#include <HistogramOnGrid.h>

Inheritance diagram for PLMD::gridtools::HistogramOnGrid:

[legend]

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

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

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

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

void	addOneKernelEachTimeOnly ()

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

double	getNorm () const

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

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

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

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

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

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

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

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

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

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

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

bool	noDiscreteKernels () const

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

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

void	resize () override
	Set the size of the buffer equal to nper*npoints. 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) override
	Set the minimum and maximum of the grid. More...

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

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

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

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

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

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

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

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

void	setValueAndDerivatives (const unsigned &, const unsigned &, const double &, const std::vector< double > &)
	Set the values and derivatives of a particular element. More...

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

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

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

double	von_misses_norm

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

bool	discrete

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

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

bool	noderiv
	Do we have derivatives. 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_max

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

bool	wasforced
	Is forced. More...

Private Types
enum	{ flat, fibonacci }
	The way that grid points are constructed. More...

Private Attributes
ActionWithVessel *	action
	The action that this vessel is created within. More...

bool	addOneKernelAtATime

std::vector< double >	bandwidths

bool	bounds_set
	Have the minimum and maximum for the grid been set. More...

unsigned	bufsize
	The number of elements in this vessel's buffered data. More...

double	cube_units
	Units for Gaussian Cube file. More...

unsigned	currentGridPoint
	The grid point that was requested last by getGridPointCoordinates. More...

std::vector< double >	data
	The data that is being averaged. More...

double	fib_increment

std::vector< std::vector< unsigned > >	fib_nlist

double	fib_offset
	Fib increment here is equal to 2pi(INVERSE GOLDEN RATIO) More...

double	fib_shift

std::vector< double >	finalForces
	The forces that will be output at the end of the calculation. More...

bool	finished_read
	This just checks we have done checkRead. More...

bool	foundprint
	This flag is used to check if the user has created a valid input. More...

double	golden

enum PLMD::gridtools::GridVessel:: { ... }	gtype
	The way that grid points are constructed. More...

double	igolden

std::string	kerneltype

const PLMD::Keywords &	keywords
	The keywords. More...

std::vector< std::string >	line
	Directive line. More...

double	log_golden2

std::vector< double >	max

std::vector< double >	min
	The minimum and maximum of the grid stored as doubles. More...

std::string	mylabel
	The label for the vessel for referencing. More...

std::string	myname
	The keyword for the vessel in the input file. More...

std::vector< unsigned >	nbin
	The number of bins in each grid direction. More...

unsigned	neigh_tot

std::vector< unsigned >	nneigh

unsigned	npoints
	The number of points in the grid. More...

const int	numlab
	The numerical label for this object. More...

double	root5
	Stuff for fibonacci grids. More...

std::vector< unsigned >	stride
	The numerical distance between adjacent grid points. More...

bool	unormalised
	Are we outputting unormalised data. More...

bool	wascleared
	The grid was recently cleared and bounds can be set. More...

Member Enumeration Documentation

◆ anonymous enum

anonymous enum

privateinherited

The way that grid points are constructed.

Enumerator
flat
fibonacci

Constructor & Destructor Documentation

◆ HistogramOnGrid()

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

explicit

Member Function Documentation

◆ accumulate()

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

virtual

Reimplemented in PLMD::gridtools::AverageOnGrid.

◆ accumulateForce()

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

virtual

Reimplemented in PLMD::gridtools::AverageOnGrid.

◆ 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 ( )

inline

◆ 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 )

overridevirtualinherited

And retrieve the forces.

Implements PLMD::vesselbase::Vessel.

◆ calculate()

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

overridevirtual

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 ( )

overridevirtualinherited

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 )

overridevirtual

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

overridevirtual

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::HistogramOnGrid::getFinalForces	(	const std::vector< double > &	buffer,
		std::vector< double > &	finalForces
	)

overridevirtual

This retrieves the final force.

Reimplemented from PLMD::gridtools::GridVessel.

◆ 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::GridVessel::getGridElement	(	const std::vector< unsigned > &	indices,
		const unsigned &	jelement
	)		const

inherited

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

◆ getGridElement() [2/2]

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

virtualinherited

Get the value of the ith grid element.

Reimplemented in PLMD::gridtools::AverageOnGrid.

◆ 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 std::vector< double > &	point,
		std::vector< unsigned > &	indices
	)		const

inherited

Get the indices of a particular point.

◆ getIndices() [2/2]

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

inherited

Get the indices fof a 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()

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

◆ 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

inlineoverridevirtual

Get the number of points needed in the buffer.

Reimplemented from PLMD::gridtools::GridVessel.

◆ getNumberOfComponents()

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

inlinevirtualinherited

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

Reimplemented in PLMD::gridtools::AverageOnGrid.

◆ 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,
		unsigned &	nneighbors,
		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< std::unique_ptr< Value > > PLMD::gridtools::HistogramOnGrid::getVectorOfValues ( ) const

◆ 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

◆ 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::HistogramOnGrid::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 ( )

overridevirtualinherited

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
	)

overridevirtual

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 std::vector< unsigned > &	indices,
		const unsigned &	jelement,
		const double &	value
	)

inherited

◆ setGridElement() [2/2]

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.

◆ 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.

◆ setValueAndDerivatives()

void PLMD::gridtools::GridVessel::setValueAndDerivatives	(	const unsigned &	ipoint,
		const unsigned &	jelement,
		const double &	value,
		const std::vector< double > &	der
	)

inherited

Set the values and derivatives of a particular element.

◆ 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

◆ action

ActionWithVessel* PLMD::vesselbase::Vessel::action

privateinherited

The action that this vessel is created within.

◆ active

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

protectedinherited

Which grid points are we actively accumulating.

◆ addOneKernelAtATime

bool PLMD::gridtools::HistogramOnGrid::addOneKernelAtATime

private

◆ arg_names

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

protectedinherited

The names of the various columns in the grid file.

◆ bandwidths

std::vector<double> PLMD::gridtools::HistogramOnGrid::bandwidths

private

◆ bounds_set

bool PLMD::gridtools::GridVessel::bounds_set

privateinherited

Have the minimum and maximum for the grid been set.

◆ bufsize

unsigned PLMD::vesselbase::Vessel::bufsize

privateinherited

The number of elements in this vessel's buffered data.

◆ bufstart

unsigned PLMD::vesselbase::Vessel::bufstart

protectedinherited

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

◆ cube_units

double PLMD::gridtools::GridVessel::cube_units

privateinherited

Units for Gaussian Cube file.

◆ currentGridPoint

unsigned PLMD::gridtools::GridVessel::currentGridPoint

privateinherited

The grid point that was requested last by getGridPointCoordinates.

◆ data

std::vector<double> PLMD::vesselbase::AveragingVessel::data

privateinherited

The data that is being averaged.

◆ dimension

unsigned PLMD::gridtools::GridVessel::dimension

protectedinherited

The dimensionality of the grid.

◆ discrete

bool PLMD::gridtools::HistogramOnGrid::discrete

protected

◆ dx

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

protectedinherited

The spacing between grid points.

◆ fib_increment

double PLMD::gridtools::GridVessel::fib_increment

privateinherited

◆ fib_nlist

std::vector<std::vector<unsigned> > PLMD::gridtools::GridVessel::fib_nlist

privateinherited

◆ fib_offset

double PLMD::gridtools::GridVessel::fib_offset

privateinherited

Fib increment here is equal to 2*pi*(INVERSE GOLDEN RATIO)

◆ fib_shift

double PLMD::gridtools::GridVessel::fib_shift

privateinherited

◆ finalForces

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

privateinherited

The forces that will be output at the end of the calculation.

◆ finished_read

bool PLMD::vesselbase::Vessel::finished_read

privateinherited

This just checks we have done checkRead.

◆ forces

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

protectedinherited

Forces acting on grid elements.

◆ foundprint

bool PLMD::gridtools::GridVessel::foundprint

privateinherited

This flag is used to check if the user has created a valid input.

◆ golden

double PLMD::gridtools::GridVessel::golden

privateinherited

◆ gtype

enum { ... } PLMD::gridtools::GridVessel::gtype

The way that grid points are constructed.

◆ igolden

double PLMD::gridtools::GridVessel::igolden

privateinherited

◆ kerneltype

std::string PLMD::gridtools::HistogramOnGrid::kerneltype

private

◆ keywords

const PLMD::Keywords& PLMD::vesselbase::Vessel::keywords

privateinherited

The keywords.

◆ line

std::vector<std::string> PLMD::vesselbase::Vessel::line

privateinherited

Directive line.

This line is progressively erased during vessel construction so as to check if all the present keywords are correct.

◆ log_golden2

double PLMD::gridtools::GridVessel::log_golden2

privateinherited

◆ max

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

privateinherited

◆ min

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

privateinherited

The minimum and maximum of the grid stored as doubles.

◆ mylabel

std::string PLMD::vesselbase::Vessel::mylabel

privateinherited

The label for the vessel for referencing.

◆ myname

std::string PLMD::vesselbase::Vessel::myname

privateinherited

The keyword for the vessel in the input file.

◆ nbin

std::vector<unsigned> PLMD::gridtools::GridVessel::nbin

privateinherited

The number of bins in each grid direction.

◆ neigh_tot

unsigned PLMD::gridtools::HistogramOnGrid::neigh_tot

private

◆ nneigh

std::vector<unsigned> PLMD::gridtools::HistogramOnGrid::nneigh

private

◆ 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.

◆ npoints

unsigned PLMD::gridtools::GridVessel::npoints

privateinherited

The number of points in the grid.

◆ numlab

const int PLMD::vesselbase::Vessel::numlab

privateinherited

The numerical label for this object.

◆ pbc

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

protectedinherited

Is this direction periodic.

◆ root5

double PLMD::gridtools::GridVessel::root5

privateinherited

Stuff for fibonacci grids.

◆ 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.

◆ stride

std::vector<unsigned> PLMD::gridtools::GridVessel::stride

privateinherited

The numerical distance between adjacent grid points.

◆ unormalised

bool PLMD::vesselbase::AveragingVessel::unormalised

privateinherited

Are we outputting unormalised data.

◆ von_misses_concentration

double PLMD::gridtools::HistogramOnGrid::von_misses_concentration

◆ von_misses_norm

double PLMD::gridtools::HistogramOnGrid::von_misses_norm

◆ wascleared

bool PLMD::vesselbase::AveragingVessel::wascleared

privateinherited

The grid was recently cleared and bounds can be set.

◆ wasforced

bool PLMD::gridtools::GridVessel::wasforced

protectedinherited

Is forced.

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

gridtools/HistogramOnGrid.h
gridtools/HistogramOnGrid.cpp

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Types

Private Attributes

Member Enumeration Documentation

◆ anonymous enum

Constructor & Destructor Documentation

◆ HistogramOnGrid()

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()