PLMD::Pbc Class Reference

#include <Pbc.h>

Public Member Functions
	Pbc ()
	Constructor.
void	apply (std::vector< Vector > &dlist, unsigned max_index=0) const
void	apply (VectorView dlist, unsigned max_index=0) const
	Apply PBC to a set of positions or distance vectors.
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.
Vector	distance (const Vector &, const Vector &, int *nshifts=nullptr) const
	Computes v2-v1, using minimal image convention if specified, also returns the number of attempted shifts.
void	fullSearch (Vector &) const
	Full search (for testing).
const Tensor &	getBox () const
	Returns the box.
const Tensor &	getInvBox () const
	Returns the inverse matrix of box.
bool	isOrthorombic () const
	Returns true if the box vectors are orthogonal.
bool	isSet () const
	Returns true if box is set and non zero.
Vector	realToScaled (const Vector &) const
	Transform a vector in real space to a vector in scaled coordinates.
Vector	scaledToReal (const Vector &) const
	Transform a vector in scaled coordinates to a vector in real space.
void	setBox (const Tensor &b)
	Set the lattice vectors.

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

Private Member Functions
void	buildShifts (gch::small_vector< Vector, maxshiftsize > shifts[2][2][2]) const
	Build list of shifts.

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

Static Private Attributes
static constexpr unsigned	maxshiftsize =6
	This is the maximum expected size for general boxes.

Member Enumeration Documentation

anonymous enum

anonymous enum

private

Type of box.

Enumerator
unset
orthorombic
generic

Constructor & Destructor Documentation

Pbc()

PLMD::Pbc::Pbc

(

)

Constructor.

Member Function Documentation

apply() [1/2]

void PLMD::Pbc::apply	(	std::vector< Vector > &	dlist,
		unsigned	max_index = 0 ) const

apply() [2/2]

void PLMD::Pbc::apply	(	VectorView	dlist,
		unsigned	max_index = 0 ) const

Apply PBC to a set of positions or distance vectors.

buildShifts()

void PLMD::Pbc::buildShifts ( gch::small_vector< Vector, maxshiftsize > 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.

distance() [1/2]

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.

distance() [2/2]

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

Computes v2-v1, using minimal image convention if specified, also returns the number of attempted shifts.

fullSearch()

void PLMD::Pbc::fullSearch

(

Vector &

d

)

const

Full search (for testing).

Perform a full search on vector

getBox()

const Tensor & PLMD::Pbc::getBox

(

)

const

Returns the box.

getInvBox()

const Tensor & PLMD::Pbc::getInvBox

(

)

const

Returns the inverse matrix of box.

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

isOrthorombic()

bool PLMD::Pbc::isOrthorombic

(

)

const

Returns true if the box vectors are orthogonal.

isSet()

bool PLMD::Pbc::isSet ( ) const

inline

Returns true if box is set and non zero.

realToScaled()

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)));

scaledToReal()

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);

setBox()

void PLMD::Pbc::setBox

(

const Tensor &

b

)

Set the lattice vectors.

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

Member Data Documentation

box

Tensor PLMD::Pbc::box

private

Box.

diag

Vector PLMD::Pbc::diag

private

Alternative representation for orthorombic cells.

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

hdiag

Vector PLMD::Pbc::hdiag

private

invBox

Tensor PLMD::Pbc::invBox

private

Inverse box.

invReduced

Tensor PLMD::Pbc::invReduced

private

Inverse of the reduced box.

maxshiftsize

unsigned PLMD::Pbc::maxshiftsize =6

staticconstexprprivate

This is the maximum expected size for general boxes.

I found this empirically by manually modifying regtest basic/rt-make-1 Since it uses randomly generated boxes it should be correct. In any case, this is just used as a hint for small_vector, which will then switch to heap allocations if more shifts are needed

mdiag

Vector PLMD::Pbc::mdiag

private

reduced

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.

shifts

gch::small_vector<Vector,maxshiftsize> 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.

[]

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