Inheritance diagram for AreaVTK:

Public Member Functions
	AreaVTK (std::string const &wallSource)

void	setupInitialConditions () override
	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...

double	getTotalsurfaceAreaFromFile (std::string const &fileName)

Public Member Functions inherited from Mercury3D
	Mercury3D ()
	This is the default constructor. All it does is set sensible defaults. More...

	Mercury3D (const DPMBase &other)
	Copy-constructor for creates an Mercury3D problem from an existing MD problem. More...

	Mercury3D (const Mercury3D &other)
	Copy-constructor. More...

void	constructor ()
	Function that sets the SystemDimension and ParticleDimension to 3. More...

std::vector< BaseParticle * >	hGridFindParticleContacts (const BaseParticle *obj) override
	Returns all particles that have a contact with a given particle. More...

Public Member Functions inherited from MercuryBase
	MercuryBase ()
	This is the default constructor. It sets sensible defaults. More...

	~MercuryBase () override
	This is the default destructor. More...

	MercuryBase (const MercuryBase &mercuryBase)
	Copy-constructor. More...

void	constructor ()
	This is the actual constructor, it is called do both constructors above. More...

void	hGridActionsBeforeTimeLoop () override
	This sets up the broad phase information, has to be done at this stage because it requires the particle size. More...

void	hGridActionsBeforeTimeStep () override
	Performs all necessary actions before a time-step, like updating the particles and resetting all the bucket information, etc. More...

void	read (std::istream &is, ReadOptions opt=ReadOptions::ReadAll) override
	Reads the MercuryBase from an input stream, for example a restart file. More...

void	write (std::ostream &os, bool writeAllParticles=true) const override
	Writes all data into a restart file. More...

Mdouble	getHGridCurrentMaxRelativeDisplacement () const
	Returns hGridCurrentMaxRelativeDisplacement_. More...

Mdouble	getHGridTotalCurrentMaxRelativeDisplacement () const
	Returns hGridTotalCurrentMaxRelativeDisplacement_. More...

void	setHGridUpdateEachTimeStep (bool updateEachTimeStep)
	Sets whether or not the HGrid must be updated every time step. More...

bool	getHGridUpdateEachTimeStep () const final
	Gets whether or not the HGrid is updated every time step. More...

void	setHGridMaxLevels (unsigned int HGridMaxLevels)
	Sets the maximum number of levels of the HGrid in this MercuryBase. More...

unsigned int	getHGridMaxLevels () const
	Gets the maximum number of levels of the HGrid in this MercuryBase. More...

HGridMethod	getHGridMethod () const
	Gets whether the HGrid in this MercuryBase is BOTTOMUP or TOPDOWN. More...

void	setHGridMethod (HGridMethod hGridMethod)
	Sets the HGridMethod to either BOTTOMUP or TOPDOWN. More...

HGridDistribution	getHGridDistribution () const
	Gets how the sizes of the cells of different levels are distributed. More...

void	setHGridDistribution (HGridDistribution hGridDistribution)
	Sets how the sizes of the cells of different levels are distributed. More...

Mdouble	getHGridCellOverSizeRatio () const
	Gets the ratio of the smallest cell over the smallest particle. More...

void	setHGridCellOverSizeRatio (Mdouble cellOverSizeRatio)
	Sets the ratio of the smallest cell over the smallest particle. More...

bool	hGridNeedsRebuilding ()
	Gets if the HGrid needs rebuilding before anything else happens. More...

virtual unsigned int	getHGridTargetNumberOfBuckets () const
	Gets the desired number of buckets, which is the maximum of the number of particles and 10. More...

virtual Mdouble	getHGridTargetMinInteractionRadius () const
	Gets the desired size of the smallest cells of the HGrid. More...

virtual Mdouble	getHGridTargetMaxInteractionRadius () const
	Gets the desired size of the largest cells of the HGrid. More...

bool	checkParticleForInteraction (const BaseParticle &P) final
	Checks if given BaseParticle has an interaction with a BaseWall or other BaseParticle. More...

bool	checkParticleForInteractionLocal (const BaseParticle &P) final
	Checks if the given BaseParticle has an interaction with a BaseWall or other BaseParticles in a local domain. More...

virtual Mdouble	userHGridCellSize (unsigned int level)
	Virtual function that enables inheriting classes to implement a function to let the user set the cell size of the HGrid. More...

void	hGridInfo (std::ostream &os=std::cout) const
	Writes the info of the HGrid to the screen in a nice format. More...

Public Member Functions inherited from DPMBase
void	constructor ()
	A function which initialises the member variables to default values, so that the problem can be solved off the shelf; sets up a basic two dimensional problem which can be solved off the shelf. It is called in the constructor DPMBase(). More...

	DPMBase ()
	Constructor that calls the "void constructor()". More...

	DPMBase (const DPMBase &other)
	Copy constructor type-2. More...

virtual	~DPMBase ()
	virtual destructor More...

void	autoNumber ()
	The autoNumber() function calls three functions: setRunNumber(), readRunNumberFromFile() and incrementRunNumberInFile(). More...

std::vector< int >	get1DParametersFromRunNumber (int size_x) const
	This turns a counter into 1 index, which is a useful feature for performing 1D parameter study. The index run from 1:size_x, while the study number starts at 0 (initially the counter=1 in COUNTER_DONOTDEL) More...

std::vector< int >	get2DParametersFromRunNumber (int size_x, int size_y) const
	This turns a counter into 2 indices which is a very useful feature for performing a 2D study. 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...

std::vector< int >	get3DParametersFromRunNumber (int size_x, int size_y, int size_z) const
	This turns a counter into 3 indices, which is a useful feature for performing a 3D parameter study. The indices run from 1:size_x, 1:size_y and 1:size_z, 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...

virtual void	decompose ()
	Sends particles from processorId to the root processor. More...

void	solve ()
	The work horse of the code. More...

void	initialiseSolve ()
	Beginning of the solve routine, before time stepping. More...

void	finaliseSolve ()
	End of the solve routine, after time stepping. More...

virtual void	computeOneTimeStep ()
	Performs everything needed for one time step, used in the time-loop of solve(). More...

void	checkSettings ()
	Checks if the essentials are set properly to go ahead with solving the problem. More...

void	forceWriteOutputFiles ()
	Writes output files immediately, even if the current time step was not meant to be written. Also resets the last saved time step. More...

virtual void	writeOutputFiles ()
	Writes simulation data to all the main Mercury files: .data, .ene, .fstat, .xballs and .restart (see the Mercury website for more details regarding these files). More...

void	solve (int argc, char *argv[])
	The work horse of the code. Can handle flags from the command line. 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 Mdouble	getInfo (const BaseParticle &P) const
	A virtual function that returns some user-specified information about a particle. More...

ParticleVtkWriter *	getVtkWriter () const

virtual void	writeRestartFile ()
	Stores all the particle data for current save time step to a "restart" file, which is a file simply intended to store all the information necessary to "restart" a simulation from a given time step (see also MercuryDPM.org for more information on restart files). More...

void	writeDataFile ()

void	writeEneFile ()

void	writeFStatFile ()

void	fillDomainWithParticles (unsigned N=50)

bool	readRestartFile (ReadOptions opt=ReadOptions::ReadAll)
	Reads all the particle data corresponding to a given, existing . restart file (for more details regarding restart files, refer to the training materials on the MercuryDPM website).Returns true if it is successful, false otherwise. More...

int	readRestartFile (std::string fileName, ReadOptions opt=ReadOptions::ReadAll)
	The same as readRestartFile(bool), but also reads all the particle data corresponding to the current saved time step. More...

virtual BaseWall *	readUserDefinedWall (const std::string &type) const
	Allows you to read in a wall defined in a Driver directory; see USER/Luca/ScrewFiller. More...

virtual void	readOld (std::istream &is)
	Reads all data from a restart file, e.g. domain data and particle data; old version. More...

bool	readDataFile (std::string fileName="", unsigned int format=0)
	This allows particle data to be reloaded from data files. More...

bool	readParAndIniFiles (std::string fileName)
	Allows the user to read par.ini files (useful to read files produced by the MDCLR simulation code - external to MercuryDPM) 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 Visualising data in xballs. More...

void	readNextFStatFile ()
	Reads the next fstat file. More...

bool	findNextExistingDataFile (Mdouble tMin, bool verbose=true)
	Finds and opens the next data file, if such a file exists. More...

bool	readArguments (int argc, char *argv[])
	Can interpret main function input arguments that are passed by the driver codes. More...

bool	checkParticleForInteractionLocalPeriodic (const BaseParticle &P)

void	readSpeciesFromDataFile (bool read=true)

void	importParticlesAs (ParticleHandler &particleHandler, InteractionHandler &interactionHandler, const ParticleSpecies *species)
	Copies particles, interactions assigning species from a local simulation to a global one. Useful for the creation of a cluster. More...

MERCURYDPM_DEPRECATED File &	getDataFile ()
	The non const version. Allows one to edit the File::dataFile. More...

MERCURYDPM_DEPRECATED File &	getEneFile ()
	The non const version. Allows to edit the File::eneFile. More...

MERCURYDPM_DEPRECATED File &	getFStatFile ()
	The non const version. Allows to edit the File::fStatFile. More...

MERCURYDPM_DEPRECATED File &	getRestartFile ()
	The non const version. Allows to edit the File::restartFile. More...

MERCURYDPM_DEPRECATED File &	getStatFile ()
	The non const version. Allows to edit the File::statFile. More...

File &	getInteractionFile ()
	Return a reference to the file InteractionsFile. More...

MERCURYDPM_DEPRECATED const File &	getDataFile () const
	The const version. Does not allow for any editing of the File::dataFile. More...

MERCURYDPM_DEPRECATED const File &	getEneFile () const
	The const version. Does not allow for any editing of the File::eneFile. More...

MERCURYDPM_DEPRECATED const File &	getFStatFile () const
	The const version. Does not allow for any editing of the File::fStatFile. More...

MERCURYDPM_DEPRECATED const File &	getRestartFile () const
	The const version. Does not allow for any editing of the File::restartFile. More...

MERCURYDPM_DEPRECATED const File &	getStatFile () const
	The const version. Does not allow for any editing of the File::statFile. More...

const File &	getInteractionFile () const

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	closeFiles ()
	Closes all files (ene, data, fstat, restart, stat) that were opened to read or write. More...

void	setLastSavedTimeStep (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...

Mdouble	getTime () const
	Returns the current simulation time. More...

Mdouble	getNextTime () const
	Returns the current simulation time. More...

unsigned int	getNumberOfTimeSteps () const
	Returns the current counter of time-steps, i.e. the number of time-steps that the simulation has undergone so far. More...

void	setTime (Mdouble time)
	Sets a new value for the current simulation time. More...

void	setTimeMax (Mdouble newTMax)
	Sets a new value for the maximum simulation duration. More...

Mdouble	getTimeMax () const
	Returns the maximum simulation duration. More...

void	setLogarithmicSaveCount (Mdouble logarithmicSaveCountBase)
	Sets File::logarithmicSaveCount_ for all files (ene, data, fstat, restart, stat) More...

void	setNToWrite (int nToWrite)
	set the number of elements to write to the screen More...

int	getNToWrite () const
	get the number of elements to write to the More...

void	setRotation (bool rotation)
	Sets whether particle rotation is enabled or disabled. More...

bool	getRotation () const
	Indicates whether particle rotation is enabled or disabled. More...

MERCURYDPM_DEPRECATED void	setWallsWriteVTK (FileType writeWallsVTK)
	Sets whether walls are written into a VTK file. More...

MERCURYDPM_DEPRECATED void	setWallsWriteVTK (bool)
	Sets whether walls are written into a VTK file. More...

MERCURYDPM_DEPRECATED void	setInteractionsWriteVTK (bool)
	Sets whether interactions are written into a VTK file. More...

void	setParticlesWriteVTK (bool writeParticlesVTK)
	Sets whether particles are written in a VTK file. More...

void	setSuperquadricParticlesWriteVTK (bool writeSuperquadricParticlesVTK)

MERCURYDPM_DEPRECATED FileType	getWallsWriteVTK () const
	Returns whether walls are written in a VTK file. More...

bool	getParticlesWriteVTK () const
	Returns whether particles are written in a VTK file. More...

bool	getSuperquadricParticlesWriteVTK () 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...

Mdouble	getXCenter () const

Mdouble	getYCenter () const

Mdouble	getZCenter () const

Vec3D	getMin () const

Vec3D	getMax () const

void	setXMin (Mdouble newXMin)
	Sets the value of XMin, the lower bound of the problem domain in the x-direction. More...

void	setYMin (Mdouble newYMin)
	Sets the value of YMin, the lower bound of the problem domain in the y-direction. More...

void	setZMin (Mdouble newZMin)
	Sets the value of ZMin, the lower bound of the problem domain in the z-direction. More...

void	setXMax (Mdouble newXMax)
	Sets the value of XMax, the upper bound of the problem domain in the x-direction. More...

void	setYMax (Mdouble newYMax)
	Sets the value of YMax, the upper bound of the problem domain in the y-direction. More...

void	setZMax (Mdouble newZMax)
	Sets the value of ZMax, the upper bound of the problem domain in the z-direction. More...

void	setMax (const Vec3D &max)
	Sets the maximum coordinates of the problem domain. More...

void	setMax (Mdouble, Mdouble, Mdouble)
	Sets the maximum coordinates of the problem domain. More...

void	setDomain (const Vec3D &min, const Vec3D &max)
	Sets the minimum coordinates of the problem domain. More...

void	setMin (const Vec3D &min)
	Sets the minimum coordinates of the problem domain. More...

void	setMin (Mdouble, Mdouble, Mdouble)
	Sets the minimum coordinates of the problem domain. More...

void	setTimeStep (Mdouble newDt)
	Sets a new value for the simulation time step. More...

Mdouble	getTimeStep () const
	Returns the simulation time step. More...

void	setNumberOfOMPThreads (int numberOfOMPThreads)

int	getNumberOfOMPThreads () const

void	setXBallsColourMode (int newCMode)
	Set the xballs output mode. More...

int	getXBallsColourMode () const
	Get the xballs colour mode (CMode). More...

void	setXBallsVectorScale (double newVScale)
	Set the scale of vectors in xballs. More...

double	getXBallsVectorScale () const
	Returns the scale of vectors used in xballs. More...

void	setXBallsAdditionalArguments (std::string newXBArgs)
	Set the additional arguments for xballs. More...

std::string	getXBallsAdditionalArguments () const
	Returns the additional arguments for xballs. More...

void	setXBallsScale (Mdouble newScale)
	Sets the scale of the view (either normal, zoom in or zoom out) to display in xballs. The default is fit to screen. More...

double	getXBallsScale () const
	Returns the scale of the view in xballs. More...

void	setGravity (Vec3D newGravity)
	Sets a new value for the gravitational acceleration. More...

Vec3D	getGravity () const
	Returns the gravitational acceleration. More...

void	setBackgroundDrag (Mdouble backgroundDrag)
	Simple access function to turn on a background drag. The force of particleVelocity*drag is applied (note, it allowd to be negaitve i.e. create energy) More...

const Mdouble	getBackgroundDrag () const
	Return the background drag. More...

void	setDimension (unsigned int newDim)
	Sets both the system dimensions and the particle dimensionality. More...

void	setSystemDimensions (unsigned int newDim)
	Sets the system dimensionality. More...

unsigned int	getSystemDimensions () const
	Returns the system dimensionality. More...

void	setParticleDimensions (unsigned int particleDimensions)
	Sets the particle dimensionality. More...

unsigned int	getParticleDimensions () const
	Returns the particle dimensionality. 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 whether the "append" option is on or off. More...

void	setAppend (bool newAppendFlag)
	Sets whether the "append" option is on or off. More...

Mdouble	getElasticEnergy () const
	Returns the global elastic energy within the system. More...

Mdouble	getKineticEnergy () const
	Returns the global kinetic energy stored in the system. More...

Mdouble	getGravitationalEnergy () const
	Returns the global gravitational potential energy stored in the system. More...

Mdouble	getRotationalEnergy () const
	JMFT Returns the global rotational energy stored in the system. More...

Mdouble	getTotalEnergy () const

Mdouble	getTotalMass () const
	JMFT: Return the total mass of the system, excluding fixed particles. More...

Vec3D	getCentreOfMass () const
	JMFT: Return the centre of mass of the system, excluding fixed particles. More...

Vec3D	getTotalMomentum () const
	JMFT: Return the total momentum of the system, excluding fixed particles. More...

double	getCPUTime ()

double	getWallTime ()

virtual void	hGridInsertParticle (BaseParticle *obj UNUSED)

virtual void	hGridUpdateParticle (BaseParticle *obj UNUSED)

virtual void	hGridRemoveParticle (BaseParticle *obj UNUSED)

bool	mpiIsInCommunicationZone (BaseParticle *particle)
	Checks if the position of the particle is in an mpi communication zone or not. More...

bool	mpiInsertParticleCheck (BaseParticle *P)
	Function that checks if the mpi particle should really be inserted by the current domain. More...

void	insertGhostParticle (BaseParticle *P)
	This function inserts a particle in the mpi communication boundaries. More...

void	updateGhostGrid (BaseParticle *P)
	Checks if the Domain/periodic interaction distance needs to be updated and updates it accordingly. More...

virtual void	gatherContactStatistics (unsigned int index1, int index2, Vec3D Contact, Mdouble delta, Mdouble ctheta, Mdouble fdotn, Mdouble fdott, Vec3D P1_P2_normal_, Vec3D P1_P2_tangential)
	//Not unsigned index because of possible wall collisions. More...

void	setNumberOfDomains (std::vector< unsigned > direction)
	Sets the number of domains in x-,y- and z-direction. Required for parallel computations. More...

void	splitDomain (DomainSplit domainSplit)

std::vector< unsigned >	getNumberOfDomains ()
	returns the number of domains More...

Domain *	getCurrentDomain ()
	Function that returns a pointer to the domain corresponding to the processor. More...

void	removeOldFiles () const

void	setMeanVelocity (Vec3D V_mean_goal)
	This function will help you set a fixed kinetic energy and mean velocity in your system. More...

void	setMeanVelocityAndKineticEnergy (Vec3D V_mean_goal, Mdouble Ek_goal)
	This function will help you set a fixed kinetic energy and mean velocity in your system. More...

Mdouble	getTotalVolume () const
	Get the total volume of the cuboid system. More...

Matrix3D	getKineticStress () const
	Calculate the kinetic stress tensor in the system averaged over the whole volume. More...

Matrix3D	getStaticStress () const
	Calculate the static stress tensor in the system averaged over the whole volume. More...

Matrix3D	getTotalStress () const
	Calculate the total stress tensor in the system averaged over the whole volume. More...

virtual void	handleParticleRemoval (unsigned int id)
	Handles the removal of particles from the particleHandler. More...

virtual void	handleParticleAddition (unsigned int id, BaseParticle *p)

void	writePythonFileForVTKVisualisation () const

void	setWritePythonFileForVTKVisualisation (bool forceWritePythonFileForVTKVisualisation)

bool	getWritePythonFileForVTKVisualisation () const

WallVTKWriter &	getWallVTKWriter ()

Private Attributes
LinearViscoelasticSpecies *	species_

std::string	wallSource_

Additional Inherited Members
Public Types inherited from DPMBase
enum class	ReadOptions : int { ReadAll , ReadNoInteractions , ReadNoParticlesAndInteractions }

enum class	DomainSplit { X , Y , Z , XY , XZ , YZ , XYZ }

Static Public Member Functions inherited from DPMBase
static 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...

static int	readRunNumberFromFile ()
	Read the run number or the counter from the counter file (COUNTER_DONOTDEL) More...

static bool	areInContact (const BaseParticle pI, const BaseParticle pJ)
	Checks if two particle are in contact or is there any positive overlap. More...

Public Attributes inherited from DPMBase
SpeciesHandler	speciesHandler
	A handler to that stores the species type i.e. LinearViscoelasticSpecies, etc. 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...

ParticleHandler	paoloParticleHandler
	Fake particleHandler created by Paolo needed temporary by just Paolo. 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...

PeriodicBoundaryHandler	periodicBoundaryHandler
	Internal handler that deals with periodic boundaries, especially in a parallel build. More...

DomainHandler	domainHandler
	An object of the class DomainHandler which deals with parallel code. More...

InteractionHandler	interactionHandler
	An object of the class InteractionHandler. More...

CGHandler	cgHandler
	Object of the class cgHandler. More...

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...

File	interactionFile
	File class to handle in- and output into .interactions file. This file hold information about interactions. More...

Time	clock_
	record when the simulation started More...

Protected Member Functions inherited from Mercury3D
void	hGridFindContactsWithinTargetCell (int x, int y, int z, unsigned int l)
	Finds contacts between particles in the target cell. More...

void	hGridFindContactsWithTargetCell (int x, int y, int z, unsigned int l, BaseParticle *obj)
	Finds contacts between the BaseParticle and the target cell. More...

void	computeWallForces (BaseWall *w) override
	Compute contacts with a wall. More...

void	hGridFindParticlesWithTargetCell (int x, int y, int z, unsigned int l, BaseParticle obj, std::vector< BaseParticle > &list)
	Finds particles within target cell and stores them in a list. More...

void	hGridGetInteractingParticleList (BaseParticle obj, std::vector< BaseParticle > &list) override
	Obtains all neighbour particles of a given object, obtained from the hgrid. More...

void	computeInternalForces (BaseParticle *obj) override
	Finds contacts with the BaseParticle; avoids multiple checks. More...

bool	hGridHasContactsInTargetCell (int x, int y, int z, unsigned int l, const BaseParticle *obj) const
	Tests if the BaseParticle has contacts with other Particles in the target cell. More...

bool	hGridHasParticleContacts (const BaseParticle *obj) override
	Tests if a BaseParticle has any contacts in the HGrid. More...

void	hGridRemoveParticle (BaseParticle *obj) override
	Removes a BaseParticle from the HGrid. More...

void	hGridUpdateParticle (BaseParticle *obj) override
	Updates the cell (not the level) of a BaseParticle. More...

Protected Member Functions inherited from MercuryBase
void	hGridRebuild ()
	This sets up the parameters required for the contact model. More...

void	hGridInsertParticle (BaseParticle *obj) final
	Inserts a single Particle to current grid. More...

void	hGridUpdateMove (BaseParticle *iP, Mdouble move) final
	Computes the relative displacement of the given BaseParticle and updates the currentMaxRelativeDisplacement_ accordingly. More...

void	hGridActionsBeforeIntegration () override
	Resets the currentMaxRelativeDisplacement_ to 0. More...

void	hGridActionsAfterIntegration () override
	This function has to be called before integrateBeforeForceComputation. More...

HGrid *	getHGrid ()
	Gets the HGrid used by this problem. More...

const HGrid *	getHGrid () const
	Gets the HGrid used by this problem, const version. More...

bool	readNextArgument (int &i, int argc, char *argv[]) override
	Reads the next command line argument. More...

Protected Member Functions inherited from DPMBase
virtual void	computeAllForces ()
	Computes all the forces acting on the particles using the BaseInteractable::setForce() and BaseInteractable::setTorque() More...

virtual void	computeInternalForce (BaseParticle , BaseParticle )
	Computes the forces between two particles (internal in the sense that the sum over all these forces is zero i.e. fully modelled forces) More...

virtual void	computeExternalForces (BaseParticle *)
	Computes the external forces, such as gravity, acting on particles. More...

virtual void	computeForcesDueToWalls (BaseParticle , BaseWall )
	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	actionsBeforeTimeStep ()
	A virtual function which allows to define operations to be executed before the new time step. More...

virtual void	computeAdditionalForces ()
	A virtual function which allows to define operations to be executed prior to the OMP force collect. 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...

void	writeVTKFiles () const

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. For more information on the XBalls program, see Visualising data in xballs. More...

virtual void	outputXBallsDataParticle (unsigned int i, 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. For more information on the XBalls program, see Visualising data in xballs. 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
	Write the global kinetic, potential energy, etc. in the system. More...

virtual void	initialiseStatistics ()

virtual void	outputStatistics ()

void	gatherContactStatistics ()

virtual void	processStatistics (bool)

virtual void	finishStatistics ()

virtual void	integrateBeforeForceComputation ()
	Update particles' and walls' positions and velocities before force computation. More...

virtual void	integrateAfterForceComputation ()
	Update particles' and walls' positions and velocities after force computation. 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...

void	setFixedParticles (unsigned int n)
	Sets a number, `n`, of particles in the particleHandler as "fixed particles". More...

virtual void	printTime () const
	Displays the current simulation time and the maximum simulation duration. More...

virtual bool	continueSolve () const
	A virtual function for deciding whether to continue the simulation, based on a user-specified criterion. More...

void	outputInteractionDetails () const
	Displays the interaction details corresponding to the pointer objects in the interaction handler. More...

bool	isTimeEqualTo (Mdouble time) const
	Checks whether the input variable "time" is the current time in the simulation. More...

void	removeDuplicatePeriodicParticles ()
	Removes periodic duplicate Particles. More...

void	checkAndDuplicatePeriodicParticles ()
	For simulations using periodic boundaries, checks and adds particles when necessary into the particle handler. See DPMBase.cc and PeriodicBoundary.cc for more details. More...

void	performGhostParticleUpdate ()
	When the Verlet scheme updates the positions and velocities of particles, ghost particles will need an update as wel. Their status will also be updated accordingly. More...

void	deleteGhostParticles (std::set< BaseParticle * > &particlesToBeDeleted)

void	synchroniseParticle (BaseParticle *, unsigned fromProcessor=0)

void	performGhostVelocityUpdate ()
	updates the final time-step velocity of the ghost particles More...

void	setSoftStop ()
	function for setting sigaction constructor. More...

Static Protected Member Functions inherited from DPMBase
static void	signalHandler (int signal)
	signal handler function. More...

Constructor & Destructor Documentation

◆ AreaVTK()

AreaVTK::AreaVTK ( std::string const & wallSource )

inline

         : wallSource_(wallSource)
     {
         species_ = speciesHandler.copyAndAddObject(LinearViscoelasticSpecies());
     }

References BaseHandler< T >::copyAndAddObject(), species_, and DPMBase::speciesHandler.

Member Function Documentation

◆ getTotalsurfaceAreaFromFile()

double AreaVTK::getTotalsurfaceAreaFromFile ( std::string const & fileName )

inline

     {
         FILE* fp = fopen(fileName.c_str(), "r");
         if (fp == NULL) {
             logger(ERROR, "%", strerror(errno));
         }
  
         auto trimLine = [this](char* line) {
             char* start = line;
             while (isspace(*start)) {
                 start++;
             }
  
             char* end = line + strlen(line) - 1;
  
             while (isspace(*end)) {
                 end--;
             }
  
             int length = end - start + 1;
             if (length <= 0) {
                 logger(ERROR, "Unable to trim `%`", line);
             }
  
             return std::string(start, length);
         };
  
         auto getDouble = [this](std::string const& str) {
             char* next;
             double val = strtod(str.c_str(), &next);
             if ((next == str) || (*next != '\0')) {
                 logger(ERROR, "Invalid number: `%`", str);
             };
             return val;
         };
  
         char line[1024];
         bool inSurfaceArea = false;
         double totalSurfaceArea = 0;
         size_t numberOfSurfaces = 0;
  
         while (fgets(line, sizeof(line), fp)) {
             if (strstr(line, "SurfaceArea") != NULL) {
                 inSurfaceArea = true;
             } else if (inSurfaceArea && strstr(line, "</DataArray>") != NULL) {
                 inSurfaceArea = false;
                 break;
             } else if (inSurfaceArea) {
                 numberOfSurfaces++;
                 double surfaceArea = getDouble(trimLine(line));
                 totalSurfaceArea += surfaceArea;
             } else {
                 // do nothing
             }
         }
  
         if (numberOfSurfaces == 0) {
             logger(ERROR, "No 'SurfaceArea' found in %", fileName);
         }
  
         if (inSurfaceArea) {
             logger(ERROR, "Corrupted 'SurfaceArea' in %", fileName);
         }
  
         fclose(fp);
  
         return totalSurfaceArea;
     }

References ERROR, and logger.

Referenced by main().

◆ setupInitialConditions()

void AreaVTK::setupInitialConditions ( )

inlineoverridevirtual

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 distributed

Reimplemented from DPMBase.

     {
         setName(wallSource_);
  
         setTimeStep(1);
         setTimeMax(1);
  
         removeOldFiles();
         setSaveCount(1);
         setFileType(FileType::NO_FILE);
         setWritePythonFileForVTKVisualisation(false);
         setParticlesWriteVTK(false);
         wallHandler.setWriteVTK(true);
         wallHandler.setWriteWallSurfaceAreaVTK(true);
  
         setMin({ -1, -1, -1 });
         setMax({ 1, 1, 1 });
  
         if (wallSource_ == "InfiniteWall") {
             InfiniteWall w0;
             w0.setSpecies(species_);
             w0.set(Vec3D(0.0, 0.0, -1.0), Vec3D(0, 0, 0));
             wallHandler.copyAndAddObject(w0);
         } else {
             wallHandler.readTriangleWall(wallSource_, species_);
         }
     }