#include <AverageOnGrid.h>

Inheritance diagram for PLMD::gridtools::AverageOnGrid:

[legend]

Public Member Functions
	AverageOnGrid (const vesselbase::VesselOptions &da)

void	accumulate (const unsigned &ipoint, const double &weight, const double &dens, const std::vector< double > &der, std::vector< double > &buffer) const

void	accumulateForce (const unsigned &ipoint, const double &weight, const std::vector< double > &der, std::vector< double > &intforce) const

double	getGridElement (const unsigned &ipoint, const unsigned &jelement) const
	Get the value of the ith grid element. More...

unsigned	getNumberOfComponents () const
	Get the number of components in the vector stored on each grid point. More...

void	getFinalForces (const std::vector< double > &buffer, std::vector< double > &finalForces)
	This retrieves the final force. More...

void	setBounds (const std::vector< std::string > &smin, const std::vector< std::string > &smax, const std::vector< unsigned > &nbins, const std::vector< double > &spacing)
	Set the minimum and maximum of the grid. More...

void	calculate (const unsigned &current, MultiValue &myvals, std::vector< double > &buffer, std::vector< unsigned > &der_list) const
	Copy data from the action into the grid. More...

void	finish (const std::vector< double > &buffer)
	Finish the calculation. More...

unsigned	getNumberOfBufferPoints () const
	Get the number of points needed in the buffer. More...

KernelFunctions *	getKernelAndNeighbors (std::vector< double > &point, unsigned &num_neigh, std::vector< unsigned > &neighbors) const

std::vector< Value * >	getVectorOfValues () const

void	addOneKernelEachTimeOnly ()

bool	noDiscreteKernels () const

double	getFibonacciCutoff () const
	Get the cutoff to use for the Fibonacci spheres. More...

unsigned	getIndex (const std::vector< unsigned > &indices) const
	Flatten the grid and get the grid index for a point. More...

void	setNoDerivatives ()
	Remove the derivatives. More...

std::string	getType () const
	Get the type of grid we are using. More...

void	setupFibonacciGrid (const unsigned &np)
	Setup the grid if it is a fibonacci grid on the surface of a sphere. More...

std::string	description ()
	Get a description of the grid to output to the log. More...

void	convertIndexToIndices (const unsigned &index, const std::vector< unsigned > &nnbin, std::vector< unsigned > &indices) const
	Convert an index into indices. More...

void	getIndices (const unsigned &index, std::vector< unsigned > &indices) const
	Get the indices fof a point. More...

void	getIndices (const std::vector< double > &point, std::vector< unsigned > &indices) const
	Get the indices of a particular point. More...

void	setGridElement (const unsigned &, const unsigned &, const double &)
	Operations on one of the elements of grid point i. More...

void	setGridElement (const std::vector< unsigned > &, const unsigned &, const double &)

void	addToGridElement (const unsigned &ipoint, const unsigned &jelement, const double &value)
	Add data to an element of the grid. More...

double	getGridElement (const std::vector< unsigned > &, const unsigned &) const
	Operations on one of the elements of grid point specified by vector. More...

virtual void	resize ()
	Set the size of the buffer equal to nper*npoints. More...

unsigned	getNumberOfPoints () const
	Get the number of points in the grid. More...

void	getGridPointCoordinates (const unsigned &, std::vector< double > &) const
	Get the coordinates for a point in the grid. More...

void	getGridPointCoordinates (const unsigned &, std::vector< unsigned > &, std::vector< double > &) const

unsigned	getDimension () const
	Get the dimensionality of the function. More...

bool	isPeriodic (const unsigned &i) const
	Is the grid periodic in the ith direction. More...

unsigned	getNumberOfQuantities () const
	Get the number of quantities we have stored at each grid point. More...

std::vector< unsigned >	getNbin () const
	Get the number of grid points for each dimension. More...

std::string	getComponentName (const unsigned &i) const
	Get the name of the ith component. More...

std::vector< std::string >	getMin () const
	Get the vector containing the minimum value of the grid in each dimension. More...

std::vector< std::string >	getMax () const
	Get the vector containing the maximum value of the grid in each dimension. More...

const std::vector< unsigned > &	getStride () const
	Get the stride (the distance between the grid points of an index) More...

double	getCellVolume () const
	Return the volume of one of the grid cells. More...

void	getNeighbors (const std::vector< double > &pp, const std::vector< unsigned > &nneigh, unsigned &num_neighbours, std::vector< unsigned > &neighbors) const
	Get the set of points neighouring a particular location in space. More...

void	getNeighbors (const std::vector< unsigned > &indices, const std::vector< unsigned > &nneigh, unsigned &num_neighbors, std::vector< unsigned > &neighbors) const
	Get the neighbors for a set of indices of a point. More...

void	getSplineNeighbors (const unsigned &mybox, std::vector< unsigned > &mysneigh) const
	Get the points neighboring a particular spline point. More...

const std::vector< double > &	getGridSpacing () const
	Get the spacing between grid points. More...

double	getGridExtent (const unsigned &i) const
	Get the extent of the grid in one of the axis. More...

void	setCubeUnits (const double &units)
	This ensures that Gaussian cube fies are in correct units. More...

double	getCubeUnits () const
	This ensures that Gaussian cube files are in correct units. More...

std::string	getInputString () const
	Return a string containing the input to the grid so we can clone it. More...

bool	noDerivatives () const
	Does this have derivatives. More...

double	getValueAndDerivatives (const std::vector< double > &x, const unsigned &ind, std::vector< double > &der) const
	Get the value and derivatives at a particular location using spline interpolation. More...

void	activateThesePoints (const std::vector< bool > &to_activate)
	Deactivate all the grid points. More...

bool	inactive (const unsigned &ip) const
	Is this point active. More...

void	setForce (const std::vector< double > &inforces)
	Apply the forces. More...

bool	wasForced () const
	Was a force added to the grid. More...

bool	applyForce (std::vector< double > &fforces)
	And retrieve the forces. More...

bool	wasreset () const
	Was the grid cleared on the last step. More...

virtual void	clear ()
	Clear all the data stored on the grid. More...

virtual void	reset ()
	Reset the grid so that it is cleared at start of next time it is calculated. More...

void	setNorm (const double &snorm)
	Functions for dealing with normalisation constant. More...

double	getNorm () const

std::string	getName () const
	Return the name. More...

std::string	getLabel () const
	Return the label. More...

void	checkRead ()
	Check that readin was fine. More...

virtual void	setBufferStart (unsigned &start)
	Set the start of the buffer. More...

virtual void	prepare ()
	Do something before the loop. More...

virtual MultiValue &	transformDerivatives (const unsigned &current, MultiValue &myvals, MultiValue &bvals)
	This is replaced in bridges so we can transform the derivatives. More...

Static Public Member Functions
static void	registerKeywords (Keywords &keys)

static std::string	transformName (const std::string &name)
	Convert the name to the label of the component. More...

Public Attributes
double	von_misses_norm

double	von_misses_concentration

Log &	log
	Reference to the log on which to output details. More...

Protected Member Functions
unsigned	getIndex (const std::vector< double > &p) const
	Convert a point in space the the correspoinding grid point. More...

unsigned	getFibonacciIndex (const std::vector< double > &p) const
	Get the index of the closest point on the fibonacci sphere. More...

void	getFlatGridCoordinates (const unsigned &ipoint, std::vector< unsigned > &tindices, std::vector< double > &x) const
	Get the flat grid coordinates. More...

void	getFibonacciCoordinates (const unsigned &ipoint, std::vector< double > &x) const
	Get the coordinates on the Fibonacci grid. More...

void	setDataSize (const unsigned &size)
	Set the size of the data vector. More...

void	setDataElement (const unsigned &myelem, const double &value)
	Set an element of the data array. More...

void	addDataElement (const unsigned &myelem, const double &value)
	Add some value to an element of the data array. More...

double	getDataElement (const unsigned &myelem) const
	Get the value of one of the data element. More...

bool	noAverage () const
	Are we averaging the data. More...

int	getNumericalLabel () const
	Return the numerical label. More...

void	error (const std::string &errmsg)
	Report an error. More...

template<class T >
void	parse (const std::string &key, T &t)
	Parse something from the input. More...

template<class T >
void	parseVector (const std::string &key, std::vector< T > &t)
	Parse one keyword as std::vector. More...

void	parseFlag (const std::string &key, bool &t)
	Parse one keyword as boolean flag. More...

std::string	getAllInput ()
	This returns the whole input line (it is used for less_than/more_than/between) More...

