Computes the 2D projection of the multidimensional CrystalFp object. More...

#include <CrystalFpScatterplot.h>

Public Types
enum	ValueType { VAL_TOTAL_ENERGY, VAL_PER_ATOM_ENERGY, VAL_STRESS, VAL_GROUP, VAL_STEP }
	Type of value associated to the points. More...

enum	DiagnosticType { DIAG_DISTANCES, DIAG_BINNED_DISTANCES, DIAG_DO_NOTHING }
	Type of diagnostic requested. More...

Public Member Functions
	CrystalFpScatterplot ()
	Constructor.

	~CrystalFpScatterplot ()
	Destructor.

void	setNamedParam (const std::string &aName, const std::string &aValue)
	Set the parameter identified by the name.

size_t	initScatterplot (const CrystalFp *aCfp)
	Initialize the scatterplot computation for the given CrystalFp object.

void	getPoints (float *aCoords) const
	Get the points coordinates.

void	getValues (float *aValues, ValueType aValueType) const
	Return the values associated to the points.

float	stepScatterplot (float aTimestep)
	Move the points one step ahead.

void	perturbPositions (void)
	Check if the current solution is the best.

size_t	initDiagnostic (DiagnosticType aDiagnostic)
	Compute scatterplot diagnostic chart.

void	getDiagnosticValues (float aCoords, float aValues) const
	Return the diagnostic chart points.

void	dumpParams (void) const
	Prints the params values (the one set with setNamedParam()).

Detailed Description

Computes the 2D projection of the multidimensional CrystalFp object.

The points are projected in 2D trying to preserve the original distances. Normal usage is:

CrystalFpScatterplot sp;
npoints = sp.initScatterplot(&cfp);
allocate npoints*2 float for cooordinates (coords) and  for values (vals)
sp.getPoints(coords);
sp.getValues(vals, CrystalFpScatterplot::VAL_TOTAL_ENERGY);
for(num. retries) {
    for(num. iterations) {
        energy = sp.stepScatterplot(timestep);
        sp.getPoints(coords);
        sp.getValues(vals, CrystalFpScatterplot::VAL_TOTAL_ENERGY);
        if(energy < min_energy) break;
    }
    sp.perturbPositions();
    sp.getPoints(coords);
    sp.getValues(vals, CrystalFpScatterplot::VAL_TOTAL_ENERGY);
}
sp.getPoints(coords);
sp.getValues(vals, CrystalFpScatterplot::VAL_TOTAL_ENERGY);

Author: Mario Valle - Swiss National Supercomputing Centre (CSCS)

Date: 2011-06-01 (initial version)

Version: 1.0

Definition at line 42 of file CrystalFpScatterplot.h.

Member Enumeration Documentation

enum cfp::CrystalFpScatterplot::DiagnosticType

Type of diagnostic requested.

Enumerator:

DIAG_DISTANCES	Return all inter-point distances.
DIAG_BINNED_DISTANCES	Bin the interpoint distances.
DIAG_DO_NOTHING	To simplify visualization of the scatterplot only.

Definition at line 126 of file CrystalFpScatterplot.h.

enum cfp::CrystalFpScatterplot::ValueType

Type of value associated to the points.

Enumerator:

VAL_TOTAL_ENERGY	The total energy associated to the structure.
VAL_PER_ATOM_ENERGY	Per atom energy associated to the structure.
VAL_STRESS	The stress computed by the multidimensional scaling algorithm.
VAL_GROUP	Group to which the point pertains.
VAL_STEP	The step value.

Definition at line 83 of file CrystalFpScatterplot.h.

Constructor & Destructor Documentation

cfp::CrystalFpScatterplot::CrystalFpScatterplot ( )

Constructor.

cfp::CrystalFpScatterplot::~CrystalFpScatterplot ( )

Destructor.

Member Function Documentation

void cfp::CrystalFpScatterplot::dumpParams ( void ) const

Prints the params values (the one set with setNamedParam()).

The print is on cerr

void cfp::CrystalFpScatterplot::getDiagnosticValues	(	float *	aCoords,
		float *	aValues
	)		const

Return the diagnostic chart points.

Parameters

[out]	aCoords	A preallocated array that will be filled by the point coordinates (x, y)
[out]	aValues	A preallocated array that will be filled with the point's values

void cfp::CrystalFpScatterplot::getPoints ( float * aCoords ) const

Get the points coordinates.

If no points, then do nothing.

Parameters

[out] aCoords Array of x,y coordinates filled on output.

void cfp::CrystalFpScatterplot::getValues	(	float *	aValues,
		ValueType	aValueType
	)		const

Return the values associated to the points.

It is an independent routine so you can change the visualized value without redisplaying the points.

Parameters

[out]	aValues	An array where the values will be stored.
[in]	aValueType	The value to be returned.

Exceptions

CrystalFpFatal If aValueType is invalid.

size_t cfp::CrystalFpScatterplot::initDiagnostic ( DiagnosticType aDiagnostic )

Compute scatterplot diagnostic chart.

The chart shows distances on the scatterplot vs. distances in real space (both distances are normalized between 0 and 1).

Parameters

[in] aDiagnostic The diagnostic to be computed

Returns: The number of points

Exceptions

CrystalFpFatal If aDiagnostic is invalid.

size_t cfp::CrystalFpScatterplot::initScatterplot ( const CrystalFp * aCfp )

Initialize the scatterplot computation for the given CrystalFp object.

The method used is the ball and spring simple method.

Parameters

[in] aCfp Pointer to the already computed CrystalFp structure.

Exceptions

CrystalFpFatal If CrystalFp has no distances available.

void cfp::CrystalFpScatterplot::perturbPositions ( void )

Check if the current solution is the best.

If the current solution is not an improvement, then reload the previous optimum solution. Perturb the point positions to escape a local minima. The perturbation is proportional to the point stress and is slowly reduced every restart.

void cfp::CrystalFpScatterplot::setNamedParam	(	const std::string &	aName,
		const std::string &	aValue
	)

Set the parameter identified by the name.

Mainly used to set parameters from the command line. The accepted codes are:

retry Number of retries (used only here to compute the decay coefficient)
mass Ball mass
stiffness Of the spring
damping Damping factor for the movement
perturb Perturb scale for the retries (it perturb the initial position of the masses)
bins Number of bins for the binned distances diagnostics
wobble Wobble scale for the position of the binned points

Parameters

aName	Name of the parameter to be set (see above)
aValue	String representation of the value to be set (internally it is converted to the needed data type)

Exceptions

CrystalFpFatal If the param name is invalid

float cfp::CrystalFpScatterplot::stepScatterplot ( float aTimestep )

Move the points one step ahead.

Parameters

[in] aTimestep The time from the previous step.

Returns: The cinetic energy of the points (to decide when they are sufficiently "calm")

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

CrystalFpScatterplot.h

Public Types

Public Member Functions

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation