revision: v0.14
statistics_while_running< T > Class Template Reference
+ Inheritance diagram for statistics_while_running< T >:

Public Member Functions

 statistics_while_running ()
 
void actionsBeforeTimeStep ()
 A virtual function which allows to define operations to be executed before the new time step. More...
 
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...
 
void printTime () const
 Displays the current simulation time and the maximum simulation duration. More...
 
void auto_set_domain ()
 
 statistics_while_running ()
 
void actionsBeforeTimeStep ()
 A virtual function which allows to define operations to be executed before the new time step. More...
 
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...
 
void printTime () const
 Displays the current simulation time and the maximum simulation duration. More...
 
void auto_set_domain ()
 
 statistics_while_running ()
 
void run (int argc, char *argv[])
 
void actionsBeforeTimeStep ()
 A virtual function which allows to define operations to be executed before the new time step. More...
 
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...
 
void printTime ()
 
void auto_set_z ()
 
void initialiseStatistics ()
 
void processStatistics ()
 
void finishStatistics ()
 
bool writeToFile (string filename, string text)
 
bool appendToFile (string filename, string text)
 
 statistics_while_running ()
 
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...
 
 statistics_while_running ()
 
void actionsBeforeTimeStep ()
 A virtual function which allows to define operations to be executed before the new time step. More...
 
void actionsBeforeTimeLoop ()
 A virtual function. Allows one to carry out any operations before the start of the time loop. More...
 
void printTime ()
 
void auto_set_z ()
 
 statistics_while_running ()
 
void actionsBeforeTimeStep ()
 A virtual function which allows to define operations to be executed before the new time step. More...
 
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...
 
void printTime ()
 
void auto_set_z ()
 
 statistics_while_running ()
 
void run (int argc, char *argv[])
 
void actionsBeforeTimeStep () override
 A virtual function which allows to define operations to be executed before the new time step. More...
 
void setupInitialConditions () override
 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...
 
void printTime () const override
 Displays the current simulation time and the maximum simulation duration. More...
 
void auto_set_z ()
 
void initialiseStatistics () override
 
void finishStatistics () override
 
bool writeToFile (std::string filename, std::string text)
 
bool appendToFile (std::string filename, std::string text)
 
- Public Member Functions inherited from StatisticsVector< T >
void constructor ()
 this is the actual constructor, sets up all basic things More...
 
void constructor (std::string name)
 
 StatisticsVector ()
 Basic constructor only calls constructor() More...
 
 StatisticsVector (std::string name)
 
 StatisticsVector (StatisticsVector &other)
 Copy constructor. More...
 
 StatisticsVector (int argc, char *argv[])
 Advanced constructor that accepts arguments from the command line. More...
 
void readStatArguments (int argc, char *argv[])
 
std::string printStat ()
 Outputs member variable values to a std::string. More...
 
void set_statType ()
 
void writeOutputFiles ()
 
void print_help ()
 
void setNX (int new_)
 
void set_hx (Mdouble hx)
 
void setNY (int new_)
 
void set_hy (Mdouble hy)
 
void setNZ (int new_)
 
void set_hz (Mdouble hz)
 
void setN (int n)
 
void set_h (Mdouble h)
 
int getNX ()
 
int getNY ()
 
int getNZ ()
 
void setCGTimeMin (Mdouble t)
 
void setTimeMaxStat (Mdouble t)
 
void setCGTimeAveragingInterval (Mdouble t)
 
Mdouble getCGTimeMin ()
 
Mdouble getTimeMaxStat ()
 
Mdouble getCGTimeAveragingInterval ()
 
bool check_current_time_for_statistics ()
 
void setCGShape (const char *new_)
 
void setCGShape (CG_TYPE new_)
 
CG_TYPE getCGShape ()
 
void setN (int nx_, int ny_, int nz_)
 
void getN (int &nx_, int &ny_, int &nz_)
 
void setCGWidth (Mdouble w)
 Set CG variables w2 and CG_invvolume. More...
 
void setCGWidth2 (Mdouble new_)
 Set CG variables w2 and CG_invvolume. More...
 
Mdouble getCGWidth ()
 
Mdouble getCGWidthSquared ()
 
Mdouble getCutoff ()
 
Mdouble getCutoff2 ()
 
std::string print_CG ()
 Output coarse graining variables. More...
 
StatisticsPoint< T > average (std::vector< StatisticsPoint< T > > &P)
 Output average of statistical variables. More...
 
virtual void reset_statistics ()
 Set all statistical variables to zero. More...
 
void statistics_from_fstat_and_data ()
 get StatisticsPoint More...
 
void statistics_from_p3 ()
 
void jump_p3c ()
 
void setDoTimeAverage (bool new_)
 
bool getDoTimeAverage ()
 
void setStressTypeForFixedParticles (int new_)
 
int getStressTypeForFixedParticles ()
 
void set_infiniteStressForFixedParticles (bool new_)
 
void setMirrorAtDomainBoundary (Mdouble new_)
 
Mdouble getMirrorAtDomainBoundary ()
 
void setDoVariance (bool new_)
 
bool getDoVariance ()
 
void setDoGradient (bool new_)
 
bool getDoGradient ()
 
void setSuperExact (bool new_)
 
bool getSuperExact ()
 
void setDoIgnoreFixedParticles (bool new_)
 
bool getDoIgnoreFixedParticles ()
 
void verbose ()
 
void setVerbosityLevel (int new_)
 
int getVerbosityLevel () const
 
void setCGWidthalls (bool new_)
 
bool getCGWidthalls ()
 
void setDoPeriodicWalls (bool new_)
 
bool getDoPeriodicWalls ()
 
void setCGWidth_over_rmax (Mdouble new_)
 
Mdouble getCGWidth_over_rmax ()
 
void setPositions ()
 Set position of StatisticsPoint points and set variables to 0. More...
 
bool readNextDataFile (unsigned int format)
 
void gather_force_statistics_from_fstat_and_data ()
 
void gather_force_statistics_from_p3c (int version)
 
void gather_force_statistics_from_p3w (int version, std::vector< int > &index)
 
void evaluate_force_statistics (int wp=0)
 
void evaluate_wall_force_statistics (Vec3D P, int wp=0)
 
void jump_fstat ()
 
void initialiseStatistics ()
 Initializes statistics, i.e. setting w2, setting the grid and writing the header lines in the .stat file. More...
 
void outputStatistics ()
 Calculates statistics for Particles (i.e. not collisions) More...
 
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)
 Calculates statistics for one collision (can be any kind of collision) More...
 
void processStatistics (bool usethese)
 Processes all gathered statistics and resets them afterwards. (Processing means either calculating time averages or writing out statistics) More...
 
void finishStatistics ()
 Finish all statistics (i.e. write out final data) More...
 
void write_statistics ()
 Writes regular statistics. More...
 
void write_time_average_statistics ()
 Writes out time averaged statistics. More...
 
void evaluate_particle_statistics (std::vector< BaseParticle * >::iterator P, int wp=0)
 Calculates statistics for a single Particle. More...
 
std::vector< StatisticsPoint< T > > getCGPoints ()
 
Mdouble getXMinStat ()
 Functions to acces and change the domain of statistics. More...
 
