hemo::HemoCell Class Reference

#include <hemocell.h>

Collaboration diagram for hemo::HemoCell:

Public Types
enum class	MPIHandle { Internal , External }
	Switch to indicate if the MPI instance is managed externally. The MPI instance is typically invoked when initialising the HemoCell class through the plb::plbInit routine. However, in some scenarios we might want to manually control the MPI environment and do not want HemoCell to setup MPI environment. More...

Public Member Functions
	HemoCell (char *configFileName, int argc, char *argv[])
	HemoCell (char *configFileName, int argc, char *argv[], HemoCell::MPIHandle mpi_handle)
	~HemoCell ()
void	latticeEquilibrium (T rho, hemo::Array< T, 3 > vel)
void	initializeCellfield ()
template<class Mechanics >
void	addCellType (string name, int constructType)
void	setOutputs (string name, vector< int > outputs)
void	setRepulsion (T repulsionConstant, T repulsionCutoff)
void	setMaterialTimeScaleSeparation (string name, unsigned int separation)
void	enableSolidifyMechanics (string name)
void	setParticleVelocityUpdateTimeScaleSeparation (unsigned int separation)
void	setRepulsionTimeScaleSeperation (unsigned int separation)
void	setSolidifyTimeScaleSeperation (unsigned int separation)
void	setInteriorViscosityTimeScaleSeperation (unsigned int separation, unsigned int separation_entire_grid)
void	enableBoundaryParticles (T boundaryRepulsionConstant, T boundaryRepulsionCutoff, unsigned int timestep=1)
void	setInitialMinimumDistanceFromSolid (string name, T distance)
void	setFluidOutputs (vector< int > outputs)
void	setCEPACOutputs (vector< int > outputs)
void	setSystemPeriodicity (unsigned int axis, bool bePeriodic)
void	setSystemPeriodicityLimit (unsigned int axis, int limit)
void	loadParticles ()
	Load the particles from their .pos files.
void	loadCheckPoint ()
	Load a checkpoint.
void	saveCheckPoint ()
	Save a checkpoint.
void	writeOutput ()
	Write the specified output to hdf5 files.
void	iterate ()
void	checkExitSignals ()
	Check if any exis signal was caught.
T	calculateFractionalLoadImbalance ()
	Calculate and return the fractional load imbalance.
void	doLoadBalance ()
	Load balance the domain (only necessary with nAtomic blocks > nMpi processors, also checkpoints.
void	doRestructure (bool checkpoint_avail=true)
	Restructure the grid, has an optional argument to specify whether a checkpoint from this iteration is available, default is YES!
void	initializeLattice (MultiBlockManagement3D const &management)
	Initialize the fluid field with the given management, should be done after specifing the pre inlets and before initializing the cellfields.

Public Attributes
bool	repulsionEnabled = false
bool	boundaryRepulsionEnabled = false
bool	leesEdwardsBC = false
double *	LEcurrentDisplacement
bool	outputInSiUnits = true
	Specify whether the output is in SI or LBM units.
PreInlet *	preInlet = 0
bool	partOfpreInlet = false
map< plint, plint >	BlockToMpi
LoadBalancer *	loadBalancer = 0
MultiBlockLattice3D< T, DESCRIPTOR > *	lattice = 0
	The fluid lattice.
MultiBlockLattice3D< T, DESCRIPTOR > *	preinlet_lattice = 0
MultiBlockLattice3D< T, DESCRIPTOR > *	domain_lattice = 0
MultiBlockManagement3D *	preinlet_lattice_management = 0
MultiBlockManagement3D *	domain_lattice_management = 0
Config *	cfg = 0
HemoCellFields *	cellfields = 0
	The cellfields contains the particle field and all celltypes.
unsigned int	iter = 0
XMLreader *	documentXML = 0

Private Member Functions
void	sanityCheck ()
	To be run right before the first iteration, all checking should move here.

Private Attributes
bool	loadParticlesIsCalled = false
unsigned int	lastOutputAt = 0
	Store the last time (iteration) output occured.
std::chrono::high_resolution_clock::duration	lastOutput = std::chrono::high_resolution_clock::duration::zero()
bool	sanityCheckDone = false
	Checked in iteration, do sanity check when not yet done.

Detailed Description

The HemoCell class contains all the information, data and methods to set up a basic HemoCell simulation.

Most importantly:

• It contains one Palabos FluidField
• It contains one CellFields

After everything is set HemoCell::iterate() is used to iterate the simulation.

Member Enumeration Documentation

MPIHandle

enum class hemo::HemoCell::MPIHandle

strong

Switch to indicate if the MPI instance is managed externally. The MPI instance is typically invoked when initialising the HemoCell class through the plb::plbInit routine. However, in some scenarios we might want to manually control the MPI environment and do not want HemoCell to setup MPI environment.

Enumerator
Internal
External

Constructor & Destructor Documentation

HemoCell() [1/2]

hemo::HemoCell::HemoCell ( char *  configFileName, int  argc, char *  argv[]  )

inline

Creates an hemocell object

Parameters

configFileName

the location of the main config file

Unfortunately, due to palabos regulations, it is required to pass the commandline arguments

HemoCell() [2/2]

HemoCell::HemoCell	(	char *	configFileName,
		int	argc,
		char *	argv[],
		HemoCell::MPIHandle	mpi_handle
	)

Creates an HemoCell object and allows to indicate the MPI environment is managed externally. If so, this constructor avoids plb::plbInit().

Parameters

mpi_handle

the MPIHanndle indicator.

~HemoCell()

HemoCell::~HemoCell

(

)

Member Function Documentation

addCellType()

template<class Mechanics >

void hemo::HemoCell::addCellType ( string  name, int  constructType  )

inline

Add a celltype valid options for constructType are: RBC_FROM_SPHERE <- RBC ELLIPSOID_FROM_SPHERE <- platelet STRING_FROM_VERTEXES ->von willibrand factor use as addCelltype<RbcHO>("RBC", RBC_FROM_SPHERE) for example Since it is a template, it must be in the header class, maybe move to .hh file for readability ...

calculateFractionalLoadImbalance()

T HemoCell::calculateFractionalLoadImbalance

(

)

Calculate and return the fractional load imbalance.

checkExitSignals()

void HemoCell::checkExitSignals

(

)

Check if any exis signal was caught.

doLoadBalance()

void hemo::HemoCell::doLoadBalance

(

)

Load balance the domain (only necessary with nAtomic blocks > nMpi processors, also checkpoints.

doRestructure()

void HemoCell::doRestructure

(

bool

checkpoint_avail = true

)

Restructure the grid, has an optional argument to specify whether a checkpoint from this iteration is available, default is YES!

enableBoundaryParticles()

void HemoCell::enableBoundaryParticles	(	T	boundaryRepulsionConstant,
		T	boundaryRepulsionCutoff,
		unsigned int	timestep = 1
	)

enableSolidifyMechanics()

void hemo::HemoCell::enableSolidifyMechanics ( string  name )

inline

initializeCellfield()

void HemoCell::initializeCellfield

(

)

Initialice the cellfields structure (and thus also the particlefield)

initializeLattice()

void HemoCell::initializeLattice

(

MultiBlockManagement3D const &

management

)

Initialize the fluid field with the given management, should be done after specifing the pre inlets and before initializing the cellfields.

iterate()

void HemoCell::iterate

(

)

Do an iteration, If the system is driven by an external vector, you must set it again after calling iterate

latticeEquilibrium()

void HemoCell::latticeEquilibrium	(	T	rho,
		hemo::Array< T, 3 >	vel
	)

Set all the fluid nodes to these values

Parameters

rho	the desired density in lbm units
vel	the desired macroscopic velocity of each node

loadCheckPoint()

void HemoCell::loadCheckPoint

(

)

Load a checkpoint.

loadParticles()

void HemoCell::loadParticles

(

)

Load the particles from their .pos files.

sanityCheck()

void HemoCell::sanityCheck ( )

private

To be run right before the first iteration, all checking should move here.

saveCheckPoint()

void HemoCell::saveCheckPoint

(

)

Save a checkpoint.

