MercuryDPM  Trunk
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
MercuryBase Class Referenceabstract

This is the base class for both Mercury2D and Mercury3D. Note the actually abstract grid is defined in the class Grid defined below. More...

#include <MercuryBase.h>

+ Inheritance diagram for MercuryBase:

Public Member Functions

 MercuryBase ()
 This is the default constructor. It sets sensible defaults. More...
 
 ~MercuryBase () override
 This is the default destructor. More...
 
 MercuryBase (const MercuryBase &mercuryBase)
 Copy-constructor. More...
 
void constructor ()
 This is the actual constructor, it is called do both constructors above. More...
 
void hGridActionsBeforeTimeLoop () override
 This sets up the broad phase information, has to be done at this stage because it requires the particle size. More...
 
void hGridActionsBeforeTimeStep () override
 Performs all necessary actions before a time-step, like updating the particles and resetting all the bucket information, etc. More...
 
void read (std::istream &is, ReadOptions opt=ReadOptions::ReadAll) override
 Reads the MercuryBase from an input stream, for example a restart file. More...
 
void write (std::ostream &os, bool writeAllParticles=true) const override
 Writes all data into a restart file. More...
 
Mdouble getHGridCurrentMaxRelativeDisplacement () const
 Returns hGridCurrentMaxRelativeDisplacement_. More...
 
Mdouble getHGridTotalCurrentMaxRelativeDisplacement () const
 Returns hGridTotalCurrentMaxRelativeDisplacement_. More...
 
void setHGridUpdateEachTimeStep (bool updateEachTimeStep)
 Sets whether or not the HGrid must be updated every time step. More...
 
bool getHGridUpdateEachTimeStep () const final
 Gets whether or not the HGrid is updated every time step. More...
 
void setHGridMaxLevels (unsigned int HGridMaxLevels)
 Sets the maximum number of levels of the HGrid in this MercuryBase. More...
 
unsigned int getHGridMaxLevels () const
 Gets the maximum number of levels of the HGrid in this MercuryBase. More...
 
HGridMethod getHGridMethod () const
 Gets whether the HGrid in this MercuryBase is BOTTOMUP or TOPDOWN. More...
 
void setHGridMethod (HGridMethod hGridMethod)
 Sets the HGridMethod to either BOTTOMUP or TOPDOWN. More...
 
HGridDistribution getHGridDistribution () const
 Gets how the sizes of the cells of different levels are distributed. More...
 
void setHGridDistribution (HGridDistribution hGridDistribution)
 Sets how the sizes of the cells of different levels are distributed. More...
 
Mdouble getHGridCellOverSizeRatio () const
 Gets the ratio of the smallest cell over the smallest particle. More...
 
void setHGridCellOverSizeRatio (Mdouble cellOverSizeRatio)
 Sets the ratio of the smallest cell over the smallest particle. More...
 
bool hGridNeedsRebuilding ()
 Gets if the HGrid needs rebuilding before anything else happens. More...
 
virtual unsigned int getHGridTargetNumberOfBuckets () const
 Gets the desired number of buckets, which is the maximum of the number of particles and 10. More...
 
virtual Mdouble getHGridTargetMinInteractionRadius () const
 Gets the desired size of the smallest cells of the HGrid. More...
 
virtual Mdouble getHGridTargetMaxInteractionRadius () const
 Gets the desired size of the largest cells of the HGrid. More...
 
bool checkParticleForInteraction (const BaseParticle &P) final
 Checks if given BaseParticle has an interaction with a BaseWall or other BaseParticle. More...
 
bool checkParticleForInteractionLocal (const BaseParticle &P) final
 Checks if the given BaseParticle has an interaction with a BaseWall or other BaseParticles in a local domain. More...
 
virtual Mdouble userHGridCellSize (unsigned int level)
 Virtual function that enables inheriting classes to implement a function to let the user set the cell size of the HGrid. More...
 
virtual std::vector
< BaseParticle * > 
hGridFindParticleContacts (const BaseParticle *obj)=0
 Purely virtual function that returns all particles that have a contact with a given particle. More...
 
void hGridInfo (std::ostream &os=std::cout) const
 Writes the info of the HGrid to the screen in a nice format. More...
 
- Public Member Functions inherited from DPMBase
void constructor ()
 A function which initialises the member variables to default values, so that the problem can be solved off the shelf; sets up a basic two dimensional problem which can be solved off the shelf. It is called in the constructor DPMBase(). More...
 
 DPMBase ()
 Constructor that calls the "void constructor()". More...
 
 DPMBase (const DPMBase &other)
 Copy constructor type-2. More...
 
virtual ~DPMBase ()
 virtual destructor More...
 
void autoNumber ()
 The autoNumber() function calls three functions: setRunNumber(), readRunNumberFromFile() and incrementRunNumberInFile(). More...
 
std::vector< int > get1DParametersFromRunNumber (int size_x) const
 This turns a counter into 1 index, which is a useful feature for performing 1D parameter study. The index run from 1:size_x, while the study number starts at 0 (initially the counter=1 in COUNTER_DONOTDEL) More...
 
std::vector< int > get2DParametersFromRunNumber (int size_x, int size_y) const
 This turns a counter into 2 indices which is a very useful feature for performing a 2D study. The indices run from 1:size_x and 1:size_y, while the study number starts at 0 ( initially the counter=1 in COUNTER_DONOTDEL) More...
 
std::vector< int > get3DParametersFromRunNumber (int size_x, int size_y, int size_z) const
 This turns a counter into 3 indices, which is a useful feature for performing a 3D parameter study. The indices run from 1:size_x, 1:size_y and 1:size_z, while the study number starts at 0 ( initially the counter=1 in COUNTER_DONOTDEL) More...
 
int launchNewRun (const char *name, bool quick=false)
 This launches a code from within this code. Please pass the name of the code to run. More...
 
void setRunNumber (int runNumber)
 This sets the counter/Run number, overriding the defaults. More...
 
int getRunNumber () const
 This returns the current value of the counter (runNumber_) More...
 
virtual void decompose ()
 Sends particles from processorId to the root processor. More...
 
void solve ()
 The work horse of the code. More...
 
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...
 
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 (Mdouble logarithmicSaveCountBase)
 Sets File::logarithmicSaveCount_ for all files (ene, data, fstat, restart, stat) More...
 
void setNToWrite (int nToWrite)
 set the number of elements to write to the screen More...
 
int getNToWrite () const
 get the number of elements to write to the More...
 
void setRotation (bool rotation)
 Sets whether particle rotation is enabled or disabled. More...
 
bool getRotation () const
 Indicates whether particle rotation is enabled or disabled. More...
 
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 setNumberOfOMPThreads (int numberOfOMPThreads)
 
int getNumberOfOMPThreads () const
 
void setXBallsColourMode (int newCMode)
 Set the xballs output mode. More...
 
int getXBallsColourMode () const
 Get the xballs colour mode (CMode). More...
 
void setXBallsVectorScale (double newVScale)
 Set the scale of vectors in xballs. More...
 
double getXBallsVectorScale () const
 Returns the scale of vectors used in xballs. More...
 
void setXBallsAdditionalArguments (std::string newXBArgs)
 Set the additional arguments for xballs. More...
 
std::string getXBallsAdditionalArguments () const
 Returns the additional arguments for xballs. More...
 
void setXBallsScale (Mdouble newScale)
 Sets the scale of the view (either normal, zoom in or zoom out) to display in xballs. The default is fit to screen. More...
 
double getXBallsScale () const
 Returns the scale of the view in xballs. More...
 
void setGravity (Vec3D newGravity)
 Sets a new value for the gravitational acceleration. More...
 
Vec3D getGravity () const
 Returns the gravitational acceleration. More...
 
void setDimension (unsigned int newDim)
 Sets both the system dimensions and the particle dimensionality. More...
 
void setSystemDimensions (unsigned int newDim)
 Sets the system dimensionality. More...
 
unsigned int getSystemDimensions () const
 Returns the system dimensionality. More...
 
void setParticleDimensions (unsigned int particleDimensions)
 Sets the particle dimensionality. More...
 
unsigned int getParticleDimensions () const
 Returns the particle dimensionality. More...
 
std::string getRestartVersion () const
 This is to take into account for different Mercury versions. Returns the version of the restart file. More...
 
void setRestartVersion (std::string newRV)
 Sets restart_version. More...
 
bool getRestarted () const
 Returns the flag denoting if the simulation was restarted or not. More...
 
void setRestarted (bool newRestartedFlag)
 Allows to set the flag stating if the simulation is to be restarted or not. More...
 
bool getAppend () const
 Returns whether the "append" option is on or off. More...
 
void setAppend (bool newAppendFlag)
 Sets whether the "append" option is on or off. More...
 
Mdouble getElasticEnergy () const
 Returns the global elastic energy within the system. More...
 
Mdouble getKineticEnergy () const
 Returns the global kinetic energy stored in the system. More...
 
Mdouble getGravitationalEnergy () const
 Returns the global gravitational potential energy stored in the system. More...
 
Mdouble getRotationalEnergy () const
 JMFT Returns the global rotational energy stored in the system. More...
 
Mdouble getTotalEnergy () const
 
Mdouble getTotalMass () const
 JMFT: Return the total mass of the system, excluding fixed particles. More...
 
Vec3D getCentreOfMass () const
 JMFT: Return the centre of mass of the system, excluding fixed particles. More...
 
