Crystallography

Classes
class	Pscf::Prdc::Basis< D >
	Symmetry-adapted Fourier basis for pseudo-spectral scft. More...
class	Pscf::Prdc::BFieldComparison
	Comparator for fields in symmetry-adapted basis format. More...
class	Pscf::Prdc::SpaceGroup< D >
	Crystallographic space group. More...
class	Pscf::Prdc::SpaceSymmetry< D >
	A SpaceSymmetry represents a crystallographic space group symmetry. More...
class	Pscf::Prdc::SymmetryGroup< Symmetry >
	Class template for a group of elements. More...
struct	Pscf::Prdc::TWave< D >
	Simple wave struct for use within Basis construction. More...
struct	Pscf::Prdc::TWaveNormComp< D >
	Comparator for TWave objects, based on TWave::sqNorm. More...
struct	Pscf::Prdc::TWaveDftComp< D >
	Comparator for TWave objects, based on TWave::indicesDft. More...
struct	Pscf::Prdc::TWaveBzComp< D >
	Comparator for TWave objects, based on TWave::indicesBz. More...
class	Pscf::Prdc::UnitCell< D >
	Base template for UnitCell<D> classes, D=1, 2 or 3. More...
class	Pscf::Prdc::UnitCell< 1 >
	1D crystal unit cell. More...
class	Pscf::Prdc::UnitCell< 2 >
	2D crystal unit cell. More...
class	Pscf::Prdc::UnitCell< 3 >
	3D crystal unit cell. More...
class	Pscf::Prdc::UnitCellBase< D >
	Base class template for a crystallographic unit cell. More...

Functions
template<int D>
void	Pscf::Prdc::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	Pscf::Prdc::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).
std::string	Pscf::Prdc::makeGroupFileName (int D, std::string groupName)
	Generates the file name from a group name.
template<int D>
int	Pscf::Prdc::convertFullParamIdToReduced (const int fullId, const typename UnitCell< D >::LatticeSystem lattice)
	Convert full lattice parameter index to a reduced index.
template<int D>
int	Pscf::Prdc::convertReducedParamIdToFull (const int reducedId, const typename UnitCell< D >::LatticeSystem lattice)
	Convert reduced lattice parameter index to a full index.
template<int D>
IntVec< D >	Pscf::Prdc::shiftToMinimum (IntVec< D > &v, IntVec< D > d, UnitCell< D > const &cell)
	Returns minimum magnitude image of DFT wavevector.
template<int D>
std::ostream &	Pscf::Prdc::operator<< (std::ostream &out, SpaceGroup< D > const &g)
	Output stream inserter operator for a SpaceGroup<D>.
template<int D>
std::istream &	Pscf::Prdc::operator>> (std::istream &in, SpaceGroup< D > &g)
	Input stream extractor operator for a SpaceGroup<D>.
template<int D>
void	Pscf::Prdc::readGroup (std::string groupName, SpaceGroup< D > &group)
	Open and read a group file.
template<int D>
void	Pscf::Prdc::writeGroup (std::string filename, SpaceGroup< D > const &group)
	Open and write a group file.
template<int D>
bool	Pscf::Prdc::operator== (const SpaceSymmetry< D > &A, const SpaceSymmetry< D > &B)
	Are two SpaceSymmetry objects equivalent?
template<int D>
bool	Pscf::Prdc::operator!= (const SpaceSymmetry< D > &A, const SpaceSymmetry< D > &B)
	Are two SpaceSymmetry objects not equivalent?
template<int D>
SpaceSymmetry< D >	Pscf::Prdc::operator* (const SpaceSymmetry< D > &A, const SpaceSymmetry< D > &B)
	Return the product A*B of two symmetry objects.
template<int D>
IntVec< D >	Pscf::Prdc::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 >	Pscf::Prdc::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 &	Pscf::Prdc::operator<< (std::ostream &out, const SpaceSymmetry< D > &A)
	Output stream inserter for a SpaceSymmetry<D>
template<int D>
std::istream &	Pscf::Prdc::operator>> (std::istream &in, SpaceSymmetry< D > &A)
	Input stream extractor for a SpaceSymmetry<D>
template<int D>
std::istream &	Pscf::Prdc::operator>> (std::istream &in, UnitCell< D > &cell)
	istream input extractor for a UnitCell<D>.
template<int D>
std::ostream &	Pscf::Prdc::operator<< (std::ostream &out, UnitCell< D > const &cell)
	ostream output inserter for a UnitCell<D>.
template<class Archive , int D>
void	Pscf::Prdc::serialize (Archive &ar, UnitCell< D > &cell, const unsigned int version)
	Serialize to/from an archive.
template<int D>
void	Pscf::Prdc::readUnitCellHeader (std::istream &in, UnitCell< D > &cell)
	Read UnitCell<D> from a field file header (fortran PSCF format).
template<int D>
void	Pscf::Prdc::writeUnitCellHeader (std::ostream &out, UnitCell< D > const &cell)
	Write UnitCell<D> to a field file header (fortran PSCF format).
std::istream &	Pscf::Prdc::operator>> (std::istream &in, UnitCell< 1 >::LatticeSystem &lattice)
	istream extractor for a 1D UnitCell<1>::LatticeSystem.
std::ostream &	Pscf::Prdc::operator<< (std::ostream &out, UnitCell< 1 >::LatticeSystem lattice)
	ostream inserter for a 1D UnitCell<1>::LatticeSystem.
std::istream &	Pscf::Prdc::operator>> (std::istream &in, UnitCell< 2 >::LatticeSystem &lattice)
	istream extractor for a 2D UnitCell<2>::LatticeSystem.
std::istream &	Pscf::Prdc::operator>> (std::istream &in, UnitCell< 3 >::LatticeSystem &lattice)
	istream extractor for a 3D UnitCell<3>::LatticeSystem.
std::ostream &	Pscf::Prdc::operator<< (std::ostream &out, UnitCell< 3 >::LatticeSystem lattice)
	ostream inserter for an 3D UnitCell<3>::LatticeSystem.