ActionWithVessel *	getAction () const
	Return a pointer to the action we are working in. More...

double	getTolerance () const
	Return the value of the tolerance. More...

double	getNLTolerance () const
	Return the value of the neighbor list tolerance. More...

unsigned	getSizeOfBuffer () const
	Return the size of the buffer. More...

void	resizeBuffer (const unsigned &n)
	Set the size of the data buffer. More...

Protected Attributes
bool	discrete

bool	wasforced
	Is forced. More...

std::vector< double >	forces
	Forces acting on grid elements. More...

bool	noderiv
	Do we have derivatives. More...

std::vector< std::string >	arg_names
	The names of the various columns in the grid file. More...

unsigned	nper
	The number of pieces of information we are storing for each point in the grid. More...

std::vector< bool >	pbc
	Is this direction periodic. More...

std::vector< std::string >	str_min
	The minimum and maximum in the grid stored as strings. More...

std::vector< std::string >	str_max

std::vector< double >	dx
	The spacing between grid points. More...

unsigned	dimension
	The dimensionality of the grid. More...

std::vector< bool >	active
	Which grid points are we actively accumulating. More...

unsigned	bufstart
	The start of this Vessel's buffer in buffer in the underlying ActionWithVessel. More...

Communicator &	comm
	A copy of the communicator. More...

Constructor & Destructor Documentation

◆ AverageOnGrid()

PLMD::gridtools::AverageOnGrid::AverageOnGrid ( const vesselbase::VesselOptions & da )

explicit

Member Function Documentation

◆ accumulate()

void PLMD::gridtools::AverageOnGrid::accumulate	(	const unsigned &	ipoint,
		const double &	weight,
		const double &	dens,
		const std::vector< double > &	der,
		std::vector< double > &	buffer
	)		const

virtual

Reimplemented from PLMD::gridtools::HistogramOnGrid.

◆ accumulateForce()

void PLMD::gridtools::AverageOnGrid::accumulateForce	(	const unsigned &	ipoint,
		const double &	weight,
		const std::vector< double > &	der,
		std::vector< double > &	intforce
	)		const

inlinevirtual

Reimplemented from PLMD::gridtools::HistogramOnGrid.

◆ activateThesePoints()

void PLMD::gridtools::GridVessel::activateThesePoints ( const std::vector< bool > & to_activate )

inherited

Deactivate all the grid points.

◆ addDataElement()

void PLMD::vesselbase::AveragingVessel::addDataElement	(	const unsigned &	myelem,
		const double &	value
	)

inlineprotectedinherited

Add some value to an element of the data array.

◆ addOneKernelEachTimeOnly()

void PLMD::gridtools::HistogramOnGrid::addOneKernelEachTimeOnly ( )

inlineinherited

◆ addToGridElement()

void PLMD::gridtools::GridVessel::addToGridElement	(	const unsigned &	ipoint,
		const unsigned &	jelement,
		const double &	value
	)

inherited

Add data to an element of the grid.

◆ applyForce()

bool PLMD::gridtools::GridVessel::applyForce ( std::vector< double > & fforces )

virtualinherited

And retrieve the forces.

Reimplemented from PLMD::vesselbase::AveragingVessel.

◆ calculate()

void PLMD::gridtools::HistogramOnGrid::calculate	(	const unsigned &	current,
		MultiValue &	myvals,
		std::vector< double > &	buffer,
		std::vector< unsigned > &	der_list
	)		const

virtualinherited

Copy data from the action into the grid.

Reimplemented from PLMD::gridtools::GridVessel.

◆ checkRead()

void PLMD::vesselbase::Vessel::checkRead ( )

inherited

Check that readin was fine.

◆ clear()

void PLMD::vesselbase::AveragingVessel::clear ( )

virtualinherited

Clear all the data stored on the grid.

◆ convertIndexToIndices()

void PLMD::gridtools::GridVessel::convertIndexToIndices	(	const unsigned &	index,
		const std::vector< unsigned > &	nnbin,
		std::vector< unsigned > &	indices
	)		const

inherited

Convert an index into indices.

◆ description()

std::string PLMD::gridtools::GridVessel::description ( )

virtualinherited

Get a description of the grid to output to the log.

Implements PLMD::vesselbase::Vessel.

◆ error()

void PLMD::vesselbase::Vessel::error ( const std::string & errmsg )

protectedinherited

Report an error.

◆ finish()

void PLMD::gridtools::HistogramOnGrid::finish ( const std::vector< double > & buffer )

virtualinherited

Finish the calculation.

Reimplemented from PLMD::gridtools::GridVessel.

◆ getAction()

ActionWithVessel * PLMD::vesselbase::Vessel::getAction ( ) const

inlineprotectedinherited

Return a pointer to the action we are working in.

◆ getAllInput()

std::string PLMD::vesselbase::Vessel::getAllInput ( )

protectedinherited

This returns the whole input line (it is used for less_than/more_than/between)

◆ getCellVolume()

double PLMD::gridtools::GridVessel::getCellVolume ( ) const

inlineinherited

Return the volume of one of the grid cells.

◆ getComponentName()

std::string PLMD::gridtools::GridVessel::getComponentName ( const unsigned & i ) const

inlineinherited

Get the name of the ith component.

◆ getCubeUnits()

double PLMD::gridtools::GridVessel::getCubeUnits ( ) const

inherited

This ensures that Gaussian cube files are in correct units.

◆ getDataElement()

double PLMD::vesselbase::AveragingVessel::getDataElement ( const unsigned & myelem ) const

inlineprotectedinherited

Get the value of one of the data element.

◆ getDimension()

unsigned PLMD::gridtools::GridVessel::getDimension ( ) const

inlineinherited

Get the dimensionality of the function.

◆ getFibonacciCoordinates()

void PLMD::gridtools::GridVessel::getFibonacciCoordinates	(	const unsigned &	ipoint,
		std::vector< double > &	x
	)		const

protectedinherited

Get the coordinates on the Fibonacci grid.

◆ getFibonacciCutoff()

double PLMD::gridtools::HistogramOnGrid::getFibonacciCutoff ( ) const

virtualinherited

Get the cutoff to use for the Fibonacci spheres.

Reimplemented from PLMD::gridtools::GridVessel.

◆ getFibonacciIndex()

unsigned PLMD::gridtools::GridVessel::getFibonacciIndex ( const std::vector< double > & p ) const

protectedinherited

Get the index of the closest point on the fibonacci sphere.

◆ getFinalForces()

void PLMD::gridtools::AverageOnGrid::getFinalForces	(	const std::vector< double > &	buffer,
		std::vector< double > &	finalForces
	)

inlinevirtual

This retrieves the final force.

Reimplemented from PLMD::gridtools::HistogramOnGrid.

◆ getFlatGridCoordinates()

void PLMD::gridtools::GridVessel::getFlatGridCoordinates	(	const unsigned &	ipoint,
		std::vector< unsigned > &	tindices,
		std::vector< double > &	x
	)		const

protectedinherited

Get the flat grid coordinates.

◆ getGridElement() [1/2]

double PLMD::gridtools::AverageOnGrid::getGridElement	(	const unsigned &	ipoint,
		const unsigned &	jelement
	)		const

virtual

Get the value of the ith grid element.

Reimplemented from PLMD::gridtools::GridVessel.

