NFsim: NFcore::DumpSystem Class Reference

This class is useful for outputting and dumping all the states of the molecules in the system. This is ideal for then determining complex output values such as average aggregate size. DumpSystem objects are initialized at most once per system by the createSystemDumper() function defined in the NFinput.hh file.

to invoke: use -dump flag as: -dump [t1;t2;t3;...tn]->/optional/path/to/directory where t1 to tn are the output times you want dumped. you can also list the output times in a matlab style sequence as: -dump [t_start:step:t_end] if no step is given, the step is assumed to be at one second intervals. the path to the output directory is optional, and if omitted the files will be dumped to the current directory.

For each output time, a number of files will be created. There will be one header file that contains the number of molecules and other MoleculeType information needed to correctly read the binary files. Then, there will be one binary file for each MoleculeType giving the details of each molecule as

moleculeId,complexId,state_1,partner_1, ... state_n,partner_n,localFuncValue_1 ... localFuncValue_n the moleculeId is the unique identifier of the molecule. The complexId gives the unique id of the complex the molecule is in. For each component, the state value and the binding partner if any is given. Finally, each local function's value is given.

If you don't want to worry about all of that, take a look at the NFanalysis matlab library for tools that let you easily read the binary files into a nice data structure that can be used to analyze output.


Public Member Functions
	DumpSystem (System *s, vector< double > dumpTimes, string pathToFolder, bool verbose)
	The only constructor of DumpSystem objects.
	~DumpSystem ()
	Deconstructor that does nothing - DumpSystems don't tie up any heap memory.
void	tryToDump (double simTime)
	Key function of the DumpSystem class that is called at each simulation step.
Protected Member Functions
void	dumpHeaderFile (double dumpTime)
	Protected function for dumping the header file at the given time step.
void	dumpMoleculeTypeFiles (double dumpTime)
	Protected function for dumping the MoleculeType files at the given time step.
Protected Attributes
System *	s
int	currentDumpTimeIndex
vector< double >	dumpTimes
string	pathToFolder
bool	verbose

Constructor & Destructor Documentation

DumpSystem::DumpSystem	(	System *	s,
		vector< double >	dumpTimes,
		string	pathToFolder,
		bool	verbose
	)

The only constructor of DumpSystem objects.

Takes a reference to the system, a sorted list of double valued number corresponding to the simulation times that a dump is required. The relative path to the output directory of all your folders, and a flag that tells us whether or not to output random things.

DumpSystem::~DumpSystem ( )

Deconstructor that does nothing - DumpSystems don't tie up any heap memory.

Member Function Documentation

void DumpSystem::tryToDump ( double simTime )

Key function of the DumpSystem class that is called at each simulation step.

The System will call this function at each step, and the DumpSystem will determine whether or not to dump its files based on the output times originally provided.

void DumpSystem::dumpHeaderFile ( double dumpTime ) [protected]

Protected function for dumping the header file at the given time step.

void DumpSystem::dumpMoleculeTypeFiles ( double dumpTime ) [protected]

Protected function for dumping the MoleculeType files at the given time step.

Member Data Documentation

System* NFcore::DumpSystem::s [protected]

reference to the system being dumped

int NFcore::DumpSystem::currentDumpTimeIndex [protected]

keeps track of when we have dumped so far

vector<double> NFcore::DumpSystem::dumpTimes [protected]

the list of the times to dump

string NFcore::DumpSystem::pathToFolder [protected]