Reference Class Reference

A reference is used to compare to simulated data. More...

#include <Reference.h>

Classes
struct	timeStep
	private structure with monitors for a time step More...

Public Member Functions
bool	getDistanceToTriangularMesh (double pos[3], double &dist)
	get distance to a triangular mesh, the target of the reference must contain triangles. More...
bool	getMonitoredData (std::string type, double ref[])
	get the the values of a given monitor which do not depend of time or an atom (e.g. More...
bool	getMonitoredData (std::string type, double time, double &realTime, double ref[])
	get the the values of a given monitor at a given time which do not depend an atom (e.g. More...
bool	getMonitoredData (std::string type, double time, int index, double &realTime, double ref[])
	get the the values of a given monitor at a given time and a given atom's index (e.g. More...
bool	getNearest (double pos[3], double time, double ref[3])
	get the nearest reference point in the "target" using "Position" monitor at given time More...
bool	getNearest (double pos[3], double ref[3])
	get the nearest reference point in the "target" using "Position" monitor of the PML Reference. More...
	Reference (mml::Reference reference, MonitoringManager *monitoringManager)
	constructor More...
std::string	toString ()
	return a string relative to Reference type More...
virtual	~Reference ()
	destructor More...

Private Attributes
int	CurrentIndex
	current data index, stored to avoid search from beginning in the data vector More...
std::vector< timeStep * >	data
	vector which contain alls monitors for each time step More...
std::unique_ptr< mml::MonitoringOut >	mmlOut
	Object in the file generated by xsdcxx. More...
std::string	mmlOutFile
	the mmlOut document More...
MonitoringManager *	monitoringManager
	monitoring manager More...
PhysicalModel *	pml
	pml of the reference More...
std::string	target
	target More...

Detailed Description

A reference is used to compare to simulated data.

An instance of this class corresponds to the data-binding for type Reference of MonitoringModel.xsd.

A reference therefore contains:

• a MMLout (xml type MonitoringOut)
• a target to consider inside the MMLout

All MonitoringOut data is also managed by this class. A MonitoringOut contains:

• the path to a PML document, this is managed by the pml private attribute.
• vector of timestep that contains (time, vector values), this is managed by inner struct timeStep.

The PML document given in the MMLout is called the PML Reference.

The PML Reference can either be at any state (beginning, rest shape, final step...etc...) It is mainly used to get the list of Structure/Component to be used in correlation with the target field of the reference.

Note

Some monitors are directly using the position of the atoms given in the PML Reference to compute their values. Therefore it is STONGLY advised to give a PML Reference that corresponds to the FINAL step of the simulation (position at the end of the simulation/experiments).

Constructor & Destructor Documentation

Reference()

Reference::Reference	(	mml::Reference	reference,
		MonitoringManager *	monitoringManager
	)

constructor

References MonitorFactory::createMonitor(), CurrentIndex, data, MonitoringManager::getmmlFileFolder(), Monitor::getTypeName(), mmlOut, mmlOutFile, monitoringManager, Reference::timeStep::monitorsMap, pml, target, and Reference::timeStep::time.

~Reference()

Reference::~Reference ( )

virtual

destructor

References data, Reference::timeStep::monitorsMap, and pml.

Member Function Documentation

getDistanceToTriangularMesh()

bool Reference::getDistanceToTriangularMesh	(	double	pos[3],
		double &	dist
	)

get distance to a triangular mesh, the target of the reference must contain triangles.

This is a fast method that gives the distance relatively to the triangles in the PML Reference.

Note

This is a heuristic version, which means, it does not test all triangles to find the lowest. It first look for the nearest atom in the PML Reference and then only check the triangles around this nearest atom.

This is not the exact distance to the nearest triangle, but an approximation given by the function distanceToTrianglePlane().

Parameters

pos	atom's position (with eventual offset)
dist	the distance

Returns

true if method succeded (a triangular mesh was found)

References a, AtomIterator::begin(), AtomIterator::currentAtom(), distance(), distanceToTrianglePlane(), AtomIterator::end(), Structure::getAllStructuralComponents(), Atom::getPosition(), Cell::getProperties(), StructuralComponent::getStructure(), StructureProperties::getType(), AtomIterator::next(), pml, target, and StructureProperties::TRIANGLE.

getMonitoredData() [1/3]

bool Reference::getMonitoredData	(	std::string	type,
		double	ref[]
	)

get the the values of a given monitor which do not depend of time or an atom (e.g.

geometrical data)

Parameters

type	name of the monitor, must be a existing monitor in the mmlOut document
ref	a table where data will be stored

Returns

true if method succeded (an existing monitor named "type" was found)

Referenced by getNearest().

getMonitoredData() [2/3]

bool Reference::getMonitoredData	(	std::string	type,
		double	time,
		double &	realTime,
		double	ref[]
	)

get the the values of a given monitor at a given time which do not depend an atom (e.g.

volume) if there is no corresponding time in reference, it return data for the first higher time.

Parameters

type	name of the monitor, must be a existing monitor in the mmlOut document
time	time to get the values
realTime	the nearest time found if realTime=infinity, the nearest is the final state
ref	a table where data will be stored

Returns

true if method succeded

References CurrentIndex, data, and Monitor::SCALAR.

getMonitoredData() [3/3]

bool Reference::getMonitoredData	(	std::string	type,
		double	time,
		int	index,
		double &	realTime,
		double	ref[]
	)

get the the values of a given monitor at a given time and a given atom's index (e.g.

position)

Parameters

type	name of the monitor, must be a existing monitor in the mmlOut document
time	time to get the values
index	atom's index
realTime	the nearest time found if realTime=infinity, the nearest is the final state
ref	a table where data will be stored

Returns

true if method succeded

References CurrentIndex, and data.

getNearest() [1/2]

bool Reference::getNearest	(	double	pos[3],
		double	time,
		double	ref[3]
	)

get the nearest reference point in the "target" using "Position" monitor at given time

Parameters

pos	atom's position (with eventual offset)
time	time to get the Position
ref	a table where positon of the nearest atom in reference will be stored

Returns

true if method succeded (a nearest atom was found in reference)

References AtomIterator::begin(), AtomIterator::currentAtom(), distance(), AtomIterator::end(), Structure::getIndex(), getMonitoredData(), AtomIterator::next(), pml, and target.

getNearest() [2/2]

bool Reference::getNearest	(	double	pos[3],
		double	ref[3]
	)

get the nearest reference point in the "target" using "Position" monitor of the PML Reference.

This is a fast method that gives the nearest position relatively to the PML Reference.

Parameters

pos	atom's position (with eventual offset)
ref	a table where positon of the nearest atom in reference will be stored

Returns

true if method succeded (a nearest atom was found in reference)

References AtomIterator::begin(), AtomIterator::currentAtom(), distance(), AtomIterator::end(), Atom::getPosition(), AtomIterator::next(), pml, and target.

toString()

std::string Reference::toString

(

)

return a string relative to Reference type

References mmlOutFile.

Member Data Documentation

CurrentIndex

int Reference::CurrentIndex

private

current data index, stored to avoid search from beginning in the data vector

Referenced by getMonitoredData(), and Reference().

data

std::vector<timeStep*> Reference::data

private

vector which contain alls monitors for each time step

Referenced by getMonitoredData(), Reference(), and ~Reference().

mmlOut

std::unique_ptr<mml::MonitoringOut> Reference::mmlOut

private

Object in the file generated by xsdcxx.

Referenced by Reference().

mmlOutFile

std::string Reference::mmlOutFile

private

the mmlOut document

Referenced by Reference(), and toString().

monitoringManager

MonitoringManager* Reference::monitoringManager

private

monitoring manager

Referenced by Reference().

pml

PhysicalModel* Reference::pml

private

pml of the reference

Referenced by getDistanceToTriangularMesh(), getNearest(), Reference(), and ~Reference().

target

std::string Reference::target

private

target

Referenced by getDistanceToTriangularMesh(), getNearest(), and Reference().

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

• Reference.h
• Reference.cpp