ParticleSpecies Class Reference

#include <ParticleSpecies.h>

Inheritance diagram for ParticleSpecies:

Public Types
typedef BaseInteraction	InteractionType
typedef BaseSpecies	MixedSpeciesType

Public Member Functions
	ParticleSpecies ()
	The default constructor. More...
	ParticleSpecies (const ParticleSpecies &p)
	The default copy constructor. More...
	ParticleSpecies (BaseNormalForce *normalForce, BaseFrictionForce *frictionForce, BaseAdhesiveForce *adhesiveForce)
	~ParticleSpecies ()
	The default destructor. More...
ParticleSpecies *	copy () const override=0
	Creates a deep copy of the object from which it is called. More...
virtual BaseSpecies *	copyMixed () const =0
	Creates a new MixedSpecies with the same force properties as the Species from which it is called. See Species::copyMixed for details. More...
void	read (std::istream &is) override
	Reads the species properties from an input stream. More...
void	write (std::ostream &os) const override
	Writes the species properties to an output stream. More...
std::string	getBaseName () const
	Used in Species::getName to obtain a unique name for each Species. More...
void	setDensity (Mdouble density)
Mdouble	getMassFromRadius (Mdouble radius) const
Mdouble	getMassFromRadius (const Mdouble radius, SpeciesHandler &speciesHandler)
Mdouble	getVolumeFromRadius (Mdouble radius) const
Mdouble	getDensity () const
	Allows density_ to be accessed. More...
void	computeMass (BaseParticle *p) const
	Compute Particle mass function, which required a reference to the Species vector. It computes the Particles mass, Inertia and the inverses. More...
void	setTemperatureDependentDensity (const std::function< double(double)> &temperatureDependentDensity)
const std::function< double(double)> &	getTemperatureDependentDensity () const
Mdouble	getSmallestParticleMass () const
	Computes mass of the lightest particle (by mass) belonging to this species. This computation calls getLightestInverseParticleMassLocal, such that the computation is done on each node. More...
Mdouble	getMaxInteractionDistance () const
	returns the largest separation distance at which adhesive short-range forces can occur. More...
void	setMaxInteractionDistance (Mdouble interactionDistance=0)
	Sets maxInteractionDistance_. More...
const BaseSpecies *	getMixedSpecies (const ParticleSpecies *s) const
Public Member Functions inherited from BaseSpecies
	BaseSpecies ()
	The default constructor. More...
	BaseSpecies (BaseNormalForce *normalForce, BaseFrictionForce *frictionForce_, BaseAdhesiveForce *adhesiveForce)
	BaseSpecies (const BaseSpecies &p)
	The copy constructor. More...
	~BaseSpecies ()
	The default destructor. More...
virtual void	copyInto (BaseSpecies *s) const =0
void	setHandler (SpeciesHandler *handler)
	Sets the pointer to the handler to which this species belongs. More...
SpeciesHandler *	getHandler () const
	Returns the pointer to the handler to which this species belongs. More...
virtual void	mixAll (BaseSpecies *S, BaseSpecies *T)=0
	creates default values for mixed species More...
virtual bool	getUseAngularDOFs () const =0
	Returns true if torques (i.e. angular degrees of freedom) have to be calculated. More...
virtual BaseInteraction *	getNewInteraction (BaseInteractable *P, BaseInteractable *I, unsigned timeStamp) const =0
	returns new Interaction object. More...
virtual BaseInteraction *	getEmptyInteraction () const =0
virtual void	deleteEmptyInteraction (BaseInteraction *interaction) const =0
Mdouble	getInteractionDistance () const
	returns the largest separation distance at which adhesive short-range forces can occur. More...
BaseNormalForce *	getNormalForce () const
BaseFrictionForce *	getFrictionForce () const
BaseAdhesiveForce *	getAdhesiveForce () const
void	setInteractionDistance (Mdouble interactionDistance)
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 std::string	getName () const =0
	A purely virtual function. 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 Member Functions
Mdouble	getLargestInverseParticleMassLocal () const
	Computes inverse mass of the lightest particle (by mass) belonging to this species. If MPI is used, this computation is done locally on each node. More...

Private Attributes
Mdouble	density_
	The mass density. More...
std::function< double(double temperature)>	temperatureDependentDensity_
Mdouble	maxInteractionDistance_

Additional Inherited Members
Static Public Member Functions inherited from BaseSpecies
static Mdouble	average (Mdouble a, Mdouble b)
	Returns the harmonic mean of two variables. More...
static Mdouble	averageInf (Mdouble a, Mdouble b)
	Returns the harmonic mean of two variables, returning inf if either is inf. More...
Protected Attributes inherited from BaseSpecies
BaseNormalForce *	normalForce_
	A pointer to the normal force parameters \detail This pointer is used by the Interaction's to get a pointer to the species The pointer is set in the constructors of SPecies and MixedSpecies. More...
BaseFrictionForce *	frictionForce_
	A pointer to the friction force parameters \detail This pointer is used by the Interaction's to get a pointer to the species The pointer is set in the constructors of SPecies and MixedSpecies. More...
BaseAdhesiveForce *	adhesiveForce_
	A pointer to the adhesive force parameters \detail This pointer is used by the Interaction's to get a pointer to the species The pointer is set in the constructors of SPecies and MixedSpecies. More...