Mdouble getYMinStat ()
 
Mdouble getZMinStat ()
 
Mdouble getXMaxStat ()
 
Mdouble getYMaxStat ()
 
Mdouble getZMaxStat ()
 
void setXMinStat (Mdouble xMinStat_)
 
void setYMinStat (Mdouble yMinStat_)
 
void setZMinStat (Mdouble zMinStat_)
 
void setXMaxStat (Mdouble xMaxStat_)
 
void setYMaxStat (Mdouble yMaxStat_)
 
void setZMaxStat (Mdouble zMaxStat_)
 
int getNTimeAverage ()
 
Mdouble setInfinitelyLongDistance ()
 
void set_Polynomial (std::vector< Mdouble > new_coefficients, unsigned int new_dim)
 
void set_Polynomial (Mdouble *new_coefficients, unsigned int num_coeff, unsigned int new_dim)
 
void setPolynomialName (const char *new_name)
 
std::string getPolynomialName ()
 
void setDoDoublePoints (bool new_)
 
bool getDoDoublePoints ()
 
void setNTimeAverageReset (int new_)
 
bool getNTimeAverageReset ()
 
void set_rmin (Mdouble new_)
 
void set_rmax (Mdouble new_)
 
void set_hmax (Mdouble new_)
 
Mdouble evaluatePolynomial (Mdouble r)
 
Mdouble evaluatePolynomialGradient (Mdouble r)
 
Mdouble evaluateIntegral (Mdouble n1, Mdouble n2, Mdouble t)
 
unsigned int getStepSize () const
 
void setStepSize (unsigned int stepSize)
 
void setIndSpecies (unsigned int indSpecies)
 
- Public Member Functions inherited from Chute
 Chute ()
 This is the default constructor. All it does is set sensible defaults. More...
 
 Chute (const DPMBase &other)
 Copy constructor, converts an existing DPMBase problem into a Chute problem. More...
 
 Chute (const MercuryBase &other)
 Copy constructor, converts an existing MercuryBase problem into a Chute problem. More...
 
 Chute (const Mercury3D &other)
 Copy constructor, converts an existing Mercury3D problem into a Chute problem. More...
 
 Chute (const Chute &other)
 Default copy constructor. More...
 
void constructor ()
 This is the actual constructor METHOD; it is called by all constructors above (except the default copy constructor). More...
 
bool readNextArgument (int &i, int argc, char *argv[]) override
 This method can be used for reading object properties from a string. More...
 
void setupSideWalls ()
 Creates chute side walls (either solid or periodic) More...
 
void makeChutePeriodic ()
 This makes the chute periodic in Y. More...
 
bool getIsPeriodic () const
 Returns whether the chute is periodic in Y. More...
 
void setupInitialConditions () override
 Creates bottom, side walls and a particle insertion boundary. More...
 
void read (std::istream &is, ReadOptions opt=ReadOptions::ReadAll) override
 Reads all chute properties from an istream. More...
 
void write (std::ostream &os, bool writeAllParticles=true) const override
 This function writes the Chute properties to an ostream, and adds the properties of ALL chute particles as well. More...
 
void setFixedParticleRadius (Mdouble fixedParticleRadius)
 Sets the particle radius of the fixed particles which constitute the (rough) chute bottom. More...
 
Mdouble getFixedParticleRadius () const
 Returns the particle radius of the fixed particles which constitute the (rough) chute bottom. More...
 
void setRoughBottomType (RoughBottomType roughBottomType)
 Sets the type of rough bottom of the chute. More...
 
void setRoughBottomType (std::string roughBottomTypeString)
 Sets the type of rough bottom of the chute, using a string with the EXACT enum type as input. More...
 
RoughBottomType getRoughBottomType () const
 Returns the type of (rough) bottom of the chute. More...
 
void setChuteAngle (Mdouble chuteAngle)
 Sets gravity vector according to chute angle (in degrees) More...
 
void setChuteAngleAndMagnitudeOfGravity (Mdouble chuteAngle, Mdouble gravity)
 Sets gravity vector according to chute angle (in degrees) More...
 
Mdouble getChuteAngle () const
 Returns the chute angle (in radians) More...
 
Mdouble getChuteAngleDegrees () const
 Returns the chute angle (in degrees) More...
 
void setMaxFailed (unsigned int maxFailed)
 Sets the number of times a particle will be tried to be added to the insertion boundary. More...
 
unsigned int getMaxFailed () const
 Returns the number of times a particle will be tried to be added to the insertion boundary. More...
 
void setInflowParticleRadius (Mdouble inflowParticleRadius)
 Sets the radius of the inflow particles to a single one (i.e. ensures a monodisperse inflow). More...
 
void setInflowParticleRadius (Mdouble minInflowParticleRadius, Mdouble maxInflowParticleRadius)
 Sets the minimum and maximum radius of the inflow particles. More...
 
void setMinInflowParticleRadius (Mdouble minInflowParticleRadius)
 sets the minimum radius of inflow particles More...
 
void setMaxInflowParticleRadius (Mdouble maxInflowParticleRadius)
 Sets the maximum radius of inflow particles. More...
 
Mdouble getInflowParticleRadius () const
 Returns the average radius of inflow particles. More...
 
Mdouble getMinInflowParticleRadius () const
 returns the minimum radius of inflow particles More...
 
Mdouble getMaxInflowParticleRadius () const
 Returns the maximum radius of inflow particles. More...
 
void setInflowHeight (Mdouble inflowHeight)
 Sets maximum inflow height (Z-direction) More...
 
Mdouble getInflowHeight () const
 Returns the maximum inflow height (Z-direction) More...
 
void setInflowVelocity (Mdouble inflowVelocity)
 Sets the average inflow velocity. More...
 
Mdouble getInflowVelocity () const
 Returns the average inflow velocity. More...
 
void setInflowVelocityVariance (Mdouble inflowVelocityVariance)
 Sets the inflow velocity variance. More...
 
Mdouble getInflowVelocityVariance () const
 Returns the inflow velocity variance. More...
 
void setChuteWidth (Mdouble chuteWidth)
 Sets the chute width (Y-direction) More...
 
Mdouble getChuteWidth () const
 Returns the chute width (Y-direction) More...
 
virtual void setChuteLength (Mdouble chuteLength)
 Sets the chute length (X-direction) More...
 
Mdouble getChuteLength () const
 Returns the chute length (X-direction) More...
 
void setInsertionBoundary (InsertionBoundary *insertionBoundary)
 Sets the chute insertion boundary. More...
 
- Public Member Functions inherited from Mercury3D
 Mercury3D ()
 This is the default constructor. All it does is set sensible defaults. More...
 
 Mercury3D (const DPMBase &other)
 Copy-constructor for creates an Mercury3D problem from an existing MD problem. More...
 
 Mercury3D (const Mercury3D &other)
 Copy-constructor. More...
 
void constructor ()
 Function that sets the SystemDimension and ParticleDimension to 3. More...
 
std::vector< BaseParticle * > hGridFindParticleContacts (const BaseParticle *obj) override
 Returns all particles that have a contact with a given particle. More...
 
- Public Member Functions inherited from MercuryBase
 MercuryBase ()
 This is the default constructor. It sets sensible defaults. More...
 
 ~MercuryBase () override
 This is the default destructor. More...
 
 MercuryBase (const MercuryBase &mercuryBase)
 Copy-constructor. More...
 
void constructor ()
 This is the actual constructor, it is called do both constructors above. More...
 
void hGridActionsBeforeTimeLoop () override
 This sets up the broad phase information, has to be done at this stage because it requires the particle size. More...
 
void hGridActionsBeforeTimeStep () override
 Performs all necessary actions before a time-step, like updating the particles and resetting all the bucket information, etc. More...
 
void read (std::istream &is, ReadOptions opt=ReadOptions::ReadAll) override
 Reads the MercuryBase from an input stream, for example a restart file. More...
 
void write (std::ostream &os, bool writeAllParticles=true) const override
 Writes 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...
 
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< intget1DParametersFromRunNumber (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< intget2DParametersFromRunNumber (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< intget3DParametersFromRunNumber (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 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)
 
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
 
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
 

Public Attributes

Mdouble TimeAverageSurface
 
Mdouble TimeAverageSurface2
 
Mdouble TimeAverageBase
 
Mdouble TimeAverageBase2
 
int nTimeAvg
 
- 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...
 

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...
 
- Protected Member Functions inherited from StatisticsVector< T >
bool satisfiesInclusionCriteria (BaseParticle *P)
 
bool loadVelocityProfile (const char *filename)
 
bool loadPositions (const char *filename)
 
Vec3D getVelocityProfile (Vec3D Position)
 
bool read_next_from_p3p_file ()
 
void autoSetSystemDimensions ()
 
- Protected Member Functions inherited from Chute
void actionsBeforeTimeStep () override
 Calls Chute::cleanChute(). More...
 
void cleanChute ()
 Deletes all outflow particles once every 100 time steps. More...
 
virtual void createBottom ()
 Creates the chute bottom, which can be either flat or one of three flavours of rough. More...
 
virtual void addFlowParticlesCompactly ()
 Add initial flow particles in a dense packing. More...
 
virtual SphericalParticle createFlowParticle ()
 
void printTime () const override
 prints time, max time and number of particles More...
 
- Protected Member Functions inherited from Mercury3D
void hGridFindContactsWithinTargetCell (int x, int y, int z, unsigned int l)
 Finds contacts between particles in the target cell. More...
 
void hGridFindContactsWithTargetCell (int x, int y, int z, unsigned int l, BaseParticle *obj)
 Finds contacts between the BaseParticle and the target cell. More...
 
void computeWallForces (BaseWall *w) override
 Compute contacts with a wall. More...
 
void hGridFindParticlesWithTargetCell (int x, int y, int z, unsigned int l, BaseParticle *obj, std::vector< BaseParticle * > &list)
 Finds particles within target cell and stores them in a list. More...
 
void hGridGetInteractingParticleList (BaseParticle *obj, std::vector< BaseParticle * > &list) override
 Obtains all neighbour particles of a given object, obtained from the hgrid. More...
 
void computeInternalForces (BaseParticle *obj) override
 Finds contacts with the BaseParticle; avoids multiple checks. More...
 
bool hGridHasContactsInTargetCell (int x, int y, int z, unsigned int l, const BaseParticle *obj) const
 Tests if the BaseParticle has contacts with other Particles in the target cell. More...
 
bool hGridHasParticleContacts (const BaseParticle *obj) override
 Tests if a BaseParticle has any contacts in the HGrid. More...
 
void hGridRemoveParticle (BaseParticle *obj) override
 Removes a BaseParticle from the HGrid. More...
 
void hGridUpdateParticle (BaseParticle *obj) override
 Updates the cell (not the level) of a BaseParticle. More...
 
- Protected Member Functions inherited from MercuryBase
void hGridRebuild ()
 This sets up the parameters required for the contact model. More...
 
void hGridInsertParticle (BaseParticle *obj) final
 Inserts a single Particle to current grid. More...
 
void hGridUpdateMove (BaseParticle *iP, Mdouble move) final
 Computes the relative displacement of the given BaseParticle and updates the currentMaxRelativeDisplacement_ accordingly. More...
 
void hGridActionsBeforeIntegration () override
 Resets the currentMaxRelativeDisplacement_ to 0. More...
 
void hGridActionsAfterIntegration () override
 This function has to be called before integrateBeforeForceComputation. More...
 
HGridgetHGrid ()
 Gets the HGrid used by this problem. More...
 
const HGridgetHGrid () const
 Gets the HGrid used by this problem, const version. More...
 
bool readNextArgument (int &i, int argc, char *argv[]) override
 Reads the next command line argument. More...
 
- Protected Member Functions inherited from DPMBase
virtual void computeAllForces ()
 Computes all the forces acting on the particles using the BaseInteractable::setForce() and BaseInteractable::setTorque() More...
 
virtual void computeInternalForce (BaseParticle *, BaseParticle *)
 Computes the forces between two particles (internal in the sense that the sum over all these forces is zero i.e. fully modelled forces) More...
 
virtual void computeExternalForces (BaseParticle *)
 Computes the external forces, such as gravity, acting on particles. More...
 
void computeForcesDueToWalls (BaseParticle *, BaseWall *)
 Computes the forces on the particles due to the walls (normals are outward normals) More...
 
virtual void actionsOnRestart ()
 A virtual function where the users can add extra code which is executed only when the code is restarted. More...
 
virtual void 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 outputStatistics ()
 
void gatherContactStatistics ()
 
virtual void processStatistics (bool)
 
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 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...
 
- Static Protected Member Functions inherited from DPMBase
static void signalHandler (int signal)
 signal handler function. More...
 
- Protected Attributes inherited from StatisticsVector< T >
StatType statType
 Possible values X,Y,Z,XY,XZ,YZ,XYZ,RAZ,RA,RZ,AZ,R,A are used to determine if the statistics are averaged; f.e. StatType X is averaged over y and z. More...
 
int nx
 Grid size nx,ny,nz (by default the points of evaluation are placed in an grid on the domain [xMinStat,xMaxStat]x[yMinStat,yMaxStat]x[zMinStat,zMaxStat]. More...
 
int ny
 see nx More...
 
int nz
 see nx More...
 
Mdouble xMinStat
 By default the domain is set to the domain of the MD problem (indicated by setting the stat-domain values to nan), but can be resized. More...
 
Mdouble xMaxStat
 
Mdouble yMinStat
 
Mdouble yMaxStat
 
Mdouble zMinStat
 
Mdouble zMaxStat
 
int nxMirrored
 extension of grid size from mirrored points More...
 
int nyMirrored
 
int nzMirrored
 
std::vector< StatisticsPoint< T > > Points
 A vector that stores the values of the statistical variables at a given position. More...
 
std::vector< StatisticsPoint< T > > dx
 A vector that stores the gradient in x of all statistical variables at a given position. More...
 
std::vector< StatisticsPoint< T > > dy
 A vector that stores the gradient in y of all statistical variables at a given position. More...
 
std::vector< StatisticsPoint< T > > dz
 A vector that stores the gradient in z of all statistical variables at a given position. More...
 
std::vector< StatisticsPoint< T > > timeAverage
 A vector used to sum up all statistical values in Points for time-averaging. More...
 
std::vector< StatisticsPoint< T > > timeVariance
 a vector used to sum up the variance in time of all statistical values More...
 
std::vector< StatisticsPoint< T > > dxTimeAverage
 a vector used to sum up all statistical gradients in dx for time-averaging More...
 
std::vector< StatisticsPoint< T > > dyTimeAverage
 a vector used to sum up all statistical gradients in dy for time-averaging More...
 
std::vector< StatisticsPoint< T > > dzTimeAverage
 a vector used to sum up all statistical gradients in dz for time-averaging More...
 
bool doTimeAverage
 Determines if output is averaged over time. More...
 
int nTimeAverageReset
 Determines after how many time steps the time average is reset. More...
 
bool doVariance
 Determines if variance is outputted. More...
 
bool doGradient
 Determines if gradient is outputted. More...
 
int nTimeAverage
 A counter needed to average over time. More...
 
CG_TYPE CG_type
 coarse graining type (Gaussian, Heaviside, Polynomial) More...
 
NORMALIZED_POLYNOMIAL< T > CGPolynomial
 Stores the Polynomial, if the cg function is an axisymmetric function Polynomial in r. More...
 
Mdouble w2
 coarse graining width squared; for HeavisideSphere and Gaussian More...
 
Mdouble cutoff
 The distance from the origin at which the cg function vanishes; cutoff=w for HeavisideSphere or Polynomial, 3*w for Gaussian. More...
 
Mdouble cutoff2
 
Mdouble w_over_rmax
 if w is not set manually then w will be set by multiplying this value by the largest particle radius at t=0 More...
 
Mdouble tMinStat
 Statistical output will only be created if t>tMinStat. More...
 
Mdouble tMaxStat
 Statistical output will only be created if t<tMaxStat. More...
 
Mdouble tIntStat
 Statistical output will only be created if tMaxStat-tIntStat< t< tMaxStat. More...
 
Mdouble indSpecies
 defines the species for which statistics are extracted (-1 for all species) More...
 
Mdouble rmin
 defines the minimum radius of the particles for which statistics are extracted More...
 
Mdouble rmax
 defines the maximum radius of the particles for which statistics are extracted More...
 
Mdouble hmax
 defines the maximum height of the particles for which statistics are extracted More...
 
bool walls
 Turns off walls before evaluation. More...
 
bool periodicWalls
 Turns off periodic walls before evaluation (needed for averaging, because we do not yet check if particle is in domain) More...
 
bool ignoreFixedParticles
 Determines if fixed particles contribute to particle statistics (density, ...) More...
 
int StressTypeForFixedParticles
 Stress type for fixed particles. More...
 
int verbosity
 Determines how much is outputted to the terminal. More...
 
int format
 format of the data input file More...
 
Mdouble mirrorAtDomainBoundary
 0: Statistics near the wall are equal to statistics away from the wall; 1: Statistics are mirrored at the domain boundaries; up to a maximum depth specified by this number More...
 
bool isMDCLR
 
bool superexact
 If true, cutoff radius for Gaussian is set to 5*w (from 3*w) More...
 
bool doDoublePoints
 
Vec3D P1
 Position of first contact point. More...
 
Vec3D P2
 Position of second contact point. More...
 
Vec3D P1_P2_normal
 Direction of contact. More...
 
Mdouble P1_P2_distance
 Length of contact line. More...
 
Matrix3D P1_P2_NormalStress
 Contact stress from normal forces along the line of contact. More...
 
Matrix3D P1_P2_ContactCoupleStress
 
Vec3D P1_P2_Contact
 
Matrix3D P1_P2_TangentialStress
 Contact stress from tangential forces along the line of contact. More...
 
Vec3D P1_P2_NormalTraction
 Traction from normal forces at contact of flow with fixed particles or walls. More...
 
Vec3D P1_P2_TangentialTraction
 Traction from tangential forces at contact of flow with fixed particles or walls. More...
 
MatrixSymmetric3D P1_P2_Fabric
 Fabric. More...
 
Vec3D P1_P2_CollisionalHeatFlux
 not yet working More...
 
Mdouble P1_P2_Dissipation
 not yet working More...
 
Mdouble P1_P2_Potential
 not yet working More...
 
std::vector< Vec3DVelocityProfile
 
Vec3D VelocityProfile_Min
 
Vec3D VelocityProfile_D
 
std::fstream p3p_file
 
std::fstream p3c_file
 
std::fstream p3w_file
 
bool p3Format = true
 
unsigned int stepSize_
 
std::vector< Vec3Dpositions_
 
bool centerPointInFStat_ = true
 

Constructor & Destructor Documentation

◆ statistics_while_running() [1/7]

template<StatType T>
statistics_while_running< T >::statistics_while_running ( )
inline
32 : StatisticsVector<T>() , Chute() {}

◆ statistics_while_running() [2/7]

template<StatType T>
statistics_while_running< T >::statistics_while_running ( )
inline
33 : StatisticsVector<T>() , Chute() {}

◆ statistics_while_running() [3/7]

template<StatType T>
statistics_while_running< T >::statistics_while_running ( )
inline
34 : StatisticsVector<T>() , Chute() {}

◆ statistics_while_running() [4/7]

template<StatType T>
statistics_while_running< T >::statistics_while_running ( )
inline

◆ statistics_while_running() [5/7]

template<StatType T>
statistics_while_running< T >::statistics_while_running ( )
inline
33 : StatisticsVector<T>() , Chute() {}

◆ statistics_while_running() [6/7]

template<StatType T>
statistics_while_running< T >::statistics_while_running ( )
inline
33 : StatisticsVector<T>() , Chute() {}

◆ statistics_while_running() [7/7]

template<StatType T>
statistics_while_running< T >::statistics_while_running ( )
inline
33 : StatisticsVector<T>() , Chute() {}

Member Function Documentation

◆ actionsBeforeTimeLoop()

template<StatType T>
void statistics_while_running< T >::actionsBeforeTimeLoop ( )
inlinevirtual

A virtual function. Allows one to carry out any operations before the start of the time loop.

no implementation but can be overriden in its derived classes.

Reimplemented from DPMBase.

37  {
38  fix_hgrid();
39  write(std::cout,false);
40  cout<< endl
42  << endl;
43  //~ for (unsigned int i=0; i<particleHandler.getNumberOfObjects(); i++) {
44  //~ if (particleHandler.getObject(i)->isFixed() || i>10) {removeParticle(i); i--;}
45  //~ }
46  };

◆ actionsBeforeTimeStep() [1/6]

template<StatType T>
void statistics_while_running< T >::actionsBeforeTimeStep ( )
inlinevirtual

A virtual function which allows to define operations to be executed before the new time step.

no implementation but can be overidden in its derived classes.

Reimplemented from DPMBase.

34 {}

◆ actionsBeforeTimeStep() [2/6]

template<StatType T>
void statistics_while_running< T >::actionsBeforeTimeStep ( )
inlinevirtual

A virtual function which allows to define operations to be executed before the new time step.

no implementation but can be overidden in its derived classes.

Reimplemented from DPMBase.

35 {};

◆ actionsBeforeTimeStep() [3/6]

template<StatType T>
void statistics_while_running< T >::actionsBeforeTimeStep ( )
inlinevirtual

A virtual function which allows to define operations to be executed before the new time step.

no implementation but can be overidden in its derived classes.

Reimplemented from DPMBase.

94 {};

◆ actionsBeforeTimeStep() [4/6]

template<StatType T>
void statistics_while_running< T >::actionsBeforeTimeStep ( )
inlinevirtual

A virtual function which allows to define operations to be executed before the new time step.

no implementation but can be overidden in its derived classes.

Reimplemented from DPMBase.

35 {};

◆ actionsBeforeTimeStep() [5/6]

template<StatType T>
void statistics_while_running< T >::actionsBeforeTimeStep ( )
inlinevirtual

A virtual function which allows to define operations to be executed before the new time step.

no implementation but can be overidden in its derived classes.

Reimplemented from DPMBase.

35 {};

◆ actionsBeforeTimeStep() [6/6]

template<StatType T>
void statistics_while_running< T >::actionsBeforeTimeStep ( )
inlineoverridevirtual

A virtual function which allows to define operations to be executed before the new time step.

no implementation but can be overidden in its derived classes.

Reimplemented from DPMBase.

120  {};

◆ appendToFile() [1/2]

template<StatType T>
bool statistics_while_running< T >::appendToFile ( std::string  filename,
std::string  text 
)
inline
199  {
200  std::fstream file;
201  file.open(filename.c_str(),std::fstream::out | std::fstream::app);
202  file << text;
203  file.close();
204  return true;
205  }

◆ appendToFile() [2/2]

template<StatType T>
bool statistics_while_running< T >::appendToFile ( string  filename,
string  text 
)
inline
180  {
181  fstream file;
182  file.open(filename.c_str(),fstream::out | fstream::app);
183  file << text;
184  file.close();
185  return true;
186  }

◆ auto_set_domain() [1/2]

template<StatType T>
void statistics_while_running< T >::auto_set_domain ( )
inline
48  {
51  Vec3D Min= - particleHandler.getObject(0)->getRadius()*Vec3D(1,1,1) + particleHandler.getObject(0)->getPosition();//Particles[0].Position-Particles[0].Radius;
52  for (unsigned int i=0; i<particleHandler.getNumberOfObjects(); i++) {
55  }
56  setXMax(Max.X+.05*(Max.X-Min.X));
57  setXMin(Min.X-.05*(Max.X-Min.X));
58  setYMax(Max.Y+.05*(Max.Y-Min.Y));
59  setYMin(Min.Y-.05*(Max.Y-Min.Y));
60  setZMax(Max.Z+.05*(Max.Z-Min.Z));
61  setZMin(Min.Z-.05*(Max.Z-Min.Z));
62  }
63  }

References ParticleHandler::getNumberOfObjects(), BaseHandler< T >::getObject(), BaseInteractable::getPosition(), BaseParticle::getRadius(), constants::i, Vec3D::max(), Vec3D::min(), DPMBase::particleHandler, DPMBase::setXMax(), DPMBase::setXMin(), DPMBase::setYMax(), DPMBase::setYMin(), DPMBase::setZMax(), DPMBase::setZMin(), Vec3D::X, Vec3D::Y, and Vec3D::Z.

Referenced by main().

◆ auto_set_domain() [2/2]

template<StatType T>
void statistics_while_running< T >::auto_set_domain ( )
inline
50  {
52  Vec3D Max= particleHandler.getObject(0)->getRadius()*Vec3D(1,1,1) +particleHandler.getObject(0)->getPosition();//Particles[0].Position+Particles[0].Radius;
53  Vec3D Min=-particleHandler.getObject(0)->getRadius()*Vec3D(1,1,1) +particleHandler.getObject(0)->getPosition();//Particles[0].Position-Particles[0].Radius;
54  for (unsigned int i=0; i<particleHandler.getNumberOfObjects(); i++) {
57  }
58  setXMax(Max.X+.05*(Max.X-Min.X));
59  setXMin(Min.X-.05*(Max.X-Min.X));
60  setYMax(Max.Y+.05*(Max.Y-Min.Y));
61  setYMin(Min.Y-.05*(Max.Y-Min.Y));
62  setZMax(Max.Z+.05*(Max.Z-Min.Z));
63  setZMin(Min.Z-.05*(Max.Z-Min.Z));
64  }
65  }

References ParticleHandler::getNumberOfObjects(), BaseHandler< T >::getObject(), BaseInteractable::getPosition(), BaseParticle::getRadius(), constants::i, Vec3D::max(), Vec3D::min(), DPMBase::particleHandler, DPMBase::setXMax(), DPMBase::setXMin(), DPMBase::setYMax(), DPMBase::setYMin(), DPMBase::setZMax(), DPMBase::setZMin(), Vec3D::X, Vec3D::Y, and Vec3D::Z.

◆ auto_set_z() [1/4]

template<StatType T>
void statistics_while_running< T >::auto_set_z ( )
inline
112  {
114  Mdouble zmin=particleHandler.getObject(0)->->getPosition().Z+particleHandler.getObject(0)->->getRadius();
115  Mdouble zmax=particleHandler.getObject(0)->->getPosition().Z-particleHandler.getObject(0)->->getRadius();
116  for (unsigned int i=0; i<particleHandler.getNumberOfObjects(); i++) {
119  }
120  setZMax(zmax+.05*(zmax-zmin));
121  setZMin(zmin-.05*(zmax-zmin));
122  }
123  }

References constants::i.

Referenced by main(), and statistics_while_running< T >::run().

◆ auto_set_z() [2/4]

template<StatType T>
void statistics_while_running< T >::auto_set_z ( )
inline
59  {
61  Mdouble zmin=particleHandler.getObject(0)->->getPosition().Z+particleHandler.getObject(0)->->getRadius();
62  Mdouble zmax=particleHandler.getObject(0)->->getPosition().Z-particleHandler.getObject(0)->->getRadius();
63  for (unsigned int i=0; i<particleHandler.getNumberOfObjects(); i++) {
66  }
67  setZMax(zmax+.05*(zmax-zmin));
68  setZMin(zmin-.05*(zmax-zmin));
69  }
70  }

References constants::i.

◆ auto_set_z() [3/4]

template<StatType T>
void statistics_while_running< T >::auto_set_z ( )
inline
50  {
52  Mdouble zmin=particleHandler.getObject(0)->->getPosition().Z+particleHandler.getObject(0)->->getRadius();
53  Mdouble zmax=particleHandler.getObject(0)->->getPosition().Z-particleHandler.getObject(0)->->getRadius();
54  for (unsigned int i=0; i<particleHandler.getNumberOfObjects(); i++) {
57  }
58  setZMax(zmax+.05*(zmax-zmin));
59  setZMin(zmin-.05*(zmax-zmin));
60  }
61  }

References constants::i.

◆ auto_set_z() [4/4]

◆ finishStatistics() [1/2]

template<StatType T>
void statistics_while_running< T >::finishStatistics ( )
inlinevirtual

This function is overridden by StatisticsVector

Reimplemented from DPMBase.

158  {
164  stringstream filename("");
165  filename << getName() << ".height";
166  stringstream text("");
169  writeToFile(filename.str(),text.str());
170  }

References StatisticsVector< T >::finishStatistics(), getName(), mathsFunc::square(), and helpers::writeToFile().

◆ finishStatistics() [2/2]

template<StatType T>
void statistics_while_running< T >::finishStatistics ( )
inlineoverridevirtual

◆ initialiseStatistics() [1/2]

template<StatType T>
void statistics_while_running< T >::initialiseStatistics ( )
inlinevirtual

This function is overridden by StatisticsVector

Reimplemented from DPMBase.

132  {
134  TimeAverageSurface = 0.0;
135  TimeAverageSurface2 = 0.0;
136  TimeAverageBase = 0.0;
137  TimeAverageBase2 = 0.0;
138  nTimeAvg = 0;
139  }

References StatisticsVector< T >::initialiseStatistics().

◆ initialiseStatistics() [2/2]

◆ printTime() [1/6]

template<StatType T>
void statistics_while_running< T >::printTime ( )
inline
104  {
105  if (this->getVerbosityLevel()<1) return;
106  static Mdouble tint = getTimeMax()-getTime();
107  cout << "\r" << setprecision(2) << setw(5) << (int)100.*(1-(getTimeMax()-getTime())/tint) << "%\r";
108  cout.flush();
109  }

◆ printTime() [2/6]

template<StatType T>
void statistics_while_running< T >::printTime ( )
inline
48  {
49  static Mdouble tint = getTimeMax()-getTime();
50  cout << "\r"
51  << setprecision(7) << setw(10) << getTime() << ", dt" << tint << ", "
52  << setprecision(2) << setw(5) << (int)100.*(1-(getTimeMax()-getTime())/tint)
53  << "%\r"
54  ;
55  cout.flush();
56  }

◆ printTime() [3/6]

template<StatType T>
void statistics_while_running< T >::printTime ( )
inline
43  {
44  static Mdouble tint = getTimeMax()-getTime();
45  cout << "\r" << setprecision(2) << setw(5) << (int)100.*(1-(getTimeMax()-getTime())/tint) << "%\r";
46  cout.flush();
47  }

◆ printTime() [4/6]

template<StatType T>
void statistics_while_running< T >::printTime ( ) const
inlinevirtual

Displays the current simulation time and the maximum simulation duration.

Gets and prints the current simulation time (getTime()) and the currently set maximum simulation time (getTimeMax()) .

Reimplemented from DPMBase.

42  {
43  static Mdouble tint = getTimeMax()-getTime();
44  logger(INFO, "\r2.5%%\r", static_cast<int>(100. * (1 - (getTimeMax() - getTime()) / tint)));
45  }

References DPMBase::getTime(), DPMBase::getTimeMax(), INFO, and logger.

◆ printTime() [5/6]

template<StatType T>
void statistics_while_running< T >::printTime ( ) const
inlinevirtual

Displays the current simulation time and the maximum simulation duration.

Gets and prints the current simulation time (getTime()) and the currently set maximum simulation time (getTimeMax()) .

Reimplemented from DPMBase.

44  {
45  static Mdouble tint = getTimeMax()-getTime();
46  logger(INFO, "\rProgress: %2.10%\r", (int) 100. * (1 - (getTimeMax() - getTime()) / tint));
47  }

References DPMBase::getTime(), DPMBase::getTimeMax(), INFO, and logger.

◆ printTime() [6/6]

template<StatType T>
void statistics_while_running< T >::printTime ( ) const
inlineoverridevirtual

Displays the current simulation time and the maximum simulation duration.

Gets and prints the current simulation time (getTime()) and the currently set maximum simulation time (getTimeMax()) .

Reimplemented from DPMBase.

132  {
133  if (this->getVerbosityLevel() < 1)
134  {
135  return;
136  }
137  static Mdouble tint = getTimeMax() - getTime();
138  logger(INFO, "\r%2.5%\r", (int) 100. * (1 - (getTimeMax() - getTime()) / tint));
139  }

References DPMBase::getTime(), DPMBase::getTimeMax(), StatisticsVector< T >::getVerbosityLevel(), INFO, and logger.

◆ processStatistics()

template<StatType T>
void statistics_while_running< T >::processStatistics ( )
inline
142  {
144  Mdouble Base = 1e20, Surface=-1e20;
145  for (unsigned int i=0; i<particleHandler.getNumberOfObjects(); i++) if (!particleHandler.getObject(i)->isFixed()) {
146  Base=min(Base,particleHandler.getObject(i)->getPosition().Z);
147  Surface=max(Surface,particleHandler.getObject(i)->getPosition().Z);
148  }
149  TimeAverageSurface += Surface;
151  TimeAverageBase += Base;
153  nTimeAvg++;
154  //~ cout << "Height " << setprecision(14) << Surface << "_" << Base << endl;
155  }

References constants::i, StatisticsVector< T >::processStatistics(), and mathsFunc::square().

◆ run() [1/2]

template<StatType T>
void statistics_while_running< T >::run ( int  argc,
char argv[] 
)
inline
36  {
37  //select file name to restart from
38  string name;
39  if (argc>1) {name=argv[1]; argv++; argc--;} else { cout << "please provide a name" << endl; exit(-1); }
40  //select time interval
41  Mdouble tint=.2;
42  if (argc>1) {tint=atof(argv[1]); argv++; argc--; cout << "tint=" << tint << endl;}
43  argv--; argc++;
44  //create class and set name
45  setName(name.c_str());
46  //load restart data
47  int i;
48  for (i = 1; i<argc; i++) if (!strcmp(argv[i],"-restartfilename")) break;
49  if (i<argc) {
50  string filename(argv[i+1]);
51  cout << "loading restart data:: " << filename << endl;
52  load_restart_data(filename);
53  } else {
54  cout << "loading restart data: " << name << ".restart" << endl;
55  load_restart_data();
56  }
57  //save restart data
58  //restartFile.setFileType(FileType::ONE_FILE);
59  //writeRestartFile();
60  //automatic depth range detection
61  auto_set_z();
62  //keep file name but create files in the local directory, i.e. remove folder
63  cout << "changed name from " << getName();
64  size_t found=name.find_last_of("/\\");
65  setName(name.substr(found+1).c_str());
66  cout << " to " << getName() << endl;
67  //save restart data
68  //restartFile.setFileType(FileType::ONE_FILE);
69  //writeRestartFile();
70  //set output to minimum
71  dataFile.setFileType(FileType::NO_FILE);
72  restartFile.setFileType(FileType::NO_FILE);
73  fStatFile.setFileType(FileType::NO_FILE);
74  eneFile.setFileType(FileType::NO_FILE);
75  //automatic depth range decection
76  auto_set_z();
77  //set statistical parameters
78  this->setDoPeriodicWalls(false);
79  //~ setZMinStat(-1);
80  this->setN(200);
82  cout << "by default w=InflowParticleRadius=" << this->getCGWidth() << endl;
83  setSaveCount(25);
84  //~ setStressTypeForFixedParticles(3); //default 1
86  setTimeMax(getTime()+tint);
87  //solve and create live statistics
88  cout << "read arguments" << endl;
89  this->readStatArguments(argc, argv);
90  solve();
91  }

References getName(), constants::i, and units::name.

Referenced by main().

◆ run() [2/2]

template<StatType T>
void statistics_while_running< T >::run ( int  argc,
char argv[] 
)
inline
35  {
36  //select file name to restart from
37  std::string name;
38  if (argc > 1)
39  {
40  name = argv[1];
41  argv++;
42  argc--;
43  }
44  else
45  {
46  logger(ERROR, "please provide a name");
47  }
48  //select time interval
49  Mdouble tint = .2;
50  if (argc > 1)
51  {
52  tint = atof(argv[1]);
53  argv++;
54  argc--;
55  logger(INFO, "tint=%", tint);
56  }
57  argv--;
58  argc++;
59  //create class and set name
60  setName(name.c_str());
61  //load restart data
62  int i;
63  for (i = 1; i < argc; i++)
64  {
65  if (!strcmp(argv[i], "-restartfilename"))
66  {
67  break;
68  }
69  }
70  if (i < argc)
71  {
72  std::string filename(argv[i + 1]);
73  logger(INFO, "loading restart data: %\n", filename, Flusher::NO_FLUSH);
74  readRestartFile(filename);//load_restart_data(filename);
75  }
76  else
77  {
78  logger(INFO, "loading restart data: %.restart\n", name, Flusher::NO_FLUSH);
79  readRestartFile();//load_restart_data();
80  }
81  //save restart data
82  //restartFile.setFileType(FileType::ONE_FILE);
83  //writeRestartFile();
84  //automatic depth range detection
85  auto_set_z();
86  //keep file name but create files in the local directory, i.e. remove folder
87  logger(INFO, "changed name from %\n", getName(), Flusher::NO_FLUSH);
88  size_t found = name.find_last_of("/\\");
89  setName(name.substr(found + 1).c_str());
90  logger(INFO, " to %\n", getName(), Flusher::NO_FLUSH);
91  //set output to minimum
92  restartFile.setFileType(FileType::NO_FILE);
93  fStatFile.setFileType(FileType::NO_FILE);
94  dataFile.setFileType(FileType::NO_FILE);
95  eneFile.setFileType(FileType::NO_FILE);
96  //dataFile.setFileType(FileType::NO_FILE);
97  //restartFile.setFileType(FileType::NO_FILE);
98  //fStatFile.setFileType(FileType::NO_FILE);
99  //eneFile.setFileType(FileType::NO_FILE);
100  //automatic depth range decection
101  auto_set_z();
102  //set statistical parameters
103  this->setDoPeriodicWalls(false);
104  //~ setZMinStat(-1);
105  this->setN(200);
107  logger(INFO, "by default w=InflowParticleRadius=%", this->getCGWidth());
108  setSaveCount(25);
109  //~ setStressTypeForFixedParticles(3); //default 1
111  setTimeMax(getTime() + tint);
112  //solve and create live statistics
113  logger(VERBOSE, "read arguments");
114  this->readStatArguments(argc, argv);
115  solve();
116  }

References statistics_while_running< T >::auto_set_z(), DPMBase::dataFile, DPMBase::eneFile, ERROR, FLUSH, DPMBase::fStatFile, StatisticsVector< T >::getCGWidth(), Chute::getInflowParticleRadius(), DPMBase::getName(), DPMBase::getTime(), constants::i, INFO, logger, units::name, DPMBase::readRestartFile(), StatisticsVector< T >::readStatArguments(), DPMBase::restartFile, StatisticsVector< T >::setCGTimeMin(), StatisticsVector< T >::setCGWidth(), StatisticsVector< T >::setDoPeriodicWalls(), File::setFileType(), StatisticsVector< T >::setN(), DPMBase::setName(), DPMBase::setSaveCount(), DPMBase::setTimeMax(), DPMBase::solve(), and VERBOSE.

◆ setupInitialConditions() [1/6]

template<StatType T>
void statistics_while_running< T >::setupInitialConditions ( )
inlinevirtual

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.

A virtual function with no implementation but can be overriden.

Todo:
I (Anthony) wants to change this to be an external function. This has a lot of advantages especially when using copy-constructors. This is a major change and will break other codes, so therefore has to be done carefully.

This sets up the particles initial conditions it is as you expect the user to override this. By default the particles are randomly distributed

Reimplemented from DPMBase.

37  //~ for (unsigned int i=0; i<particleHandler.getNumberOfObjects(); i++) {
38  //~ if (particleHandler.getObject(i)->isFixed() || i>10) {removeParticle(i); i--;}
39  //~ }
40  }

References StatisticsVector< T >::printStat().

◆ setupInitialConditions() [2/6]

template<StatType T>
void statistics_while_running< T >::setupInitialConditions ( )
inlinevirtual

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.

A virtual function with no implementation but can be overriden.

Todo:
I (Anthony) wants to change this to be an external function. This has a lot of advantages especially when using copy-constructors. This is a major change and will break other codes, so therefore has to be done carefully.

This sets up the particles initial conditions it is as you expect the user to override this. By default the particles are randomly distributed

Reimplemented from DPMBase.

37  {
39  //~ for (unsigned int i=0; i<particleHandler.getNumberOfObjects(); i++) {
40  //~ if (particleHandler.getObject(i)->isFixed() || i>10) {removeParticle(i); i--;}
41  //~ }
42  };

References StatisticsVector< T >::printStat(), and StatisticsVector< T >::verbose().

◆ setupInitialConditions() [3/6]

template<StatType T>
void statistics_while_running< T >::setupInitialConditions ( )
inlinevirtual

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.

A virtual function with no implementation but can be overriden.

Todo:
I (Anthony) wants to change this to be an external function. This has a lot of advantages especially when using copy-constructors. This is a major change and will break other codes, so therefore has to be done carefully.

This sets up the particles initial conditions it is as you expect the user to override this. By default the particles are randomly distributed

Reimplemented from DPMBase.

96  {
97  write(std::cout,false);
99  //~ for (unsigned int i=0; i<particleHandler.getNumberOfObjects(); i++) {
100  //~ if (particleHandler.getObject(i)->isFixed() || i>10) {removeParticle(i); i--;}
101  //~ }
102  };

◆ setupInitialConditions() [4/6]

template<StatType T>
void statistics_while_running< T >::setupInitialConditions ( )
inlinevirtual

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.

A virtual function with no implementation but can be overriden.

Todo:
I (Anthony) wants to change this to be an external function. This has a lot of advantages especially when using copy-constructors. This is a major change and will break other codes, so therefore has to be done carefully.

This sets up the particles initial conditions it is as you expect the user to override this. By default the particles are randomly distributed

Reimplemented from DPMBase.

38  {
39  setXMax(1);
40  setYMax(1.2);
41  setZMax(1);
42 
43 
44  set_N(3);
45  particleHandler.getObject(0)->->setPosition(Vec3D(0.4, 0.4, 0.0));
46  particleHandler.getObject(0)->->setVelocity(Vec3D(0.0, 1.0, 0.0));
47  particleHandler.getObject(0)->->getRadius()=0.1;
48 
49  particleHandler.getObject(1)->setPosition(Vec3D(0.4, 0.8, 0.0));
50  particleHandler.getObject(1)->setVelocity(Vec3D(0.0,-1.0, 0.0));
52 
53  particleHandler.getObject(2)->Position=Vec3D(0.2, 0.7, 0.0);
54  particleHandler.getObject(2)->Velocity=Vec3D(-1.0,-1.0, 0.0);
55  particleHandler.getObject(2)->Radius=0.1;
56 
57 
58  set_NWall(2);
59  wallHandler.getObject(0)->set(Vec3D(0.0, 1.0,0.0), getYMax());
60  Walls[1].set(Vec3D(0.0,-1.0,0.0),-getYMin());
61 
62  set_NWallPeriodic(1);
63  WallsPeriodic[0].set(Vec3D(1,0,0), getXMin(), getXMax());
64  }

References BaseHandler< T >::getObject(), BaseParticle::getRadius(), DPMBase::getXMax(), DPMBase::getXMin(), DPMBase::getYMax(), DPMBase::getYMin(), DPMBase::particleHandler, BaseInteractable::setPosition(), BaseInteractable::setVelocity(), DPMBase::setXMax(), DPMBase::setYMax(), DPMBase::setZMax(), and DPMBase::wallHandler.

◆ setupInitialConditions() [5/6]

template<StatType T>
void statistics_while_running< T >::setupInitialConditions ( )
inlinevirtual

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.

A virtual function with no implementation but can be overriden.

Todo:
I (Anthony) wants to change this to be an external function. This has a lot of advantages especially when using copy-constructors. This is a major change and will break other codes, so therefore has to be done carefully.

This sets up the particles initial conditions it is as you expect the user to override this. By default the particles are randomly distributed

Reimplemented from DPMBase.

38  //~ for (unsigned int i=0; i<particleHandler.getNumberOfObjects(); i++) {
39  //~ if (particleHandler.getObject(i)->isFixed() || i>10) {removeParticle(i); i--;}
40  //~ }
41  };

◆ setupInitialConditions() [6/6]

template<StatType T>
void statistics_while_running< T >::setupInitialConditions ( )
inlineoverridevirtual

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.

A virtual function with no implementation but can be overriden.

Todo:
I (Anthony) wants to change this to be an external function. This has a lot of advantages especially when using copy-constructors. This is a major change and will break other codes, so therefore has to be done carefully.

This sets up the particles initial conditions it is as you expect the user to override this. By default the particles are randomly distributed

Reimplemented from DPMBase.

123  {
124  write(std::cout, false);
126  //~ for (unsigned int i=0; i<particleHandler.getNumberOfObjects(); i++) {
127  //~ if (particleHandler.getObject(i)->isFixed() || i>10) {removeParticle(i); i--;}
128  //~ }
129  };

References StatisticsVector< T >::printStat(), and Chute::write().

◆ writeToFile() [1/2]

template<StatType T>
bool statistics_while_running< T >::writeToFile ( std::string  filename,
std::string  text 
)
inline
191  {
192  std::fstream file;
193  file.open(filename.c_str(),std::fstream::out);
194  file << text;
195  file.close();
196  return true;
197  }

◆ writeToFile() [2/2]

template<StatType T>
bool statistics_while_running< T >::writeToFile ( string  filename,
string  text 
)
inline
172  {
173  fstream file;
174  file.open(filename.c_str(),fstream::out);
175  file << text;
176  file.close();
177  return true;
178  }

Referenced by statistics_while_running< T >::finishStatistics().

Member Data Documentation

◆ nTimeAvg

◆ TimeAverageBase

◆ TimeAverageBase2

◆ TimeAverageSurface

◆ TimeAverageSurface2


The documentation for this class was generated from the following files:
StatisticsVector::finishStatistics
void finishStatistics()
Finish all statistics (i.e. write out final data)
StatisticsVector::printStat
std::string printStat()
Outputs member variable values to a std::string.
mathsFunc::square
T square(const T val)
squares a number
Definition: ExtendedMath.h:106
DPMBase::setName
void setName(const std::string &name)
Allows to set the name of all the files (ene, data, fstat, restart, stat)
Definition: DPMBase.cc:420
File::setFileType
void setFileType(FileType fileType)
Sets the type of file needed to write into or read from. File::fileType_.
Definition: File.cc:215
DPMBase::readRestartFile
bool readRestartFile(ReadOptions opt=ReadOptions::ReadAll)
Reads all the particle data corresponding to a given, existing . restart file (for more details regar...
Definition: DPMBase.cc:2921
Flusher::FLUSH
@ FLUSH
StatisticsVector::setN
void setN(int n)
Definition: StatisticsVector.h:179
DPMBase::getXMax
Mdouble getXMax() const
If the length of the problem domain in x-direction is XMax - XMin, then getXMax() returns XMax.
Definition: DPMBase.h:607
BaseInteractable::setPosition
void setPosition(const Vec3D &position)
Sets the position of this BaseInteractable.
Definition: BaseInteractable.h:239
logger
Logger< MERCURY_LOGLEVEL > logger("MercuryKernel")
Definition of different loggers with certain modules. A user can define its own custom logger here.
ParticleHandler::getNumberOfObjects
unsigned int getNumberOfObjects() const override
Returns the number of objects in the container. In parallel code this practice is forbidden to avoid ...
Definition: ParticleHandler.cc:1315
Vec3D::X
Mdouble X
the vector components
Definition: Vector.h:65
statistics_while_running::TimeAverageSurface2
Mdouble TimeAverageSurface2
Definition: obsolete_codes/statistics_while_running.cpp:126
DPMBase::setYMax
void setYMax(Mdouble newYMax)
Sets the value of YMax, the upper bound of the problem domain in the y-direction.
Definition: DPMBase.cc:1182
DPMBase::restartFile
File restartFile
An instance of class File to handle in- and output into a .restart file.
Definition: DPMBase.h:1451
INFO
LL< Log::INFO > INFO
Info log level.
Definition: Logger.cc:55
StatisticsVector
This class is used to extract statistical data from MD simulations.
Definition: StatisticsVector.h:62
Mercury3D::Mercury3D
Mercury3D()
This is the default constructor. All it does is set sensible defaults.
Definition: Mercury3D.cc:29
Vec3D
Definition: Vector.h:50
DPMBase::solve
void solve()
The work horse of the code.
Definition: DPMBase.cc:4003
DPMBase::fStatFile
File fStatFile
An instance of class File to handle in- and output into a .fstat file.
Definition: DPMBase.h:1441
DPMBase::getYMin
Mdouble getYMin() const
If the length of the problem domain in y-direction is YMax - YMin, then getYMin() returns YMin.
Definition: DPMBase.h:613
DPMBase::setZMax
void setZMax(Mdouble newZMax)
Sets the value of ZMax, the upper bound of the problem domain in the z-direction.
Definition: DPMBase.cc:1208
Mdouble
double Mdouble
Definition: GeneralDefine.h:34
BaseParticle::getRadius
Mdouble getRadius() const
Returns the particle's radius.
Definition: BaseParticle.h:348
statistics_while_running::writeToFile
bool writeToFile(string filename, string text)
Definition: obsolete_codes/statistics_while_running.cpp:172
BaseInteractable::setVelocity
void setVelocity(const Vec3D &velocity)
set the velocity of the BaseInteractable.
Definition: BaseInteractable.cc:350
VERBOSE
LL< Log::VERBOSE > VERBOSE
Verbose information.
Definition: Logger.cc:57
ERROR
LL< Log::ERROR > ERROR
Error log level.
Definition: Logger.cc:53
DPMBase::getTime
Mdouble getTime() const
Returns the current simulation time.
Definition: DPMBase.cc:805
StatisticsVector::setDoPeriodicWalls
void setDoPeriodicWalls(bool new_)
Definition: StatisticsVector.h:563
StatisticsVector::setCGTimeMin
void setCGTimeMin(Mdouble t)
Definition: StatisticsVector.h:223
DPMBase::setXMax
void setXMax(Mdouble newXMax)
Sets the value of XMax, the upper bound of the problem domain in the x-direction.
Definition: DPMBase.cc:1156
statistics_while_running::TimeAverageBase2
Mdouble TimeAverageBase2
Definition: obsolete_codes/statistics_while_running.cpp:128
DPMBase::wallHandler
WallHandler wallHandler
An object of the class WallHandler. Contains pointers to all the walls created.
Definition: DPMBase.h:1405
StatisticsVector::getVerbosityLevel
int getVerbosityLevel() const
Definition: StatisticsVector.h:539
StatisticsVector::setCGWidth
void setCGWidth(Mdouble w)
Set CG variables w2 and CG_invvolume.
Definition: StatisticsVector.h:317
DPMBase::setTimeMax
void setTimeMax(Mdouble newTMax)
Sets a new value for the maximum simulation duration.
Definition: DPMBase.cc:870
Vec3D::Y
Mdouble Y
Definition: Vector.h:65
statistics_while_running::TimeAverageBase
Mdouble TimeAverageBase
Definition: obsolete_codes/statistics_while_running.cpp:127
Vec3D::min
static Vec3D min(const Vec3D &a, const Vec3D &b)
Calculates the pointwise minimum of two Vec3D.
Definition: Vector.cc:102
DPMBase::getName
const std::string & getName() const
Returns the name of the file. Does not allow to change it though.
Definition: DPMBase.cc:397
constants::i
const std::complex< Mdouble > i
Definition: ExtendedMath.h:51
DPMBase::setYMin
void setYMin(Mdouble newYMin)
Sets the value of YMin, the lower bound of the problem domain in the y-direction.
Definition: DPMBase.cc:1025
Chute::Chute
Chute()
This is the default constructor. All it does is set sensible defaults.
Definition: Chute.cc:42
BaseHandler::getObject
T * getObject(const unsigned int id)
Gets a pointer to the Object at the specified index in the BaseHandler.
Definition: BaseHandler.h:613
Mdouble
Chute::write
void write(std::ostream &os, bool writeAllParticles=true) const override
This function writes the Chute properties to an ostream, and adds the properties of ALL chute particl...
Definition: Chute.cc:206
DPMBase::eneFile
File eneFile
An instance of class File to handle in- and output into a .ene file.
Definition: DPMBase.h:1446
statistics_while_running::nTimeAvg
int nTimeAvg
Definition: obsolete_codes/statistics_while_running.cpp:129
StatisticsVector::verbose
void verbose()
Definition: StatisticsVector.h:523
DPMBase::getYMax
Mdouble getYMax() const
If the length of the problem domain in y-direction is YMax - YMin, then getYMax() returns XMax.
Definition: DPMBase.h:619
DPMBase::setXMin
void setXMin(Mdouble newXMin)
Sets the value of XMin, the lower bound of the problem domain in the x-direction.
Definition: DPMBase.cc:1001
Vec3D::max
static Vec3D max(const Vec3D &a, const Vec3D &b)
Calculates the pointwise maximum of two Vec3D.
Definition: Vector.cc:89
BaseParticle::isFixed
bool isFixed() const override
Is fixed Particle function. It returns whether a Particle is fixed or not, by checking its inverse Ma...
Definition: BaseParticle.h:93
DPMBase::particleHandler
ParticleHandler particleHandler
An object of the class ParticleHandler, contains the pointers to all the particles created.
Definition: DPMBase.h:1395
Vec3D::Z
Mdouble Z
Definition: Vector.h:65
DPMBase::setSaveCount
void setSaveCount(unsigned int saveCount)
Sets File::saveCount_ for all files (ene, data, fstat, restart, stat)
Definition: DPMBase.cc:406
statistics_while_running::auto_set_z
void auto_set_z()
Definition: obsolete_codes/statistics_while_running.cpp:112
DPMBase::dataFile
File dataFile
An instance of class File to handle in- and output into a .data file.
Definition: DPMBase.h:1436
StatisticsVector::getCGWidth
Mdouble getCGWidth()
Definition: StatisticsVector.h:331
StatisticsVector::initialiseStatistics
void initialiseStatistics()
Initializes statistics, i.e. setting w2, setting the grid and writing the header lines in the ....
units::name
std::string name
Definition: MercuryProb.h:48
statistics_while_running::TimeAverageSurface
Mdouble TimeAverageSurface
Definition: obsolete_codes/statistics_while_running.cpp:125
DPMBase::setZMin
void setZMin(Mdouble newZMin)
Sets the value of ZMin, the lower bound of the problem domain in the z-direction.
Definition: DPMBase.cc:1049
StatisticsVector::readStatArguments
void readStatArguments(int argc, char *argv[])
Chute::getInflowParticleRadius
Mdouble getInflowParticleRadius() const
Returns the average radius of inflow particles.
Definition: Chute.cc:856
StatisticsVector::processStatistics
void processStatistics(bool usethese)
Processes all gathered statistics and resets them afterwards. (Processing means either calculating ti...
DPMBase::getXMin
Mdouble getXMin() const
If the length of the problem domain in x-direction is XMax - XMin, then getXMin() returns XMin.
Definition: DPMBase.h:600
BaseInteractable::getPosition
const Vec3D & getPosition() const
Returns the position of this BaseInteractable.
Definition: BaseInteractable.h:218
DPMBase::getTimeMax
Mdouble getTimeMax() const
Returns the maximum simulation duration.
Definition: DPMBase.cc:885
int