PLMD::forceBoxTrajectory Class Reference

A decorator for forcing a box in the trajectory. More...

Inheritance diagram for PLMD::forceBoxTrajectory:

Public Member Functions
	forceBoxTrajectory (std::unique_ptr< AtomDistribution > &&d, std::array< double, 9 > mybox)
void	frame (std::vector< Vector > &posToUpdate, std::vector< double > &box, unsigned step, Random &rng)
	Update the input vectors with the position and the box of the frame.
void	frame (View< Vector > posToUpdate, View< double, 9 > box, unsigned step, Random &rng) override
	Update the input vectors with the position and the box of the frame.
bool	overrideNat (unsigned &natoms) override
	If necessary changes the number of atoms, returns true if that number has been changed.

Static Public Member Functions
static std::unique_ptr< AtomDistribution >	decorate (std::unique_ptr< AtomDistribution > &&d, std::string_view cmd)
static std::unique_ptr< AtomDistribution >	decorateAtomDistribution (std::unique_ptr< AtomDistribution > &&ad, std::string_view decoratorsDistr)
static std::unique_ptr< AtomDistribution >	getAtomDistribution (std::string_view atomicDistr)
static std::vector< documentation >	getDecoratorsDocumentation ()
static std::vector< std::string >	getDecoratorsList ()
static std::vector< documentation >	getDistributionDocumentation ()
static std::vector< std::string >	getDistributionList ()

Static Public Attributes
static constexpr auto	doc
static constexpr auto	id ="box"

Private Attributes
std::unique_ptr< AtomDistribution >	distribution
std::array< double, 9 >	fixedbox

Detailed Description

A decorator for forcing a box in the trajectory.

Constructor & Destructor Documentation

forceBoxTrajectory()

PLMD::forceBoxTrajectory::forceBoxTrajectory ( std::unique_ptr< AtomDistribution > && d, std::array< double, 9 > mybox )

inline

Member Function Documentation

decorate()

static std::unique_ptr< AtomDistribution > PLMD::forceBoxTrajectory::decorate ( std::unique_ptr< AtomDistribution > && d, std::string_view cmd )

inlinestatic

decorateAtomDistribution()

std::unique_ptr< AtomDistribution > PLMD::AtomDistribution::decorateAtomDistribution ( std::unique_ptr< AtomDistribution > && ad, std::string_view decoratorsDistr )

staticinherited

frame() [1/2]

void PLMD::AtomDistribution::frame ( std::vector< Vector > & posToUpdate, std::vector< double > & box, unsigned step, Random & rng )

inherited

Update the input vectors with the position and the box of the frame.

frame() [2/2]

void PLMD::forceBoxTrajectory::frame ( View< Vector > posToUpdate, View< double, 9 > box, unsigned step, Random & rng )

inlineoverridevirtual

Update the input vectors with the position and the box of the frame.

Implements PLMD::AtomDistribution.

getAtomDistribution()

std::unique_ptr< AtomDistribution > PLMD::AtomDistribution::getAtomDistribution ( std::string_view atomicDistr )

staticinherited

getDecoratorsDocumentation()

std::vector< AtomDistribution::documentation > PLMD::AtomDistribution::getDecoratorsDocumentation ( )

staticinherited

getDecoratorsList()

std::vector< std::string > PLMD::AtomDistribution::getDecoratorsList ( )

staticinherited

getDistributionDocumentation()

std::vector< AtomDistribution::documentation > PLMD::AtomDistribution::getDistributionDocumentation ( )

staticinherited

getDistributionList()

std::vector< std::string > PLMD::AtomDistribution::getDistributionList ( )

staticinherited

overrideNat()

bool PLMD::forceBoxTrajectory::overrideNat ( unsigned & )

inlineoverridevirtual

If necessary changes the number of atoms, returns true if that number has been changed.

This is used principally in the benchmark. All the atoms distributions usually acts all the atoms passed by the vector of positions, so this does not change the input

But the "reading file" ones will only work if the number of atoms is the same of the one in the file, so this set the input to that number

And in case of the ones that replicate the trajectory this multiplies the input by the number of replicated "systems" this this is needed to inform benchmark that if you asked for replicating N atoms X*Y*Z times it will need an array of N*X*Y*Z atoms Outside of the specific usecase of the benchmark this is less important, because replicate will generate the inner trjectory on a limited number of atoms and the it will replicate it

Reimplemented from PLMD::AtomDistribution.

Member Data Documentation

distribution

std::unique_ptr<AtomDistribution> PLMD::forceBoxTrajectory::distribution

private

doc

auto PLMD::forceBoxTrajectory::doc

staticconstexpr

Initial value:

=R"=(Forces a box on the atom distribution
usage:
  box xx yy zz
 or
  box xx xy xy yx yy yz zx zy zz)="

fixedbox

std::array<double,9> PLMD::forceBoxTrajectory::fixedbox

private

id

auto PLMD::forceBoxTrajectory::id ="box"

staticconstexpr

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

• tools/AtomDistribution.cpp