Periodic fields and crystallography. More...

Namespaces
namespace	Cpu
	Fields and FFTs for periodic boundary conditions (CPU)
namespace	Cuda
	Fields, FFTs, and utilities for periodic boundary conditions (CUDA).

Classes
class	Basis
	Symmetry-adapted Fourier basis for pseudo-spectral SCFT. More...
class	BFieldComparison
	Comparator for fields in symmetry-adapted basis format. More...
struct	BWave
	Wave struct designed for use within Basis construction. More...
struct	BWaveMinComp
	Comparator for BWave objects, based on BWave::indicesMin. More...
struct	BWaveNormComp
	Comparator for BWave objects, based on BWave::sqNorm. More...
struct	BWaveStdComp
	Comparator for BWave objects, based on BWave::indicesStd. More...
class	Environment
	Base class mask and external field generator for variable-cell SCFT. More...
class	FieldGenerator
	Base class field generator for MixAndMatchEnv in variable-cell SCFT. More...
class	FieldState
	Record of a state of a periodic system (fields + unit cell). More...
class	FilmFieldGenExtBase
	Base class Field Generator for external fields in thin-film systems. More...
class	FilmFieldGenMaskBase
	Base class Field Generator for thin-film masks. More...
class	MixAndMatchEnv
	Environment that can mix and match field generators in variable-cell SCFT. More...
class	SpaceGroup
	Crystallographic space group. More...
class	SpaceSymmetry
	A SpaceSymmetry represents a crystallographic space group symmetry. More...
class	SymmetryGroup
	Class template for a group of elements. More...
class	UnitCell
	Base template for UnitCell<D> classes, D=1, 2 or 3. More...
class	UnitCell< 1 >
	1D crystal unit cell. More...
class	UnitCell< 2 >
	2D crystal unit cell. More...
class	UnitCell< 3 >
	3D crystal unit cell. More...
class	UnitCellBase
	Base class template for a crystallographic unit cell. More...

