This class calculates the Radial Distribution Function (RDF). More...

#include <RDF.h>

Inheritance diagram for RDF:

Public Member Functions
void	readXML (XMLfileUnits &xmlconfig)
	Read in XML configuration for RDFWriter. More...

void	afterForces (ParticleContainer particleContainer, DomainDecompBase domainDecomp, unsigned long simstep)
	Method afterForces will be called after forcefields have been applied no sitewise Forces can be applied here. More...

void	init (ParticleContainer particleContainer, DomainDecompBase domainDecomp, Domain *domain)
	Method init will be called at the begin of the simulation. More...

void	finish (ParticleContainer particleContainer, DomainDecompBase domainDecomp, Domain *domain)
	Method finish will be called at the end of the simulation. More...

std::string	getPluginName ()
	return the name of the plugin More...

void	setOutputTimestep (unsigned int timestep)

void	setOutputPrefix (std::string prefix)

void	endStep (ParticleContainer particleContainer, DomainDecompBase domainDecomposition, Domain *domain, unsigned long simStep)
	plot all the statistics calculated to one or several files More...

void	tickRDF ()

void	accumulateNumberOfMolecules (std::vector< Component > &components)

void	observeARDFMolecule (double dd, double cosPhi, double cosPhiReverse, unsigned cid1, unsigned cid2)

void	observeRDF (Molecule const &mi, Molecule const &mj, double dd)

void	observeRDFMolecule (double dd, unsigned i, unsigned j)

void	observeRDFSite (double dd, unsigned i, unsigned j, unsigned m, unsigned n)

bool	isEnabledSiteRDF () const

bool	doARDF () const

void	reset ()
	reset all values to 0, except the accumulated ones.

Public Member Functions inherited from PluginBase
	PluginBase ()
	Subclasses should use their constructur to pass parameters (e.g. filenames)

virtual void	beforeEventNewTimestep (ParticleContainer particleContainer, DomainDecompBase domainDecomp, unsigned long simstep)
	Method will be called first thing in a new timestep. More...

virtual void	beforeForces (ParticleContainer particleContainer, DomainDecompBase domainDecomp, unsigned long simstep)
	Method beforeForces will be called before forcefields have been applied no alterations w.r.t. Forces shall be made here. More...

virtual void	siteWiseForces (ParticleContainer particleContainer, DomainDecompBase domainDecomp, unsigned long simstep)
	Method siteWiseForces will be called before forcefields have been applied alterations to sitewise forces and fullMolecule forces can be made here. More...

virtual void	registerCallbacks (std::map< std::string, FunctionWrapper > &callbackMap)

virtual void	accessAllCallbacks (const std::map< std::string, FunctionWrapper > &callbackMap)

Static Public Member Functions
static PluginBase *	createInstance ()

Friends
class	RDFTest

Detailed Description

This class calculates the Radial Distribution Function (RDF).

The RDF "describes how the atomic density varies as a function of the distance from one particular atom." (see http://en.wikipedia.org/wiki/Radial_distribution_function ). For example, it should be possible to recognize the aggregate state of a system (see http://matdl.org/matdlwiki/index.php/softmatter:Radial_Distribution_Function ).

Note: The RDF is only determined for molecule pairs within the cutoff radius of the force and potential calculation. This means that bins outside the cut-off will always be computed to be zero.

Calculation:

calculate the distance of the pair, discretize it to intervalls with length dr (i.e. sort the pairs into bins to obtain a histogram).
for each bin: calculate the number density (i.e. number of particles per volume) of the corresponding shell
divide the number density by the number density of the system.

Update: Optionally, the RDF can be additionally resolved in angular direction, by chosing angularbins > 1 in the input. Phi is the angle between the central molecules orientation vector and the vector connecting the pair of molecules. The angular coordinate is given and discretized in terms of the cosine of the angle cos(phi), to ensure equal control volume sizes for equal distance R

Member Function Documentation

◆ accumulateNumberOfMolecules()

void RDF::accumulateNumberOfMolecules ( std::vector< Component > & components )

count the number of molecules per component

Todo:: : remove it and replace it by component.getNumMolecules()

◆ afterForces()

void RDF::afterForces	(	ParticleContainer *	particleContainer,
		DomainDecompBase *	domainDecomp,
		unsigned long	simstep
	)

virtual

Method afterForces will be called after forcefields have been applied no sitewise Forces can be applied here.

Reimplemented from PluginBase.

◆ endStep()

void RDF::endStep	(	ParticleContainer *	particleContainer,
		DomainDecompBase *	domainDecomposition,
		Domain *	domain,
		unsigned long	simStep
	)

virtual

plot all the statistics calculated to one or several files

Implements PluginBase.

◆ finish()

void RDF::finish	(	ParticleContainer *	particleContainer,
		DomainDecompBase *	domainDecomp,
		Domain *	domain
	)

virtual

Method finish will be called at the end of the simulation.

This method will be called once at the end of the simulation. It can be used e.g. to closing output files or writing final statistics.

Parameters

particleContainer	particle container storing the (local) molecules
domainDecomp	domain decomposition in use
domain

Implements PluginBase.

◆ getPluginName()

std::string RDF::getPluginName ( )

inlinevirtual

return the name of the plugin

Implements PluginBase.

◆ init()

void RDF::init	(	ParticleContainer *	particleContainer,
		DomainDecompBase *	domainDecomp,
		Domain *	domain
	)

virtual

Method init will be called at the begin of the simulation.

This method will be called once at the begin of the simulation just right before the main time step loop. It can be used e.g. to open output files or initialize statistics.

Parameters

particleContainer	particle container storing the (local) molecules
domainDecomp	domain decomposition in use
domain

Implements PluginBase.

◆ observeRDFMolecule()

void RDF::observeRDFMolecule	(	double	dd,
		unsigned	i,
		unsigned	j
	)

inline

This method "really" counts the number of molecule pairs within a certain distance.

◆ observeRDFSite()

void RDF::observeRDFSite	(	double	dd,
		unsigned	i,
		unsigned	j,
		unsigned	m,
		unsigned	n
	)

inline

Count center pairing for particle pair for molecules i and j and centers m_i, n_j at distance dd.

◆ readXML()

void RDF::readXML ( XMLfileUnits & xmlconfig )

virtual

Read in XML configuration for RDFWriter.

The following xml object structure is handled by this method:

<outputplugin name="RDF">
  <writefrequency>INTEGER</writefrequency>
  <outputprefix>STRING</outputprefix>
  <bins>INTEGER</bins>
  <intervallength>DOUBLE</intervallength>
</outputplugin>

Implements PluginBase.

◆ setOutputPrefix()

void RDF::setOutputPrefix ( std::string prefix )

inline

Todo:: put this in the constructor (when the transition to the xml file is done), or create a seperate output component.

◆ setOutputTimestep()

void RDF::setOutputTimestep ( unsigned int timestep )

inline

Todo:: put this in the constructor (when the transition to the xml file is done), or create a seperate output component.

◆ tickRDF()

void RDF::tickRDF ( )

inline

increment the counter indicating for how many iterations the molecule pairs have been counted.

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

src/io/RDF.h
src/io/RDF.cpp

Public Member Functions

Static Public Member Functions

Friends

Detailed Description

Member Function Documentation

◆ accumulateNumberOfMolecules()

◆ afterForces()

◆ endStep()

◆ finish()

◆ getPluginName()

◆ init()

◆ observeRDFMolecule()

◆ observeRDFSite()

◆ readXML()

◆ setOutputPrefix()

◆ setOutputTimestep()

◆ tickRDF()