MercuryDPM  Beta
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)

void setMaxWallTime (Mdouble maxWallTime)

Mdouble getMaxWallTime () const

Mdouble getInitialWallTime () const

int 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...

Public Member Functions inherited from MercuryBase
MercuryBase ()
This is the default constructor. It sets sensible defaults. More...

~MercuryBase ()
This is the default destructor. More...

MercuryBase (const MercuryBase &mercuryBase)
Copy-constructor. More...

void constructor ()
This is the actual constructor, it is called do both constructors above. More...

void hGridActionsBeforeTimeLoop () override
This sets up the broad phase information, has to be done at this stage because it requires the particle size. More...

void hGridActionsBeforeTimeStep () override
Performs all necessary actions before a time-step, like updating the particles and resetting all the bucket information, etc. More...

void read (std::istream &is) override
Reads the MercuryBase from an input stream, for example a restart file. More...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

virtual Mdouble getHGridTargetMinInteractionRadius () const
Gets the desired size of the smallest cells of the HGrid. More...

virtual Mdouble getHGridTargetMaxInteractionRadius () const
Gets the desired size of the largest cells of the HGrid. More...

bool checkParticleForInteraction (const BaseParticle &P) override
Checks if given BaseParticle has an interaction with a BaseWall or other BaseParticle. More...

virtual Mdouble userHGridCellSize (unsigned int level)
Virtual function that enables inheriting classes to implement a function to let the user set the cell size of the HGrid. More...

void hGridInfo () const
Writes the info of the HGrid to the screen in a nice format. More...

Public Member Functions inherited from DPMBase
void constructor ()
A function which initialises the member variables to default values, so that the problem can be solved off the shelf; sets up a basic two dimensional problem which can be solved off the shelf. It is called in the constructor DPMBase(). More...

DPMBase ()
Constructor that calls the "void constructor()". More...

DPMBase (const FilesAndRunNumber &other)
Copy constructor type-1. More...

DPMBase (const DPMBase &other)
Copy constructor type-2. More...

virtual ~DPMBase ()
virtual destructor More...

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

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

void solve (int argc, char *argv[])
The solve function is the work horse of the code with the user input. More...

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

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

virtual double getInfo (const BaseParticle &P) const
A virtual method that allows the user to overrride and set what is written into the info column in the data file. By default it returns the Species ID number. More...

virtual void writeRestartFile ()
Stores all the particle data for current save time step. Calls the write function. More...

Reads all the particle data corresponding to the current saved time step. Which is what the restart file basically stores. The problem description with the latest particle data. More...

int readRestartFile (std::string fileName)
Also reads all the particle data corresponding to the current saved time step. More...

virtual void readOld (std::istream &is)
Reads all particle data into a restart file; old version. More...

bool readDataFile (const std::string fileName, unsigned int format=0)
This allows particle data to be reloaded from data files. More...

bool readParAndIniFiles (const std::string fileName)
Allows the user to read par.ini files (useful to read MDCLR files) More...

bool readNextDataFile (unsigned int format=0)
Reads the next data file with default format=0. However, one can modify the format based on whether the particle data corresponds to 3D or 2D data. See XBalls/xballs.txt. More...

bool findNextExistingDataFile (Mdouble tMin, bool verbose=true)
Useful when fileType is chosen as Multiple Files or Multiple files with padded. More...

bool readArguments (int argc, char *argv[])
Can interpret main function input arguments that are passed by the driver codes. More...

Mdouble getTime () const
Access function for the time. More...

unsigned int getNtimeSteps () const
Returns the current counter of time steps. More...

void setTime (Mdouble time)
Access function for the time. More...

void setTimeMax (Mdouble newTMax)
Allows the upper time limit to be changed. More...

Mdouble getTimeMax () const
Allows the user to access the total simulation time during the simulation. Cannot change it though. More...

void setDoCGAlways (bool newDoCGFlag)

void setRotation (bool newRotFlag)
Allows to set the flag for enabling or disabling particle rotation in the simulations. More...

bool getRotation () const
Returns a flag indicating if particle rotation is enabled or disabled. More...

bool getDoCGAlways () const

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

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

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

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

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

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

void setXMin (Mdouble newXMin)
If the length of the problem domain in x-direction is XMax - XMin, this method sets XMin. More...

void setYMin (Mdouble newYMin)
If the length of the problem domain in y-direction is YMax - YMin, this method sets YMin. More...

void setZMin (Mdouble newZMin)
If the length of the problem domain in z-direction is ZMax - ZMin, this method sets ZMin. More...

void setXMax (Mdouble newXMax)
If the length of the problem domain in x-direction is XMax - XMin, this method sets XMax. More...

void setYMax (Mdouble newYMax)
If the length of the problem domain in y-direction is YMax - YMin, this method sets YMax. More...

void setZMax (Mdouble newZMax)
If the length of the problem domain in z-direction is XMax - XMin, this method sets ZMax. More...

void setTimeStep (Mdouble newDt)
Allows the time step dt to be changed. More...

Mdouble getTimeStep () const
Allows the time step dt to be accessed. More...

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

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

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

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

void setXBallsAdditionalArguments (std::string newXBArgs)
Set the additional arguments for xballs. More...

std::string getXBallsAdditionalArguments () const

void setXBallsScale (Mdouble newScale)
Sets the scale of the view (either normal, zoom in or zoom out) to display in xballs. The default is fit to screen. More...

double getXBallsScale () const
Returns the scale of the view in xballs. More...

void setGravity (Vec3D newGravity)
Allows to modify the gravity vector. More...

Vec3D getGravity () const
Returns the gravity vector. More...

void setDimension (unsigned int newDim)
Sets the system and particle dimension. More...

void setSystemDimensions (unsigned int newDim)
Allows for the dimension of the simulation to be changed. More...

unsigned int getSystemDimensions () const
Returns the dimension of the simulation. Note there is also a particle dimension. More...

void setParticleDimensions (unsigned int particleDimensions)
Allows the dimension of the particle (f.e. for mass) to be changed. e.g. discs or spheres. More...

unsigned int getParticleDimensions () const
Returns the particle dimensions. More...

std::string getRestartVersion () const
This is to take into account for different Mercury versions. Returns the version of the restart file. More...

void setRestartVersion (std::string newRV)
Sets restart_version. More...

bool getRestarted () const
Returns the flag denoting if the simulation was restarted or not. More...

void setRestarted (bool newRestartedFlag)
Allows to set the flag stating if the simulation is to be restarted or not. More...

bool getAppend () const
Returns the flag denoting if the append option is on or off. More...

void setAppend (bool newAppendFlag)
Allows to set the append option. More...

Mdouble getElasticEnergy () const
Returns the global elastic energy within the system. More...

Mdouble getKineticEnergy () const
Returns the global kinetic energy stored in the system. More...

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

virtual void hGridInsertParticle (BaseParticle *obj UNUSED)
no implementation but can be overidden in its derived classes. More...

virtual void hGridUpdateParticle (BaseParticle *obj UNUSED)
no implementation but can be overidden in its derived classes. More...

virtual void hGridRemoveParticle (BaseParticle *obj UNUSED)
no implementation but can be overidden in its derived classes. More...

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

Public Member Functions inherited from FilesAndRunNumber
FilesAndRunNumber ()
Constructor. More...

FilesAndRunNumber (const FilesAndRunNumber &other)
Copy constructor. More...

virtual ~FilesAndRunNumber ()
Constructor. More...

void constructor ()
a function called by the FilesAndRunNumber() (constructor) More...

void incrementRunNumberInFile ()
Increment the run Number (counter value) stored in the file_counter (COUNTER_DONOTDEL) by 1 and store the new value in the counter file. More...

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

void autoNumber ()
The autoNumber() function is the trigger. It calls three functions. setRunNumber(), readRunNumberFromFile() and incrementRunNumberInFile(). More...

std::vector< int > get2DParametersFromRunNumber (int size_x, int size_y)
This turns a counter into two indices which is an amazing feature for doing two dimensional parameter studies. The indices run from 1:size_x and 1:size_y, while the study number starts at 0 ( initially the counter=1 in COUNTER_DONOTDEL) More...

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

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

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

void read (std::istream &is)
Accepts an input stream std::istream. More...

void write (std::ostream &os) const
Accepts an output stream read function, which accepts an input stream std::ostream. More...

Public Member Functions inherited from Files
Files ()
A constructor. More...

virtual ~Files ()
A destructor, watch out its a virtual destructor. More...

Files (const Files &other)
Copy constructor. More...

MERCURY_DEPRECATED 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...

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 std::string & getName () const
Returns the name of the file. Does not allow to change it though. More...

void setName (const std::string &name)
Allows to set the name of all the files (ene, data, fstat, restart, stat) More...

void setName (const char *name)
Calls setName(std::string) More...

void setSaveCount (unsigned int saveCount)
Sets File::saveCount_ for all files (ene, data, fstat, restart, stat) More...

void setFileType (FileType fileType)
Sets File::fileType_ for all files (ene, data, fstat, restart, stat) More...

void setOpenMode (std::fstream::openmode openMode)
Sets File::openMode_ for all files (ene, data, fstat, restart, stat) More...

void resetFileCounter ()
Resets the file counter for each file i.e. for ene, data, fstat, restart, stat) More...

void read (std::istream &is)
Extracts data from the input stream (which is basically a file you want to read from) into name_, restartFile .... More...

void write (std::ostream &os) const
Writes data into a file from the member variables name_, restartFile, dataFile etc. More...

void openFiles ()
Opens all the files (ene, data, fstat, restart, stat) for reading and writing purposes. More...

void closeFiles ()
Closes all files (ene, data, fstat, restart, stat) that were opened to read or write. More...

void setNextSavedTimeStep (unsigned int nextSavedTimeStep)
Sets the next time step for all the files (ene, data, fstat, restart, stat) at which the data is to be written or saved. More...

## Private Member Functions

void writeOutputFiles ()
Writes the simulation data onto all the files i.e. .data, .ene, .fstat ... 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...

## Additional Inherited Members

Public Attributes inherited from DPMBase
SpeciesHandler speciesHandler
A handler to that stores the species type i.e. elastic, linear visco-elastic... et cetera. More...

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

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

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

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

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

Public Attributes inherited from Files
File dataFile
An instance of class File to handle in- and output into a .data file. More...

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

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

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

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

Protected Member Functions inherited from Mercury3D
virtual void hGridFindContactsWithinTargetCell (int x, int y, int z, unsigned int l)
Finds contacts between particles in the target cell. More...

virtual void hGridFindContactsWithTargetCell (int x, int y, int z, unsigned int l, BaseParticle *obj)
Finds contacts between the BaseParticle and the target cell. More...

void hGridFindOneSidedContacts (BaseParticle *obj) override
Finds contacts with the BaseParticle; avoids multiple checks. More...

bool hGridHasContactsInTargetCell (int x, int y, int z, unsigned int l, const BaseParticle *obj) const
Tests if the BaseParticle has contacts with other Particles in the target cell. More...

bool hGridHasParticleContacts (const BaseParticle *obj) override
Tests if a BaseParticle has any contacts in the HGrid. More...

void hGridRemoveParticle (BaseParticle *obj)
Removes a BaseParticle from the HGrid. More...

void hGridUpdateParticle (BaseParticle *obj) override
Updates the cell (not the level) of a BaseParticle. More...

Protected Member Functions inherited from MercuryBase
void hGridRebuild ()
This sets up the parameters required for the contact model. More...

void hGridInsertParticle (BaseParticle *obj) override
Inserts a single Particle to current grid. More...

void broadPhase (BaseParticle *i) override
This checks particles in the HGRID to see if for closer enough for possible contact. More...

void hGridUpdateMove (BaseParticle *iP, Mdouble move) override
Computes the relative displacement of the given BaseParticle and updates the currentMaxRelativeDisplacement_ accordingly. More...

void hGridActionsBeforeIntegration () override
Resets the currentMaxRelativeDisplacement_ to 0. More...

void hGridActionsAfterIntegration () override
Sets the totalCurrentMaxRelativeDisplacement_ as 2*currentMaxRelativeDisplacement_. More...

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 by using the setTorque and setForce methods. See BaseInteractible.cc. More...

virtual void computeInternalForces (BaseParticle *i)
Computes the forces between particles (internal in the sense that the sum over all these forces is zero i.e. fully modelled forces) More...

virtual void computeInternalForces (BaseParticle *P1, BaseParticle *P2)
Computes the forces between particles (internal in the sense that the sum over all these forces is zero i.e. fully modelled forces) More...

virtual void computeExternalForces (BaseParticle *PI)
Computes the external forces acting on particles (e.g. gravitational) More...

virtual void computeForcesDueToWalls (BaseParticle *PI)
Computes the forces on the particles due to the walls (normals are outward normals) More...

virtual void actionsOnRestart ()
A virtual function where the users can add extra code which is executed only when the code is restarted. More...

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

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

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

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

virtual void outputXBallsData (std::ostream &os) const
This function writes the location of the walls and particles in a format the XBalls program can read. See XBalls/xballs.txt. However, MercuryDPM supports a much better viewer now called Paraview. See the tutorials section in the documentation. More...

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

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

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

virtual void writeEneTimestep (std::ostream &os) const
This function enables one to write the global energy available in the system after each time step. The default is to compute the rotational and translational kinetic energy, potential energy and the centre of mass. More...

virtual void initialiseStatistics ()
no implementation but can be overidden in its derived classes. More...

virtual void outputStatistics ()
no implementation but can be overidden in its derived classes. More...

void gatherContactStatistics ()

virtual void processStatistics (bool usethese UNUSED)
no implementation but can be overidden in its derived classes. More...

virtual void finishStatistics ()
no implementation but can be overidden in its derived classes. More...

virtual void integrateBeforeForceComputation ()
This is were the integration is done, at the moment it is velocity Verlet integration and is done before the forces are computed. See http://en.wikipedia.org/wiki/Verlet_integration#Velocity_Verlet. More...

virtual void integrateAfterForceComputation ()
Integration is done after force computations. We apply the Velocity verlet scheme. See http://en.wikipedia.org/wiki/Verlet_integration#Velocity_Verlet. More...

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

void setFixedParticles (unsigned int n)

void initialiseTangentialSprings ()

virtual void printTime () const
Displays the current simulation time onto your screen for example. More...

virtual bool continueSolve () const

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

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

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

void checkAndDuplicatePeriodicParticles ()
In case of periodic boundaries, the below methods checks and adds particles when necessary into the particle handler. See DPMBase.cc and PeriodicBoundary.cc for more details. More...

## 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 37 of file Mercury3DRestart.h.

## Constructor & Destructor Documentation

 Mercury3DRestart::Mercury3DRestart ( )
inline

Definition at line 41 of file Mercury3DRestart.h.

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

42  {
44  maxWallTime_ = 10;
45  clusterCommand_ = "";
46  }
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

 Mdouble Mercury3DRestart::getInitialWallTime ( ) const
inline

Definition at line 63 of file Mercury3DRestart.h.

References initialWallTime_.

64  {
65  return initialWallTime_;
66  }
double initialWallTime_
Internal variable (i.e.
 Mdouble Mercury3DRestart::getMaxWallTime ( ) const
inline

Definition at line 58 of file Mercury3DRestart.h.

References maxWallTime_.

59  {
60  return maxWallTime_;
61  }
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 92 of file Mercury3DRestart.h.

Referenced by Mercury3DRestart(), and writeOutputFiles().

93  {
94  struct timeval time;
95  if (gettimeofday(&time, NULL))
96  {
97  std::cerr << "Error in getWallTime: Wall time could not be read" << std::endl;
98  return 0;
99  }
100  return (double) time.tv_sec + (double) time.tv_usec * .000001;
101  }
 int 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 71 of file Mercury3DRestart.h.

72  {
73  if (!strcmp(argv[i], "-restart") || !strcmp(argv[i], "-r"))
74  {
75  setName(argv[i + 1]);
76  std::cout << "Reading file " << restartFile.getName() << std::endl;
78  std::cout << "tmax= " << getTimeMax() << std::endl;
79  restartFile.getFstream().precision(18);
80  setAppend(true);
81  printTime();
82  }
83  else
84  {
85  return Mercury3D::readNextArgument(i, argc, argv);
86  }
87  return true;
88  }
File restartFile
An instance of class File to handle in- and output into a .restart file.
Definition: Files.h:219
void setAppend(bool newAppendFlag)
Allows to set the append option.
Definition: DPMBase.cc:544
std::fstream & getFstream()
Allows to access the member variable File::fstream_.
Definition: File.cc:150
Reads all the particle data corresponding to the current saved time step. Which is what the restart f...
Definition: DPMBase.cc:1375
void setName(const std::string &name)
Allows to set the name of all the files (ene, data, fstat, restart, stat)
Definition: Files.cc:149
bool readNextArgument(int &i, int argc, char *argv[]) override
Reads the next command line argument.
Definition: MercuryBase.cc:419
virtual void printTime() const
Displays the current simulation time onto your screen for example.
Definition: DPMBase.cc:758
Mdouble getTimeMax() const
Allows the user to access the total simulation time during the simulation. Cannot change it though...
Definition: DPMBase.cc:194
const std::string & getName() const
Allows to access the file name, e.g., "problem.data".
Definition: File.cc:162
 void Mercury3DRestart::setClusterCommand ( std::string clusterCommand )
inline

Definition at line 48 of file Mercury3DRestart.h.

References clusterCommand_.

49  {
50  clusterCommand_ = clusterCommand;
51  }
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 53 of file Mercury3DRestart.h.

References maxWallTime_.

54  {
55  maxWallTime_ = maxWallTime;
56  }
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 the simulation data onto all the files i.e. .data, .ene, .fstat ...

Reimplemented from DPMBase.

Definition at line 109 of file Mercury3DRestart.h.

110  {
112
114  {
117  closeFiles();
118  std::cout << "Exiting for restarting after "
119  << getWallTime() - initialWallTime_ << "s" << std::endl;
120
121  //set the restart command
122  std::stringstream com("");
123  //check if filename contaion a dot
124  //this is so the code works for autonumbered files
125  std::size_t found = getName().find('.');
126  if (found==std::string::npos) {
127  com << clusterCommand_ << " ./" << getName() << " -r " << getName();
128  } else {
129  com << clusterCommand_ << " ./" << getName().substr (0,found) << " -r " << getName();
130  }
131  //std::cout << com << std::endl;
132  std::cout << "system output:" << system(com.str().c_str()) << std::endl;
133  exit(0);
134  }
135  }
std::string clusterCommand_
Command required to execute code on a cluster; for einder, the command is ~/bin/sclusterscriptexecute...
void closeFiles()
Closes all files (ene, data, fstat, restart, stat) that were opened to read or write.
Definition: Files.cc:250
virtual void writeOutputFiles()
Writes the simulation data onto all the files i.e. .data, .ene, .fstat ...
Definition: DPMBase.cc:1848
double getWallTime() const
Returns wall time (uses sys command, thus might not work on Windows)
double initialWallTime_
Internal variable (i.e.
virtual void actionsAfterSolve()
A virtual function which allows to define operations to be executed after the solve().
Definition: DPMBase.cc:662
double maxWallTime_
Time in seconds after which the code is automatically restarted for einder, this should be set to ~10...
virtual void finishStatistics()
no implementation but can be overidden in its derived classes.
Definition: DPMBase.cc:710
const std::string & getName() const
Returns the name of the file. Does not allow to change it though.
Definition: Files.cc:131

## 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 140 of file Mercury3DRestart.h.

Referenced by 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 150 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 145 of file Mercury3DRestart.h.

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

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