DeletionBoundary Class Reference

Used for removing particles from the problem. Inherits from BaseBoundary. By default, a plane that deletes everything past it, but there are derived classes such as CubeDeletionBoundary. More...

#include <DeletionBoundary.h>

Inheritance diagram for DeletionBoundary:

Public Member Functions
	DeletionBoundary ()
	default constructor More...
	DeletionBoundary (DeletionBoundary const &d)
	default copy constructor More...
	~DeletionBoundary () override
	destructor More...
DeletionBoundary *	copy () const override
	Copy method; creates copy on the heap and returns a pointer to it. More...
void	set (const Vec3D &normal, Mdouble distance)
	Sets boundary position based on a normal and distance. More...
void	move (Mdouble position)
	Sets the boundary's distance property to the given one. More...
virtual Mdouble	getDistance (const Vec3D &position) const
	Returns a negative value if and only if the particle is inside the boundary (and therefore to be deleted). More...
bool	checkBoundaryAfterParticleMoved (BaseParticle *p, ParticleHandler &pH)
	Checks if particle is inside the boundary, and deletes the particle if so. More...
void	checkBoundaryAfterParticlesMove (ParticleHandler &pH) override
unsigned int	getNumberOfParticlesDeleted () const
	Gets the number of particles deleted by the boundary. More...
double	getMassOfParticlesDeleted () const
double	getVolumeOfParticlesDeleted () const
void	reset ()
void	activate ()
	Turns on the DeletionBoundary. More...
void	deactivate ()
	Turns off the DeletionBoundary. More...
void	trackOutflow (bool trackOutflow=true)
	Turns on the outflow tracker. More...
void	read (std::istream &is) override
	Reads some boundary properties from an std::istream. More...
MERCURYDPM_DEPRECATED void	oldRead (std::istream &is)
	Deprecated read method. use DeletionBoundary::read() instead. More...
void	write (std::ostream &os) const override
	Writes the boundary properties to an std::ostream. More...
std::string	getName () const override
	Returns the name of the object. More...
Public Member Functions inherited from BaseBoundary
	BaseBoundary ()
	default constructor. More...
	BaseBoundary (const BaseBoundary &b)
	copy constructor More...
	~BaseBoundary () override
	destructor More...
virtual void	createPeriodicParticle (BaseParticle *p UNUSED, ParticleHandler &pH UNUSED)
	Creates a periodic particle in case of periodic boundaries in serial build. More...
virtual void	createPeriodicParticles (ParticleHandler &pH UNUSED)
	Creates periodic copies of given particle in case of periodic boundaries. More...
virtual void	checkBoundaryBeforeTimeStep (DPMBase *md)
	Virtual function that does things before each time step. More...
virtual void	actionsBeforeTimeLoop ()
	Virtual function that does something after DPMBase::setupInitialConditions but before the first time step. More...
virtual void	modifyGhostAfterCreation (BaseParticle *particle, int i)
virtual void	writeVTK (std::fstream &file)
void	setHandler (BoundaryHandler *handler)
	Sets the boundary's BoundaryHandler. More...
BoundaryHandler *	getHandler () const
	Returns the boundary's BoundaryHandler. More...
Public Member Functions inherited from BaseObject
	BaseObject ()=default
	Default constructor. More...
	BaseObject (const BaseObject &p)=default
	Copy constructor, copies all the objects BaseObject contains. More...
virtual	~BaseObject ()=default
	virtual destructor More...
virtual void	moveInHandler (unsigned int index)
	Except that it is virtual, it does the same thing as setIndex() does. More...
void	setIndex (unsigned int index)
	Allows one to assign an index to an object in the handler/container. More...
void	setId (unsigned long id)
	Assigns a unique identifier to each object in the handler (container) which remains constant even after the object is deleted from the container/handler. More...
unsigned int	getIndex () const
	Returns the index of the object in the handler. More...
unsigned int	getId () const
	Returns the unique identifier of any particular object. More...
void	setGroupId (unsigned groupId)
unsigned	getGroupId () const

Private Attributes
Vec3D	normal_
	outward unit normal vector More...
Mdouble	scaleFactor_
	This is the factor to rescale the given normal vector to a unit vectors. More...
Mdouble	distance_
	The boundary's distance from the origin. More...
unsigned int	numberOfParticlesDeleted_
	Number of particles that have been deleted by this boundary. More...
double	massDeleted_
double	trackMassDeleted_
double	volumeDeleted_
bool	isActivated_
	The DeletionBoundary is activated by default. If the DeletionBoundary is deactivated, then it deletes no particles. More...
bool	trackOutflow_
std::ofstream	tracker

Detailed Description

Used for removing particles from the problem. Inherits from BaseBoundary. By default, a plane that deletes everything past it, but there are derived classes such as CubeDeletionBoundary.

Constructor & Destructor Documentation

DeletionBoundary() [1/2]

DeletionBoundary::DeletionBoundary

(

)

default constructor

Default constructor (calls the parent-constructor of BaseBoundary as well)

        : BaseBoundary()
{
    distance_ = std::numeric_limits<double>::quiet_NaN();
    scaleFactor_ = std::numeric_limits<double>::quiet_NaN();
    isActivated_ = true;
    trackOutflow_ = false;
    numberOfParticlesDeleted_ = 0;
    massDeleted_ = 0;
    volumeDeleted_ = 0;
    
    logger(DEBUG, "DeletionBoundary::DeletionBoundary() finished", true);
}

References DEBUG, distance_, isActivated_, logger, massDeleted_, numberOfParticlesDeleted_, scaleFactor_, trackOutflow_, and volumeDeleted_.

Referenced by copy().

DeletionBoundary() [2/2]

DeletionBoundary::DeletionBoundary ( DeletionBoundary const &  d )

inline

default copy constructor

        : normal_(d.normal_), scaleFactor_(d.scaleFactor_), distance_(d.distance_),
          numberOfParticlesDeleted_(d.numberOfParticlesDeleted_), massDeleted_(d.massDeleted_),
          volumeDeleted_(d.volumeDeleted_), isActivated_(d.isActivated_), trackOutflow_(d.trackOutflow_) {}

~DeletionBoundary()

DeletionBoundary::~DeletionBoundary ( )

override

destructor

Destructor

{
    logger(DEBUG, "DeletionBoundary::~DeletionBoundary() finished", true);
}

References DEBUG, and logger.

Member Function Documentation

activate()

void DeletionBoundary::activate

(

)

Turns on the DeletionBoundary.

{
    isActivated_ = true;
}

References isActivated_.

checkBoundaryAfterParticleMoved()

bool DeletionBoundary::checkBoundaryAfterParticleMoved	(	BaseParticle *	p,
		ParticleHandler &	pH
	)

Checks if particle is inside the boundary, and deletes the particle if so.

Todo:

: MX: update the above comment

Checks if particle has passed the boundary, and if so, deletes the particle.

Parameters

[in]	p	pointer to the particle which is to be checked
[out]	pH	the particle's ParticleHandler, from which the particle is removed in case it has passed the boundary.

Returns

TRUE if the particle has actually passed the boundary and is thus deleted.

Todo:

JMFT: The mass and volume counters need to be updated in the MPI code.

{
    if (getDistance(p->getPosition()) < 0)
    {
        if (trackOutflow_) {
            auto dpm = getHandler()->getDPMBase();
            trackMassDeleted_ += p->getMass();
            if (!tracker.is_open()) {
                std::string name  = dpm->getName()
                        + helpers::toString(getIndex())
                        + ".out" + (NUMBER_OF_PROCESSORS==1?"":std::to_string(PROCESSOR_ID));
                logger(INFO, "Open file %", name);
                tracker.open(name);
                tracker << std::setw(13) << "Time "
                        << std::setw(8) << "Species "
                        << std::setw(8) << "ID "
                        << std::setw(13) << "Position_x "
                        << std::setw(13) << "Position_y "
                        << std::setw(13) << "Position_z "
                        << std::setw(13) << "Velocity_x "
                        << std::setw(13) << "Velocity_y "
                        << std::setw(13) << "Velocity_z "
                        << std::setw(13) << "Radius "
                        << std::setw(13) << "AnVelocity_x "
                        << std::setw(13) << "AnVelocity_y "
                        << std::setw(13) << "AnVelocity_z "
                        << std::setw(13) << "Mass "
                        << std::setw(13) << "TotalMass"
                        << '\n';
            }
            tracker << std::setw(12) << dpm->getTime() << ' '
                    << std::setw(8) << p->getIndSpecies() << ' '
                    << std::setw(8) << p->getId() << ' '
                    << std::setw(12) << p->getPosition().X << ' '
                    << std::setw(12) << p->getPosition().Y << ' '
                    << std::setw(12) << p->getPosition().Z << ' '
                    << std::setw(12) << p->getVelocity().X << ' '
                    << std::setw(12) << p->getVelocity().Y << ' '
                    << std::setw(12) << p->getVelocity().Z << ' '
                    << std::setw(12) << p->getRadius() << ' '
                    << std::setw(12) << p->getAngularVelocity().X << ' '
                    << std::setw(12) << p->getAngularVelocity().Y << ' '
                    << std::setw(12) << p->getAngularVelocity().Z << ' '
                    << std::setw(12) << p->getMass() << ' '
                    << std::setw(12) << trackMassDeleted_ << '\n';
        }
 
