IO-plugin: Used to create instances of CavityEnsemble and output the corresponding files containing the detected Cavity coordinates. More...

#include <CavityWriter.h>

Inheritance diagram for CavityWriter:

Public Member Functions
	CavityWriter ()=default
	Initialisation of all necessary field is done in readXML and init.

void	readXML (XMLfileUnits &xmlconfig) final
	reads in parameters for CavityEnsemble and output writefrequency: output timestep frequency AFTER initStatistics timesteps componentid: can be multiple. Starts separate CavityEnsembles for each component. radius: search radius around pseudo-molecules to look for neighbors with componentid=0/1... maxNeighbours: number of neighbours allowed in radius for a pseudo-molecule to count as a cavity Nx,Ny,Nz: grid numbers for grid of pseudo-molecules, sampling cavity properties at their grid position for non-overlapping coverage: radius*N_xyz = domainSize_xyz More...

void	init (ParticleContainer particleContainer, DomainDecompBase domainDecomp, Domain *domain) final
	Set all necessary variables for each CavityEnsemble. One is used per Component. Ensembles are assigned subDomains depending on the rank of the MPI process. Also, if a smaller controlVolume is specified it gets passed here. More...

void	beforeEventNewTimestep (ParticleContainer particleContainer, DomainDecompBase domainDecomp, unsigned long simstep) final
	Method will be called first thing in a new timestep. If the writeFrequency is reached and this is the first time, this will set the required Quaternions for the pseudo-molecules. More...

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

void	endStep (ParticleContainer particleContainer, DomainDecompBase domainDecomp, Domain *domain, unsigned long simstep) final
	Output the sampled cavity information from all ensembles to file. More...

void	finish (ParticleContainer particleContainer, DomainDecompBase domainDecomp, Domain *domain)
	Nothing done here. Necessary for inheritance from PluginBase. More...

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

std::map< unsigned, CavityEnsemble * >	getMcav ()

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

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 ()

Detailed Description

IO-plugin: Used to create instances of CavityEnsemble and output the corresponding files containing the detected Cavity coordinates.

Member Function Documentation

◆ afterForces()

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

finalvirtual

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

If the writeFrequency is reached, this will trigger a loop through all pseudo-molecules to determine their status as either cavity or non-cavity and start the communication.

Reimplemented from PluginBase.

◆ beforeEventNewTimestep()

void CavityWriter::beforeEventNewTimestep	(	ParticleContainer *	particleContainer,
		DomainDecompBase *	domainDecomp,
		unsigned long	simstep
	)

finalvirtual

Method will be called first thing in a new timestep. If the writeFrequency is reached and this is the first time, this will set the required Quaternions for the pseudo-molecules.

Reimplemented from PluginBase.

◆ endStep()

void CavityWriter::endStep	(	ParticleContainer *	particleContainer,
		DomainDecompBase *	domainDecomp,
		Domain *	domain,
		unsigned long	simstep
	)

finalvirtual

Output the sampled cavity information from all ensembles to file.

Parameters

particleContainer
domainDecomp
domain
simstep

Implements PluginBase.

◆ finish()

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

virtual

Nothing done here. Necessary for inheritance from PluginBase.

Parameters

particleContainer
domainDecomp
domain

Implements PluginBase.

◆ getPluginName()

std::string CavityWriter::getPluginName ( )

inlinefinalvirtual

return the name of the plugin

Implements PluginBase.

◆ init()

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

finalvirtual

Set all necessary variables for each CavityEnsemble. One is used per Component. Ensembles are assigned subDomains depending on the rank of the MPI process. Also, if a smaller controlVolume is specified it gets passed here.

Parameters

particleContainer
domainDecomp
domain

Implements PluginBase.

◆ readXML()

void CavityWriter::readXML ( XMLfileUnits & xmlconfig )

finalvirtual

reads in parameters for CavityEnsemble and output
writefrequency: output timestep frequency AFTER initStatistics timesteps
componentid: can be multiple. Starts separate CavityEnsembles for each component.
radius: search radius around pseudo-molecules to look for neighbors with componentid=0/1...
maxNeighbours: number of neighbours allowed in radius for a pseudo-molecule to count as a cavity
Nx,Ny,Nz: grid numbers for grid of pseudo-molecules, sampling cavity properties at their grid position

for non-overlapping coverage: radius*N_xyz = domainSize_xyz

<plugin name="CavityWriter" enabled="1">
         <writefrequency>10</writefrequency>
         <componentid>0</componentid>
         <componentid>1</componentid>
         <radius>2.0</radius>
         <maxNeighbours>1</maxNeighbours>
         <Nx>40</Nx>
         <Ny>40</Ny>
         <Nz>40</Nz>
         <ControlVolume>
             <x0> LowerBound (1.0) </x0>
             <x1> UpperBound (2.0) </x1>
             <y0> LowerBound (1.0) </y0>
             <y1> UpperBound (2.0) </y1>
             <z0> LowerBound (1.0) </z0>
             <z1> UpperBound (2.0) </z1>
         </ControlVolume>
     </plugin>

Parameters

xmlconfig

Implements PluginBase.

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

src/io/CavityWriter.h
src/io/CavityWriter.cpp

Public Member Functions

Static Public Member Functions

Detailed Description

Member Function Documentation

◆ afterForces()

◆ beforeEventNewTimestep()

◆ endStep()

◆ finish()

◆ getPluginName()

◆ init()

◆ readXML()