◆ getGridElement() [2/2]

double PLMD::gridtools::GridVessel::getGridElement	(	const std::vector< unsigned > &	indices,
		const unsigned &	jelement
	)		const

inherited

Operations on one of the elements of grid point specified by vector.

◆ getGridExtent()

double PLMD::gridtools::GridVessel::getGridExtent ( const unsigned & i ) const

inlineinherited

Get the extent of the grid in one of the axis.

◆ getGridPointCoordinates() [1/2]

void PLMD::gridtools::GridVessel::getGridPointCoordinates	(	const unsigned &	ipoint,
		std::vector< double > &	x
	)		const

inherited

Get the coordinates for a point in the grid.

◆ getGridPointCoordinates() [2/2]

void PLMD::gridtools::GridVessel::getGridPointCoordinates	(	const unsigned &	ipoint,
		std::vector< unsigned > &	tindices,
		std::vector< double > &	x
	)		const

inherited

◆ getGridSpacing()

const std::vector< double > & PLMD::gridtools::GridVessel::getGridSpacing ( ) const

inlineinherited

Get the spacing between grid points.

◆ getIndex() [1/2]

unsigned PLMD::gridtools::GridVessel::getIndex ( const std::vector< double > & p ) const

protectedinherited

Convert a point in space the the correspoinding grid point.

◆ getIndex() [2/2]

unsigned PLMD::gridtools::GridVessel::getIndex ( const std::vector< unsigned > & indices ) const

inherited

Flatten the grid and get the grid index for a point.

◆ getIndices() [1/2]

void PLMD::gridtools::GridVessel::getIndices	(	const unsigned &	index,
		std::vector< unsigned > &	indices
	)		const

inherited

Get the indices fof a point.

◆ getIndices() [2/2]

void PLMD::gridtools::GridVessel::getIndices	(	const std::vector< double > &	point,
		std::vector< unsigned > &	indices
	)		const

inherited

Get the indices of a particular point.

◆ getInputString()

std::string PLMD::gridtools::GridVessel::getInputString ( ) const

inherited

Return a string containing the input to the grid so we can clone it.

◆ getKernelAndNeighbors()

KernelFunctions * PLMD::gridtools::HistogramOnGrid::getKernelAndNeighbors	(	std::vector< double > &	point,
		unsigned &	num_neigh,
		std::vector< unsigned > &	neighbors
	)		const

inherited

◆ getLabel()

std::string PLMD::vesselbase::Vessel::getLabel ( ) const

inherited

Return the label.

◆ getMax()

std::vector< std::string > PLMD::gridtools::GridVessel::getMax ( ) const

inherited

Get the vector containing the maximum value of the grid in each dimension.

◆ getMin()

std::vector< std::string > PLMD::gridtools::GridVessel::getMin ( ) const

inherited

Get the vector containing the minimum value of the grid in each dimension.

◆ getName()

std::string PLMD::vesselbase::Vessel::getName ( ) const

inherited

Return the name.

◆ getNbin()

std::vector< unsigned > PLMD::gridtools::GridVessel::getNbin ( ) const

inherited

Get the number of grid points for each dimension.

◆ getNeighbors() [1/2]

void PLMD::gridtools::GridVessel::getNeighbors	(	const std::vector< double > &	pp,
		const std::vector< unsigned > &	nneigh,
		unsigned &	num_neighbours,
		std::vector< unsigned > &	neighbors
	)		const

inherited

Get the set of points neighouring a particular location in space.

◆ getNeighbors() [2/2]

void PLMD::gridtools::GridVessel::getNeighbors	(	const std::vector< unsigned > &	indices,
		const std::vector< unsigned > &	nneigh,
		unsigned &	num_neighbors,
		std::vector< unsigned > &	neighbors
	)		const

inherited

Get the neighbors for a set of indices of a point.

◆ getNLTolerance()

double PLMD::vesselbase::Vessel::getNLTolerance ( ) const

inlineprotectedinherited

Return the value of the neighbor list tolerance.

◆ getNorm()

double PLMD::vesselbase::AveragingVessel::getNorm ( ) const

inlineinherited

◆ getNumberOfBufferPoints()

unsigned PLMD::gridtools::HistogramOnGrid::getNumberOfBufferPoints ( ) const

inlinevirtualinherited

Get the number of points needed in the buffer.

Reimplemented from PLMD::gridtools::GridVessel.

◆ getNumberOfComponents()

unsigned PLMD::gridtools::AverageOnGrid::getNumberOfComponents ( ) const

inlinevirtual

Get the number of components in the vector stored on each grid point.

Reimplemented from PLMD::gridtools::GridVessel.

◆ getNumberOfPoints()

unsigned PLMD::gridtools::GridVessel::getNumberOfPoints ( ) const

inlineinherited

Get the number of points in the grid.

◆ getNumberOfQuantities()

unsigned PLMD::gridtools::GridVessel::getNumberOfQuantities ( ) const

inlineinherited

Get the number of quantities we have stored at each grid point.

◆ getNumericalLabel()

int PLMD::vesselbase::Vessel::getNumericalLabel ( ) const

inlineprotectedinherited

Return the numerical label.

◆ getSizeOfBuffer()

unsigned PLMD::vesselbase::Vessel::getSizeOfBuffer ( ) const

inlineprotectedinherited

Return the size of the buffer.

◆ getSplineNeighbors()

void PLMD::gridtools::GridVessel::getSplineNeighbors	(	const unsigned &	mybox,
		std::vector< unsigned > &	mysneigh
	)		const

inherited

Get the points neighboring a particular spline point.

◆ getStride()

const std::vector< unsigned > & PLMD::gridtools::GridVessel::getStride ( ) const

inlineinherited

Get the stride (the distance between the grid points of an index)

◆ getTolerance()

double PLMD::vesselbase::Vessel::getTolerance ( ) const

inlineprotectedinherited

Return the value of the tolerance.

◆ getType()

std::string PLMD::gridtools::GridVessel::getType ( ) const

inlineinherited

Get the type of grid we are using.

◆ getValueAndDerivatives()

double PLMD::gridtools::GridVessel::getValueAndDerivatives	(	const std::vector< double > &	x,
		const unsigned &	ind,
		std::vector< double > &	der
	)		const

inherited

Get the value and derivatives at a particular location using spline interpolation.

◆ getVectorOfValues()

std::vector< Value * > PLMD::gridtools::HistogramOnGrid::getVectorOfValues ( ) const

inherited

◆ inactive()

bool PLMD::gridtools::GridVessel::inactive ( const unsigned & ip ) const

inlineinherited

Is this point active.

◆ isPeriodic()

bool PLMD::gridtools::GridVessel::isPeriodic ( const unsigned & i ) const

inlineinherited

Is the grid periodic in the ith direction.

◆ noAverage()

bool PLMD::vesselbase::AveragingVessel::noAverage ( ) const

inlineprotectedinherited

Are we averaging the data.

◆ noDerivatives()

bool PLMD::gridtools::GridVessel::noDerivatives ( ) const

inlineinherited

Does this have derivatives.

◆ noDiscreteKernels()

bool PLMD::gridtools::HistogramOnGrid::noDiscreteKernels ( ) const

inherited

◆ parse()

template<class T >

void PLMD::vesselbase::Vessel::parse	(	const std::string &	key,
		T &	t
	)

protectedinherited

Parse something from the input.

◆ parseFlag()

void PLMD::vesselbase::Vessel::parseFlag	(	const std::string &	key,
		bool &	t
	)

protectedinherited

Parse one keyword as boolean flag.

◆ parseVector()

template<class T >

void PLMD::vesselbase::Vessel::parseVector	(	const std::string &	key,
		std::vector< T > &	t
	)

protectedinherited

Parse one keyword as std::vector.

◆ prepare()

virtual void PLMD::vesselbase::Vessel::prepare ( )

inlinevirtualinherited

Do something before the loop.

Reimplemented in PLMD::vesselbase::BridgeVessel, and PLMD::mapping::SpathVessel.

◆ registerKeywords()

void PLMD::gridtools::AverageOnGrid::registerKeywords ( Keywords & keys )

static

◆ reset()

void PLMD::vesselbase::AveragingVessel::reset ( )

virtualinherited

Reset the grid so that it is cleared at start of next time it is calculated.

◆ resize()

void PLMD::gridtools::GridVessel::resize ( )

virtualinherited

Set the size of the buffer equal to nper*npoints.

Implements PLMD::vesselbase::Vessel.

◆ resizeBuffer()

void PLMD::vesselbase::Vessel::resizeBuffer ( const unsigned & n )

inlineprotectedinherited

Set the size of the data buffer.

◆ setBounds()

void PLMD::gridtools::HistogramOnGrid::setBounds	(	const std::vector< std::string > &	smin,
		const std::vector< std::string > &	smax,
		const std::vector< unsigned > &	nbins,
		const std::vector< double > &	spacing
	)

virtualinherited

Set the minimum and maximum of the grid.

Reimplemented from PLMD::gridtools::GridVessel.

◆ setBufferStart()

void PLMD::vesselbase::Vessel::setBufferStart ( unsigned & start )

inlinevirtualinherited

Set the start of the buffer.

Reimplemented in PLMD::vesselbase::BridgeVessel.

◆ setCubeUnits()

void PLMD::gridtools::GridVessel::setCubeUnits ( const double & units )

inherited

This ensures that Gaussian cube fies are in correct units.

◆ setDataElement()

void PLMD::vesselbase::AveragingVessel::setDataElement	(	const unsigned &	myelem,
		const double &	value
	)

inlineprotectedinherited

Set an element of the data array.

◆ setDataSize()

void PLMD::vesselbase::AveragingVessel::setDataSize ( const unsigned & size )

protectedinherited

Set the size of the data vector.

◆ setForce()

void PLMD::gridtools::GridVessel::setForce ( const std::vector< double > & inforces )

inherited

Apply the forces.

◆ setGridElement() [1/2]

void PLMD::gridtools::GridVessel::setGridElement	(	const unsigned &	ipoint,
		const unsigned &	jelement,
		const double &	value
	)

inherited

Operations on one of the elements of grid point i.

◆ setGridElement() [2/2]

void PLMD::gridtools::GridVessel::setGridElement	(	const std::vector< unsigned > &	indices,
		const unsigned &	jelement,
		const double &	value
	)

inherited

◆ setNoDerivatives()

void PLMD::gridtools::GridVessel::setNoDerivatives ( )

inherited

Remove the derivatives.

◆ setNorm()

void PLMD::vesselbase::AveragingVessel::setNorm ( const double & snorm )

inlineinherited

Functions for dealing with normalisation constant.

◆ setupFibonacciGrid()

void PLMD::gridtools::GridVessel::setupFibonacciGrid ( const unsigned & np )

inherited

Setup the grid if it is a fibonacci grid on the surface of a sphere.

◆ transformDerivatives()

MultiValue & PLMD::vesselbase::Vessel::transformDerivatives	(	const unsigned &	current,
		MultiValue &	myvals,
		MultiValue &	bvals
	)

inlinevirtualinherited

This is replaced in bridges so we can transform the derivatives.

Reimplemented in PLMD::vesselbase::BridgeVessel.

◆ transformName()

std::string PLMD::vesselbase::Vessel::transformName ( const std::string & name )

staticinherited

Convert the name to the label of the component.

◆ wasForced()

bool PLMD::gridtools::GridVessel::wasForced ( ) const

inherited

Was a force added to the grid.

◆ wasreset()

bool PLMD::vesselbase::AveragingVessel::wasreset ( ) const

inherited

Was the grid cleared on the last step.

Member Data Documentation

◆ active

std::vector<bool> PLMD::gridtools::GridVessel::active

protectedinherited

Which grid points are we actively accumulating.

◆ arg_names

std::vector<std::string> PLMD::gridtools::GridVessel::arg_names

protectedinherited

The names of the various columns in the grid file.

◆ bufstart

unsigned PLMD::vesselbase::Vessel::bufstart

protectedinherited

The start of this Vessel's buffer in buffer in the underlying ActionWithVessel.

◆ comm

Communicator& PLMD::vesselbase::Vessel::comm

protectedinherited

A copy of the communicator.

◆ dimension

unsigned PLMD::gridtools::GridVessel::dimension

protectedinherited

The dimensionality of the grid.

◆ discrete

bool PLMD::gridtools::HistogramOnGrid::discrete

protectedinherited

◆ dx

std::vector<double> PLMD::gridtools::GridVessel::dx

protectedinherited

The spacing between grid points.

◆ forces

std::vector<double> PLMD::gridtools::GridVessel::forces

protectedinherited

Forces acting on grid elements.

◆ log

Log& PLMD::vesselbase::Vessel::log

inherited

Reference to the log on which to output details.

◆ noderiv

bool PLMD::gridtools::GridVessel::noderiv

protectedinherited

Do we have derivatives.

◆ nper

unsigned PLMD::gridtools::GridVessel::nper

protectedinherited

The number of pieces of information we are storing for each point in the grid.

◆ pbc

std::vector<bool> PLMD::gridtools::GridVessel::pbc

protectedinherited

Is this direction periodic.

◆ str_max

std::vector<std::string> PLMD::gridtools::GridVessel::str_max

protectedinherited

◆ str_min

std::vector<std::string> PLMD::gridtools::GridVessel::str_min

protectedinherited

The minimum and maximum in the grid stored as strings.

◆ von_misses_concentration

double PLMD::gridtools::HistogramOnGrid::von_misses_concentration

inherited

◆ von_misses_norm

double PLMD::gridtools::HistogramOnGrid::von_misses_norm

inherited

◆ wasforced

bool PLMD::gridtools::GridVessel::wasforced

protectedinherited

Is forced.

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

gridtools/AverageOnGrid.h
gridtools/AverageOnGrid.cpp

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

◆ AverageOnGrid()

Member Function Documentation

◆ accumulate()

◆ accumulateForce()

◆ activateThesePoints()

◆ addDataElement()

◆ addOneKernelEachTimeOnly()

◆ addToGridElement()

◆ applyForce()

◆ calculate()

◆ checkRead()

◆ clear()

◆ convertIndexToIndices()

◆ description()

◆ error()

◆ finish()

◆ getAction()

◆ getAllInput()

◆ getCellVolume()

◆ getComponentName()

◆ getCubeUnits()

◆ getDataElement()

◆ getDimension()

◆ getFibonacciCoordinates()

◆ getFibonacciCutoff()

◆ getFibonacciIndex()

◆ getFinalForces()

◆ getFlatGridCoordinates()

◆ getGridElement() [1/2]

◆ getGridElement() [2/2]

◆ getGridExtent()

◆ getGridPointCoordinates() [1/2]

◆ getGridPointCoordinates() [2/2]

◆ getGridSpacing()

◆ getIndex() [1/2]

◆ getIndex() [2/2]

◆ getIndices() [1/2]

◆ getIndices() [2/2]

◆ getInputString()

◆ getKernelAndNeighbors()

◆ getLabel()

◆ getMax()

◆ getMin()

◆ getName()

◆ getNbin()

◆ getNeighbors() [1/2]

◆ getNeighbors() [2/2]

◆ getNLTolerance()

◆ getNorm()

◆ getNumberOfBufferPoints()

◆ getNumberOfComponents()

◆ getNumberOfPoints()

◆ getNumberOfQuantities()

◆ getNumericalLabel()

◆ getSizeOfBuffer()

◆ getSplineNeighbors()

◆ getStride()

◆ getTolerance()

◆ getType()

◆ getValueAndDerivatives()

◆ getVectorOfValues()

◆ inactive()

◆ isPeriodic()

◆ noAverage()

◆ noDerivatives()

◆ noDiscreteKernels()

◆ parse()

◆ parseFlag()

◆ parseVector()

◆ prepare()

◆ registerKeywords()

◆ reset()

◆ resize()

◆ resizeBuffer()