A representation of the simulation that is used to input or output from an HDF5 file. More...

#include <SimulationFile.h>

Classes
struct	ReplicateHandles
	A handle for the different replicates that may be stored in the HDF5 file. More...

Public Member Functions
	SimulationFile (const string filename)
	Create a SimulationFile with the specified filename.
	SimulationFile (const char *filename)
	Create a SimulationFile with the specified filename.
virtual	~SimulationFile ()
	Destroy the SimulationFile.
virtual void	close ()
	Close the file.
virtual void	flush ()
	Flush the current buffered data to the file.
virtual string	checkpoint ()
	Create the current checkpoint to the HDF5 file.
virtual map< string, string >	getParameters ()
	Get all the parameters from the current replicate.
virtual string	getParameter (string key, string defaultValue="")
	Get the specified parameter from the current replicate.
virtual void	setParameter (string key, string value)
	Set the specified parameter to the value.
virtual void	getReactionModel (lm::io::ReactionModel *reactionModel)
	Pops the reaction model from the HDF5 file.
virtual void	setReactionModel (lm::io::ReactionModel *reactionModel)
	Pushes the reaction model into the HDF5 file.
virtual void	getDiffusionModel (lm::io::DiffusionModel *diffusionModel)
	Pops the diffusion model from the HDF5 file.
virtual void	getDiffusionModelLattice (lm::io::DiffusionModel diffusionModel, byte lattice, size_t latticeMaxSize, byte *latticeSites, size_t latticeSitesMaxSize)
	Pops the diffusion lattice from the HDF5 file.
virtual void	getDiffusionModelLattice (lm::io::DiffusionModel diffusionModel, lm::rdme::Lattice lattice)
	Pops the diffusion lattice from the HDF5 file.
virtual void	setDiffusionModel (lm::io::DiffusionModel *diffusionModel)
	Pushes the diffusion model into the HDF5 file.
virtual void	setDiffusionModelLattice (lm::io::DiffusionModel m, uint8_t lattice, uint8_t *latticeSites)
	Pushes the diffusion lattice into the HDF5 file.
virtual void	setDiffusionModelLattice (lm::io::DiffusionModel m, uint32_t lattice, uint8_t *latticeSites)
	Pushes the diffusion lattice into the HDF5 file.
virtual void	setDiffusionModelLattice (lm::io::DiffusionModel m, lm::rdme::ByteLattice lattice)
	Pushes the diffusion lattice into the HDF5 file.
virtual void	setDiffusionModelLattice (lm::io::DiffusionModel m, lm::rdme::IntLattice lattice)
	Pushes the diffusion lattice into the HDF5 file.
virtual void	setSpatialModel (lm::io::SpatialModel *model)
	Pushes the spacial model (i.e. obstacles) into the HDF5 file.
virtual void	getSpatialModel (lm::io::SpatialModel *model)
	Pops the spacial model (i.e. obstacles) from the HDF5 file.
virtual bool	replicateExists (unsigned int replicate)
	Checks if the specified replicate exists.
virtual void	openReplicate (unsigned int replicate)
	Opens the specified replicate for reading.
virtual void	appendSpeciesCounts (unsigned int replicate, lm::io::SpeciesCounts *speciesCounts)
	Appends the species counts in the various sites into the replicate.
virtual void	appendLattice (unsigned int replicate, lm::io::Lattice lattice, byte latticeData, size_t latticeDataSize)
	Appends the lattice to the current replicate.
virtual void	appendLattice_U32LE (unsigned int replicate, lm::io::Lattice lattice, uint32_t latticeData, size_t latticeDataSize)
virtual void	arbitraryH5 (byte *ptr)
virtual void	arbitraryH5Lookup (byte in, byte &out, size_t &out_sz)
virtual void	appendSites (unsigned int replicate, lm::io::Lattice lattice, uint8_t siteData, size_t siteDataSize)
virtual void	appendParameterValues (unsigned int replicate, lm::io::ParameterValues *parameterValues)
	Adds all the parameter values to the replicate.
virtual void	setFirstPassageTimes (unsigned int replicate, lm::io::FirstPassageTimes *speciesCounts)
	Adds all the first passage times to the replicate.
virtual vector< double >	getLatticeTimes (unsigned int replicate)
	Get the timestep times for the replicate.
virtual void	getLattice (unsigned int replicate, unsigned int latticeIndex, lm::rdme::Lattice *lattice)
	Get the lattice for the replicate.
virtual void	closeReplicate (unsigned int replicate)
	Close the specified replicate.
virtual void	closeAllReplicates ()
	Close all the replicates.
std::map< uint32_t, uint >	getParticleCounts (unsigned int replicate, unsigned int latticeIndex)
std::map< double, vector< int > >	getSpeciesCounts (unsigned int replicate)
vector< double >	getSpeciesCountTimes (unsigned int replicate)
std::map< uint, string >	getSpeciesNames ()
std::map< uint, string >	getSiteTypeNames ()

Static Public Member Functions
static bool	isValidFile (const string filename)
	Check that the HDF5 file is valid.
static bool	isValidFile (const char *filename)
	Check that the HDF5 file is valid.
static void	create (const string filename)
	Create an HDF5 file.
static void	create (const char *filename)
	Create an HDF5 file.
static void	create (const string filename, unsigned int numberSpecies)
	Create an HDF5 file with the specified number of species.
static void	create (const char *filename, unsigned int numberSpecies)
	Create an HDF5 file with the specified number of species.
static void	create (const char *filename, bool initializeModel, unsigned int numberSpecies=0)
	Create an HDF5 file and initialize the model with an optional number of species.

Static Public Attributes
static const uint	MIN_VERSION = 2
static const uint	CURRENT_VERSION = 4
static const uint	MAX_REACTION_RATE_CONSTANTS = 10
static const uint	MAX_SHAPE_PARAMETERS = 10

Protected Member Functions
void	writeParticleLattice_U8LE (const char path, uint8_t data, unsigned int x, unsigned int y, unsigned int z, unsigned int w)
void	writeParticleLattice_U32LE (hid_t handle, const char path, unsigned int data, unsigned int x, unsigned int y, unsigned int z, unsigned int w)
void	write3DLattice_U8LE (const char path, uint8_t data, unsigned int x, unsigned int y, unsigned int z)
void	appendToDataset (H5MetaData header, byte data)
void	makeNewDataset (H5MetaData header, byte data)
void	appendDsToGroup (H5MetaData header, byte data)
void	readDataset (H5Lookup req, byte &data, size_t &sz)
void	readAttr (H5Lookup req, byte &data, size_t &sz)
virtual void	open ()
virtual void	openGroups ()
virtual void	loadParameters ()
virtual void	loadModel ()
virtual ReplicateHandles *	openReplicateHandles (unsigned int replicate)
virtual ReplicateHandles *	createReplicateHandles (string replicateString)
virtual void	closeReplicateHandles (ReplicateHandles *handles)

Static Protected Member Functions
static herr_t	parseParameter (hid_t location_id, const char attr_name, const H5A_info_t ainfo, void *op_data)

Protected Attributes
string	filename
hid_t	file
unsigned int	version
hid_t	parametersGroup
hid_t	modelGroup
hid_t	simulationsGroup
map< string, string >	parameterMap
bool	modelLoaded
unsigned int	numberSpecies
map< unsigned int, ReplicateHandles * >	openReplicates

Detailed Description

A representation of the simulation that is used to input or output from an HDF5 file.

Constructor & Destructor Documentation

◆ SimulationFile() [1/2]

lm::io::hdf5::SimulationFile::SimulationFile ( const string filename )

Create a SimulationFile with the specified filename.

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◆ SimulationFile() [2/2]

lm::io::hdf5::SimulationFile::SimulationFile ( const char * filename )

Create a SimulationFile with the specified filename.

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◆ ~SimulationFile()

lm::io::hdf5::SimulationFile::~SimulationFile ( )

virtual

Destroy the SimulationFile.

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Member Function Documentation

◆ appendDsToGroup()

void lm::io::hdf5::SimulationFile::appendDsToGroup	(	H5MetaData *	header,
		byte *	data )

protected

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◆ appendLattice()

void lm::io::hdf5::SimulationFile::appendLattice	(	unsigned int	replicate,
		lm::io::Lattice *	lattice,
		byte *	latticeData,
		size_t	latticeDataSize )

virtual

Appends the lattice to the current replicate.

Parameters

replicate	Replicate number
lattice	Lattice to add to replicate
latticeData	The actual data of the lattice
latticeDataSize	The size of the lattice

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◆ appendLattice_U32LE()

void lm::io::hdf5::SimulationFile::appendLattice_U32LE	(	unsigned int	replicate,
		lm::io::Lattice *	lattice,
		uint32_t *	latticeData,
		size_t	latticeDataSize )

virtual

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◆ appendParameterValues()

void lm::io::hdf5::SimulationFile::appendParameterValues	(	unsigned int	replicate,
		lm::io::ParameterValues *	parameterValues )

virtual

Adds all the parameter values to the replicate.

Parameters

replicate	Replicate number
parameterValues	Actual values to store

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◆ appendSites()

void lm::io::hdf5::SimulationFile::appendSites	(	unsigned int	replicate,
		lm::io::Lattice *	lattice,
		uint8_t *	siteData,
		size_t	siteDataSize )

virtual

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◆ appendSpeciesCounts()

void lm::io::hdf5::SimulationFile::appendSpeciesCounts	(	unsigned int	replicate,
		lm::io::SpeciesCounts *	speciesCounts )

virtual

Appends the species counts in the various sites into the replicate.

Parameters

replicate	Replicate number
speciesCounts	Protocol buffers object with species counts in lattice

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◆ appendToDataset()

void lm::io::hdf5::SimulationFile::appendToDataset	(	H5MetaData *	header,
		byte *	data )

protected

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◆ arbitraryH5()

void lm::io::hdf5::SimulationFile::arbitraryH5 ( byte * ptr )

virtual

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◆ arbitraryH5Lookup()

void lm::io::hdf5::SimulationFile::arbitraryH5Lookup	(	byte *	in,
		byte *&	out,
		size_t &	out_sz )

virtual

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◆ checkpoint()

string lm::io::hdf5::SimulationFile::checkpoint ( )

virtual

Create the current checkpoint to the HDF5 file.

Parameters

checkpointFilename Name of the new checkpoint file

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◆ close()

void lm::io::hdf5::SimulationFile::close ( )

virtual

Close the file.

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◆ closeAllReplicates()

void lm::io::hdf5::SimulationFile::closeAllReplicates ( )

virtual

Close all the replicates.

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◆ closeReplicate()

void lm::io::hdf5::SimulationFile::closeReplicate ( unsigned int replicate )

virtual

Close the specified replicate.

Parameters

replicate Replicate number

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◆ closeReplicateHandles()

void lm::io::hdf5::SimulationFile::closeReplicateHandles ( ReplicateHandles * handles )

protectedvirtual

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◆ create() [1/5]

void lm::io::hdf5::SimulationFile::create ( const char * filename )

static

Create an HDF5 file.

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◆ create() [2/5]

void lm::io::hdf5::SimulationFile::create	(	const char *	filename,
		bool	initializeModel,
		unsigned int	numberSpecies = 0 )

static

Create an HDF5 file and initialize the model with an optional number of species.

◆ create() [3/5]

void lm::io::hdf5::SimulationFile::create	(	const char *	filename,
		unsigned int	numberSpecies )

static

Create an HDF5 file with the specified number of species.

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◆ create() [4/5]

void lm::io::hdf5::SimulationFile::create ( const string filename )

static

Create an HDF5 file.

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◆ create() [5/5]

void lm::io::hdf5::SimulationFile::create	(	const string	filename,
		unsigned int	numberSpecies )

static

Create an HDF5 file with the specified number of species.

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◆ createReplicateHandles()

SimulationFile::ReplicateHandles * lm::io::hdf5::SimulationFile::createReplicateHandles ( string replicateString )

protectedvirtual

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◆ flush()

void lm::io::hdf5::SimulationFile::flush ( )

virtual

Flush the current buffered data to the file.

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◆ getDiffusionModel()

void lm::io::hdf5::SimulationFile::getDiffusionModel ( lm::io::DiffusionModel * diffusionModel )

virtual

Pops the diffusion model from the HDF5 file.

Parameters

diffusionModel Memory at which to place the diffusionModel

◆ getDiffusionModelLattice() [1/2]

void lm::io::hdf5::SimulationFile::getDiffusionModelLattice	(	lm::io::DiffusionModel *	diffusionModel,
		byte *	lattice,
		size_t	latticeMaxSize,
		byte *	latticeSites,
		size_t	latticeSitesMaxSize )

virtual

Pops the diffusion lattice from the HDF5 file.

