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MercuryDPM
Beta
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MercuryDPM
Beta
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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... | |
| Public Member Functions inherited from MercuryBase | |
| MercuryBase () | |
| This is the default constructor. It sets sensible defaults. More... | |
| ~MercuryBase () | |
| This is the default destructor. More... | |
| MercuryBase (const MercuryBase &mercuryBase) | |
| Copy-constructor. More... | |
| void | constructor () |
| This is the actual constructor, it is called do both constructors above. More... | |
| void | hGridActionsBeforeTimeLoop () override |
| This sets up the broad phase information, has to be done at this stage because it requires the particle size. More... | |
| void | hGridActionsBeforeTimeStep () override |
| Performs all necessary actions before a time-step, like updating the particles and resetting all the bucket information, etc. More... | |
| void | read (std::istream &is) override |
| Reads the MercuryBase from an input stream, for example a restart file. More... | |
| void | write (std::ostream &os, bool writeAllParticles=true) const override |
| Writes the MercuryBase to an output stream, for example a restart file. More... | |
| Mdouble | getHGridCurrentMaxRelativeDisplacement () const |
| Returns hGridCurrentMaxRelativeDisplacement_. More... | |
| Mdouble | getHGridTotalCurrentMaxRelativeDisplacement () const |
| Returns hGridTotalCurrentMaxRelativeDisplacement_. More... | |
| void | setHGridUpdateEachTimeStep (bool updateEachTimeStep) |
| Sets whether or not the HGrid must be updated every time step. More... | |
| bool | getHGridUpdateEachTimeStep () const override |
| 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) override |
| Checks if given BaseParticle has an interaction with a BaseWall or other BaseParticle. 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 () 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 FilesAndRunNumber &other) | |
| Copy constructor type-1. More... | |
| DPMBase (const DPMBase &other) | |
| Copy constructor type-2. More... | |
| virtual | ~DPMBase () |
| virtual destructor More... | |
| void | solve () |
| The work horse of the code. More... | |
| void | checkSettings () |
| Checks if the essentials are set properly to go ahead with solving the problem. More... | |
| virtual void | writeOutputFiles () |
| Writes the simulation data onto all the files i.e. .data, .ene, .fstat ... More... | |
| void | solve (int argc, char *argv[]) |
| The solve function is the work horse of the code with the user input. More... | |
| virtual void | setupInitialConditions () |
| This function allows to set the initial conditions for our problem to be solved, by default particle locations are randomly set. Remember particle properties must also be defined here. More... | |
| virtual void | writeXBallsScript () const |
| This writes a script which can be used to load the xballs problem to display the data just generated. More... | |
| virtual double | getInfo (const BaseParticle &P) const |
| A virtual method that allows the user to overrride and set what is written into the info column in the data file. By default it returns the Species ID number. More... | |
| virtual void | writeRestartFile () |
| Stores all the particle data for current save time step. Calls the write function. More... | |
| int | readRestartFile () |
| Reads all the particle data corresponding to the current saved time step. Which is what the restart file basically stores. The problem description with the latest particle data. More... | |
| int | readRestartFile (std::string fileName) |
| Also reads all the particle data corresponding to the current saved time step. More... | |
| virtual void | readOld (std::istream &is) |
| Reads all particle data into a restart file; old version. More... | |
| bool | readDataFile (const std::string fileName, unsigned int format=0) |
| This allows particle data to be reloaded from data files. More... | |
| bool | readParAndIniFiles (const std::string fileName) |
| Allows the user to read par.ini files (useful to read MDCLR files) More... | |
| bool | readNextDataFile (unsigned int format=0) |
| Reads the next data file with default format=0. However, one can modify the format based on whether the particle data corresponds to 3D or 2D data. See XBalls/xballs.txt. More... | |
| bool | findNextExistingDataFile (Mdouble tMin, bool verbose=true) |
| Useful when fileType is chosen as Multiple Files or Multiple files with padded. More... | |
| bool | readArguments (int argc, char *argv[]) |
| Can interpret main function input arguments that are passed by the driver codes. More... | |
