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Mercury3D Class Reference

This adds on the hierarchical grid code for 3D problems. More...

#include <Mercury3D.h>

+ Inheritance diagram for Mercury3D:

Public Member Functions

 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) 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 the MercuryBase to an output stream, for example 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 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 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 a very useful feature for performing 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...
 
virtual void decompose ()
 Sends particles from processorId to the root processor. More...
 
void solve ()
 The work horse of the code. 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 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 Mdouble getInfo (const BaseParticle &P) const
 A virtual function that returns some user-specified information about a particle. More...
 
ParticleVtkWritergetVtkWriter () 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)
 Inserts particles in the whole domain. More...
 
bool readRestartFile ()
 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)
 The same as readRestartFile(bool), but also reads all the particle data corresponding to the current saved time step. More...
 
virtual BaseWallreadUserDefinedWall (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...
 
bool readNextDataFileMPI (unsigned int format=0)
 
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)
 
MERCURY_DEPRECATED FilegetDataFile ()
 The non const version. Allows one to edit the File::dataFile. More...
 
MERCURY_DEPRECATED FilegetEneFile ()
 The non const version. Allows to edit the File::eneFile. More...
 
MERCURY_DEPRECATED FilegetFStatFile ()
 The non const version. Allows to edit the File::fStatFile. More...
 
MERCURY_DEPRECATED FilegetRestartFile ()
 The non const version. Allows to edit the File::restartFile. More...
 
MERCURY_DEPRECATED FilegetStatFile ()
 The non const version. Allows to edit the File::statFile. More...
 
FilegetInteractionFile ()
 Return a reference to the file InteractionsFile. More...
 
MERCURY_DEPRECATED const FilegetDataFile () const
 The const version. Does not allow for any editing of the File::dataFile. More...
 
MERCURY_DEPRECATED const FilegetEneFile () const
 The const version. Does not allow for any editing of the File::eneFile. More...
 
MERCURY_DEPRECATED const FilegetFStatFile () const
 The const version. Does not allow for any editing of the File::fStatFile. More...
 
MERCURY_DEPRECATED const FilegetRestartFile () const
 The const version. Does not allow for any editing of the File::restartFile. More...
 
MERCURY_DEPRECATED const FilegetStatFile () const
 The const version. Does not allow for any editing of the File::statFile. More...
 
const FilegetInteractionFile () 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 (const Mdouble logarithmicSaveCountBase)
 Sets File::logarithmicSaveCount_ for all files (ene, data, fstat, restart, stat) 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...
 
void setWallsWriteVTK (FileType writeWallsVTK)
 Sets whether walls are written into a VTK file. More...
 
void setWallsWriteVTK (bool)
 Sets whether walls are written into a VTK file. More...
 
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)
 
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...
 
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 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 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 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...
 
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)
 
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...
 
std::vector< unsignedgetNumberOfDomains ()
 returns the number of domains More...
 
DomaingetCurrentDomain ()
 Function that returns a pointer to the domain corresponding to the processor. More...
 
void removeOldFiles () const
 
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...
 
void writePythonFileForVTKVisualisation () const
 record when the simulation started More...
 
void setReadInteractions (const bool readInteractions)
 
bool getReadInteractions () const
 

Protected Member Functions

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...
 
HGridgetHGrid ()
 Gets the HGrid used by this problem. More...
 
const HGridgetHGrid () 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...
 
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 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...
 

Additional Inherited Members

- 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...
 
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...
 

Detailed Description

This adds on the hierarchical grid code for 3D problems.

Definition at line 34 of file Mercury3D.h.

Constructor & Destructor Documentation

Mercury3D::Mercury3D ( )

This is the default constructor. All it does is set sensible defaults.

Definition at line 29 of file Mercury3D.cc.

References constructor(), DEBUG, and logger.

30 {
31  constructor();
32  logger(DEBUG, "Mercury3D::Mercury3D() finished");
33 }
Logger< MERCURY_LOGLEVEL > logger("MercuryKernel")
void constructor()
Function that sets the SystemDimension and ParticleDimension to 3.
Definition: Mercury3D.cc:59
Mercury3D::Mercury3D ( const DPMBase other)
explicit

Copy-constructor for creates an Mercury3D problem from an existing MD problem.

Parameters
[in]otherDPMBase which has to be copied and converted to a Mercury3D.

Constructor that makes a Mercury3D out of a DPMBase. The "copy"-constructor of DPMBase has to be called because the link from DPMBase to MercuryBase is virtual.

Definition at line 52 of file Mercury3D.cc.

References constructor(), DEBUG, and logger.

53  : DPMBase(other), MercuryBase()
54 {
55  constructor();
56  logger(DEBUG, "Mercury3D::Mercury3D(DPMBase& other) constructor finished");
57 }
Logger< MERCURY_LOGLEVEL > logger("MercuryKernel")
void constructor()
Function that sets the SystemDimension and ParticleDimension to 3.
Definition: Mercury3D.cc:59
MercuryBase()
This is the default constructor. It sets sensible defaults.
Definition: MercuryBase.cc:31
DPMBase()
Constructor that calls the "void constructor()".
Definition: DPMBase.cc:191
Mercury3D::Mercury3D ( const Mercury3D other)

Copy-constructor.

Parameters
[in]otherMercury3D that must be copied.

Copy constructor, note that the copy-constructor of DPMBase has to be called because the link from DPMBase to MercuryBase is virtual.

Definition at line 40 of file Mercury3D.cc.

References DEBUG, and logger.

41  : DPMBase(other), MercuryBase(other)
42 {
43  logger(DEBUG, "Mercury3D::Mercury3D(Mercury3D& other) copy constructor finished.");
44 }
Logger< MERCURY_LOGLEVEL > logger("MercuryKernel")
MercuryBase()
This is the default constructor. It sets sensible defaults.
Definition: MercuryBase.cc:31
DPMBase()
Constructor that calls the "void constructor()".
Definition: DPMBase.cc:191

Member Function Documentation

void Mercury3D::computeInternalForces ( BaseParticle obj)
overrideprotectedvirtual

Finds contacts with the BaseParticle; avoids multiple checks.

Parameters
[in]objA pointer to the BaseParticle for which we want to check for contacts.

Computes all collision between given BaseParticle and all other particles in the grid. Please note that we're looking only one way, so that interactions are not detected twice.

Reimplemented from DPMBase.

Definition at line 220 of file Mercury3D.cc.

References MercuryBase::getHGrid(), BaseParticle::getHGridLevel(), MercuryBase::getHGridMethod(), BaseParticle::getHGridX(), BaseParticle::getHGridY(), BaseParticle::getHGridZ(), HGrid::getInvCellSize(), BaseParticle::getMaxInteractionRadius(), HGrid::getNumberOfLevels(), HGrid::getOccupiedLevelsMask(), BaseInteractable::getPosition(), hGridFindContactsWithinTargetCell(), hGridFindContactsWithTargetCell(), TOPDOWN, Vec3D::X, Vec3D::Y, and Vec3D::Z.

