hemo::HemoCellFields Class Reference

#include <hemoCellFields.h>

Collaboration diagram for hemo::HemoCellFields:

Classes
class	HemoAdvanceParticles
class	HemoApplyConstitutiveModel
class	HemoBoundaryRepulsionForce
class	HemoDeleteIncompleteCells
class	HemoDeleteNonLocalParticles
class	HemoFindInternalParticleGridPoints
class	HemoGetParticles
class	HemoInternalGridPointsMembrane
class	HemoInterpolateFluidVelocity
class	HemoPopulateBindingSites
class	HemoPopulateBoundaryParticles
class	HemoPrepareSolidification
class	HemoRepulsionForce
class	HemoSeperateForceVectors
class	HemoSetParticles
class	HemoSolidifyCells
class	HemoSpreadParticleForce
class	HemoSyncEnvelopes
class	HemoUnifyForceVectors
class	HemoupdateResidenceTime

Public Member Functions
	HemoCellFields (plb::MultiBlockLattice3D< T, DESCRIPTOR > &lattice_, unsigned int particleEnvelopeWidth, HemoCell &)
	Default constructor, needs an palabos lattice, envelope width (lbm units), and hemocell reference.
void	createParticleField (plb::SparseBlockStructure3D *sbStructure_=0, plb::ThreadAttribution *tAttribution_=0)
void	createCEPACfield ()
void	InitAfterLoadCheckpoint ()
	Used to set variables inside the celltypes for correct access, called through createParticleField.
	~HemoCellFields ()
	Generic Destructor.
HemoCellField *	addCellType (std::string name_, int constructType)
	Add an celltype with a certain mesh, the name also specifies <name_>.xml and <name_>.pos.
HemoCellField *	operator[] (unsigned int index)
	Easy access to contained celltypes.
HemoCellField *	operator[] (string name)
	Easy access to contained celltypes.
unsigned int	size ()
	Get the number of celltypes.
void	load (plb::XMLreader *documentXML, unsigned int &iter, Config *cfg=NULL)
	Load a checkpoint, store the current iteration in &iter.
void	save (plb::XMLreader *documentXML, unsigned int iter, Config *cfg=NULL)
	Save a checkpoint.
plb::MultiParticleField3D< HemoCellParticleField > &	getParticleField3D ()
	Legacy Helper function to get the particle field, mostly unused as direct access is available.
void	readPositionsCellFields (std::string particlePosFile)
	Legacy reads in only RBC an PLT from a single pos file.
void	advanceParticles ()
	Advance the particles in an iteration.
void	findInternalParticleGridPoints ()
void	internalGridPointsMembrane ()
void	interpolateFluidVelocity ()
	Interpolate the velocity of the fluid to the individual particles.
void	spreadParticleForce ()
	Spread the force of all particles over the fluid in this iteration.
void	separate_force_vectors ()
	Separate the force vectors of particles so it becomes clear what the vector for each separate force is.
void	unify_force_vectors ()
	Unify the force vectors of particles to point to a single force.
void	applyRepulsionForce ()
	Apply (and calculate) the repulsion force between particles.
void	applyBoundaryRepulsionForce ()
	Apply (and calculate) the repulsion force between particles and the boundary.
void	deleteIncompleteCells (bool verbose=true)
	Delete any incomplete cells on a block.
void	applyConstitutiveModel (bool forced=false)
	Apply the material model of the cells to the particles, updating their force.
void	syncEnvelopes ()
	Sync the particle envelopes between domains.
void	getParticles (vector< HemoCellParticle * > &particles, plb::Box3D &domain)
	Get particles in a given domain.
void	addParticles (vector< HemoCellParticle > &particles)
	Add particles to local processors.
void	populateBoundaryParticles ()
	Add boundary particles on the fluid-solid boundary.
void	populateBindingSites (plb::Box3D *box=0)
	Add bindingSites.
void	deleteNonLocalParticles (int envelope)
	Delete non local particles (do not delete in envelopesize)
void	solidifyCells ()
	Conditionally solidify cells if requested.
void	prepareSolidification ()
void	updateResidenceTime (unsigned int rtime)
	increment cell residence time
int	base_cell_id (int wrapped)
void	calculateCommunicationStructure ()

Public Attributes
plb::MultiBlockLattice3D< T, DESCRIPTOR > *	lattice
	the fluid lattice
vector< int >	desiredFluidOutputVariables
	A vector specifying the output variables (from const_defaults.h)
vector< int >	desiredCEPACfieldOutputVariables
HemoCell &	hemocell
	Reference to parent.
vector< HemoCellField * >	cellFields
	Vector containing the cellTypes.
pluint	envelopeSize
	The envelopeSize for the particles.
plb::MultiParticleField3D< HemoCellParticleField > *	immersedParticles = 0
	palabos field storing the particles
plb::MultiParticleField3D< HemoCellParticleField > *	preinlet_immersedParticles = 0
	seperate preinlet and domain pointers whenever necessary
plb::MultiParticleField3D< HemoCellParticleField > *	domain_immersedParticles = 0
plb::MultiBlockLattice3D< T, CEPAC_DESCRIPTOR > *	CEPACfield = 0
	palabos field for storing the CPAC scalar field if used
T	repulsionCutoff = 0.0
	Repulsion variable set through hemocell.h.
T	repulsionConstant = 0.0
	Repulsion variable set through hemocell.h.
pluint	repulsionTimescale = 1
	Timescale seperation for repulsion, set through hemocell.h.
T	boundaryRepulsionCutoff = 0.0
	Boundary repulsion variable set through hemocell.h.
T	boundaryRepulsionConstant = 0.0
	Boundary repulsion variable set through hemocell.h.
pluint	boundaryRepulsionTimescale = 1
	Timescale seperation for boundary repulsion, set through hemocell.h.
pluint	particleVelocityUpdateTimescale = 1
	Timescale seperation for the velocity interpolation from the fluid to the particle.
pluint	solidifyTimescale = 1
pluint	interiorViscosityTimescale = 1
pluint	interiorViscosityEntireGridTimescale = 1
int	periodicity_limit [3] = {100}
	Limit of cycles in a direction (xyz)
int	periodicity_limit_offset_y = 100
int	periodicity_limit_offset_z = 10000
int	number_of_cells = 0
unsigned int	max_neighbours = 0
plb::CommunicationStructure3D *	large_communicator = 0
plb::ParallelBlockCommunicator3D	envelope_communicator

Private Member Functions
void	copyXMLreader2XMLwriter (plb::XMLreader const &reader, plb::XMLwriter &writer)
void	copyXMLreader2XMLwriter (plb::XMLreaderProxy readerProxy, plb::XMLwriter &writer)

Private Attributes
vector< vector< NoInitChar > >	sendBuffers
vector< vector< NoInitChar > >	recvBuffers

Detailed Description

This class can contain many cellTypes, it keeps track of all the particles of all types. The option exists to get exclusive access to a single cellType if necessary. all the particles are stored in a single particlefield

Constructor & Destructor Documentation

HemoCellFields()

hemo::HemoCellFields::HemoCellFields	(	plb::MultiBlockLattice3D< T, DESCRIPTOR > &	lattice_,
		unsigned int	particleEnvelopeWidth,
		HemoCell &
	)

Default constructor, needs an palabos lattice, envelope width (lbm units), and hemocell reference.

~HemoCellFields()

hemo::HemoCellFields::~HemoCellFields

(

)

Generic Destructor.

Member Function Documentation

addCellType()

HemoCellField * hemo::HemoCellFields::addCellType	(	std::string	name_,
		int	constructType
	)

Add an celltype with a certain mesh, the name also specifies <name_>.xml and <name_>.pos.

addParticles()

void hemo::HemoCellFields::addParticles

(

vector< HemoCellParticle > &

particles

)

Add particles to local processors.

advanceParticles()

void hemo::HemoCellFields::advanceParticles

(

)

Advance the particles in an iteration.

applyBoundaryRepulsionForce()

void hemo::HemoCellFields::applyBoundaryRepulsionForce

(

)

Apply (and calculate) the repulsion force between particles and the boundary.

applyConstitutiveModel()

void hemo::HemoCellFields::applyConstitutiveModel

(

bool

forced = false

)

Apply the material model of the cells to the particles, updating their force.

applyRepulsionForce()

void hemo::HemoCellFields::applyRepulsionForce

(

)

Apply (and calculate) the repulsion force between particles.

base_cell_id()

int hemo::HemoCellFields::base_cell_id ( int  wrapped )

inline

calculateCommunicationStructure()

void hemo::HemoCellFields::calculateCommunicationStructure

(

)

copyXMLreader2XMLwriter() [1/2]

void hemo::HemoCellFields::copyXMLreader2XMLwriter ( plb::XMLreader const &  reader, plb::XMLwriter &  writer  )

private

copyXMLreader2XMLwriter() [2/2]

void hemo::HemoCellFields::copyXMLreader2XMLwriter ( plb::XMLreaderProxy  readerProxy, plb::XMLwriter &  writer  )

private

createCEPACfield()

void hemo::HemoCellFields::createCEPACfield

(

)

createParticleField()

void hemo::HemoCellFields::createParticleField	(	plb::SparseBlockStructure3D *	sbStructure_ = 0,
		plb::ThreadAttribution *	tAttribution_ = 0
	)

deleteIncompleteCells()

void hemo::HemoCellFields::deleteIncompleteCells

(

bool

verbose = true

)

Delete any incomplete cells on a block.

deleteNonLocalParticles()

void hemo::HemoCellFields::deleteNonLocalParticles

(

int

envelope

)

Delete non local particles (do not delete in envelopesize)

findInternalParticleGridPoints()

void hemo::HemoCellFields::findInternalParticleGridPoints

(

)

getParticleField3D()

MultiParticleField3D< HemoCellParticleField > & hemo::HemoCellFields::getParticleField3D

(

)

Legacy Helper function to get the particle field, mostly unused as direct access is available.

getParticles()

void hemo::HemoCellFields::getParticles	(	vector< HemoCellParticle * > &	particles,
		plb::Box3D &	domain
	)

Get particles in a given domain.

InitAfterLoadCheckpoint()

void hemo::HemoCellFields::InitAfterLoadCheckpoint

(

)

Used to set variables inside the celltypes for correct access, called through createParticleField.

internalGridPointsMembrane()

void hemo::HemoCellFields::internalGridPointsMembrane

(

)

interpolateFluidVelocity()

void hemo::HemoCellFields::interpolateFluidVelocity

(

)

Interpolate the velocity of the fluid to the individual particles.

load()

void hemo::HemoCellFields::load	(	plb::XMLreader *	documentXML,
		unsigned int &	iter,
		Config *	cfg = NULL
	)

Load a checkpoint, store the current iteration in &iter.

operator[]() [1/2]

HemoCellField * hemo::HemoCellFields::operator[]

(

string

name

)

Easy access to contained celltypes.

operator[]() [2/2]

HemoCellField * hemo::HemoCellFields::operator[]

(

unsigned int

index

)

Easy access to contained celltypes.

populateBindingSites()

void hemo::HemoCellFields::populateBindingSites

(

plb::Box3D *

box = 0

)

Add bindingSites.

populateBoundaryParticles()

void hemo::HemoCellFields::populateBoundaryParticles

(

)

Add boundary particles on the fluid-solid boundary.

prepareSolidification()

void hemo::HemoCellFields::prepareSolidification

(

)

readPositionsCellFields()

void hemo::HemoCellFields::readPositionsCellFields

(

std::string

particlePosFile

)

Legacy reads in only RBC an PLT from a single pos file.

save()

void hemo::HemoCellFields::save	(	plb::XMLreader *	documentXML,
		unsigned int	iter,
		Config *	cfg = NULL
	)

Save a checkpoint.

separate_force_vectors()

void hemo::HemoCellFields::separate_force_vectors

(

)

Separate the force vectors of particles so it becomes clear what the vector for each separate force is.

size()

unsigned int hemo::HemoCellFields::size

(

)

Get the number of celltypes.

solidifyCells()

void hemo::HemoCellFields::solidifyCells

(

)

Conditionally solidify cells if requested.

spreadParticleForce()

void hemo::HemoCellFields::spreadParticleForce

(

)

Spread the force of all particles over the fluid in this iteration.

syncEnvelopes()

void hemo::HemoCellFields::syncEnvelopes

(

)

Sync the particle envelopes between domains.

unify_force_vectors()

void hemo::HemoCellFields::unify_force_vectors

(

)

Unify the force vectors of particles to point to a single force.

updateResidenceTime()

void hemo::HemoCellFields::updateResidenceTime

(

unsigned int

rtime

)

increment cell residence time

Member Data Documentation

boundaryRepulsionConstant

T hemo::HemoCellFields::boundaryRepulsionConstant = 0.0

Boundary repulsion variable set through hemocell.h.

boundaryRepulsionCutoff

T hemo::HemoCellFields::boundaryRepulsionCutoff = 0.0

Boundary repulsion variable set through hemocell.h.

boundaryRepulsionTimescale

pluint hemo::HemoCellFields::boundaryRepulsionTimescale = 1

Timescale seperation for boundary repulsion, set through hemocell.h.

cellFields

vector<HemoCellField *> hemo::HemoCellFields::cellFields

Vector containing the cellTypes.

CEPACfield

plb::MultiBlockLattice3D<T,CEPAC_DESCRIPTOR>* hemo::HemoCellFields::CEPACfield = 0

palabos field for storing the CPAC scalar field if used

desiredCEPACfieldOutputVariables

vector<int> hemo::HemoCellFields::desiredCEPACfieldOutputVariables

desiredFluidOutputVariables

vector<int> hemo::HemoCellFields::desiredFluidOutputVariables

A vector specifying the output variables (from const_defaults.h)

domain_immersedParticles

plb::MultiParticleField3D<HemoCellParticleField> * hemo::HemoCellFields::domain_immersedParticles = 0

envelope_communicator

plb::ParallelBlockCommunicator3D hemo::HemoCellFields::envelope_communicator

envelopeSize

pluint hemo::HemoCellFields::envelopeSize

The envelopeSize for the particles.

hemocell

HemoCell& hemo::HemoCellFields::hemocell

Reference to parent.

immersedParticles

plb::MultiParticleField3D<HemoCellParticleField>* hemo::HemoCellFields::immersedParticles = 0

palabos field storing the particles

interiorViscosityEntireGridTimescale

pluint hemo::HemoCellFields::interiorViscosityEntireGridTimescale = 1

interiorViscosityTimescale

pluint hemo::HemoCellFields::interiorViscosityTimescale = 1

large_communicator

plb::CommunicationStructure3D* hemo::HemoCellFields::large_communicator = 0

lattice

plb::MultiBlockLattice3D<T, DESCRIPTOR>* hemo::HemoCellFields::lattice

the fluid lattice

max_neighbours

unsigned int hemo::HemoCellFields::max_neighbours = 0

number_of_cells

int hemo::HemoCellFields::number_of_cells = 0

Total number of cells in the simulation, should be constant Is set through hemocell::loadParticles() is added (TODO: also when removed)

particleVelocityUpdateTimescale

pluint hemo::HemoCellFields::particleVelocityUpdateTimescale = 1

Timescale seperation for the velocity interpolation from the fluid to the particle.

periodicity_limit

int hemo::HemoCellFields::periodicity_limit[3] = {100}

Limit of cycles in a direction (xyz)

periodicity_limit_offset_y

int hemo::HemoCellFields::periodicity_limit_offset_y = 100

periodicity_limit_offset_z

int hemo::HemoCellFields::periodicity_limit_offset_z = 10000

preinlet_immersedParticles

plb::MultiParticleField3D<HemoCellParticleField>* hemo::HemoCellFields::preinlet_immersedParticles = 0

seperate preinlet and domain pointers whenever necessary

recvBuffers

vector<vector<NoInitChar> > hemo::HemoCellFields::recvBuffers

private

repulsionConstant

T hemo::HemoCellFields::repulsionConstant = 0.0

Repulsion variable set through hemocell.h.

repulsionCutoff

T hemo::HemoCellFields::repulsionCutoff = 0.0

Repulsion variable set through hemocell.h.

repulsionTimescale

pluint hemo::HemoCellFields::repulsionTimescale = 1

Timescale seperation for repulsion, set through hemocell.h.

sendBuffers

vector<vector<NoInitChar> > hemo::HemoCellFields::sendBuffers

private

solidifyTimescale

pluint hemo::HemoCellFields::solidifyTimescale = 1