MercuryDPM  Trunk
Mercury3DRestart Class Reference

This class adds to Mercury3D the ability to restart after a certain wall time. More...

#include <Mercury3DRestart.h>

Inheritance diagram for Mercury3DRestart:

## Public Member Functions

Mercury3DRestart ()

void setClusterCommand (std::string clusterCommand)

std::string getClusterCommand () const

void setMaxWallTime (Mdouble maxWallTime)

Mdouble getMaxWallTime () const

Mdouble getInitialWallTime () const

bool readNextArgument (int &i, int argc, char *argv[])
the -r option is used to restart the code; this should probably be moved to DPMBase More...

double getWallTime () const
Returns wall time (uses sys command, thus might not work on Windows) 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...

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

void write (std::ostream &os, bool writeAllParticles=true) const override
Writes the MercuryBase to an output stream, for example a restart file. More...

Mdouble getHGridCurrentMaxRelativeDisplacement () const
Returns hGridCurrentMaxRelativeDisplacement_. More...

Mdouble getHGridTotalCurrentMaxRelativeDisplacement () const
Returns hGridTotalCurrentMaxRelativeDisplacement_. More...

void setHGridUpdateEachTimeStep (bool updateEachTimeStep)
Sets whether or not the HGrid must be updated every time step. More...

bool getHGridUpdateEachTimeStep () const final
Gets whether or not the HGrid is updated every time step. More...

void setHGridMaxLevels (unsigned int HGridMaxLevels)
Sets the maximum number of levels of the HGrid in this MercuryBase. More...

unsigned int getHGridMaxLevels () const
Gets the maximum number of levels of the HGrid in this MercuryBase. More...

HGridMethod getHGridMethod () const
Gets whether the HGrid in this MercuryBase is BOTTOMUP or TOPDOWN. More...

void setHGridMethod (HGridMethod hGridMethod)
Sets the HGridMethod to either BOTTOMUP or TOPDOWN. More...

HGridDistribution getHGridDistribution () const
Gets how the sizes of the cells of different levels are distributed. More...

void setHGridDistribution (HGridDistribution hGridDistribution)
Sets how the sizes of the cells of different levels are distributed. More...

Mdouble getHGridCellOverSizeRatio () const
Gets the ratio of the smallest cell over the smallest particle. More...

void setHGridCellOverSizeRatio (Mdouble cellOverSizeRatio)
Sets the ratio of the smallest cell over the smallest particle. More...

bool hGridNeedsRebuilding ()
Gets if the HGrid needs rebuilding before anything else happens. More...

virtual unsigned int getHGridTargetNumberOfBuckets () const
Gets the desired number of buckets, which is the maximum of the number of particles and 10. More...

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

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< int > get1DParametersFromRunNumber (int size_x) const
This turns a counter into 1 index, which is a useful feature for performing 1D parameter study. The index run from 1:size_x, while the study number starts at 0 (initially the counter=1 in COUNTER_DONOTDEL) More...

std::vector< int > get2DParametersFromRunNumber (int size_x, int size_y) const
This turns a counter into 2 indices which is a very useful feature for performing a 2D study. The indices run from 1:size_x and 1:size_y, while the study number starts at 0 ( initially the counter=1 in COUNTER_DONOTDEL) More...

std::vector< int > get3DParametersFromRunNumber (int size_x, int size_y, int size_z) const
This turns a counter into 3 indices, which is a useful feature for performing a 3D parameter study. The indices run from 1:size_x, 1:size_y and 1:size_z, while the study number starts at 0 ( initially the counter=1 in COUNTER_DONOTDEL) More...

int launchNewRun (const char *name, bool quick=false)
This launches a code from within this code. Please pass the name of the code to run. More...

void setRunNumber (int runNumber)
This sets the counter/Run number, overriding the defaults. More...

int getRunNumber () const
This returns the current value of the counter (runNumber_) More...

virtual void decompose ()
Sends particles from processorId to the root processor. More...

void solve ()
The work horse of the code. More...

virtual void computeOneTimeStep ()
Performs everything needed for one time step, used in the time-loop of solve(). More...

void checkSettings ()
Checks if the essentials are set properly to go ahead with solving the problem. More...

void forceWriteOutputFiles ()
Writes output files immediately, even if the current time step was not meant to be written. Also resets the last saved time step. More...

void solve (int argc, char *argv[])
The work horse of the code. Can handle flags from the command line. More...

virtual void setupInitialConditions ()
This function allows to set the initial conditions for our problem to be solved, by default particle locations are randomly set. Remember particle properties must also be defined here. More...

virtual void writeXBallsScript () const
This writes a script which can be used to load the xballs problem to display the data just generated. More...

virtual Mdouble getInfo (const BaseParticle &P) const
A virtual function that returns some user-specified information about a particle. More...

ParticleVtkWritergetVtkWriter () const

virtual void writeRestartFile ()
Stores all the particle data for current save time step to a "restart" file, which is a file simply intended to store all the information necessary to "restart" a simulation from a given time step (see also MercuryDPM.org for more information on restart files). More...

void writeDataFile ()

void writeEneFile ()

void writeFStatFile ()

void fillDomainWithParticles (unsigned N=50)
Inserts particles in the whole domain. More...

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...

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...

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...

Allows the user to read par.ini files (useful to read files produced by the MDCLR simulation code - external to MercuryDPM) More...

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...

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 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 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...

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...

Mdouble getXMin () const
If the length of the problem domain in x-direction is XMax - XMin, then getXMin() returns XMin. More...

Mdouble getXMax () const
If the length of the problem domain in x-direction is XMax - XMin, then getXMax() returns XMax. More...

Mdouble getYMin () const
If the length of the problem domain in y-direction is YMax - YMin, then getYMin() returns YMin. More...

Mdouble getYMax () const
If the length of the problem domain in y-direction is YMax - YMin, then getYMax() returns XMax. More...

Mdouble getZMin () const
If the length of the problem domain in z-direction is ZMax - ZMin, then getZMin() returns ZMin. More...

Mdouble getZMax () const
If the length of the problem domain in z-direction is ZMax - ZMin, then getZMax() returns ZMax. More...

Vec3D getMin () const

Vec3D getMax () const

void setXMin (Mdouble newXMin)
Sets the value of XMin, the lower bound of the problem domain in the x-direction. More...

void setYMin (Mdouble newYMin)
Sets the value of YMin, the lower bound of the problem domain in the y-direction. More...

void setZMin (Mdouble newZMin)
Sets the value of ZMin, the lower bound of the problem domain in the z-direction. More...

void setXMax (Mdouble newXMax)
Sets the value of XMax, the upper bound of the problem domain in the x-direction. More...

void setYMax (Mdouble newYMax)
Sets the value of YMax, the upper bound of the problem domain in the y-direction. More...

void setZMax (Mdouble newZMax)
Sets the value of ZMax, the upper bound of the problem domain in the z-direction. More...

void setMax (const Vec3D &max)
Sets the maximum coordinates of the problem domain. More...

void setMax (Mdouble, Mdouble, Mdouble)
Sets the maximum coordinates of the problem domain. More...

void setDomain (const Vec3D &min, const Vec3D &max)
Sets the minimum coordinates of the problem domain. More...

void setMin (const Vec3D &min)
Sets the minimum coordinates of the problem domain. More...

void setMin (Mdouble, Mdouble, Mdouble)
Sets the minimum coordinates of the problem domain. More...

void setTimeStep (Mdouble newDt)
Sets a new value for the simulation time step. More...

Mdouble getTimeStep () const
Returns the simulation time step. More...

void setXBallsColourMode (int newCMode)
Set the xballs output mode. More...

int getXBallsColourMode () const
Get the xballs colour mode (CMode). More...

void setXBallsVectorScale (double newVScale)
Set the scale of vectors in xballs. More...

double getXBallsVectorScale () const
Returns the scale of vectors used in xballs. More...

Set the additional arguments for xballs. More...

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...

virtual void hGridInsertParticle (BaseParticle *obj UNUSED)

virtual void hGridUpdateParticle (BaseParticle *obj UNUSED)

virtual void hGridRemoveParticle (BaseParticle *obj UNUSED)

bool mpiIsInCommunicationZone (BaseParticle *particle)
Checks if the position of the particle is in an mpi communication zone or not. More...

bool mpiInsertParticleCheck (BaseParticle *P)
Function that checks if the mpi particle should really be inserted by the current domain. More...

void insertGhostParticle (BaseParticle *P)
This function inserts a particle in the mpi communication boundaries. More...

void updateGhostGrid (BaseParticle *P)
Checks if the Domain/periodic interaction distance needs to be updated and updates it accordingly. More...

virtual void gatherContactStatistics (unsigned int index1, int index2, Vec3D Contact, Mdouble delta, Mdouble ctheta, Mdouble fdotn, Mdouble fdott, Vec3D P1_P2_normal_, Vec3D P1_P2_tangential)
//Not unsigned index because of possible wall collisions. More...

void setNumberOfDomains (std::vector< unsigned > direction)
Sets the number of domains in x-,y- and z-direction. Required for parallel computations. More...

void splitDomain (DomainSplit domainSplit)

std::vector< unsignedgetNumberOfDomains ()
returns the number of domains More...

DomaingetCurrentDomain ()
Function that returns a pointer to the domain corresponding to the processor. More...

void removeOldFiles () const

void setMeanVelocity (Vec3D V_mean_goal)
This function will help you set a fixed kinetic energy and mean velocity in your system. More...

void setMeanVelocityAndKineticEnergy (Vec3D V_mean_goal, Mdouble Ek_goal)
This function will help you set a fixed kinetic energy and mean velocity in your system. More...

Mdouble getTotalVolume () const
Get the total volume of the cuboid system. More...

Matrix3D getKineticStress () const
Calculate the kinetic stress tensor in the system averaged over the whole volume. More...

Matrix3D getStaticStress () const
Calculate the static stress tensor in the system averaged over the whole volume. More...

Matrix3D getTotalStress () const
Calculate the total stress tensor in the system averaged over the whole volume. More...

void writePythonFileForVTKVisualisation () const
record when the simulation started More...

## Private Member Functions

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...

## Private Attributes

std::string clusterCommand_
Command required to execute code on a cluster; for einder, the command is ~/bin/sclusterscriptexecute. More...

double maxWallTime_
Time in seconds after which the code is automatically restarted for einder, this should be set to ~10*3600. More...

double initialWallTime_
Internal variable (i.e. More...

Public Types inherited from DPMBase

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...

Read the run number or the counter from the counter file (COUNTER_DONOTDEL) More...

static bool areInContact (const BaseParticle *pI, const BaseParticle *pJ)
Checks if two particle are in contact or is there any positive overlap. More...

Public Attributes inherited from DPMBase
SpeciesHandler speciesHandler
A handler to that stores the species type i.e. LinearViscoelasticSpecies, etc. More...

RNG random
This is a random generator, often used for setting up the initial conditions etc... More...

ParticleHandler particleHandler
An object of the class ParticleHandler, contains the pointers to all the particles created. More...

ParticleHandler paoloParticleHandler
Fake particleHandler created by Paolo needed temporary by just Paolo. More...

WallHandler wallHandler
An object of the class WallHandler. Contains pointers to all the walls created. More...

BoundaryHandler boundaryHandler
An object of the class BoundaryHandler which concerns insertion and deletion of particles into or from regions. More...

PeriodicBoundaryHandler periodicBoundaryHandler
Internal handler that deals with periodic boundaries, especially in a parallel build. More...

DomainHandler domainHandler
An object of the class DomainHandler which deals with parallel code. More...

InteractionHandler interactionHandler
An object of the class InteractionHandler. More...

CGHandler cgHandler
Object of the class cgHandler. More...

File dataFile
An instance of class File to handle in- and output into a .data file. More...

File fStatFile
An instance of class File to handle in- and output into a .fstat file. More...

File eneFile
An instance of class File to handle in- and output into a .ene file. More...

File restartFile
An instance of class File to handle in- and output into a .restart file. More...

File statFile
An instance of class File to handle in- and output into a .stat file. More...

File interactionFile
File class to handle in- and output into .interactions file. This file hold information about interactions. More...

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

virtual void actionsBeforeTimeStep ()
A virtual function which allows to define operations to be executed before the new time step. More...

virtual void actionsAfterSolve ()
A virtual function which allows to define operations to be executed after the solve(). More...

virtual void actionsAfterTimeStep ()
A virtual function which allows to define operations to be executed after time step. More...

void writeVTKFiles () const

virtual void outputXBallsData (std::ostream &os) const
This function writes the location of the walls and particles in a format the XBalls program can read. For more information on the XBalls program, see Visualising data in xballs. More...

virtual void outputXBallsDataParticle (unsigned int i, unsigned int format, std::ostream &os) const
This function writes out the particle locations into an output stream in a format the XBalls program can read. For more information on the XBalls program, see Visualising data in xballs. More...

virtual void writeEneHeader (std::ostream &os) const
Writes a header with a certain format for ENE file. More...

virtual void writeFstatHeader (std::ostream &os) const
Writes a header with a certain format for FStat file. More...

virtual void writeEneTimeStep (std::ostream &os) const
Write the global kinetic, potential energy, etc. in the system. More...

virtual void initialiseStatistics ()

virtual void outputStatistics ()

void gatherContactStatistics ()

virtual void processStatistics (bool)

virtual void finishStatistics ()

virtual void integrateBeforeForceComputation ()
Update particles' and walls' positions and velocities before force computation. More...

virtual void integrateAfterForceComputation ()
Update particles' and walls' positions and velocities after force computation. More...

virtual void checkInteractionWithBoundaries ()
There are a range of boundaries one could implement depending on ones' problem. This methods checks for interactions between particles and such range of boundaries. See BaseBoundary.h and all the boundaries in the Boundaries folder. More...

void setFixedParticles (unsigned int n)
Sets a number, n, of particles in the particleHandler as "fixed particles". More...

virtual void printTime () const
Displays the current simulation time and the maximum simulation duration. More...

virtual bool continueSolve () const
A virtual function for deciding whether to continue the simulation, based on a user-specified criterion. More...

void outputInteractionDetails () const
Displays the interaction details corresponding to the pointer objects in the interaction handler. More...

bool isTimeEqualTo (Mdouble time) const
Checks whether the input variable "time" is the current time in the simulation. More...

void removeDuplicatePeriodicParticles ()
Removes periodic duplicate Particles. More...

void checkAndDuplicatePeriodicParticles ()
For simulations using periodic boundaries, checks and adds particles when necessary into the particle handler. See DPMBase.cc and PeriodicBoundary.cc for more details. More...

void performGhostParticleUpdate ()
When the Verlet scheme updates the positions and velocities of particles, ghost particles will need an update as wel. Their status will also be updated accordingly. More...

void deleteGhostParticles (std::set< BaseParticle * > &particlesToBeDeleted)

void synchroniseParticle (BaseParticle *, unsigned fromProcessor=0)

void performGhostVelocityUpdate ()
updates the final time-step velocity of the ghost particles More...

## Detailed Description

This class adds to Mercury3D the ability to restart after a certain wall time.

This was made necessary to run codes on clusters with wall-time limits. For an example of use, see CSCRun.cpp.

Definition at line 38 of file Mercury3DRestart.h.

## Constructor & Destructor Documentation

 Mercury3DRestart::Mercury3DRestart ( )
inline

Definition at line 42 of file Mercury3DRestart.h.

References clusterCommand_, getWallTime(), initialWallTime_, and maxWallTime_.

43  {
45  maxWallTime_ = 10;
46  clusterCommand_ = "";
47  }
std::string clusterCommand_
Command required to execute code on a cluster; for einder, the command is ~/bin/sclusterscriptexecute...
double getWallTime() const
Returns wall time (uses sys command, thus might not work on Windows)
double initialWallTime_
Internal variable (i.e.
double maxWallTime_
Time in seconds after which the code is automatically restarted for einder, this should be set to ~10...

## Member Function Documentation

 std::string Mercury3DRestart::getClusterCommand ( ) const
inline

Definition at line 54 of file Mercury3DRestart.h.

References clusterCommand_.

55  {
56  return clusterCommand_;
57  }
std::string clusterCommand_
Command required to execute code on a cluster; for einder, the command is ~/bin/sclusterscriptexecute...
 Mdouble Mercury3DRestart::getInitialWallTime ( ) const
inline

Definition at line 69 of file Mercury3DRestart.h.

References initialWallTime_.

70  {
71  return initialWallTime_;
72  }
double initialWallTime_
Internal variable (i.e.
 Mdouble Mercury3DRestart::getMaxWallTime ( ) const
inline

Definition at line 64 of file Mercury3DRestart.h.

References maxWallTime_.

65  {
66  return maxWallTime_;
67  }
double maxWallTime_
Time in seconds after which the code is automatically restarted for einder, this should be set to ~10...
 double Mercury3DRestart::getWallTime ( ) const
inline

Returns wall time (uses sys command, thus might not work on Windows)

Definition at line 111 of file Mercury3DRestart.h.

Referenced by Mercury3DRestart(), and writeOutputFiles().

112  {
113  struct timeval time;
114  if (gettimeofday(&time, NULL))
115  {
116  std::cerr << "Error in getWallTime: Wall time could not be read" << std::endl;
117  return 0;
118  }
119  return (double) time.tv_sec + (double) time.tv_usec * .000001;
120  }
 bool Mercury3DRestart::readNextArgument ( int & i, int argc, char * argv[] )
inlinevirtual

the -r option is used to restart the code; this should probably be moved to DPMBase

Reimplemented from DPMBase.

Definition at line 77 of file Mercury3DRestart.h.

78  {
79  if (!strcmp(argv[i], "-restart") || !strcmp(argv[i], "-r"))
80  {
81  setName(argv[i + 1]);
82
83  //if a restart file is given
84  std::size_t found = getName().find(".restart");
85  if (found == std::string::npos)
86  {
87  std::cout << "Reading file " << restartFile.getName() << std::endl;
89  }
90  else
91  {
92  std::cout << "Reading file " << argv[i + 1] << std::endl;
94  //setName(getName().substr(0,found));
95  std::cout << "Read file " << getName() << std::endl;
96  }
97  std::cout << "tmax= " << getTimeMax() << std::endl;
98  //restartFile.getFstream().precision(18);
99  setAppend(true);
100  printTime();
101  }
102  else
103  {
105  }
106  return true;
107  }
const std::complex< Mdouble > i
Definition: ExtendedMath.h:50
const std::string & getName() const
Returns the name of the file. Does not allow to change it though.
Definition: DPMBase.cc:389
void setAppend(bool newAppendFlag)
Sets whether the "append" option is on or off.
Definition: DPMBase.cc:1482
bool readNextArgument(int &i, int argc, char *argv[]) override
Reads the next command line argument.
Definition: MercuryBase.cc:396
virtual void printTime() const
Displays the current simulation time and the maximum simulation duration.
Definition: DPMBase.cc:1930
void setName(const std::string &name)
Allows to set the name of all the files (ene, data, fstat, restart, stat)
Definition: DPMBase.cc:412
File restartFile
An instance of class File to handle in- and output into a .restart file.
Definition: DPMBase.h:1385
Reads all the particle data corresponding to a given, existing . restart file (for more details regar...
Definition: DPMBase.cc:2896
Mdouble getTimeMax() const
Returns the maximum simulation duration.
Definition: DPMBase.cc:855
const std::string & getName() const
Allows to access the file name, e.g., "problem.data".
Definition: File.cc:166
 void Mercury3DRestart::setClusterCommand ( std::string clusterCommand )
inline

Definition at line 49 of file Mercury3DRestart.h.

References clusterCommand_.

50  {
51  clusterCommand_ = clusterCommand;
52  }
std::string clusterCommand_
Command required to execute code on a cluster; for einder, the command is ~/bin/sclusterscriptexecute...
 void Mercury3DRestart::setMaxWallTime ( Mdouble maxWallTime )
inline

Definition at line 59 of file Mercury3DRestart.h.

References maxWallTime_.

60  {
61  maxWallTime_ = maxWallTime;
62  }
double maxWallTime_
Time in seconds after which the code is automatically restarted for einder, this should be set to ~10...
 void Mercury3DRestart::writeOutputFiles ( )
inlineprivatevirtual

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).

Writes headers and all relevant information to the relevant output files. Note that the writeFstatHeader() actually contains within it the functionality to write the full fstat data, whereas for .ene files the functions to write the headers and main data are separate. Note that the interaction file is not written here: it is written with the start and end of each interaction.

The function [X].saveCurrentTimeStep(numberOfTimeSteps_) returns true if:

a) The current time step is greater than or equal to the time step at which the next write or read operation is supposed to happen.

b) The FileType is not "NO_FILE".

c) The file is open.

Reimplemented from DPMBase.

Definition at line 128 of file Mercury3DRestart.h.

129  {
131
133  {
136  closeFiles();
137  std::cout << "Exiting for restarting after "
138  << getWallTime() - initialWallTime_ << "s" << std::endl;
139
140  //set the restart command
141  std::stringstream com("");
142  //check if filename contaion a dot
143  //this is so the code works for autonumbered files
144  std::size_t found = getName().find('.');
145  if (found == std::string::npos)
146  {
147  com << clusterCommand_ << " ./" << getName() << " -r " << getName();
148  }
149  else
150  {
151  com << clusterCommand_ << " ./" << getName().substr(0, found) << " -r " << getName();
152  }
153  //std::cout << com << std::endl;
154  std::cout << "system output:" << system(com.str().c_str()) << std::endl;
155  exit(0);
156  }
157  }
std::string clusterCommand_
Command required to execute code on a cluster; for einder, the command is ~/bin/sclusterscriptexecute...
const std::string & getName() const
Returns the name of the file. Does not allow to change it though.
Definition: DPMBase.cc:389
virtual void writeOutputFiles()
Writes simulation data to all the main Mercury files: .data, .ene, .fstat, .xballs and ...
Definition: DPMBase.cc:3846
double getWallTime() const
Returns wall time (uses sys command, thus might not work on Windows)
double initialWallTime_
Internal variable (i.e.
void closeFiles()
Closes all files (ene, data, fstat, restart, stat) that were opened to read or write.
Definition: DPMBase.cc:492
virtual void actionsAfterSolve()
A virtual function which allows to define operations to be executed after the solve().
Definition: DPMBase.cc:1831
double maxWallTime_
Time in seconds after which the code is automatically restarted for einder, this should be set to ~10...
virtual void finishStatistics()
Definition: DPMBase.cc:1885

## Member Data Documentation

 std::string Mercury3DRestart::clusterCommand_
private

Command required to execute code on a cluster; for einder, the command is ~/bin/sclusterscriptexecute.

Definition at line 162 of file Mercury3DRestart.h.

Referenced by getClusterCommand(), Mercury3DRestart(), setClusterCommand(), and writeOutputFiles().

 double Mercury3DRestart::initialWallTime_
private

Internal variable (i.e.

not to be set by the user); stores the wall time before solve is executed

Definition at line 172 of file Mercury3DRestart.h.

Referenced by getInitialWallTime(), Mercury3DRestart(), and writeOutputFiles().

 double Mercury3DRestart::maxWallTime_
private

Time in seconds after which the code is automatically restarted for einder, this should be set to ~10*3600.

Definition at line 167 of file Mercury3DRestart.h.

Referenced by getMaxWallTime(), Mercury3DRestart(), setMaxWallTime(), and writeOutputFiles().

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