MPICheckpointWriter Class Reference

Inheritance diagram for MPICheckpointWriter:

Public Member Functions
	MPICheckpointWriter (unsigned long writeFrequency, std::string outputPrefix, bool incremental=true, std::string datarep=std::string(""))
	writes a checkpoint file that can be used to continue the simulation using MPIIO More...
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...
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 ()

Constructor & Destructor Documentation

MPICheckpointWriter()

MPICheckpointWriter::MPICheckpointWriter	(	unsigned long	writeFrequency,
		std::string	outputPrefix,
		bool	incremental = true,
		std::string	datarep = std::string("")
	)

writes a checkpoint file that can be used to continue the simulation using MPIIO

The format of the checkpointfile written by this method is Byte offset 0 - 5, 6: string "MarDyn" Byte offset 6 - 19, 14: string version: "20150122trunk\0" Byte offset 20 - 51, 32: reserved for version string extension Byte offset 52 - 55, 4: int store 0x0a0b0c0d=168496141 to check endianess Byte offset 56 - 63, 8: unsigned int gap_to_data=data_displ-64=18+numBB*64 Byte offset 64 - 70, 7: string tuple structure "ICRVQD\0" Byte offset 71 - 73, 3: string "BB\0" Byte offset 74 - 81, 8: unsigned long number of bounding boxes Byte offset 82 - (81+numBB*(6*8+2*8)), numBB*64: numBB*(6*double+2*unsigned long) bounding boxes Byte offset (64+gap_to_data) - : data tuples

Parameters

writeFrequency	Controls the frequency of writing out the data (every timestep, every 10th, 100th, ... timestep)
outputPrefix	path and prefix for file name used
incremental	add simulation step to file name
datarep	data representation (e.g. "external32")

Member Function Documentation

endStep()

void MPICheckpointWriter::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 MPICheckpointWriter::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 MPICheckpointWriter::getPluginName ( )

inlinevirtual

return the name of the plugin

Implements PluginBase.

init()

void MPICheckpointWriter::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.

readXML()

void MPICheckpointWriter::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.

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

• src/io/MPICheckpointWriter.h
• src/io/MPICheckpointWriter.cpp