Functions
std::string	makeGroupFileName (int D, std::string groupName)
	Generates the file name from a group name.
template<int D>
bool	hasVariableAngle (typename UnitCell< D >::LatticeSystem lattice)
	Return true if lattice type has variable angle parameters.
template<int D>
int	convertFullParamIdToReduced (const int fullId, const typename UnitCell< D >::LatticeSystem lattice)
	Convert full lattice parameter index to a reduced index.
template<int D>
int	convertReducedParamIdToFull (const int reducedId, const typename UnitCell< D >::LatticeSystem lattice)
	Convert reduced lattice parameter index to a full index.
template<>
void	replicateUnitCell (IntVec< 1 > const &replicas, UnitCell< 1 > const &cellIn, UnitCell< 1 > &cellOut)
	Create a replicated UnitCell<1>.
template<>
void	replicateUnitCell (IntVec< 2 > const &replicas, UnitCell< 2 > const &cellIn, UnitCell< 2 > &cellOut)
	Create a replicated UnitCell<2>.
template<>
void	replicateUnitCell (IntVec< 3 > const &replicas, UnitCell< 3 > const &cellIn, UnitCell< 3 > &cellOut)
	Create a replicated UnitCell<3>.
template<int D>
void	replicateUnitCell (IntVec< D > const &replicas, UnitCell< D > const &cellIn, UnitCell< D > &cellOut)
	Create a replicated UnitCell<D> (base template).
template<>
void	replicateUnitCell (IntVec< 1 > const &replicas, UnitCell< 1 > const &cellIn, UnitCell< 1 > &cellOut)
	Create a replicated UnitCell<1>.
template<>
void	replicateUnitCell (IntVec< 2 > const &replicas, UnitCell< 2 > const &cellIn, UnitCell< 2 > &cellOut)
	Create a replicated UnitCell<2>.
template<>
void	replicateUnitCell (IntVec< 3 > const &replicas, UnitCell< 3 > const &cellIn, UnitCell< 3 > &cellOut)
	Create a replicated UnitCell<3>.
template<int D>
IntVec< D >	shiftToMinimum (IntVec< D > const &v, IntVec< D > const &d, UnitCell< D > const &cell)
	Returns minimum magnitude image of DFT wavevector.
template<int D>
void	sortWaves (UnitCell< D > const &cell, IntVec< D > const &meshDimensions, std::vector< Sort::Item< double > > &items, GArray< Sort::Bunch > &bunches, double epsilon, bool isRealField)
	Sorted waves and identify bunches of equal magnitude.
template<int D>
std::ostream &	operator<< (std::ostream &out, SpaceGroup< D > const &g)
	Output stream inserter operator for a SpaceGroup<D>.
template<int D>
std::istream &	operator>> (std::istream &in, SpaceGroup< D > &g)
	Input stream extractor operator for a SpaceGroup<D>.
template<int D>
void	readGroup (std::string groupName, SpaceGroup< D > &group)
	Open and read a group file.
template<int D>
void	writeGroup (std::string filename, SpaceGroup< D > const &group)
	Open and write a group file.
template<int D>
bool	operator== (const SpaceSymmetry< D > &A, const SpaceSymmetry< D > &B)
	Are two SpaceSymmetry objects equivalent?
template<int D>
bool	operator!= (const SpaceSymmetry< D > &A, const SpaceSymmetry< D > &B)
	Are two SpaceSymmetry objects not equivalent?
template<int D>
SpaceSymmetry< D >	operator* (const SpaceSymmetry< D > &A, const SpaceSymmetry< D > &B)
	Return the product A*B of two symmetry objects.
template<int D>
IntVec< D >	operator* (const SpaceSymmetry< D > &S, const IntVec< D > &V)
	Return the IntVec<D> product S*V of a rotation matrix and an IntVec<D>.
template<int D>
IntVec< D >	operator* (const IntVec< D > &V, const SpaceSymmetry< D > &S)
	Return the IntVec<D> product V*S of an IntVec<D> and a rotation matrix.
template<int D>
std::ostream &	operator<< (std::ostream &out, const SpaceSymmetry< D > &A)
	Output stream inserter for a SpaceSymmetry<D>
template<int D>
std::istream &	operator>> (std::istream &in, SpaceSymmetry< D > &A)
	Input stream extractor for a SpaceSymmetry<D>
template<int D>
std::istream &	operator>> (std::istream &in, UnitCell< D > &cell)
	istream input extractor for a UnitCell<D>.
template<int D>
std::ostream &	operator<< (std::ostream &out, UnitCell< D > const &cell)
	ostream output inserter for a UnitCell<D>.
template<class Archive, int D>
void	serialize (Archive &ar, UnitCell< D > &cell, const unsigned int version)
	Serialize to/from an archive.
std::istream &	operator>> (std::istream &in, UnitCell< 1 >::LatticeSystem &lattice)
	istream extractor for a 1D UnitCell<1>::LatticeSystem.
std::ostream &	operator<< (std::ostream &out, UnitCell< 1 >::LatticeSystem lattice)
	ostream inserter for a 1D UnitCell<1>::LatticeSystem.
template<class Archive>
void	serialize (Archive &ar, UnitCell< 1 >::LatticeSystem &lattice, const unsigned int version)
	Serialize a UnitCell<1>::LatticeSystem enumeration value.
std::istream &	operator>> (std::istream &in, UnitCell< 2 >::LatticeSystem &lattice)
	istream extractor for a 2D UnitCell<2>::LatticeSystem.
std::ostream &	operator<< (std::ostream &out, UnitCell< 2 >::LatticeSystem lattice)
	ostream inserter for a 2D UnitCell<2>::LatticeSystem.
template<class Archive>
void	serialize (Archive &ar, UnitCell< 2 >::LatticeSystem &lattice, const unsigned int version)
	Serialize a UnitCell<2>::LatticeSystem enumeration value.
std::istream &	operator>> (std::istream &in, UnitCell< 3 >::LatticeSystem &lattice)
	istream extractor for a 3D UnitCell<3>::LatticeSystem.
std::ostream &	operator<< (std::ostream &out, UnitCell< 3 >::LatticeSystem lattice)
	ostream inserter for an 3D UnitCell<3>::LatticeSystem.
template<class Archive>
void	serialize (Archive &ar, UnitCell< 3 >::LatticeSystem &lattice, const unsigned int version)
	Serialize a UnitCell<3>::LatticeSystem enumeration value.
template<int D>
void	readUnitCellHeader (std::istream &in, UnitCell< D > &cell)
	Read UnitCell<D> from a field file header (fortran PSCF format).
template<int D>
void	writeUnitCellHeader (std::ostream &out, UnitCell< D > const &cell)
	Write UnitCell<D> to a field file header (fortran PSCF format).
template<int D, class AT>
void	readCFieldsData (std::istream &in, DArray< AT > &fields, IntVec< D > const &dimensions)
	Read data for an array of complex fields, with no header section.
template<int D, class AT>
void	readCFieldData (std::istream &in, AT &field, IntVec< D > const &dimensions)
	Read data for a single complex field, with no header section.
template<int D, class AT, typename CT, typename RT>
void	writeCFieldsData (std::ostream &out, DArray< AT > const &fields, IntVec< D > const &dimensions)
	Write data for an array of complex fields, with no header section.
template<int D, class AT, typename CT, typename RT>
void	writeCFieldData (std::ostream &out, AT const &field, IntVec< D > const &dimensions)
	Write data for a single complex field, with no header section.
template<int D, class FT>
void	allocateFields (DArray< FT > &fields, int n, IntVec< D > const &dimension)
	Allocate a DArray of fields.
template<int D, class FT>
void	checkAllocateField (FT &field, IntVec< D > const &dimensions)
	Check allocation of a single field, allocate if necessary.
template<int D, class FT>
void	checkAllocateFields (DArray< FT > &fields, int nMonomer, IntVec< D > const &dimensions)
	Check allocation of an array of fields, allocate if necessary.
template<int D, class FT>
void	inspectFields (DArray< FT > const &fields, int &nMonomer, IntVec< D > &dimensions)
	Inspect dimensions of a DArray of fields, each of type FT.
template<class AT>
void	allocateArrays (DArray< AT > &arrays, int n, int capacity)
	Allocate an array of arrays.
template<int D, class AT>
void	checkAllocateArrays (DArray< AT > &arrays, int nMonomer, int capacity)
	Check allocation of a DArray of 1D arrays, allocate if necessary.
template<class AT>
void	inspectArrays (DArray< AT > const &arrays, int &nMonomer, int &capacity)
	Inspect dimensions of a DArray of 1D arrays, each of type AT.
template<class OAT, class IAT>
void	copyArrays (DArray< OAT > &out, DArray< IAT > const &in)
	Copy a DArray of 1D arrays.
template<int D>
void	readFieldHeader (std::istream &in, int &ver1, int &ver2, UnitCell< D > &cell, std::string &groupName, int &nMonomer)
	Read common part of field header (fortran PSCF format).
template<int D>
void	writeFieldHeader (std::ostream &out, int ver1, int ver2, UnitCell< D > const &cell, std::string const &groupName, int nMonomer)
	Write common part of field header (fortran PSCF format).
template<int D>
void	readMeshDimensions (std::istream &in, IntVec< D > const &meshDimensions)
	Read mesh dimensions from a field file header.
template<int D>
void	writeMeshDimensions (std::ostream &out, IntVec< D > const &meshDimensions)
	Write mesh dimensions to a field file header.
int	readNBasis (std::istream &in)
	Read the number of basis functions from a basis field file header.
void	writeNBasis (std::ostream &out, int nBasis)
	Write the number of basis functions to a basis field file header.
template<int D, class AT>
void	readRGridData (std::istream &in, DArray< AT > &fields, int nMonomer, IntVec< D > const &dimensions)
	Read data for array of r-grid fields, with no header section.
template<int D, class AT>
void	readRGridData (std::istream &in, AT &field, IntVec< D > const &dimensions)
	Read data for a single r-grid field, with no header section.
template<int D, class AT>
void	writeRGridData (std::ostream &out, DArray< AT > const &fields, int nMonomer, IntVec< D > const &dimensions)
	Write data for array of r-grid fields, with no header section.
template<int D, class AT>
void	writeRGridData (std::ostream &out, AT const &field, IntVec< D > const &dimensions)
	Write data for a single r-grid field, with no header section.
template<int D, class AT>
void	readKGridData (std::istream &in, DArray< AT > &fields, int nMonomer, IntVec< D > const &dftDimensions)
	Read data for array of k-grid fields, with no header section.
template<int D, class AT>
void	readKGridData (std::istream &in, AT &field, IntVec< D > const &dftDimensions)
	Read data for a single k-grid field, with no header section.
template<int D, class AT>
void	writeKGridData (std::ostream &out, DArray< AT > const &fields, int nMonomer, IntVec< D > const &dftDimensions)
	Write data for array of k-grid fields, with no header section.
template<int D, class AT>
void	writeKGridData (std::ostream &in, AT const &field, IntVec< D > const &dftDimensions)
	Write data for a single k-grid field, with no header section.
template<int D>
void	readBasisData (std::istream &in, DArray< DArray< double > > &fields, UnitCell< D > const &unitCell, Mesh< D > const &mesh, Basis< D > const &basis, int nStarIn)
	Read an array of fields in basis format, without a header.
template<int D>
void	readBasisData (std::istream &in, DArray< double > &field, UnitCell< D > const &unitCell, Mesh< D > const &mesh, Basis< D > const &basis, int nStarIn)
	Read data section of a single field in basis format.
template<int D>
void	writeBasisData (std::ostream &out, DArray< DArray< double > > const &fields, Basis< D > const &basis)
	Write data section of an array of fields in basis format.
template<int D>
void	writeBasisData (std::ostream &out, DArray< double > const &field, Basis< D > const &basis)
	Write data section of a single field in basis format.
template<int D, class AT>
void	convertBasisToKGrid (DArray< double > const &components, AT &dft, Basis< D > const &basis, IntVec< D > const &dftDimensions)
	Convert a real field from symmetrized basis to Fourier grid.
template<int D, class AT>
void	convertKGridToBasis (AT const &in, DArray< double > &out, Basis< D > const &basis, IntVec< D > const &dftDimensions, bool checkSymmetry=true, double epsilon=1.0e-8)
	Convert a real field from Fourier grid to symmetrized basis.
template<int D, class AT>
bool	hasSymmetry (AT const &in, Basis< D > const &basis, IntVec< D > const &dftDimensions, double epsilon=1.0e-8, bool verbose=true)
	Check if a k-grid field has the declared space group symmetry.
template<int D, class AT>
void	replicateUnitCell (std::ostream &out, DArray< AT > const &fields, IntVec< D > const &meshDimensions, UnitCell< D > const &unitCell, IntVec< D > const &replicas)
	Write r-grid fields in a replicated unit cell to std::ostream.
template<int D, class AT>
void	expandRGridDimension (std::ostream &out, DArray< AT > const &fields, IntVec< D > const &meshDimensions, UnitCell< D > const &unitCell, int d, DArray< int > newGridDimensions)
	Expand the dimensionality of space from D to d.

