Mercury2PVD Class Reference

Inheritance diagram for Mercury2PVD:

Public Member Functions
void	setupInitialConditions ()
	This function allows to set the initial conditions for our problem to be solved, by default particle locations are randomly set. Remember particle properties must also be defined here. More...
Public Member Functions inherited from DPMBase
void	constructor ()
	A function which initialises the member variables to default values, so that the problem can be solved off the shelf; sets up a basic two dimensional problem which can be solved off the shelf. It is called in the constructor DPMBase(). More...
	DPMBase ()
	Constructor that calls the "void constructor()". More...
	DPMBase (const FilesAndRunNumber &other)
	Copy constructor type-1. More...
	DPMBase (const DPMBase &other)
	Copy constructor type-2. More...
virtual	~DPMBase ()
	virtual destructor More...
void	solve ()
	The work horse of the code. More...
void	checkSettings ()
	Checks if the essentials are set properly to go ahead with solving the problem. More...
virtual void	writeOutputFiles ()
	Writes the simulation data onto all the files i.e. .data, .ene, .fstat ... More...
void	solve (int argc, char *argv[])
	The solve function is the work horse of the code with the user input. More...
virtual void	writeXBallsScript () const
	This writes a script which can be used to load the xballs problem to display the data just generated. More...
virtual double	getInfo (const BaseParticle &P) const
	A virtual method that allows the user to overrride and set what is written into the info column in the data file. By default it returns the Species ID number. More...
virtual void	writeRestartFile ()
	Stores all the particle data for current save time step. Calls the write function. More...
bool	readRestartFile (bool restarted=true)
	Reads all the particle data corresponding to the current saved time step. Which is what the restart file basically stores. The problem description with the latest particle data. Returns 0 if it is successful, 1 otherwise. More...
int	readRestartFile (std::string fileName)
	The same as readRestartFile(bool), but also reads all the particle data corresponding to the current saved time step. More...
virtual void	write (std::ostream &os, bool writeAllParticles=true) const
	Loads all MD data and plots statistics for all timesteps in the .data file. More...
virtual void	read (std::istream &is)
	Reads all data from a restart file, e.g. domain data and particle data. More...
virtual bool	readUserDefinedWall (std::string type, std::istream &is)
virtual void	readOld (std::istream &is)
	Reads all data from a restart file, e.g. domain data and particle data; old version. More...
bool	readDataFile (const std::string fileName, unsigned int format=0)
	This allows particle data to be reloaded from data files. More...
bool	readParAndIniFiles (const std::string fileName)
	Allows the user to read par.ini files (useful to read MDCLR files) More...
bool	readNextDataFile (unsigned int format=0)
	Reads the next data file with default format=0. However, one can modify the format based on whether the particle data corresponds to 3D or 2D data. See XBalls/xballs.txt. More...
bool	findNextExistingDataFile (Mdouble tMin, bool verbose=true)
	Useful when fileType is chosen as Multiple Files or Multiple files with padded. More...
bool	readArguments (int argc, char *argv[])
	Can interpret main function input arguments that are passed by the driver codes. More...
virtual bool	readNextArgument (int &i, int argc, char *argv[])
	Interprets the i^th command-line argument. More...
virtual bool	checkParticleForInteraction (const BaseParticle &P)
	Checks if the particle having any interaction with walls or other particles. More...
virtual bool	checkParticleForInteractionLocal (const BaseParticle &P)
	Checks if a particle P has any interaction with walls or other particles in the local domain. More...
bool	checkParticleForInteractionLocalPeriodic (const BaseParticle &P)
Mdouble	getTime () const
	Access function for the time. More...
unsigned int	getNtimeSteps () const
	Returns the current counter of time steps. More...
void	setTime (Mdouble time)
	Access function for the time. More...
void	setTimeMax (Mdouble newTMax)
	Allows the upper time limit to be changed. More...
Mdouble	getTimeMax () const
	Allows the user to access the total simulation time during the simulation. Cannot change it though. More...
void	setDoCGAlways (bool newDoCGFlag)
void	setRotation (bool newRotFlag)
	Allows to set the flag for enabling or disabling particle rotation in the simulations. More...
bool	getRotation () const
	Returns a flag indicating if particle rotation is enabled or disabled. More...
void	setWallsWriteVTK (FileType writeWallsVTK)
	Allows to set the flag for enabling or disabling particle rotation in the simulations. More...
void	setParticlesWriteVTK (bool writeParticlesVTK)
	Allows to set the flag for enabling or disabling particle rotation in the simulations. More...
FileType	getWallsWriteVTK () const
	Returns a flag indicating if particle rotation is enabled or disabled. More...
bool	getParticlesWriteVTK () const
	Returns a flag indicating if particle rotation is enabled or disabled. More...
bool	getDoCGAlways () const
Vec3D	getMin () const
	Return the "bottom left" corner of the domain, a vector with xMin_, yMin_ and zMin_. More...
Vec3D	getMax () const
	Return the "upper right" corner of the domain, a vector with xMin_, yMin_ and zMin_. More...
Mdouble	getXMin () const
	If the length of the problem domain in x-direction is XMax - XMin, then getXMin() returns XMin,. More...
Mdouble	getXMax () const
	If the length of the problem domain in x-direction is XMax - XMin, then getXMax() returns XMax,. More...
Mdouble	getYMin () const
	If the length of the problem domain in y-direction is YMax - YMin, then getYMin() returns YMin,. More...
Mdouble	getYMax () const
	If the length of the problem domain in y-direction is YMax - YMin, then getYMax() returns XMax,. More...
Mdouble	getZMin () const
	If the length of the problem domain in z-direction is ZMax - ZMin, then getZMin() returns ZMin,. More...
Mdouble	getZMax () const
	If the length of the problem domain in z-direction is ZMax - ZMin, then getZMax() returns ZMax,. More...
void	setMin (Vec3D min)
	Sets the values xMin, yMin, zMin of the problem domain, which is [xMin,xMax]x[yMin,yMax]x[zMin,zMax]. More...
void	setMax (Vec3D max)
	Sets the values xMax, yMax, zMax of the problem domain, which is [xMin,xMax]x[yMin,yMax]x[zMin,zMax]. More...
void	setXMin (Mdouble newXMin)
	If the length of the problem domain in x-direction is XMax - XMin, this method sets XMin. More...
void	setYMin (Mdouble newYMin)
	If the length of the problem domain in y-direction is YMax - YMin, this method sets YMin. More...
void	setZMin (Mdouble newZMin)
	If the length of the problem domain in z-direction is ZMax - ZMin, this method sets ZMin. More...
void	setXMax (Mdouble newXMax)
	If the length of the problem domain in x-direction is XMax - XMin, this method sets XMax. More...
void	setYMax (Mdouble newYMax)
	If the length of the problem domain in y-direction is YMax - YMin, this method sets YMax. More...
void	setZMax (Mdouble newZMax)
	If the length of the problem domain in z-direction is XMax - XMin, this method sets ZMax. More...
int	getAddLarge () const
	returns the number of large particles that are to be added on restart. More...
int	getAddSmall () const
	returns the number of small particles that are to be added on restart. More...
void	setAddLarge (int new_addL)
	sets the number of large particles that are to be added on restart. More...
void	setAddSmall (int new_addS)
	sets the number of small particles that are to be added on restart. More...
void	setTimeStep (Mdouble newDt)
	Allows the time step dt to be changed. More...
Mdouble	getTimeStep () const
	Allows the time step dt to be accessed. More...
void	setXBallsColourMode (int newCMode)
	Set the xball output mode. More...
int	getXBallsColourMode () const
	Get the xball colour mode (CMode) More...
void	setXBallsVectorScale (double newVScale)
	Set the scale of vectors in xballs. More...
double	getXBallsVectorScale () const
	Returns the scale of vectors used in xballs. More...
void	setXBallsAdditionalArguments (std::string newXBArgs)
	Set the additional arguments for xballs. More...
std::string	getXBallsAdditionalArguments () const
	Returns the additional arguments for xballs. More...
void	setXBallsScale (Mdouble newScale)
	Sets the scale of the view (either normal, zoom in or zoom out) to display in xballs. The default is fit to screen. More...
double	getXBallsScale () const
	Returns the scale of the view in xballs. More...
void	setGravity (Vec3D newGravity)
	Allows to modify the gravity vector. More...
Vec3D	getGravity () const
	Returns the gravity vector. More...
void	setDimension (unsigned int newDim)
	Sets the system and particle dimension. More...
void	setSystemDimensions (unsigned int newDim)
	Allows for the dimension of the simulation to be changed. More...
unsigned int	getSystemDimensions () const
	Returns the dimension of the simulation. Note there is also a particle dimension. More...
void	setParticleDimensions (unsigned int particleDimensions)
	Allows the dimension of the particle (f.e. for mass) to be changed. e.g. discs or spheres. More...
unsigned int	getParticleDimensions () const
	Returns the particle dimensions. More...
std::string	getRestartVersion () const
	This is to take into account for different Mercury versions. Returns the version of the restart file. More...
void	setRestartVersion (std::string newRV)
	Sets restart_version. More...
bool	getRestarted () const
	Returns the flag denoting if the simulation was restarted or not. More...
void	setRestarted (bool newRestartedFlag)
	Allows to set the flag stating if the simulation is to be restarted or not. More...
bool	getAppend () const
	Returns the flag denoting if the append option is on or off. More...
void	setAppend (bool newAppendFlag)
	Allows to set the append option. More...
Mdouble	getElasticEnergy () const
	Returns the global elastic energy within the system. More...
Mdouble	getKineticEnergy () const
	Returns the global kinetic energy stored in the system. More...
Mdouble	getGravitationalEnergy () const
	Returns the global gravitational potential energy stored in the system. More...
bool	areInContact (const BaseParticle *pI, const BaseParticle *pJ) const
	Checks if two particle are in contact or is there any positive overlap. More...
virtual void	hGridInsertParticle (BaseParticle *obj UNUSED)
	no implementation but can be overidden in its derived classes. More...
virtual void	hGridUpdateParticle (BaseParticle *obj UNUSED)
	no implementation but can be overidden in its derived classes. More...
virtual void	hGridRemoveParticle (BaseParticle *obj UNUSED)
	no implementation but can be overidden in its derived classes. More...
virtual void	hGridUpdateMove (BaseParticle *, Mdouble)
	no implementation but can be overidden in its derived classes. More...
virtual void	gatherContactStatistics (unsigned int index1 UNUSED, int index2 UNUSED, Vec3D Contact UNUSED, Mdouble delta UNUSED, Mdouble ctheta UNUSED, Mdouble fdotn UNUSED, Mdouble fdott UNUSED, Vec3D P1_P2_normal_ UNUSED, Vec3D P1_P2_tangential UNUSED)
	//Not unsigned index because of possible wall collisions. More...
Public Member Functions inherited from FilesAndRunNumber
	FilesAndRunNumber ()
	Constructor. More...
	FilesAndRunNumber (const FilesAndRunNumber &other)
	Copy constructor. More...
virtual	~FilesAndRunNumber ()
	Constructor. More...
void	constructor ()
	a function called by the FilesAndRunNumber() (constructor) More...
void	incrementRunNumberInFile ()
	Increment the run Number (counter value) stored in the file_counter (COUNTER_DONOTDEL) by 1 and store the new value in the counter file. More...
int	readRunNumberFromFile ()
	Read the run number or the counter from the counter file (COUNTER_DONOTDEL) More...
void	autoNumber ()
	The autoNumber() function is the trigger. It calls three functions. setRunNumber(), readRunNumberFromFile() and incrementRunNumberInFile(). More...
std::vector< int >	get2DParametersFromRunNumber (int size_x, int size_y)
	This turns a counter into two indices which is an amazing feature for doing two dimensional parameter studies. The indices run from 1:size_x and 1:size_y, while the study number starts at 0 ( initially the counter=1 in COUNTER_DONOTDEL) More...
int	launchNewRun (const char *name, bool quick=false)
	This launches a code from within this code. Please pass the name of the code to run. More...
void	setRunNumber (int runNumber)
	This sets the counter/Run number, overriding the defaults. More...
int	getRunNumber () const
	This returns the current value of the counter (runNumber_) More...
void	read (std::istream &is)
	Accepts an input stream std::istream. More...
void	write (std::ostream &os) const
	Accepts an output stream read function, which accepts an input stream std::ostream. More...
Public Member Functions inherited from Files
	Files ()
	A constructor. More...
virtual	~Files ()
	A destructor, watch out its a virtual destructor. More...
	Files (const Files &other)
	Copy constructor. More...
MERCURY_DEPRECATED File &	getDataFile ()
	The non const version. Allows one to edit the File::dataFile. More...
MERCURY_DEPRECATED File &	getEneFile ()
	The non const version. Allows to edit the File::eneFile. More...
MERCURY_DEPRECATED File &	getFStatFile ()
	The non const version. Allows to edit the File::fStatFile. More...
MERCURY_DEPRECATED File &	getRestartFile ()
	The non const version. Allows to edit the File::restartFile. More...
MERCURY_DEPRECATED File &	getStatFile ()
	The non const version. Allows to edit the File::statFile. More...
MERCURY_DEPRECATED const File &	getDataFile () const
	The const version. Does not allow for any editing of the File::dataFile. More...
MERCURY_DEPRECATED const File &	getEneFile () const
	The const version. Does not allow for any editing of the File::eneFile. More...
MERCURY_DEPRECATED const File &	getFStatFile () const
	The const version. Does not allow for any editing of the File::fStatFile. More...
MERCURY_DEPRECATED const File &	getRestartFile () const
	The const version. Does not allow for any editing of the File::restartFile. More...
MERCURY_DEPRECATED const File &	getStatFile () const
	The const version. Does not allow for any editing of the File::statFile. More...
const std::string &	getName () const
	Returns the name of the file. Does not allow to change it though. More...
void	setName (const std::string &name)
	Allows to set the name of all the files (ene, data, fstat, restart, stat) More...
void	setName (const char *name)
	Calls setName(std::string) More...
void	setSaveCount (unsigned int saveCount)
	Sets File::saveCount_ for all files (ene, data, fstat, restart, stat) More...
void	setFileType (FileType fileType)
	Sets File::fileType_ for all files (ene, data, fstat, restart, stat) More...
void	setOpenMode (std::fstream::openmode openMode)
	Sets File::openMode_ for all files (ene, data, fstat, restart, stat) More...
void	resetFileCounter ()
	Resets the file counter for each file i.e. for ene, data, fstat, restart, stat) More...
void	read (std::istream &is)
	Extracts data from the input stream (which is basically a file you want to read from) into name_, restartFile .... More...
void	write (std::ostream &os) const
	Writes data into a file from the member variables name_, restartFile, dataFile etc. More...
void	openFiles ()
	Opens all the files (ene, data, fstat, restart, stat) for reading and writing purposes. More...
void	closeFiles ()
	Closes all files (ene, data, fstat, restart, stat) that were opened to read or write. More...
void	setNextSavedTimeStep (unsigned int nextSavedTimeStep)
	Sets the next time step for all the files (ene, data, fstat, restart, stat) at which the data is to be written or saved. More...

Additional Inherited Members
Public Attributes inherited from DPMBase
SpeciesHandler	speciesHandler
	A handler to that stores the species type i.e. elastic, linear visco-elastic... et cetera. More...
RNG	random
	This is a random generator, often used for setting up the initial conditions etc... More...
ParticleHandler	particleHandler
	An object of the class ParticleHandler, contains the pointers to all the particles created. More...
WallHandler	wallHandler
	An object of the class WallHandler. Contains pointers to all the walls created. More...
BoundaryHandler	boundaryHandler
	An object of the class BoundaryHandler which concerns insertion and deletion of particles into or from regions. More...
InteractionHandler	interactionHandler
	An object of the class InteractionHandler. More...
Public Attributes inherited from Files
File	dataFile
	An instance of class File to handle in- and output into a .data file. More...
File	fStatFile
	An instance of class File to handle in- and output into a .fstat file. More...
File	eneFile
	An instance of class File to handle in- and output into a .ene file. More...
File	restartFile
	An instance of class File to handle in- and output into a .restart file. More...
File	statFile
	An instance of class File to handle in- and output into a .stat file. More...
Protected Member Functions inherited from DPMBase
virtual void	computeAllForces ()
	Computes all the forces acting on the particles by using the setTorque and setForce methods. See BaseInteractible.cc. More...
virtual void	computeInternalForces (BaseParticle *i)
	Computes the forces between particles (internal in the sense that the sum over all these forces is zero i.e. fully modelled forces) More...
virtual void	computeInternalForces (BaseParticle *P1, BaseParticle *P2)
	Computes the forces between particles (internal in the sense that the sum over all these forces is zero i.e. fully modelled forces) More...
virtual void	computeExternalForces (BaseParticle *PI)
	Computes the external forces acting on particles (e.g. gravitational) More...
virtual void	computeForcesDueToWalls (BaseParticle *PI)
	Computes the forces on the particles due to the walls (normals are outward normals) More...
virtual void	actionsOnRestart ()
	A virtual function where the users can add extra code which is executed only when the code is restarted. More...
virtual void	actionsBeforeTimeLoop ()
	A virtual function. Allows one to carry out any operations before the start of the time loop. More...
virtual void	hGridActionsBeforeTimeLoop ()
	A virtual function that allows one to carry out hGrid operations before the start of the time loop. More...
virtual void	hGridActionsBeforeTimeStep ()
	A virtual function that allows one to set or execute hGrid parameters or operations before every simulation time step. More...
virtual bool	getHGridUpdateEachTimeStep () const
virtual void	actionsBeforeTimeStep ()
	A virtual function which allows to define operations to be executed before the new time step. More...
virtual void	actionsAfterSolve ()
	A virtual function which allows to define operations to be executed after the solve(). More...
virtual void	actionsAfterTimeStep ()
	A virtual function which allows to define operations to be executed after time step. More...
virtual void	outputXBallsData (std::ostream &os) const
	This function writes the location of the walls and particles in a format the XBalls program can read. See XBalls/xballs.txt. However, MercuryDPM supports a much better viewer now called Paraview. See the tutorials section in the documentation. More...
virtual void	outputXBallsDataParticle (const unsigned int i, const unsigned int format, std::ostream &os) const
	This function writes out the particle locations into an output stream in a format the XBalls program can read. More...
virtual void	writeEneHeader (std::ostream &os) const
	Writes a header with a certain format for ENE file. More...