Vec3D getTotalMomentum () const
 JMFT: Return the total momentum of the system, excluding fixed particles. More...
 
double getCPUTime ()
 
double getWallTime ()
 
virtual void hGridInsertParticle (BaseParticle *obj UNUSED)
 
virtual void hGridUpdateParticle (BaseParticle *obj UNUSED)
 
virtual void hGridRemoveParticle (BaseParticle *obj UNUSED)
 
bool mpiIsInCommunicationZone (BaseParticle *particle)
 Checks if the position of the particle is in an mpi communication zone or not. More...
 
bool mpiInsertParticleCheck (BaseParticle *P)
 Function that checks if the mpi particle should really be inserted by the current domain. More...
 
void insertGhostParticle (BaseParticle *P)
 This function inserts a particle in the mpi communication boundaries. More...
 
void updateGhostGrid (BaseParticle *P)
 Checks if the Domain/periodic interaction distance needs to be updated and updates it accordingly. More...
 
virtual void gatherContactStatistics (unsigned int index1, int index2, Vec3D Contact, Mdouble delta, Mdouble ctheta, Mdouble fdotn, Mdouble fdott, Vec3D P1_P2_normal_, Vec3D P1_P2_tangential)
 //Not unsigned index because of possible wall collisions. More...
 
void setNumberOfDomains (std::vector< unsigned > direction)
 Sets the number of domains in x-,y- and z-direction. Required for parallel computations. More...
 
void splitDomain (DomainSplit domainSplit)
 
std::vector< unsignedgetNumberOfDomains ()
 returns the number of domains More...
 
DomaingetCurrentDomain ()
 Function that returns a pointer to the domain corresponding to the processor. More...
 
void removeOldFiles () const
 
virtual void hGridGetInteractingParticleList (BaseParticle *obj, std::vector< BaseParticle * > &list)
 Creates a list of neighbour particles obtained from the hgrid. More...
 
virtual void computeWallForces (BaseWall *w)
 
void setMeanVelocity (Vec3D V_mean_goal)
 This function will help you set a fixed kinetic energy and mean velocity in your system. More...
 
void setMeanVelocityAndKineticEnergy (Vec3D V_mean_goal, Mdouble Ek_goal)
 This function will help you set a fixed kinetic energy and mean velocity in your system. More...
 
Mdouble getTotalVolume () const
 Get the total volume of the cuboid system. More...
 
Matrix3D getKineticStress () const
 Calculate the kinetic stress tensor in the system averaged over the whole volume. More...
 
Matrix3D getStaticStress () const
 Calculate the static stress tensor in the system averaged over the whole volume. More...
 
Matrix3D getTotalStress () const
 Calculate the total stress tensor in the system averaged over the whole volume. More...
 
virtual void handleParticleRemoval (unsigned int id)
 Handles the removal of particles from the particleHandler. More...
 
virtual void handleParticleAddition (unsigned int id, BaseParticle *p)
 
void writePythonFileForVTKVisualisation () const
 

Protected Member Functions

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...
 
virtual bool hGridHasParticleContacts (const BaseParticle *obj)=0
 Purely virtual function that checks if the given particle has a possible contact with any other BaseParticle in the HGrid. 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 computeInternalForces (BaseParticle *)
 Computes the internal forces on particle i (internal in the sense that the sum over all these forces is zero i.e. fully modelled forces) 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 computeAdditionalForces ()
 A virtual function which allows to define operations to be executed prior to the OMP force collect. More...
 
virtual void actionsAfterSolve ()
 A virtual function which allows to define operations to be executed after the solve(). More...
 
virtual void actionsAfterTimeStep ()
 A virtual function which allows to define operations to be executed after time step. More...
 
void writeVTKFiles () const
 
virtual void outputXBallsData (std::ostream &os) const
 This function writes the location of the walls and particles in a format the XBalls program can read. For more information on the XBalls program, see Visualising data in xballs. More...
 
virtual void outputXBallsDataParticle (unsigned int i, unsigned int format, std::ostream &os) const
 This function writes out the particle locations into an output stream in a format the XBalls program can read. For more information on the XBalls program, see Visualising data in xballs. More...
 
virtual void writeEneHeader (std::ostream &os) const
 Writes a header with a certain format for ENE file. More...
 
virtual void writeFstatHeader (std::ostream &os) const
 Writes a header with a certain format for FStat file. More...
 
virtual void writeEneTimeStep (std::ostream &os) const
 Write the global kinetic, potential energy, etc. in the system. More...
 
virtual void initialiseStatistics ()
 
virtual void outputStatistics ()
 
void gatherContactStatistics ()
 
virtual void processStatistics (bool)
 
virtual void finishStatistics ()
 
virtual void integrateBeforeForceComputation ()
 Update particles' and walls' positions and velocities before force computation. More...
 
virtual void integrateAfterForceComputation ()
 Update particles' and walls' positions and velocities after force computation. More...
 
virtual void checkInteractionWithBoundaries ()
 There are a range of boundaries one could implement depending on ones' problem. This methods checks for interactions between particles and such range of boundaries. See BaseBoundary.h and all the boundaries in the Boundaries folder. More...
 
void setFixedParticles (unsigned int n)
 Sets a number, n, of particles in the particleHandler as "fixed particles". More...
 
virtual void printTime () const
 Displays the current simulation time and the maximum simulation duration. More...
 
virtual bool continueSolve () const
 A virtual function for deciding whether to continue the simulation, based on a user-specified criterion. More...
 
void outputInteractionDetails () const
 Displays the interaction details corresponding to the pointer objects in the interaction handler. More...
 
bool isTimeEqualTo (Mdouble time) const
 Checks whether the input variable "time" is the current time in the simulation. More...
 
void removeDuplicatePeriodicParticles ()
 Removes periodic duplicate Particles. More...
 
void checkAndDuplicatePeriodicParticles ()
 For simulations using periodic boundaries, checks and adds particles when necessary into the particle handler. See DPMBase.cc and PeriodicBoundary.cc for more details. More...
 
void performGhostParticleUpdate ()
 When the Verlet scheme updates the positions and velocities of particles, ghost particles will need an update as wel. Their status will also be updated accordingly. More...
 
void deleteGhostParticles (std::set< BaseParticle * > &particlesToBeDeleted)
 
void synchroniseParticle (BaseParticle *, unsigned fromProcessor=0)
 
void performGhostVelocityUpdate ()
 updates the final time-step velocity of the ghost particles More...
 
void setSoftStop ()
 function for setting sigaction constructor. More...
 

Private Attributes

HGridgrid
 A pointer to the HGrid associated with this MercuryBase. More...
 
HGridMethod hGridMethod_
 Indicator of which way the interactions between different levels are tested. More...
 
HGridDistribution hGridDistribution_
 Indicator for the distribution of the sizes of the cells of different levels of the HGrid. The default is EXPONENTIAL. More...
 
Mdouble currentMaxRelativeDisplacement_
 Mdouble that denotes the maximum of the displacement of a particle divided by the cell size of the level of that particle at the current time step. This is useful to see whether a particle could have moved more than one cell. More...
 
Mdouble totalCurrentMaxRelativeDisplacement_
 After each time step, this Mdouble is increased by 2*currentMaxRelativeDisplacement_. More...
 
bool gridNeedsUpdate_
 Boolean that indicates whether or not the grid needs to be updated. More...
 
bool updateEachTimeStep_
 Boolean which indicates whether or not the cell in which a particle is must be updated every time step. More...
 
unsigned int hGridMaxLevels_
 Unsigned integer that indicates the maximum number of levels of the HGrid. More...
 
Mdouble hGridCellOverSizeRatio_
 The maximum ratio between the size of the cells and the BaseParticle they contain. 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
}
 
- Static Public Member Functions inherited from DPMBase
static void incrementRunNumberInFile ()
 Increment the run Number (counter value) stored in the file_counter (COUNTER_DONOTDEL) by 1 and store the new value in the counter file. More...
 
static int readRunNumberFromFile ()
 Read the run number or the counter from the counter file (COUNTER_DONOTDEL) More...
 
static bool areInContact (const BaseParticle *pI, const BaseParticle *pJ)
 Checks if two particle are in contact or is there any positive overlap. More...
 
- Public Attributes inherited from DPMBase
SpeciesHandler speciesHandler
 A handler to that stores the species type i.e. LinearViscoelasticSpecies, etc. More...
 
RNG random
 This is a random generator, often used for setting up the initial conditions etc... More...
 
ParticleHandler particleHandler
 An object of the class ParticleHandler, contains the pointers to all the particles created. More...
 
ParticleHandler paoloParticleHandler
 Fake particleHandler created by Paolo needed temporary by just Paolo. More...
 
WallHandler wallHandler
 An object of the class WallHandler. Contains pointers to all the walls created. More...
 
BoundaryHandler boundaryHandler
 An object of the class BoundaryHandler which concerns insertion and deletion of particles into or from regions. More...
 
PeriodicBoundaryHandler periodicBoundaryHandler
 Internal handler that deals with periodic boundaries, especially in a parallel build. More...
 
DomainHandler domainHandler
 An object of the class DomainHandler which deals with parallel code. More...
 
InteractionHandler interactionHandler
 An object of the class InteractionHandler. More...
 
CGHandler cgHandler
 Object of the class cgHandler. More...
 
File dataFile
 An instance of class File to handle in- and output into a .data file. More...
 
File fStatFile
 An instance of class File to handle in- and output into a .fstat file. More...
 
File eneFile
 An instance of class File to handle in- and output into a .ene file. More...
 
File restartFile
 An instance of class File to handle in- and output into a .restart file. More...
 