| Mdouble | getTime () const |
| Access function for the time. More... | |
| unsigned int | getNtimeSteps () const |
| Returns the current counter of time steps. More... | |
| void | setTime (Mdouble time) |
| Access function for the time. More... | |
| void | setTimeMax (Mdouble newTMax) |
| Allows the upper time limit to be changed. More... | |
| Mdouble | getTimeMax () const |
| Allows the user to access the total simulation time during the simulation. Cannot change it though. More... | |
| void | setDoCGAlways (bool newDoCGFlag) |
| void | setRotation (bool newRotFlag) |
| Allows to set the flag for enabling or disabling particle rotation in the simulations. More... | |
| bool | getRotation () const |
| Returns a flag indicating if particle rotation is enabled or disabled. More... | |
| bool | getDoCGAlways () const |
| Mdouble | getXMin () const |
| If the length of the problem domain in x-direction is XMax - XMin, then getXMin() returns XMin,. More... | |
| Mdouble | getXMax () const |
| If the length of the problem domain in x-direction is XMax - XMin, then getXMax() returns XMax,. More... | |
| Mdouble | getYMin () const |
| If the length of the problem domain in y-direction is YMax - YMin, then getYMin() returns YMin,. More... | |
| Mdouble | getYMax () const |
| If the length of the problem domain in y-direction is YMax - YMin, then getYMax() returns XMax,. More... | |
| Mdouble | getZMin () const |
| If the length of the problem domain in z-direction is ZMax - ZMin, then getZMin() returns ZMin,. More... | |
| Mdouble | getZMax () const |
| If the length of the problem domain in z-direction is ZMax - ZMin, then getZMax() returns ZMax,. More... | |
| void | setXMin (Mdouble newXMin) |
| If the length of the problem domain in x-direction is XMax - XMin, this method sets XMin. More... | |
| void | setYMin (Mdouble newYMin) |
| If the length of the problem domain in y-direction is YMax - YMin, this method sets YMin. More... | |
| void | setZMin (Mdouble newZMin) |
| If the length of the problem domain in z-direction is ZMax - ZMin, this method sets ZMin. More... | |
| void | setXMax (Mdouble newXMax) |
| If the length of the problem domain in x-direction is XMax - XMin, this method sets XMax. More... | |
| void | setYMax (Mdouble newYMax) |
| If the length of the problem domain in y-direction is YMax - YMin, this method sets YMax. More... | |
| void | setZMax (Mdouble newZMax) |
| If the length of the problem domain in z-direction is XMax - XMin, this method sets ZMax. More... | |
| void | setTimeStep (Mdouble newDt) |
| Allows the time step dt to be changed. More... | |
| Mdouble | getTimeStep () const |
| Allows the time step dt to be accessed. More... | |
| void | setXBallsColourMode (int newCMode) |
| Set the xball output mode. More... | |
| int | getXBallsColourMode () const |
| Get the xball colour mode (CMode) More... | |
| void | setXBallsVectorScale (double newVScale) |
| Set the scale of vectors in xballs. More... | |
| double | getXBallsVectorScale () const |
| Returns the scale of vectors used in xballs. More... | |
| void | setXBallsAdditionalArguments (std::string newXBArgs) |
| Set the additional arguments for xballs. More... | |
| std::string | getXBallsAdditionalArguments () const |
| void | setXBallsScale (Mdouble newScale) |
| Sets the scale of the view (either normal, zoom in or zoom out) to display in xballs. The default is fit to screen. More... | |
| double | getXBallsScale () const |
| Returns the scale of the view in xballs. More... | |
| void | setGravity (Vec3D newGravity) |
| Allows to modify the gravity vector. More... | |
| Vec3D | getGravity () const |
| Returns the gravity vector. More... | |
| void | setDimension (unsigned int newDim) |
| Sets the system and particle dimension. More... | |
| void | setSystemDimensions (unsigned int newDim) |
| Allows for the dimension of the simulation to be changed. More... | |
| unsigned int | getSystemDimensions () const |
| Returns the dimension of the simulation. Note there is also a particle dimension. More... | |
| void | setParticleDimensions (unsigned int particleDimensions) |
| Allows the dimension of the particle (f.e. for mass) to be changed. e.g. discs or spheres. More... | |
| unsigned int | getParticleDimensions () const |
| Returns the particle dimensions. More... | |
| std::string | getRestartVersion () const |
| This is to take into account for different Mercury versions. Returns the version of the restart file. More... | |
| void | setRestartVersion (std::string newRV) |
| Sets restart_version. More... | |
| bool | getRestarted () const |
| Returns the flag denoting if the simulation was restarted or not. More... | |
| void | setRestarted (bool newRestartedFlag) |
| Allows to set the flag stating if the simulation is to be restarted or not. More... | |