Detailed Description

Classes that describe crystallographic information.

Function Documentation

readFieldHeader()

template<int D>

void Pscf::Prdc::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).

If the group_name label and value are absent, then this function returns an empty groupName string, groupName == "".

Parameters

in	input stream
ver1	major file format version number (output)
ver2	major file format version number (output)
cell	UnitCell<D> object (output)
groupName	string identifier for space group (output)
nMonomer	number of monomers (output)

Definition at line 26 of file fieldHeader.tpp.

References Pscf::Prdc::readUnitCellHeader(), and UTIL_CHECK.

Referenced by Pscf::Rpc::System< D >::basisToKGrid(), Pscf::Rpg::System< D >::basisToKGrid(), Pscf::Rpc::System< D >::basisToRGrid(), Pscf::Rpg::System< D >::basisToRGrid(), Pscf::Rpc::System< D >::checkRGridFieldSymmetry(), Pscf::Rpg::System< D >::checkRGridFieldSymmetry(), Pscf::Rpc::System< D >::estimateWfromC(), Pscf::Rpg::System< D >::estimateWfromC(), Pscf::Rpc::System< D >::kGridToBasis(), Pscf::Rpg::System< D >::kGridToBasis(), Pscf::Rpc::System< D >::kGridToRGrid(), Pscf::Rpg::System< D >::kGridToRGrid(), Pscf::Rpc::FieldIo< D >::readFieldRGrid(), Pscf::Rpg::FieldIo< D >::readFieldRGrid(), Pscf::Rpc::FieldIo< D >::readFieldsKGrid(), Pscf::Rpg::FieldIo< D >::readFieldsKGrid(), Pscf::Rpc::FieldIo< D >::readFieldsRGrid(), Pscf::Rpg::FieldIo< D >::readFieldsRGrid(), Pscf::Rpc::Domain< D >::readRGridFieldHeader(), Pscf::Rpg::Domain< D >::readRGridFieldHeader(), Pscf::Rpc::System< D >::readWBasis(), Pscf::Rpg::System< D >::readWBasis(), Pscf::Rpc::System< D >::readWRGrid(), Pscf::Rpg::System< D >::readWRGrid(), Pscf::Rpc::System< D >::rGridToBasis(), Pscf::Rpg::System< D >::rGridToBasis(), Pscf::Rpc::System< D >::rGridToKGrid(), Pscf::Rpg::System< D >::rGridToKGrid(), Pscf::Rpc::System< D >::scaleFieldsBasis(), Pscf::Rpg::System< D >::scaleFieldsBasis(), and Pscf::Prdc::FieldIoReal< D, RField< D >, RFieldDft< D >, FFT< D > >::setFileMaster().

writeFieldHeader()

template<int D>

void Pscf::Prdc::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).

If the groupName parameter is an empty string (groupName == ""), then this function does not write the group_name label or value.

Parameters

out	output stream
ver1	major file format version number (input)
ver2	major file format version number (input)
cell	UnitCell<D> object (input)
groupName	string identifier for space group (input)
nMonomer	number of monomers (input)

Definition at line 69 of file fieldHeader.tpp.

References Pscf::Prdc::writeUnitCellHeader().

Referenced by Pscf::Rpc::FieldIo< D >::writeFieldRGrid(), Pscf::Rpg::FieldIo< D >::writeFieldRGrid(), Pscf::Rpc::FieldIo< D >::writeFieldsKGrid(), Pscf::Rpg::FieldIo< D >::writeFieldsKGrid(), Pscf::Rpc::FieldIo< D >::writeFieldsRGrid(), and Pscf::Rpg::FieldIo< D >::writeFieldsRGrid().

makeGroupFileName()

std::string Pscf::Prdc::makeGroupFileName	(	int	D,
		std::string	groupName )

Generates the file name from a group name.

Parameters

D	dimensionality of space (D=1,2 or 3)
groupName	standard name of space group

Definition at line 26 of file groupFile.cpp.

References UTIL_THROW.

Referenced by Pscf::Prdc::readGroup().

convertFullParamIdToReduced()

template<int D>

int Pscf::Prdc::convertFullParamIdToReduced	(	const int	fullId,
		const typename UnitCell< D >::LatticeSystem	lattice )

Convert full lattice parameter index to a reduced index.

Here, we define the "full" list of lattice parameters to be {a, b, c, alpha, beta, gamma}, and we define the "reduced" list of lattice parameters to be the list of independent parameters as defined by a particular lattice system (e.g., {a, c} for a tetragonal lattice). This function converts an index of a parameter in the full list, fullId, into the corresponding index in the reduced list, reducedId.

If fullId denotes a parameter that is able to vary but is not independent, then the index of the corresponding independent parameter in the reduced list is returned. For example, in a tetragonal lattice a == b, so a fullId of 1 would correspond to a reducedId of 0.

If fullId denotes a parameter that is rigid in a given lattice, then reducedId is set to -1. For example, all three angles are fixed at 90° in a tetragonal lattice, so a fullId value of 3, 4, or 5 would result in a reducedId of -1.

Parameters

fullId	the value of fullId to convert
lattice	the lattice system

Referenced by Pscf::Rpc::MaskGenFilm< D >::generate(), Pscf::Rpg::MaskGenFilm< D >::generate(), Pscf::Rpc::MaskGenFilm< D >::modifyStress(), Pscf::Rpg::MaskGenFilm< D >::modifyStress(), Pscf::Rpc::ExtGenFilm< D >::stressTerm(), Pscf::Rpc::MaskGenFilm< D >::stressTerm(), Pscf::Rpg::ExtGenFilm< D >::stressTerm(), and Pscf::Rpg::MaskGenFilm< D >::stressTerm().

convertReducedParamIdToFull()

template<int D>

int Pscf::Prdc::convertReducedParamIdToFull	(	const int	reducedId,
		const typename UnitCell< D >::LatticeSystem	lattice )

Convert reduced lattice parameter index to a full index.

Here, we define the "full" list of lattice parameters to be {a, b, c, alpha, beta, gamma}, and we define the "reduced" list of lattice parameters to be the list of independent parameters as defined by a particular lattice system (e.g., {a, c} for a tetragonal lattice). This function converts an index of a parameter in the reduced list, reducedId, into the corresponding index in the full list, fullId.

Parameters

reducedId	the value of reducedId to convert
lattice	the lattice system

shiftToMinimum()

template<int D>

IntVec< D > Pscf::Prdc::shiftToMinimum	(	IntVec< D > &	v,
		IntVec< D >	d,
		UnitCell< D > const &	cell )

Returns minimum magnitude image of DFT wavevector.

Parameters

v	IntVec<D> containing integer indices of wavevector.
d	dimensions of the discrete Fourier transform grid.
cell	UnitCell

operator<<() [1/5]

template<int D>

std::ostream & Pscf::Prdc::operator<<	(	std::ostream &	out,
		SpaceGroup< D > const &	g )

Output stream inserter operator for a SpaceGroup<D>.

Parameters

out	output stream
g	space group

Definition at line 108 of file SpaceGroup.h.

operator>>() [1/6]

template<int D>

std::istream & Pscf::Prdc::operator>>	(	std::istream &	in,
		SpaceGroup< D > &	g )

Input stream extractor operator for a SpaceGroup<D>.

Parameters

in	input stream
g	space group

Definition at line 129 of file SpaceGroup.h.

References UTIL_CHECK.

readGroup()

template<int D>

void Pscf::Prdc::readGroup	(	std::string	groupName,
		SpaceGroup< D > &	group )

Open and read a group file.

Parameters

groupName	name of group, or group file (input)
group	space group (output)

Definition at line 162 of file SpaceGroup.tpp.

References Util::Log::file(), Pscf::Prdc::SymmetryGroup< Symmetry >::makeCompleteGroup(), Pscf::Prdc::makeGroupFileName(), UTIL_CHECK, and UTIL_THROW.

writeGroup()

template<int D>

void Pscf::Prdc::writeGroup	(	std::string	filename,
		SpaceGroup< D > const &	group )

Open and write a group file.

Parameters

filename	output file name
group	space group

Definition at line 201 of file SpaceGroup.tpp.

operator==()

template<int D>

bool Pscf::Prdc::operator==	(	const SpaceSymmetry< D > &	A,
		const SpaceSymmetry< D > &	B )

Are two SpaceSymmetry objects equivalent?

Parameters

A	first symmetry
B	second symmetry

Returns

True if A == B, false otherwise

Definition at line 371 of file SpaceSymmetry.h.

operator!=()

template<int D>

bool Pscf::Prdc::operator!= ( const SpaceSymmetry< D > & A, const SpaceSymmetry< D > & B )

inline

Are two SpaceSymmetry objects not equivalent?

Parameters

A	first symmetry
B	second symmetry

Returns

True if A != B, false otherwise

Definition at line 319 of file SpaceSymmetry.h.

operator*() [1/3]

template<int D>

SpaceSymmetry< D > Pscf::Prdc::operator*	(	const SpaceSymmetry< D > &	A,
		const SpaceSymmetry< D > &	B )

Return the product A*B of two symmetry objects.

Parameters

A	first symmetry
B	second symmetry

Returns

product A*B

Definition at line 392 of file SpaceSymmetry.h.

operator*() [2/3]

template<int D>

IntVec< D > Pscf::Prdc::operator*	(	const SpaceSymmetry< D > &	S,
		const IntVec< D > &	V )

Return the IntVec<D> product S*V of a rotation matrix and an IntVec<D>.

The product is defined to be the matrix product of the rotation matrix and the integer vector S.R * V.

Parameters

S	symmetry operation
V	integer vector

Returns

product S*V

Definition at line 425 of file SpaceSymmetry.h.

operator*() [3/3]

template<int D>

IntVec< D > Pscf::Prdc::operator*	(	const IntVec< D > &	V,
		const SpaceSymmetry< D > &	S )

Return the IntVec<D> product V*S of an IntVec<D> and a rotation matrix.

The product is defined to be the matrix product of the integer vector and the space group rotation matrix S.R * V.

Parameters

V	integer vector
S	symmetry operation

Returns

product V*S

Definition at line 442 of file SpaceSymmetry.h.

operator<<() [2/5]

template<int D>

std::ostream & Pscf::Prdc::operator<<	(	std::ostream &	out,
		const SpaceSymmetry< D > &	A )

Output stream inserter for a SpaceSymmetry<D>

Parameters

out	output stream
A	SpaceSymmetry<D> object to be output

Returns

modified output stream

Definition at line 459 of file SpaceSymmetry.h.

operator>>() [2/6]

template<int D>

std::istream & Pscf::Prdc::operator>>	(	std::istream &	in,
		SpaceSymmetry< D > &	A )

Input stream extractor for a SpaceSymmetry<D>

Parameters

in	input stream
A	SpaceSymmetry<D> object to be input

Returns

modified input stream

Definition at line 479 of file SpaceSymmetry.h.

operator>>() [3/6]

template<int D>

std::istream & Pscf::Prdc::operator>>	(	std::istream &	in,
		UnitCell< D > &	cell )

istream input extractor for a UnitCell<D>.

If cell.lattice() is not Null, the lattice type read from stream must match the existing lattice type, or an Exception is thrown.

Parameters

in	input stream
cell	UnitCell<D> to be read

Returns

modified input stream

Definition at line 22 of file UnitCell.tpp.

operator<<() [3/5]

template<int D>

std::ostream & Pscf::Prdc::operator<<	(	std::ostream &	out,
		UnitCell< D > const &	cell )

ostream output inserter for a UnitCell<D>.

Parameters

out	output stream
cell	UnitCell<D> to be written

Returns

modified output stream

Definition at line 36 of file UnitCell.tpp.

serialize()

template<class Archive , int D>

void Pscf::Prdc::serialize	(	Archive &	ar,
		UnitCell< D > &	cell,
		const unsigned int	version )

Serialize to/from an archive.

Parameters

ar	input or output archive
cell	UnitCell<D> object to be serialized
version	archive version id

Definition at line 50 of file UnitCell.tpp.

readUnitCellHeader()

template<int D>

void Pscf::Prdc::readUnitCellHeader	(	std::istream &	in,
		UnitCell< D > &	cell )

Read UnitCell<D> from a field file header (fortran PSCF format).

If the unit cell has a non-null lattice system on entry, the value read from file must match this existing value, or this function throws an exception. If the lattice system is null on entry, the lattice system value is read from file. In either case, unit cell parameters (dimensions and angles) are updated using values read from file.

Parameters

in	input stream
cell	UnitCell<D> to be read

Definition at line 61 of file UnitCell.tpp.

Referenced by Pscf::Prdc::readFieldHeader().

writeUnitCellHeader()

template<int D>

void Pscf::Prdc::writeUnitCellHeader	(	std::ostream &	out,
		UnitCell< D > const &	cell )

Write UnitCell<D> to a field file header (fortran PSCF format).

Parameters

out	output stream
cell	UnitCell<D> to be written

Definition at line 91 of file UnitCell.tpp.

Referenced by Pscf::Prdc::writeFieldHeader().

operator>>() [4/6]

std::istream & Pscf::Prdc::operator>>	(	std::istream &	in,
		UnitCell< 1 >::LatticeSystem &	lattice )

istream extractor for a 1D UnitCell<1>::LatticeSystem.

Parameters

in	input stream
lattice	UnitCell<1>::LatticeSystem to be read

Returns

modified input stream

Definition at line 52 of file UnitCell1.cpp.

References UTIL_THROW.

operator<<() [4/5]

std::ostream & Pscf::Prdc::operator<<	(	std::ostream &	out,
		UnitCell< 1 >::LatticeSystem	lattice )

ostream inserter for a 1D UnitCell<1>::LatticeSystem.

Parameters

out	output stream
lattice	UnitCell<1>::LatticeSystem to be written

Returns

modified output stream

Definition at line 69 of file UnitCell1.cpp.

References UTIL_THROW.

operator>>() [5/6]

std::istream & Pscf::Prdc::operator>>	(	std::istream &	in,
		UnitCell< 2 >::LatticeSystem &	lattice )

istream extractor for a 2D UnitCell<2>::LatticeSystem.

Parameters

in	input stream
lattice	UnitCell<2>::LatticeSystem to be read

Returns

modified input stream

Definition at line 157 of file UnitCell2.cpp.

References UTIL_THROW.

operator>>() [6/6]

std::istream & Pscf::Prdc::operator>>	(	std::istream &	in,
		UnitCell< 3 >::LatticeSystem &	lattice )

istream extractor for a 3D UnitCell<3>::LatticeSystem.

Parameters

in	input stream
lattice	UnitCell<3>::LatticeSystem to be read

Returns

modified input stream

Definition at line 326 of file UnitCell3.cpp.

References UTIL_THROW.

operator<<() [5/5]

std::ostream & Pscf::Prdc::operator<<	(	std::ostream &	out,
		UnitCell< 3 >::LatticeSystem	lattice )

ostream inserter for an 3D UnitCell<3>::LatticeSystem.

Parameters

out	output stream
lattice	UnitCell<3>::LatticeSystem to be written

Returns

modified output stream

Definition at line 361 of file UnitCell3.cpp.

References UTIL_THROW.