Detailed Description

Periodic fields and crystallography.

Function Documentation

◆ hasVariableAngle()

template<int D>

bool Pscf::Prdc::hasVariableAngle ( typename UnitCell< D >::LatticeSystem lattice )

Return true if lattice type has variable angle parameters.

This base template is not defined, but explicit specializations are defined for D=1, 2, and 3.

Parameters

lattice lattice system enumeration value

Returns: true iff lattice type has variable angles

References hasVariableAngle().

Referenced by Pscf::Prdc::Cpu::WaveList< D >::clearUnitCellData(), Pscf::Prdc::Cuda::WaveList< D >::clearUnitCellData(), and hasVariableAngle().

◆ serialize() [1/3]

template<class Archive>

void Pscf::Prdc::serialize	(	Archive &	ar,
		UnitCell< 1 >::LatticeSystem &	lattice,
		const unsigned int	version )

inline

Serialize a UnitCell<1>::LatticeSystem enumeration value.

Parameters

ar	archive
lattice	enumeration data to be serialized
version	version id

Definition at line 235 of file UnitCell.h.

References Util::serializeEnum().

◆ operator<<()

std::ostream & Pscf::Prdc::operator<<	(	std::ostream &	out,
		UnitCell< 2 >::LatticeSystem	lattice )

ostream inserter for a 2D UnitCell<2>::LatticeSystem.

Parameters

out	output stream
lattice	UnitCell<2>::LatticeSystem to be written

Returns: modified output stream

Definition at line 248 of file UnitCell2.cpp.

References UTIL_THROW.

◆ serialize() [2/3]

template<class Archive>

void Pscf::Prdc::serialize	(	Archive &	ar,
		UnitCell< 2 >::LatticeSystem &	lattice,
		const unsigned int	version )

inline

Serialize a UnitCell<2>::LatticeSystem enumeration value.

Parameters

ar	archive
lattice	enumeration data to be serialized
version	version id

Definition at line 377 of file UnitCell.h.

References Util::serializeEnum().

◆ serialize() [3/3]

template<class Archive>

void Pscf::Prdc::serialize	(	Archive &	ar,
		UnitCell< 3 >::LatticeSystem &	lattice,
		const unsigned int	version )

inline

Serialize a UnitCell<3>::LatticeSystem enumeration value.

Parameters

ar	archive
lattice	enumeration data to be serialized
version	version id

Definition at line 538 of file UnitCell.h.

References Util::serializeEnum().

◆ allocateFields()

template<int D, class FT>

void Pscf::Prdc::allocateFields	(	DArray< FT > &	fields,
		int	n,
		IntVec< D > const &	dimension )

Allocate a DArray of fields.

Parameters

fields	DArray of fields of type FT
n	number of inner arrays
dimension	mesh dimensions

Definition at line 24 of file fieldCheck.tpp.

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

Referenced by Pscf::Cp::FieldIo< D, CFT, FFT >::convertKGridToRGrid(), and Pscf::Cp::FieldIo< D, CFT, FFT >::convertRGridToKGrid().

◆ allocateArrays()

template<class AT>

void Pscf::Prdc::allocateArrays	(	DArray< AT > &	arrays,
		int	n,
		int	capacity )

Allocate an array of arrays.

Parameters

arrays	DArray of arrays
n	number of inner arrays
capacity	capacity of each inner array

Definition at line 95 of file fieldCheck.tpp.

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

Referenced by Pscf::Rpg::FieldIo< D >::expandRGridDimension(), Pscf::Rpg::FieldIo< D >::readFieldsKGrid(), Pscf::Rpg::FieldIo< D >::readFieldsRGrid(), Pscf::Rpg::FieldIo< D >::readFieldsRGridData(), Pscf::Rpg::FieldIo< D >::replicateUnitCell(), Pscf::Rpg::FieldIo< D >::writeFieldsKGrid(), and Pscf::Rpg::FieldIo< D >::writeFieldsRGrid().

Namespaces

Classes

Functions

Detailed Description

Function Documentation

◆ hasVariableAngle()

◆ serialize() [1/3]

◆ operator<<()

◆ serialize() [2/3]

◆ serialize() [3/3]

◆ allocateFields()

◆ allocateArrays()