Detailed Description

A monoclinic periodic unit cell.

Definition at line 42 of file MonoclinicBoundary.h.

#include <MonoclinicBoundary.h>

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

void	setMonoclinic (const Vector &lengths, const double d)
	Set unit cell dimensions for orthorhombic boundary. More...

void	setOrthorhombic (const Vector &lengths)
	Invalid function for monoclinic - throws Exception. More...

template<class Archive >
void	serialize (Archive &ar, const unsigned int version)
	Serialize to/from an archive. More...

Periodic Boundary Conditions - Coordinate Shifting
void	shift (Vector &r) const
	Shift Vector r to its image within the primary unit cell. More...

void	shift (Vector &r, IntVector &shift) const
	Shift Vector r to its image within the primary unit cell. More...

void	shiftGen (Vector &r) const
	Shift generalized Vector r to its primary image. More...

void	shiftGen (Vector &r, IntVector &shift) const
	Shift generalized Vector r to its primary image. More...

void	applyShift (Vector &r, int i, int t) const
	Shift Cartesian Vector r by multiple t of a Bravais lattice vector. More...

Periodic Boundary Conditions - Minimum Image Separations
double	distanceSq (const Vector &r1, const Vector &r2) const
	Return square distance between r1 and r2, with minimum image convention. More...

double	distanceSq (const Vector &r1, const Vector &r2, IntVector &shift) const
	Return square distance between r1 and r2, with minimum image convention. More...

double	distanceSq (const Vector &r1, const Vector &r2, Vector &dr) const
	Return square distance between r1 and r2, with minimum image convention. More...

Coordinate Transformations
void	transformCartToGen (const Vector &Rc, Vector &Rg) const
	Transform Vector of Cartesian coordinates to generalized coordinates. More...

void	transformGenToCart (const Vector &Rg, Vector &Rc) const
	Transform Vector of generalized coordinates to Cartesian coordinates. More...

Accessors
LatticeSystem	latticeSystem ()
	Return actual lattice system. More...

const Vector &	lengths () const
	Get Vector of distances between faces of primitive cell. More...

double	length (int i) const
	Get distance across primitive cell along reciprocal basis vector i. More...

double	minLength () const
	Get minimum length across primitive unit cell. More...

double	volume () const
	Return unit cell volume. More...

const Vector &	bravaisBasisVector (int i) const
	Return Bravais lattice vector i. More...

const Vector &	reciprocalBasisVector (int i) const
	Return reciprocal lattice basis vector i. More...

void	randomPosition (Random &random, Vector &r) const
	Generate random Cartesian position within the primary unit cell. More...

bool	isValid ()
	Return true if valid, or throw Exception. More...

Friends
class	::MonoclinicBoundaryTest
	Unit test. More...

std::istream &	operator>> (std::istream &in, MonoclinicBoundary &boundary)
	istream extractor More...

std::ostream &	operator<< (std::ostream &out, const MonoclinicBoundary &boundary)
	ostream inserter More...

Constructor & Destructor Documentation

Simp::MonoclinicBoundary::MonoclinicBoundary ( )

Constructor.

Definition at line 23 of file MonoclinicBoundary.cpp.

References Util::Dimension, Util::Constants::Pi, and Util::Vector::Zero.

Member Function Documentation

void Simp::MonoclinicBoundary::setMonoclinic	(	const Vector &	lengths,
		const double	d
	)

Set unit cell dimensions for orthorhombic boundary.

Also sets all related lengths and volume.

Parameters

lengths	Vector of unit cell dimensions, orthogonal box.
d	displacement along z axis.

Definition at line 50 of file MonoclinicBoundary.cpp.

References lengths().

void Simp::MonoclinicBoundary::setOrthorhombic ( const Vector & lengths )

Invalid function for monoclinic - throws Exception.

Parameters

lengths Vector of unit cell dimensions, orthogonal box.

Definition at line 60 of file MonoclinicBoundary.cpp.

References Util::Dimension, lengths(), and Util::Constants::Pi.

template<class Archive >

void Simp::MonoclinicBoundary::serialize	(	Archive &	ar,
		const unsigned int	version
	)

Serialize to/from an archive.

Parameters

ar	saving or loading archive
version	archive version id

Definition at line 730 of file MonoclinicBoundary.h.

References Util::bcast< MonoclinicBoundary >(), isValid(), Util::recv< MonoclinicBoundary >(), and Util::send< MonoclinicBoundary >().

void Simp::MonoclinicBoundary::shift ( Vector & r ) const

inline

Shift Vector r to its image within the primary unit cell.

On output the vector r is shifted its image in the primary unit cell.

Parameters

r	Vector of coordinates

Definition at line 402 of file MonoclinicBoundary.h.

void Simp::MonoclinicBoundary::shift	(	Vector &	r,
		IntVector &	shift
	)		const

inline

Shift Vector r to its image within the primary unit cell.

This method shifts a vector to its image in the primary unit cell, and also increments a corresponding atomic shift IntVector:

If the Vector r is shifted by r -> r - sum_i t[i]*a_i, then the IntVector shift parameter is incremented by shift -> shift + t, where t is an IntVector and a_i is Bravais basis vector number i.

See also: Atom:shift()

Parameters

r	Vector of Cartesian coordinates
shift	integer shifts required to obtain "true" coordinates.

Definition at line 436 of file MonoclinicBoundary.h.

void Simp::MonoclinicBoundary::shiftGen ( Vector & r ) const

inline

Shift generalized Vector r to its primary image.

One output, each coordinate r[i] is shifted by an integer, so as to lie within the range 0 < r[i] < 1.0

Precondition: The algorithm assumes that on input, for each i=0,..,2, -1.0 < r[i] < 2.0, and throws an Exception otherwise.

Parameters

r	Vector of generalized coordinates

Definition at line 495 of file MonoclinicBoundary.h.

References Util::Dimension.

void Simp::MonoclinicBoundary::shiftGen	(	Vector &	r,
		IntVector &	shift
	)		const

inline

Shift generalized Vector r to its primary image.

This method maps a vector of generalized coordinates to lie in the primary cell, and also increments the atomic shift IntVector:

If r[i] -> r[i] - t, then shift[i] -> shift[i] + t.

See also: Atom:shift()

Parameters

r	Vector of generalized coordinates (in/out)
shift	integer shifts, modified on output (in/out)

Definition at line 513 of file MonoclinicBoundary.h.

References Util::Dimension.

void Simp::MonoclinicBoundary::applyShift	(	Vector &	r,
		int	i,
		int	t
	)		const

inline

Shift Cartesian Vector r by multiple t of a Bravais lattice vector.

This method shifts the Vector r by a specified amount:

r -> r + t*a_i

where a_i is Bravais lattice basis vector number i.

Parameters

r	Vector of Cartesian coordinates
i	index for direction (basis vector) of shift
t	multiple added of Bravais basis vector a_i

Definition at line 476 of file MonoclinicBoundary.h.

double Simp::MonoclinicBoundary::distanceSq	(	const Vector &	r1,
		const Vector &	r2
	)		const

inline

Return square distance between r1 and r2, with minimum image convention.

Parameters

r1	first position Vector
r2	second position Vector

Returns: square of distance between r1 and r2, using nearest image.

Definition at line 588 of file MonoclinicBoundary.h.

double Simp::MonoclinicBoundary::distanceSq	(	const Vector &	r1,
		const Vector &	r2,
		IntVector &	shift
	)		const

inline

Return square distance between r1 and r2, with minimum image convention.

Parameters

r1	first position Vector
r2	second position Vector
shift	shift added to r1 to create nearest image of r2.

Returns: square of distance between r1 and r2, using nearest image.

Definition at line 533 of file MonoclinicBoundary.h.

double Simp::MonoclinicBoundary::distanceSq	(	const Vector &	r1,
		const Vector &	r2,
		Vector &	dr
	)		const

inline

Return square distance between r1 and r2, with minimum image convention.

Upon return, Vector dr contains the separation r1 - r2, using the nearest image convention. Returns the square of the absolute magnitude of the separation dr.

Parameters

r1	first position Vector
r2	second position Vector
dr	separation Vector (upon return)

Returns: square of separation dr

Definition at line 632 of file MonoclinicBoundary.h.

References operator<<, and operator>>.

void Simp::MonoclinicBoundary::transformCartToGen	(	const Vector &	Rc,
		Vector &	Rg
	)		const

inline

Transform Vector of Cartesian coordinates to generalized coordinates.

Returns the generalized coordinates of Cartesian input Rc in output Rg.

Generalized coordinates range from 0.0 <= Rg[i] < 1.0 within the primitive cell, for i = 0,..,2.

Parameters

Rc	Vector of Cartesian coordinates (input)
Rg	Vector of generalized coordinates (output)

Definition at line 706 of file MonoclinicBoundary.h.

void Simp::MonoclinicBoundary::transformGenToCart	(	const Vector &	Rg,
		Vector &	Rc
	)		const

inline

Transform Vector of generalized coordinates to Cartesian coordinates.

Returns the Cartesian coordinates of input Rg in output Rc.

Parameters

Rg	Vector of generalized coordinates (input)
Rc	Vector of Cartesian coordinates (output)

Definition at line 718 of file MonoclinicBoundary.h.

Referenced by randomPosition().

LatticeSystem Simp::MonoclinicBoundary::latticeSystem ( )

inline

Return actual lattice system.

Return value for this class is Monoclinic.

Definition at line 699 of file MonoclinicBoundary.h.

const Vector & Simp::MonoclinicBoundary::lengths ( ) const

inline

Get Vector of distances between faces of primitive cell.

Each component of this vector is projection of a Bravais lattice unit vector onto a line parallel to the corresponding reciprocal lattice basis vector. The resulting distances are distances between faces of the primitive unit cell, which are normal to the reciprocal lattice unit vectors.

Definition at line 366 of file MonoclinicBoundary.h.

Referenced by setMonoclinic(), and setOrthorhombic().

double Simp::MonoclinicBoundary::length ( int i ) const

inline

Get distance across primitive cell along reciprocal basis vector i.

Parameters

i	index of Cartesian direction, 0 <= i < Dimension

Definition at line 372 of file MonoclinicBoundary.h.

double Simp::MonoclinicBoundary::minLength ( ) const

inline

Get minimum length across primitive unit cell.

Definition at line 396 of file MonoclinicBoundary.h.

double Simp::MonoclinicBoundary::volume ( ) const

inline

Return unit cell volume.

Definition at line 378 of file MonoclinicBoundary.h.

const Vector & Simp::MonoclinicBoundary::bravaisBasisVector ( int i ) const

inline

Return Bravais lattice vector i.

Parameters

i	basis Vector index.

Definition at line 384 of file MonoclinicBoundary.h.

const Vector & Simp::MonoclinicBoundary::reciprocalBasisVector ( int i ) const

inline

Return reciprocal lattice basis vector i.

Parameters

i	basis Vector index.

Definition at line 390 of file MonoclinicBoundary.h.

void Simp::MonoclinicBoundary::randomPosition	(	Random &	random,
		Vector &	r
	)		const

Generate random Cartesian position within the primary unit cell.

Parameters

random	random number generator object
r	Vector of random Cartesian coordinates (upon return)

Definition at line 106 of file MonoclinicBoundary.cpp.

References Util::Dimension, transformGenToCart(), and Util::Random::uniform().

bool Simp::MonoclinicBoundary::isValid ( )

Return true if valid, or throw Exception.

Definition at line 118 of file MonoclinicBoundary.cpp.

References Util::Dimension, Util::feq(), Util::Constants::Pi, and UTIL_THROW.

Referenced by serialize().

Friends And Related Function Documentation

friend class ::MonoclinicBoundaryTest

friend

Unit test.

Definition at line 333 of file MonoclinicBoundary.h.

std::istream& operator>>	(	std::istream &	in,
		MonoclinicBoundary &	boundary
	)

friend

istream extractor

Parameters

in	input stream
boundary	MonoclinicBoundary to be read from stream

Returns: modified input stream

Definition at line 161 of file MonoclinicBoundary.cpp.

Referenced by distanceSq().

std::ostream& operator<<	(	std::ostream &	out,
		const MonoclinicBoundary &	boundary
	)

friend

ostream inserter

Parameters

out	output stream
boundary	MonoclinicBoundary to be written to stream

Returns: modified output stream

Definition at line 178 of file MonoclinicBoundary.cpp.

Referenced by distanceSq().

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

Detailed Description

Public Member Functions

Friends

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation