The DPMBase header includes quite a few header files, defining all the handlers, which are essential. Moreover, it defines and solves a DPM problem. It is inherited from FilesAndRunNumber (public). More...

#include <DPMBase.h>

Inheritance diagram for DPMBase:

Public Member Functions
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	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...

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...

int	readRestartFile ()
	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. More...

int	readRestartFile (std::string fileName)
	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 particle data into a restart file. More...

virtual void	readOld (std::istream &is)
	Reads all particle data into a restart file; 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[])

virtual bool	checkParticleForInteraction (const BaseParticle &P)
	Checks if the particle having any interaction with walls or other particles. More...

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...

bool	getDoCGAlways () const

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	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...

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

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...

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...

Public Attributes
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
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...

Private Attributes
unsigned int	systemDimensions_
	The dimensions of the simulation i.e. 2D or 3D. More...

unsigned int	particleDimensions_
	determines if 2D or 3D particle volume is used for mass calculations More...

Vec3D	gravity_
	Gravity vector. More...

Mdouble	xMin_
	If the length of the problem domain in x-direction is XMax - XMin, the above variable stores XMin. More...

Mdouble	xMax_
	If the length of the problem domain in x-direction is XMax - XMin, the above variable stores XMax. More...

Mdouble	yMin_
	If the length of the problem domain in y-direction is YMax - YMin, the above variable stores YMin. More...

Mdouble	yMax_
	If the length of the problem domain in y-direction is YMax - XMin, the above variable stores YMax. More...

Mdouble	zMin_
	If the length of the problem domain in z-direction is ZMax - ZMin, the above variable stores ZMin. More...

Mdouble	zMax_
	If the length of the problem domain in z-direction is ZMax - ZMin, the above variable stores ZMax. More...

Mdouble	time_
	Stores the current simulation time. More...

unsigned int	ntimeSteps_
	Stores the number of time steps. More...

Mdouble	timeStep_
	Stores the simulation time step. More...

Mdouble	timeMax_
	Stores the duration of the simulation. More...

Mdouble	elasticEnergy_
	used in force calculations More...

std::string	restartVersion_
	Previous versions of MercuryDPM had a different restart file format, the below member variable allows one to specify the version in order to choose between the available version support. More...

bool	restarted_
	A bool to check if the simulation was restarted or not. More...

bool	append_
	A flag to determine if the file has to be appended or not. See DPMBase::Solve() for example. More...

bool	rotation_
	A flag to turn on/off particle rotation. More...

int	xBallsColourMode_
	XBalls is a package to view the particle data. As an alternative MercuryDPM also supports Paraview. The below variable is used to set the argument cmode in xballs script (see XBalls/xballs.txt) More...

Mdouble	xBallsVectorScale_
	sets the xballs argument vscale (see XBalls/xballs.txt) More...

Mdouble	xBallsScale_
	sets the xballs argument scale (see XBalls/xballs.txt) More...

std::string	xBallsAdditionalArguments_
	A string of additional arguments for xballs can be specified (see XBalls/xballs.txt). e.g. "-solidf -v0". More...

Friends
std::ostream &	operator<< (std::ostream &os, const DPMBase &md)
	Operator overloading of DPMBase class. More...

Detailed Description

The DPMBase header includes quite a few header files, defining all the handlers, which are essential. Moreover, it defines and solves a DPM problem. It is inherited from FilesAndRunNumber (public).

Bug:: When restarting the first time step is not saved, therefore there is a missing time step after a restart

Definition at line 61 of file DPMBase.h.

Constructor & Destructor Documentation

DPMBase::DPMBase ( )

Constructor that calls the "void constructor()".

Definition at line 135 of file DPMBase.cc.

References constructor().

 {
     constructor();
 }

DPMBase::DPMBase ( const FilesAndRunNumber & other )

Copy constructor type-1.

Parameters

[in] other

Definition at line 83 of file DPMBase.cc.

References constructor().

         : FilesAndRunNumber(other)
 {
     constructor();
 }

DPMBase::DPMBase ( const DPMBase & other )

Copy constructor type-2.

Parameters

[in] other

Definition at line 92 of file DPMBase.cc.

References append_, boundaryHandler, gravity_, interactionHandler, ntimeSteps_, particleDimensions_, particleHandler, random, restarted_, restartVersion_, rotation_, BaseHandler< T >::setDPMBase(), speciesHandler, systemDimensions_, time_, timeMax_, timeStep_, wallHandler, xBallsAdditionalArguments_, xBallsColourMode_, xBallsScale_, xBallsVectorScale_, xMax_, xMin_, yMax_, yMin_, zMax_, and zMin_.

 {
     systemDimensions_ = other.systemDimensions_;
     particleDimensions_ = other.particleDimensions_;
     gravity_ = other.gravity_;
     xMin_ = other.xMin_;
     xMax_ = other.xMax_;
     yMin_ = other.yMin_;
     yMax_ = other.yMax_;
     zMin_ = other.zMin_;
     zMax_ = other.zMax_;
     time_ = other.time_;
     timeStep_ = other.timeStep_;
     ntimeSteps_ = other.ntimeSteps_;
     timeMax_ = other.timeMax_;
     restartVersion_ = other.restartVersion_; //to read new and old restart data
     restarted_ = other.restarted_; //to see if it was restarted or not
     append_ = other.append_;
     rotation_ = other.rotation_;
     xBallsColourMode_ = other.xBallsColourMode_; // sets the xballs argument cmode (see xballs.txt)
     xBallsVectorScale_ = other.xBallsVectorScale_; // sets the xballs argument vscale (see xballs.txt)
     xBallsScale_ = other.xBallsScale_; // sets the xballs argument scale (see xballs.txt)
     xBallsAdditionalArguments_ = other.xBallsAdditionalArguments_; // std::string where additional xballs argument can be specified (see xballs.txt)
 #ifdef CONTACT_LIST_HGRID
             possibleContactList=other.possibleContactList;
 #endif
     random = other.random;
 
     boundaryHandler.setDPMBase(this);
     particleHandler.setDPMBase(this);
     interactionHandler.setDPMBase(this);
     speciesHandler.setDPMBase(this);
     wallHandler.setDPMBase(this);
 
     speciesHandler = other.speciesHandler;
     particleHandler = other.particleHandler;
     wallHandler = other.wallHandler;
     boundaryHandler = other.boundaryHandler;
     interactionHandler = other.interactionHandler;
 }

DPMBase::~DPMBase ( )

virtual

virtual destructor

Definition at line 142 of file DPMBase.cc.

 {
 
 }

Member Function Documentation

void DPMBase::actionsAfterSolve ( )

protectedvirtual

A virtual function which allows to define operations to be executed after the solve().

no implementation but can be overidden in its derived classes.

Definition at line 662 of file DPMBase.cc.

Referenced by solve(), and Mercury3DRestart::writeOutputFiles().

663 {

664 }

void DPMBase::actionsAfterTimeStep ( )

protectedvirtual

A virtual function which allows to define operations to be executed after time step.

no implementation but can be overidden in its derived classes.

Definition at line 669 of file DPMBase.cc.

Referenced by solve().

670 {

671 }

void DPMBase::actionsBeforeTimeLoop ( )

protectedvirtual

A virtual function. Allows one to carry out any operations before the start of the time loop.

no implementation but can be overriden in its derived classes.

Definition at line 598 of file DPMBase.cc.

Referenced by solve().

599 {

600 }

void DPMBase::actionsBeforeTimeStep ( )

protectedvirtual

A virtual function which allows to define operations to be executed before the new time step.

no implementation but can be overidden in its derived classes.

Reimplemented in Chute, and ChuteBottom.

Definition at line 655 of file DPMBase.cc.

Referenced by solve().

656 {

657 }

void DPMBase::actionsOnRestart ( )

protectedvirtual

A virtual function where the users can add extra code which is executed only when the code is restarted.

no implementation but can be overidden in its derived classes.

Definition at line 612 of file DPMBase.cc.

Referenced by solve().

613 {

614 }

bool DPMBase::areInContact	(	const BaseParticle *	pI,
		const BaseParticle *	pJ
	)		const

Checks if two particle are in contact or is there any positive overlap.

Parameters

[in]	pI
[in]	pJ

Returns: bool (True or False)

Definition at line 590 of file DPMBase.cc.

References Vec3D::getDistanceSquared(), BaseParticle::getInteractionRadius(), BaseInteractable::getPosition(), and mathsFunc::square().

Referenced by Mercury3D::hGridHasContactsInTargetCell().

 {
     return pI != pJ && Vec3D::getDistanceSquared(pI->getPosition(), pJ->getPosition()) < mathsFunc::square(pI->getInteractionRadius() + pJ->getInteractionRadius());
 }

void DPMBase::broadPhase ( BaseParticle * i )

protectedvirtual

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.

Parameters

[in] i

Reimplemented in MercuryBase.

Definition at line 738 of file DPMBase.cc.

References BaseHandler< T >::begin(), computeInternalForces(), and particleHandler.

Referenced by computeInternalForces().

 {
     for (std::vector<BaseParticle*>::iterator it = particleHandler.begin(); (*it) != i; ++it)
     {
         computeInternalForces(i, *it);
     }
 }

void DPMBase::checkAndDuplicatePeriodicParticles ( )

protected

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.

Definition at line 2409 of file DPMBase.cc.

References boundaryHandler, BaseHandler< T >::getNumberOfObjects(), BaseHandler< T >::getObject(), and particleHandler.

Referenced by solve().

 {
     for (BaseBoundary* it : boundaryHandler) // For all pointers of type BaseBoundary in Boundary handler
     {
         unsigned int N = particleHandler.getNumberOfObjects(); //Required because the number of particles increases
         for (unsigned int i = 0; i < N; i++)
         {
             it->createPeriodicParticles(particleHandler.getObject(i), particleHandler);
         }
     }
 }

void DPMBase::checkInteractionWithBoundaries ( )

protectedvirtual

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.

\\ calls checkBoundaryAfterParticleMoved()

Definition at line 1509 of file DPMBase.cc.

References BaseHandler< T >::begin(), boundaryHandler, BaseHandler< T >::end(), and particleHandler.

Referenced by solve().

 {
     for (std::vector<BaseBoundary*>::iterator B = boundaryHandler.begin(); B != boundaryHandler.end(); ++B)
     {
         for (std::vector<BaseParticle*>::iterator P = particleHandler.begin(); P != particleHandler.end(); ++P)
         {
             if ((*B)->checkBoundaryAfterParticleMoved(*P, particleHandler)) //Returns true if the particle is deleted
                 --P;
         }
     }
 }

bool DPMBase::checkParticleForInteraction ( const BaseParticle & p )

virtual

Checks if the particle having any interaction with walls or other particles.

A very useful feature. For e.g. when one wants to have an initial condition with particles free of interactions with other particles or walls, one could use this method and check for particles if they are interacting. If yes, then it would not consider this particle for insertion and continue onto next particle. However can prove expensive if the number of particles is large.

Parameters

[in] p

Returns: bool (True or False)

Todo:: tw check against periodic copies (see ShearCell3DInitialConditions.cpp)

Reimplemented in MercuryBase.

Definition at line 2353 of file DPMBase.cc.

References BaseHandler< T >::begin(), BaseHandler< T >::end(), Vec3D::getDistanceSquared(), BaseParticle::getInteractionRadius(), BaseInteractable::getPosition(), particleHandler, mathsFunc::square(), and wallHandler.

Referenced by InsertionBoundary::checkBoundaryBeforeTimeStep().

 {
     Mdouble distance;
     Vec3D normal;
     
     //Check if it has no collision with walls
     for (std::vector<BaseWall*>::const_iterator it = wallHandler.begin(); it != wallHandler.end(); it++)
     {
         if ((*it)->getDistanceAndNormal(p, distance, normal))
         {
             //std::cout<<"failure: Collision with wall: "<<**it<<std::endl;
             return false;
         }
         else
         {
             //std::cout<<"No collision with wall: "<<**it<<std::endl;
         }
     }
     
     //Check if it has no collision with other particles
     for (std::vector<BaseParticle*>::const_iterator it = particleHandler.begin(); it != particleHandler.end(); it++)
     {
         if (Vec3D::getDistanceSquared(p.getPosition(), (*it)->getPosition()) < mathsFunc::square(p.getInteractionRadius() + (*it)->getInteractionRadius()))
         {
             //std::cout<<"failure: Collision with particle "<<**it<<std::endl;
             return false;
         }
         else
         {
             //std::cout<<"No collision with particle "<<**it<<std::endl;
         }
     }
     return true;
 }

void DPMBase::checkSettings ( )

Checks if the essentials are set properly to go ahead with solving the problem.

Checks if at least one species exists in the SpeciesHandler.
1. Checks if particle dimensions are set.
2. Checks if system dimensions are set.
3. Checks if the time step is set or not.

Definition at line 1824 of file DPMBase.cc.

References BaseHandler< T >::getNumberOfObjects(), getParticleDimensions(), getSystemDimensions(), getTimeStep(), and speciesHandler.

Referenced by solve().

 {
     if (speciesHandler.getNumberOfObjects() == 0)
     {
         std::cerr << "Error in solve(): at least one species has to be defined" << std::endl;
         exit(-1);
     }
     if (getParticleDimensions() == 0)
     {
         std::cerr << "Error in solve(): particleDimensions not specified" << std::endl;
         exit(-1);
     }
     if (getSystemDimensions() == 0)
     {
         std::cerr << "Error in solve(): systemDimensions not specified" << std::endl;
         exit(-1);
     }
     if (getTimeStep() == 0.0)
     {
         std::cerr << "Error in solve(): timeStep not specified" << std::endl;
         exit(-1);
     }
 }

void DPMBase::computeAllForces ( )

protectedvirtual

Computes all the forces acting on the particles by using the setTorque and setForce methods. See BaseInteractible.cc.

Reset all forces to zero

Now loop over all particles contacts computing force contributions

Now loop over all other particles looking for contacts

Definition at line 1586 of file DPMBase.cc.

References BaseHandler< T >::begin(), computeExternalForces(), computeInternalForces(), BaseHandler< T >::end(), PossibleContact::getNext(), PossibleContact::getP1(), PossibleContact::getP2(), particleHandler, and wallHandler.

Referenced by solve().

 {
     for (std::vector<BaseParticle*>::iterator it = particleHandler.begin(); it != particleHandler.end(); ++it)
     {
         (*it)->setForce(Vec3D(0.0, 0.0, 0.0));
         (*it)->setTorque(Vec3D(0.0, 0.0, 0.0));
     }
     for (std::vector<BaseWall*>::iterator it = wallHandler.begin(); it != wallHandler.end(); ++it)
     {
         (*it)->setForce(Vec3D(0.0, 0.0, 0.0));
         (*it)->setTorque(Vec3D(0.0, 0.0, 0.0));
     } //end reset forces loop
     
 #ifdef DEBUG_OUTPUT
     std::cerr << "Have all forces set to zero " << std::endl;
 #endif
     
     
     for (std::vector<BaseParticle*>::iterator it = particleHandler.begin(); it != particleHandler.end(); ++it)
     {
         
         computeInternalForces(*it);
         //end inner loop over contacts.
         
         computeExternalForces(*it);
         
     }
     
 #ifdef CONTACT_LIST_HGRID
     //possibleContactList.write(std::cout);
     PossibleContact* Curr=possibleContactList.getFirstPossibleContact();
     while(Curr)
     {   
         computeInternalForces(Curr->getP1(),Curr->getP2());
         Curr=Curr->getNext();
     }
 #endif
     //end outer loop over contacts.
     
 }

void DPMBase::computeExternalForces ( BaseParticle * CI )

protectedvirtual

Computes the external forces acting on particles (e.g. gravitational)

Todo:

take out computeWalls() from compute External Forces method.

Parameters

[in] CI

Definition at line 1451 of file DPMBase.cc.

References BaseInteractable::addForce(), computeForcesDueToWalls(), getGravity(), BaseParticle::getMass(), and BaseParticle::isFixed().

Referenced by computeAllForces().

 {
     if (!CI->isFixed())
     {
         // Gravitational force
         CI->addForce(getGravity() * CI->getMass());
         // Still calls this in compute External Forces.
         computeForcesDueToWalls(CI);
     }
 }

void DPMBase::computeForcesDueToWalls ( BaseParticle * pI )

protectedvirtual

Computes the forces on the particles due to the walls (normals are outward normals)

Parameters

[in] pI

Todo:: TW: I think this torque has the wrong sign

Definition at line 1465 of file DPMBase.cc.

References BaseInteractable::addForce(), BaseInteractable::addTorque(), BaseHandler< T >::begin(), BaseInteraction::computeForce(), Vec3D::cross(), BaseHandler< T >::end(), BaseInteraction::getContactPoint(), BaseInteraction::getForce(), BaseParticle::getPeriodicFromParticle(), BaseInteractable::getPosition(), getRotation(), getTime(), BaseInteraction::getTorque(), interactionHandler, and wallHandler.

Referenced by computeExternalForces().

 {
     //No need to compute interactions between periodic particle images and walls
     if (pI->getPeriodicFromParticle() != nullptr)
         return;
 
     for (std::vector<BaseWall*>::iterator it = wallHandler.begin(); it != wallHandler.end(); ++it)
     {
         BaseInteraction* C = (*it)->getInteractionWith(pI, getTime(), &interactionHandler);
 
         if (C != nullptr)
         {
             C->computeForce();
 
             pI->addForce(C->getForce());
             (*it)->addForce(-C->getForce());
 
             if (getRotation()) // getRotation() returns a boolean.
             {
                 pI->addTorque(C->getTorque() - Vec3D::cross(pI->getPosition() - C->getContactPoint(), C->getForce()));
                 (*it)->addTorque(-C->getTorque() + Vec3D::cross((*it)->getPosition() - C->getContactPoint(), C->getForce()));
             }
         }
     }
 }

void DPMBase::computeInternalForces ( BaseParticle * i )

protectedvirtual

Computes the forces between particles (internal in the sense that the sum over all these forces is zero i.e. fully modelled forces)

Parameters

[in] i

Definition at line 1633 of file DPMBase.cc.

References broadPhase().

Referenced by broadPhase(), computeAllForces(), Mercury3D::hGridFindContactsWithinTargetCell(), Mercury2D::hGridFindContactsWithinTargetCell(), Mercury2D::hGridFindContactsWithTargetCell(), and Mercury3D::hGridFindContactsWithTargetCell().

 {
     broadPhase(i);
 }

void DPMBase::computeInternalForces	(	BaseParticle *	P1,
		BaseParticle *	P2
	)

protectedvirtual

Computes the forces between particles (internal in the sense that the sum over all these forces is zero i.e. fully modelled forces)

Parameters

[in]	P1
[in]	P2

Definition at line 1405 of file DPMBase.cc.

References BaseInteractable::addForce(), BaseInteractable::addTorque(), BaseInteraction::computeForce(), Vec3D::cross(), BaseInteraction::getContactPoint(), BaseInteraction::getForce(), BaseObject::getId(), BaseParticle::getInteractionWith(), BaseParticle::getPeriodicFromParticle(), BaseInteractable::getPosition(), getRotation(), getTime(), BaseInteraction::getTorque(), interactionHandler, and BaseParticle::isFixed().

 {
     //this is because the rough bottom allows overlapping fixed particles
     if (P1->isFixed() && P2->isFixed())
     {
         return;
     }
 
     if (P1->getPeriodicFromParticle() && P2->getPeriodicFromParticle())
     {
         return;
     }
 
     BaseParticle *PI, *PJ;
     if (P1->getId() > P2->getId())
     {
         PI = P2;
         PJ = P1;
     }
     else
     {
         PI = P1;
         PJ = P2;
     }
 
     //if statement above ensures that the PI has the lower id than PJ
     BaseInteraction* C = PJ->getInteractionWith(PI, getTime(), &interactionHandler);
     if (C != 0)
     {
         C->computeForce();
 
         PI->addForce(C->getForce());
         PJ->addForce(-C->getForce());
 
         if (getRotation())
         {
             PI->addTorque(C->getTorque() - Vec3D::cross(PI->getPosition() - C->getContactPoint(), C->getForce()));
             PJ->addTorque(-C->getTorque() + Vec3D::cross(PJ->getPosition() - C->getContactPoint(), C->getForce()));
         }
     }
 }

void DPMBase::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().

Definition at line 777 of file DPMBase.cc.

References boundaryHandler, gravity_, interactionHandler, loggerOutput, logWriteAndDie(), ntimeSteps_, LoggerOutput::onFatal, particleHandler, random, setAppend(), BaseHandler< T >::setDPMBase(), Files::setName(), setParticleDimensions(), RNG::setRandomSeed(), setRestarted(), Files::setSaveCount(), BaseHandler< T >::setStorageCapacity(), setSystemDimensions(), speciesHandler, time_, timeMax_, timeStep_, wallHandler, xBallsAdditionalArguments_, xBallsColourMode_, xBallsScale_, xBallsVectorScale_, xMax_, xMin_, yMax_, yMin_, zMax_, and zMin_.

Referenced by DPMBase().

 {
     //These are the particle parameters like dissipation etc..
     setRestarted(false);
 
     //This sets the maximum number of particles
     boundaryHandler.setDPMBase(this);
     speciesHandler.setDPMBase(this);
     particleHandler.setDPMBase(this);
     interactionHandler.setDPMBase(this);
     wallHandler.setDPMBase(this);
     interactionHandler.setDPMBase(this);
 
     particleHandler.setStorageCapacity(2);
     setSystemDimensions(2);
     setParticleDimensions(2);
 
     // Set gravitational acceleration
     gravity_ = Vec3D(0.0, -9.8, 0.0);
     
     //This is the parameter of the numerical part
     time_ = 0.0;
     timeStep_ = 0.0; // if dt is not user-specified, this is set in actionsBeforeTimeLoop()
     ntimeSteps_ = 0;
     setSaveCount(20);
     timeMax_ = 1.0;
     
     //This sets the default xballs domain
     xMin_ = 0.0;
     xMax_ = 0.01;
     yMin_ = 0.0;
     yMax_ = 0.01;
     zMin_ = 0.0;
     zMax_ = 0.0;
     
     loggerOutput->onFatal = logWriteAndDie;
     
     setName("");
     
     //Default mode is energy with no scale of the vectors
     xBallsColourMode_ = 0;
     xBallsVectorScale_ = -1;
     xBallsScale_ = -1;
     xBallsAdditionalArguments_ = "";
     setAppend(false);
 
     //The default random seed is 0
     random.setRandomSeed(0);
 #ifdef DEBUG_OUTPUT
     std::cerr << "MD problem constructor finished " << std::endl;
 #endif
 }

bool DPMBase::continueSolve ( ) const

protectedvirtual

Returns: bool (True or False)

Definition at line 769 of file DPMBase.cc.

Referenced by solve().

 {
     return true;
 }

bool DPMBase::findNextExistingDataFile	(	Mdouble	tMin,
		bool	verbose = `true`
	)

Useful when fileType is chosen as Multiple Files or Multiple files with padded.

Parameters

[in]	tMin
[in]	verbose

Returns: bool (True or False)

Definition at line 1191 of file DPMBase.cc.

References Files::dataFile, File::getCounter(), File::getFileType(), File::getFstream(), File::getName(), MULTIPLE_FILES, MULTIPLE_FILES_PADDED, and File::openNextFile().

 {
     if (dataFile.getFileType() == FileType::MULTIPLE_FILES || dataFile.getFileType() == FileType::MULTIPLE_FILES_PADDED)
     {
         while (true)// This true corresponds to the if s
         {
             dataFile.openNextFile();
             //check if file exists and contains data
             int N;
             dataFile.getFstream() >> N;
             if (dataFile.getFstream().eof() || dataFile.getFstream().peek() == -1)
             {
                 std::cout << "file " << dataFile.getName() << " not found" << std::endl;
                 return false;
             }
             //check if tmin condition is satisfied
             Mdouble t;
             dataFile.getFstream() >> t;
             if (t > tMin)
             {
                 //set_file_counter(get_file_counter()-1);
                 return true;
             }
             if (verbose)
                 std::cout << "Jumping file counter: " << dataFile.getCounter() << std::endl;
         }
     }
     return true;
 }

void DPMBase::finishStatistics ( )

protectedvirtual

no implementation but can be overidden in its derived classes.

Reimplemented in StatisticsVector< T >.

Definition at line 710 of file DPMBase.cc.

Referenced by solve(), and Mercury3DRestart::writeOutputFiles().

711 {

712 }

void DPMBase::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
	)

virtual

//Not unsigned index because of possible wall collisions.

no implementation but can be overidden in its derived classes.

Reimplemented in StatisticsVector< T >.

Definition at line 696 of file DPMBase.cc.

Referenced by BaseInteraction::gatherContactStatistics().

697 {

698 }

void DPMBase::gatherContactStatistics ( )

protected

Definition at line 687 of file DPMBase.cc.

References BaseHandler< T >::begin(), BaseHandler< T >::end(), and interactionHandler.

 {
     for (std::vector<BaseInteraction*>::const_iterator it = interactionHandler.begin(); it != interactionHandler.end(); ++it)
         (*it)->gatherContactStatistics();
 }

bool DPMBase::getAppend ( ) const

Returns the flag denoting if the append option is on or off.

Returns: bool (True or False)

Definition at line 536 of file DPMBase.cc.

References append_.

Referenced by solve(), and writeEneHeader().

 {
     return append_;
 }

bool DPMBase::getDoCGAlways ( ) const

Mdouble DPMBase::getElasticEnergy ( ) const

Returns the global elastic energy within the system.

Returns: Mdouble elasticEnergy

Definition at line 552 of file DPMBase.cc.

References BaseHandler< T >::begin(), BaseHandler< T >::end(), and interactionHandler.

Referenced by writeEneTimestep().

 {
     Mdouble elasticEnergy = 0.0;
     for (std::vector<BaseInteraction*>::const_iterator it = interactionHandler.begin(); it != interactionHandler.end(); ++it)
         elasticEnergy += (*it)->getElasticEnergy();
     return elasticEnergy;
 }

Vec3D DPMBase::getGravity ( ) const

Returns the gravity vector.

Returns: Vec3D gravity_

Definition at line 438 of file DPMBase.cc.

References gravity_.

Referenced by computeExternalForces(), ChuteWithHopper::getMaximumVelocityInducedByGravity(), Chute::setChuteAngle(), write(), and writeEneTimestep().

 {
     return gravity_;
 }

bool DPMBase::getHGridUpdateEachTimeStep ( ) const

protectedvirtual

Returns: bool (True or False)

Reimplemented in MercuryBase.

Definition at line 647 of file DPMBase.cc.

 {
     return true;
 }

double DPMBase::getInfo ( const BaseParticle & P ) const

virtual

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.

Returns: double

Definition at line 580 of file DPMBase.cc.

References BaseObject::getId(), and BaseInteractable::getSpecies().

 {
     return P.getSpecies()->getId(); // was getIndex()
 }

Mdouble DPMBase::getKineticEnergy ( ) const

Returns the global kinetic energy stored in the system.

Returns: Mdouble kineticEnergy

Definition at line 563 of file DPMBase.cc.

References BaseHandler< T >::begin(), BaseHandler< T >::end(), and particleHandler.

 {
     Mdouble kineticEnergy = 0;
     for (std::vector<BaseParticle*>::const_iterator it = particleHandler.begin(); it != particleHandler.end(); ++it)
     {
         if (!(*it)->isFixed())
         {
             kineticEnergy += .5 * (*it)->getMass() * (*it)->getVelocity().getLengthSquared();
         }
     }
     return kineticEnergy;
 
 }

unsigned int DPMBase::getNtimeSteps ( ) const

Returns the current counter of time steps.

Returns: ntimeSteps_

Definition at line 165 of file DPMBase.cc.

References ntimeSteps_.

 {
     return ntimeSteps_;
 }

unsigned int DPMBase::getParticleDimensions ( ) const

Returns the particle dimensions.

Returns: particleDimensions_

Definition at line 492 of file DPMBase.cc.

References particleDimensions_.

Referenced by checkSettings(), ParticleSpecies::getMassFromRadius(), BaseParticle::getParticleDimensions(), and write().

 {
     return particleDimensions_;
 }

bool DPMBase::getRestarted ( ) const

Returns the flag denoting if the simulation was restarted or not.

Returns: restarted_

Definition at line 519 of file DPMBase.cc.

References restarted_.

Referenced by solve(), and writeOutputFiles().

 {
     return restarted_;
 }

std::string DPMBase::getRestartVersion ( ) const

This is to take into account for different Mercury versions. Returns the version of the restart file.

Returns: restartVersion_

Definition at line 501 of file DPMBase.cc.

References restartVersion_.

Referenced by Chute::read().

 {
     return restartVersion_;
 }

bool DPMBase::getRotation ( ) const

Returns a flag indicating if particle rotation is enabled or disabled.

Returns: bool (True or False)

Definition at line 217 of file DPMBase.cc.

References rotation_.

Referenced by computeForcesDueToWalls(), and computeInternalForces().

 {
     return rotation_;
 }

unsigned int DPMBase::getSystemDimensions ( ) const

Returns the dimension of the simulation. Note there is also a particle dimension.

Returns: systemDimensions_

Definition at line 466 of file DPMBase.cc.

References systemDimensions_.

Referenced by checkSettings(), HGridOptimiser::initialise(), outputXBallsData(), readNextDataFile(), StatisticsVector< T >::setNZ(), and write().

 {
     return systemDimensions_;
 }

Mdouble DPMBase::getTime ( ) const

Access function for the time.

Returns: time_

Definition at line 158 of file DPMBase.cc.

References time_.

Referenced by StatisticsVector< T >::check_current_time_for_statistics(), computeForcesDueToWalls(), computeInternalForces(), integrateAfterForceComputation(), integrateBeforeForceComputation(), isTimeEqualTo(), outputXBallsData(), Chute::printTime(), printTime(), LeesEdwardsBoundary::shiftVerticalPosition(), solve(), LeesEdwardsBoundary::write(), write(), writeEneTimestep(), and writeFstatHeader().

 {
     return time_;
 }

Mdouble DPMBase::getTimeMax ( ) const

Allows the user to access the total simulation time during the simulation. Cannot change it though.

Returns: timeMax_

Definition at line 194 of file DPMBase.cc.

References timeMax_.

Referenced by StatisticsVector< T >::getTimeMaxStat(), Chute::printTime(), printTime(), Mercury3DRestart::readNextArgument(), readNextArgument(), solve(), and write().

 {
     return timeMax_;
 }

Mdouble DPMBase::getTimeStep ( ) const

Allows the time step dt to be accessed.

Returns: timeStep_

Definition at line 368 of file DPMBase.cc.

References timeStep_.

Referenced by StatisticsVector< T >::check_current_time_for_statistics(), checkSettings(), SlidingFrictionInteraction::computeFrictionForce(), FrictionInteraction::computeFrictionForce(), ChuteWithHopper::getTimeStepRatio(), integrateAfterForceComputation(), integrateBeforeForceComputation(), isTimeEqualTo(), ChuteBottom::makeRoughBottom(), readNextArgument(), readParAndIniFiles(), solve(), and write().

 {
     return timeStep_;
 }

std::string DPMBase::getXBallsAdditionalArguments ( ) const

Returns: xBallsAdditionalArguments_

Definition at line 410 of file DPMBase.cc.

References xBallsAdditionalArguments_.

 {
     return xBallsAdditionalArguments_;
 }

int DPMBase::getXBallsColourMode ( ) const

Get the xball colour mode (CMode)

Returns: int xBallsColourMode_

Definition at line 382 of file DPMBase.cc.

References xBallsColourMode_.

 {
     return xBallsColourMode_;
 }

double DPMBase::getXBallsScale ( ) const

Returns the scale of the view in xballs.

Returns: double xBallsScale_

Definition at line 424 of file DPMBase.cc.

References xBallsScale_.

 {
     return xBallsScale_;
 }

double DPMBase::getXBallsVectorScale ( ) const

Returns the scale of vectors used in xballs.

Returns: double xBallsVectorScale_

Definition at line 396 of file DPMBase.cc.

References xBallsVectorScale_.

 {
     return xBallsVectorScale_;
 }

Mdouble DPMBase::getXMax ( ) const

If the length of the problem domain in x-direction is XMax - XMin, then getXMax() returns XMax,.

Returns: xMax_

Definition at line 231 of file DPMBase.cc.

References xMax_.

Referenced by Chute::cleanChute(), Chute::createBottom(), ChuteWithHopper::getChuteLength(), Chute::getChuteLength(), ChuteWithHopper::getMaximumVelocityInducedByGravity(), StatisticsVector< T >::getXMaxStat(), HGridOptimiser::initialise(), outputXBallsData(), readParAndIniFiles(), ChuteWithHopper::setHopperShift(), ChuteBottom::setupInitialConditions(), Chute::setupInitialConditions(), setXMin(), write(), and writeFstatHeader().

 {
     return xMax_;
 }

Mdouble DPMBase::getXMin ( ) const

If the length of the problem domain in x-direction is XMax - XMin, then getXMin() returns XMin,.

Returns: xMin_

Definition at line 224 of file DPMBase.cc.

References xMin_.

Referenced by Chute::cleanChute(), Chute::createBottom(), StatisticsVector< T >::getXMinStat(), HGridOptimiser::initialise(), outputXBallsData(), readParAndIniFiles(), ChuteBottom::setupInitialConditions(), Chute::setupInitialConditions(), setXMax(), write(), and writeFstatHeader().

 {
     return xMin_;
 }

Mdouble DPMBase::getYMax ( ) const

If the length of the problem domain in y-direction is YMax - YMin, then getYMax() returns XMax,.

Returns: yMax_

Definition at line 245 of file DPMBase.cc.

References yMax_.

Referenced by ChuteWithHopper::addHopper(), Chute::createBottom(), Chute::getChuteWidth(), StatisticsVector< T >::getYMaxStat(), HGridOptimiser::initialise(), outputXBallsData(), readParAndIniFiles(), ChuteBottom::setupInitialConditions(), Chute::setupInitialConditions(), ChuteWithHopper::setupInitialConditions(), Chute::setupSideWalls(), setYMin(), write(), and writeFstatHeader().

 {
     return yMax_;
 }

Mdouble DPMBase::getYMin ( ) const

If the length of the problem domain in y-direction is YMax - YMin, then getYMin() returns YMin,.

Returns: yMin_

Definition at line 238 of file DPMBase.cc.

References yMin_.

Referenced by ChuteWithHopper::addHopper(), Chute::createBottom(), StatisticsVector< T >::getYMinStat(), HGridOptimiser::initialise(), outputXBallsData(), readParAndIniFiles(), ChuteBottom::setupInitialConditions(), Chute::setupInitialConditions(), ChuteWithHopper::setupInitialConditions(), Chute::setupSideWalls(), setYMax(), write(), and writeFstatHeader().

 {
     return yMin_;
 }

Mdouble DPMBase::getZMax ( ) const

If the length of the problem domain in z-direction is ZMax - ZMin, then getZMax() returns ZMax,.

Returns: zMax_

Definition at line 259 of file DPMBase.cc.

References zMax_.

Referenced by StatisticsVector< T >::getZMaxStat(), HGridOptimiser::initialise(), outputXBallsData(), readParAndIniFiles(), ChuteBottom::setupInitialConditions(), Chute::setupInitialConditions(), setZMin(), write(), and writeFstatHeader().

 {
     return zMax_;
 }

Mdouble DPMBase::getZMin ( ) const

If the length of the problem domain in z-direction is ZMax - ZMin, then getZMin() returns ZMin,.

Returns: zMin_

Definition at line 252 of file DPMBase.cc.

References zMin_.

Referenced by Chute::createBottom(), StatisticsVector< T >::getZMinStat(), HGridOptimiser::initialise(), outputXBallsData(), readParAndIniFiles(), ChuteBottom::setupInitialConditions(), Chute::setupInitialConditions(), setZMax(), write(), and writeFstatHeader().

 {
     return zMin_;
 }

void DPMBase::hGridActionsAfterIntegration ( )

protectedvirtual

no implementation but can be overidden in its derived classes.

Reimplemented in MercuryBase.

Definition at line 731 of file DPMBase.cc.

Referenced by solve().

732 {

733 }

void DPMBase::hGridActionsBeforeIntegration ( )

protectedvirtual

no implementation but can be overidden in its derived classes.

Reimplemented in MercuryBase.

Definition at line 724 of file DPMBase.cc.

Referenced by solve().

725 {

726 }

void DPMBase::hGridActionsBeforeTimeLoop ( )

protectedvirtual

A virtual function that allows one to carry out hGrid operations before the start of the time loop.

no implementation but can be overidden in its derived classes.

Reimplemented in MercuryBase.

Definition at line 605 of file DPMBase.cc.

Referenced by solve().

606 {

607 }

void DPMBase::hGridActionsBeforeTimeStep ( )

protectedvirtual

A virtual function that allows one to set or execute hGrid parameters or operations before every simulation time step.

no implementation but can be overidden in its derived classes.

Reimplemented in MercuryBase.

Definition at line 619 of file DPMBase.cc.

Referenced by solve().

620 {

621 }

void DPMBase::hGridInsertParticle ( BaseParticle *obj UNUSED )

virtual

no implementation but can be overidden in its derived classes.

Bug:: Why are the hGRID actions public, this seems wrong. Someone please comment [Ant].

Definition at line 626 of file DPMBase.cc.

Referenced by ParticleHandler::addObject().

627 {

628 }

void DPMBase::hGridRemoveParticle ( BaseParticle *obj UNUSED )

virtual

no implementation but can be overidden in its derived classes.

Definition at line 640 of file DPMBase.cc.

Referenced by ParticleHandler::removeLastObject(), and ParticleHandler::removeObject().

641 {

642 }

void DPMBase::hGridUpdateMove	(	BaseParticle *	,
		Mdouble
	)

virtual

no implementation but can be overidden in its derived classes.

Reimplemented in MercuryBase.

Definition at line 717 of file DPMBase.cc.

Referenced by BaseParticle::integrateBeforeForceComputation().

718 {

719 }

void DPMBase::hGridUpdateParticle ( BaseParticle *obj UNUSED )

virtual

no implementation but can be overidden in its derived classes.

Definition at line 633 of file DPMBase.cc.

Referenced by ParticleHandler::addObject(), MercuryBase::hGridActionsBeforeTimeStep(), and MercuryBase::hGridRebuild().

634 {

635 }

void DPMBase::initialiseStatistics ( )

protectedvirtual

no implementation but can be overidden in its derived classes.

Reimplemented in StatisticsVector< T >.

Definition at line 676 of file DPMBase.cc.

Referenced by solve().

677 {

678 }

void DPMBase::initialiseTangentialSprings ( )

protected

void DPMBase::integrateAfterForceComputation ( )

protectedvirtual

Integration is done after force computations. We apply the Velocity verlet scheme. See http://en.wikipedia.org/wiki/Verlet_integration#Velocity_Verlet.

Definition at line 1524 of file DPMBase.cc.

References BaseHandler< T >::begin(), BaseHandler< T >::end(), getTime(), getTimeStep(), particleHandler, and wallHandler.

Referenced by solve().

 {
     for_each(particleHandler.begin(), particleHandler.end(), [this] (BaseParticle* p)
     {
         p->integrateAfterForceComputation(getTime(),getTimeStep());
     });
     for_each(wallHandler.begin(), wallHandler.end(), [this] (BaseWall* w)
     {
         w->integrateAfterForceComputation(getTime(),getTimeStep());
     });
 }

void DPMBase::integrateBeforeForceComputation ( )

protectedvirtual

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.

Definition at line 1495 of file DPMBase.cc.

References BaseHandler< T >::begin(), BaseHandler< T >::end(), getTime(), getTimeStep(), particleHandler, and wallHandler.

Referenced by solve().

 {
     for_each(particleHandler.begin(), particleHandler.end(), [this] (BaseParticle* p)
     {
         p->integrateBeforeForceComputation(getTime(),getTimeStep());
     });
     for_each(wallHandler.begin(), wallHandler.end(), [this] (BaseWall* w)
     {
         w->integrateBeforeForceComputation(getTime(),getTimeStep());
     });
 }

bool DPMBase::isTimeEqualTo ( Mdouble time ) const

protected

Checks if the input variable "time" is the current time in the simulation.

Returns: bool (True or False)

Definition at line 2446 of file DPMBase.cc.

References getTime(), and getTimeStep().

 {
     return getTime()<=time && getTime()+getTimeStep()>time;
 }

void DPMBase::outputInteractionDetails ( ) const

protected

Displays the interaction details corresponding to the pointer objects in the interaction handler.

Skims through all the object pointers of type BaseInteraction in the interaction handler. Outputs the type of interaction between two particles P and I.

Definition at line 2424 of file DPMBase.cc.

References BaseHandler< T >::begin(), BaseHandler< T >::end(), and interactionHandler.

 {
     std::cout << "Interactions currently in the handler:" << std::endl;
     for (std::vector<BaseInteraction*>::const_iterator it = interactionHandler.begin(); it != interactionHandler.end(); ++it)
     {
         (*it)->write(std::cout);
         std::cout << std::endl;
         std::cout << "Interaction " << (*it)->getName() << " " << (*it)->getId() << " between " << (*it)->getP()->getId() << " and " << (*it)->getI()->getId() << std::endl;
     }
     /*std::cout << "Interactions currently in the particles:" << std::endl;
      for (std::vector<BaseParticle*>::const_iterator it = particleHandler.begin(); it != particleHandler.end(); ++it)
      {
      std::cout << "Base particle " << (*it)->getId() << " has interactions:" << std::endl;
      for (std::list<BaseInteraction*>::const_iterator it2 = (*it)->getInteractions().begin(); it2 != (*it)->getInteractions().end(); ++it2)
      {
      std::cout << (*it2)->getId() << " between " << (*it2)->getP()->getId() << " and " << (*it2)->getI()->getId() << std::endl;
      }
      }*/
 }

void DPMBase::outputStatistics ( )

protectedvirtual

no implementation but can be overidden in its derived classes.

Reimplemented in StatisticsVector< T >.

Definition at line 683 of file DPMBase.cc.

684 {

685 }

void DPMBase::outputXBallsData ( std::ostream & os ) const

protectedvirtual

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.

Parameters

[in] os

Definition at line 947 of file DPMBase.cc.

References BaseHandler< T >::getNumberOfObjects(), getSystemDimensions(), getTime(), getXMax(), getXMin(), getYMax(), getYMin(), getZMax(), getZMin(), outputXBallsDataParticle(), and particleHandler.

Referenced by writeOutputFiles().

         {
     //Set the correct formation based of dimension if the formation is not specified by the user
     unsigned int format;
     switch (getSystemDimensions())
     {
         case 2:
             format = 8;
             break;
         case 3:
             format = 14;
             break;
         default:
             std::cerr << "Unknown systemdimension" << std::endl;
             exit(-1);
     }
     
     // This outputs the location of walls and how many particles there are to file this is required by the xballs plotting
     if (format != 14) // dim = 1 or 2
     {
         os << particleHandler.getNumberOfObjects() << " " << getTime() << " " << getXMin() << " " << getYMin() << " " << getXMax() << " " << getYMax() << " " << std::endl;
     }
     else
     {
         //dim==3
         os << particleHandler.getNumberOfObjects() << " " << getTime() << " " << getXMin() << " " << getYMin() << " " << getZMin() << " " << getXMax() << " " << getYMax() << " " << getZMax() << " " << std::endl;
     }
     // This outputs the particle data
     for (unsigned int i = 0; i < particleHandler.getNumberOfObjects(); i++)
     {
         outputXBallsDataParticle(i, format, os);
     }
 #ifdef DEBUG_OUTPUT
     std::cerr << "Have output the properties of the problem to disk " << std::endl;
 #endif
 }

virtual void DPMBase::outputXBallsDataParticle	(	const unsigned int	i,
		const unsigned int	format,
		std::ostream &	os
	)		const

protectedvirtual

This function writes out the particle locations into an output stream in a format the XBalls program can read.

Referenced by outputXBallsData().

void DPMBase::printTime ( ) const

protectedvirtual

Displays the current simulation time onto your screen for example.

Reimplemented in Chute.

Definition at line 758 of file DPMBase.cc.

References getTime(), and getTimeMax().

Referenced by Mercury3DRestart::readNextArgument(), and writeOutputFiles().

 {
     std::cout << "t=" << std::setprecision(3) << std::left << std::setw(6) << getTime()
         << ", tmax=" << std::setprecision(3) << std::left << std::setw(6) << getTimeMax()
         << std::endl;
     std::cout.flush();
 }

void DPMBase::processStatistics ( bool usethese UNUSED )

protectedvirtual

no implementation but can be overidden in its derived classes.

Reimplemented in StatisticsVector< T >.

Definition at line 703 of file DPMBase.cc.

704 {

705 }

void DPMBase::read ( std::istream & is )

virtual

Reads all particle data into a restart file.

Parameters

[in] is

todo{Do we want to calculate the mass?}

Reimplemented in ChuteWithHopper, Chute, and MercuryBase.

Definition at line 1695 of file DPMBase.cc.

References boundaryHandler, BaseHandler< T >::clear(), ParticleHandler::clear(), FATAL, helpers::getLineFromStringStream(), gravity_, INFO, interactionHandler, logger, ntimeSteps_, particleDimensions_, particleHandler, BaseHandler< T >::read(), FilesAndRunNumber::read(), BoundaryHandler::readObject(), WallHandler::readObject(), ParticleHandler::readObject(), readOld(), restartVersion_, speciesHandler, systemDimensions_, time_, timeMax_, timeStep_, wallHandler, xMax_, xMin_, yMax_, yMin_, zMax_, and zMin_.

Referenced by MercuryBase::read(), and readRestartFile().

 {
     std::string dummy;
     is >> dummy;
     if (strcmp(dummy.c_str(), "restart_version"))
     {
         //only very old files did not have a restart_version
         logger.log(Log::FATAL, "Error in DPMBase::read(is): this is not a valid restart file");
     }
     else
     {
         is >> restartVersion_;
         if (!restartVersion_.compare("1.0"))
         {
             FilesAndRunNumber::read(is);
             is >> dummy >> xMin_
                 >> dummy >> xMax_
                 >> dummy >> yMin_
                 >> dummy >> yMax_
                 >> dummy >> zMin_
                 >> dummy >> zMax_
                 >> dummy >> timeStep_
                 >> dummy >> time_
                 >> dummy >> ntimeSteps_
                 >> dummy >> timeMax_
                 >> dummy >> systemDimensions_
                 >> dummy >> particleDimensions_
                 >> dummy >> gravity_;
             speciesHandler.read(is);
 
             unsigned int N;
             std::stringstream line(std::stringstream::in | std::stringstream::out);
             is >> dummy >> N;
             wallHandler.clear();
             helpers::getLineFromStringStream(is, line);
             for (unsigned int i = 0; i < N; i++)
             {
                 helpers::getLineFromStringStream(is, line);
                 wallHandler.readObject(line);
             }
 
             is >> dummy >> N;
             boundaryHandler.clear();
             helpers::getLineFromStringStream(is, line);
             for (unsigned int i = 0; i < N; i++)
             {
                 helpers::getLineFromStringStream(is, line);
                 boundaryHandler.readObject(line);
             }
 
             is >> dummy >> N;
             particleHandler.clear();
             helpers::getLineFromStringStream(is, line);
             for (unsigned int i = 0; i < N; i++)
             {
                 helpers::getLineFromStringStream(is, line);
                 particleHandler.readObject(line);
                 //particleHandler.getLastObject()->computeMass();
             }
             interactionHandler.read(is);
         }
         else if (!restartVersion_.compare("3"))
         {
             logger.log(Log::INFO, "DPMBase::read(is): restarting from an old restart file (restart_version %).", restartVersion_);
             readOld(is);
         }
         else
         {
             //only very old files did not have a restart_version
             logger.log(Log::FATAL, "Error in DPMBase::read(is): restart_version % cannot be read; use an older version of Mercury to upgrade the file", restartVersion_);
         }
     }
 }

bool DPMBase::readArguments	(	int	argc,
		char *	argv[]
	)

Can interpret main function input arguments that are passed by the driver codes.

Parameters

[in]	argc
[in]	*argv[]

Definition at line 2029 of file DPMBase.cc.

References readNextArgument().

Referenced by solve().

 {
     bool isRead = true;
     for (int i = 1; i < argc; i += 2)
     {
         std::cout << "interpreting input argument " << argv[i];
         for (int j = i + 1; j < argc; j++)
         {
             if (argv[j][0] == '-')
                 break;
             std::cout << " " << argv[j];
         }
         std::cout << std::endl;
         isRead &= readNextArgument(i, argc, argv);
         if (!isRead)
         {
             std::cerr << "Warning: not all arguments read correctly!" << std::endl;
         }
     }
     return isRead;
 }

bool DPMBase::readDataFile	(	const std::string	fileName,
		unsigned int	format = `0`
	)

This allows particle data to be reloaded from data files.

E.g. If one has a data file. This function loads data from the .data file i.e. you get position, velocity, angular velocty, radius .. info. See also MD::readRestartFile For XBalls: Can read in format_ 14 - 8 or format_ 7 data format. This code saves in format_ 8 for 2D and format_ 14 for 3D. So if no extra parameters are specified it will assume things many parameters, like density cannot be set using the data file.

Parameters

[in]	fileName
[in]	format	(format for specifying if its for 2D or 3D data)

Returns: bool (True or False)

Definition at line 989 of file DPMBase.cc.

References File::close(), Files::dataFile, File::getFileType(), File::getFstream(), File::getName(), ONE_FILE, File::open(), readNextDataFile(), File::setFileType(), and File::setName().

Referenced by readNextArgument().

 {
     std::string oldFileName = dataFile.getName();
     //This opens the file the data will be recalled from
     dataFile.setName(fileName);
     dataFile.open(std::fstream::in);
     if (!dataFile.getFstream().is_open() || dataFile.getFstream().bad())
     {
         std::cout << "Loading data file " << fileName << " failed" << std::endl;
         return false;
     }
 
     //dataFile.getFileType() is ignored
     FileType fileTypeData = dataFile.getFileType();
     dataFile.setFileType(FileType::ONE_FILE);
     readNextDataFile(format);
     dataFile.setFileType(fileTypeData);
 
     dataFile.close();
     dataFile.setName(oldFileName);
 
     //std::cout << "Loaded data file " << filename << " (t=" << getTime() << ")" << std::endl;
     return true;
 }

bool DPMBase::readNextArgument	(	int &	i,
		int	argc,
		char *	argv[]
	)

virtual

Parameters

[in]	i
[in]	argc
[in]	*argv[]

Returns: bool (True or False)

argv[i+1] interpreted as argument of type char*, Mdouble, integer or boolean unless noted

-gravity_ requires three arguments

-restart or -r loads a restart file. By default, it loads <name>.restart. If an argument "arg" is given it loads the file "arg", or "arg".restart (if the ending is not given).

-clean of -c removes all files <name>.*.

Reimplemented in MercuryBase, ChuteWithHopper, Chute, and Mercury3DRestart.

Definition at line 2057 of file DPMBase.cc.

References FilesAndRunNumber::autoNumber(), Files::dataFile, Files::eneFile, Files::fStatFile, Files::getName(), getTimeMax(), getTimeStep(), random, RNG::randomise(), readDataFile(), readRestartFile(), Files::restartFile, setAppend(), File::setFileType(), Files::setFileType(), setFixedParticles(), setGravity(), Files::setName(), FilesAndRunNumber::setRunNumber(), File::setSaveCount(), Files::setSaveCount(), setSystemDimensions(), setTimeMax(), setTimeStep(), setXMax(), setXMin(), setYMax(), setYMin(), setZMax(), setZMin(), Files::statFile, and to_string_padded().

Referenced by readArguments(), and MercuryBase::readNextArgument().

 {
     if (!strcmp(argv[i], "-name"))
     {
         setName(argv[i + 1]);
     }
     else if (!strcmp(argv[i], "-xmin"))
     {
         setXMin(atof(argv[i + 1]));
     }
     else if (!strcmp(argv[i], "-ymin"))
     {
         setYMin(atof(argv[i + 1]));
     }
     else if (!strcmp(argv[i], "-zmin"))
     {
         setZMin(atof(argv[i + 1]));
     }
     else if (!strcmp(argv[i], "-xmax"))
     {
         setXMax(atof(argv[i + 1]));
     }
     else if (!strcmp(argv[i], "-ymax"))
     {
         setYMax(atof(argv[i + 1]));
     }
     else if (!strcmp(argv[i], "-zmax"))
     {
         setZMax(atof(argv[i + 1]));
         //} else if (!strcmp(argv[i],"-svn")) {
         //  std::cout << "svn version " << SVN_VERSION << std::endl;
         //  i--;
     }
     else if (!strcmp(argv[i], "-dt"))
     {
         Mdouble old = getTimeStep();
         setTimeStep(atof(argv[i + 1]));
         std::cout << "  reset dt from " << old << " to " << getTimeStep() << std::endl;
     }
 //    else if (!strcmp(argv[i], "-Hertz"))
 //    {
 //        speciesHandler.getObject(0)->setForceType(ForceType::HERTZ);
 //        i--;
 //    }
     else if (!strcmp(argv[i], "-tmax"))
     {
         Mdouble old = getTimeMax();
         setTimeMax(atof(argv[i + 1]));
         std::cout << "  reset timeMax from " << old << " to " << getTimeMax() << std::endl;
     }
     else if (!strcmp(argv[i], "-saveCount"))
     {
         setSaveCount(static_cast<unsigned int>(atoi(argv[i + 1])));
     }
     else if (!strcmp(argv[i], "-saveCountData"))
     {
         dataFile.setSaveCount(static_cast<unsigned int>(atoi(argv[i + 1])));
     }
     else if (!strcmp(argv[i], "-saveCountFStat"))
     {
         fStatFile.setSaveCount(static_cast<unsigned int>(atoi(argv[i + 1])));
     }
     else if (!strcmp(argv[i], "-saveCountStat"))
     {
         statFile.setSaveCount(static_cast<unsigned int>(atoi(argv[i + 1])));
     }
     else if (!strcmp(argv[i], "-saveCountEne"))
     {
         eneFile.setSaveCount(static_cast<unsigned int>(atoi(argv[i + 1])));
     }
     else if (!strcmp(argv[i], "-saveCountRestart"))
     {
         restartFile.setSaveCount(static_cast<unsigned int>(atoi(argv[i + 1])));
     }
     else if (!strcmp(argv[i], "-dim"))
     {
         setSystemDimensions(static_cast<unsigned int>(atoi(argv[i + 1])));
     }
     else if (!strcmp(argv[i], "-gravity"))
     {
         setGravity(Vec3D(atof(argv[i + 1]), atof(argv[i + 2]), atof(argv[i + 3])));
         i += 2;
     }
     else if (!strcmp(argv[i], "-fileType"))
     { //uses int input
         setFileType(static_cast<FileType>(atoi(argv[i + 1])));
     }
     else if (!strcmp(argv[i], "-fileTypeFStat"))
     { //uses int input
         fStatFile.setFileType(static_cast<FileType>(atoi(argv[i + 1])));
     }
     else if (!strcmp(argv[i], "-fileTypeRestart"))
     {
         restartFile.setFileType(static_cast<FileType>(atoi(argv[i + 1])));
     }
     else if (!strcmp(argv[i], "-fileTypeData"))
     {
         dataFile.setFileType(static_cast<FileType>(atoi(argv[i + 1])));
     }
     else if (!strcmp(argv[i], "-fileTypeStat"))
     {
         statFile.setFileType(static_cast<FileType>(atoi(argv[i + 1])));
     }
     else if (!strcmp(argv[i], "-fileTypeEne"))
     {
         eneFile.setFileType(static_cast<FileType>(atoi(argv[i + 1])));
     }
     else if (!strcmp(argv[i], "-auto_number"))
     {
         autoNumber();
         i--;
     }
 //    else if (!strcmp(argv[i], "-number_of_saves"))
 //    {
 //        set_number_of_saves_all(atof(argv[i + 1]));
 //    }
     else if (!strcmp(argv[i], "-restart") || !strcmp(argv[i], "-r"))
     {
         std::string filename;
         
         //use default filename if no argument is given
         if (i + 1 >= argc || argv[i + 1][0] == '-')
         {
             i--;
             filename = getName();
             std::cout << getName() << std::endl;
         }
         else
             filename = argv[i + 1];
         
         //add ".restart" if necessary
         if (filename.find(".restart") == std::string::npos)
         {            
             filename = filename + ".restart";
         }
         
         std::cout << "restart from " << filename << std::endl;
         readRestartFile(filename);
     }    
     else if (!strcmp(argv[i], "-clean") || !strcmp(argv[i], "-c"))
     {
         std::cout<< "Remove old " << getName() << ".* files" << std::endl;
 //        std::string filename;
         std::ostringstream filename;
         std::vector<std::string> ext {".restart",".stat",".fstat",".data",".ene",".xballs"};
         for (unsigned int j=0; j<ext.size(); j++)
         {
             // remove files with given extension for FileType::ONE_FILE
             filename.clear();
             filename << getName() <<ext[j];
             if( !remove( filename.str().c_str() ) )
             {
                 std::cout<< "  File " << filename.str() << " successfully deleted" << std::endl;
             }
             // remove files with given extension for FileType::MULTIPLE_FILES
             unsigned int k=0;
             filename.clear(); filename << getName() << ext[j] << '.' << k;
             while( !remove( filename.str().c_str() ) )
             {
                 std::cout<< "  File " << filename.str() << " successfully deleted" << std::endl;
                 filename.clear();
                 filename << getName() << ext[j] << '.' << ++k;
             }
             // remove files with given extension for FileType::MULTIPLE_FILES_PADDED
             k=0;           
             filename.clear(); filename << getName() << ext[j] << '.' << to_string_padded(k);
             while( !remove( filename.str().c_str() ) )
             {
                 std::cout<< "  File " << filename.str() << " successfully deleted" << std::endl;
                 filename.clear();
                 filename << getName() << ext[j] << '.' << to_string_padded(++k);
             }
         }
         i--;
     }
     else if (!strcmp(argv[i], "-data"))
     {
         std::string filename = argv[i + 1];
         readDataFile(filename.c_str());
     }
 //    else if (!strcmp(argv[i], "-k"))
 //    {
 //        Mdouble old = getSpecies(0)->getStiffness();
 //        getSpecies(0)->setStiffness(atof(argv[i + 1]));
 //        std::cout << "  reset k from " << old << " to " << getSpecies(0)->getStiffness() << std::endl;
 //    }
 //    else if (!strcmp(argv[i], "-dissipation") || !strcmp(argv[i], "-disp"))
 //    {
 //        Mdouble old = getSpecies(0)->getDissipation();
 //        getSpecies(0)->setDissipation(atof(argv[i + 1]));
 //        std::cout << "  reset getDissipation() from " << old << " to " << getSpecies(0)->getDissipation() << std::endl;
 //    }
 //    else if (!strcmp(argv[i], "-kt"))
 //    {
 //        Mdouble old = getSpecies(0)->getSlidingStiffness();
 //        getSpecies(0)->setSlidingStiffness(atof(argv[i + 1]));
 //        std::cout << "  reset kt from " << old << " to " << getSpecies(0)->getSlidingStiffness() << std::endl;
 //    }
 //    else if (!strcmp(argv[i], "-dispt"))
 //    {
 //        Mdouble old = getSpecies(0)->getSlidingDissipation();
 //        getSpecies(0)->setSlidingDissipation(atof(argv[i + 1]));
 //        std::cout << "  reset dispt from " << old << " to " << getSpecies(0)->getSlidingDissipation() << std::endl;
 //    }
 //    else if (!strcmp(argv[i], "-krolling"))
 //    {
 //        Mdouble old = getSpecies(0)->getRollingStiffness();
 //        getSpecies(0)->setRollingStiffness(atof(argv[i + 1]));
 //        std::cout << "  reset krolling from " << old << " to " << getSpecies(0)->getRollingStiffness() << std::endl;
 //    }
 //    else if (!strcmp(argv[i], "-disprolling"))
 //    {
 //        Mdouble old = getSpecies(0)->getRollingDissipation();
 //        getSpecies(0)->setRollingDissipation(atof(argv[i + 1]));
 //        std::cout << "  reset disprolling from " << old << " to " << getSpecies(0)->getRollingDissipation() << std::endl;
 //    }
 //    else if (!strcmp(argv[i], "-mu"))
 //    {
 //        Mdouble old = getSpecies(0)->getSlidingFrictionCoefficient();
 //        getSpecies(0)->setSlidingFrictionCoefficient(atof(argv[i + 1]));
 //        std::cout << "  reset mu from " << old << " to " << getSpecies(0)->getSlidingFrictionCoefficient() << std::endl;
 //    }
 //    else if (!strcmp(argv[i], "-murolling"))
 //    {
 //        Mdouble old = getSpecies(0)->getRollingFrictionCoefficient();
 //        getSpecies(0)->setRollingFrictionCoefficient(atof(argv[i + 1]));
 //        std::cout << "  reset murolling from " << old << " to " << getSpecies(0)->getRollingFrictionCoefficient() << std::endl;
 //    }
     else if (!strcmp(argv[i], "-randomise") || !strcmp(argv[i], "-randomize"))
     {
         random.randomise();
         i--;
     }
 //    else if (!strcmp(argv[i], "-k0"))
 //    {
 //        Mdouble old = speciesHandler.getObject(0)->getAdhesionStiffness();
 //        speciesHandler.getObject(0)->setAdhesionStiffness(atof(argv[i + 1]));
 //        std::cout << "  reset k0 from " << old << " to " << speciesHandler.getObject(0)->getAdhesionStiffness() << std::endl;
 //    }
 //    else if (!strcmp(argv[i], "-f0"))
 //    {
 //        Mdouble old = speciesHandler.getObject(0)->getAdhesionForceMax();
 //        speciesHandler.getObject(0)->setAdhesionForceMax(atof(argv[i + 1]));
 //        std::cout << "  reset f0 from " << old << " to " << speciesHandler.getObject(0)->getAdhesionForceMax() << std::endl;
 //    }
 //    else if (!strcmp(argv[i], "-AdhesionForceType"))
 //    {
 //        AdhesionForceType old = speciesHandler.getObject(0)->getAdhesionForceType();
 //        speciesHandler.getObject(0)->setAdhesionForceType(argv[i + 1]);
 //        std::cout << "  reset AdhesionForceType from "
 //                << static_cast<signed char>(old) << " to "
 //                << static_cast<signed char>(speciesHandler.getObject(0)->getAdhesionForceType()) << std::endl;
 //    }
     else if (!strcmp(argv[i], "-append"))
     {
         setAppend(true);
         i--;
     }
     else if (!strcmp(argv[i], "-fixedParticles"))
     {
         setFixedParticles(static_cast<unsigned int>(atoi(argv[i + 1])));
     }
 //    else if (!strcmp(argv[i], "-rho"))
 //    {
 //        Mdouble old = speciesHandler.getObject(0)->getDensity();
 //        speciesHandler.getObject(0)->setDensity(atof(argv[i + 1]));
 //        std::cout << "  reset rho from " << old << " to " << speciesHandler.getObject(0)->getDensity() << std::endl;
 //    }
 //    else if (!strcmp(argv[i], "-dim_particle"))
 //    {
 //        setParticleDimensions(atoi(argv[i + 1]));
 //    }
     else if (!strcmp(argv[i], "-counter"))
     {
         setRunNumber(atoi(argv[i + 1]));
     }
     else
         return false;
     return true; //returns true if argv is found
 }

bool DPMBase::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.

Parameters

[in] format

Definition at line 1224 of file DPMBase.cc.

References BaseHandler< T >::begin(), ParticleHandler::computeAllMasses(), BaseHandler< T >::copyAndAddObject(), Files::dataFile, BaseHandler< T >::end(), File::getFstream(), BaseHandler< T >::getNumberOfObjects(), getSystemDimensions(), File::openNextFile(), particleHandler, ParticleHandler::removeLastObject(), setTime(), setXMax(), setXMin(), setYMax(), setYMin(), setZMax(), setZMin(), time_, Vec3D::X, xMax_, xMin_, Vec3D::Y, yMax_, yMin_, Vec3D::Z, zMax_, and zMin_.

Referenced by readDataFile().

 {
     dataFile.openNextFile(std::fstream::in);
     //fStatFile.openNextFile();
     //Set the correct formation based of dimension if the formation is not specified by the user
     if (format == 0)
     {
         switch (getSystemDimensions())
         {
             case 1:
                 case 2:
                 format = 8;
                 break;
             case 3:
                 format = 14;
                 break;
         }
         //end case
         
     }
     //end if
     
     unsigned int N=0;
     Mdouble dummy;
     dataFile.getFstream() >> N;
 
     //read first parameter and check if we reached the end of the file
     if (N==0)
         return false;
     
     BaseParticle* P0 = new BaseParticle();
     if (particleHandler.getNumberOfObjects() < N)
         while (particleHandler.getNumberOfObjects() < N)
             particleHandler.copyAndAddObject(P0);
     else
         while (particleHandler.getNumberOfObjects() > N)
             particleHandler.removeLastObject();
     delete P0;
 
 #ifdef DEBUG_OUTPUT
     std::cout << "Number of particles read from file "<<N << std::endl;
 #endif
     
     //read all other data available for the time step
     switch (format)
     {
         //This is the format_ that Stefan's and Vitaley's code saves in - note the axis rotation_
         case 7:
             {
             dataFile.getFstream() >> dummy;
             setTime(dummy);
             dataFile.getFstream() >> dummy;
             setXMin(dummy);
             dataFile.getFstream() >> dummy;
             setYMin(dummy);
             dataFile.getFstream() >> dummy;
             setZMin(dummy);
             dataFile.getFstream() >> dummy;
             setXMax(dummy);
             dataFile.getFstream() >> dummy;
             setYMax(dummy);
             dataFile.getFstream() >> dummy;
             setZMax(dummy);
             //std::cout << " time " << t <<  std::endl;
             Mdouble radius;
             Vec3D position, velocity;
             for (std::vector<BaseParticle*>::iterator it = particleHandler.begin(); it != particleHandler.end(); ++it)
             {
                 dataFile.getFstream() >> position.X >> position.Z >> position.Y >> velocity.X >> velocity.Z >> velocity.Y >> radius >> dummy;
                 (*it)->setPosition(position);
                 (*it)->setVelocity(velocity);
                 (*it)->setOrientation(Vec3D(0.0, 0.0, 0.0));
                 (*it)->setAngularVelocity(Vec3D(0.0, 0.0, 0.0));
                 (*it)->setRadius(radius);
             }
             //End the interator over all particles
             break;
         }
             //This is a 2D format_
         case 8:
             {
             dataFile.getFstream() >> time_ >> xMin_ >> yMin_ >> xMax_ >> yMax_;
             zMin_ = 0.0;
             zMax_ = 0.0;
             Mdouble radius;
             Vec3D position, velocity, angle, angularVelocity;
             for (std::vector<BaseParticle*>::iterator it = particleHandler.begin(); it != particleHandler.end(); ++it)
             {
                 dataFile.getFstream() >> position.X >> position.Y >> velocity.X >> velocity.Y >> radius >> angle.Z >> angularVelocity.Z >> dummy;
                 (*it)->setPosition(position);
                 (*it)->setVelocity(velocity);
                 (*it)->setOrientation(-angle);
                 (*it)->setAngularVelocity(-angularVelocity);
                 (*it)->setRadius(radius);
             } //end for all particles
             break;
         }
             //This is a 3D format_
         case 14:
             {
             dataFile.getFstream() >> time_ >> xMin_ >> yMin_ >> zMin_ >> xMax_ >> yMax_ >> zMax_;
             Mdouble radius;
             Vec3D position, velocity, angle, angularVelocity;
             for (std::vector<BaseParticle*>::iterator it = particleHandler.begin(); it != particleHandler.end(); ++it)
             {
                 dataFile.getFstream() >> position >> velocity >> radius >> angle >> angularVelocity >> dummy;
                 (*it)->setPosition(position);
                 (*it)->setVelocity(velocity);
                 (*it)->setOrientation(angle);
                 (*it)->setAngularVelocity(angularVelocity);
                 (*it)->setRadius(radius);
             } //end for all particles
             break;
         }
             //This is a 3D format_
         case 15:
             {
             dataFile.getFstream() >> time_ >> xMin_ >> yMin_ >> zMin_ >> xMax_ >> yMax_ >> zMax_;
             Mdouble radius;
             Vec3D position, velocity, angle, angularVelocity;
             for (std::vector<BaseParticle*>::iterator it = particleHandler.begin(); it != particleHandler.end(); ++it)
             {
                 dataFile.getFstream() >> position >> velocity >> radius >> angle >> angularVelocity >> dummy >> dummy;
                 (*it)->setPosition(position);
                 (*it)->setVelocity(velocity);
                 (*it)->setOrientation(angle);
                 (*it)->setAngularVelocity(angularVelocity);
                 (*it)->setRadius(radius);
                 
             } //end for all particles
             break;
         }
     } //end switch statement
     particleHandler.computeAllMasses();
     
     return true;
 }

void DPMBase::readOld ( std::istream & is )

virtual

Reads all particle data into a restart file; old version.

Parameters

[in] is

Definition at line 1772 of file DPMBase.cc.

References boundaryHandler, Files::dataFile, Files::eneFile, Files::fStatFile, gravity_, particleHandler, BaseHandler< T >::read(), Files::restartFile, File::setFileType(), Files::setName(), File::setSaveCount(), speciesHandler, Files::statFile, systemDimensions_, time_, timeMax_, timeStep_, wallHandler, xMax_, xMin_, yMax_, yMin_, zMax_, and zMin_.

Referenced by read().

 {
     std::string dummy;
     is >> dummy >> dummy;
     setName(dummy);
 
     unsigned int saveCountData, saveCountEne, saveCountStat, saveCountFStat;
     unsigned int fileTypeFstat, fileTypeData, fileTypeEne, fileTypeRestart;
     is >> dummy >> xMin_
         >> dummy >> xMax_
         >> dummy >> yMin_
         >> dummy >> yMax_
         >> dummy >> zMin_
         >> dummy >> zMax_
         >> dummy >> timeStep_
         >> dummy >> time_
         >> dummy >> timeMax_
         >> dummy >> saveCountData
         >> dummy >> saveCountEne
         >> dummy >> saveCountStat
         >> dummy >> saveCountFStat
         >> dummy >> systemDimensions_
         >> dummy >> gravity_
         >> dummy >> fileTypeFstat
         >> dummy >> fileTypeData
         >> dummy >> fileTypeEne;
     dataFile.setSaveCount(saveCountData);
     eneFile.setSaveCount(saveCountEne);
     statFile.setSaveCount(saveCountStat);
     fStatFile.setSaveCount(saveCountFStat);
     
     fStatFile.setFileType(static_cast<FileType>(fileTypeFstat));
     dataFile.setFileType(static_cast<FileType>(fileTypeData));
     eneFile.setFileType(static_cast<FileType>(fileTypeEne));
     
     //this is optional to allow restart files with and without restartFile.getFileType()
     is >> dummy;
     if (!strcmp(dummy.c_str(), "options_restart"))
     {
         is >> fileTypeRestart;
         restartFile.setFileType(static_cast<FileType>(fileTypeRestart));
     }
 
     speciesHandler.read(is);
     wallHandler.read(is);
     boundaryHandler.read(is);
     particleHandler.read(is);
 }

bool DPMBase::readParAndIniFiles ( const std::string fileName )

Allows the user to read par.ini files (useful to read MDCLR files)

Parameters

[in] fileName

Returns: bool (True or False)

Definition at line 1018 of file DPMBase.cc.

References SpeciesHandler::addObject(), boundaryHandler, BaseHandler< T >::clear(), BaseHandler< T >::copyAndAddObject(), Files::dataFile, Files::fStatFile, getTimeStep(), getXMax(), getXMin(), getYMax(), getYMin(), getZMax(), getZMin(), PeriodicBoundary::set(), InfiniteWall::set(), setGravity(), setParticleDimensions(), File::setSaveCount(), Files::setSaveCount(), setTime(), setTimeMax(), setTimeStep(), speciesHandler, and wallHandler.

 {
     //Opens the par.ini file
     std::fstream file;
     file.open(fileName, std::fstream::in);
     if (!file.is_open() || file.bad())
     {
         //std::cout << "Loading par.ini file " << filename << " failed" << std::endl;
         return false;
     }
     
     Mdouble doubleValue;
     int integerValue;
     
     // inputfile par.ini 
     // line 1 =============================================================
     // Example: 1 1 0
     //   1: integer (0|1) switches from non-periodic to periodic
     //      integer (5|6) does 2D integration only (y-coordinates fixed)
     //                    and switches from non-periodic to periodic
     //      integer (11) uses a quarter system with circular b.c.
     file >> integerValue;
     //~ std::cout << "11" << integerValue << std::endl;
     if (integerValue == 0)
     {
         InfiniteWall w0;
         w0.set(Vec3D(-1, 0, 0), Vec3D(getXMin(), 0, 0));
         wallHandler.copyAndAddObject(w0);
         w0.set(Vec3D( 1, 0, 0), Vec3D(getXMax(), 0, 0));
         wallHandler.copyAndAddObject(w0);
         w0.set(Vec3D(0, -1, 0), Vec3D(0, getYMin(), 0));
         wallHandler.copyAndAddObject(w0);
         w0.set(Vec3D(0,  1, 0), Vec3D(0, getYMax(), 0));
         wallHandler.copyAndAddObject(w0);
         w0.set(Vec3D(0, 0, -1), Vec3D(0, 0, getZMin()));
         wallHandler.copyAndAddObject(w0);
         w0.set(Vec3D(0, 0,  1), Vec3D(0, 0, getZMax()));
         wallHandler.copyAndAddObject(w0);
     }
     else if (integerValue == 1)
     {
         PeriodicBoundary b0;
         b0.set(Vec3D(1, 0, 0), getXMin(), getXMax());
         boundaryHandler.copyAndAddObject(b0);
         b0.set(Vec3D(0, 1, 0), getYMin(), getYMax());
         boundaryHandler.copyAndAddObject(b0);
         b0.set(Vec3D(0, 0, 1), getZMin(), getZMax());
         boundaryHandler.copyAndAddObject(b0);
     }
     else if (integerValue == 5)
     {
         InfiniteWall w0;
         w0.set(Vec3D(-1, 0, 0), Vec3D(-getXMin(), 0, 0));
         wallHandler.copyAndAddObject(w0);
         w0.set(Vec3D(1, 0, 0), Vec3D(getXMax(), 0, 0));
         wallHandler.copyAndAddObject(w0);
         w0.set(Vec3D(0, -1, 0), Vec3D(0, -getYMin(), 0));
         wallHandler.copyAndAddObject(w0);
         w0.set(Vec3D(0, 1, 0), Vec3D(0, getYMax(), 0));
         wallHandler.copyAndAddObject(w0);
         
     }
     else if (integerValue == 6)
     {
         PeriodicBoundary b0;
         b0.set(Vec3D(1, 0, 0), getXMin(), getXMax());
         boundaryHandler.copyAndAddObject(b0);
         b0.set(Vec3D(0, 1, 0), getYMin(), getYMax());
         boundaryHandler.copyAndAddObject(b0);
         b0.set(Vec3D(0, 0, 1), getZMin(), getZMax());
         boundaryHandler.copyAndAddObject(b0);
     }
     else
     {
         std::cerr << "Error in par.ini: line 1, value 1 is " << integerValue << std::endl;
         exit(-1);
     }
     
     //   2: integer (0|1) dont use | use the search pattern for linked cells
     file >> integerValue; //ignore
             
     //   3: real - gravity in z direction: positive points upwards
     file >> doubleValue;
     setGravity(Vec3D(0.0, 0.0, doubleValue));
     
     // line 2 =============================================================
     // Example: -10000 .5e-2
     //   1: time end of simulation - (negative resets start time to zero
     //                                and uses -time as end-time)   
     file >> doubleValue;
     if (doubleValue < 0)
         setTime(0);
     setTimeMax(fabs(doubleValue));
     
     //   2: time-step of simulation
     file >> doubleValue;
     setTimeStep(doubleValue);
     
     // line 3 =============================================================
     // Example: 1e-1 100
     file >> doubleValue;
     if (doubleValue >= 0)
     {
         //   1: time-step for output on time-series protocoll file  -> "ene"
         unsigned int savecount = static_cast<unsigned int>(round(doubleValue / getTimeStep()));
         setSaveCount(savecount);
         
         //   2: time-step for output on film (coordinate) file      -> "c3d"
         //      (fstat-output is coupled to c3d-output time-step)
         file >> doubleValue;
         savecount = static_cast<unsigned int>(round(doubleValue / getTimeStep()));
         dataFile.setSaveCount(savecount);
         fStatFile.setSaveCount(savecount);
     }
     else
     {
         //  or: ---------------------------------------------------------------
         //   1: negative number is multiplied to the previous log-output-time
         //   2: requires initial log-output time
         //   3: negative number is multiplied to the previous film-output-time
         //   4: requires initial film-output time
         std::cerr << "Error in par.ini: line 3, value 1 is " << doubleValue << std::endl;
         exit(-1);
     }
     
     // line 4 =============================================================
     // Example: 2000 1e5 1e3 1e2
     //   1: particle density (mass=4/3*constants::pi*density*rad^3)
     file >> doubleValue;
 
     //clear species handler
     speciesHandler.clear();
     auto S = new LinearViscoelasticSlidingFrictionSpecies;
     speciesHandler.addObject(S);
 
     setParticleDimensions(3);
     S->setDensity(doubleValue);
 
     //   2: linear spring constant
     file >> doubleValue;
     S->setStiffness(doubleValue);
 
     //   3: linear dashpot constant
     file >> doubleValue;
     S->setDissipation(doubleValue);
 
     //   4: background damping dashpot constant
     file >> doubleValue;
     if (doubleValue != 0.0)
         std::cerr << "Warning in par.ini: ignored background damping " << doubleValue << std::endl;
     
     // line 5 =============================================================
     // Example: 0 0
     //   1: growth rate:  d(radius) = xgrow * dt
     file >> doubleValue;
     if (doubleValue != 0.0)
         std::cerr << "Warning in par.ini: ignored growth rate " << doubleValue << std::endl;
     
     //   2: target volume_fraction
     file >> doubleValue;
     if (doubleValue != 0.0)
         std::cerr << "Warning in par.ini: ignored target volume_fraction " << doubleValue << std::endl;
     
     file.close();
     //std::cout << "Loaded par.ini file " << filename << std::endl;
     return true;
 }

int DPMBase::readRestartFile ( )

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.

Calls the read() and sets the restarted_ flag to true (if the file is found)

Returns: int

Definition at line 1375 of file DPMBase.cc.

References File::close(), File::getFstream(), File::getName(), File::open(), read(), Files::restartFile, and setRestarted().

Referenced by Mercury3DRestart::readNextArgument(), readNextArgument(), and readRestartFile().

 {
     if (restartFile.open(std::fstream::in))
     {
         read(restartFile.getFstream());
         restartFile.close();
         setRestarted(true);
         return (1);
     }
     else
     {
         std::cerr << restartFile.getName() << " could not be loaded" << std::endl;
         return (0);
     }
 }

int DPMBase::readRestartFile ( std::string fileName )

Also reads all the particle data corresponding to the current saved time step.

Parameters

[in] fileName

Returns: int

Definition at line 1395 of file DPMBase.cc.

References readRestartFile(), Files::restartFile, and File::setName().

 {
     restartFile.setName(fileName);
     return readRestartFile();
 }

void DPMBase::removeDuplicatePeriodicParticles ( )

protected

Removes periodic duplicate Particles.

Removes particles created by CheckAndDuplicatePeriodicParticle(int i, int nWallPeriodic)). Note that between these two functions it is not allowed to create additional functions

Definition at line 2394 of file DPMBase.cc.

References BaseInteractable::getInteractions(), BaseHandler< T >::getNumberOfObjects(), BaseHandler< T >::getObject(), BaseParticle::getPeriodicFromParticle(), interactionHandler, particleHandler, ParticleHandler::removeObject(), and InteractionHandler::removeObjectKeepingPeriodics().

Referenced by solve().

 {
     for (unsigned int i = particleHandler.getNumberOfObjects(); i >= 1 && particleHandler.getObject(i - 1)->getPeriodicFromParticle() != nullptr; i--)
     {
         while (particleHandler.getObject(i - 1)->getInteractions().size() > 0)
         {
             interactionHandler.removeObjectKeepingPeriodics(particleHandler.getObject(i - 1)->getInteractions().front()->getIndex());
         }
         particleHandler.removeObject(i - 1);
     }
 }

void DPMBase::setAppend ( bool newAppendFlag )

Allows to set the append option.

Parameters

[in] newAppendFlag

Definition at line 544 of file DPMBase.cc.

References append_.

Referenced by constructor(), Mercury3DRestart::readNextArgument(), and readNextArgument().

 {
     append_ = newAppendFlag;
 }

void DPMBase::setDimension ( unsigned int newDim )

Sets the system and particle dimension.

Parameters

[in] newDim

Definition at line 445 of file DPMBase.cc.

References setParticleDimensions(), and setSystemDimensions().

 {
     setSystemDimensions(newDim);
     setParticleDimensions(newDim);
 }

void DPMBase::setDoCGAlways ( bool newDoCGFlag )

void DPMBase::setFixedParticles ( unsigned int n )

protected

Parameters

[in] n

Definition at line 749 of file DPMBase.cc.

References BaseParticle::fixParticle(), BaseHandler< T >::getNumberOfObjects(), BaseHandler< T >::getObject(), and particleHandler.

Referenced by readNextArgument().

 {
     for (unsigned int i = 0; i < std::min(particleHandler.getNumberOfObjects(), n); i++)
         particleHandler.getObject(i)->fixParticle();
 }

void DPMBase::setGravity ( Vec3D newGravity )

Allows to modify the gravity vector.

Parameters

[in] newGravity

Definition at line 431 of file DPMBase.cc.

References gravity_.

Referenced by readNextArgument(), readParAndIniFiles(), and Chute::setChuteAngleAndMagnitudeOfGravity().

 {
     gravity_ = newGravity;
 }

void DPMBase::setParticleDimensions ( unsigned int particleDimensions )

Allows the dimension of the particle (f.e. for mass) to be changed. e.g. discs or spheres.

Parameters

[in] particleDimensions

Definition at line 474 of file DPMBase.cc.

References ParticleHandler::computeAllMasses(), particleDimensions_, and particleHandler.

Referenced by Mercury2D::constructor(), Mercury3D::constructor(), constructor(), SpeciesHandler::readOldObject(), readParAndIniFiles(), and setDimension().

 {
     if (particleDimensions >= 1 && particleDimensions <= 3)
     {
         particleDimensions_ = particleDimensions;
         particleHandler.computeAllMasses();
     }
     else
     {
         std::cerr << "Error in setParticleDimensions" << std::endl;
         exit(-1);
     }
 }

void DPMBase::setRestarted ( bool newRestartedFlag )

Allows to set the flag stating if the simulation is to be restarted or not.

Parameters

[in] newRestartedFlag

Definition at line 527 of file DPMBase.cc.

References restarted_.

Referenced by constructor(), and readRestartFile().

 {
     restarted_ = newRestartedFlag;
     //setAppend(new_);
 }

void DPMBase::setRestartVersion ( std::string newRV )

Sets restart_version.

Parameters

[in] newRV

Definition at line 510 of file DPMBase.cc.

References restartVersion_.

 {
     restartVersion_ = newRV;
 }

void DPMBase::setRotation ( bool newRotFlag )

Allows to set the flag for enabling or disabling particle rotation in the simulations.

Todo:: {these functions should also update the mixed species}

Parameters

[in] newRotFlag

Definition at line 210 of file DPMBase.cc.

References rotation_.

Referenced by SpeciesHandler::addObject(), and SpeciesHandler::removeObject().

 {
     rotation_ = newRotFlag;
 }

void DPMBase::setSystemDimensions ( unsigned int newDim )

Allows for the dimension of the simulation to be changed.

Parameters

[in] newDim

Definition at line 453 of file DPMBase.cc.

References systemDimensions_.

Referenced by Mercury2D::constructor(), Mercury3D::constructor(), constructor(), readNextArgument(), and setDimension().

 {
     if (newDim >= 1 && newDim <= 3)
         systemDimensions_ = newDim;
     else
     {
         std::cerr << "Error in setSystemDimensions" << std::endl;
         exit(-1);
     }
 }

void DPMBase::setTime ( Mdouble time )

Access function for the time.

Parameters

[in] time

Definition at line 172 of file DPMBase.cc.

References time_.

Referenced by readNextDataFile(), readParAndIniFiles(), and solve().

 {
     time_ = time;
 }

void DPMBase::setTimeMax ( Mdouble newTMax )

Allows the upper time limit to be changed.

Parameters

[in] newTMmax

Definition at line 179 of file DPMBase.cc.

References timeMax_.

Referenced by ChuteBottom::makeRoughBottom(), readNextArgument(), and readParAndIniFiles().

 {
     if (newTMax >= 0)
     {
         timeMax_ = newTMax;
     }
     else
     {
         std::cerr << "Error in setTimeMax, newTMax=" << newTMax << std::endl;
         exit(-1);
     }
 }

void DPMBase::setTimeStep ( Mdouble timeStep )

Allows the time step dt to be changed.

Parameters

[in] timeStep

Definition at line 353 of file DPMBase.cc.

References timeStep_.

Referenced by ChuteBottom::makeRoughBottom(), readNextArgument(), and readParAndIniFiles().

 {
     if (timeStep >= 0.0)
     {
         timeStep_ = timeStep;
     }
     else
     {
         std::cerr << "Error in setTimeStep" << std::endl;
         exit(-1);
     }
 }

void DPMBase::setupInitialConditions ( )

virtual

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 in ChuteWithHopper, Chute, and ChuteBottom.

Definition at line 833 of file DPMBase.cc.

Referenced by solve().

834 {

835 }

void DPMBase::setXBallsAdditionalArguments ( std::string newXBArgs )

Set the additional arguments for xballs.

Parameters

[in] newXBArgs

Definition at line 403 of file DPMBase.cc.

References xBallsAdditionalArguments_.

 {
     xBallsAdditionalArguments_ = newXBArgs.c_str();
 }

void DPMBase::setXBallsColourMode ( int newCMode )

Set the xball output mode.

Parameters

[in] newCMode

Definition at line 375 of file DPMBase.cc.

References xBallsColourMode_.

 {
     xBallsColourMode_ = newCMode;
 }

void DPMBase::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.

Parameters

[in] newScale

Definition at line 417 of file DPMBase.cc.

References xBallsScale_.

 {
     xBallsScale_ = newScale;
 }

void DPMBase::setXBallsVectorScale ( double newVScale )

Set the scale of vectors in xballs.

Parameters

[in] newVScale

Definition at line 389 of file DPMBase.cc.

References xBallsVectorScale_.

 {
     xBallsVectorScale_ = newVScale;
 }

void DPMBase::setXMax ( Mdouble newXMax )

If the length of the problem domain in x-direction is XMax - XMin, this method sets XMax.

Parameters

[in] newXMax

Definition at line 309 of file DPMBase.cc.

References getXMin(), and xMax_.

Referenced by readNextArgument(), readNextDataFile(), ChuteWithHopper::setChuteLength(), Chute::setChuteLength(), and ChuteWithHopper::setHopperShift().

 {
     if (newXMax >= getXMin())
     {
         xMax_ = newXMax;
     }
     else
     {
         std::cerr << "Error in setXMax(" << newXMax << "): xMin=" << getXMin() << std::endl;
         exit(-1);
     }
 }

void DPMBase::setXMin ( Mdouble newXMin )

If the length of the problem domain in x-direction is XMax - XMin, this method sets XMin.

Parameters

[in] newXMin

Definition at line 266 of file DPMBase.cc.

References getXMax(), and xMin_.

Referenced by readNextArgument(), readNextDataFile(), and ChuteWithHopper::setChuteLength().

 {
     if (newXMin <= getXMax())
     {
         xMin_ = newXMin;
     }
     else
     {
         std::cerr << "Warning in setXMin(" << newXMin << "): xMax=" << getXMax() << std::endl;
     }
 }

void DPMBase::setYMax ( Mdouble newYMax )

If the length of the problem domain in y-direction is YMax - YMin, this method sets YMax.

Parameters

[in] newYMax

Definition at line 324 of file DPMBase.cc.

References getYMin(), and yMax_.

Referenced by readNextArgument(), readNextDataFile(), and Chute::setChuteWidth().

 {
     if (newYMax >= getYMin())
     {
         yMax_ = newYMax;
     }
     else
     {
         std::cerr << "Warning in setYMax(" << newYMax << "): yMin=" << getYMin() << std::endl;
     }
 }

void DPMBase::setYMin ( Mdouble newYMin )

If the length of the problem domain in y-direction is YMax - YMin, this method sets YMin.

Parameters

[in] newYMin

Definition at line 280 of file DPMBase.cc.

References getYMax(), and yMin_.

Referenced by readNextArgument(), and readNextDataFile().

 {
     if (newYMin <= getYMax())
     {
         yMin_ = newYMin;
     }
     else
     {
         std::cerr << "Error in setYMin(" << newYMin << "): yMax=" << getYMax() << std::endl;
         exit(-1);
     }
 }

void DPMBase::setZMax ( Mdouble newZMax )

If the length of the problem domain in z-direction is XMax - XMin, this method sets ZMax.

Parameters

[in] newZMax

Definition at line 338 of file DPMBase.cc.

References getZMin(), and zMax_.

Referenced by ChuteWithHopper::addHopper(), Chute::readNextArgument(), readNextArgument(), readNextDataFile(), and Chute::setInflowHeight().

 {
     if (newZMax >= getZMin())
     {
         zMax_ = newZMax;
     }
     else
     {
         std::cerr << "Error in setZMax(" << newZMax << "): zMin=" << getZMin() << std::endl;
         exit(-1);
     }
 }

void DPMBase::setZMin ( Mdouble newZMin )

If the length of the problem domain in z-direction is ZMax - ZMin, this method sets ZMin.

Parameters

[in] newZMin

Definition at line 295 of file DPMBase.cc.

References getZMax(), and zMin_.

Referenced by readNextArgument(), and readNextDataFile().

 {
     if (newZMin <= getZMax())
     {
         zMin_ = newZMin;
     }
     else
     {
         std::cerr << "Warning in setZMin(" << newZMin << "): zMax=" << getZMax() << std::endl;
     }
 }

void DPMBase::solve ( )

The work horse of the code.

Initialises the time, sets up the initial conditions for the simulation by calling the setupInitialConditions() and resets the counter using setNExtSavedTimeStep().
- HGrid operations which is the contact detection algorithm.
- Checks if the basic essentials are set for carrying out the simulations using checkSettings()
- And many more vital operations. See below ;)
  Todo:
  Is it neccesarry to reset initial conditions here and in setTimeStepByParticle (i.e. should it be in constructor) Thomas: I agree, setTimeStepByParticle should be rewritten to work without calling setupInitialConditions

Initialise the time and sets up the initial conditions for the simulation

Todo:: Is it neccesarry to reset initial conditions here and in setTimeStepByParticle (i.e. should it be in constructor)? Thomas: I agree, setTimeStepByParticle should be rewritten to work without calling setupInitialConditions

Bug:: {In chute particles are added in actions_before_time_set(), however they are not written to the xballs data yet, but can have a collison and be written to the fstat data}

Definition at line 1895 of file DPMBase.cc.

References actionsAfterSolve(), actionsAfterTimeStep(), actionsBeforeTimeLoop(), actionsBeforeTimeStep(), actionsOnRestart(), BaseHandler< T >::begin(), boundaryHandler, checkAndDuplicatePeriodicParticles(), checkInteractionWithBoundaries(), checkSettings(), Files::closeFiles(), computeAllForces(), ParticleHandler::computeAllMasses(), continueSolve(), BaseHandler< T >::end(), InteractionHandler::eraseOldInteractions(), finishStatistics(), getAppend(), Files::getName(), getRestarted(), FilesAndRunNumber::getRunNumber(), getTime(), getTimeMax(), getTimeStep(), hGridActionsAfterIntegration(), hGridActionsBeforeIntegration(), hGridActionsBeforeTimeLoop(), hGridActionsBeforeTimeStep(), initialiseStatistics(), integrateAfterForceComputation(), integrateBeforeForceComputation(), interactionHandler, ntimeSteps_, particleHandler, removeDuplicatePeriodicParticles(), Files::resetFileCounter(), Files::restartFile, Files::setName(), Files::setNextSavedTimeStep(), File::setOpenMode(), Files::setOpenMode(), setTime(), setupInitialConditions(), time_, timeStep_, and writeOutputFiles().

Referenced by ChuteBottom::makeRoughBottom(), and solve().

 {
 #ifdef DEBUG_OUTPUT
     std::cerr << "Entered solve" << std::endl;
 #endif
 #ifdef CONTACT_LIST_HGRID
     std::cout << "Using CONTACT_LIST_HGRID"<<std::endl;
 #endif
     
     if (getRestarted()==false)
     {
         ntimeSteps_ = 0;
         resetFileCounter();
         setTime(0.0);
         //this is to ensure that the interaction time stamps agree with the resetting of the time value
         for (auto& i : interactionHandler)
             i->setTimeStamp(0);
         setupInitialConditions();
         setNextSavedTimeStep(0); //reset the counter
 #ifdef DEBUG_OUTPUT
         std::cerr << "Have created the particles initial conditions " << std::endl;
 #endif
     }
     else
     {
         actionsOnRestart();
     }
 
     checkSettings();
 
     if (getRunNumber()>0) 
     {
         std::stringstream name;
         name << getName() << "." << getRunNumber();
         setName(name.str());
     }
     
     //append_ determines if files have to be appended or not
     if (getAppend())
     {
         setOpenMode(std::fstream::out | std::fstream::app);
         restartFile.setOpenMode(std::fstream::out); //Restart files should always be overwritten.
     }
     else
         setOpenMode(std::fstream::out);
 
     initialiseStatistics();
 
     // Setup the mass of each particle.
     particleHandler.computeAllMasses();
 
     // Other initialisations
     //max_radius = getLargestParticle()->getRadius();
     actionsBeforeTimeLoop();
     hGridActionsBeforeTimeLoop();
 
     // do a first force computation
     checkAndDuplicatePeriodicParticles();
     hGridActionsBeforeTimeStep();
     computeAllForces();
     removeDuplicatePeriodicParticles();
 
 
 #ifdef DEBUG_OUTPUT
     std::cerr << "Have computed the initial values for the forces " << std::endl;
 #endif
 
     // This is the main loop over advancing time
     while (getTime() < getTimeMax() && continueSolve())
     {
         writeOutputFiles(); //everything is written at the beginning of the timestep!
         
         // Loop over all particles doing the time integration step
         hGridActionsBeforeIntegration();
         integrateBeforeForceComputation();
         checkInteractionWithBoundaries(); // INSERTION boundaries handled
         hGridActionsAfterIntegration();
 
         // Compute forces
         
         // INSERTION/DELETION boundary flag change
         for (std::vector<BaseBoundary*>::iterator it = boundaryHandler.begin(); it != boundaryHandler.end(); ++it)
         {
             (*it)->checkBoundaryBeforeTimeStep(this);
         }
 
         actionsBeforeTimeStep();
 
         checkAndDuplicatePeriodicParticles();
 
         hGridActionsBeforeTimeStep();
 
         computeAllForces();
 
         removeDuplicatePeriodicParticles();
 
         actionsAfterTimeStep();
 
         // Loop over all particles doing the time integration step
         hGridActionsBeforeIntegration();
         integrateAfterForceComputation();
 
         checkInteractionWithBoundaries(); // DELETION boundaries handled
         hGridActionsAfterIntegration();
 
         //erase interactions that have not been used during the last timestep
         interactionHandler.eraseOldInteractions(getTime() - getTimeStep() * 0.5);
 
         time_ += timeStep_;
         ntimeSteps_ ++;
     }
     //force writing of the last time step
     setNextSavedTimeStep(ntimeSteps_);
     writeOutputFiles();
 
     //end loop over interaction count
     actionsAfterSolve();
     
     std::cout << std::endl;
     //To make sure getTime gets the correct time for outputting statistics
     finishStatistics();
     
     closeFiles();
 }

void DPMBase::solve	(	int	argc,
		char *	argv[]
	)

The solve function is the work horse of the code with the user input.

Parameters

[in]	argc
[in]	argv

Definition at line 150 of file DPMBase.cc.

References readArguments(), and solve().

 {
     readArguments(argc, argv);
     solve();
 }

void DPMBase::write	(	std::ostream &	os,
		bool	writeAllParticles = `true`
	)		const

virtual

Loads all MD data and plots statistics for all timesteps in the .data file.

Writes all particle data into a restart file

Parameters

[in]	os
[in]	writeAllParticles

Todo:: TW: random number seed is not stored

Todo:: TW: xBalls arguments are not stored

Reimplemented in ChuteWithHopper, Chute, and MercuryBase.

Definition at line 1642 of file DPMBase.cc.

References BaseHandler< T >::begin(), boundaryHandler, BaseHandler< T >::end(), getGravity(), BaseHandler< T >::getNumberOfObjects(), BaseHandler< T >::getObject(), getParticleDimensions(), getSystemDimensions(), getTime(), getTimeMax(), getTimeStep(), getXMax(), getXMin(), getYMax(), getYMin(), getZMax(), getZMin(), interactionHandler, ntimeSteps_, particleHandler, speciesHandler, wallHandler, SpeciesHandler::write(), InteractionHandler::write(), FilesAndRunNumber::write(), and ParticleHandler::write().

Referenced by operator<<(), MercuryBase::write(), and writeRestartFile().

 {
     os << "restart_version " << "1.0";
     FilesAndRunNumber::write(os);
     os << "xMin " << getXMin()
         << " xMax " << getXMax()
         << " yMin " << getYMin()
         << " yMax " << getYMax()
         << " zMin " << getZMin()
         << " zMax " << getZMax() << std::endl
         << "timeStep " << getTimeStep()
         << " time " << getTime()
         << " ntimeSteps " << ntimeSteps_
         << " timeMax " << getTimeMax() << std::endl
         << "systemDimensions " << getSystemDimensions()
         << " particleDimensions " << getParticleDimensions()
         << " gravity " << getGravity() << std::endl;
     speciesHandler.write(os);
     os << "Walls " << wallHandler.getNumberOfObjects() << std::endl;
     for (std::vector<BaseWall*>::const_iterator it = wallHandler.begin(); it != wallHandler.end(); ++it)
         os << (**it) << std::endl;
     os << "Boundaries " << boundaryHandler.getNumberOfObjects() << std::endl;
     for (std::vector<BaseBoundary*>::const_iterator it = boundaryHandler.begin(); it != boundaryHandler.end(); ++it)
         os << (**it) << std::endl;
     if (writeAllParticles || particleHandler.getNumberOfObjects() < 4)
     {
         particleHandler.write(os);
     }
     else
     {
         os << "Particles " << particleHandler.getNumberOfObjects() << std::endl;
         for (unsigned int i = 0; i < 2; i++)
             os << *particleHandler.getObject(i) << std::endl;
         os << "..." << std::endl;
     }
     if (writeAllParticles || interactionHandler.getNumberOfObjects() < 4)
     {
         interactionHandler.write(os);
     }
     else
     {
         os << "Interactions " << interactionHandler.getNumberOfObjects() << std::endl;
         for (unsigned int i = 0; i < 2; i++)
             os << *interactionHandler.getObject(i) << std::endl;
         os << "..." << std::endl;
     }
 }

void DPMBase::writeEneHeader ( std::ostream & os ) const

protectedvirtual

Writes a header with a certain format for ENE file.

Parameters

[in] os

todo{Why is there a +6 here? TW: to get the numbers and title aligned}

Definition at line 840 of file DPMBase.cc.

References getAppend().

Referenced by writeOutputFiles().

 {
     //only write if we don't restart
     if (getAppend())
         return;
     
     long width = os.precision() + 6;
     os << std::setw(width) << "t" << " " << std::setw(width)
             << "ene_gra" << " " << std::setw(width)
             << "ene_kin" << " " << std::setw(width)
             << "ene_rot" << " " << std::setw(width)
             << "ene_ela" << " " << std::setw(width)
             << "X_COM" << " " << std::setw(width)
             << "Y_COM" << " " << std::setw(width)
             << "Z_COM" << std::endl;
 }

void DPMBase::writeEneTimestep ( std::ostream & os ) const

protectedvirtual

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.

Parameters

[in] os

todo{Why is there a +6 here? TW: to ensure the numbers fit into a constant width column}

Definition at line 912 of file DPMBase.cc.

References BaseHandler< T >::begin(), Vec3D::dot(), BaseHandler< T >::end(), getElasticEnergy(), getGravity(), getTime(), and particleHandler.

Referenced by writeOutputFiles().

 {
     Mdouble ene_kin = 0, ene_elastic = 0, ene_rot = 0, ene_gra = 0, mass_sum = 0, x_masslength = 0, y_masslength = 0, z_masslength = 0;
 
     for (std::vector<BaseParticle*>::const_iterator it = particleHandler.begin(); it != particleHandler.end(); ++it)
         if (!(*it)->isFixed())
         {
             ene_kin += .5 * (*it)->getMass() * (*it)->getVelocity().getLengthSquared();
             ene_rot += .5 * (*it)->getInertia() * (*it)->getAngularVelocity().getLengthSquared();
             ene_gra -= (*it)->getMass() * Vec3D::dot(getGravity(), (*it)->getPosition());
             mass_sum += (*it)->getMass();
             x_masslength += (*it)->getMass() * (*it)->getPosition().X;
             y_masslength += (*it)->getMass() * (*it)->getPosition().Y;
             z_masslength += (*it)->getMass() * (*it)->getPosition().Z;
         } //end for loop over Particles
 
     ene_elastic = getElasticEnergy();
 
     long width = os.precision() + 6;
     os << std::setw(width) << getTime()
             << " " << std::setw(width) << ene_gra
             << " " << std::setw(width) << ene_kin
             << " " << std::setw(width) << ene_rot
             << " " << std::setw(width) << ene_elastic
             << " " << std::setw(width) << (mass_sum != 0.0 ? x_masslength / mass_sum : std::numeric_limits<double>::quiet_NaN())
             << " " << std::setw(width) << (mass_sum != 0.0 ? y_masslength / mass_sum : std::numeric_limits<double>::quiet_NaN())
             << " " << std::setw(width) << (mass_sum != 0.0 ? z_masslength / mass_sum : std::numeric_limits<double>::quiet_NaN()) << std::endl;
 
     //sliding = sticking = 0;
 }

void DPMBase::writeFstatHeader ( std::ostream & os ) const

protectedvirtual

Writes a header with a certain format for FStat file.

Parameters

[in] os

Definition at line 861 of file DPMBase.cc.

References BaseHandler< T >::begin(), BaseHandler< T >::end(), ParticleHandler::getLargestParticle(), BaseParticle::getRadius(), ParticleHandler::getSmallestParticle(), getTime(), getXMax(), getXMin(), getYMax(), getYMin(), getZMax(), getZMin(), interactionHandler, and particleHandler.

Referenced by writeOutputFiles().

         {
     // line #1: time, volume fraction
     // line #2: wall box: wx0, wy0, wz0, wx1, wy1, wz1
     // line #3: radii-min-max & moments: rad_min, rad_max, r1, r2, r3, r4
     os << "#"
             << " " << getTime()
             << " " << 0
             << std::endl;
     os << "#"
             << " " << getXMin()
             << " " << getYMin()
             << " " << getZMin()
             << " " << getXMax()
             << " " << getYMax()
             << " " << getZMax()
             << std::endl;
     os << "#"
             << " ";
     if (particleHandler.getSmallestParticle())
     {
         os << particleHandler.getSmallestParticle()->getRadius();
     }
     else
     {
         os << std::numeric_limits<double>::quiet_NaN();
     }
     os << " ";
     if (particleHandler.getLargestParticle())
     {
         os << particleHandler.getLargestParticle()->getRadius();
     }
     else
     {
         os << std::numeric_limits<double>::quiet_NaN();
     }
     os << " " << 0
             << " " << 0
             << " " << 0
             << " " << 0
             << std::endl;
     //B: write data
     for (std::vector<BaseInteraction*>::const_iterator it = interactionHandler.begin(); it != interactionHandler.end(); ++it)
     {
         (*it)->writeToFStat(os);
     }
 }

void DPMBase::writeOutputFiles ( )

virtual

Writes the simulation data onto all the files i.e. .data, .ene, .fstat ...

Reimplemented in StatisticsVector< T >, and Mercury3DRestart.

Definition at line 1848 of file DPMBase.cc.

References File::close(), Files::dataFile, Files::eneFile, Files::fStatFile, File::getCounter(), File::getFileType(), File::getFstream(), getRestarted(), MULTIPLE_FILES, MULTIPLE_FILES_PADDED, NO_FILE, ntimeSteps_, outputXBallsData(), printTime(), Files::restartFile, File::saveCurrentTimestep(), writeEneHeader(), writeEneTimestep(), writeFstatHeader(), writeRestartFile(), and writeXBallsScript().

Referenced by solve(), and Mercury3DRestart::writeOutputFiles().

 {
     if (fStatFile.saveCurrentTimestep(ntimeSteps_))
         writeFstatHeader(fStatFile.getFstream());
 
     if (eneFile.saveCurrentTimestep(ntimeSteps_))
     {
         if (eneFile.getCounter()==1 || eneFile.getFileType()==FileType::MULTIPLE_FILES || eneFile.getFileType()==FileType::MULTIPLE_FILES_PADDED)
             writeEneHeader(eneFile.getFstream());
         writeEneTimestep(eneFile.getFstream());
     }
 
     if (dataFile.saveCurrentTimestep(ntimeSteps_))
     {
         printTime();
         if ((getRestarted() ||dataFile.getCounter()==1) && dataFile.getFileType()!= FileType::NO_FILE)
             writeXBallsScript();
         outputXBallsData(dataFile.getFstream());
     }
 
 //    if (statFile.saveCurrentTimestep(ntimeSteps_))
 //    {
 //        outputStatistics();
 //        gatherContactStatistics();
 //        processStatistics(true);
 //    }
 
     //write restart file last, otherwise the output cunters are wrong
     if (restartFile.saveCurrentTimestep(ntimeSteps_))
     {
         writeRestartFile();
         restartFile.close(); //overwrite old restart file if FileType::ONE_FILE
     }
 }

void DPMBase::writeRestartFile ( )

virtual

Stores all the particle data for current save time step. Calls the write function.

/// See also MD::readRestartFile

Definition at line 1365 of file DPMBase.cc.

References File::getFstream(), Files::restartFile, and write().

Referenced by writeOutputFiles().

 {
     write(restartFile.getFstream());
 }

virtual void DPMBase::writeXBallsScript ( ) const

virtual

This writes a script which can be used to load the xballs problem to display the data just generated.

Referenced by writeOutputFiles().

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	os,
		const DPMBase &	md
	)

friend

Operator overloading of DPMBase class.

Member Data Documentation

bool DPMBase::append_

private

A flag to determine if the file has to be appended or not. See DPMBase::Solve() for example.

Definition at line 826 of file DPMBase.h.

Referenced by DPMBase(), getAppend(), and setAppend().

BoundaryHandler DPMBase::boundaryHandler

An object of the class BoundaryHandler which concerns insertion and deletion of particles into or from regions.

Definition at line 888 of file DPMBase.h.

Referenced by checkAndDuplicatePeriodicParticles(), checkInteractionWithBoundaries(), constructor(), DPMBase(), read(), readOld(), readParAndIniFiles(), ChuteBottom::setupInitialConditions(), Chute::setupInitialConditions(), ChuteWithHopper::setupInitialConditions(), Chute::setupSideWalls(), solve(), and write().

Mdouble DPMBase::elasticEnergy_

private

used in force calculations

Stores the potential energy in the elastic springs (global, because it has to be calculated in the force loop

Definition at line 808 of file DPMBase.h.

Vec3D DPMBase::gravity_

private

Gravity vector.

Definition at line 745 of file DPMBase.h.

Referenced by constructor(), DPMBase(), getGravity(), read(), readOld(), and setGravity().

InteractionHandler DPMBase::interactionHandler

An object of the class InteractionHandler.

Definition at line 893 of file DPMBase.h.

Referenced by computeForcesDueToWalls(), computeInternalForces(), constructor(), DPMBase(), gatherContactStatistics(), getElasticEnergy(), outputInteractionDetails(), read(), removeDuplicatePeriodicParticles(), solve(), write(), and writeFstatHeader().

unsigned int DPMBase::ntimeSteps_

private

Stores the number of time steps.

Definition at line 791 of file DPMBase.h.

Referenced by constructor(), DPMBase(), getNtimeSteps(), read(), solve(), write(), and writeOutputFiles().

unsigned int DPMBase::particleDimensions_

private

determines if 2D or 3D particle volume is used for mass calculations

Definition at line 740 of file DPMBase.h.

Referenced by DPMBase(), getParticleDimensions(), read(), and setParticleDimensions().

ParticleHandler DPMBase::particleHandler

An object of the class ParticleHandler, contains the pointers to all the particles created.

Definition at line 878 of file DPMBase.h.

Referenced by ChuteWithHopper::addHopper(), SpeciesHandler::addObject(), broadPhase(), checkAndDuplicatePeriodicParticles(), InsertionBoundary::checkBoundaryBeforeTimeStep(), checkInteractionWithBoundaries(), checkParticleForInteraction(), Chute::cleanChute(), computeAllForces(), constructor(), Chute::createBottom(), DPMBase(), MercuryBase::getHGridTargetMaxInteractionRadius(), MercuryBase::getHGridTargetMinInteractionRadius(), MercuryBase::getHGridTargetNumberOfBuckets(), getKineticEnergy(), MercuryBase::hGridActionsBeforeTimeStep(), MercuryBase::hGridNeedsRebuilding(), MercuryBase::hGridRebuild(), HGridOptimiser::initialise(), integrateAfterForceComputation(), integrateBeforeForceComputation(), ChuteBottom::makeRoughBottom(), outputXBallsData(), Chute::printTime(), read(), readNextDataFile(), InteractionHandler::readObject(), readOld(), removeDuplicatePeriodicParticles(), ParticleSpecies::setDensity(), setFixedParticles(), setParticleDimensions(), BaseParticle::setSpecies(), ChuteBottom::setupInitialConditions(), solve(), write(), writeEneTimestep(), and writeFstatHeader().

RNG DPMBase::random

This is a random generator, often used for setting up the initial conditions etc...

Definition at line 873 of file DPMBase.h.

Referenced by InsertionBoundary::checkBoundaryBeforeTimeStep(), constructor(), Chute::createBottom(), DPMBase(), readNextArgument(), and ChuteBottom::setupInitialConditions().

bool DPMBase::restarted_

private

A bool to check if the simulation was restarted or not.

Definition at line 820 of file DPMBase.h.

Referenced by DPMBase(), getRestarted(), and setRestarted().

std::string DPMBase::restartVersion_

private

Previous versions of MercuryDPM had a different restart file format, the below member variable allows one to specify the version in order to choose between the available version support.

Definition at line 815 of file DPMBase.h.

Referenced by DPMBase(), getRestartVersion(), read(), and setRestartVersion().

bool DPMBase::rotation_

private

A flag to turn on/off particle rotation.

Definition at line 831 of file DPMBase.h.

Referenced by DPMBase(), getRotation(), and setRotation().

SpeciesHandler DPMBase::speciesHandler

A handler to that stores the species type i.e. elastic, linear visco-elastic... et cetera.

Definition at line 868 of file DPMBase.h.

Referenced by MaserBoundary::addParticleToMaser(), checkSettings(), constructor(), DPMBase(), InteractionHandler::getInteraction(), ChuteBottom::makeRoughBottom(), read(), readOld(), readParAndIniFiles(), BaseParticle::setIndSpecies(), Chute::setupInitialConditions(), ChuteWithHopper::setupInitialConditions(), and write().

unsigned int DPMBase::systemDimensions_

private

The dimensions of the simulation i.e. 2D or 3D.

Definition at line 735 of file DPMBase.h.

Referenced by DPMBase(), getSystemDimensions(), read(), readOld(), and setSystemDimensions().

Mdouble DPMBase::time_

private

Stores the current simulation time.

Definition at line 786 of file DPMBase.h.

Referenced by constructor(), DPMBase(), getTime(), read(), readNextDataFile(), readOld(), setTime(), and solve().

Mdouble DPMBase::timeMax_

private

Stores the duration of the simulation.

Definition at line 801 of file DPMBase.h.

Referenced by constructor(), DPMBase(), getTimeMax(), read(), readOld(), and setTimeMax().

Mdouble DPMBase::timeStep_

private

Stores the simulation time step.

Definition at line 796 of file DPMBase.h.

Referenced by constructor(), DPMBase(), getTimeStep(), read(), readOld(), setTimeStep(), and solve().

WallHandler DPMBase::wallHandler

An object of the class WallHandler. Contains pointers to all the walls created.

Definition at line 883 of file DPMBase.h.

Referenced by ChuteWithHopper::addHopper(), MercuryBase::checkParticleForInteraction(), checkParticleForInteraction(), computeAllForces(), computeForcesDueToWalls(), constructor(), Chute::createBottom(), DPMBase(), integrateAfterForceComputation(), integrateBeforeForceComputation(), read(), InteractionHandler::readObject(), readOld(), readParAndIniFiles(), BaseWall::setSpecies(), ChuteBottom::setupInitialConditions(), Chute::setupSideWalls(), and write().

std::string DPMBase::xBallsAdditionalArguments_

private

A string of additional arguments for xballs can be specified (see XBalls/xballs.txt). e.g. "-solidf -v0".

Definition at line 854 of file DPMBase.h.

Referenced by constructor(), DPMBase(), getXBallsAdditionalArguments(), and setXBallsAdditionalArguments().

int DPMBase::xBallsColourMode_

private

XBalls is a package to view the particle data. As an alternative MercuryDPM also supports Paraview. The below variable is used to set the argument cmode in xballs script (see XBalls/xballs.txt)

Definition at line 839 of file DPMBase.h.

Referenced by constructor(), DPMBase(), getXBallsColourMode(), and setXBallsColourMode().