A flux is defined between a pair of types, and acts on the state vector between a pair of instances. More...

#include <tfFlux.h>

Collaboration diagram for TissueForge::Fluxes:

[legend]

Public Member Functions
std::string	toString ()
	Get a JSON string representation.

Static Public Member Functions
static Fluxes *	newFluxes (int32_t init_size)

static Fluxes *	create (FluxKind kind, ParticleType a, ParticleType b, const std::string &name, FPTYPE k, FPTYPE decay, FPTYPE target, FPTYPE cutoff=-FPTYPE_ONE)

static Fluxes *	addFlux (FluxKind kind, Fluxes *fluxes, int16_t typeId_a, int16_t typeId_b, int32_t index_a, int32_t index_b, FPTYPE k, FPTYPE decay, FPTYPE target, FPTYPE cutoff)

static Fluxes *	fluxFick (ParticleType A, ParticleType B, const std::string &name, const FPTYPE &k, const FPTYPE &decay=FPTYPE_ZERO, const FPTYPE &cutoff=-FPTYPE_ONE)
	Creates and binds a Fickian diffusion flux.

static Fluxes *	flux (ParticleType A, ParticleType B, const std::string &name, const FPTYPE &k, const FPTYPE &decay=FPTYPE_ZERO, const FPTYPE &cutoff=-FPTYPE_ONE)
	Alias of fluxFick.

static Fluxes *	secrete (ParticleType A, ParticleType B, const std::string &name, const FPTYPE &k, const FPTYPE &target, const FPTYPE &decay=FPTYPE_ZERO, const FPTYPE &cutoff=-FPTYPE_ONE)
	Creates a secretion flux by active pumping.

static Fluxes *	uptake (ParticleType A, ParticleType B, const std::string &name, const FPTYPE &k, const FPTYPE &target, const FPTYPE &decay=FPTYPE_ZERO, const FPTYPE &cutoff=-FPTYPE_ONE)
	Creates an uptake flux by active pumping.

static Fluxes *	fromString (const std::string &str)
	Create from a JSON string representation.

Public Attributes
int32_t	size

int32_t	fluxes_size

Flux	fluxes []

Detailed Description

A flux is defined between a pair of types, and acts on the state vector between a pair of instances.

The indices of the species in each state vector are most likely different, so Tissue Forge tracks the indices in each type, and the transport constatants.

A flux between a pair of types, and pair of respective species needs:

(1) type A, (2) type B, (3) species id in A, (4) species id in B, (5) transport constant.

Allocates Flux as a single block, member pointers point to offsets in these blocks.

Allocated size is: sizeof(Fluxes) + 2 * alloc_size * sizeof(int32) + alloc_size * sizeof(FPTYPE)

Member Function Documentation

◆ flux()

static Fluxes * TissueForge::Fluxes::flux	(	ParticleType *	A,
		ParticleType *	B,
		const std::string &	name,
		const FPTYPE &	k,
		const FPTYPE &	decay = FPTYPE_ZERO,
		const FPTYPE &	cutoff = -FPTYPE_ONE )

static

Alias of fluxFick.

Parameters

A	first type
B	second type
name	name of species
k	transport coefficient
decay	optional decay. Defaults to 0.0.
cutoff	optional cutoff distance. Defaults to global cutoff

Returns: Fluxes*

◆ fluxFick()

static Fluxes * TissueForge::Fluxes::fluxFick	(	ParticleType *	A,
		ParticleType *	B,
		const std::string &	name,
		const FPTYPE &	k,
		const FPTYPE &	decay = FPTYPE_ZERO,
		const FPTYPE &	cutoff = -FPTYPE_ONE )

static

Creates and binds a Fickian diffusion flux.

