MmpldWriter Class Reference

Output plugin to generate a MegaMol™ Particle List Data file (*.mmpld). More...

#include <MmpldWriter.h>

Inheritance diagram for MmpldWriter:

Public Member Functions
void	readXML (XMLfileUnits &xmlconfig)
	Method readXML will be called once for each plugin section in the input file. More...
void	init (ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
	Method init will be called at the begin of the simulation. More...
void	endStep (ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
	Method endStep will be called at the end of each time step. 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	SetInitSphereDataParameters (const uint8_t &bInitSphereData, const std::string &strSphereDataFilename)
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	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...
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 ()

Protected Member Functions
	MmpldWriter (uint64_t startTimestep, uint64_t writeFrequency, uint64_t stopTimestep, uint64_t numFramesPerFile, std::string outputPrefix)
	: writes a mmspd file used by MegaMol More...
virtual void	SetNumSphereTypes ()
virtual void	CalcNumSpheresPerType (ParticleContainer *particleContainer, uint64_t *numSpheresPerType)
virtual bool	GetSpherePos (float *spherePos, Molecule *mol, uint8_t &nSphereTypeIndex)
void	InitSphereData ()
std::string	getOutputFilename ()
void	MultiFileApproachReset (ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
void	PrepareWriteControl ()
long	get_data_frame_header_size ()
long	get_seekTable_size ()
void	writeSeekTableEntry (int id, uint64_t offset)
long	get_data_list_header_size ()
long	get_particle_data_size ()
long	get_data_list_size (uint64_t particle_count)
void	write_frame_header (uint32_t num_data_lists)
void	write_particle_list_header (uint64_t particle_count, int sphereId)
void	write_frame (ParticleContainer *particleContainer, DomainDecompBase *domainDecomp)

Protected Attributes
uint64_t	_startTimestep
uint64_t	_writeFrequency
uint64_t	_stopTimestep
long	_writeBufferSize
std::string	_outputPrefix
std::string	_timestampString
uint32_t	_frameCount
uint8_t	_numComponents
uint8_t	_numSitesTotal
uint8_t	_numSphereTypes
std::vector< uint64_t >	_seekTable
std::vector< uint8_t >	_numSitesPerComp
std::vector< uint8_t >	_nCompSitesOffset
std::string	_strSphereDataFilename
uint8_t	_bInitSphereData
bool	_bWriteControlPrepared
long	_fileCount
uint32_t	_numFramesPerFile
uint16_t	_mmpldversion
uint32_t	_numSeekEntries
MMPLD_Vertex_type	_vertex_type
MMPLD_Color_type	_color_type
std::vector< float >	_global_radius
std::vector< std::array< uint8_t, 4 > >	_global_rgba
std::vector< std::array< float, 2 > >	_global_intensity_range
MPI_File	_mpifh
MPI_Info_object	_mpiinfo

Detailed Description

Output plugin to generate a MegaMol™ Particle List Data file (*.mmpld).

Constructor & Destructor Documentation

MmpldWriter()

MmpldWriter::MmpldWriter ( uint64_t  startTimestep, uint64_t  writeFrequency, uint64_t  stopTimestep, uint64_t  numFramesPerFile, std::string  outputPrefix  )

protected

: writes a mmspd file used by MegaMol

Depending on write frequency (for example: every timestep, or every 10th, 100th, 1000th ...) number of frames can be controlled. The *.mmspd-file can be visualized by visualization software like MegaMol. (for detail information visit: https://svn.vis.uni-stuttgart.de/trac/megamol/)

Parameters

filename	Name of the *.mmspd-file (including path)
particleContainer	The molecules that have to be written to the file are stored here
domainDecomp	In the parallel version, the file has to be written by more than one process. Methods to achieve this are available in domainDecomp
writeFrequency	Controls the frequency of writing out the data (every timestep, every 10th, 100th, ... timestep)

Member Function Documentation

endStep()

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

virtual

Method endStep will be called at the end of each time step.

This method will be called every time step passing the simstep as an additional parameter. It can be used e.g. to write per time step data to a file or perform additional computations.

Parameters

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

Implements PluginBase.

finish()

void MmpldWriter::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

Todo:

end of frame offset may not be identical to file end!

Implements PluginBase.

getPluginName()

std::string MmpldWriter::getPluginName ( )

inlinevirtual

return the name of the plugin

Implements PluginBase.

init()

void MmpldWriter::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

Todo:

MMPLD writer takes into account only LJ sites at the moment, here

Implements PluginBase.

readXML()

void MmpldWriter::readXML ( XMLfileUnits &  xmlconfig )

virtual

Method readXML will be called once for each plugin section in the input file.

This method can be used to read in parameters from the corresponding plugin section in the xml config file. The method will be called once after an instance of the plugin is created.

Note

The same plugins may be specified multiple times in the xml config file. It is the responsibility of the plugin to handle this case in a propper way.

The following xml object structure will be provided to the plugin:

<plugin name="plugin name">
  <!-- options for the specific plugin -->
</plugin>

Parameters

xmlconfig

section of the xml file

Implements PluginBase.

Member Data Documentation

_startTimestep

uint64_t MmpldWriter::_startTimestep

protected

First time step to be recorded

_stopTimestep

uint64_t MmpldWriter::_stopTimestep

protected

Max time step up to which shall be recorded

_writeFrequency

uint64_t MmpldWriter::_writeFrequency

protected

time steps between two records

---

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

• src/io/MmpldWriter.h
• src/io/MmpldWriter.cpp