Parameters

diffusionModel	Memoryfrom which to get the lattice
lattice	Memory in which to place lattice
latticeMaxSize	Total size of the lattice (i.e. number of bytes)
latticeSites	Actual lattice site data in byte format
latticeSitesMaxSize	Max size of a lattice site (i.e. number of particles it can contain)

◆ getDiffusionModelLattice() [2/2]

void lm::io::hdf5::SimulationFile::getDiffusionModelLattice	(	lm::io::DiffusionModel *	diffusionModel,
		lm::rdme::Lattice *	lattice )

virtual

Pops the diffusion lattice from the HDF5 file.

Parameters

diffusionModel	Memoryfrom which to get the lattice
lattice	Memory at which to place the lattice

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◆ getLattice()

void lm::io::hdf5::SimulationFile::getLattice	(	unsigned int	replicate,
		unsigned int	latticeIndex,
		lm::rdme::Lattice *	lattice )

virtual

Get the lattice for the replicate.

Parameters

replicate	Replicate number
latticeIndex	Seems to be unused...
lattice	The lattice object in which to store the data

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◆ getLatticeTimes()

vector< double > lm::io::hdf5::SimulationFile::getLatticeTimes ( unsigned int replicate )

virtual

Get the timestep times for the replicate.

Parameters

replicate Replicate number

Returns: A set of timestep times

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◆ getParameter()

string lm::io::hdf5::SimulationFile::getParameter	(	string	key,
		string	defaultValue = "" )

virtual

Get the specified parameter from the current replicate.

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◆ getParameters()

map< string, string > lm::io::hdf5::SimulationFile::getParameters ( )

virtual

Get all the parameters from the current replicate.

◆ getParticleCounts()

std::map< uint32_t, uint > lm::io::hdf5::SimulationFile::getParticleCounts	(	unsigned int	replicate,
		unsigned int	latticeIndex )

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◆ getReactionModel()

void lm::io::hdf5::SimulationFile::getReactionModel ( lm::io::ReactionModel * reactionModel )

virtual

Pops the reaction model from the HDF5 file.

Parameters

reactionModel Memory at which to place the reactionModel

◆ getSiteTypeNames()

std::map< uint, string > lm::io::hdf5::SimulationFile::getSiteTypeNames ( )

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◆ getSpatialModel()

void lm::io::hdf5::SimulationFile::getSpatialModel ( lm::io::SpatialModel * model )

virtual

Pops the spacial model (i.e. obstacles) from the HDF5 file.

Parameters

model The model in which to store the object

◆ getSpeciesCounts()

std::map< double, vector< int > > lm::io::hdf5::SimulationFile::getSpeciesCounts ( unsigned int replicate )

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◆ getSpeciesCountTimes()

vector< double > lm::io::hdf5::SimulationFile::getSpeciesCountTimes ( unsigned int replicate )

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◆ getSpeciesNames()

std::map< uint, string > lm::io::hdf5::SimulationFile::getSpeciesNames ( )

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◆ isValidFile() [1/2]

bool lm::io::hdf5::SimulationFile::isValidFile ( const char * filename )

static

Check that the HDF5 file is valid.

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◆ isValidFile() [2/2]

bool lm::io::hdf5::SimulationFile::isValidFile ( const string filename )

static

Check that the HDF5 file is valid.

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◆ loadModel()

void lm::io::hdf5::SimulationFile::loadModel ( )

protectedvirtual

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◆ loadParameters()

void lm::io::hdf5::SimulationFile::loadParameters ( )

protectedvirtual

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◆ makeNewDataset()

void lm::io::hdf5::SimulationFile::makeNewDataset	(	H5MetaData *	header,
		byte *	data )

protected

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◆ open()

void lm::io::hdf5::SimulationFile::open ( )

protectedvirtual

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◆ openGroups()

void lm::io::hdf5::SimulationFile::openGroups ( )

protectedvirtual

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◆ openReplicate()

void lm::io::hdf5::SimulationFile::openReplicate ( unsigned int replicate )

virtual

Opens the specified replicate for reading.

Parameters

replicate Replicate number

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◆ openReplicateHandles()

SimulationFile::ReplicateHandles * lm::io::hdf5::SimulationFile::openReplicateHandles ( unsigned int replicate )

protectedvirtual

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◆ parseParameter()

herr_t lm::io::hdf5::SimulationFile::parseParameter	(	hid_t	location_id,
		const char *	attr_name,
		const H5A_info_t *	ainfo,
		void *	op_data )

staticprotected

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◆ readAttr()

void lm::io::hdf5::SimulationFile::readAttr	(	H5Lookup *	req,
		byte *&	data,
		size_t &	sz )

protected

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◆ readDataset()

void lm::io::hdf5::SimulationFile::readDataset	(	H5Lookup *	req,
		byte *&	data,
		size_t &	sz )

protected

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◆ replicateExists()

bool lm::io::hdf5::SimulationFile::replicateExists ( unsigned int replicate )

virtual

Checks if the specified replicate exists.

Parameters

replicate Replicate number

Returns: true/false

◆ setDiffusionModel()

void lm::io::hdf5::SimulationFile::setDiffusionModel ( lm::io::DiffusionModel * diffusionModel )

virtual

Pushes the diffusion model into the HDF5 file.

Parameters

diffusionModel Memory from which to place the diffusionModel

◆ setDiffusionModelLattice() [1/4]

void lm::io::hdf5::SimulationFile::setDiffusionModelLattice	(	lm::io::DiffusionModel *	m,
		lm::rdme::ByteLattice *	lattice )

virtual

Pushes the diffusion lattice into the HDF5 file.

Parameters

diffusionModel	Memory from which to get the lattice
lattice	Memory from which to place the lattice

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◆ setDiffusionModelLattice() [2/4]

void lm::io::hdf5::SimulationFile::setDiffusionModelLattice	(	lm::io::DiffusionModel *	m,
		lm::rdme::IntLattice *	lattice )

virtual

Pushes the diffusion lattice into the HDF5 file.

Parameters

diffusionModel	Memory from which to get the lattice
lattice	Memory from which to place the lattice

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◆ setDiffusionModelLattice() [3/4]

void lm::io::hdf5::SimulationFile::setDiffusionModelLattice	(	lm::io::DiffusionModel *	m,
		uint32_t *	lattice,
		uint8_t *	latticeSites )

virtual

Pushes the diffusion lattice into the HDF5 file.

Parameters

diffusionModel	Memoryfrom which to get the lattice
lattice	Memory from which to place the lattice - uint32_t particle lattice
latticeSites	Memory from which to place lattice contents

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◆ setDiffusionModelLattice() [4/4]

void lm::io::hdf5::SimulationFile::setDiffusionModelLattice	(	lm::io::DiffusionModel *	m,
		uint8_t *	lattice,
		uint8_t *	latticeSites )

virtual

Pushes the diffusion lattice into the HDF5 file.

Parameters

diffusionModel	Memoryfrom which to get the lattice
lattice	Memory from which to place the lattice - uint8_t particle lattice
latticeSites	Memory from which to place lattice contents

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◆ setFirstPassageTimes()

void lm::io::hdf5::SimulationFile::setFirstPassageTimes	(	unsigned int	replicate,
		lm::io::FirstPassageTimes *	speciesCounts )

virtual

Adds all the first passage times to the replicate.

Parameters

replicate	Replicate number
speciesCounts	Actual passage times to store

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◆ setParameter()

void lm::io::hdf5::SimulationFile::setParameter	(	string	key,
		string	value )

virtual

Set the specified parameter to the value.

◆ setReactionModel()

void lm::io::hdf5::SimulationFile::setReactionModel ( lm::io::ReactionModel * reactionModel )

virtual

Pushes the reaction model into the HDF5 file.

Parameters

reactionModel Memory from which to place the reactionModel

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◆ setSpatialModel()

void lm::io::hdf5::SimulationFile::setSpatialModel ( lm::io::SpatialModel * model )

virtual

Pushes the spacial model (i.e. obstacles) into the HDF5 file.

Parameters

model The model object

◆ write3DLattice_U8LE()

void lm::io::hdf5::SimulationFile::write3DLattice_U8LE	(	const char *	path,
		uint8_t *	data,
		unsigned int	x,
		unsigned int	y,
		unsigned int	z )

protected

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◆ writeParticleLattice_U32LE()

void lm::io::hdf5::SimulationFile::writeParticleLattice_U32LE	(	hid_t	handle,
		const char *	path,
		unsigned int *	data,
		unsigned int	x,
		unsigned int	y,
		unsigned int	z,
		unsigned int	w )

protected

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◆ writeParticleLattice_U8LE()

void lm::io::hdf5::SimulationFile::writeParticleLattice_U8LE	(	const char *	path,
		uint8_t *	data,
		unsigned int	x,
		unsigned int	y,
		unsigned int	z,
		unsigned int	w )

protected

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Member Data Documentation

◆ CURRENT_VERSION

const uint lm::io::hdf5::SimulationFile::CURRENT_VERSION = 4

static

◆ file

hid_t lm::io::hdf5::SimulationFile::file

protected

◆ filename

string lm::io::hdf5::SimulationFile::filename

protected

◆ MAX_REACTION_RATE_CONSTANTS

const uint lm::io::hdf5::SimulationFile::MAX_REACTION_RATE_CONSTANTS = 10

static

◆ MAX_SHAPE_PARAMETERS

const uint lm::io::hdf5::SimulationFile::MAX_SHAPE_PARAMETERS = 10

static

◆ MIN_VERSION

const uint lm::io::hdf5::SimulationFile::MIN_VERSION = 2

static

◆ modelGroup

hid_t lm::io::hdf5::SimulationFile::modelGroup

protected

◆ modelLoaded

bool lm::io::hdf5::SimulationFile::modelLoaded

protected

◆ numberSpecies

unsigned int lm::io::hdf5::SimulationFile::numberSpecies

protected

◆ openReplicates

map<unsigned int,ReplicateHandles *> lm::io::hdf5::SimulationFile::openReplicates

protected

◆ parameterMap

map<string,string> lm::io::hdf5::SimulationFile::parameterMap

protected

◆ parametersGroup

hid_t lm::io::hdf5::SimulationFile::parametersGroup

protected

◆ simulationsGroup

hid_t lm::io::hdf5::SimulationFile::simulationsGroup

protected

◆ version

unsigned int lm::io::hdf5::SimulationFile::version

protected

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

/data2/LM_zls_github/Lattice-Microbes/src/io/SimulationFile.h
/data2/LM_zls_github/Lattice-Microbes/src/io/SimulationFile.cpp
/data2/LM_zls_github/Lattice-Microbes/src/io/SimulationFile_create.cpp

Classes

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SimulationFile() [1/2]

◆ SimulationFile() [2/2]

◆ ~SimulationFile()

Member Function Documentation

◆ appendDsToGroup()

◆ appendLattice()

◆ appendLattice_U32LE()

◆ appendParameterValues()

◆ appendSites()

◆ appendSpeciesCounts()

◆ appendToDataset()

◆ arbitraryH5()

◆ arbitraryH5Lookup()

◆ checkpoint()

◆ close()

◆ closeAllReplicates()

◆ closeReplicate()

◆ closeReplicateHandles()

◆ create() [1/5]

◆ create() [2/5]

◆ create() [3/5]

◆ create() [4/5]

◆ create() [5/5]

◆ createReplicateHandles()

◆ flush()

◆ getDiffusionModel()

◆ getDiffusionModelLattice() [1/2]

◆ getDiffusionModelLattice() [2/2]

◆ getLattice()

◆ getLatticeTimes()

◆ getParameter()

◆ getParameters()

◆ getParticleCounts()

◆ getReactionModel()

◆ getSiteTypeNames()

◆ getSpatialModel()

◆ getSpeciesCounts()

◆ getSpeciesCountTimes()

◆ getSpeciesNames()

◆ isValidFile() [1/2]

◆ isValidFile() [2/2]

◆ loadModel()

◆ loadParameters()

◆ makeNewDataset()

◆ open()

◆ openGroups()

◆ openReplicate()

◆ openReplicateHandles()

◆ parseParameter()

◆ readAttr()

◆ readDataset()

◆ replicateExists()

◆ setDiffusionModel()

◆ setDiffusionModelLattice() [1/4]

◆ setDiffusionModelLattice() [2/4]

◆ setDiffusionModelLattice() [3/4]

◆ setDiffusionModelLattice() [4/4]

◆ setFirstPassageTimes()

◆ setParameter()

◆ setReactionModel()

◆ setSpatialModel()

◆ write3DLattice_U8LE()

◆ writeParticleLattice_U32LE()

◆ writeParticleLattice_U8LE()

Member Data Documentation

◆ CURRENT_VERSION

◆ file

◆ filename

◆ MAX_REACTION_RATE_CONSTANTS

◆ MAX_SHAPE_PARAMETERS

◆ MIN_VERSION