| bool | getAppend () const |
| Returns the flag denoting if the append option is on or off. More... | |
| void | setAppend (bool newAppendFlag) |
| Allows to set the append option. More... | |
| Mdouble | getElasticEnergy () const |
| Returns the global elastic energy within the system. More... | |
| Mdouble | getKineticEnergy () const |
| Returns the global kinetic energy stored in the system. More... | |
| bool | areInContact (const BaseParticle *pI, const BaseParticle *pJ) const |
| Checks if two particle are in contact or is there any positive overlap. More... | |
| virtual void | hGridInsertParticle (BaseParticle *obj UNUSED) |
| no implementation but can be overidden in its derived classes. More... | |
| virtual void | hGridUpdateParticle (BaseParticle *obj UNUSED) |
| no implementation but can be overidden in its derived classes. More... | |
| virtual void | hGridRemoveParticle (BaseParticle *obj UNUSED) |
| no implementation but can be overidden in its derived classes. More... | |
| virtual void | gatherContactStatistics (unsigned int index1 UNUSED, int index2 UNUSED, Vec3D Contact UNUSED, Mdouble delta UNUSED, Mdouble ctheta UNUSED, Mdouble fdotn UNUSED, Mdouble fdott UNUSED, Vec3D P1_P2_normal_ UNUSED, Vec3D P1_P2_tangential UNUSED) |
| //Not unsigned index because of possible wall collisions. More... | |
| Public Member Functions inherited from FilesAndRunNumber | |
| FilesAndRunNumber () | |
| Constructor. More... | |
| FilesAndRunNumber (const FilesAndRunNumber &other) | |
| Copy constructor. More... | |
| virtual | ~FilesAndRunNumber () |
| Constructor. More... | |
| void | constructor () |
| a function called by the FilesAndRunNumber() (constructor) More... | |
| void | incrementRunNumberInFile () |
| Increment the run Number (counter value) stored in the file_counter (COUNTER_DONOTDEL) by 1 and store the new value in the counter file. More... | |
| int | readRunNumberFromFile () |
| Read the run number or the counter from the counter file (COUNTER_DONOTDEL) More... | |
| void | autoNumber () |
| The autoNumber() function is the trigger. It calls three functions. setRunNumber(), readRunNumberFromFile() and incrementRunNumberInFile(). More... | |
| std::vector< int > | get2DParametersFromRunNumber (int size_x, int size_y) |
| This turns a counter into two indices which is an amazing feature for doing two dimensional parameter studies. The indices run from 1:size_x and 1:size_y, while the study number starts at 0 ( initially the counter=1 in COUNTER_DONOTDEL) More... | |
| int | launchNewRun (const char *name, bool quick=false) |
| This launches a code from within this code. Please pass the name of the code to run. More... | |
| void | setRunNumber (int runNumber) |
| This sets the counter/Run number, overriding the defaults. More... | |
| int | getRunNumber () const |
| This returns the current value of the counter (runNumber_) More... | |
| void | read (std::istream &is) |
| Accepts an input stream std::istream. More... | |
| void | write (std::ostream &os) const |
| Accepts an output stream read function, which accepts an input stream std::ostream. More... | |
| Public Member Functions inherited from Files | |
| Files () | |
| A constructor. More... | |
| virtual | ~Files () |
| A destructor, watch out its a virtual destructor. More... | |
| Files (const Files &other) | |
| Copy constructor. More... | |
| MERCURY_DEPRECATED File & | getDataFile () |
| The non const version. Allows one to edit the File::dataFile. More... | |
| MERCURY_DEPRECATED File & | getEneFile () |
| The non const version. Allows to edit the File::eneFile. More... | |
| MERCURY_DEPRECATED File & | getFStatFile () |
| The non const version. Allows to edit the File::fStatFile. More... | |
| MERCURY_DEPRECATED File & | getRestartFile () |
| The non const version. Allows to edit the File::restartFile. More... | |
| MERCURY_DEPRECATED File & | getStatFile () |
| The non const version. Allows to edit the File::statFile. More... | |
| MERCURY_DEPRECATED const File & | getDataFile () const |
| The const version. Does not allow for any editing of the File::dataFile. More... | |
| MERCURY_DEPRECATED const File & | getEneFile () const |
| The const version. Does not allow for any editing of the File::eneFile. More... | |
| MERCURY_DEPRECATED const File & | getFStatFile () const |
| The const version. Does not allow for any editing of the File::fStatFile. More... | |
| MERCURY_DEPRECATED const File & | getRestartFile () const |
| The const version. Does not allow for any editing of the File::restartFile. More... | |
| MERCURY_DEPRECATED const File & | getStatFile () const |
| The const version. Does not allow for any editing of the File::statFile. More... | |
| const std::string & | getName () const |
| Returns the name of the file. Does not allow to change it though. More... | |
| void | setName (const std::string &name) |
| Allows to set the name of all the files (ene, data, fstat, restart, stat) More... | |
| void | setName (const char *name) |
| Calls setName(std::string) More... | |
| void | setSaveCount (unsigned int saveCount) |
| Sets File::saveCount_ for all files (ene, data, fstat, restart, stat) More... | |
| void | setFileType (FileType fileType) |
| Sets File::fileType_ for all files (ene, data, fstat, restart, stat) More... | |
| void | setOpenMode (std::fstream::openmode openMode) |
| Sets File::openMode_ for all files (ene, data, fstat, restart, stat) More... | |
| void | resetFileCounter () |
| Resets the file counter for each file i.e. for ene, data, fstat, restart, stat) More... | |
| void | read (std::istream &is) |
| Extracts data from the input stream (which is basically a file you want to read from) into name_, restartFile .... More... | |
| void | write (std::ostream &os) const |
| Writes data into a file from the member variables name_, restartFile, dataFile etc. More... | |
| void | openFiles () |
| Opens all the files (ene, data, fstat, restart, stat) for reading and writing purposes. More... | |
| void | closeFiles () |
| Closes all files (ene, data, fstat, restart, stat) that were opened to read or write. More... | |
| void | setNextSavedTimeStep (unsigned int nextSavedTimeStep) |
| Sets the next time step for all the files (ene, data, fstat, restart, stat) at which the data is to be written or saved. More... | |
Protected Member Functions | |
| virtual void | hGridFindContactsWithinTargetCell (int x, int y, int z, unsigned int l) |
| Finds contacts between particles in the target cell. More... | |
| virtual void | hGridFindContactsWithTargetCell (int x, int y, int z, unsigned int l, BaseParticle *obj) |
| Finds contacts between the BaseParticle and the target cell. More... | |
| void | hGridFindOneSidedContacts (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) |
| 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) override |
| Inserts a single Particle to current grid. More... | |
| void | broadPhase (BaseParticle *i) override |
| This checks particles in the HGRID to see if for closer enough for possible contact. More... | |
| void | hGridUpdateMove (BaseParticle *iP, Mdouble move) override |
| 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 |
| Sets the totalCurrentMaxRelativeDisplacement_ as 2*currentMaxRelativeDisplacement_. More... | |
| HGrid * | getHGrid () |
| Gets the HGrid used by this problem. More... | |
| const HGrid * | getHGrid () const |
| Gets the HGrid used by this problem, const version. More... | |
| bool | readNextArgument (int &i, int argc, char *argv[]) override |
| Reads the next command line argument. More... | |
| Protected Member Functions inherited from DPMBase | |
| virtual void | computeAllForces () |
| Computes all the forces acting on the particles by using the setTorque and setForce methods. See BaseInteractible.cc. More... | |
| virtual void | computeInternalForces (BaseParticle *i) |
| Computes the forces between particles (internal in the sense that the sum over all these forces is zero i.e. fully modelled forces) More... | |
| virtual void | computeInternalForces (BaseParticle *P1, BaseParticle *P2) |
| Computes the forces between particles (internal in the sense that the sum over all these forces is zero i.e. fully modelled forces) More... | |
| virtual void | computeExternalForces (BaseParticle *PI) |
| Computes the external forces acting on particles (e.g. gravitational) More... | |
| virtual void | computeForcesDueToWalls (BaseParticle *PI) |
| Computes the forces on the particles due to the walls (normals are outward normals) More... | |
| virtual void | actionsOnRestart () |
| A virtual function where the users can add extra code which is executed only when the code is restarted. More... | |
| virtual void | actionsBeforeTimeLoop () |
| A virtual function. Allows one to carry out any operations before the start of the time loop. More... | |
| virtual void | actionsBeforeTimeStep () |
| A virtual function which allows to define operations to be executed before the new time step. More... | |
| virtual void | actionsAfterSolve () |
| A virtual function which allows to define operations to be executed after the solve(). More... | |
| virtual void | actionsAfterTimeStep () |
| A virtual function which allows to define operations to be executed after time step. More... | |
| virtual void | outputXBallsData (std::ostream &os) const |
| This function writes the location of the walls and particles in a format the XBalls program can read. See XBalls/xballs.txt. However, MercuryDPM supports a much better viewer now called Paraview. See the tutorials section in the documentation. More... | |
| virtual void | outputXBallsDataParticle (const unsigned int i, const unsigned int format, std::ostream &os) const |
| This function writes out the particle locations into an output stream in a format the XBalls program can read. More... | |
| virtual void | writeEneHeader (std::ostream &os) const |
| Writes a header with a certain format for ENE file. More... | |
| virtual void | writeFstatHeader (std::ostream &os) const |
| Writes a header with a certain format for FStat file. More... | |
| virtual void | writeEneTimestep (std::ostream &os) const |
| This function enables one to write the global energy available in the system after each time step. The default is to compute the rotational and translational kinetic energy, potential energy and the centre of mass. More... | |
| virtual void | initialiseStatistics () |
| no implementation but can be overidden in its derived classes. More... | |
| virtual void | outputStatistics () |
| no implementation but can be overidden in its derived classes. More... | |
| void | gatherContactStatistics () |
| virtual void | processStatistics (bool usethese UNUSED) |
| no implementation but can be overidden in its derived classes. More... | |
| virtual void | finishStatistics () |
| no implementation but can be overidden in its derived classes. More... | |
| virtual void | integrateBeforeForceComputation () |
| This is were the integration is done, at the moment it is velocity Verlet integration and is done before the forces are computed. See http://en.wikipedia.org/wiki/Verlet_integration#Velocity_Verlet. More... | |
| virtual void | integrateAfterForceComputation () |
| Integration is done after force computations. We apply the Velocity verlet scheme. See http://en.wikipedia.org/wiki/Verlet_integration#Velocity_Verlet. More... | |
| virtual void | checkInteractionWithBoundaries () |
| There are a range of boundaries one could implement depending on ones' problem. This methods checks for interactions between particles and such range of boundaries. See BaseBoundary.h and all the boundaries in the Boundaries folder. More... | |
| void | setFixedParticles (unsigned int n) |
| void | initialiseTangentialSprings () |
| virtual void | printTime () const |
| Displays the current simulation time onto your screen for example. More... | |
| virtual bool | continueSolve () const |
| void | outputInteractionDetails () const |
| Displays the interaction details corresponding to the pointer objects in the interaction handler. More... | |
| bool | isTimeEqualTo (Mdouble time) const |
| Checks if the input variable "time" is the current time in the simulation. More... | |
| void | removeDuplicatePeriodicParticles () |
| Removes periodic duplicate Particles. More... | |
| void | checkAndDuplicatePeriodicParticles () |
| In case of periodic boundaries, the below methods checks and adds particles when necessary into the particle handler. See DPMBase.cc and PeriodicBoundary.cc for more details. More... | |
Additional Inherited Members | |
| Public Attributes inherited from DPMBase | |
| SpeciesHandler | speciesHandler |
| A handler to that stores the species type i.e. elastic, linear visco-elastic... et cetera. More... | |
| RNG | random |
| This is a random generator, often used for setting up the initial conditions etc... More... | |
| ParticleHandler | particleHandler |
| An object of the class ParticleHandler, contains the pointers to all the particles created. More... | |
| WallHandler | wallHandler |
| An object of the class WallHandler. Contains pointers to all the walls created. More... | |
| BoundaryHandler | boundaryHandler |
| An object of the class BoundaryHandler which concerns insertion and deletion of particles into or from regions. More... | |
| InteractionHandler | interactionHandler |
| An object of the class InteractionHandler. More... | |
| Public Attributes inherited from Files | |
| File | dataFile |
| An instance of class File to handle in- and output into a .data file. More... | |
| File | fStatFile |
| An instance of class File to handle in- and output into a .fstat file. More... | |
| File | eneFile |
| An instance of class File to handle in- and output into a .ene file. More... | |
| File | restartFile |
| An instance of class File to handle in- and output into a .restart file. More... | |
| File | statFile |
| An instance of class File to handle in- and output into a .stat file. More... | |
This adds on the hierarchical grid code for 3D problems.
Definition at line 35 of file Mercury3D.h.
| 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.
| Mercury3D::Mercury3D | ( | const DPMBase & | other | ) |
Copy-constructor for creates an Mercury3D problem from an existing MD problem.
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.
| Mercury3D::Mercury3D | ( | const Mercury3D & | other | ) |
Copy-constructor.
| [in] | other | Mercury3D 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.
| 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().
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protectedvirtual |
Finds contacts between particles in the target cell.
| [in] | x | Coordinate of the target cell in x direction. |
| [in] | y | Coordinate of the target cell in y direction. |
| [in] | z | Coordinate of the target cell in z direction. |
| [in] | l | Level 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.
Definition at line 73 of file Mercury3D.cc.
References HGrid::computeHashBucketIndex(), DPMBase::computeInternalForces(), HGrid::getBucketIsChecked(), HGrid::getFirstBaseParticleInBucket(), MercuryBase::getHGrid(), BaseParticle::getHGridLevel(), BaseParticle::getHGridNextObject(), BaseParticle::getHGridX(), BaseParticle::getHGridY(), BaseParticle::getHGridZ(), and HGrid::setBucketIsChecked().
Referenced by hGridFindOneSidedContacts().
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protectedvirtual |
Finds contacts between the BaseParticle and the target cell.
| [in] | x | The coordinate of the target cell in x direction. |
| [in] | y | The coordinate of the target cell in y direction. |
| [in] | z | The coordinate of the target cell in z direction. |
| [in] | l | The level in the HGrid of the target cell. |
| [in] | obj | A 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::computeInternalForces(), HGrid::getFirstBaseParticleInBucket(), MercuryBase::getHGrid(), BaseParticle::getHGridLevel(), BaseParticle::getHGridNextObject(), BaseParticle::getHGridX(), BaseParticle::getHGridY(), and BaseParticle::getHGridZ().
Referenced by hGridFindOneSidedContacts().
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overrideprotectedvirtual |
Finds contacts with the BaseParticle; avoids multiple checks.
| [in] | obj | A 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.
Implements MercuryBase.
Definition at line 149 of file Mercury3D.cc.
References BOTTOMUP, MercuryBase::getHGrid(), BaseParticle::getHGridLevel(), MercuryBase::getHGridMethod(), BaseParticle::getHGridX(), BaseParticle::getHGridY(), BaseParticle::getHGridZ(), BaseParticle::getInteractionRadius(), HGrid::getInvCellSize(), HGrid::getNumberOfLevels(), HGrid::getOccupiedLevelsMask(), BaseInteractable::getPosition(), hGridFindContactsWithinTargetCell(), hGridFindContactsWithTargetCell(), TOPDOWN, Vec3D::X, Vec3D::Y, and Vec3D::Z.
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protected |
Tests if the BaseParticle has contacts with other Particles in the target cell.
| [in] | x | The coordinate of the target cell in x direction. |
| [in] | y | The coordinate of the target cell in y direction. |
| [in] | z | The coordinate of the target cell in z direction. |
| [in] | l | The level of the HGrid of the target cell. |
| [in] | obj | A 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 381 of file Mercury3D.cc.
References DPMBase::areInContact(), HGrid::computeHashBucketIndex(), HGrid::getFirstBaseParticleInBucket(), MercuryBase::getHGrid(), BaseParticle::getHGridLevel(), BaseParticle::getHGridNextObject(), BaseParticle::getHGridX(), BaseParticle::getHGridY(), and BaseParticle::getHGridZ().
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overrideprotectedvirtual |
Tests if a BaseParticle has any contacts in the HGrid.
| [in] | obj | A 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 409 of file Mercury3D.cc.
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protected |
Removes a BaseParticle from the HGrid.
| [in] | obj | A pointer to the BaseParticle that needs to be removed. |
Removes the given BaseParticle from the HGrid.
Definition at line 347 of file Mercury3D.cc.
References HGrid::computeHashBucketIndex(), HGrid::getFirstBaseParticleInBucket(), MercuryBase::getHGrid(), BaseParticle::getHGridLevel(), BaseParticle::getHGridNextObject(), BaseParticle::getHGridPrevObject(), BaseParticle::getHGridX(), BaseParticle::getHGridY(), BaseParticle::getHGridZ(), HGrid::setFirstBaseParticleInBucket(), BaseParticle::setHGridNextObject(), and BaseParticle::setHGridPrevObject().
Referenced by hGridUpdateParticle().
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overrideprotected |
Updates the cell (not the level) of a BaseParticle.
| [in] | obj | A pointer to the BaseParticle that must be updated. |
Updates the HGrid positions (x, y and z) of the given BaseParticle.
Definition at line 287 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.
1.8.7 