        #ifdef MERCURYDPM_USE_MPI
            //Check if the particle is in the mpi communication zone
            if(p->isInMPIDomain())
            {
                //Add the particle to a list so we can flush it later on
                //The particles are not deleted yet. This is done in dpmBase after this function is called
                particlesToBeDeleted_.insert(p);
                return false;
            }
            else
            {
                pH.removeGhostObject(p->getIndex());
                return true;
            }
        #else
            numberOfParticlesDeleted_++;
            massDeleted_ += p->getMass();
            volumeDeleted_ += p->getVolume();
            pH.removeObject(p->getIndex());
            pH.computeLargestParticle();
            pH.computeSmallestParticle();
            return true;
        #endif
    }
    else
    {
        return false;
    }
}

References ParticleHandler::computeLargestParticle(), ParticleHandler::computeSmallestParticle(), BaseInteractable::getAngularVelocity(), getDistance(), BaseHandler< T >::getDPMBase(), BaseBoundary::getHandler(), BaseObject::getId(), BaseObject::getIndex(), BaseInteractable::getIndSpecies(), BaseParticle::getMass(), BaseInteractable::getPosition(), BaseParticle::getRadius(), BaseInteractable::getVelocity(), BaseParticle::getVolume(), INFO, BaseParticle::isInMPIDomain(), logger, massDeleted_, units::name, NUMBER_OF_PROCESSORS, numberOfParticlesDeleted_, PROCESSOR_ID, ParticleHandler::removeGhostObject(), ParticleHandler::removeObject(), helpers::toString(), tracker, trackMassDeleted_, trackOutflow_, volumeDeleted_, Vec3D::X, Vec3D::Y, and Vec3D::Z.

Referenced by checkBoundaryAfterParticlesMove().

checkBoundaryAfterParticlesMove()

void DeletionBoundary::checkBoundaryAfterParticlesMove ( ParticleHandler &  pH )

overridevirtual

Todo:

MX: I changed the syntax to a more mpi compatible (and neater) code. Need to update the comments of the checkBoundaryAfterParticleMoved function

Reimplemented from BaseBoundary.

{
    if (!isActivated_)
        return;
 
#ifdef MERCURYDPM_USE_MPI
    particlesToBeDeleted_.clear();
#endif
    for (unsigned int i = 0; i < pH.getSize(); i++)
    {
        //If the particle is deleted, change the iterator
        if (checkBoundaryAfterParticleMoved(pH.getObject(i), pH))
        {
            i--;
        }
    }
}

References checkBoundaryAfterParticleMoved(), BaseHandler< T >::getObject(), BaseHandler< T >::getSize(), constants::i, and isActivated_.

copy()

DeletionBoundary * DeletionBoundary::copy ( ) const

overridevirtual

Copy method; creates copy on the heap and returns a pointer to it.

Copy function, which creates a copy and returns a pointer to that copy (on the heap)

Returns

pointer to the copy

Implements BaseBoundary.

{
    return new DeletionBoundary(*this);
}

References DeletionBoundary().

deactivate()

void DeletionBoundary::deactivate

(

)

Turns off the DeletionBoundary.

{
    isActivated_ = false;
}

References isActivated_.

getDistance()

Mdouble DeletionBoundary::getDistance ( const Vec3D &  position ) const

virtual

Returns a negative value if and only if the particle is inside the boundary (and therefore to be deleted).

The default DeletionBoundary is a half-space (specified by a plane) but the geometry can be overridden (e.g. by CubeDeletionBoundary). Calculates the shortest distance between the wall and given position.

Parameters

[in]

position

the position of which the distance should be calculated.

Reimplemented in CubeDeletionBoundary.

{
    return distance_ - Vec3D::dot(position, normal_);
}

References distance_, Vec3D::dot(), and normal_.

Referenced by checkBoundaryAfterParticleMoved().

getMassOfParticlesDeleted()

double DeletionBoundary::getMassOfParticlesDeleted

(

)

const

{
    return massDeleted_;
}

References massDeleted_.

Referenced by BoundariesSelfTest::actionsAfterTimeStep().

getName()

std::string DeletionBoundary::getName ( ) const

overridevirtual

Returns the name of the object.

Returns the object's class name (i.e. 'DeletionBoundary').

Returns

the object's class name

Implements BaseObject.

{
    return "DeletionBoundary";
}

getNumberOfParticlesDeleted()

unsigned int DeletionBoundary::getNumberOfParticlesDeleted

(

)

const

Gets the number of particles deleted by the boundary.

Returns the number of particles deleted by this boundary. TODO For some reason, this causes a segfault — DO NOT USE. valgrind complains that 'numberOfParticlesDeleted_' is not initialised.

{
    return numberOfParticlesDeleted_;
}

References numberOfParticlesDeleted_.

Referenced by T_protectiveWall::actionsAfterTimeStep(), BoundariesSelfTest::actionsAfterTimeStep(), and protectiveWall::actionsAfterTimeStep().

getVolumeOfParticlesDeleted()

double DeletionBoundary::getVolumeOfParticlesDeleted

(

)

const

{
    return volumeDeleted_;
}

References volumeDeleted_.

Referenced by BoundariesSelfTest::actionsAfterTimeStep().

move()

void DeletionBoundary::move

(

Mdouble

distance

)

Sets the boundary's distance property to the given one.

Resets the boundary's 'distance' from the origin to be the one given.

Parameters

[in]

distance

the new 'distance' between boundary and origin. see also comments of DeletionBoundary::set().

{
    distance_ = distance * scaleFactor_;
}

References distance_, and scaleFactor_.

oldRead()

void DeletionBoundary::oldRead

(

std::istream &

is

)

Deprecated read method. use DeletionBoundary::read() instead.

the deprecated version of the read-method. Should not be used by new users!

Deprecated:

Should be gone by Mercury 2.0. Use DeletionBoundary::read() instead.

{
    std::string dummy;
    is >> dummy >> normal_ >> dummy >> scaleFactor_ >> dummy >> distance_;
}

References distance_, normal_, and scaleFactor_.

read()

void DeletionBoundary::read ( std::istream &  is )

overridevirtual

Reads some boundary properties from an std::istream.

Reads a number of boundary properties from the given std::istream.

Parameters

[in,out]

is

the istream

Implements BaseBoundary.

{
    BaseBoundary::read(is);
    std::string dummy;
    is >> dummy >> normal_
       >> dummy >> scaleFactor_
       >> dummy >> distance_
       >> dummy >> numberOfParticlesDeleted_
       >> dummy >> massDeleted_
       >> dummy >> volumeDeleted_
       >> dummy >> isActivated_
       >> dummy >> trackOutflow_;
}

References distance_, isActivated_, massDeleted_, normal_, numberOfParticlesDeleted_, BaseBoundary::read(), scaleFactor_, trackOutflow_, and volumeDeleted_.

Referenced by CubeDeletionBoundary::read().

reset()

void DeletionBoundary::reset

(

)

{
    numberOfParticlesDeleted_ = 0;
    massDeleted_ = 0;
    volumeDeleted_ = 0;
}

References massDeleted_, numberOfParticlesDeleted_, and volumeDeleted_.

set()

void DeletionBoundary::set	(	const Vec3D &	normal,
		Mdouble	distance
	)

Sets boundary position based on a normal and distance.

Defines the placing of the (2D) boundary based on the given normal and distance.

Parameters

[in]	normal	boundary normal vector
[in]	distance	'distance' between the origin and the boundary, such that the following relation is satisfied: \[ \mathbf{r} \cdot \mathbf{\hat{n}} = d \] in which \( \mathbf{\hat{n}} \) and \( d \) are the given normal vector and distance, respectively. NB: If the distance is the ACTUAL distance from the origin, the normal vector must be of UNIT LENGTH for the placing of the boundary to be done correctly.

{
    scaleFactor_ = 1. / std::sqrt(Vec3D::dot(normal, normal));
    normal_ = normal * scaleFactor_;
    distance_ = distance * scaleFactor_;
}

References distance_, Vec3D::dot(), normal_, and scaleFactor_.

Referenced by GranuHeap::actionsAfterTimeStep(), BoundariesSelfTest::BoundariesSelfTest(), FluxBoundarySelfTest::FluxBoundarySelfTest(), protectiveWall::protectiveWall(), Silo::setupInitialConditions(), DeletionBoundarySelfTest::setupInitialConditions(), FullRestartTest::setupInitialConditions(), and T_protectiveWall::T_protectiveWall().

trackOutflow()

void DeletionBoundary::trackOutflow ( bool  trackOutflow = true )

inline

Turns on the outflow tracker.

{trackOutflow_ = trackOutflow;}

References trackOutflow(), and trackOutflow_.

Referenced by trackOutflow().

write()

void DeletionBoundary::write ( std::ostream &  os ) const

overridevirtual

Writes the boundary properties to an std::ostream.

Writes the boundary properties to an std::ostream.

Parameters

[out]

os

the ostream the properties are to be written to.

Implements BaseBoundary.

{
    BaseBoundary::write(os);
    os << " normal " << normal_
       << " scaleFactor " << scaleFactor_
       << " distance " << distance_
       << " numberOfParticlesDeleted " << numberOfParticlesDeleted_
       << " massDeleted " << massDeleted_
       << " volumeDeleted " << volumeDeleted_
       << " isActivated " << isActivated_
       << " trackOutflow " << trackOutflow_;
}

References distance_, isActivated_, massDeleted_, normal_, numberOfParticlesDeleted_, scaleFactor_, trackOutflow_, volumeDeleted_, and BaseBoundary::write().

Referenced by CubeDeletionBoundary::write().

Member Data Documentation

distance_

Mdouble DeletionBoundary::distance_

private

The boundary's distance from the origin.

Referenced by DeletionBoundary(), getDistance(), move(), oldRead(), read(), set(), and write().

isActivated_

bool DeletionBoundary::isActivated_

private

The DeletionBoundary is activated by default. If the DeletionBoundary is deactivated, then it deletes no particles.

Referenced by activate(), checkBoundaryAfterParticlesMove(), deactivate(), DeletionBoundary(), read(), and write().

massDeleted_

double DeletionBoundary::massDeleted_

private

Referenced by checkBoundaryAfterParticleMoved(), DeletionBoundary(), getMassOfParticlesDeleted(), read(), reset(), and write().

normal_

Vec3D DeletionBoundary::normal_

private

outward unit normal vector

Referenced by getDistance(), oldRead(), read(), set(), and write().

numberOfParticlesDeleted_

unsigned int DeletionBoundary::numberOfParticlesDeleted_

private

Number of particles that have been deleted by this boundary.

Referenced by checkBoundaryAfterParticleMoved(), DeletionBoundary(), getNumberOfParticlesDeleted(), read(), reset(), and write().

scaleFactor_

Mdouble DeletionBoundary::scaleFactor_

private

This is the factor to rescale the given normal vector to a unit vectors.

NB: Not only the normal vector is rescaled by this factor, also the 'distance' from the origin of the boundary is scaled by this factor! Also, once the boundary position is set with DeletionBoundary::set(), the arguments of any reset of the distance_ property (i.e. usage of DeletionBoundary::move()) will be rescaled by the same factor!

Referenced by DeletionBoundary(), move(), oldRead(), read(), set(), and write().

tracker

std::ofstream DeletionBoundary::tracker

private

Referenced by checkBoundaryAfterParticleMoved().

trackMassDeleted_

double DeletionBoundary::trackMassDeleted_

private

Referenced by checkBoundaryAfterParticleMoved().

trackOutflow_

bool DeletionBoundary::trackOutflow_

private

Referenced by checkBoundaryAfterParticleMoved(), DeletionBoundary(), read(), trackOutflow(), and write().

volumeDeleted_

double DeletionBoundary::volumeDeleted_

private

Referenced by checkBoundaryAfterParticleMoved(), DeletionBoundary(), getVolumeOfParticlesDeleted(), read(), reset(), and write().

---

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

• DeletionBoundary.h
• DeletionBoundary.cc