Member Typedef Documentation

InteractionType

typedef BaseInteraction ParticleSpecies::InteractionType

MixedSpeciesType

typedef BaseSpecies ParticleSpecies::MixedSpeciesType

Constructor & Destructor Documentation

ParticleSpecies() [1/3]

ParticleSpecies::ParticleSpecies

(

)

The default constructor.

    : BaseSpecies(), density_(1.0)
{
#ifdef DEBUG_CONSTRUCTOR
    std::cout<<"ParticleSpecies::ParticleSpecies() finished"<<std::endl;
#endif
}

ParticleSpecies() [2/3]

ParticleSpecies::ParticleSpecies

(

const ParticleSpecies &

p

)

The default copy constructor.

Parameters

[in]

p

the species that is copied

    : BaseSpecies(p)
{
    density_ = p.density_;
    temperatureDependentDensity_ = p.temperatureDependentDensity_;
#ifdef DEBUG_CONSTRUCTOR
    std::cout<<"ParticleSpecies::ParticleSpecies(const ParticleSpecies &p) finished"<<std::endl;
#endif
}

References density_, and temperatureDependentDensity_.

ParticleSpecies() [3/3]

ParticleSpecies::ParticleSpecies	(	BaseNormalForce *	normalForce,
		BaseFrictionForce *	frictionForce,
		BaseAdhesiveForce *	adhesiveForce
	)

    : BaseSpecies(normalForce,frictionForce, adhesiveForce), density_(1.0)
{
#ifdef DEBUG_CONSTRUCTOR
    std::cout<<"ParticleSpecies::ParticleSpecies(n,f,a) finished"<<std::endl;
#endif
}

~ParticleSpecies()

ParticleSpecies::~ParticleSpecies

(

)

The default destructor.

{
#ifdef DEBUG_DESTRUCTOR
    std::cout<<"ParticleSpecies::~ParticleSpecies() finished"<<std::endl;
#endif
}

Member Function Documentation

computeMass()

void ParticleSpecies::computeMass

(

BaseParticle *

p

)

const

Compute Particle mass function, which required a reference to the Species vector. It computes the Particles mass, Inertia and the inverses.

Compute BaseParticle mass function, which required a reference to the Species vector. It computes the Particles mass, Inertia and the inverses. this function is called, if BaseParticleHandler::addObject, SpeciesHandler::addObject, ParticleSpecies::setDensity, BaseParticle::setRadius or DPMBase::setParticleDimensions is called

{
    p->computeMass(*this);
}

References BaseParticle::computeMass().

Referenced by ParticleHandler::addExistingObject(), ParticleHandler::addGhostObject(), ParticleHandler::addObject(), SuperQuadricParticle::setAxes(), SuperQuadricParticle::setExponents(), BaseParticle::setRadius(), WallParticleCollision::setupInitialConditions(), and BaseParticle::unfix().

copy()

ParticleSpecies* ParticleSpecies::copy ( ) const

overridepure virtual

Creates a deep copy of the object from which it is called.

See BaseSpecies::copy for details

Implements BaseSpecies.

Referenced by CurvyChute::createBottom().

copyMixed()

virtual BaseSpecies* ParticleSpecies::copyMixed ( ) const

pure virtual

Creates a new MixedSpecies with the same force properties as the Species from which it is called. See Species::copyMixed for details.

Referenced by SpeciesHandler::addObject().

getBaseName()

std::string ParticleSpecies::getBaseName

(

)

const

Used in Species::getName to obtain a unique name for each Species.

Returns

a string containing the name of the species (minus the word "Species")

{
    return "Particle";
}

getDensity()

Mdouble ParticleSpecies::getDensity

(

)

const

Allows density_ to be accessed.

Returns

the particle density

{
    return density_;
}

References density_.

Referenced by Membrane::adjustVertexParticleSize(), Membrane::buildMesh(), BaseParticle::computeMass(), SuperQuadricParticle::computeMass(), HertzianSinterNormalSpecies::computeTimeStep(), FlowRule::getDensityVariation(), getMassFromRadius(), LinearViscoelasticNormalSpecies::setCollisionTimeAndRestitutionCoefficient(), FlowRule::setDensityVariation(), and SuperQuadricParticle::setInertia().

getLargestInverseParticleMassLocal()

Mdouble ParticleSpecies::getLargestInverseParticleMassLocal ( ) const

private

Computes inverse mass of the lightest particle (by mass) belonging to this species. If MPI is used, this computation is done locally on each node.

Returns

A pointer to the to the lightest BaseParticle (by mass) in this ParticleHandler.

{
    Mdouble maxInvMass = 0;
    logger.assert_debug(getHandler() != nullptr && getHandler()->getDPMBase() != nullptr,"speciesHandler must be set");
    for (BaseParticle* const p : getHandler()->getDPMBase()->particleHandler)
    {
        if (p->getSpecies()==this && !(p->isFixed() || p->isMPIParticle() || p->isPeriodicGhostParticle()) && p->getInvMass() > maxInvMass)
        {
            maxInvMass = p->getInvMass();
        }
    }
    return maxInvMass;
}

References BaseSpecies::getHandler(), and logger.

Referenced by getSmallestParticleMass().

getMassFromRadius() [1/2]

Mdouble ParticleSpecies::getMassFromRadius	(	const Mdouble	radius,
		SpeciesHandler &	speciesHandler
	)

{
    setHandler(&speciesHandler);
    return getMassFromRadius(radius);
}

References getMassFromRadius(), and BaseSpecies::setHandler().

getMassFromRadius() [2/2]

Mdouble ParticleSpecies::getMassFromRadius

(

Mdouble

radius

)

const

Todo:

TW: should getMassFromRadius be removed? IFCD: it is used in at least one driver (AxisymmetricHopper).

{
    return getDensity() * getVolumeFromRadius(radius);
}

References getDensity(), and getVolumeFromRadius().

Referenced by BaseCluster::calculateTimeStep(), getMassFromRadius(), and ChuteBottom::makeRoughBottom().

getMaxInteractionDistance()

Mdouble ParticleSpecies::getMaxInteractionDistance ( ) const

inline

returns the largest separation distance at which adhesive short-range forces can occur.

returns the largest separation distance (negative overlap) at which (adhesive) short-range forces can occur (needed for contact detection). Defined in each of the AdhesiveForceSpecies It is defined as a virtual function here to allow the function to be called from a BaseSpecies pointer (which is the kind of pointer used for MixedSpecies).

{return maxInteractionDistance_;}

References maxInteractionDistance_.

Referenced by BaseParticle::getMaxInteractionRadius().

getMixedSpecies()

const BaseSpecies * ParticleSpecies::getMixedSpecies

(

const ParticleSpecies *

s

)

const

                                                                                  {
    return (getIndex()==s->getIndex())?this:getHandler()->getMixedObject(getIndex(),s->getIndex());
}

References BaseSpecies::getHandler(), BaseObject::getIndex(), and SpeciesHandler::getMixedObject().

Referenced by BaseParticle::getInteractionDistance().

getSmallestParticleMass()

Mdouble ParticleSpecies::getSmallestParticleMass

(

)

const

Computes mass of the lightest particle (by mass) belonging to this species. This computation calls getLightestInverseParticleMassLocal, such that the computation is done on each node.

{
#ifdef MERCURY_USE_MPI
    Mdouble maxInvMass = 0;
    Mdouble invMassLocal = getLargestInverseParticleMassLocal();
    //Obtain the global value
    MPIContainer::Instance().allReduce(invMassLocal, maxInvMass, MPI_MAX);
    //return value
    return 1.0 / maxInvMass;
#else
    return 1.0 / getLargestInverseParticleMassLocal();
#endif
 
}

References getLargestInverseParticleMassLocal(), and MPIContainer::Instance().

getTemperatureDependentDensity()

const std::function< double(double)> & ParticleSpecies::getTemperatureDependentDensity

(

)

const

{
    return temperatureDependentDensity_;
}

References temperatureDependentDensity_.

Referenced by ThermalParticle::actionsAfterTimeStep().

getVolumeFromRadius()

Mdouble ParticleSpecies::getVolumeFromRadius

(

Mdouble

radius

)

const

Todo:

this should depend on the particle shape; thus, it should be a static function of BaseParticle

{
    if (getHandler() == nullptr)
    {
        logger(ERROR,
               "[Species::VolumeFromRadius()] No handler has been set, therefore, I can't figure out the dimensions.");
        return 0;
    }
    
    unsigned int particleDimensions = getHandler()->getDPMBase()->getParticleDimensions();
    if (particleDimensions == 3)
    {
        return 4.0 / 3.0 * constants::pi * radius * radius * radius;
    }
    else if (particleDimensions == 2)
    {
        return constants::pi * radius * radius;
    }
    else if (particleDimensions == 1)
    {
        return 2.0 * radius;
    }
    else
    {
        logger(ERROR, "[Species::VolumeFromRadius()] the dimension of the particle is wrongly set to %",
               particleDimensions);
        return 0.0;
    }
}

References ERROR, BaseHandler< T >::getDPMBase(), BaseSpecies::getHandler(), DPMBase::getParticleDimensions(), logger, and constants::pi.

Referenced by getMassFromRadius().

read()

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

overridevirtual

Reads the species properties from an input stream.

Parameters

[in]

is

input stream (typically the restart file)

Reimplemented from BaseSpecies.

{
    BaseObject::read(is);
    std::string dummy;
    is >> dummy >> density_;
    BaseSpecies::read(is);
}

References density_, BaseSpecies::read(), and BaseObject::read().

Referenced by Species< NormalForceSpecies, FrictionForceSpecies, AdhesiveForceSpecies >::read().

setDensity()

void ParticleSpecies::setDensity

(

Mdouble

density

)

Allows density_ to be changed

Todo:

recalculate masses when setting dim_particle or rho

Parameters

[in]

density

the particle density

{
    logger.assert_always(density >= 0, "[ParticleSpecies::setDensity(%)] value cannot be negative", density);
    density_ = density;
    if (getHandler()) getHandler()->getDPMBase()->particleHandler.computeAllMasses(getIndex());
}

References ParticleHandler::computeAllMasses(), density_, BaseHandler< T >::getDPMBase(), BaseSpecies::getHandler(), BaseObject::getIndex(), logger, and DPMBase::particleHandler.

Referenced by Membrane::buildMesh(), main(), and FlowRule::setDensityVariation().

setMaxInteractionDistance()

void ParticleSpecies::setMaxInteractionDistance

(

Mdouble

interactionDistance = 0

)

Sets maxInteractionDistance_.

Parameters

interactionDistance

the interaction distance that has been changed

Sets maxInteractionDistance_

Parameters

interactionDistance

the interaction distance that has been changed

                                                                           {
    // if maxInteractionDistance_ has increased it's simple
    if (interactionDistance>=maxInteractionDistance_) {
        maxInteractionDistance_ = interactionDistance;
    } else /*else we need to recompute*/ {
        maxInteractionDistance_ = 0;
        int j = getIndex();
        for (int i=0; i<getHandler()->getSize(); ++i) {
            const auto mixedSpecies = getHandler()->getMixedObject(i,j);
            if (mixedSpecies) { //this check is necessary because the mixed species handler might not yet be built fully
                maxInteractionDistance_ = std::max(maxInteractionDistance_,
                        mixedSpecies->getInteractionDistance());
            }
        }
    }
}

References BaseSpecies::getHandler(), BaseObject::getIndex(), SpeciesHandler::getMixedObject(), BaseHandler< T >::getSize(), constants::i, and maxInteractionDistance_.

Referenced by SpeciesHandler::addObject(), and BaseSpecies::setInteractionDistance().

setTemperatureDependentDensity()

void ParticleSpecies::setTemperatureDependentDensity

(

const std::function< double(double)> &

temperatureDependentDensity

)

{
    temperatureDependentDensity_ = temperatureDependentDensity;
//    density_ = temperatureDependentDensity_(0);
//    logger(INFO,"Setting initial density to %",temperature_);
}

References temperatureDependentDensity_.

write()

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

overridevirtual

Writes the species properties to an output stream.

Parameters

[out]

os

output stream (typically the restart file)

Reimplemented from BaseSpecies.

{
    //note we inherit from BaseObject, not BaseParticle
    BaseObject::write(os);
    os << " density " << density_;
    BaseSpecies::write(os);
    //todo flip the two values
}

References density_, BaseObject::write(), and BaseSpecies::write().

Referenced by Species< NormalForceSpecies, FrictionForceSpecies, AdhesiveForceSpecies >::write().

Member Data Documentation

density_

Mdouble ParticleSpecies::density_

private

The mass density.

Referenced by getDensity(), ParticleSpecies(), read(), setDensity(), and write().

maxInteractionDistance_

Mdouble ParticleSpecies::maxInteractionDistance_

private

Returns the max distance between particles of this species and any other species below which adhesive forces can occur (needed for contact detection)

Referenced by getMaxInteractionDistance(), and setMaxInteractionDistance().

temperatureDependentDensity_

std::function<double(double temperature)> ParticleSpecies::temperatureDependentDensity_

private

Change this function to let the particles expand due to temperature. The default value (empty) stands for constant density.

Referenced by getTemperatureDependentDensity(), ParticleSpecies(), and setTemperatureDependentDensity().

---

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

• ParticleSpecies.h
• ParticleSpecies.cc