in,
		DArray< RField< D > > &	out ) const

Convert an array of fields from basis to r-grid format.

Parameters

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

◆ convertBasisToRGrid() [3/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::convertBasisToRGrid	(	std::string const &	inFileName,
		std::string const &	outFileName ) const

Convert a field file from basis format to r-grid format.

This function reads a field file in basis format, converts the fields to r-grid format, and writes the fields in r-grid format to a different file.

This and other field file format conversion functions read field data into private workspace in which memory is allocated for nMonomer fields, where nMonomer is the value set by the setNMonomer(int i) member function. The number of monomer types in the input file must thus be equal to this stored value of nMonomer.

Parameters

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

◆ convertRGridToBasis() [1/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::convertRGridToBasis	(	RField< D > const &	in,
		DArray< double > &	out,
		bool	checkSymmetry = true,
		double	epsilon = 1.0e-8 ) const

Convert a single field from r-grid to basis form.

If the boolean checkSymmetry parameter is true, this function checks whether the the input field has the correct space group symmetry to within an error threshhold given by the epsilon parameter. If this error threshhold is exceeded, a warning is written to Log::file().

Parameters

in	field defined on real-space grid
out	field in symmetry adapted basis form
checkSymmetry	if true, check space group symmetry
epsilon	error threshhold for symmetry test

Referenced by Pscf::Rpc::System< D >::readCommands().

◆ convertRGridToBasis() [2/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::convertRGridToBasis	(	DArray< RField< D > > const &	in,
		DArray< DArray< double > > &	out,
		bool	checkSymmetry = true,
		double	epsilon = 1.0e-8 ) const

Convert an array of fields from r-grid to basis format.

If the boolean checkSymmetry parameter is true, this function checks whether the input fields all have the correct space group symmetry to within an error threshhold given by the epsilon parameter. If this error threshhold is exceeded by an field, a warning is written to Log::file().

Parameters

in	fields defined on real-space grid
out	fields in symmetry adapted basis form
checkSymmetry	if true, check space group symmetry
epsilon	error threshhold for symmetry test

◆ convertRGridToBasis() [3/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::convertRGridToBasis	(	std::string const &	inFileName,
		std::string const &	outFileName ) const

Convert a field file from r-grid to basis format.

The number of monomers in the input file must equal the number set by the setNMonomer(int) member function.

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 field in unpredictable ways.

Parameters

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

◆ convertKGridToRGrid() [1/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::convertKGridToRGrid	(	DArray< RFieldDft< D > > const &	in,
		DArray< RField< D > > &	out ) const

Convert an array of field from k-grid to r-grid format.

This function simply calls the inverse FFT for an array of fields.

Parameters

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

Referenced by Pscf::Rpc::System< D >::readCommands().

◆ convertKGridToRGrid() [2/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::convertKGridToRGrid	(	RFieldDft< D > const &	in,
		RField< D > &	out ) const

Convert a single field from k-grid to r-grid format.

This function simply calls the inverse FFT for a single field.

Parameters

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

◆ convertKGridToRGrid() [3/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::convertKGridToRGrid	(	std::string const &	inFileName,
		std::string const &	outFileName ) const

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

The number of monomers in the input file must equal the number set by the setNMonomer(int) member function.

Parameters

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

◆ convertRGridToKGrid() [1/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::convertRGridToKGrid	(	DArray< RField< D > > const &	in,
		DArray< RFieldDft< D > > &	out ) const

Convert an array of fields from r-grid to k-grid (Fourier) format.

This function simply calls the forward FFT repeatedly for an array of fields.

Parameters

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

Referenced by Pscf::Rpc::System< D >::readCommands().

◆ convertRGridToKGrid() [2/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::convertRGridToKGrid	(	RField< D > const &	in,
		RFieldDft< D > &	out ) const

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

This function simply calls the forward FFT for a single field.

Parameters

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

◆ convertRGridToKGrid() [3/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::convertRGridToKGrid	(	std::string const &	inFileName,
		std::string const &	outFileName ) const

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

The number of monomers in the input file must equal the number set by the setNMonomer(int) member function.

Parameters

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

◆ hasSymmetry() [2/3]

template<int D>

bool Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::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.

This function checks whether a field defined on the nodes of a regular real-space grid is invariant under all the symmetry operations of a declared space group to within an error threshhold given by function parameter epsilon. If parameter verbose is true and the deviation from symmetry exceeds the error threshhold, errors are written to Log::file().

Parameters

in	field in real space grid (r-grid) format
epsilon	error threshold used to test for symmetry
verbose	if true, write error to Log::file()

Returns: true if the field is symmetric, false otherwise

◆ hasSymmetry() [3/3]

template<int D>

bool Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::hasSymmetry	(	std::string const &	inFileName,
		double	epsilon = 1.0E-8 ) const

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

Parameters

inFileName	name of input r-grid field file
epsilon	error threshold used when testing for symmetry

Returns: true if fields all have symmetry, false otherwise

◆ compareFieldsBasis() [1/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::compareFieldsBasis	(	DArray< DArray< double > > const &	field1,
		DArray< DArray< double > > const &	field2 ) const

Compare array of fields in basis form, write a report to Log file.

Outputs maximum and root-mean-squared differences to the standard Log file.

Parameters

field1	first array of fields (basis form)
field2	second array of fields (basis form)

Referenced by Pscf::Rpc::System< D >::readCommands().

◆ compareFieldsBasis() [2/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::compareFieldsBasis	(	std::string const &	filename1,
		std::string const &	filename2 ) const

Compare two r-grid field files, write a report to Log file.

Parameters

filename1	name of 1st field file
filename2	name of 2nd field file

◆ compareFieldsRGrid() [2/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::compareFieldsRGrid	(	std::string const &	filename1,
		std::string const &	filename2 ) const

Compare two r-grid field files, write a report to Log file.

Parameters

filename1	name of 1st field file
filename2	name of 2nd field file

◆ scaleFieldsBasis() [1/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::scaleFieldsBasis	(	DArray< DArray< double > > &	fields,
		double	factor ) const

Multiply an array of fields in basis format by a real scalar.

This function takes an array of real periodic fields and multiplies all components in place by a common real scalar, thereby modifying the input.

Parameters

fields	array of fields in basis form to be rescaled
factor	factor by which to multiply every field element

Referenced by Pscf::Rpc::System< D >::readCommands().

◆ scaleFieldsBasis() [2/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::scaleFieldsBasis	(	std::string const &	inFileName,
		std::string const &	outFileName,
		double	factor ) const

Multiply all fields in a basis field file by a scalar.

Parameters

inFileName	name of input field file
outFileName	name of file for rescaled output fields
factor	factor by which to multiply every field element

◆ scaleFieldsRGrid() [1/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::scaleFieldsRGrid	(	DArray< RField< D > > &	fields,
		double	factor ) const

Scale an array of r-grid fields by a scalar.

This function takes an array of real periodic fields and multiplies all elements in place by a common real scalar, thereby modifying the input.

Parameters

fields	array of r-grid (RFT) fields to be rescaled
factor	factor by which to multiply every field element

Referenced by Pscf::Rpc::System< D >::readCommands().

◆ scaleFieldsRGrid() [2/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::scaleFieldsRGrid	(	std::string const &	inFileName,
		const std::string &	outFileName,
		double	factor ) const

Multiply all fields in an r-grid field file by a scalar.

Read a set of fields from a file, multiply fields by a constant, and write rescaled fields to a different file.

Parameters

inFileName	name of input field file
outFileName	name of file for rescaled output fields
factor	factor by which to multiply all field elements

◆ estimateWBasis() [1/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::estimateWBasis	(	DMatrix< double > const &	chi,
		DArray< DArray< double > > &	fields ) const

Convert c fields to estimated w fields, in basis format.

This function converts an array of c-fields in place to an array of estimated w fields. The approximation starts from the SCFT equation

\[ w_{i}({\bf r}) = \sum_{j=1}^{M} \chi_{ij} \phi_{j}({\bf r}) + \xi({\bf r}) \]

in which \(\xi({\bf r})\) is a pressure like field, and simply sets \( \xi({\bf r}) = 0 \) for all \( {\bf r} \). Here, \( M \) is the number of monomer types (nMonomer), i and j are monomer type indices, \(\chi_{ij}\) is a Flory-Huggins interaction parameter, \( \phi_{j} \) is a non-dimensiona monomer concentration (or volume fraction) field (which is an input to this function), and \( w_{i}\) is a monomer chemical potential field.

Parameters

chi	matrix of Flory-Huggins chi parameters
fields	array of field in basis format

Referenced by Pscf::Rpc::System< D >::readCommands().

◆ estimateWBasis() [2/2]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::estimateWBasis	(	std::string const &	inFileName,
		std::string const &	outFileName,
		DMatrix< double > const &	chi ) const

Convert a file of c fields to estimated w fields, in basis format.

This function reads an array of monomer concentration fields (c-fields) in basis format from a file named inFileName, converts them to estimated w fields, and writes the estimated w fields to a file named outFileName.

Parameters

inFileName	name of input file of c-fields
outFileName	name of output file of w-fields
chi	matrix of Flory-Huggins chi parameters

◆ replicateUnitCell() [2/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::replicateUnitCell	(	std::string	filename,
		DArray< RField< D > > const &	fields,
		UnitCell< D > const &	unitCell,
		IntVec< D > const &	replicas ) const

Write r-grid fields in a replicated unit cell to a named file.

This function opens output file filename, writes fields within a replicated unit cell to the file, and closes the file. See documentation of the overloaded function of the same name with a std::ostream parameter, which is called internally.

Parameters

filename	output file name
fields	array of RField fields (r-space grid) needs
unitCell	original crystallographic unit cell
replicas	number of unit cell replicas in each direction

◆ replicateUnitCell() [3/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::replicateUnitCell	(	std::string const &	inFileName,
		std::string const &	outFileName,
		IntVec< D > const &	replicas ) const

Write replicated fields read from one file to another.

This function reads a field file in r-grid format, and writes replicated fields to another file.

Parameters

inFileName	name of input field file
outFileName	name of output field file
replicas	the number of replicas in each D direction

◆ expandRGridDimension() [2/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::expandRGridDimension	(	std::string	filename,
		DArray< RField< D > > const &	fields,
		UnitCell< D > const &	unitCell,
		int	d,
		DArray< int >	newGridDimensions ) const

Increase D for an array of r-grid fields, write to a named file.

This function opens an output file with the specified filename, writes expanded fields in RField<d> real-space grid format to that file, and then closes the file. The overloaded function of the same name with an std::ostream parameter is called internally.

Parameters

filename	name of output file
fields	input array of RFT objects (r-space grid)
unitCell	original crystallographic unit cell
d	expanded dimension (greater than D)
newGridDimensions	number of grid points in added dimensions

◆ expandRGridDimension() [3/3]

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::expandRGridDimension	(	std::string const &	inFileName,
		std::string const &	outFileName,
		int	d,
		DArray< int >	newGridDimensions ) const

Increase D for an r-grid field file.

This function reads an array of fields in D-dimensional space from an r-grid field file and writes expanded fields in d-dimensional space to another file.

Parameters

inFileName	filename name of input field file
outFileName	filename name of output field file
d	intended dimensions (d > D)
newGridDimensions	number of grid points in added dimensions

◆ readFieldHeader()

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::readFieldHeader	(	std::istream &	in,
		int &	nMonomer,
		UnitCell< D > &	unitCell,
		bool &	isSymmetric ) const

Reader header of field file (fortran PSCF format)

This reads the common part of the header for all PSCF field file formats. This contains the dimension of space, the lattice system, a list of unit cell parameters, the space group name as an optional parameter, and the number of monomer types. The unit cell data is used to update a UnitCell<D> that is passed as a parameter.

If a space group was declared in the parameter file but the associated Basis object is not been initialized, this function will initialize the Basis by calling Basis<D>::makeBasis via a private pointer, using the unit cell parameters found in the file header. This function may thus modify the associated Basis object as a side effect (even though this function is marked const). Because all member functions that read complete field files call this function to read the file header, any member function of FieldIo that reads a field file header may thus cause the Basis to be constructed as a side effect.

On return, parameter nMonomer contains the number of monomer types declared in the field file header. This function does not require the number of monomers declared in the field file header to match the value of nMonomer set by the setNMonomer member function.

On return, isSymmetric is set true iff a group name was found in the header.

Consistency checks (Exceptions thrown on failure):

The value of "dim" in the header file must match the template parameter D. If the UnitCell<D> object passed to this function already contains a non-null lattice type, it must match the lattice system in the header file.

If the header declares a group name, then a matching group name must have been declared in the parameter file.

Parameters

in	input stream (i.e., file)
nMonomer	number of monomer types in the header (output)
unitCell	associated crystallographic unit cell (output)
isSymmetric	Is there a group name in the header? (output)

Referenced by Pscf::Rpc::RGridTrajectoryReader< D >::readHeader().

◆ writeFieldHeader()

template<int D>

void Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::writeFieldHeader	(	std::ostream &	out,
		int	nMonomer,
		UnitCell< D > const &	unitCell,
		bool	isSymmetric = true ) const

Write header for field file (fortran pscf format).

Parameters

out	output stream (i.e., file)
nMonomer	number of monomer types or fields
unitCell	associated crystallographic unit cell
isSymmetric	Should a space group be declared?

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

◆ mesh()

template<int D>

Mesh< D > const & Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::mesh ( ) const

inline

Get spatial discretization mesh by const reference.

Definition at line 1251 of file FieldIoReal.h.

Referenced by readFieldRGrid(), readFieldsKGrid(), readFieldsRGrid(), and readFieldsRGridData().

◆ basis()

template<int D>

Basis< D > const & Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::basis ( ) const

inline

Get the associated Basis by const reference.

Definition at line 1260 of file FieldIoReal.h.

Referenced by convertBasisToKGrid(), convertKGridToBasis(), and hasSymmetry().

◆ fileMaster()

template<int D>

FileMaster const & Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::fileMaster ( ) const

inline

Get associated FileMaster by const reference.

Definition at line 1269 of file FieldIoReal.h.

◆ lattice()

template<int D>

UnitCell< D >::LatticeSystem const & Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::lattice ( ) const

inlineprotected

Get the lattice type enum value by const reference.

Definition at line 1282 of file FieldIoReal.h.

◆ hasGroup()

template<int D>

bool Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::hasGroup ( ) const

inlineprotected

Has a space group been declared externally ?

Definition at line 1291 of file FieldIoReal.h.

◆ groupName()

template<int D>

std::string const & Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::groupName ( ) const

inlineprotected

Get an associated group name string by const reference.

Definition at line 1300 of file FieldIoReal.h.

◆ group()

template<int D>

SpaceGroup< D > const & Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::group ( ) const

inlineprotected

Get an associated SpaceGroup<D> by const reference.

Definition at line 1309 of file FieldIoReal.h.

◆ fft()

template<int D>

FFT const & Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT >::fft ( ) const

inlineprotected

Get FFT object by const reference.

Definition at line 1318 of file FieldIoReal.h.

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

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

Member Typedef Documentation

◆ Base

Member Function Documentation

◆ readFieldsRGrid() [1/2]

◆ readFieldsRGridData()

◆ readFieldRGrid() [1/2]

◆ writeFieldsRGrid() [1/2]

◆ writeFieldRGrid() [1/2]

◆ readFieldsKGrid() [1/2]

◆ writeFieldsKGrid() [1/2]

◆ convertBasisToKGrid() [1/3]

◆ convertKGridToBasis() [1/3]

◆ hasSymmetry() [1/3]

◆ compareFieldsRGrid() [1/2]

◆ scaleFieldRGrid()

◆ expandRGridDimension() [1/3]

◆ replicateUnitCell() [1/3]

◆ associate()

◆ setFileMaster()

◆ readFieldsBasis() [1/2]

◆ readFieldsBasis() [2/2]

◆ readFieldBasis() [1/2]

◆ readFieldBasis() [2/2]

◆ writeFieldBasis() [1/2]

◆ writeFieldBasis() [2/2]

◆ writeFieldsBasis() [1/2]

◆ writeFieldsBasis() [2/2]

◆ readFieldsRGrid() [2/2]

◆ readFieldRGrid() [2/2]

◆ writeFieldsRGrid() [2/2]

◆ writeFieldRGrid() [2/2]

◆ readFieldsKGrid() [2/2]

◆ writeFieldsKGrid() [2/2]

◆ convertBasisToKGrid() [2/3]

◆ convertBasisToKGrid() [3/3]

◆ convertKGridToBasis() [2/3]

◆ convertKGridToBasis() [3/3]

◆ convertBasisToRGrid() [1/3]

◆ convertBasisToRGrid() [2/3]

◆ convertBasisToRGrid() [3/3]

◆ convertRGridToBasis() [1/3]

◆ convertRGridToBasis() [2/3]

◆ convertRGridToBasis() [3/3]

◆ convertKGridToRGrid() [1/3]

◆ convertKGridToRGrid() [2/3]

◆ convertKGridToRGrid() [3/3]

◆ convertRGridToKGrid() [1/3]

◆ convertRGridToKGrid() [2/3]

◆ convertRGridToKGrid() [3/3]

◆ hasSymmetry() [2/3]

◆ hasSymmetry() [3/3]

◆ compareFieldsBasis() [1/2]

◆ compareFieldsBasis() [2/2]

◆ compareFieldsRGrid() [2/2]

◆ scaleFieldsBasis() [1/2]

◆ scaleFieldsBasis() [2/2]

◆ scaleFieldsRGrid() [1/2]

◆ scaleFieldsRGrid() [2/2]

◆ estimateWBasis() [1/2]

◆ estimateWBasis() [2/2]

◆ replicateUnitCell() [2/3]

◆ replicateUnitCell() [3/3]

◆ expandRGridDimension() [2/3]

◆ expandRGridDimension() [3/3]

◆ readFieldHeader()

◆ writeFieldHeader()

◆ mesh()

◆ basis()

◆ fileMaster()

◆ lattice()

◆ hasGroup()

◆ groupName()

◆ group()

◆ fft()