setCEPACOutputs()

void HemoCell::setCEPACOutputs

(

vector< int >

outputs

)

setFluidOutputs()

void HemoCell::setFluidOutputs

(

vector< int >

outputs

)

setInitialMinimumDistanceFromSolid()

void HemoCell::setInitialMinimumDistanceFromSolid	(	string	name,
		T	distance
	)

setInteriorViscosityTimeScaleSeperation()

void HemoCell::setInteriorViscosityTimeScaleSeperation	(	unsigned int	separation,
		unsigned int	separation_entire_grid
	)

setMaterialTimeScaleSeparation()

void HemoCell::setMaterialTimeScaleSeparation	(	string	name,
		unsigned int	separation
	)

setOutputs()

void HemoCell::setOutputs	(	string	name,
		vector< int >	outputs
	)

Set the output of a celltype the outputs string should contain constants like VELOCITY_OUTPUT defined in the constants_defaults file

Parameters

outputs	a vector of constants that define the desired output
name	the name of the CellType ("RBC", "PLT")

setParticleVelocityUpdateTimeScaleSeparation()

void HemoCell::setParticleVelocityUpdateTimeScaleSeparation

(

unsigned int

separation

)

setRepulsion()

void HemoCell::setRepulsion	(	T	repulsionConstant,
		T	repulsionCutoff
	)

setRepulsionTimeScaleSeperation()

void HemoCell::setRepulsionTimeScaleSeperation

(

unsigned int

separation

)

setSolidifyTimeScaleSeperation()

void HemoCell::setSolidifyTimeScaleSeperation

(

unsigned int

separation

)

setSystemPeriodicity()

void HemoCell::setSystemPeriodicity	(	unsigned int	axis,
		bool	bePeriodic
	)

setSystemPeriodicityLimit()

void HemoCell::setSystemPeriodicityLimit	(	unsigned int	axis,
		int	limit
	)

writeOutput()

void HemoCell::writeOutput

(

)

Write the specified output to hdf5 files.

Member Data Documentation

BlockToMpi

map<plint,plint> hemo::HemoCell::BlockToMpi

boundaryRepulsionEnabled

bool hemo::HemoCell::boundaryRepulsionEnabled = false

cellfields

HemoCellFields* hemo::HemoCell::cellfields = 0

The cellfields contains the particle field and all celltypes.

cfg

Config* hemo::HemoCell::cfg = 0

documentXML

XMLreader* hemo::HemoCell::documentXML = 0

domain_lattice

MultiBlockLattice3D<T, DESCRIPTOR> * hemo::HemoCell::domain_lattice = 0

domain_lattice_management

MultiBlockManagement3D * hemo::HemoCell::domain_lattice_management = 0

iter

unsigned int hemo::HemoCell::iter = 0

lastOutput

std::chrono::high_resolution_clock::duration hemo::HemoCell::lastOutput = std::chrono::high_resolution_clock::duration::zero()

private

lastOutputAt

unsigned int hemo::HemoCell::lastOutputAt = 0

private

Store the last time (iteration) output occured.

lattice

MultiBlockLattice3D<T, DESCRIPTOR>* hemo::HemoCell::lattice = 0

The fluid lattice.

LEcurrentDisplacement

double* hemo::HemoCell::LEcurrentDisplacement

leesEdwardsBC

bool hemo::HemoCell::leesEdwardsBC = false

loadBalancer

LoadBalancer* hemo::HemoCell::loadBalancer = 0

loadParticlesIsCalled

bool hemo::HemoCell::loadParticlesIsCalled = false

private

outputInSiUnits

bool hemo::HemoCell::outputInSiUnits = true

Specify whether the output is in SI or LBM units.

partOfpreInlet

bool hemo::HemoCell::partOfpreInlet = false

preInlet

PreInlet* hemo::HemoCell::preInlet = 0

preinlet_lattice

MultiBlockLattice3D<T, DESCRIPTOR> * hemo::HemoCell::preinlet_lattice = 0

preinlet_lattice_management

MultiBlockManagement3D* hemo::HemoCell::preinlet_lattice_management = 0

repulsionEnabled

bool hemo::HemoCell::repulsionEnabled = false

sanityCheckDone

bool hemo::HemoCell::sanityCheckDone = false

private

Checked in iteration, do sanity check when not yet done.