File statFile
 An instance of class File to handle in- and output into a .stat file. More...
 
File interactionFile
 File class to handle in- and output into .interactions file. This file hold information about interactions. More...
 
Time clock_
 record when the simulation started More...
 
- Static Protected Member Functions inherited from DPMBase
static void signalHandler (int signal)
 signal handler function. More...
 

Detailed Description

This is the base class for both Mercury2D and Mercury3D. Note the actually abstract grid is defined in the class Grid defined below.

Todo:
Discuss if we want to remove Mercury2D and Mercury3D and template MercuryBase as the interface for the user.

Definition at line 125 of file MercuryBase.h.

Constructor & Destructor Documentation

MercuryBase::MercuryBase ( )

This is the default constructor. It sets sensible defaults.

Definition at line 31 of file MercuryBase.cc.

References constructor(), DEBUG, and logger.

32 {
33  constructor();
34  logger(DEBUG, "MercuryBase::MercuryBase() constructor finished");
35 }
Logger< MERCURY_LOGLEVEL > logger("MercuryKernel")
Definition of different loggers with certain modules. A user can define its own custom logger here...
void constructor()
This is the actual constructor, it is called do both constructors above.
Definition: MercuryBase.cc:77
MercuryBase::~MercuryBase ( )
override

This is the default destructor.

Definition at line 37 of file MercuryBase.cc.

References DEBUG, grid, and logger.

38 {
39  if (grid != nullptr)
40  {
41  delete grid;
42  grid = nullptr;
43  }
44  logger(DEBUG, "MercuryBase::~MercuryBase() destructor finished.");
45 }
HGrid * grid
A pointer to the HGrid associated with this MercuryBase.
Definition: MercuryBase.h:336
Logger< MERCURY_LOGLEVEL > logger("MercuryKernel")
Definition of different loggers with certain modules. A user can define its own custom logger here...
MercuryBase::MercuryBase ( const MercuryBase mercuryBase)

Copy-constructor.

Parameters
[in]mercuryBaseThe MercuryBase that needs to be copied.

Copy constructor that copies almost all properties of the given MercuryBase into the new MercuryBase. Please note that the grid is not literally copied, but everything to make that grid is copied and the gridNeedsUpdate_ is set to true, so that the grid is made before anything else happens.

Definition at line 55 of file MercuryBase.cc.

References currentMaxRelativeDisplacement_, DEBUG, grid, gridNeedsUpdate_, hGridCellOverSizeRatio_, hGridDistribution_, hGridMaxLevels_, hGridMethod_, logger, totalCurrentMaxRelativeDisplacement_, and updateEachTimeStep_.

56 {
57  grid = nullptr;
58  gridNeedsUpdate_ = true;
59 
60  hGridMethod_ = mercuryBase.hGridMethod_;
62 
65 
67  hGridMaxLevels_ = mercuryBase.hGridMaxLevels_;
69 
70  logger(DEBUG, "HGRID_base(HGrid_base& other) constructor finished.");
71 }
Mdouble totalCurrentMaxRelativeDisplacement_
After each time step, this Mdouble is increased by 2*currentMaxRelativeDisplacement_.
Definition: MercuryBase.h:368
HGrid * grid
A pointer to the HGrid associated with this MercuryBase.
Definition: MercuryBase.h:336
Logger< MERCURY_LOGLEVEL > logger("MercuryKernel")
Definition of different loggers with certain modules. A user can define its own custom logger here...
HGridDistribution hGridDistribution_
Indicator for the distribution of the sizes of the cells of different levels of the HGrid...
Definition: MercuryBase.h:354
unsigned int hGridMaxLevels_
Unsigned integer that indicates the maximum number of levels of the HGrid.
Definition: MercuryBase.h:396
Mdouble hGridCellOverSizeRatio_
The maximum ratio between the size of the cells and the BaseParticle they contain.
Definition: MercuryBase.h:404
HGridMethod hGridMethod_
Indicator of which way the interactions between different levels are tested.
Definition: MercuryBase.h:348
bool updateEachTimeStep_
Boolean which indicates whether or not the cell in which a particle is must be updated every time ste...
Definition: MercuryBase.h:382
bool gridNeedsUpdate_
Boolean that indicates whether or not the grid needs to be updated.
Definition: MercuryBase.h:376
Mdouble currentMaxRelativeDisplacement_
Mdouble that denotes the maximum of the displacement of a particle divided by the cell size of the le...
Definition: MercuryBase.h:362

Member Function Documentation

bool MercuryBase::checkParticleForInteraction ( const BaseParticle p)
finalvirtual

Checks if given BaseParticle has an interaction with a BaseWall or other BaseParticle.

Parameters
[in]pThe BaseParticle for which we want to check if there is an interaction.
Returns
A boolean which is false if there was an interaction and true if there was no interaction.

Check for the given BaseParticle if there is an interaction with any other object. First check all walls, then all particles.

Todo:
IFCD: I think it might be better if it returns true if there is an interaction.
Todo:
MX: use all reduce with the appropriate operator

Reimplemented from DPMBase.

Definition at line 594 of file MercuryBase.cc.

Referenced by Chute::addFlowParticlesCompactly(), BaseCluster::computeInternalStructure(), Chute::createBottom(), BaseCluster::particleInsertionSuccessful(), and ChuteBottom::setupInitialConditions().

595 {
596 #ifdef MERCURY_USE_MPI
597  bool interaction;
598  if (NUMBER_OF_PROCESSORS == 1)
599  {
601  }
602  else
603  {
604  //check locally and then collectively come to a global conclusion
605  bool interactionLocal = checkParticleForInteractionLocal(p);
606 
607  MPIContainer::Instance().allReduce(interactionLocal, interaction, MPI_LAND);
608  }
609 #else
610  bool interaction = checkParticleForInteractionLocalPeriodic(p);
611 #endif
612  return interaction;
613 }
static MPIContainer & Instance()
fetch the instance to be used for communication
Definition: MpiContainer.h:134
bool checkParticleForInteractionLocal(const BaseParticle &P) final
Checks if the given BaseParticle has an interaction with a BaseWall or other BaseParticles in a local...
Definition: MercuryBase.cc:622
#define NUMBER_OF_PROCESSORS
For the MPI communication routines this quantity is often required. defining this macro makes the cod...
Definition: GeneralDefine.h:62
bool checkParticleForInteractionLocalPeriodic(const BaseParticle &P)
Definition: DPMBase.cc:4687
bool MercuryBase::checkParticleForInteractionLocal ( const BaseParticle p)
finalvirtual

Checks if the given BaseParticle has an interaction with a BaseWall or other BaseParticles in a local domain.

Parameters
[in]pThe BaseParticle for which we want to check if there is an interaction.
Returns
A boolean which is false if there was an interaction and true if there was no interaction.

Check for the given BaseParticle if there is an interaction with any other object. First check all walls, then all particles in the local domain.

Todo:
IFCD: I think it might be better if it returns true if there is an interaction.

Reimplemented from DPMBase.

Definition at line 622 of file MercuryBase.cc.

References hGridHasParticleContacts(), logger, VERBOSE, and DPMBase::wallHandler.

623 {
624  Mdouble distance;
625  Vec3D normal;
626 
627  //Check if it has no collision with walls
628  for (BaseWall* w :wallHandler)
629  {
630  if (w->getDistanceAndNormal(p, distance, normal))
631  {
632  logger(VERBOSE, "Collision with wall %.", *w);
633  return false;
634  }
635  else
636  {
637  logger(VERBOSE, "No collision with wall %.", *w);
638  }
639  }
640 
641  //Check if it has no collision with other particles
642  if (hGridHasParticleContacts(&p))
643  {
644  logger(VERBOSE, "Collision with particle.");
645  return false;
646  }
647  else
648  {
649  logger(VERBOSE, "No collision with particles.");
650  }
651  return true;
652 }
Logger< MERCURY_LOGLEVEL > logger("MercuryKernel")
Definition of different loggers with certain modules. A user can define its own custom logger here...
double Mdouble
Definition: GeneralDefine.h:34
Basic class for walls.
Definition: BaseWall.h:47
WallHandler wallHandler
An object of the class WallHandler. Contains pointers to all the walls created.
Definition: DPMBase.h:1405
virtual bool hGridHasParticleContacts(const BaseParticle *obj)=0
Purely virtual function that checks if the given particle has a possible contact with any other BaseP...
Definition: Vector.h:49
void MercuryBase::constructor ( )

This is the actual constructor, it is called do both constructors above.

Function that is called by the default constructor, it sets all parameters for the MercuryBase to sensible defaults.

Definition at line 77 of file MercuryBase.cc.

References currentMaxRelativeDisplacement_, EXPONENTIAL, grid, gridNeedsUpdate_, hGridCellOverSizeRatio_, hGridDistribution_, hGridMaxLevels_, hGridMethod_, constants::inf, TOPDOWN, totalCurrentMaxRelativeDisplacement_, and updateEachTimeStep_.

Referenced by MercuryBase().

78 {
79  grid = nullptr;
80  gridNeedsUpdate_ = true;
81  hGridMaxLevels_ = 3;
83  updateEachTimeStep_ = true;
88 }
Mdouble totalCurrentMaxRelativeDisplacement_
After each time step, this Mdouble is increased by 2*currentMaxRelativeDisplacement_.
Definition: MercuryBase.h:368
HGrid * grid
A pointer to the HGrid associated with this MercuryBase.
Definition: MercuryBase.h:336
HGridDistribution hGridDistribution_
Indicator for the distribution of the sizes of the cells of different levels of the HGrid...
Definition: MercuryBase.h:354
unsigned int hGridMaxLevels_
Unsigned integer that indicates the maximum number of levels of the HGrid.
Definition: MercuryBase.h:396
Mdouble hGridCellOverSizeRatio_
The maximum ratio between the size of the cells and the BaseParticle they contain.
Definition: MercuryBase.h:404
const Mdouble inf
Definition: GeneralDefine.h:44
HGridMethod hGridMethod_
Indicator of which way the interactions between different levels are tested.
Definition: MercuryBase.h:348
bool updateEachTimeStep_
Boolean which indicates whether or not the cell in which a particle is must be updated every time ste...
Definition: MercuryBase.h:382
bool gridNeedsUpdate_
Boolean that indicates whether or not the grid needs to be updated.
Definition: MercuryBase.h:376
Mdouble currentMaxRelativeDisplacement_
Mdouble that denotes the maximum of the displacement of a particle divided by the cell size of the le...
Definition: MercuryBase.h:362
const HGrid* MercuryBase::getHGrid ( ) const
inlineprotected

Gets the HGrid used by this problem, const version.

Returns
A pointer to the HGrid associated with this MercuryBase.

Definition at line 318 of file MercuryBase.h.

References grid.

319  { return grid; }
HGrid * grid
A pointer to the HGrid associated with this MercuryBase.
Definition: MercuryBase.h:336
Mdouble MercuryBase::getHGridCellOverSizeRatio ( ) const

Gets the ratio of the smallest cell over the smallest particle.

Returns
The maximum ratio between the cells and the size of the BaseParticle it contains.

Definition at line 453 of file MercuryBase.cc.

References hGridCellOverSizeRatio_.

Referenced by hGridActionsAfterIntegration(), hGridActionsBeforeTimeStep(), and hGridRebuild().

454 {
456 }
Mdouble hGridCellOverSizeRatio_
The maximum ratio between the size of the cells and the BaseParticle they contain.
Definition: MercuryBase.h:404
Mdouble MercuryBase::getHGridCurrentMaxRelativeDisplacement ( ) const

Returns hGridCurrentMaxRelativeDisplacement_.

Returns
currentMaxRelativeDisplacement_, which is the highest relative speed of a BaseParticle compared to the cell size of the grid in which the BaseParticle is.

Definition at line 158 of file MercuryBase.cc.

References currentMaxRelativeDisplacement_.

159 {
161 }
Mdouble currentMaxRelativeDisplacement_
Mdouble that denotes the maximum of the displacement of a particle divided by the cell size of the le...
Definition: MercuryBase.h:362
HGridDistribution MercuryBase::getHGridDistribution ( ) const

Gets how the sizes of the cells of different levels are distributed.

Returns
The HGridDistribution (distribution of cell sizes) used by this MercuryBase.

Definition at line 431 of file MercuryBase.cc.

References hGridDistribution_.

Referenced by hGridRebuild().

432 {
433  return hGridDistribution_;
434 }
HGridDistribution hGridDistribution_
Indicator for the distribution of the sizes of the cells of different levels of the HGrid...
Definition: MercuryBase.h:354
unsigned int MercuryBase::getHGridMaxLevels ( ) const

Gets the maximum number of levels of the HGrid in this MercuryBase.

Returns
The maximum number of levels in the HGrid.

Definition at line 488 of file MercuryBase.cc.

References hGridMaxLevels_.

Referenced by hGridRebuild().

489 {
490  return hGridMaxLevels_;
491 }
unsigned int hGridMaxLevels_
Unsigned integer that indicates the maximum number of levels of the HGrid.
Definition: MercuryBase.h:396
HGridMethod MercuryBase::getHGridMethod ( ) const
inline

Gets whether the HGrid in this MercuryBase is BOTTOMUP or TOPDOWN.

Returns
The HGridMethod used by this MercuryBase.

Definition at line 204 of file MercuryBase.h.

References hGridMethod_.

Referenced by Mercury2D::computeInternalForces(), and Mercury3D::computeInternalForces().

205  { return hGridMethod_; }
HGridMethod hGridMethod_
Indicator of which way the interactions between different levels are tested.
Definition: MercuryBase.h:348
Mdouble MercuryBase::getHGridTargetMaxInteractionRadius ( ) const
virtual

Gets the desired size of the largest cells of the HGrid.

Returns
The interaction radius of the largest particle multiplied by the maximum ratio between the cell size and particle size.

Definition at line 574 of file MercuryBase.cc.

References ParticleHandler::getLargestInteractionRadiusLocal(), BaseHandler< T >::getSize(), and DPMBase::particleHandler.

Referenced by hGridRebuild().

575 {
576  if (particleHandler.getSize() == 0)
577  {
578  return 0.0;
579  }
580  else
581  {
583  }
584 }
unsigned int getSize() const
Gets the size of the particleHandler (including mpi and periodic particles)
Definition: BaseHandler.h:655
Mdouble getLargestInteractionRadiusLocal() const
Returns the largest interaction radius of the current domain.
ParticleHandler particleHandler
An object of the class ParticleHandler, contains the pointers to all the particles created...
Definition: DPMBase.h:1395
Mdouble MercuryBase::getHGridTargetMinInteractionRadius ( ) const
virtual

Gets the desired size of the smallest cells of the HGrid.

Returns
The interaction radius of the smallest particle multiplied by the maximum ratio between the cell size and particle size.

Definition at line 558 of file MercuryBase.cc.

References BaseHandler< T >::getSize(), ParticleHandler::getSmallestInteractionRadiusLocal(), and DPMBase::particleHandler.

Referenced by hGridRebuild().

559 {
560  if (particleHandler.getSize() == 0)
561  {
562  return 0.0;
563  }
564  else
565  {
567  }
568 }
unsigned int getSize() const
Gets the size of the particleHandler (including mpi and periodic particles)
Definition: BaseHandler.h:655
Mdouble getSmallestInteractionRadiusLocal() const
Returns the smallest interaction radius of the current domain.
ParticleHandler particleHandler
An object of the class ParticleHandler, contains the pointers to all the particles created...
Definition: DPMBase.h:1395
unsigned int MercuryBase::getHGridTargetNumberOfBuckets ( ) const
virtual

Gets the desired number of buckets, which is the maximum of the number of particles and 10.

Returns
The number of possible values the hash function can have.
Todo:
TW SpeedCheckThomas revealed that adding a factor 10 here improved performance by 20% for monodisperse particles, 45% for highly polydisperse (this seems true for particle numbers 1e3 - 1e6); a larger factor seems to little extra effect; the memory cost is small compared to the number of particles, so I added the factor permanently. please check this is ok to do.

Definition at line 540 of file MercuryBase.cc.

References BaseHandler< T >::getSize(), and DPMBase::particleHandler.

Referenced by hGridNeedsRebuilding(), and hGridRebuild().

541 {
542  unsigned int nParticles = particleHandler.getSize();
543  if (nParticles > 10)
544  {
546  return 10 * nParticles;
547  }
548  else
549  {
550  return 10;
551  }
552 }
unsigned int getSize() const
Gets the size of the particleHandler (including mpi and periodic particles)
Definition: BaseHandler.h:655
ParticleHandler particleHandler
An object of the class ParticleHandler, contains the pointers to all the particles created...
Definition: DPMBase.h:1395
Mdouble MercuryBase::getHGridTotalCurrentMaxRelativeDisplacement ( ) const

Returns hGridTotalCurrentMaxRelativeDisplacement_.

Returns
totalCurrentMaxRelativeDisplacement_, which is the cumulative value of 2*currentMaxRelativeDisplacement_

Definition at line 167 of file MercuryBase.cc.

References totalCurrentMaxRelativeDisplacement_.

Referenced by hGridActionsBeforeTimeStep().

168 {
170 }
Mdouble totalCurrentMaxRelativeDisplacement_
After each time step, this Mdouble is increased by 2*currentMaxRelativeDisplacement_.
Definition: MercuryBase.h:368
bool MercuryBase::getHGridUpdateEachTimeStep ( ) const
finalvirtual

Gets whether or not the HGrid is updated every time step.

Returns
A boolean which indicates if the HGrid must be updated every time step.

Reimplemented from DPMBase.

Definition at line 184 of file MercuryBase.cc.

References updateEachTimeStep_.

Referenced by hGridActionsBeforeTimeStep().

185 {
186  return updateEachTimeStep_;
187 }
bool updateEachTimeStep_
Boolean which indicates whether or not the cell in which a particle is must be updated every time ste...
Definition: MercuryBase.h:382
void MercuryBase::hGridActionsAfterIntegration ( )
overrideprotectedvirtual

This function has to be called before integrateBeforeForceComputation.

Sets the totalCurrentMaxRelativeDisplacement

Reimplemented from DPMBase.

Definition at line 379 of file MercuryBase.cc.

References currentMaxRelativeDisplacement_, getHGridCellOverSizeRatio(), and totalCurrentMaxRelativeDisplacement_.

380 {
383 }
Mdouble totalCurrentMaxRelativeDisplacement_
After each time step, this Mdouble is increased by 2*currentMaxRelativeDisplacement_.
Definition: MercuryBase.h:368
Mdouble getHGridCellOverSizeRatio() const
Gets the ratio of the smallest cell over the smallest particle.
Definition: MercuryBase.cc:453
Mdouble currentMaxRelativeDisplacement_
Mdouble that denotes the maximum of the displacement of a particle divided by the cell size of the le...
Definition: MercuryBase.h:362
void MercuryBase::hGridActionsBeforeIntegration ( )
overrideprotectedvirtual

Resets the currentMaxRelativeDisplacement_ to 0.

Sets the currentMaxRelativeDisplacement to zero

Reimplemented from DPMBase.

Definition at line 371 of file MercuryBase.cc.

References currentMaxRelativeDisplacement_.

372 {
374 }
Mdouble currentMaxRelativeDisplacement_
Mdouble that denotes the maximum of the displacement of a particle divided by the cell size of the le...
Definition: MercuryBase.h:362
void MercuryBase::hGridActionsBeforeTimeLoop ( )
overridevirtual

This sets up the broad phase information, has to be done at this stage because it requires the particle size.

Performs all actions that need to be done before the time loop. At the moment, this means nothing.

Reimplemented from DPMBase.

Definition at line 94 of file MercuryBase.cc.

Referenced by Chute::createBottom(), and ChuteBottom::setupInitialConditions().

95 {
96 }
void MercuryBase::hGridActionsBeforeTimeStep ( )
overridevirtual

Performs all necessary actions before a time-step, like updating the particles and resetting all the bucket information, etc.

The actions that are done before each time step, it rebuilds the HGrid if necessary, otherwise it computes which cell each particle is in.

Reimplemented from DPMBase.

Definition at line 323 of file MercuryBase.cc.

References HGrid::clearBucketIsChecked(), HGrid::clearFirstBaseParticleInBucket(), getHGrid(), getHGridCellOverSizeRatio(), getHGridTotalCurrentMaxRelativeDisplacement(), getHGridUpdateEachTimeStep(), hGridNeedsRebuilding(), hGridRebuild(), DPMBase::hGridUpdateParticle(), DPMBase::particleHandler, and totalCurrentMaxRelativeDisplacement_.

Referenced by Chute::createBottom().

324 {
325  if (hGridNeedsRebuilding())
326  {
327  //logger(INFO, "HGrid needs rebuilding at nt=%",getNumberOfTimeSteps());
328  hGridRebuild();
329  }
330  else
331  {
332 #ifndef CONTACT_LIST_HGRID
334 #endif
337  {
338 #ifndef CONTACT_LIST_HGRID
340 #endif
341  //logger(INFO, "HGrid needs updating at nt=%",getNumberOfTimeSteps());
342  for (BaseParticle* const p : particleHandler)
343  {
345  }
347  }
348  }
349 }
virtual void hGridUpdateParticle(BaseParticle *obj UNUSED)
Definition: DPMBase.cc:1695
bool hGridNeedsRebuilding()
Gets if the HGrid needs rebuilding before anything else happens.
Definition: MercuryBase.cc:496
Mdouble totalCurrentMaxRelativeDisplacement_
After each time step, this Mdouble is increased by 2*currentMaxRelativeDisplacement_.
Definition: MercuryBase.h:368
Mdouble getHGridCellOverSizeRatio() const
Gets the ratio of the smallest cell over the smallest particle.
Definition: MercuryBase.cc:453
void clearFirstBaseParticleInBucket()
For all buckets, it removes the pointer to the first BaseParticle in it, practically emptying the buc...
Definition: HGrid.cc:145
Mdouble getHGridTotalCurrentMaxRelativeDisplacement() const
Returns hGridTotalCurrentMaxRelativeDisplacement_.
Definition: MercuryBase.cc:167
ParticleHandler particleHandler
An object of the class ParticleHandler, contains the pointers to all the particles created...
Definition: DPMBase.h:1395
void clearBucketIsChecked()
Sets all buckets to not-checked.
Definition: HGrid.cc:140
void hGridRebuild()
This sets up the parameters required for the contact model.
Definition: MercuryBase.cc:204
HGrid * getHGrid()
Gets the HGrid used by this problem.
Definition: MercuryBase.h:311
bool getHGridUpdateEachTimeStep() const final
Gets whether or not the HGrid is updated every time step.
Definition: MercuryBase.cc:184
virtual std::vector<BaseParticle*> MercuryBase::hGridFindParticleContacts ( const BaseParticle obj)
pure virtual

Purely virtual function that returns all particles that have a contact with a given particle.

Implemented in Mercury3D, and Mercury2D.

Referenced by DropletBoundary::checkBoundaryAfterParticlesMove().

virtual bool MercuryBase::hGridHasParticleContacts ( const BaseParticle obj)
protectedpure virtual

Purely virtual function that checks if the given particle has a possible contact with any other BaseParticle in the HGrid.

Implemented in Mercury3D, and Mercury2D.

Referenced by checkParticleForInteractionLocal().

void MercuryBase::hGridInfo ( std::ostream &  os = std::cout) const

Writes the info of the HGrid to the screen in a nice format.

Definition at line 655 of file MercuryBase.cc.

References currentMaxRelativeDisplacement_, HGrid::getCellSizes(), HGrid::getNumberOfBuckets(), MPIContainer::getNumberOfProcessors(), grid, gridNeedsUpdate_, hGridCellOverSizeRatio_, hGridDistribution_, hGridMethod_, MPIContainer::Instance(), totalCurrentMaxRelativeDisplacement_, and updateEachTimeStep_.

Referenced by write().

656 {
657 #ifdef MERCURY_USE_MPI
658  MPIContainer& communicator = MPIContainer::Instance();
659  int numberOfProcessors = communicator.getNumberOfProcessors();
660 #else
661  int numberOfProcessors = 1;
662 #endif
663  os << "hGrid"
664  << " method " << hGridMethod_
665  << " distribution " << hGridDistribution_
666  << " cellOverSizeRatio " << hGridCellOverSizeRatio_;
667  //os << " maxLevels " << hGridMaxLevels_;
668  if (numberOfProcessors == 1 && grid != nullptr)
669  {
670  os << " numberOfBuckets " << grid->getNumberOfBuckets()
671  << " cellSizes";
672  for (const auto p: grid->getCellSizes()) os << " " << p;
673  }
674  os << " gridNeedsUpdate " << gridNeedsUpdate_
675  << " updateEachTimeStep " << updateEachTimeStep_
676  << " currentMaxRelativeDisplacement " << currentMaxRelativeDisplacement_
677  << " totalCurrentMaxRelativeDisplacement " << totalCurrentMaxRelativeDisplacement_
678  << std::endl;
679 }
This class contains all information and functions required for communication between processors...
Definition: MpiContainer.h:129
static MPIContainer & Instance()
fetch the instance to be used for communication
Definition: MpiContainer.h:134
Mdouble totalCurrentMaxRelativeDisplacement_
After each time step, this Mdouble is increased by 2*currentMaxRelativeDisplacement_.
Definition: MercuryBase.h:368
HGrid * grid
A pointer to the HGrid associated with this MercuryBase.
Definition: MercuryBase.h:336
HGridDistribution hGridDistribution_
Indicator for the distribution of the sizes of the cells of different levels of the HGrid...
Definition: MercuryBase.h:354
std::size_t getNumberOfProcessors() const
Get the total number of processors participating in this simulation.
Mdouble hGridCellOverSizeRatio_
The maximum ratio between the size of the cells and the BaseParticle they contain.
Definition: MercuryBase.h:404
HGridMethod hGridMethod_
Indicator of which way the interactions between different levels are tested.
Definition: MercuryBase.h:348
const std::vector< double > & getCellSizes() const
Gets the sizes of the cells at all levels as a vector.
Definition: HGrid.h:154
bool updateEachTimeStep_
Boolean which indicates whether or not the cell in which a particle is must be updated every time ste...
Definition: MercuryBase.h:382
bool gridNeedsUpdate_
Boolean that indicates whether or not the grid needs to be updated.
Definition: MercuryBase.h:376
Mdouble currentMaxRelativeDisplacement_
Mdouble that denotes the maximum of the displacement of a particle divided by the cell size of the le...
Definition: MercuryBase.h:362
unsigned int getNumberOfBuckets() const
Gets the number of buckets of this HGrid.
Definition: HGrid.h:199
void MercuryBase::hGridInsertParticle ( BaseParticle obj)
finalprotected

Inserts a single Particle to current grid.

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

Definition at line 311 of file MercuryBase.cc.

References grid, and HGrid::insertParticleToHgrid().

Referenced by hGridRebuild().

312 {
313  if (grid != nullptr)
314  {
316  }
317 }
HGrid * grid
A pointer to the HGrid associated with this MercuryBase.
Definition: MercuryBase.h:336
void insertParticleToHgrid(BaseParticle *obj)
Inserts the given BaseParticle in to the HGrid.
Definition: HGrid.cc:89
bool MercuryBase::hGridNeedsRebuilding ( )

Gets if the HGrid needs rebuilding before anything else happens.

Returns
A boolean which indicates if the HGrid needs to be rebuilt.

Definition at line 496 of file MercuryBase.cc.

References HGrid::getCellOverSizeRatio(), HGrid::getCellSizes(), getHGrid(), getHGridTargetNumberOfBuckets(), ParticleHandler::getLargestParticle(), BaseParticle::getMaxInteractionRadius(), HGrid::getNeedsRebuilding(), HGrid::getNumberOfBuckets(), BaseHandler< T >::getSize(), grid, gridNeedsUpdate_, hGridCellOverSizeRatio_, logger, DPMBase::particleHandler, and VERBOSE.

Referenced by hGridActionsBeforeTimeStep(), and Mercury3D::hGridGetInteractingParticleList().

497 {
498  if (grid == nullptr)
499  {
500  logger(VERBOSE, "HGrid needs updating, because there is no grid.");
501  return true;
502  }
503  else if (gridNeedsUpdate_)
504  {
505  logger(VERBOSE, "HGrid needs updating, because some of its initialisation parameters have changed.");
506  return true;
507  }
508  else if (grid->getNeedsRebuilding())
509  {
510  logger(VERBOSE, "HGrid needs updating, because said so by the grid itself");
511  return true;
512  }
513  else if (getHGrid()->getNumberOfBuckets() > 10 * getHGridTargetNumberOfBuckets() ||
514  10 * getHGrid()->getNumberOfBuckets() < getHGridTargetNumberOfBuckets())
515  {
516  logger(VERBOSE, "HGrid needs updating, because of number of buckets, current = %, target = %.",
518  return true;
519  }
520  else if (particleHandler.getLargestParticle() != nullptr &&
523  {
524  logger(VERBOSE, "HGrid needs updating, because of maximum cell size, current = %, required = %.",
527  return true;
528  }
529  else
530  {
531  //std::cout<<"HGrid does not need updating, because of number of buckets, current="<<grid->NUM_BUCKETS<<" target="<<particleHandler.getSize()<<std::endl;
532  //std::cout<<"HGrid does not need updating, because of maximum cell size, current="<<grid->cellSizes_.back()*grid->cellOverSizeRatio_<<" required="<<2.0*particleHandler.getLargestParticle()->getInteractionRadius()<<std::endl;
533  return false;
534  }
535 }
BaseParticle * getLargestParticle() const
Returns the pointer of the largest particle in the particle handler. When mercury is running in paral...
unsigned int getSize() const
Gets the size of the particleHandler (including mpi and periodic particles)
Definition: BaseHandler.h:655
HGrid * grid
A pointer to the HGrid associated with this MercuryBase.
Definition: MercuryBase.h:336
Logger< MERCURY_LOGLEVEL > logger("MercuryKernel")
Definition of different loggers with certain modules. A user can define its own custom logger here...
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:362
virtual unsigned int getHGridTargetNumberOfBuckets() const
Gets the desired number of buckets, which is the maximum of the number of particles and 10...
Definition: MercuryBase.cc:540
Mdouble getCellOverSizeRatio() const
Gets the maximum ratio of the cell to a particle it contains.
Definition: HGrid.h:139
Mdouble hGridCellOverSizeRatio_
The maximum ratio between the size of the cells and the BaseParticle they contain.
Definition: MercuryBase.h:404
const std::vector< double > & getCellSizes() const
Gets the sizes of the cells at all levels as a vector.
Definition: HGrid.h:154
ParticleHandler particleHandler
An object of the class ParticleHandler, contains the pointers to all the particles created...
Definition: DPMBase.h:1395
bool gridNeedsUpdate_
Boolean that indicates whether or not the grid needs to be updated.
Definition: MercuryBase.h:376
HGrid * getHGrid()
Gets the HGrid used by this problem.
Definition: MercuryBase.h:311
bool getNeedsRebuilding() const
Gets whether or not the grid needs to be rebuilt before something else is done with it...
Definition: HGrid.h:192
unsigned int getNumberOfBuckets() const
Gets the number of buckets of this HGrid.
Definition: HGrid.h:199
void MercuryBase::hGridRebuild ( )
protected

This sets up the parameters required for the contact model.

Rebuild the HGrid with the current data. First compute the cell sizes of the new HGrid, then delete the old HGrid and build the new HGrid. Finally add all particles to the new HGrid. First check if either the ParticleHandler is empty or the particle distribution is monodispersed. If this is the case, make a grid that contains only one level which has a cell size defined by the diameter of the particle * hGridCellOverSizeRatio_. Otherwise, make cell sizes depending on the distribution given in hGridDistribution_. LINEAR and EXPONENTIAL first compute the smallest and biggest cell size, and then compute the ones in between according to the distribution. USER just takes the cell sizes given by the user. OLDHGRID computes the smallest cell size and then makes the cells of each subsequent level twice as big.

Todo:
{This is really ugly fix to force the particle to update}

Definition at line 204 of file MercuryBase.cc.

References EXPONENTIAL, getHGridCellOverSizeRatio(), getHGridDistribution(), getHGridMaxLevels(), getHGridTargetMaxInteractionRadius(), getHGridTargetMinInteractionRadius(), getHGridTargetNumberOfBuckets(), grid, gridNeedsUpdate_, hGridInsertParticle(), DPMBase::hGridUpdateParticle(), constants::i, INFO, LINEAR, logger, OLDHGRID, DPMBase::particleHandler, USER, userHGridCellSize(), and VERBOSE.

Referenced by Mercury3D::computeWallForces(), hGridActionsBeforeTimeStep(), Mercury2D::hGridFindParticleContacts(), Mercury3D::hGridFindParticleContacts(), Mercury3D::hGridGetInteractingParticleList(), and Mercury2D::hGridHasParticleContacts().

205 {
206  std::vector<Mdouble> cellSizes;
207 
208  const Mdouble minParticleInteractionRadius = getHGridTargetMinInteractionRadius();
209  const Mdouble maxParticleInteractionRadius = getHGridTargetMaxInteractionRadius();
210  if (minParticleInteractionRadius == 0.0 || minParticleInteractionRadius == maxParticleInteractionRadius)
211  {
212  //this case is executed if the particleHandler is empty (minParticleInteractionRadius == 0)
213  //or if the particle distribution is monodispersed.
214  //nextafter(d,std::numeric_limits<Mdouble>::max()) chooses the smallest
215  // Mdouble that is bigger than d.
216  const Mdouble maxCellSize = nextafter(2.0 * maxParticleInteractionRadius * getHGridCellOverSizeRatio(),
217  std::numeric_limits<Mdouble>::max());
218  cellSizes.push_back(maxCellSize);
219  if (getHGridMaxLevels() != 1)
220  {
221 
222  logger(VERBOSE,
223  "While rebuilding the hgrid: the number of levels was set to one, as the particle distribution is monodispersed");
224  }
225  }
226  else
227  {
228  switch (getHGridDistribution())
229  {
230  case LINEAR:
231  {
232  const Mdouble minCellSize = nextafter(2.0 * minParticleInteractionRadius * getHGridCellOverSizeRatio(),
233  0.0);
234  const Mdouble maxCellSize = nextafter(2.0 * maxParticleInteractionRadius * getHGridCellOverSizeRatio(),
235  std::numeric_limits<Mdouble>::max());
236  //std::cout << "HGrid: using a linear cell size distribution from " << minCellSize << " to " << maxCellSize << " over " << getHGridMaxLevels() << " levels" << std::endl;
237  for (unsigned int i = 0; i + 1 < getHGridMaxLevels(); i++)
238  {
239  cellSizes.push_back(minCellSize + (maxCellSize - minCellSize)
240  * (static_cast<Mdouble>(i + 1)) / getHGridMaxLevels());
241  }
242  //The last cell is added separately because in some cases accuracy was lost when calculating it.
243  cellSizes.push_back(maxCellSize);
244  break;
245  }
246  case EXPONENTIAL:
247  {
248  const Mdouble minCellSize = nextafter(2.0 * minParticleInteractionRadius * getHGridCellOverSizeRatio(),
249  0.0);
250  const Mdouble maxCellSize = nextafter(2.0 * maxParticleInteractionRadius * getHGridCellOverSizeRatio(),
251  std::numeric_limits<Mdouble>::max());
252  logger(INFO,"HGrid: using exponential cell size distribution from % to % over % levels",
253  minCellSize,maxCellSize,getHGridMaxLevels());
254  for (unsigned int i = 0; i + 1 < getHGridMaxLevels(); i++)
255  {
256  cellSizes.push_back(minCellSize
257  * std::pow(maxCellSize / minCellSize, static_cast<Mdouble>(i + 1)
258  / getHGridMaxLevels()));
259  }
260  //The last cell is added separately because in some cases accuracy was lost when calculating it.
261  cellSizes.push_back(maxCellSize);
262  break;
263  }
264  case USER:
265  {
266  for (unsigned int i = 0; i < getHGridMaxLevels(); i++)
267  {
268  cellSizes.push_back(userHGridCellSize(i));
269  }
270  break;
271  }
272  case OLDHGRID:
273  {
274  const Mdouble minCellSize = nextafter(2.0 * minParticleInteractionRadius * getHGridCellOverSizeRatio(),
275  0.0);
276 
277  //std::cout<<"HGrid: using the old HGrid cell size distribution starting from " <<minCellSize<<std::endl;
278  for (unsigned int i = 0; i < getHGridMaxLevels(); i++)
279  {
280  cellSizes.push_back(minCellSize * std::pow(2, i));
281  }
282  break;
283  }
284  }
285  }
286 
287 // //Make sure the cell size is at less 10 times the smallest number
288 // for (unsigned int i = 0; i < getHGridMaxLevels(); i++)
289 // {
290 // if (cellSizes[i]<(10+i)*std::numeric_limits<double>::min()) cellSizes[i]=(10+i)*std::numeric_limits<double>::min();
291 // }
292 
293 
294  delete grid;
295 
297 
298  for (BaseParticle* const p : particleHandler)
299  {
302  p->setHGridX(9999);
304  }
305  gridNeedsUpdate_ = false;
306 }
virtual void hGridUpdateParticle(BaseParticle *obj UNUSED)
Definition: DPMBase.cc:1695
Mdouble getHGridCellOverSizeRatio() const
Gets the ratio of the smallest cell over the smallest particle.
Definition: MercuryBase.cc:453
HGrid * grid
A pointer to the HGrid associated with this MercuryBase.
Definition: MercuryBase.h:336
Logger< MERCURY_LOGLEVEL > logger("MercuryKernel")
Definition of different loggers with certain modules. A user can define its own custom logger here...
double Mdouble
Definition: GeneralDefine.h:34
virtual unsigned int getHGridTargetNumberOfBuckets() const
Gets the desired number of buckets, which is the maximum of the number of particles and 10...
Definition: MercuryBase.cc:540
virtual Mdouble getHGridTargetMinInteractionRadius() const
Gets the desired size of the smallest cells of the HGrid.
Definition: MercuryBase.cc:558
const std::complex< Mdouble > i
Definition: ExtendedMath.h:51
unsigned int getHGridMaxLevels() const
Gets the maximum number of levels of the HGrid in this MercuryBase.
Definition: MercuryBase.cc:488
virtual Mdouble getHGridTargetMaxInteractionRadius() const
Gets the desired size of the largest cells of the HGrid.
Definition: MercuryBase.cc:574
void hGridInsertParticle(BaseParticle *obj) final
Inserts a single Particle to current grid.
Definition: MercuryBase.cc:311
In the HGrid class, here all information about the HGrid is stored.
Definition: HGrid.h:42
ParticleHandler particleHandler
An object of the class ParticleHandler, contains the pointers to all the particles created...
Definition: DPMBase.h:1395
HGridDistribution getHGridDistribution() const
Gets how the sizes of the cells of different levels are distributed.
Definition: MercuryBase.cc:431
bool gridNeedsUpdate_
Boolean that indicates whether or not the grid needs to be updated.
Definition: MercuryBase.h:376
virtual Mdouble userHGridCellSize(unsigned int level)
Virtual function that enables inheriting classes to implement a function to let the user set the cell...
Definition: MercuryBase.cc:389
void MercuryBase::hGridUpdateMove ( BaseParticle iP,
Mdouble  move 
)
finalprotectedvirtual

Computes the relative displacement of the given BaseParticle and updates the currentMaxRelativeDisplacement_ accordingly.

(the factor 2.0 is because the displacement is applied after and before the force computation in velocity verlet)

Parameters
[in]iPA pointer to the BaseParticle for which we want to compare the relative speed to the currentMaxRelativeDisplacement_ to.
[in]moveAn Mdouble that represents the square of the distance the BaseParticle has moved.

Reimplemented from DPMBase.

Definition at line 359 of file MercuryBase.cc.

References currentMaxRelativeDisplacement_, getHGrid(), BaseParticle::getHGridLevel(), and mathsFunc::square().

360 {
361  const Mdouble currentRelativeDisplacement = move / mathsFunc::square(getHGrid()->getCellSize(iP->getHGridLevel()));
362  if (currentRelativeDisplacement > currentMaxRelativeDisplacement_)
363  {
364  currentMaxRelativeDisplacement_ = currentRelativeDisplacement;
365  }
366 }
double Mdouble
Definition: GeneralDefine.h:34
HGrid * getHGrid()
Gets the HGrid used by this problem.
Definition: MercuryBase.h:311
T square(const T val)
squares a number
Definition: ExtendedMath.h:106
unsigned int getHGridLevel() const
Returns particle's HGrid level.
Definition: BaseParticle.h:234
Mdouble currentMaxRelativeDisplacement_
Mdouble that denotes the maximum of the displacement of a particle divided by the cell size of the le...
Definition: MercuryBase.h:362
void MercuryBase::read ( std::istream &  is,
ReadOptions  opt = ReadOptions::ReadAll 
)
overridevirtual

Reads the MercuryBase from an input stream, for example a restart file.

Parameters
[in,out]isThe input stream from which the MercuryBase must be read.

This function reads first the properties that are DPMBase related from the given input stream, after that it reads the hGridMaxLevels_ and the hGridCellOverSizeRatio_ from the input stream.

Reimplemented from DPMBase.

Definition at line 104 of file MercuryBase.cc.

References currentMaxRelativeDisplacement_, helpers::getLineFromStringStream(), gridNeedsUpdate_, hGridCellOverSizeRatio_, hGridDistribution_, hGridMethod_, DPMBase::read(), totalCurrentMaxRelativeDisplacement_, and updateEachTimeStep_.

Referenced by Chute::read(), and BaseCluster::read().

105 {
106  DPMBase::read(is, opt);
107 
108  std::stringstream line;
110 
111  std::string dummy;
112 
113  line >> dummy;
114  // if-statement is needed in case a DPMBase (which does not contain the hGrid data)
115  // is read into MercuryBase class
116  if (dummy == "hGrid")
117  {
118  line >> dummy >> hGridMethod_;
119  line >> dummy >> hGridDistribution_;
120  line >> dummy >> hGridCellOverSizeRatio_;
121  //the extra information here is not needed
122  do
123  {
124  line >> dummy;
125  } while (dummy != "gridNeedsUpdate");
126  line >> gridNeedsUpdate_;
127  line >> dummy >> updateEachTimeStep_;
128  line >> dummy >> currentMaxRelativeDisplacement_;
129  line >> dummy >> totalCurrentMaxRelativeDisplacement_;
130  }
131 }
Mdouble totalCurrentMaxRelativeDisplacement_
After each time step, this Mdouble is increased by 2*currentMaxRelativeDisplacement_.
Definition: MercuryBase.h:368
HGridDistribution hGridDistribution_
Indicator for the distribution of the sizes of the cells of different levels of the HGrid...
Definition: MercuryBase.h:354
Mdouble hGridCellOverSizeRatio_
The maximum ratio between the size of the cells and the BaseParticle they contain.
Definition: MercuryBase.h:404
HGridMethod hGridMethod_
Indicator of which way the interactions between different levels are tested.
Definition: MercuryBase.h:348
virtual void read(std::istream &is, ReadOptions opt=ReadOptions::ReadAll)
Reads all data from a restart file, e.g. domain data and particle data.
Definition: DPMBase.cc:3530
void getLineFromStringStream(std::istream &in, std::stringstream &out)
Reads a line from one stringstream into another, and prepares the latter for reading in...
Definition: Helpers.cc:423
bool updateEachTimeStep_
Boolean which indicates whether or not the cell in which a particle is must be updated every time ste...
Definition: MercuryBase.h:382
bool gridNeedsUpdate_
Boolean that indicates whether or not the grid needs to be updated.
Definition: MercuryBase.h:376
Mdouble currentMaxRelativeDisplacement_
Mdouble that denotes the maximum of the displacement of a particle divided by the cell size of the le...
Definition: MercuryBase.h:362
bool MercuryBase::readNextArgument ( int &  i,
int  argc,
char *  argv[] 
)
overrideprotectedvirtual

Reads the next command line argument.

Parameters
[in]iThe ordinal number in the input arguments we want to read.
[in]argcThe number of arguments in the command line, not used.
[in]argvThe command line input arguments.
Returns
A boolean which is true if the argument is found and false otherwise.

Reimplemented from DPMBase.

Definition at line 402 of file MercuryBase.cc.

References DPMBase::readNextArgument(), setHGridCellOverSizeRatio(), and setHGridMaxLevels().

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

403 {
404  if (!strcmp(argv[i], "-hGridMaxLevels"))
405  {
406  setHGridMaxLevels(static_cast<unsigned int>(atoi(argv[i + 1])));
407  }
408  else if (!strcmp(argv[i], "-cellOverSizeRatio"))
409  {
410  setHGridCellOverSizeRatio(atof(argv[i + 1]));
411  }
412  else
413  {
414  return DPMBase::readNextArgument(i, argc, argv); //if argv[i] is not found, check the commands in MD
415  }
416  return true; //returns true if argv[i] is found
417 }
const std::complex< Mdouble > i
Definition: ExtendedMath.h:51
virtual bool readNextArgument(int &i, int argc, char *argv[])
Interprets the i^th command-line argument.
Definition: DPMBase.cc:4349
void setHGridCellOverSizeRatio(Mdouble cellOverSizeRatio)
Sets the ratio of the smallest cell over the smallest particle.
Definition: MercuryBase.cc:463
void setHGridMaxLevels(unsigned int HGridMaxLevels)
Sets the maximum number of levels of the HGrid in this MercuryBase.
Definition: MercuryBase.cc:476
void MercuryBase::setHGridCellOverSizeRatio ( Mdouble  hGridCellOverSizeRatio)

Sets the ratio of the smallest cell over the smallest particle.

Parameters
[in]hGridCellOverSizeRatioThe desired maximum ratio between the cells and the size of the BaseParticle it contains.
Todo:
IFCD: I changed the if unequal to if equal, can someone check this is correct?

Definition at line 463 of file MercuryBase.cc.

References gridNeedsUpdate_, hGridCellOverSizeRatio_, and mathsFunc::isEqual().

Referenced by readNextArgument().

464 {
465  //If the hGridCellOverSizeRatio changes significantly, assign the given parameter.
466  if (!mathsFunc::isEqual(hGridCellOverSizeRatio_, hGridCellOverSizeRatio, 1e-10))
467  {
468  gridNeedsUpdate_ = true;
469  hGridCellOverSizeRatio_ = hGridCellOverSizeRatio;
470  }
471 }
Mdouble hGridCellOverSizeRatio_
The maximum ratio between the size of the cells and the BaseParticle they contain.
Definition: MercuryBase.h:404
bool isEqual(Mdouble v1, Mdouble v2, Mdouble absError)
Compares the difference of two Mdouble with an absolute error, useful in UnitTests.
bool gridNeedsUpdate_
Boolean that indicates whether or not the grid needs to be updated.
Definition: MercuryBase.h:376
void MercuryBase::setHGridDistribution ( HGridDistribution  hGridDistribution)

Sets how the sizes of the cells of different levels are distributed.