Fickian diffusion flux implements the analogous reaction:

$a.S \leftrightarrow b.S ; k \left(1 - \frac{r}{r_{cutoff}} \right)\left(a.S - b.S\right) ,$

$a.S \rightarrow 0 ; \frac{d}{2} a.S ,$

$b.S \rightarrow 0 ; \frac{d}{2} b.S ,$

where $ a.S $ is a chemical species located at object $ a $ , and likewise for $ b $ , $ k $ is the flux constant, $ r $ is the distance between the two objects, $r_{cutoff}$ is the global cutoff distance, and $ d $ is an optional decay term.

Automatically updates when running on a CUDA device.

Parameters

A	first type
B	second type
name	name of species
k	transport coefficient
decay	optional decay. Defaults to 0.0.
cutoff	optional cutoff distance. Defaults to global cutoff

Returns: Fluxes*

◆ fromString()

static Fluxes * TissueForge::Fluxes::fromString ( const std::string & str )

static

Create from a JSON string representation.

Parameters

str

Returns: Fluxes*

◆ secrete()

static Fluxes * TissueForge::Fluxes::secrete	(	ParticleType *	A,
		ParticleType *	B,
		const std::string &	name,
		const FPTYPE &	k,
		const FPTYPE &	target,
		const FPTYPE &	decay = FPTYPE_ZERO,
		const FPTYPE &	cutoff = -FPTYPE_ONE )

static

Creates a secretion flux by active pumping.

Secretion flux implements the analogous reaction:

$a.S \rightarrow b.S ; k \left(1 - \frac{r}{r_{cutoff}} \right)\left(a.S - a.S_{target} \right) ,$

$a.S \rightarrow 0 ; \frac{d}{2} a.S ,$

$b.S \rightarrow 0 ; \frac{d}{2} b.S ,$

where $ a.S $ is a chemical species located at object $ a $ , and likewise for $ b $ , $ k $ is the flux constant, $ r $ is the distance between the two objects, $r_{cutoff}$ is the global cutoff distance, and $ d $ is an optional decay term.

Automatically updates when running on a CUDA device.

Parameters

A	first type
B	second type
name	name of species
k	transport coefficient
target	target concentration
decay	optional decay. Defaults to 0.0
cutoff	optional cutoff distance. Defaults to global cutoff

Returns: Fluxes*

◆ toString()

std::string TissueForge::Fluxes::toString ( )

Get a JSON string representation.

Returns: std::string

◆ uptake()

static Fluxes * TissueForge::Fluxes::uptake	(	ParticleType *	A,
		ParticleType *	B,
		const std::string &	name,
		const FPTYPE &	k,
		const FPTYPE &	target,
		const FPTYPE &	decay = FPTYPE_ZERO,
		const FPTYPE &	cutoff = -FPTYPE_ONE )

static

Creates an uptake flux by active pumping.

Uptake flux implements the analogous reaction:

$a.S \rightarrow b.S ; k \left(1 - \frac{r}{r_{cutoff}}\right)\left(b.S - b.S_{target} \right)\left(a.S\right) ,$

$a.S \rightarrow 0 ; \frac{d}{2} a.S ,$

$b.S \rightarrow 0 ; \frac{d}{2} b.S ,$

where $ a.S $ is a chemical species located at object $ a $ , and likewise for $ b $ , $ k $ is the flux constant, $ r $ is the distance between the two objects, $r_{cutoff}$ is the global cutoff distance, and $ d $ is an optional decay term.

Automatically updates when running on a CUDA device.

Parameters

A	first type
B	second type
name	name of species
k	transport coefficient
target	target concentration
decay	optional decay. Defaults to 0.0
cutoff	optional cutoff distance. Defaults to global cutoff

Returns: Fluxes*

The documentation for this struct was generated from the following file:

source/mdcore/include/tfFlux.h

Public Member Functions

Static Public Member Functions

Public Attributes

Detailed Description

Member Function Documentation

◆ flux()

◆ fluxFick()

◆ fromString()

◆ secrete()

◆ toString()

◆ uptake()