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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, 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 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 > get1DParametersFromRunNumber (int size_x)
 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)
 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)
 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...
 
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 (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 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)
 
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...
 
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 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...
 
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...
 
void splitDomain (DomainSplit domainSplit)
 
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 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...
 
void writePythonFileForVTKVisualisation () const
 record when the simulation started More...
 

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 Types inherited from DPMBase
enum  ReadOptions : int { ReadOptions::ReadAll, ReadOptions::ReadNoInteractions, ReadOptions::ReadNoParticlesAndInteractions }
 
enum  DomainSplit {
  DomainSplit::X, DomainSplit::Y, DomainSplit::Z, DomainSplit::XY,
  DomainSplit::XZ, DomainSplit::YZ, DomainSplit::XYZ
}
 
- 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...
 

Detailed Description

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

Definition at line 36 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:192
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:192

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 221 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.

222 {
223  HGrid* const hgrid = getHGrid();
224  const unsigned int startLevel = obj->getHGridLevel();
225 
226  if (getHGridMethod() == TOPDOWN)
227  {
228  int occupiedLevelsMask = hgrid->getOccupiedLevelsMask();
229  for (unsigned int level = 0; level <= startLevel && occupiedLevelsMask != 0; occupiedLevelsMask >>= 1, level++)
230  {
231  // If no objects at this level, go on to the next level
232  if ((occupiedLevelsMask & 1) == 0)
233  {
234  continue;
235  }
236 
237  if (level == startLevel)
238  {
239  const int x = obj->getHGridX();
240  const int y = obj->getHGridY();
241  const int z = obj->getHGridZ();
242 
243  hGridFindContactsWithinTargetCell(x, y, z, level);
244  hGridFindContactsWithTargetCell(x + 1, y - 1, z, level, obj);
245  hGridFindContactsWithTargetCell(x + 1, y, z, level, obj);
246  hGridFindContactsWithTargetCell(x + 1, y + 1, z, level, obj);
247  hGridFindContactsWithTargetCell(x + 1, y - 1, z + 1, level, obj);
248  hGridFindContactsWithTargetCell(x + 1, y, z + 1, level, obj);
249  hGridFindContactsWithTargetCell(x + 1, y + 1, z + 1, level, obj);
250  hGridFindContactsWithTargetCell(x + 1, y - 1, z - 1, level, obj);
251  hGridFindContactsWithTargetCell(x + 1, y, z - 1, level, obj);
252  hGridFindContactsWithTargetCell(x + 1, y + 1, z - 1, level, obj);
253  hGridFindContactsWithTargetCell(x, y + 1, z, level, obj);
254  hGridFindContactsWithTargetCell(x, y, z - 1, level, obj);
255  hGridFindContactsWithTargetCell(x, y + 1, z - 1, level, obj);
256  hGridFindContactsWithTargetCell(x, y + 1, z + 1, level, obj);
257  }
258  else
259  {
260  const Mdouble inv_size = getHGrid()->getInvCellSize(level);
261  const int xs = static_cast<int>(std::floor(
262  (obj->getPosition().X - obj->getMaxInteractionRadius()) * inv_size - 0.5));
