PLMD::Pbc Class Reference

#include <Pbc.h>

Public Member Functions
	Pbc ()
	Constructor. More...
double	distance (const bool pbc, const Vector &v1, const Vector &v2) const
	Compute modulo of (v2-v1), using or not pbc depending on bool pbc. More...
Vector	distance (const Vector &v1, const Vector &v2) const
	Computes v2-v1, using minimal image convention. More...
void	setBox (const Tensor &b)
	Set the lattice vectors. More...
const Tensor &	getBox () const
	Returns the box. More...
const Tensor &	getInvBox () const
	Returns the inverse matrix of box. More...
Vector	realToScaled (const Vector &) const
	Transform a vector in real space to a vector in scaled coordinates. More...
Vector	scaledToReal (const Vector &) const
	Transform a vector in scaled coordinates to a vector in real space. More...
bool	isOrthorombic () const
	Returns true if the box vectors are orthogonal. More...

Static Public Member Functions
static void	test ()
	Perform some check. Useful for debugging. More...

Private Types
enum	{ unset, orthorombic, generic }
	Type of box. More...

Private Member Functions
void	buildShifts (std::vector< Vector > shifts[2][2][2]) const
	Build list of shifts. More...
void	fullSearch (Vector &) const
	Full search (for testing) More...
Vector	distance (const Vector &, const Vector &, int *nshifts) const
	internal version of distance, also returns the number of attempted shifts (used in Pbc::test()). More...

Private Attributes
enum PLMD::Pbc:: { ... }	type
	Type of box. More...
Tensor	box
	Box. More...
Tensor	invBox
	Inverse box. More...
Tensor	reduced
	Reduced box. More...
Tensor	invReduced
	Inverse of the reduced box. More...
std::vector< Vector >	shifts [2][2][2]
	List of shifts that should be attempted. More...
Vector	diag
	Alternative representation for orthorombic cells. More...
Vector	hdiag
Vector	mdiag

Detailed Description

Definition at line 38 of file Pbc.h.

Member Enumeration Documentation

anonymous enum

private

Type of box.

Enumerator
unset
orthorombic
generic

Definition at line 40 of file Pbc.h.

Constructor & Destructor Documentation

PLMD::Pbc::Pbc

(

)

Constructor.

Definition at line 32 of file Pbc.cpp.

Member Function Documentation

void PLMD::Pbc::buildShifts ( std::vector< Vector >  shifts[2][2][2] ) const

private

Build list of shifts.

This is expensive, and must be called only when box is reset. It allows building a minimal set of shifts depending on the sign of the scaled coordinates representing a distance vector.

Definition at line 39 of file Pbc.cpp.

Vector PLMD::Pbc::distance ( const Vector &  v1, const Vector &  v2, int *  nshifts  ) const

private

internal version of distance, also returns the number of attempted shifts (used in Pbc::test()).

Definition at line 158 of file Pbc.cpp.

double PLMD::Pbc::distance	(	const bool	pbc,
		const Vector &	v1,
		const Vector &	v2
	)		const

Compute modulo of (v2-v1), using or not pbc depending on bool pbc.

Definition at line 153 of file Pbc.cpp.

Vector PLMD::Pbc::distance ( const Vector &  v1, const Vector &  v2  ) const

inline

Computes v2-v1, using minimal image convention.

Definition at line 98 of file Pbc.h.

void PLMD::Pbc::fullSearch ( Vector &  d ) const

private

Full search (for testing)

Definition at line 93 of file Pbc.cpp.

const Tensor & PLMD::Pbc::getBox

(

)

const

Returns the box.

Definition at line 214 of file Pbc.cpp.

const Tensor & PLMD::Pbc::getInvBox

(

)

const

Returns the inverse matrix of box.

Thus: pbc.getInvBox() == inverse(pbc.getBox()).

Definition at line 218 of file Pbc.cpp.

bool PLMD::Pbc::isOrthorombic

(

)

const

Returns true if the box vectors are orthogonal.

Definition at line 210 of file Pbc.cpp.

Vector PLMD::Pbc::realToScaled

(

const Vector &

d

)

const

Transform a vector in real space to a vector in scaled coordinates.

Thus:pbc.realToScaled(v) == matmul(transpose(inverse(pbc.getBox(),v)));

Definition at line 202 of file Pbc.cpp.

Vector PLMD::Pbc::scaledToReal

(

const Vector &

d

)

const

Transform a vector in scaled coordinates to a vector in real space.

Thus:pbc.scaledToRead(v) == matmul(transpose(pbc.getBox()),v);

Definition at line 206 of file Pbc.cpp.

void PLMD::Pbc::setBox

(

const Tensor &

b

)

Set the lattice vectors.

b[i][j] is the j-th component of the i-th vector

Definition at line 115 of file Pbc.cpp.

void PLMD::Pbc::test ( )

static

Perform some check. Useful for debugging.

Definition at line 222 of file Pbc.cpp.

Member Data Documentation

Tensor PLMD::Pbc::box

private

Box.

Definition at line 42 of file Pbc.h.

Vector PLMD::Pbc::diag

private

Alternative representation for orthorombic cells.

Not really used, but could be used to optimize search in orthorombic cells.

Definition at line 58 of file Pbc.h.

Vector PLMD::Pbc::hdiag

private

Definition at line 58 of file Pbc.h.

Tensor PLMD::Pbc::invBox

private

Inverse box.

Definition at line 44 of file Pbc.h.

Tensor PLMD::Pbc::invReduced

private

Inverse of the reduced box.

Definition at line 50 of file Pbc.h.

Vector PLMD::Pbc::mdiag

private

Definition at line 58 of file Pbc.h.

Tensor PLMD::Pbc::reduced

private

Reduced box.

This is a set of lattice vectors generating the same lattice but "minimally skewed". Useful to optimize image search.

Definition at line 48 of file Pbc.h.

std::vector<Vector> PLMD::Pbc::shifts[2][2][2]

private

List of shifts that should be attempted.

Depending on the sign of the scaled coordinates representing a distance vector, a different set of shifts must be tried.

Definition at line 54 of file Pbc.h.

enum { ... } PLMD::Pbc::type

Type of box.

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

• tools/Pbc.h
• tools/Pbc.cpp