221 {
222  HGrid* const hgrid = getHGrid();
223  const unsigned int startLevel = obj->getHGridLevel();
224 
225  if (getHGridMethod() == TOPDOWN)
226  {
227  int occupiedLevelsMask = hgrid->getOccupiedLevelsMask();
228  for (unsigned int level = 0; level <= startLevel && occupiedLevelsMask != 0; occupiedLevelsMask >>= 1, level++)
229  {
230  // If no objects at this level, go on to the next level
231  if ((occupiedLevelsMask & 1) == 0)
232  {
233  continue;
234  }
235 
236  if (level == startLevel)
237  {
238  const int x = obj->getHGridX();
239  const int y = obj->getHGridY();
240  const int z = obj->getHGridZ();
241 
242  hGridFindContactsWithinTargetCell(x, y, z, level);
243  hGridFindContactsWithTargetCell(x + 1, y - 1, z, level, obj);
244  hGridFindContactsWithTargetCell(x + 1, y, z, level, obj);
245  hGridFindContactsWithTargetCell(x + 1, y + 1, z, level, obj);
246  hGridFindContactsWithTargetCell(x + 1, y - 1, z + 1, level, obj);
247  hGridFindContactsWithTargetCell(x + 1, y, z + 1, level, obj);
248  hGridFindContactsWithTargetCell(x + 1, y + 1, z + 1, level, obj);
249  hGridFindContactsWithTargetCell(x + 1, y - 1, z - 1, level, obj);
250  hGridFindContactsWithTargetCell(x + 1, y, z - 1, level, obj);
251  hGridFindContactsWithTargetCell(x + 1, y + 1, z - 1, level, obj);
252  hGridFindContactsWithTargetCell(x, y + 1, z, level, obj);
253  hGridFindContactsWithTargetCell(x, y, z - 1, level, obj);
254  hGridFindContactsWithTargetCell(x, y + 1, z - 1, level, obj);
255  hGridFindContactsWithTargetCell(x, y + 1, z + 1, level, obj);
256  }
257  else
258  {
259  const Mdouble inv_size = getHGrid()->getInvCellSize(level);
260  const int xs = static_cast<int>(std::floor(
261  (obj->getPosition().X - obj->getMaxInteractionRadius()) * inv_size - 0.5));
262  const int xe = static_cast<int>(std::floor(
263  (obj->getPosition().X + obj->getMaxInteractionRadius()) * inv_size + 0.5));
264  const int ys = static_cast<int>(std::floor(
265  (obj->getPosition().Y - obj->getMaxInteractionRadius()) * inv_size - 0.5));
266  const int ye = static_cast<int>(std::floor(
267  (obj->getPosition().Y + obj->getMaxInteractionRadius()) * inv_size + 0.5));
268  const int zs = static_cast<int>(std::floor(
269  (obj->getPosition().Z - obj->getMaxInteractionRadius()) * inv_size - 0.5));
270  const int ze = static_cast<int>(std::floor(
271  (obj->getPosition().Z + obj->getMaxInteractionRadius()) * inv_size + 0.5));
272  for (int x = xs; x <= xe; ++x)
273  {
274  for (int y = ys; y <= ye; ++y)
275  {
276  for (int z = zs; z <= ze; ++z)
277  {
278  hGridFindContactsWithTargetCell(x, y, z, level, obj);
279  }
280  }
281  }
282  }
283  }
284  }
285  else
286  {
287  int occupiedLevelsMask = hgrid->getOccupiedLevelsMask() >> obj->getHGridLevel();
288  for (unsigned int level = startLevel; level < hgrid->getNumberOfLevels(); occupiedLevelsMask >>= 1, level++)
289  {
290  // If no objects in rest of grid, stop now
291  if (occupiedLevelsMask == 0)
292  {
293  break;
294  }
295 
296  // If no objects at this level, go on to the next level
297  if ((occupiedLevelsMask & 1) == 0)
298  {
299  continue;
300  }
301 
302  if (level == startLevel)
303  {
304  const int x = obj->getHGridX();
305  const int y = obj->getHGridY();
306  const int z = obj->getHGridZ();
307 
308  hGridFindContactsWithinTargetCell(x, y, z, level);
309  hGridFindContactsWithTargetCell(x + 1, y - 1, z, level, obj);
310  hGridFindContactsWithTargetCell(x + 1, y, z, level, obj);
311  hGridFindContactsWithTargetCell(x + 1, y + 1, z, level, obj);
312  hGridFindContactsWithTargetCell(x + 1, y - 1, z + 1, level, obj);
313  hGridFindContactsWithTargetCell(x + 1, y, z + 1, level, obj);
314  hGridFindContactsWithTargetCell(x + 1, y + 1, z + 1, level, obj);
315  hGridFindContactsWithTargetCell(x + 1, y - 1, z - 1, level, obj);
316  hGridFindContactsWithTargetCell(x + 1, y, z - 1, level, obj);
317  hGridFindContactsWithTargetCell(x + 1, y + 1, z - 1, level, obj);
318  hGridFindContactsWithTargetCell(x, y + 1, z, level, obj);
319  hGridFindContactsWithTargetCell(x, y, z - 1, level, obj);
320  hGridFindContactsWithTargetCell(x, y + 1, z - 1, level, obj);
321  hGridFindContactsWithTargetCell(x, y + 1, z + 1, level, obj);
322  }
323  else
324  {
325  const Mdouble inv_size = hgrid->getInvCellSize(level);
326  const int xs = static_cast<int>(std::floor(
327  (obj->getPosition().X - obj->getMaxInteractionRadius()) * inv_size - 0.5));
328  const int xe = static_cast<int>(std::floor(
329  (obj->getPosition().X + obj->getMaxInteractionRadius()) * inv_size + 0.5));
330  const int ys = static_cast<int>(std::floor(
331  (obj->getPosition().Y - obj->getMaxInteractionRadius()) * inv_size - 0.5));
332  const int ye = static_cast<int>(std::floor(
333  (obj->getPosition().Y + obj->getMaxInteractionRadius()) * inv_size + 0.5));
334  const int zs = static_cast<int>(std::floor(
335  (obj->getPosition().Z - obj->getMaxInteractionRadius()) * inv_size - 0.5));
336  const int ze = static_cast<int>(std::floor(
337  (obj->getPosition().Z + obj->getMaxInteractionRadius()) * inv_size + 0.5));
338  for (int x = xs; x <= xe; ++x)
339  {
340  for (int y = ys; y <= ye; ++y)
341  {
342  for (int z = zs; z <= ze; ++z)
343  {
344  hGridFindContactsWithTargetCell(x, y, z, level, obj);
345  }
346  }
347  }
348  }
349  }
350  }
351 }
const Vec3D & getPosition() const
Returns the position of this BaseInteractable.
Mdouble X
the vector components
Definition: Vector.h:65
double Mdouble
Definition: GeneralDefine.h:34
Mdouble getMaxInteractionRadius() const
Returns the particle's interaction radius, which might be different from radius_ (e.g., when dealing with wet particles)
Definition: BaseParticle.h:359
void hGridFindContactsWithinTargetCell(int x, int y, int z, unsigned int l)
Finds contacts between particles in the target cell.
Definition: Mercury3D.cc:73
HGridMethod getHGridMethod() const
Gets whether the HGrid in this MercuryBase is BOTTOMUP or TOPDOWN.
Definition: MercuryBase.h:204
int getHGridY() const
Returns particle's HGrid cell Y-coordinate.
Definition: BaseParticle.h:272
int getOccupiedLevelsMask() const
Gets the integer that represents which levels are occupied.
Definition: HGrid.h:213
In the HGrid class, here all information about the HGrid is stored.
Definition: HGrid.h:42
int getHGridZ() const
Returns particle's HGrid cell Z-coordinate.
Definition: BaseParticle.h:279
Mdouble Y
Definition: Vector.h:65
void hGridFindContactsWithTargetCell(int x, int y, int z, unsigned int l, BaseParticle *obj)
Finds contacts between the BaseParticle and the target cell.
Definition: Mercury3D.cc:115
HGrid * getHGrid()
Gets the HGrid used by this problem.
Definition: MercuryBase.h:311
unsigned long getNumberOfLevels() const
Gets the number of levels of this HGrid.
Definition: HGrid.h:206
unsigned int getHGridLevel() const
Returns particle's HGrid level.
Definition: BaseParticle.h:234
Mdouble Z
Definition: Vector.h:65
double getInvCellSize(unsigned int i) const
Gets 1/cellSize for the cells on level i.
Definition: HGrid.h:178
int getHGridX() const
Returns particle's HGrid cell X-coordinate.
Definition: BaseParticle.h:265
void Mercury3D::computeWallForces ( BaseWall w)
overrideprotectedvirtual

Compute contacts with a wall.

Reimplemented from DPMBase.

Definition at line 609 of file Mercury3D.cc.

References DPMBase::computeForcesDueToWalls(), HGrid::computeHashBucketIndex(), DPMBase::computeWallForces(), HGridCell::equals(), HGrid::getFirstBaseParticleInBucket(), MercuryBase::getHGrid(), BaseParticle::getHGridCell(), BaseParticle::getHGridNextObject(), HGrid::getInvCellSize(), HGrid::getNumberOfLevels(), HGrid::getOccupiedLevelsMask(), BaseParticle::getPeriodicFromParticle(), MercuryBase::hGridRebuild(), INFO, BaseParticle::isFixed(), BaseWall::isLocal(), logger, VERBOSE, Vec3D::X, Vec3D::Y, and Vec3D::Z.

610 {
611 
612  // if wall is not local, use the non-hGrid version for finding wall contacts
613  Vec3D min, max;
614  if (w->isLocal(min, max)==false)
615  {
616  return DPMBase::computeWallForces(w);
617  }
618 
619  //compute forces for all particles that are neither fixed or ghosts
620  if (getHGrid() == nullptr || getHGrid()->getNeedsRebuilding())
621  {
622  logger(INFO, "HGrid needs rebuilding for \"bool Mercury3D::hGridHasParticleContacts(BaseParticle *obj)\"");
623  hGridRebuild();
624  }
625 
626  HGrid* const hGrid = getHGrid();
627 
628  int occupiedLevelsMask = hGrid->getOccupiedLevelsMask();
629 
630  for (unsigned int level = 0; level < hGrid->getNumberOfLevels(); occupiedLevelsMask >>= 1, level++)
631  {
632  // If no objects in rest of grid, stop now
633  if (occupiedLevelsMask == 0)
634  {
635  logger(VERBOSE, "Level % and higher levels are empty", level);
636  break;
637  }
638 
639  // If no objects at this level, go on to the next level
640  if ((occupiedLevelsMask & 1) == 0)
641  {
642  logger(VERBOSE, "Level % is empty", level);
643  continue;
644  }
645 
646  const Mdouble inv_size = hGrid->getInvCellSize(level);
647  const int xs = static_cast<int>(std::floor(min.X * inv_size - 0.5));
648  const int xe = static_cast<int>(std::floor(max.X * inv_size + 0.5));
649  const int ys = static_cast<int>(std::floor(min.Y * inv_size - 0.5));
650  const int ye = static_cast<int>(std::floor(max.Y * inv_size + 0.5));
651  const int zs = static_cast<int>(std::floor(min.Z * inv_size - 0.5));
652  const int ze = static_cast<int>(std::floor(max.Z * inv_size + 0.5));
653  //logger(INFO, "Level % grid cells [%,%] x [%,%] x [%,%]", level, xs, xe, ys, ye, zs, ze);
654 
655  for (int x = xs; x <= xe; ++x)
656  {
657  for (int y = ys; y <= ye; ++y)
658  {
659  for (int z = zs; z <= ze; ++z)
660  {
661  // Loop through all objects in the bucket to find nearby objects
662  const unsigned int bucket = hGrid->computeHashBucketIndex(x, y, z, level);
663  BaseParticle* p = hGrid->getFirstBaseParticleInBucket(bucket);
664  while (p != nullptr)
665  {
666  if (!p->isFixed() && p->getPeriodicFromParticle() == nullptr &&
667  p->getHGridCell().equals(x, y, z, level))
668  {
669  //logger(INFO, "t % p % Size % level % cells % % %", getNumberOfTimeSteps(), p->getIndex(), hGrid->getCellSize(level), level, x,y,z);
671  //w->computeForces(p);
672  }
673  p = p->getHGridNextObject();
674  }
675  }
676  }
677  }
678  } //end for level
679 }
const HGridCell & getHGridCell() const
Definition: BaseParticle.h:643
bool equals(int x, int y, int z, unsigned int level) const
Checks if the given (x,y,z,level) is the same as the ones in this cell.
Definition: HGridCell.h:39
Mdouble X
the vector components
Definition: Vector.h:65
Logger< MERCURY_LOGLEVEL > logger("MercuryKernel")
double Mdouble
Definition: GeneralDefine.h:34
virtual bool isLocal(Vec3D &min, Vec3D &max) const
Definition: BaseWall.h:137
BaseParticle * getPeriodicFromParticle() const
Returns the 'original' particle this one's a periodic copy of.
Definition: BaseParticle.h:338
virtual void computeWallForces(BaseWall *w)
Definition: DPMBase.cc:4876
int getOccupiedLevelsMask() const
Gets the integer that represents which levels are occupied.
Definition: HGrid.h:213
In the HGrid class, here all information about the HGrid is stored.
Definition: HGrid.h:42
bool isFixed() const override
Is fixed Particle function. It returns whether a Particle is fixed or not, by checking its inverse Ma...
Definition: BaseParticle.h:93
Mdouble Y
Definition: Vector.h:65
void hGridRebuild()
This sets up the parameters required for the contact model.
Definition: MercuryBase.cc:203
HGrid * getHGrid()
Gets the HGrid used by this problem.
Definition: MercuryBase.h:311
void computeForcesDueToWalls(BaseParticle *, BaseWall *)
Computes the forces on the particles due to the walls (normals are outward normals) ...
Definition: DPMBase.cc:2978
unsigned long getNumberOfLevels() const
Gets the number of levels of this HGrid.
Definition: HGrid.h:206
const BaseParticle * getFirstBaseParticleInBucket(unsigned int i) const
Gets the first BaseParticle in the given bucket, const version.
Definition: HGrid.h:162
unsigned int computeHashBucketIndex(int x, int y, int z, unsigned int l) const
Computes hash bucket index in range [0, NUM_BUCKETS-1] for a 3D domain.
Definition: HGrid.h:76
Definition: Vector.h:49
BaseParticle * getHGridNextObject() const
Returns pointer to next object in particle's HGrid level & cell.
Definition: BaseParticle.h:242
Mdouble Z
Definition: Vector.h:65
double getInvCellSize(unsigned int i) const
Gets 1/cellSize for the cells on level i.
Definition: HGrid.h:178
void Mercury3D::constructor ( )

Function that sets the SystemDimension and ParticleDimension to 3.

Definition at line 59 of file Mercury3D.cc.

References DPMBase::setParticleDimensions(), and DPMBase::setSystemDimensions().

Referenced by Mercury3D().

60 {
63 }
void setParticleDimensions(unsigned int particleDimensions)
Sets the particle dimensionality.
Definition: DPMBase.cc:1302
void setSystemDimensions(unsigned int newDim)
Sets the system dimensionality.
Definition: DPMBase.cc:1271
void Mercury3D::hGridFindContactsWithinTargetCell ( int  x,
int  y,
int  z,
unsigned int  l 
)
protected

Finds contacts between particles in the target cell.

Parameters
[in]xCoordinate of the target cell in x direction.
[in]yCoordinate of the target cell in y direction.
[in]zCoordinate of the target cell in z direction.
[in]lLevel in the HGrid of the target cell.

Computes all collision between particles in the same bucket as cell (x,y,z,l), please note that all the particles are in the same cell.

Bug:
TW: This check is not necessary, I believe. This is the most-expensive function in most codes (the two checks in this function slows down granular jet by 15%) and the selftests are not affected.
Bug:
DK: I do think this is necessary, for example: If two cells hash to the same bucket and a particle in one of these cells check for collisions with the other cell. Then due to the hashing collision it also gets all particles in it's own cell and thus generating false collisions.

Definition at line 73 of file Mercury3D.cc.

References HGrid::computeHashBucketIndex(), DPMBase::computeInternalForce(), HGrid::getBucketIsChecked(), HGrid::getFirstBaseParticleInBucket(), MercuryBase::getHGrid(), BaseParticle::getHGridCell(), BaseParticle::getHGridNextObject(), and HGrid::setBucketIsChecked().

Referenced by computeInternalForces().

74 {
75  HGrid* const hgrid = getHGrid();
76  const unsigned int bucket = hgrid->computeHashBucketIndex(x, y, z, l);
77 
78  //Check if this function is already applied to this bucket
79  if (hgrid->getBucketIsChecked(bucket))
80  {
81  return;
82  }
83 
84  BaseParticle* p1 = hgrid->getFirstBaseParticleInBucket(bucket);
85  while (p1 != nullptr)
86  {
87  BaseParticle* p2 = p1->getHGridNextObject();
88  while (p2 != nullptr)
89  {
92  //Check if the BaseParticle* p1 and BaseParticle* p2 are really in the same cell (i.e. no hashing error has occurred)
93  if (p1->getHGridCell() == (p2->getHGridCell()))
94  {
95  computeInternalForce(p1, p2);
96  }
97  p2 = p2->getHGridNextObject();
98  }
99  p1 = p1->getHGridNextObject();
100  }
101  hgrid->setBucketIsChecked(bucket);
102 }
const HGridCell & getHGridCell() const
Definition: BaseParticle.h:643
In the HGrid class, here all information about the HGrid is stored.
Definition: HGrid.h:42
void setBucketIsChecked(unsigned int i)
Sets that the bucket with the given index is checked to true.
Definition: HGrid.h:124
virtual void computeInternalForce(BaseParticle *, BaseParticle *)
Computes the forces between two particles (internal in the sense that the sum over all these forces i...
Definition: DPMBase.cc:2903
HGrid * getHGrid()
Gets the HGrid used by this problem.
Definition: MercuryBase.h:311
const BaseParticle * getFirstBaseParticleInBucket(unsigned int i) const
Gets the first BaseParticle in the given bucket, const version.
Definition: HGrid.h:162
unsigned int computeHashBucketIndex(int x, int y, int z, unsigned int l) const
Computes hash bucket index in range [0, NUM_BUCKETS-1] for a 3D domain.
Definition: HGrid.h:76
BaseParticle * getHGridNextObject() const
Returns pointer to next object in particle's HGrid level & cell.
Definition: BaseParticle.h:242
bool getBucketIsChecked(unsigned int i) const
Gets whether or not the bucket with index i is checked.
Definition: HGrid.h:132
void Mercury3D::hGridFindContactsWithTargetCell ( int  x,
int  y,
int  z,
unsigned int  l,
BaseParticle obj 
)
protected

Finds contacts between the BaseParticle and the target cell.

Parameters
[in]xThe coordinate of the target cell in x direction.
[in]yThe coordinate of the target cell in y direction.
[in]zThe coordinate of the target cell in z direction.
[in]lThe level in the HGrid of the target cell.
[in]objA pointer to the BaseParticle for which we want to have interactions.

Computes all collisions between given BaseParticle and particles in cell (x,y,z,l). This is done by first checking if the BaseParticle is indeed from another cell, then for all BaseParticle in the target cell it is checked what the forces between that BaseParticle and given BaseParticle are.

Definition at line 115 of file Mercury3D.cc.

References HGrid::computeHashBucketIndex(), DPMBase::computeInternalForce(), HGridCell::equals(), HGrid::getFirstBaseParticleInBucket(), MercuryBase::getHGrid(), BaseParticle::getHGridCell(), BaseParticle::getHGridNextObject(), and logger.

Referenced by computeInternalForces().

116 {
117  //Check if the object is not in the same cell as being checked, CheckCell_current should handle these cases.
118  //TW a speedcheck revealed that this check costs a 10% performance decrease; it's only a safety check, so I made it an assert.
119  logger.assert(!obj->getHGridCell().equals(x, y, z, l),
120  "hGridFindContactsWithTargetCell should not be called if object is in the same cell");
121 
122  HGrid* const hgrid = getHGrid();
123 
124  // Calculate the bucket
125  const unsigned int bucket = hgrid->computeHashBucketIndex(x, y, z, l);
126 
127  // Loop through all objects in the bucket to find nearby objects
128  for (BaseParticle* p = hgrid->getFirstBaseParticleInBucket(bucket); p != nullptr; p = p->getHGridNextObject())
129  {
130  //This is the most-expensive function in most codes (the two checks in this function slows down granular jet by 15%). It is neccesary, for example: If two cells hash to the same bucket and a particle in one of these cells check for collisions with the other cell. Then due to the hashing collision it also gets all particles in it's own cell and thus generating false collisions.
131  //Check if the BaseParticle *p really is in the target cell (i.e. no hashing error has occurred)
132  //TW speedcheck revealed that this pre-check is cheaper than allowing computeInternalForces to sort out mismatches; even if a large number of hash cells (10*Np) is used.
133  if (p->getHGridCell().equals(x, y, z, l))
134  {
135  computeInternalForce(obj, p);
136  }
137  }
138 }
const HGridCell & getHGridCell() const
Definition: BaseParticle.h:643
bool equals(int x, int y, int z, unsigned int level) const
Checks if the given (x,y,z,level) is the same as the ones in this cell.
Definition: HGridCell.h:39
Logger< MERCURY_LOGLEVEL > logger("MercuryKernel")
In the HGrid class, here all information about the HGrid is stored.
Definition: HGrid.h:42
virtual void computeInternalForce(BaseParticle *, BaseParticle *)
Computes the forces between two particles (internal in the sense that the sum over all these forces i...
Definition: DPMBase.cc:2903
HGrid * getHGrid()
Gets the HGrid used by this problem.
Definition: MercuryBase.h:311
const BaseParticle * getFirstBaseParticleInBucket(unsigned int i) const
Gets the first BaseParticle in the given bucket, const version.
Definition: HGrid.h:162
unsigned int computeHashBucketIndex(int x, int y, int z, unsigned int l) const
Computes hash bucket index in range [0, NUM_BUCKETS-1] for a 3D domain.
Definition: HGrid.h:76
BaseParticle * getHGridNextObject() const
Returns pointer to next object in particle's HGrid level & cell.
Definition: BaseParticle.h:242
std::vector< BaseParticle * > Mercury3D::hGridFindParticleContacts ( const BaseParticle obj)
overridevirtual

Returns all particles that have a contact with a given particle.

Implements MercuryBase.

Definition at line 538 of file Mercury3D.cc.

References DPMBase::areInContact(), HGrid::computeHashBucketIndex(), HGridCell::equals(), HGrid::getFirstBaseParticleInBucket(), MercuryBase::getHGrid(), BaseParticle::getHGridCell(), BaseParticle::getHGridNextObject(), HGrid::getInvCellSize(), BaseParticle::getMaxInteractionRadius(), HGrid::getNumberOfLevels(), HGrid::getOccupiedLevelsMask(), BaseInteractable::getPosition(), MercuryBase::hGridRebuild(), INFO, logger, VERBOSE, Vec3D::X, Vec3D::Y, and Vec3D::Z.

539 {
540  if (getHGrid() == nullptr || getHGrid()->getNeedsRebuilding())
541  {
542  logger(INFO, "HGrid needs rebuilding for \"bool Mercury3D::hGridHasParticleContacts(BaseParticle *obj)\"");
543  hGridRebuild();
544  }
545 
546  int occupiedLevelsMask = getHGrid()->getOccupiedLevelsMask();
547 
548  std::vector<BaseParticle*> particlesInContact;
549 
550  for (unsigned int level = 0; level < getHGrid()->getNumberOfLevels(); occupiedLevelsMask >>= 1, level++)
551  {
552  // If no objects in rest of grid, stop now
553  if (occupiedLevelsMask == 0)
554  {
555  logger(VERBOSE, "Level % and higher levels are empty", level);
556  break;
557  }
558 
559  // If no objects at this level, go on to the next level
560  if ((occupiedLevelsMask & 1) == 0)
561  {
562  logger(VERBOSE, "Level % is empty", level);
563  continue;
564  }
565 
566  const Mdouble inv_size = getHGrid()->getInvCellSize(level);
567  const int xs = static_cast<int>(std::floor(
568  (obj->getPosition().X - obj->getMaxInteractionRadius()) * inv_size - 0.5));
569  const int xe = static_cast<int>(std::floor(
570  (obj->getPosition().X + obj->getMaxInteractionRadius()) * inv_size + 0.5));
571  const int ys = static_cast<int>(std::floor(
572  (obj->getPosition().Y - obj->getMaxInteractionRadius()) * inv_size - 0.5));
573  const int ye = static_cast<int>(std::floor(
574  (obj->getPosition().Y + obj->getMaxInteractionRadius()) * inv_size + 0.5));
575  const int zs = static_cast<int>(std::floor(
576  (obj->getPosition().Z - obj->getMaxInteractionRadius()) * inv_size - 0.5));
577  const int ze = static_cast<int>(std::floor(
578  (obj->getPosition().Z + obj->getMaxInteractionRadius()) * inv_size + 0.5));
579 
580  logger(VERBOSE, "Level = % grid cells [%,%] x [%,%] x [%,%]", level, xs, xe, ys, ye, zs, ze);
581  for (int x = xs; x <= xe; ++x)
582  {
583  for (int y = ys; y <= ye; ++y)
584  {
585  for (int z = zs; z <= ze; ++z)
586  {
587  // Loop through all objects in the bucket to find nearby objects
588  const unsigned int bucket = getHGrid()->computeHashBucketIndex(x, y, z, level);
590  while (p != nullptr)
591  {
592  if (p->getHGridCell().equals(x, y, z, level))
593  {
594  if (areInContact(obj, p))
595  {
596  particlesInContact.push_back(p);
597  }
598  }
599  p = p->getHGridNextObject();
600  }
601  }
602  }
603  }
604  } //end for level
605 
606  return particlesInContact;
607 }
const HGridCell & getHGridCell() const
Definition: BaseParticle.h:643
bool equals(int x, int y, int z, unsigned int level) const
Checks if the given (x,y,z,level) is the same as the ones in this cell.
Definition: HGridCell.h:39
const Vec3D & getPosition() const
Returns the position of this BaseInteractable.
Mdouble X
the vector components
Definition: Vector.h:65
bool areInContact(const BaseParticle *pI, const BaseParticle *pJ) const
Checks if two particle are in contact or is there any positive overlap.
Definition: DPMBase.cc:1511
Logger< MERCURY_LOGLEVEL > logger("MercuryKernel")
double Mdouble
Definition: GeneralDefine.h:34
Mdouble getMaxInteractionRadius() const
Returns the particle's interaction radius, which might be different from radius_ (e.g., when dealing with wet particles)
Definition: BaseParticle.h:359
int getOccupiedLevelsMask() const
Gets the integer that represents which levels are occupied.
Definition: HGrid.h:213
Mdouble Y
Definition: Vector.h:65
void hGridRebuild()
This sets up the parameters required for the contact model.
Definition: MercuryBase.cc:203
HGrid * getHGrid()
Gets the HGrid used by this problem.
Definition: MercuryBase.h:311
unsigned long getNumberOfLevels() const
Gets the number of levels of this HGrid.
Definition: HGrid.h:206
const BaseParticle * getFirstBaseParticleInBucket(unsigned int i) const
Gets the first BaseParticle in the given bucket, const version.
Definition: HGrid.h:162
unsigned int computeHashBucketIndex(int x, int y, int z, unsigned int l) const
Computes hash bucket index in range [0, NUM_BUCKETS-1] for a 3D domain.
Definition: HGrid.h:76
BaseParticle * getHGridNextObject() const
Returns pointer to next object in particle's HGrid level & cell.
Definition: BaseParticle.h:242
Mdouble Z
Definition: Vector.h:65
double getInvCellSize(unsigned int i) const
Gets 1/cellSize for the cells on level i.
Definition: HGrid.h:178
void Mercury3D::hGridFindParticlesWithTargetCell ( int  x,
int  y,
int  z,
unsigned int  l,
BaseParticle obj,
std::vector< BaseParticle * > &  list 
)
protected

Finds particles within target cell and stores them in a list.

Definition at line 142 of file Mercury3D.cc.

References HGrid::computeHashBucketIndex(), HGridCell::equals(), HGrid::getFirstBaseParticleInBucket(), MercuryBase::getHGrid(), BaseParticle::getHGridCell(), and BaseParticle::getHGridNextObject().

Referenced by hGridGetInteractingParticleList().

144 {
145  HGrid* const hgrid = getHGrid();
146 
147  // Calculate the bucket
148  const unsigned int bucket = hgrid->computeHashBucketIndex(x, y, z, l);
149 
150  // Loop through all objects in the bucket to find nearby objects
151  BaseParticle* p = hgrid->getFirstBaseParticleInBucket(bucket);
152  while (p != nullptr)
153  {
154  if (p->getHGridCell().equals(x, y, z, l))
155  {
156  list.push_back(p);
157  }
158  p = p->getHGridNextObject();
159  }
160 }
const HGridCell & getHGridCell() const
Definition: BaseParticle.h:643
bool equals(int x, int y, int z, unsigned int level) const
Checks if the given (x,y,z,level) is the same as the ones in this cell.
Definition: HGridCell.h:39
In the HGrid class, here all information about the HGrid is stored.
Definition: HGrid.h:42
HGrid * getHGrid()
Gets the HGrid used by this problem.
Definition: MercuryBase.h:311
const BaseParticle * getFirstBaseParticleInBucket(unsigned int i) const
Gets the first BaseParticle in the given bucket, const version.
Definition: HGrid.h:162
unsigned int computeHashBucketIndex(int x, int y, int z, unsigned int l) const
Computes hash bucket index in range [0, NUM_BUCKETS-1] for a 3D domain.
Definition: HGrid.h:76
BaseParticle * getHGridNextObject() const
Returns pointer to next object in particle's HGrid level & cell.
Definition: BaseParticle.h:242
void Mercury3D::hGridGetInteractingParticleList ( BaseParticle obj,
std::vector< BaseParticle * > &  list 
)
overrideprotectedvirtual

Obtains all neighbour particles of a given object, obtained from the hgrid.

Bug:
find out why this is necessary; if this is not there, the code sometimes segfaults.

Reimplemented from DPMBase.

Definition at line 162 of file Mercury3D.cc.

References DEBUG, MercuryBase::getHGrid(), BaseParticle::getHGridLevel(), HGrid::getInvCellSize(), BaseParticle::getMaxInteractionRadius(), HGrid::getNumberOfLevels(), HGrid::getOccupiedLevelsMask(), BaseInteractable::getPosition(), hGridFindParticlesWithTargetCell(), MercuryBase::hGridNeedsRebuilding(), MercuryBase::hGridRebuild(), logger, Vec3D::X, Vec3D::Y, and Vec3D::Z.

163 {
164  HGrid* hgrid = getHGrid();
165 
167  if (hGridNeedsRebuilding())
168  {
169  hGridRebuild();
170  hgrid = getHGrid();
171  }
172  logger(DEBUG, "hgrid %, object %", hgrid, obj);
173  int occupiedLevelsMask = hgrid->getOccupiedLevelsMask() >> obj->getHGridLevel();
174  for (unsigned int level = 0; level < hgrid->getNumberOfLevels(); level++)
175  {
176  // If no objects in rest of grid, stop now
177  if (occupiedLevelsMask == 0)
178  {
179  break;
180  }
181 
182  // If no objects at this level, go on to the next level
183  if ((occupiedLevelsMask & 1) == 0)
184  {
185  continue;
186  }
187 
188  const Mdouble inv_size = hgrid->getInvCellSize(level);
189  const int xs = static_cast<int>(std::floor(
190  (obj->getPosition().X - obj->getMaxInteractionRadius()) * inv_size - 0.5));
191  const int xe = static_cast<int>(std::floor(
192  (obj->getPosition().X + obj->getMaxInteractionRadius()) * inv_size + 0.5));
193  const int ys = static_cast<int>(std::floor(
194  (obj->getPosition().Y - obj->getMaxInteractionRadius()) * inv_size - 0.5));
195  const int ye = static_cast<int>(std::floor(
196  (obj->getPosition().Y + obj->getMaxInteractionRadius()) * inv_size + 0.5));
197  const int zs = static_cast<int>(std::floor(
198  (obj->getPosition().Z - obj->getMaxInteractionRadius()) * inv_size - 0.5));
199  const int ze = static_cast<int>(std::floor(
200  (obj->getPosition().Z + obj->getMaxInteractionRadius()) * inv_size + 0.5));
201  for (int x = xs; x <= xe; ++x)
202  {
203  for (int y = ys; y <= ye; ++y)
204  {
205  for (int z = zs; z <= ze; ++z)
206  {
207  hGridFindParticlesWithTargetCell(x, y, z, level, obj, list);
208  }
209  }
210  }
211  }
212 }
const Vec3D & getPosition() const
Returns the position of this BaseInteractable.
Mdouble X
the vector components
Definition: Vector.h:65
bool hGridNeedsRebuilding()
Gets if the HGrid needs rebuilding before anything else happens.
Definition: MercuryBase.cc:490
Logger< MERCURY_LOGLEVEL > logger("MercuryKernel")
double Mdouble
Definition: GeneralDefine.h:34
Mdouble getMaxInteractionRadius() const
Returns the particle's interaction radius, which might be different from radius_ (e.g., when dealing with wet particles)
Definition: BaseParticle.h:359
int getOccupiedLevelsMask() const
Gets the integer that represents which levels are occupied.
Definition: HGrid.h:213
In the HGrid class, here all information about the HGrid is stored.
Definition: HGrid.h:42
Mdouble Y
Definition: Vector.h:65
void hGridRebuild()
This sets up the parameters required for the contact model.
Definition: MercuryBase.cc:203
HGrid * getHGrid()
Gets the HGrid used by this problem.
Definition: MercuryBase.h:311
unsigned long getNumberOfLevels() const
Gets the number of levels of this HGrid.
Definition: HGrid.h:206
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.
Definition: Mercury3D.cc:142
unsigned int getHGridLevel() const
Returns particle's HGrid level.
Definition: BaseParticle.h:234
Mdouble Z
Definition: Vector.h:65
double getInvCellSize(unsigned int i) const
Gets 1/cellSize for the cells on level i.
Definition: HGrid.h:178
bool Mercury3D::hGridHasContactsInTargetCell ( int  x,
int  y,
int  z,
unsigned int  l,
const BaseParticle obj 
) const
protected

Tests if the BaseParticle has contacts with other Particles in the target cell.

Parameters
[in]xThe coordinate of the target cell in x direction.
[in]yThe coordinate of the target cell in y direction.
[in]zThe coordinate of the target cell in z direction.
[in]lThe level of the HGrid of the target cell.
[in]objA pointer to the BaseParticle which is checked for contacts.

Tests if there are any collisions between given BaseParticle and particles in cell (x, y, z, l).

Definition at line 451 of file Mercury3D.cc.

References DPMBase::areInContact(), HGrid::computeHashBucketIndex(), HGridCell::equals(), HGrid::getFirstBaseParticleInBucket(), MercuryBase::getHGrid(), BaseParticle::getHGridCell(), and BaseParticle::getHGridNextObject().

452 {
453  // Loop through all objects in the bucket to find nearby objects
454  const unsigned int bucket = getHGrid()->computeHashBucketIndex(x, y, z, l);
455 
456  const BaseParticle* p = getHGrid()->getFirstBaseParticleInBucket(bucket);
457  while (p != nullptr)
458  {
459  if (p->getHGridCell().equals(x, y, z, l))
460  {
461  if (areInContact(obj, p))
462  {
463  return true;
464  }
465  }
466  p = p->getHGridNextObject();
467  }
468  return false;
469 }
const HGridCell & getHGridCell() const
Definition: BaseParticle.h:643
bool equals(int x, int y, int z, unsigned int level) const
Checks if the given (x,y,z,level) is the same as the ones in this cell.
Definition: HGridCell.h:39
bool areInContact(const BaseParticle *pI, const BaseParticle *pJ) const
Checks if two particle are in contact or is there any positive overlap.
Definition: DPMBase.cc:1511
HGrid * getHGrid()
Gets the HGrid used by this problem.
Definition: MercuryBase.h:311
const BaseParticle * getFirstBaseParticleInBucket(unsigned int i) const
Gets the first BaseParticle in the given bucket, const version.
Definition: HGrid.h:162
unsigned int computeHashBucketIndex(int x, int y, int z, unsigned int l) const
Computes hash bucket index in range [0, NUM_BUCKETS-1] for a 3D domain.
Definition: HGrid.h:76
BaseParticle * getHGridNextObject() const
Returns pointer to next object in particle's HGrid level & cell.
Definition: BaseParticle.h:242
bool Mercury3D::hGridHasParticleContacts ( const BaseParticle obj)
overrideprotectedvirtual

Tests if a BaseParticle has any contacts in the HGrid.

Parameters
[in]objA pointer to the BaseParticle that is tested for contacts.

Tests if there are any collisions between the given BaseParticle and all other particles in the HGrid. Do this by going through all levels, find if there is a collision in any of the levels in any cell of the HGrid.

Implements MercuryBase.

Definition at line 479 of file Mercury3D.cc.

480 {
481  if (getHGrid() == nullptr || getHGrid()->getNeedsRebuilding())
482  {
483  logger(INFO, "HGrid needs rebuilding for \"bool Mercury3D::hGridHasParticleContacts(BaseParticle *obj)\"");
484  hGridRebuild();
485  }
486 
487  int occupiedLevelsMask = getHGrid()->getOccupiedLevelsMask();
488 
489  for (unsigned int level = 0; level < getHGrid()->getNumberOfLevels(); occupiedLevelsMask >>= 1, level++)
490  {
491  // If no objects in rest of grid, stop now
492  if (occupiedLevelsMask == 0)
493  {
494  logger(VERBOSE, "Level % and higher levels are empty", level);
495  break;
496  }
497 
498  // If no objects at this level, go on to the next level
499  if ((occupiedLevelsMask & 1) == 0)
500  {
501  logger(VERBOSE, "Level % is empty", level);
502  continue;
503  }
504 
505  const Mdouble inv_size = getHGrid()->getInvCellSize(level);
506  const int xs = static_cast<int>(std::floor(
507  (obj->getPosition().X - obj->getMaxInteractionRadius()) * inv_size - 0.5));
508  const int xe = static_cast<int>(std::floor(
509  (obj->getPosition().X + obj->getMaxInteractionRadius()) * inv_size + 0.5));
510  const int ys = static_cast<int>(std::floor(
511  (obj->getPosition().Y - obj->getMaxInteractionRadius()) * inv_size - 0.5));
512  const int ye = static_cast<int>(std::floor(
513  (obj->getPosition().Y + obj->getMaxInteractionRadius()) * inv_size + 0.5));
514  const int zs = static_cast<int>(std::floor(
515  (obj->getPosition().Z - obj->getMaxInteractionRadius()) * inv_size - 0.5));
516  const int ze = static_cast<int>(std::floor(
517  (obj->getPosition().Z + obj->getMaxInteractionRadius()) * inv_size + 0.5));
518 
519  logger(VERBOSE, "Level = % grid cells [%,%] x [%,%] x [%,%]", level, xs, xe, ys, ye, zs, ze);
520  for (int x = xs; x <= xe; ++x)
521  {
522  for (int y = ys; y <= ye; ++y)
523  {
524  for (int z = zs; z <= ze; ++z)
525  {
526  if (hGridHasContactsInTargetCell(x, y, z, level, obj))
527  {
528  return true;
529  }
530  }
531  }
532  }
533  } //end for level
534 
535  return false;
536 }
const Vec3D & getPosition() const
Returns the position of this BaseInteractable.
Mdouble X
the vector components
Definition: Vector.h:65
Logger< MERCURY_LOGLEVEL > logger("MercuryKernel")
double Mdouble
Definition: GeneralDefine.h:34
Mdouble getMaxInteractionRadius() const
Returns the particle's interaction radius, which might be different from radius_ (e.g., when dealing with wet particles)
Definition: BaseParticle.h:359
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.
Definition: Mercury3D.cc:451
int getOccupiedLevelsMask() const
Gets the integer that represents which levels are occupied.
Definition: HGrid.h:213
Mdouble Y
Definition: Vector.h:65
void hGridRebuild()
This sets up the parameters required for the contact model.
Definition: MercuryBase.cc:203
HGrid * getHGrid()
Gets the HGrid used by this problem.
Definition: MercuryBase.h:311
unsigned long getNumberOfLevels() const
Gets the number of levels of this HGrid.
Definition: HGrid.h:206
Mdouble Z
Definition: Vector.h:65
double getInvCellSize(unsigned int i) const
Gets 1/cellSize for the cells on level i.
Definition: HGrid.h:178
void Mercury3D::hGridRemoveParticle ( BaseParticle obj)
overrideprotected

Removes a BaseParticle from the HGrid.

Parameters
[in]objA pointer to the BaseParticle that needs to be removed.

Removes the given BaseParticle from the HGrid.

Definition at line 417 of file Mercury3D.cc.

References HGrid::computeHashBucketIndex(), HGrid::getFirstBaseParticleInBucket(), MercuryBase::getHGrid(), BaseParticle::getHGridCell(), BaseParticle::getHGridNextObject(), BaseParticle::getHGridPrevObject(), HGrid::setFirstBaseParticleInBucket(), BaseParticle::setHGridNextObject(), and BaseParticle::setHGridPrevObject().

Referenced by hGridUpdateParticle().

418 {
419  HGrid* const hGrid = getHGrid();
420  if (hGrid)
421  {
422  const unsigned int bucket = hGrid->computeHashBucketIndex(obj->getHGridCell());
423  if (obj->getHGridPrevObject())
424  {
426  }
427  else
428  {
429  if (hGrid->getFirstBaseParticleInBucket(bucket) == obj)
430  {
431  hGrid->setFirstBaseParticleInBucket(bucket, obj->getHGridNextObject());
432  }
433  }
434 
435  if (obj->getHGridNextObject())
436  {
438  }
439  }
440 }
const HGridCell & getHGridCell() const
Definition: BaseParticle.h:643
void setHGridNextObject(BaseParticle *p)
Sets the pointer to the next object in the particle's HGrid cell & level.
Definition: BaseParticle.h:477
In the HGrid class, here all information about the HGrid is stored.
Definition: HGrid.h:42
void setFirstBaseParticleInBucket(unsigned int i, BaseParticle *p)
Sets the first particle in bucket i to be the given BaseParticle.
Definition: HGrid.h:117
BaseParticle * getHGridPrevObject() const
Returns pointer to previous object in particle's HGrid level & cell.
Definition: BaseParticle.h:250
void setHGridPrevObject(BaseParticle *p)
Sets the pointer to the previous object in the particle's HGrid cell & level.
Definition: BaseParticle.h:485
HGrid * getHGrid()
Gets the HGrid used by this problem.
Definition: MercuryBase.h:311
const BaseParticle * getFirstBaseParticleInBucket(unsigned int i) const
Gets the first BaseParticle in the given bucket, const version.
Definition: HGrid.h:162
unsigned int computeHashBucketIndex(int x, int y, int z, unsigned int l) const
Computes hash bucket index in range [0, NUM_BUCKETS-1] for a 3D domain.
Definition: HGrid.h:76
BaseParticle * getHGridNextObject() const
Returns pointer to next object in particle's HGrid level & cell.
Definition: BaseParticle.h:242
void Mercury3D::hGridUpdateParticle ( BaseParticle obj)
overrideprotected

Updates the cell (not the level) of a BaseParticle.

Parameters
[in]objA pointer to the BaseParticle that must be updated.

Updates the HGrid positions (x, y and z) of the given BaseParticle.

Definition at line 357 of file Mercury3D.cc.

References HGrid::computeHashBucketIndex(), HGrid::getFirstBaseParticleInBucket(), MercuryBase::getHGrid(), BaseParticle::getHGridLevel(), BaseParticle::getHGridX(), BaseParticle::getHGridY(), BaseParticle::getHGridZ(), HGrid::getInvCellSize(), BaseInteractable::getPosition(), hGridRemoveParticle(), HGrid::setFirstBaseParticleInBucket(), BaseParticle::setHGridNextObject(), BaseParticle::setHGridPrevObject(), BaseParticle::setHGridX(), BaseParticle::setHGridY(), BaseParticle::setHGridZ(), Vec3D::X, Vec3D::Y, and Vec3D::Z.

358 {
359  HGrid* const hGrid = getHGrid();
360  if (hGrid)
361  {
362  const unsigned int l = obj->getHGridLevel();
363  const Mdouble inv_size = hGrid->getInvCellSize(l);
364 
365  int x = static_cast<int>(std::floor(obj->getPosition().X * inv_size));
366  int y = static_cast<int>(std::floor(obj->getPosition().Y * inv_size));
367  int z = static_cast<int>(std::floor(obj->getPosition().Z * inv_size));
368 
369 #ifdef CONTACT_LIST_HGRID
370  if(obj->getHGridX() != x || obj->getHGridY() != y || obj->getHGridZ() != z)
371  {
372  int bucket = hGrid->computeHashBucketIndex(x, y, z, l);
373 
374  //First the object has to be removed
375  hGridRemoveParticle(obj);
376 
377  //Also remove all contact associated with it
378  getPossibleContactList().remove_ParticlePosibleContacts(obj);
379 
380  //And now reinserted
382  obj->setHGridPrevObject(nullptr);
383  if(hGrid->getFirstBaseParticleInBucket(bucket))
384  {
386  }
387  hGrid->setFirstBaseParticleInBucket(bucket,obj);
388 
389  obj->setHGridX(x);
390  obj->setHGridY(y);
391  obj->setHGridZ(z);
392  InsertObjAgainstGrid(obj);
393  }
394 #else
395  const unsigned int bucket = hGrid->computeHashBucketIndex(x, y, z, l);
396 
398  obj->setHGridPrevObject(nullptr);
399  if (hGrid->getFirstBaseParticleInBucket(bucket))
400  {
402  }
403 
404  hGrid->setFirstBaseParticleInBucket(bucket, obj);
405 
406  obj->setHGridX(x);
407  obj->setHGridY(y);
408  obj->setHGridZ(z);
409 #endif
410  }
411 }
const Vec3D & getPosition() const
Returns the position of this BaseInteractable.
Mdouble X
the vector components
Definition: Vector.h:65
void hGridRemoveParticle(BaseParticle *obj) override
Removes a BaseParticle from the HGrid.
Definition: Mercury3D.cc:417
double Mdouble
Definition: GeneralDefine.h:34
void setHGridY(const int y)
Sets the particle's HGrid cell Y-coordinate.
Definition: BaseParticle.h:454
void setHGridNextObject(BaseParticle *p)
Sets the pointer to the next object in the particle's HGrid cell & level.
Definition: BaseParticle.h:477
int getHGridY() const
Returns particle's HGrid cell Y-coordinate.
Definition: BaseParticle.h:272
void setHGridX(const int x)
Sets the particle's HGrid cell X-coordinate.
Definition: BaseParticle.h:446
In the HGrid class, here all information about the HGrid is stored.
Definition: HGrid.h:42
int getHGridZ() const
Returns particle's HGrid cell Z-coordinate.
Definition: BaseParticle.h:279
void setFirstBaseParticleInBucket(unsigned int i, BaseParticle *p)
Sets the first particle in bucket i to be the given BaseParticle.
Definition: HGrid.h:117
void setHGridZ(const int z)
Sets the particle's HGrid cell Z-coordinate.
Definition: BaseParticle.h:462
Mdouble Y
Definition: Vector.h:65
void setHGridPrevObject(BaseParticle *p)
Sets the pointer to the previous object in the particle's HGrid cell & level.
Definition: BaseParticle.h:485
HGrid * getHGrid()
Gets the HGrid used by this problem.
Definition: MercuryBase.h:311
const BaseParticle * getFirstBaseParticleInBucket(unsigned int i) const
Gets the first BaseParticle in the given bucket, const version.
Definition: HGrid.h:162
unsigned int computeHashBucketIndex(int x, int y, int z, unsigned int l) const
Computes hash bucket index in range [0, NUM_BUCKETS-1] for a 3D domain.
Definition: HGrid.h:76
unsigned int getHGridLevel() const
Returns particle's HGrid level.
Definition: BaseParticle.h:234
Mdouble Z
Definition: Vector.h:65
double getInvCellSize(unsigned int i) const
Gets 1/cellSize for the cells on level i.
Definition: HGrid.h:178
int getHGridX() const
Returns particle's HGrid cell X-coordinate.
Definition: BaseParticle.h:265

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