Parameters
[in]hGridDistributionThe distribution of the cell sizes that will be used by this MercuryBase.

Definition at line 440 of file MercuryBase.cc.

References gridNeedsUpdate_, and hGridDistribution_.

441 {
442  if (hGridDistribution_ != hGridDistribution)
443  {
444  gridNeedsUpdate_ = true;
445  hGridDistribution_ = hGridDistribution;
446  }
447 }
HGridDistribution hGridDistribution_
Indicator for the distribution of the sizes of the cells of different levels of the HGrid...
Definition: MercuryBase.h:354
bool gridNeedsUpdate_
Boolean that indicates whether or not the grid needs to be updated.
Definition: MercuryBase.h:376
void MercuryBase::setHGridMaxLevels ( unsigned int  hGridMaxLevels)

Sets the maximum number of levels of the HGrid in this MercuryBase.

Parameters
[in]hGridMaxLevelsThe maximum number of levels that will be used in the HGrid.

Definition at line 476 of file MercuryBase.cc.

References gridNeedsUpdate_, and hGridMaxLevels_.

Referenced by readNextArgument(), and ChuteBottom::setupInitialConditions().

477 {
478  if (hGridMaxLevels_ != hGridMaxLevels)
479  {
480  gridNeedsUpdate_ = true;
481  hGridMaxLevels_ = hGridMaxLevels;
482  }
483 }
unsigned int hGridMaxLevels_
Unsigned integer that indicates the maximum number of levels of the HGrid.
Definition: MercuryBase.h:396
bool gridNeedsUpdate_
Boolean that indicates whether or not the grid needs to be updated.
Definition: MercuryBase.h:376
void MercuryBase::setHGridMethod ( HGridMethod  hGridMethod)

Sets the HGridMethod to either BOTTOMUP or TOPDOWN.

Parameters
[in]hGridMethodThe HGridMethod that will be used in this MercuryBase.

Definition at line 423 of file MercuryBase.cc.

References hGridMethod_.

424 {
425  hGridMethod_ = hGridMethod;
426 }
HGridMethod hGridMethod_
Indicator of which way the interactions between different levels are tested.
Definition: MercuryBase.h:348
void MercuryBase::setHGridUpdateEachTimeStep ( bool  updateEachTimeStep)

Sets whether or not the HGrid must be updated every time step.

Parameters
[in]updateEachTimeStepA boolean which indicates if the HGrid must be updated every time step.

Definition at line 176 of file MercuryBase.cc.

References updateEachTimeStep_.

177 {
178  updateEachTimeStep_ = updateEachTimeStep;
179 }
bool updateEachTimeStep_
Boolean which indicates whether or not the cell in which a particle is must be updated every time ste...
Definition: MercuryBase.h:382
Mdouble MercuryBase::userHGridCellSize ( unsigned int  level)
virtual

Virtual function that enables inheriting classes to implement a function to let the user set the cell size of the HGrid.

Parameters
[in]levelThe level of the cell we want to know the size set by the user for.
Returns
The size of the cells at the given level.

Definition at line 389 of file MercuryBase.cc.

References logger, and WARN.

Referenced by hGridRebuild().

390 {
391  logger(WARN, "In Mdouble MercuryBase::userHGridCellSize(unsigned int level) with level= %", level);
392  logger(WARN, "If you want to use user defined HGrid cell sizes, this function should be redefined");
393  return 0.0;
394 }
Logger< MERCURY_LOGLEVEL > logger("MercuryKernel")
Definition of different loggers with certain modules. A user can define its own custom logger here...
void MercuryBase::write ( std::ostream &  os,
bool  writeAllParticles = true 
) const
overridevirtual

Writes all data into a restart file.

Parameters
[in,out]osThe output stream to which this MercuryBase must be written.
[in]writeAllParticlesA boolean which indicates whether or not all BaseParticle from the ParticleHandler must be written to the ostream. If it is set to true or if there are at most 4 BaseParticle, all BaseParticle are written. If it is set to false, only the first two BaseParticle are written, followed by ...

Function that writes this MercuryBase to an output stream, for example a restart file. First writes the domain information, then the walls, followed by the boundaries and particles, and finally the HGrid information.

Reimplemented from DPMBase.

Definition at line 147 of file MercuryBase.cc.

References hGridInfo(), and DPMBase::write().

Referenced by Chute::write(), and BaseCluster::write().

148 {
149  DPMBase::write(os, writeAllParticles);
150  hGridInfo(os);
151 }
virtual void write(std::ostream &os, bool writeAllParticles=true) const
Loads all MD data and plots statistics for all time steps in the .data file.
Definition: DPMBase.cc:3409
void hGridInfo(std::ostream &os=std::cout) const
Writes the info of the HGrid to the screen in a nice format.
Definition: MercuryBase.cc:655

Member Data Documentation

Mdouble MercuryBase::currentMaxRelativeDisplacement_
private

Mdouble that denotes the maximum of the displacement of a particle divided by the cell size of the level of that particle at the current time step. This is useful to see whether a particle could have moved more than one cell.

Definition at line 362 of file MercuryBase.h.

Referenced by constructor(), getHGridCurrentMaxRelativeDisplacement(), hGridActionsAfterIntegration(), hGridActionsBeforeIntegration(), hGridInfo(), hGridUpdateMove(), MercuryBase(), and read().

HGrid* MercuryBase::grid
private

A pointer to the HGrid associated with this MercuryBase.

Definition at line 336 of file MercuryBase.h.

Referenced by constructor(), getHGrid(), hGridInfo(), hGridInsertParticle(), hGridNeedsRebuilding(), hGridRebuild(), MercuryBase(), and ~MercuryBase().

bool MercuryBase::gridNeedsUpdate_
private

Boolean that indicates whether or not the grid needs to be updated.

The grid needs to be updated before the HGrid is constructed and whenever something of the HGrid changes, such as the distribution, the number of levels, etc.

Definition at line 376 of file MercuryBase.h.

Referenced by constructor(), hGridInfo(), hGridNeedsRebuilding(), hGridRebuild(), MercuryBase(), read(), setHGridCellOverSizeRatio(), setHGridDistribution(), and setHGridMaxLevels().

Mdouble MercuryBase::hGridCellOverSizeRatio_
private

The maximum ratio between the size of the cells and the BaseParticle they contain.

The hGrifCellOverSizeRatio_ can be found by dividing the size of the smallest cell by the size of the smallest particle, so this can be set to give particles more space within a cell. Currently, the default is set to 1.

Definition at line 404 of file MercuryBase.h.

Referenced by constructor(), getHGridCellOverSizeRatio(), hGridInfo(), hGridNeedsRebuilding(), MercuryBase(), read(), and setHGridCellOverSizeRatio().

HGridDistribution MercuryBase::hGridDistribution_
private

Indicator for the distribution of the sizes of the cells of different levels of the HGrid. The default is EXPONENTIAL.

Definition at line 354 of file MercuryBase.h.

Referenced by constructor(), getHGridDistribution(), hGridInfo(), MercuryBase(), read(), and setHGridDistribution().

unsigned int MercuryBase::hGridMaxLevels_
private

Unsigned integer that indicates the maximum number of levels of the HGrid.

The number of levels in the HGrid is currently dependent on the maximum number of levels of the HGrid the user has given, either in the constructor or in setHGridMaxLevels, and whether the BaseParticle are monodispersed or not. If they are monodispersed, there is only one level in the HGrid, otherwise there are usually as many levels as the maximum set by the user. Note, by default the code sorts out these parameters itself but they can be overridden by the user.

Definition at line 396 of file MercuryBase.h.

Referenced by constructor(), getHGridMaxLevels(), MercuryBase(), and setHGridMaxLevels().

HGridMethod MercuryBase::hGridMethod_
private

Indicator of which way the interactions between different levels are tested.

If hGridMethod_ is TOPDOWN, then larger particles are inserted into the grid of smaller particles when looking for cross level interactions. If hGridMethod_ is BOTTOMUP, then smaller particles are inserted into the grid of larger particles when looking for cross-level interactions. The default for the hGridMethod_ is TOPDOWN.

Definition at line 348 of file MercuryBase.h.

Referenced by constructor(), getHGridMethod(), hGridInfo(), MercuryBase(), read(), and setHGridMethod().

Mdouble MercuryBase::totalCurrentMaxRelativeDisplacement_
private

After each time step, this Mdouble is increased by 2*currentMaxRelativeDisplacement_.

Definition at line 368 of file MercuryBase.h.

Referenced by constructor(), getHGridTotalCurrentMaxRelativeDisplacement(), hGridActionsAfterIntegration(), hGridActionsBeforeTimeStep(), hGridInfo(), MercuryBase(), and read().

bool MercuryBase::updateEachTimeStep_
private

Boolean which indicates whether or not the cell in which a particle is must be updated every time step.

Definition at line 382 of file MercuryBase.h.

Referenced by constructor(), getHGridUpdateEachTimeStep(), hGridInfo(), MercuryBase(), read(), and setHGridUpdateEachTimeStep().


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