PolydisperseInsertionBoundary Class Reference

Like an InsertionBoundary but generates particles of multiple types. Note that, as a child of InsertionBoundary, this class has a member called particleToCopy_, which is a pointer to a particle. This pointer needs to point to something arbitrary but it doesn't matter what the value is. More...

#include <PolydisperseInsertionBoundary.h>

Inheritance diagram for PolydisperseInsertionBoundary:

Public Member Functions
	PolydisperseInsertionBoundary ()
	Constructor; sets everything to 0. More...
	PolydisperseInsertionBoundary (const PolydisperseInsertionBoundary &other)
	Copy constructor with deep copy. More...
	~PolydisperseInsertionBoundary () override
	Destructor: default destructor. More...
PolydisperseInsertionBoundary *	copy () const override
	Creates a copy on the heap and returns a pointer. More...
void	setGeometry (int maxFailed, Vec3D posMin, Vec3D posMax, Vec3D velMin, Vec3D velMax)
	Set position and velocity of inserted particles. More...
BaseParticle *	getGenerandum (unsigned int spec) const
	Get the particles that need to be copied. More...
void	addGenerandum (BaseParticle *generandum, double probability, double sizeDispersity)
	Add a new prototype of particle to be copied. More...
void	setGenerandum (unsigned int spec, BaseParticle *generandum, double probability, double sizeDispersity)
	Change a particle to be copied. More...
BaseParticle *	generateParticle (RNG &random) override
	Generates a particle from the possible species. More...
void	placeParticle (BaseParticle *p, RNG &random) override
	Places the particle in a random position with a random velocity. More...
void	read (std::istream &is) override
	reads boundary properties from istream More...
void	write (std::ostream &os) const override
	writes boundary properties to ostream More...
std::string	getName () const override
	Returns the name of the object. More...
Public Member Functions inherited from InsertionBoundary
	InsertionBoundary ()
	InsertionBoundary (const InsertionBoundary &other)
	Copy constructor (with deep copy) More...
	~InsertionBoundary () override
	Destructor: delete the particle that has to be copied at every insertion. More...
virtual void	shiftBoundary (Vec3D shift)
	virtual function that shifts the boundary. More...
virtual void	rotateBoundary (Vec3D angle)
	virtual function that rotates the boundary. More...
void	checkBoundaryBeforeTimeStep (DPMBase *md) override
	Fills the boundary with particles. More...
void	insertParticles (DPMBase *md)
	Fill a certain domain with particles. More...
unsigned int	getNumberOfParticlesInserted () const
	Gets the number of particles inserted by the boundary. More...
Mdouble	getMassOfParticlesInserted () const
	Gets the mass of particles inserted by the boundary. More...
Mdouble	getVolumeOfParticlesInserted () const
	Gets the volume of particles inserted by the boundary. More...
void	reset ()
	resets particle property counter variables. More...
void	activate ()
	Turns on the InsertionBoundary. More...
void	deactivate ()
	Turns off the InsertionBoundary. More...
bool	isActivated ()
	Returns whether the InsertionBoundary is activated. More...
unsigned int	getMaxFailed () const
	Gets the number of times that the boundary may fail to insert a particle. More...
void	setParticleToCopy (std::vector< BaseParticle * > particleToCopy)
	Sets multiple different particles that will be inserted through the insertion boundary. More...
void	setParticleToCopy (BaseParticle *particleToCopy)
	Sets the particle that will be inserted through the insertion boundary. More...
std::vector< BaseParticle * >	getParticleToCopy ()
	Gets the particles that will be inserted through the insertion boundary. More...
Mdouble	getVolumeFlowRate () const
	Gets the volume flow rate of the insertion routine. More...
void	setVolumeFlowRate (Mdouble volumeFlowRate)
	Sets the volume flow rate of the insertion routine. More...
Mdouble	getInitialVolume () const
	Gets the initialVolume() . More...
void	setInitialVolume (Mdouble initialVolume)
	Gets the Volume which should be inserted by the insertion routine. More...
void	setPSD (const PSD psd)
	Sets the range of particle radii that may be generated from a user defined PSD. More...
void	setPSD (std::vector< PSD > psd, std::vector< Mdouble > probability)
	Sets the ranges of particle radii that may be generated from user defined PSDs. More...
std::vector< PSD >	getPSD ()
	Gets the particle size distributions set by the user. More...
void	setVariableVolumeFlowRate (const std::vector< Mdouble > &variableCumulativeVolumeFlowRate, Mdouble samplingInterval)
	Sets a variable volume flow rate. More...
bool	insertParticle (Mdouble time)
	Checks the inserted total volume and returns if a particle is still allowed to be inserted. More...
bool	getCheckParticleForInteraction () const
	Gets the variable that checks if a particle has an interaction. More...
void	setCheckParticleForInteraction (bool checkParticleForInteraction)
	Sets the variable that checks if a particle has an interaction. More...
void	setManualInsertion (bool manualInsertion)
	Set the flag for a manual PSD insertion routine. 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	checkBoundaryAfterParticlesMove (ParticleHandler &pH)
	Virtual function that does things to particles, each time step after particles have moved. 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

Public Attributes
std::vector< BaseParticle * >	generanda_
	Prototypes of the particles that can be generated. More...
std::vector< Mdouble >	probabilitates_
	The probabilities of generating each type of particle. These probabilities are not normalised. More...
std::vector< Mdouble >	sizeDispersities_
	The dispersity allowed in the particle size. More...
Vec3D	posMin_
	As in CubeInsertionBoundary. JMFT: TODO: Later we should completely separate InsertionBoundary geometry from their 'intrinsics', so that the code from CubeInsertionBoundary can be recycled. More...
Vec3D	posMax_
Vec3D	velMin_
Vec3D	velMax_
std::vector< unsigned int >	numbersInserted_
	For keeping track of how much of each prototype we have inserted. More...
std::vector< Mdouble >	massesInserted_
std::vector< Mdouble >	volumesInserted_
Public Attributes inherited from InsertionBoundary
std::vector< BaseParticle * >	particleToCopy_
	read Distribution class from file. ‍/ friend std::istream& operator>>(std::istream& is, InsertionBoundary::Distribution& type); More...
unsigned int	maxFailed_
	Number of times that the wall may fail to insert a particle. More...
unsigned int	numberOfParticlesInserted_
	Number of particles that are already inserted. More...
Mdouble	massInserted_
	Total mass of particles inserted. More...
Mdouble	volumeInserted_
	Total volume of particles inserted. More...
bool	isActivated_
	The InsertionBoundary is activated by default. If the InsertionBoundary is deactivated, then it introduces no particles (useful for trying to maintain a certain insertion rate). More...
Mdouble	volumeFlowRate_
Mdouble	initialVolume_
std::vector< Mdouble >	variableCumulativeVolumeFlowRate_
Mdouble	samplingInterval_
bool	checkParticleForInteraction_
	Checks if a particle has an interaction with a wall or other particles. More...
std::vector< PSD >	particleSizeDistributionVector_
	Defines a particle size distribution as an object of the PSD class; if particleSizeDistributionVector_ is empty, distribution_ is used instead. More...
Vec3D	velMin_
	Minimum and maximum velocity of the particles to be inserted. More...
Vec3D	velMax_
bool	isManuallyInserting_
	A flag to enable a top-down class-by-class manual insertion of a PSD; default is FALSE. More...
std::vector< Mdouble >	probability_
	vector of probabilities in range [0,1] which determine the mixing ratio of partice size distributions. More...
int	chosenSpecies_
	stores the chosen species for each timestep. More...
BaseParticle *	p0 = nullptr
	pointer to the next particle that should be inserted (needs to be stored across time steps). More...

Detailed Description

Like an InsertionBoundary but generates particles of multiple types. Note that, as a child of InsertionBoundary, this class has a member called particleToCopy_, which is a pointer to a particle. This pointer needs to point to something arbitrary but it doesn't matter what the value is.

Constructor & Destructor Documentation

PolydisperseInsertionBoundary() [1/2]

PolydisperseInsertionBoundary::PolydisperseInsertionBoundary

(

)

Constructor; sets everything to 0.

Deprecated boundary which was used to insert PSDs into Mercury.

Deprecated:

Should be gone by Mercury 2.0. Instead, use the PSD class.

{
    logger(INFO, "In PolydisperseInsertionBoundary constructor");
    /* std::vector does all the memory allocation for you. 
     * By default, these are vectors of zero length. */
    logger(INFO, "About to leave PolydisperseInsertionBoundary copy constructor");
}

References INFO, and logger.

Referenced by copy().

PolydisperseInsertionBoundary() [2/2]

PolydisperseInsertionBoundary::PolydisperseInsertionBoundary

(

const PolydisperseInsertionBoundary &

other

)

Copy constructor with deep copy.

        : InsertionBoundary(other)
{
    /* The new PolydisperseInsertionBoundary's generanda_ vector should point to
     * its own copies of each of the generanda_, so we need to copy those
     * across. */
    for (int i = 0; i < generanda_.size(); i++)
        generanda_[i] = other.generanda_[i]->copy();
    
    posMin_ = other.posMin_;
    posMax_ = other.posMax_;
    velMin_ = other.velMin_;
    velMax_ = other.velMax_;
    probabilitates_ = other.probabilitates_;
    sizeDispersities_ = other.sizeDispersities_;
    numbersInserted_ = other.numbersInserted_;
    massesInserted_ = other.massesInserted_;
    volumesInserted_ = other.volumesInserted_;
}

References generanda_, i, massesInserted_, numbersInserted_, posMax_, posMin_, probabilitates_, sizeDispersities_, velMax_, velMin_, and volumesInserted_.

~PolydisperseInsertionBoundary()

PolydisperseInsertionBoundary::~PolydisperseInsertionBoundary ( )

override

Destructor: default destructor.

{
    // JMFT: Do we need to delete the elements of generanda_?
    for (auto p : generanda_)
        
        delete p;
}

References generanda_, and p.

Member Function Documentation

addGenerandum()

void PolydisperseInsertionBoundary::addGenerandum	(	BaseParticle *	generandum,
		double	probability,
		double	sizeDispersity
	)

Add a new prototype of particle to be copied.

{
    // Give the PolydisperseInsertionBoundary its own copy of the generandum.
    generanda_.push_back(generandum->copy());
    probabilitates_.push_back(probability);
    sizeDispersities_.push_back(sizeDispersity);
    numbersInserted_.push_back(0);
    massesInserted_.push_back(0);
    volumesInserted_.push_back(0);
    logger(INFO, "PolydisperseInsertionBoundary: added a new generandum, now have %. New generandum has weighting %",
           generanda_.size(), probability);
}

References BaseParticle::copy(), generanda_, INFO, logger, massesInserted_, numbersInserted_, probabilitates_, sizeDispersities_, and volumesInserted_.

copy()

PolydisperseInsertionBoundary * PolydisperseInsertionBoundary::copy ( ) const

overridevirtual

Creates a copy on the heap and returns a pointer.

Implements BaseBoundary.

{
#ifdef DEBUG_CONSTRUCTOR
    logger(INFO, "PolydisperseInsertionBoundary::copy() const finished");
#endif
    return new PolydisperseInsertionBoundary(*this);
}

References INFO, logger, and PolydisperseInsertionBoundary().

generateParticle()

BaseParticle * PolydisperseInsertionBoundary::generateParticle ( RNG &  random )

overridevirtual

Generates a particle from the possible species.

Reimplemented from InsertionBoundary.

{
    /* First choose what particle species to generate. */
    Mdouble totalprob = 0;
    for (auto p : probabilitates_)
        totalprob += p;
    
    Mdouble check = random.getRandomNumber(0, totalprob);
    unsigned int spec = generanda_.size();
    logger(VERBOSE, "PolydisperseInsertionBoundary: check = % out of %",
           check, totalprob);
    for (int i = 0; i < generanda_.size(); i++)
    {
        if (check >= probabilitates_[i])
            check -= probabilitates_[i];
        else
        {
            spec = i;
            break;
        }
    }
    logger.assert_debug(spec<generanda_.size(),"spec set wrongly");
    
    auto P = generanda_[spec]->copy();
    
    /* The 'reference' particle for this species has a radius, but we allow some
     * sizeDispersity. */
    double radius = P->getRadius()
                    * random.getRandomNumber(1 - sizeDispersities_[spec], 1 + sizeDispersities_[spec]);
    P->setRadius(radius);
    
    /* JMFT: TODO: These do *not* give the correct values! 
     * They give the number &c. of each species that the
     * PolydisperseInsertionBoundary has _attempted_ to place, not the number
     * that have actually been placed successfully. */
    numbersInserted_[spec]++;
    massesInserted_[spec] += P->getMass();
    // volumesInserted_[spec] += P->getVolume();
    
    return P;
}

References check(), generanda_, RNG::getRandomNumber(), i, logger, massesInserted_, numbersInserted_, Global_Physical_Variables::P, p, probabilitates_, UniformPSDSelfTest::radius, sizeDispersities_, and VERBOSE.

getGenerandum()

BaseParticle* PolydisperseInsertionBoundary::getGenerandum

(

unsigned int

spec

)

const

Get the particles that need to be copied.

getName()

std::string PolydisperseInsertionBoundary::getName ( ) const

overridevirtual

Returns the name of the object.

Implements BaseObject.

{
    return "PolydisperseInsertionBoundary";
}

placeParticle()

void PolydisperseInsertionBoundary::placeParticle ( BaseParticle *  p, RNG &  random  )

overridevirtual

Places the particle in a random position with a random velocity.

Implements InsertionBoundary.

{
    Vec3D pos, vel;
    pos.X = random.getRandomNumber(posMin_.X, posMax_.X);
    pos.Y = random.getRandomNumber(posMin_.Y, posMax_.Y);
    pos.Z = random.getRandomNumber(posMin_.Z, posMax_.Z);
    vel.X = random.getRandomNumber(velMin_.X, velMax_.X);
    vel.Y = random.getRandomNumber(velMin_.Y, velMax_.Y);
    vel.Z = random.getRandomNumber(velMin_.Z, velMax_.Z);
    P->setPosition(pos);
    P->setVelocity(vel);
}

References RNG::getRandomNumber(), Global_Physical_Variables::P, posMax_, posMin_, velMax_, velMin_, Vec3D::X, Vec3D::Y, and Vec3D::Z.

read()

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

overridevirtual

reads boundary properties from istream

Reimplemented from InsertionBoundary.

{
    InsertionBoundary::read(is);
    /*
    for (int i = 0; i < generanda_.size(); i++)
    {
        BaseParticle* particleToCopy = new SphericalParticle;
        // BaseParticle::write writes the extra word 'BaseParticle', which will be
        // ignored by BaseParticle::read. To avoid an off-by-one error, we need to
        // get rid of this extra word first...
        std::string dummy;
        is >> dummy;
 
        // Now read the particleToCopy.
        particleToCopy->read(is);
        generanda_[i] = particleToCopy->copy();
        delete particleToCopy;
        generanda_[i]->setSpecies(getHandler()->getDPMBase()->speciesHandler.getObject(
                    particleToCopy_->getIndSpecies() 
                    ));
    }
    */
}

References InsertionBoundary::read().

setGenerandum()

void PolydisperseInsertionBoundary::setGenerandum	(	unsigned int	spec,
		BaseParticle *	generandum,
		double	probability,
		double	sizeDispersity
	)

Change a particle to be copied.

{
    if (spec < generanda_.size())
        logger(INFO, "Setting the %-th species of a PolydisperseInsertionBoundary that so far has % species",
               spec, generanda_.size());
    else
        logger(ERROR,
               "Setting the %-th species of a PolydiserseInsertionBoundary with only % species is illegal. Use addGenerandum instead.",
               spec, generanda_.size());
    
    if (probability == 0)
        logger(WARN, "PolydisperseInsertionBoundary: Are you sure you want to set the probability to be 0?");
    
    generanda_[spec] = generandum->copy();
    probabilitates_[spec] = probability;
    sizeDispersities_[spec] = sizeDispersity;
    
    // Reset the counters for number, mass and volume
    numbersInserted_[spec] = 0;
    massesInserted_[spec] = 0;
    volumesInserted_[spec] = 0;
}

References BaseParticle::copy(), ERROR, generanda_, INFO, logger, massesInserted_, numbersInserted_, probabilitates_, sizeDispersities_, volumesInserted_, and WARN.

setGeometry()

void PolydisperseInsertionBoundary::setGeometry	(	int	maxFailed,
		Vec3D	posMin,
		Vec3D	posMax,
		Vec3D	velMin,
		Vec3D	velMax
	)

Set position and velocity of inserted particles.

{
    maxFailed_ = maxFailed;
    posMin_ = posMin;
    posMax_ = posMax;
    velMin_ = velMin;
    velMax_ = velMax;
}

References InsertionBoundary::maxFailed_, posMax_, posMin_, velMax_, and velMin_.

write()

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

overridevirtual

writes boundary properties to ostream

Reimplemented from InsertionBoundary.

{
    logger(VERBOSE, "In PolydisperseInsertionBoundary::write");
    InsertionBoundary::write(os);
    os << " numberOfGeneranda " << generanda_.size() << " ";
    for (int i = 0; i < generanda_.size(); i++)
    {
        generanda_[i]->write(os);
        os << " weight " << probabilitates_[i] << " sizeDispersity " << sizeDispersities_[i] << " ";
    }
    os << "posMin " << posMin_ << " posMax " << posMax_
       << " velMin " << velMin_ << " velMax " << velMax_
       << " ";
}

References generanda_, i, logger, posMax_, posMin_, probabilitates_, sizeDispersities_, velMax_, velMin_, VERBOSE, and InsertionBoundary::write().

Member Data Documentation

generanda_

std::vector<BaseParticle*> PolydisperseInsertionBoundary::generanda_

Prototypes of the particles that can be generated.

Referenced by addGenerandum(), generateParticle(), PolydisperseInsertionBoundary(), setGenerandum(), write(), and ~PolydisperseInsertionBoundary().

massesInserted_

std::vector<Mdouble> PolydisperseInsertionBoundary::massesInserted_

Referenced by addGenerandum(), generateParticle(), PolydisperseInsertionBoundary(), and setGenerandum().

numbersInserted_

std::vector<unsigned int> PolydisperseInsertionBoundary::numbersInserted_

For keeping track of how much of each prototype we have inserted.

Referenced by addGenerandum(), generateParticle(), PolydisperseInsertionBoundary(), and setGenerandum().

posMax_

Vec3D PolydisperseInsertionBoundary::posMax_

Referenced by placeParticle(), PolydisperseInsertionBoundary(), setGeometry(), and write().

posMin_

Vec3D PolydisperseInsertionBoundary::posMin_

As in CubeInsertionBoundary. JMFT: TODO: Later we should completely separate InsertionBoundary geometry from their 'intrinsics', so that the code from CubeInsertionBoundary can be recycled.

Referenced by placeParticle(), PolydisperseInsertionBoundary(), setGeometry(), and write().

probabilitates_

std::vector<Mdouble> PolydisperseInsertionBoundary::probabilitates_

The probabilities of generating each type of particle. These probabilities are not normalised.

Referenced by addGenerandum(), generateParticle(), PolydisperseInsertionBoundary(), setGenerandum(), and write().

sizeDispersities_

std::vector<Mdouble> PolydisperseInsertionBoundary::sizeDispersities_

The dispersity allowed in the particle size.

Referenced by addGenerandum(), generateParticle(), PolydisperseInsertionBoundary(), setGenerandum(), and write().

velMax_

Vec3D PolydisperseInsertionBoundary::velMax_

Referenced by placeParticle(), PolydisperseInsertionBoundary(), setGeometry(), and write().

velMin_

Vec3D PolydisperseInsertionBoundary::velMin_

Referenced by placeParticle(), PolydisperseInsertionBoundary(), setGeometry(), and write().

volumesInserted_

std::vector<Mdouble> PolydisperseInsertionBoundary::volumesInserted_

Referenced by addGenerandum(), PolydisperseInsertionBoundary(), and setGenerandum().

---

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

• PolydisperseInsertionBoundary.h
• PolydisperseInsertionBoundary.cc