virtual void	writeFstatHeader (std::ostream &os) const
	Writes a header with a certain format for FStat file. More...
virtual void	writeEneTimestep (std::ostream &os) const
	This function enables one to write the global energy available in the system after each time step. The default is to compute the rotational and translational kinetic energy, potential energy and the centre of mass. More...
virtual void	initialiseStatistics ()
	no implementation but can be overidden in its derived classes. More...
virtual void	outputStatistics ()
	no implementation but can be overidden in its derived classes. More...
void	gatherContactStatistics ()
virtual void	processStatistics (bool usethese UNUSED)
	no implementation but can be overidden in its derived classes. More...
virtual void	finishStatistics ()
	no implementation but can be overidden in its derived classes. More...
virtual void	integrateBeforeForceComputation ()
	This is were the integration is done, at the moment it is velocity Verlet integration and is done before the forces are computed. See http://en.wikipedia.org/wiki/Verlet_integration#Velocity_Verlet. More...
virtual void	integrateAfterForceComputation ()
	Integration is done after force computations. We apply the Velocity verlet scheme. See http://en.wikipedia.org/wiki/Verlet_integration#Velocity_Verlet. More...
virtual void	checkInteractionWithBoundaries ()
	There are a range of boundaries one could implement depending on ones' problem. This methods checks for interactions between particles and such range of boundaries. See BaseBoundary.h and all the boundaries in the Boundaries folder. More...
virtual void	hGridActionsBeforeIntegration ()
	no implementation but can be overidden in its derived classes. More...
virtual void	hGridActionsAfterIntegration ()
	no implementation but can be overidden in its derived classes. More...
virtual void	broadPhase (BaseParticle *i)
	By broad one means to screen and determine an approximate number of particles that a given particle can be in contact with. Hence the word "Broad phase" of contact detection. More...
void	setFixedParticles (unsigned int n)
void	initialiseTangentialSprings ()
virtual void	printTime () const
	Displays the current simulation time onto your screen for example. More...
virtual bool	continueSolve () const
void	outputInteractionDetails () const
	Displays the interaction details corresponding to the pointer objects in the interaction handler. More...
bool	isTimeEqualTo (Mdouble time) const
	Checks if the input variable "time" is the current time in the simulation. More...
void	removeDuplicatePeriodicParticles ()
	Removes periodic duplicate Particles. More...
void	checkAndDuplicatePeriodicParticles ()
	In case of periodic boundaries, the below methods checks and adds particles when necessary into the particle handler. See DPMBase.cc and PeriodicBoundary.cc for more details. More...
Mdouble	domainSize () const
void	writeVTK () const

Detailed Description

Definition at line 28 of file mercury2pvd.cpp.

Member Function Documentation

void Mercury2PVD::setupInitialConditions ( )

inlinevirtual

This function allows to set the initial conditions for our problem to be solved, by default particle locations are randomly set. Remember particle properties must also be defined here.

A virtual function with no implementation but can be overriden.

Todo:

I (Anthony) wants to change this to be an external function. This has a lot of advantages especially when using copy-constructors. This is a major change and will break other codes, so therefore has to be done carefully.

This sets up the particles initial conditions it is as you expect the user to override this. By default the particles are randomly disibuted

Reimplemented from DPMBase.

Definition at line 32 of file mercury2pvd.cpp.

    {
    }

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

• /usr/local/www/mercury/repo/Alpha/Tools/mercury2pvd.cpp