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MercuryDPM
Alpha
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MercuryDPM
Alpha
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This adds on the hierarchical grid code for 2D problems. More...
#include <Mercury2D.h>
Inheritance diagram for Mercury2D:Public Member Functions | |
| Mercury2D () | |
| This is the default constructor. All it does is set sensible defaults. More... | |
| Mercury2D (const DPMBase &other) | |
| Copy-constructor for creates an Mercury2D problem from an existing MD problem. More... | |
| Mercury2D (const Mercury2D &other) | |
| Copy-constructor. More... | |
| void | constructor () |
| Function that sets the ParticleDimensions and SystemDimensions to 2. 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... | |
| bool | checkParticleForInteractionLocal (const BaseParticle &P) override |
| 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... | |
| bool | readRestartFile (bool restarted=true) |
| 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. Returns 0 if it is successful, 1 otherwise. More... | |
| int | readRestartFile (std::string fileName) |
| The same as readRestartFile(bool), but also reads all the particle data corresponding to the current saved time step. More... | |
| virtual bool | readUserDefinedWall (std::string type, std::istream &is) |
| 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 (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... | |
| bool | checkParticleForInteractionLocalPeriodic (const BaseParticle &P) |
| 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... | |
| void | setWallsWriteVTK (FileType writeWallsVTK) |
| Allows to set the flag for enabling or disabling particle rotation in the simulations. More... | |
| void | setParticlesWriteVTK (bool writeParticlesVTK) |
| Allows to set the flag for enabling or disabling particle rotation in the simulations. More... | |
| FileType | getWallsWriteVTK () const |
| Returns a flag indicating if particle rotation is enabled or disabled. More... | |
| bool | getParticlesWriteVTK () const |
| Returns a flag indicating if particle rotation is enabled or disabled. More... | |
| bool | getDoCGAlways () const |
| Vec3D | getMin () const |
| Return the "bottom left" corner of the domain, a vector with xMin_, yMin_ and zMin_. More... | |
| Vec3D | getMax () const |
| Return the "upper right" corner of the domain, a vector with xMin_, yMin_ and zMin_. More... | |
| 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 | setMin (Vec3D min) |
| Sets the values xMin, yMin, zMin of the problem domain, which is [xMin,xMax]x[yMin,yMax]x[zMin,zMax]. More... | |
| void | setMax (Vec3D max) |
| Sets the values xMax, yMax, zMax of the problem domain, which is [xMin,xMax]x[yMin,yMax]x[zMin,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... | |
| int | getAddLarge () const |
| returns the number of large particles that are to be added on restart. More... | |
| int | getAddSmall () const |
| returns the number of small particles that are to be added on restart. More... | |
| void | setAddLarge (int new_addL) |
| sets the number of large particles that are to be added on restart. More... | |
| void | setAddSmall (int new_addS) |
| sets the number of small particles that are to be added on restart. 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 |
| 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) |
| 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... | |
| Mdouble | getGravitationalEnergy () const |
| Returns the global gravitational potential 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, unsigned int l) |
| Finds contacts between particles the in the target cell. More... | |
| virtual void | hGridFindContactsWithTargetCell (int x, int y, unsigned int l, BaseParticle *obj) |
| Finds contacts between given BaseParticle and the BaseParticle in the target cell. More... | |
| void | hGridFindOneSidedContacts (BaseParticle *obj) override |
| Finds contacts with the BaseParticle; avoids multiple checks. More... | |
| bool | hGridHasContactsInTargetCell (int x, int y, 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 |
| Test if a BaseParticle has any contacts in the HGrid. More... | |
| void | hGridRemoveParticle (BaseParticle *obj) override |
| Removes a BaseParticle to 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... | |
| Mdouble | domainSize () const |
| void | writeVTK () const |
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 2D problems.
Definition at line 35 of file Mercury2D.h.
| Mercury2D::Mercury2D | ( | ) |
This is the default constructor. All it does is set sensible defaults.
Definition at line 29 of file Mercury2D.cc.
References constructor(), DEBUG, and logger.
| Mercury2D::Mercury2D | ( | const DPMBase & | other | ) |
Copy-constructor for creates an Mercury2D problem from an existing MD problem.
Makes a Mercury2D class from a DPMBase class, so it adds the HGrid functionality to the class. Note that the copy-constructor of DPMBase has to be called because the link from DPMBase to MercuryBase is virtual.
Definition at line 52 of file Mercury2D.cc.
References constructor(), DEBUG, and logger.
| Mercury2D::Mercury2D | ( | const Mercury2D & | other | ) |
Copy-constructor.
| [in] | other | Mercury2D 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 Mercury2D.cc.
| void Mercury2D::constructor | ( | ) |
Function that sets the ParticleDimensions and SystemDimensions to 2.
Definition at line 59 of file Mercury2D.cc.
References DPMBase::setParticleDimensions(), and DPMBase::setSystemDimensions().
Referenced by Mercury2D().
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protectedvirtual |
Finds contacts between particles the in the target cell.
| [in] | x | Coordinate of this cell in x direction. |
| [in] | y | Coordinate of this cell in y direction. |
| [in] | l | Level in the HGrid of this cell. |
Computes all collision between particles in the same bucket as cell (x,y,l), for all particles from the same cell.
Definition at line 72 of file Mercury2D.cc.
References HGrid::computeHashBucketIndex(), DPMBase::computeInternalForces(), HGrid::getBucketIsChecked(), HGrid::getFirstBaseParticleInBucket(), MercuryBase::getHGrid(), BaseParticle::getHGridLevel(), BaseParticle::getHGridNextObject(), BaseParticle::getHGridX(), BaseParticle::getHGridY(), and HGrid::setBucketIsChecked().
Referenced by hGridFindOneSidedContacts().
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protectedvirtual |
Finds contacts between given BaseParticle and the BaseParticle in the target cell.
| [in] | x | Coordinate in x direction of the cell we want to find collisions for. |
| [in] | y | Coordinate in y direction of the cell we want to find collisions for. |
| [in] | l | The level in the HGrid of the cell we want to find collisions for. |
| [in] | obj | The BaseParticle we want to check for collisions in the cell (x,y,l). |
Computes all collisions between given BaseParticle and particles in cell (x,y,l), where the given BaseParticle does currently not belong to that cell. First this function makes sure this BaseParticle is not in the target cell, then it computes the internal forces between the given BaseParticle and the BaseParticle in the target cell.
Definition at line 114 of file Mercury2D.cc.
References HGrid::computeHashBucketIndex(), DPMBase::computeInternalForces(), HGrid::getFirstBaseParticleInBucket(), MercuryBase::getHGrid(), BaseParticle::getHGridLevel(), BaseParticle::getHGridNextObject(), BaseParticle::getHGridX(), and BaseParticle::getHGridY().
Referenced by hGridFindOneSidedContacts().
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overrideprotectedvirtual |
Finds contacts with the BaseParticle; avoids multiple checks.
| [in] | obj | The BaseParticle we want to check for collisions in the HGrid. |
Computes all collision between given BaseParticle and all other particles in the grid (of all levels).
Implements MercuryBase.
Definition at line 145 of file Mercury2D.cc.
References BOTTOMUP, MercuryBase::getHGrid(), BaseParticle::getHGridLevel(), MercuryBase::getHGridMethod(), BaseParticle::getHGridX(), BaseParticle::getHGridY(), BaseParticle::getInteractionRadius(), HGrid::getInvCellSize(), HGrid::getNumberOfLevels(), HGrid::getOccupiedLevelsMask(), BaseInteractable::getPosition(), hGridFindContactsWithinTargetCell(), hGridFindContactsWithTargetCell(), TOPDOWN, Vec3D::X, and Vec3D::Y.
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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] | l | The level in the HGrid of the target cell. |
| [in] | obj | A pointer to the BaseParticle for which we want to find contacts. |
Tests if there are any collisions between given BaseParticle and particles in cell (x, y, l). Do this by going through all BaseParticle in the bucket, and return true if there is a contact between the given BaseParticle and the BaseParticle we're checking for. If there is no contact, go on to the next BaseParticle until either a contact has been found or all BaseParticle have been tested. If there were no contacts, return false.
Definition at line 352 of file Mercury2D.cc.
Referenced by hGridHasParticleContacts().
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overrideprotectedvirtual |
Test if a BaseParticle has any contacts in the HGrid.
| [in] | obj | A pointer to the BaseParticle which we want to check for contacts. |
Tests if there are any collisions between given BaseParticle and all other particles in the HGrid. It does this by first rebuilding the HGrid if necessary, and then for all levels first computing what the area for checking needs to be, and then check for interactions in the appropriate grid cells.
Implements MercuryBase.
Definition at line 380 of file Mercury2D.cc.
References MercuryBase::getHGrid(), BaseParticle::getInteractionRadius(), HGrid::getInvCellSize(), HGrid::getNumberOfLevels(), HGrid::getOccupiedLevelsMask(), BaseInteractable::getPosition(), hGridHasContactsInTargetCell(), MercuryBase::hGridRebuild(), INFO, logger, VERBOSE, Vec3D::X, and Vec3D::Y.
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overrideprotected |
Removes a BaseParticle to the HGrid.
| [in] | obj | The BaseParticle that has to be removed from the HGrid. |
Removes BaseParticle from the HGrid. First check which bucket the BaseParticle is in, then set the pointers correctly again.
Definition at line 311 of file Mercury2D.cc.
References HGrid::computeHashBucketIndex(), HGrid::getFirstBaseParticleInBucket(), MercuryBase::getHGrid(), BaseParticle::getHGridLevel(), BaseParticle::getHGridNextObject(), BaseParticle::getHGridPrevObject(), BaseParticle::getHGridX(), BaseParticle::getHGridY(), 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 | The BaseParticle we want to update the position in the grid for. |
Updates the HGrid positions (x and y) of the given BaseParticle.
Definition at line 253 of file Mercury2D.cc.
References HGrid::computeHashBucketIndex(), HGrid::getFirstBaseParticleInBucket(), MercuryBase::getHGrid(), BaseParticle::getHGridLevel(), BaseParticle::getHGridX(), BaseParticle::getHGridY(), HGrid::getInvCellSize(), BaseInteractable::getPosition(), hGridRemoveParticle(), HGrid::setFirstBaseParticleInBucket(), BaseParticle::setHGridNextObject(), BaseParticle::setHGridPrevObject(), BaseParticle::setHGridX(), BaseParticle::setHGridY(), Vec3D::X, and Vec3D::Y.
1.8.7 