263  const int xe = static_cast<int>(std::floor(
264  (obj->getPosition().X + obj->getMaxInteractionRadius()) * inv_size + 0.5));
265  const int ys = static_cast<int>(std::floor(
266  (obj->getPosition().Y - obj->getMaxInteractionRadius()) * inv_size - 0.5));
267  const int ye = static_cast<int>(std::floor(
268  (obj->getPosition().Y + obj->getMaxInteractionRadius()) * inv_size + 0.5));
269  const int zs = static_cast<int>(std::floor(
270  (obj->getPosition().Z - obj->getMaxInteractionRadius()) * inv_size - 0.5));
271  const int ze = static_cast<int>(std::floor(
272  (obj->getPosition().Z + obj->getMaxInteractionRadius()) * inv_size + 0.5));
273  for (int x = xs; x <= xe; ++x)
274  {
275  for (int y = ys; y <= ye; ++y)
276  {
277  for (int z = zs; z <= ze; ++z)
278  {
279  hGridFindContactsWithTargetCell(x, y, z, level, obj);
280  }
281  }
282  }
283  }
284  }
285  }
286  else
287  {
288  int occupiedLevelsMask = hgrid->getOccupiedLevelsMask() >> obj->getHGridLevel();
289  for (unsigned int level = startLevel; level < hgrid->getNumberOfLevels(); occupiedLevelsMask >>= 1, level++)
290  {
291  // If no objects in rest of grid, stop now
292  if (occupiedLevelsMask == 0)
293  {
294  break;
295  }
296 
297  // If no objects at this level, go on to the next level
298  if ((occupiedLevelsMask & 1) == 0)
299  {
300  continue;
301  }
302 
303  if (level == startLevel)
304  {
305  const int x = obj->getHGridX();
306  const int y = obj->getHGridY();
307  const int z = obj->getHGridZ();
308 
309  hGridFindContactsWithinTargetCell(x, y, z, level);
310  hGridFindContactsWithTargetCell(x + 1, y - 1, z, level, obj);
311  hGridFindContactsWithTargetCell(x + 1, y, z, level, obj);
312  hGridFindContactsWithTargetCell(x + 1, y + 1, z, level, obj);
313  hGridFindContactsWithTargetCell(x + 1, y - 1, z + 1, level, obj);
314  hGridFindContactsWithTargetCell(x + 1, y, z + 1, level, obj);
315  hGridFindContactsWithTargetCell(x + 1, y + 1, z + 1, level, obj);
316  hGridFindContactsWithTargetCell(x + 1, y - 1, z - 1, level, obj);
317  hGridFindContactsWithTargetCell(x + 1, y, z - 1, level, obj);
318  hGridFindContactsWithTargetCell(x + 1, y + 1, z - 1, level, obj);
319  hGridFindContactsWithTargetCell(x, y + 1, z, level, obj);
320  hGridFindContactsWithTargetCell(x, y, z - 1, level, obj);
321  hGridFindContactsWithTargetCell(x, y + 1, z - 1, level, obj);
322  hGridFindContactsWithTargetCell(x, y + 1, z + 1, level, obj);
323  }
324  else
325  {
326  const Mdouble inv_size = hgrid->getInvCellSize(level);
327  const int xs = static_cast<int>(std::floor(
328  (obj->getPosition().X - obj->getMaxInteractionRadius()) * inv_size - 0.5));
329  const int xe = static_cast<int>(std::floor(
330  (obj->getPosition().X + obj->getMaxInteractionRadius()) * inv_size + 0.5));
331  const int ys = static_cast<int>(std::floor(
332  (obj->getPosition().Y - obj->getMaxInteractionRadius()) * inv_size - 0.5));
333  const int ye = static_cast<int>(std::floor(
334  (obj->getPosition().Y + obj->getMaxInteractionRadius()) * inv_size + 0.5));
335  const int zs = static_cast<int>(std::floor(
336  (obj->getPosition().Z - obj->getMaxInteractionRadius()) * inv_size - 0.5));
337  const int ze = static_cast<int>(std::floor(
338  (obj->getPosition().Z + obj->getMaxInteractionRadius()) * inv_size + 0.5));
339  for (int x = xs; x <= xe; ++x)
340  {
341  for (int y = ys; y <= ye; ++y)
342  {
343  for (int z = zs; z <= ze; ++z)
344  {
345  hGridFindContactsWithTargetCell(x, y, z, level, obj);
346  }
347  }
348  }
349  }
350  }
351  }
352 }
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 611 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.

612 {
613 
614  // if wall is not local, use the non-hGrid version for finding wall contacts
615  Vec3D min, max;
616  if (w->isLocal(min, max)==false)
617  {
618  return DPMBase::computeWallForces(w);
619  }
620 
621  //compute forces for all particles that are neither fixed or ghosts
622  if (getHGrid() == nullptr || getHGrid()->getNeedsRebuilding())
623  {
624  logger(INFO, "HGrid needs rebuilding for \"bool Mercury3D::hGridHasParticleContacts(BaseParticle *obj)\"");
625  hGridRebuild();
626  }
627 
628  HGrid* const hGrid = getHGrid();
629 
630  int occupiedLevelsMask = hGrid->getOccupiedLevelsMask();
631 
632  for (unsigned int level = 0; level < hGrid->getNumberOfLevels(); occupiedLevelsMask >>= 1, level++)
633  {
634  // If no objects in rest of grid, stop now
635  if (occupiedLevelsMask == 0)
636  {
637  logger(VERBOSE, "Level % and higher levels are empty", level);
638  break;
639  }
640 
641  // If no objects at this level, go on to the next level
642  if ((occupiedLevelsMask & 1) == 0)
643  {
644  logger(VERBOSE, "Level % is empty", level);
645  continue;
646  }
647 
648  const Mdouble inv_size = hGrid->getInvCellSize(level);
649  const int xs = static_cast<int>(std::floor(min.X * inv_size - 0.5));
650  const int xe = static_cast<int>(std::floor(max.X * inv_size + 0.5));
651  const int ys = static_cast<int>(std::floor(min.Y * inv_size - 0.5));
652  const int ye = static_cast<int>(std::floor(max.Y * inv_size + 0.5));
653  const int zs = static_cast<int>(std::floor(min.Z * inv_size - 0.5));
654  const int ze = static_cast<int>(std::floor(max.Z * inv_size + 0.5));
655  //logger(INFO, "Level % grid cells [%,%] x [%,%] x [%,%]", level, xs, xe, ys, ye, zs, ze);
656 
657  for (int x = xs; x <= xe; ++x)
658  {
659  for (int y = ys; y <= ye; ++y)
660  {
661  for (int z = zs; z <= ze; ++z)
662  {
663  // Loop through all objects in the bucket to find nearby objects
664  const unsigned int bucket = hGrid->computeHashBucketIndex(x, y, z, level);
665  BaseParticle* p = hGrid->getFirstBaseParticleInBucket(bucket);
666  while (p != nullptr)
667  {
668  if (!p->isFixed() && p->getPeriodicFromParticle() == nullptr &&
669  p->getHGridCell().equals(x, y, z, level))
670  {
671  //logger(INFO, "t % p % Size % level % cells % % %", getNumberOfTimeSteps(), p->getIndex(), hGrid->getCellSize(level), level, x,y,z);
673  //w->computeForces(p);
674  }
675  p = p->getHGridNextObject();
676  }
677  }
678  }
679  }
680  } //end for level
681 }
const HGridCell & getHGridCell() const
Definition: BaseParticle.h:645
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:5088
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:3076
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:1377
void setSystemDimensions(unsigned int newDim)
Sets the system dimensionality.
Definition: DPMBase.cc:1346
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:645
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:3001
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(), Vec3D::getDistanceSquared(), HGrid::getFirstBaseParticleInBucket(), MercuryBase::getHGrid(), BaseParticle::getHGridCell(), BaseParticle::getHGridNextObject(), BaseParticle::getMaxInteractionRadius(), BaseInteractable::getPosition(), logger, and mathsFunc::square().

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  if (Vec3D::getDistanceSquared(p->getPosition(),obj->getPosition()) < mathsFunc::square(p->getMaxInteractionRadius()+obj->getMaxInteractionRadius()))
136  computeInternalForce(obj, p);
137  }
138  }
139 }
const HGridCell & getHGridCell() const
Definition: BaseParticle.h:645
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.
Logger< MERCURY_LOGLEVEL > logger("MercuryKernel")
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
In the HGrid class, here all information about the HGrid is stored.
Definition: HGrid.h:42
static Mdouble getDistanceSquared(const Vec3D &a, const Vec3D &b)
Calculates the squared distance between two Vec3D: .
Definition: Vector.h:295
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:3001
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
T square(const T val)
squares a number
Definition: ExtendedMath.h:104
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 540 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.

541 {
542  if (getHGrid() == nullptr || getHGrid()->getNeedsRebuilding())
543  {
544  logger(INFO, "HGrid needs rebuilding for \"bool Mercury3D::hGridHasParticleContacts(BaseParticle *obj)\"");
545  hGridRebuild();
546  }
547 
548  int occupiedLevelsMask = getHGrid()->getOccupiedLevelsMask();
549 
550  std::vector<BaseParticle*> particlesInContact;
551 
552  for (unsigned int level = 0; level < getHGrid()->getNumberOfLevels(); occupiedLevelsMask >>= 1, level++)
553  {
554  // If no objects in rest of grid, stop now
555  if (occupiedLevelsMask == 0)
556  {
557  logger(VERBOSE, "Level % and higher levels are empty", level);
558  break;
559  }
560 
561  // If no objects at this level, go on to the next level
562  if ((occupiedLevelsMask & 1) == 0)
563  {
564  logger(VERBOSE, "Level % is empty", level);
565  continue;
566  }
567 
568  const Mdouble inv_size = getHGrid()->getInvCellSize(level);
569  const int xs = static_cast<int>(std::floor(
570  (obj->getPosition().X - obj->getMaxInteractionRadius()) * inv_size - 0.5));
571  const int xe = static_cast<int>(std::floor(
572  (obj->getPosition().X + obj->getMaxInteractionRadius()) * inv_size + 0.5));
573  const int ys = static_cast<int>(std::floor(
574  (obj->getPosition().Y - obj->getMaxInteractionRadius()) * inv_size - 0.5));
575  const int ye = static_cast<int>(std::floor(
576  (obj->getPosition().Y + obj->getMaxInteractionRadius()) * inv_size + 0.5));
577  const int zs = static_cast<int>(std::floor(
578  (obj->getPosition().Z - obj->getMaxInteractionRadius()) * inv_size - 0.5));
579  const int ze = static_cast<int>(std::floor(
580  (obj->getPosition().Z + obj->getMaxInteractionRadius()) * inv_size + 0.5));
581 
582  logger(VERBOSE, "Level = % grid cells [%,%] x [%,%] x [%,%]", level, xs, xe, ys, ye, zs, ze);
583  for (int x = xs; x <= xe; ++x)
584  {
585  for (int y = ys; y <= ye; ++y)
586  {
587  for (int z = zs; z <= ze; ++z)
588  {
589  // Loop through all objects in the bucket to find nearby objects
590  const unsigned int bucket = getHGrid()->computeHashBucketIndex(x, y, z, level);
592  while (p != nullptr)
593  {
594  if (p->getHGridCell().equals(x, y, z, level))
595  {
596  if (areInContact(obj, p))
597  {
598  particlesInContact.push_back(p);
599  }
600  }
601  p = p->getHGridNextObject();
602  }
603  }
604  }
605  }
606  } //end for level
607 
608  return particlesInContact;
609 }
const HGridCell & getHGridCell() const
Definition: BaseParticle.h:645
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:1590
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 143 of file Mercury3D.cc.

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

Referenced by hGridGetInteractingParticleList().

145 {
146  HGrid* const hgrid = getHGrid();
147 
148  // Calculate the bucket
149  const unsigned int bucket = hgrid->computeHashBucketIndex(x, y, z, l);
150 
151  // Loop through all objects in the bucket to find nearby objects
152  BaseParticle* p = hgrid->getFirstBaseParticleInBucket(bucket);
153  while (p != nullptr)
154  {
155  if (p->getHGridCell().equals(x, y, z, l))
156  {
157  list.push_back(p);
158  }
159  p = p->getHGridNextObject();
160  }
161 }
const HGridCell & getHGridCell() const
Definition: BaseParticle.h:645
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 163 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.

164 {
165  HGrid* hgrid = getHGrid();
166 
168  if (hGridNeedsRebuilding())
169  {
170  hGridRebuild();
171  hgrid = getHGrid();
172  }
173  logger(DEBUG, "hgrid %, object %", hgrid, obj);
174  int occupiedLevelsMask = hgrid->getOccupiedLevelsMask() >> obj->getHGridLevel();
175  for (unsigned int level = 0; level < hgrid->getNumberOfLevels(); level++)
176  {
177  // If no objects in rest of grid, stop now
178  if (occupiedLevelsMask == 0)
179  {
180  break;
181  }
182 
183  // If no objects at this level, go on to the next level
184  if ((occupiedLevelsMask & 1) == 0)
185  {
186  continue;
187  }
188 
189  const Mdouble inv_size = hgrid->getInvCellSize(level);
190  const int xs = static_cast<int>(std::floor(
191  (obj->getPosition().X - obj->getMaxInteractionRadius()) * inv_size - 0.5));
192  const int xe = static_cast<int>(std::floor(
193  (obj->getPosition().X + obj->getMaxInteractionRadius()) * inv_size + 0.5));
194  const int ys = static_cast<int>(std::floor(
195  (obj->getPosition().Y - obj->getMaxInteractionRadius()) * inv_size - 0.5));
196  const int ye = static_cast<int>(std::floor(
197  (obj->getPosition().Y + obj->getMaxInteractionRadius()) * inv_size + 0.5));
198  const int zs = static_cast<int>(std::floor(
199  (obj->getPosition().Z - obj->getMaxInteractionRadius()) * inv_size - 0.5));
200  const int ze = static_cast<int>(std::floor(
201  (obj->getPosition().Z + obj->getMaxInteractionRadius()) * inv_size + 0.5));
202  for (int x = xs; x <= xe; ++x)
203  {
204  for (int y = ys; y <= ye; ++y)
205  {
206  for (int z = zs; z <= ze; ++z)
207  {
208  hGridFindParticlesWithTargetCell(x, y, z, level, obj, list);
209  }
210  }
211  }
212  }
213 }
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:143
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 452 of file Mercury3D.cc.

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

453 {
454  // Loop through all objects in the bucket to find nearby objects
455  const unsigned int bucket = getHGrid()->computeHashBucketIndex(x, y, z, l);
456 
457  const BaseParticle* p = getHGrid()->getFirstBaseParticleInBucket(bucket);
458  while (p != nullptr)
459  {
460  if (p->getHGridCell().equals(x, y, z, l))
461  {
462  if (areInContact(obj, p))
463  {
464  return true;
465  }
466  }
467  //std::cout << "HERE!" << std::endl;
468  p = p->getHGridNextObject();
469  }
470  return false;
471 }
const HGridCell & getHGridCell() const
Definition: BaseParticle.h:645
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:1590
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 481 of file Mercury3D.cc.

482 {
483  if (getHGrid() == nullptr || getHGrid()->getNeedsRebuilding())
484  {
485  logger(INFO, "HGrid needs rebuilding for \"bool Mercury3D::hGridHasParticleContacts(BaseParticle *obj)\"");
486  hGridRebuild();
487  }
488 
489  int occupiedLevelsMask = getHGrid()->getOccupiedLevelsMask();
490 
491  for (unsigned int level = 0; level < getHGrid()->getNumberOfLevels(); occupiedLevelsMask >>= 1, level++)
492  {
493  // If no objects in rest of grid, stop now
494  if (occupiedLevelsMask == 0)
495  {
496  logger(VERBOSE, "Level % and higher levels are empty", level);
497  break;
498  }
499 
500  // If no objects at this level, go on to the next level
501  if ((occupiedLevelsMask & 1) == 0)
502  {
503  logger(VERBOSE, "Level % is empty", level);
504  continue;
505  }
506 
507  const Mdouble inv_size = getHGrid()->getInvCellSize(level);
508  const int xs = static_cast<int>(std::floor(
509  (obj->getPosition().X - obj->getMaxInteractionRadius()) * inv_size - 0.5));
510  const int xe = static_cast<int>(std::floor(
511  (obj->getPosition().X + obj->getMaxInteractionRadius()) * inv_size + 0.5));
512  const int ys = static_cast<int>(std::floor(
513  (obj->getPosition().Y - obj->getMaxInteractionRadius()) * inv_size - 0.5));
514  const int ye = static_cast<int>(std::floor(
515  (obj->getPosition().Y + obj->getMaxInteractionRadius()) * inv_size + 0.5));
516  const int zs = static_cast<int>(std::floor(
517  (obj->getPosition().Z - obj->getMaxInteractionRadius()) * inv_size - 0.5));
518  const int ze = static_cast<int>(std::floor(
519  (obj->getPosition().Z + obj->getMaxInteractionRadius()) * inv_size + 0.5));
520 
521  logger(VERBOSE, "Level = % grid cells [%,%] x [%,%] x [%,%]", level, xs, xe, ys, ye, zs, ze);
522  for (int x = xs; x <= xe; ++x)
523  {
524  for (int y = ys; y <= ye; ++y)
525  {
526  for (int z = zs; z <= ze; ++z)
527  {
528  if (hGridHasContactsInTargetCell(x, y, z, level, obj))
529  {
530  return true;
531  }
532  }
533  }
534  }
535  } //end for level
536 
537  return false;
538 }
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:452
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 418 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().

419 {
420  HGrid* const hGrid = getHGrid();
421  if (hGrid)
422  {
423  const unsigned int bucket = hGrid->computeHashBucketIndex(obj->getHGridCell());
424  if (obj->getHGridPrevObject())
425  {
427  }
428  else
429  {
430  if (hGrid->getFirstBaseParticleInBucket(bucket) == obj)
431  {
432  hGrid->setFirstBaseParticleInBucket(bucket, obj->getHGridNextObject());
433  }
434  }
435 
436  if (obj->getHGridNextObject())
437  {
439  }
440  }
441 }
const HGridCell & getHGridCell() const
Definition: BaseParticle.h:645
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 358 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.

359 {
360  HGrid* const hGrid = getHGrid();
361  if (hGrid)
362  {
363  const unsigned int l = obj->getHGridLevel();
364  const Mdouble inv_size = hGrid->getInvCellSize(l);
365 
366  int x = static_cast<int>(std::floor(obj->getPosition().X * inv_size));
367  int y = static_cast<int>(std::floor(obj->getPosition().Y * inv_size));
368  int z = static_cast<int>(std::floor(obj->getPosition().Z * inv_size));
369 
370 #ifdef CONTACT_LIST_HGRID
371  if(obj->getHGridX() != x || obj->getHGridY() != y || obj->getHGridZ() != z)
372  {
373  int bucket = hGrid->computeHashBucketIndex(x, y, z, l);
374 
375  //First the object has to be removed
376  hGridRemoveParticle(obj);
377 
378  //Also remove all contact associated with it
379  getPossibleContactList().remove_ParticlePosibleContacts(obj);
380 
381  //And now reinserted
383  obj->setHGridPrevObject(nullptr);
384  if(hGrid->getFirstBaseParticleInBucket(bucket))
385  {
387  }
388  hGrid->setFirstBaseParticleInBucket(bucket,obj);
389 
390  obj->setHGridX(x);
391  obj->setHGridY(y);
392  obj->setHGridZ(z);
393  InsertObjAgainstGrid(obj);
394  }
395 #else
396  const unsigned int bucket = hGrid->computeHashBucketIndex(x, y, z, l);
397 
399  obj->setHGridPrevObject(nullptr);
400  if (hGrid->getFirstBaseParticleInBucket(bucket))
401  {
403  }
404 
405  hGrid->setFirstBaseParticleInBucket(bucket, obj);
406 
407  obj->setHGridX(x);
408  obj->setHGridY(y);
409  obj->setHGridZ(z);
410 #endif
411  }
412 }
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:418
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: