#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)
	Allows density_ to be changed. More...

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)
	Sets BaseSpecies::interactionDistance_. 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 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_
	Returns the max distance between particles of this species and any other species below which adhesive forces can occur (needed for contact detection) More...

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 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 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 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...

Detailed Description

Definition at line 36 of file ParticleSpecies.h.

Member Typedef Documentation

typedef BaseInteraction ParticleSpecies::InteractionType

Definition at line 39 of file ParticleSpecies.h.

typedef BaseSpecies ParticleSpecies::MixedSpeciesType

Definition at line 40 of file ParticleSpecies.h.

Constructor & Destructor Documentation

ParticleSpecies::ParticleSpecies ( )

The default constructor.

Definition at line 36 of file ParticleSpecies.cc.

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

ParticleSpecies::ParticleSpecies ( const ParticleSpecies & p )

The default copy constructor.

Parameters

[in] p the species that is copied

Definition at line 56 of file ParticleSpecies.cc.

References density_, and temperatureDependentDensity_.

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

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

Definition at line 44 of file ParticleSpecies.cc.

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

ParticleSpecies::~ParticleSpecies ( )

The default destructor.

Definition at line 66 of file ParticleSpecies.cc.

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

Member Function Documentation

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

Definition at line 166 of file ParticleSpecies.cc.

References BaseParticle::computeMass().

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

 {
     p->computeMass(*this);
 }

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.

Implemented in Species< NormalForceSpecies, FrictionForceSpecies, AdhesiveForceSpecies >.

Referenced by CurvyChute::createBottom().

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.

Implemented in Species< NormalForceSpecies, FrictionForceSpecies, AdhesiveForceSpecies >.

Referenced by SpeciesHandler::addObject().

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")

Definition at line 99 of file ParticleSpecies.cc.

 {
     return "Particle";
 }

Mdouble ParticleSpecies::getDensity ( ) const

Allows density_ to be accessed.

Returns: the particle density

Definition at line 117 of file ParticleSpecies.cc.

References density_.

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

 {
     return density_;
 }

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.

Definition at line 187 of file ParticleSpecies.cc.

References BaseSpecies::getHandler(), and logger.

Referenced by getSmallestParticleMass().

 {
     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;
 }

Mdouble ParticleSpecies::getMassFromRadius ( Mdouble radius ) const

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

Definition at line 122 of file ParticleSpecies.cc.

References getDensity(), and getVolumeFromRadius().

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

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

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

Definition at line 127 of file ParticleSpecies.cc.

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

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

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).

Definition at line 113 of file ParticleSpecies.h.

References maxInteractionDistance_.

Referenced by BaseParticle::getMaxInteractionRadius().

113 {return maxInteractionDistance_;}

ParticleSpecies::maxInteractionDistance_

Mdouble maxInteractionDistance_

Returns the max distance between particles of this species and any other species below which adhesive...

Definition: ParticleSpecies.h:145

const BaseSpecies * ParticleSpecies::getMixedSpecies ( const ParticleSpecies * s ) const

Definition at line 237 of file ParticleSpecies.cc.

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

Referenced by BaseParticle::getInteractionDistance().

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

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.

Definition at line 201 of file ParticleSpecies.cc.

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

 {
 #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
 
 }

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

Definition at line 171 of file ParticleSpecies.cc.

References temperatureDependentDensity_.

Referenced by ThermalParticle::actionsAfterTimeStep().

 {
     return temperatureDependentDensity_;
 }

Mdouble ParticleSpecies::getVolumeFromRadius ( Mdouble radius ) const

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

Definition at line 134 of file ParticleSpecies.cc.

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

Referenced by getMassFromRadius().

 {
     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;
     }
 }

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.

Reimplemented in Species< NormalForceSpecies, FrictionForceSpecies, AdhesiveForceSpecies >.

Definition at line 88 of file ParticleSpecies.cc.

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

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

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

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

Definition at line 107 of file ParticleSpecies.cc.

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

Referenced by Membrane::buildMesh(), FileReader::read(), and SpeciesHandler::readOldObject().

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

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

Definition at line 220 of file ParticleSpecies.cc.

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

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

                                                                            {
     // 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());
             }
         }
     }
 }

void ParticleSpecies::setTemperatureDependentDensity ( const std::function< double(double)> & temperatureDependentDensity )

Definition at line 176 of file ParticleSpecies.cc.

References temperatureDependentDensity_.

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

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.

Reimplemented in Species< NormalForceSpecies, FrictionForceSpecies, AdhesiveForceSpecies >.

Definition at line 76 of file ParticleSpecies.cc.

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

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

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

Member Data Documentation

Mdouble ParticleSpecies::density_

private

The mass density.

Definition at line 134 of file ParticleSpecies.h.

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

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)

Definition at line 145 of file ParticleSpecies.h.

Referenced by getMaxInteractionDistance(), and setMaxInteractionDistance().

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.

Definition at line 140 of file ParticleSpecies.h.

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

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

Species/ParticleSpecies.h
Species/ParticleSpecies.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation