Models::SimpleModel Struct Reference

Rod-shaped cell growing on glucose, dividing on a timer. More...

#include <simple_model.hpp>

Public Types
enum class	particle_var : int {   length = 0 , age , t_div , phi_s ,   __COUNT__ }
using	uniform_weight = std::true_type
using	Self = SimpleModel
using	FloatType = float
using	Config = std::nullopt_t
using	SelfParticle = MC::ParticlesModel<Self::n_var, Self::FloatType>
using	SelfContribs = MC::ParticlesContribs<Self::n_c, Self::FloatType>

Static Public Member Functions
static KOKKOS_INLINE_FUNCTION void	init (const MC::pool_type &random_pool, std::size_t idx, const SelfParticle &arr)
static KOKKOS_INLINE_FUNCTION MC::Status	update (const MC::pool_type &random_pool, FloatType d_t, std::size_t idx, const SelfParticle &arr, const SelfContribs &arr_contribs, std::size_t position_index, const MC::LocalConcentration &c)
static KOKKOS_INLINE_FUNCTION void	division (const MC::pool_type &random_pool, std::size_t idx, std::size_t idx2, const SelfParticle &arr, const SelfParticle &buffer_arr)
static KOKKOS_INLINE_FUNCTION double	mass (std::size_t idx, const SelfParticle &arr)
static std::vector< std::string_view >	names ()
static std::vector< std::size_t >	get_number ()
static std::vector< std::string_view >	species ()

Public Attributes
MODEL_CONSTANT std::size_t	n_var = INDEX_FROM_ENUM(particle_var::__COUNT__)
MODEL_CONSTANT std::size_t	n_c = 1
MODEL_CONSTANT std::string_view	name = "simple"
MODEL_CONSTANT FloatType	l_dot_max = 8 * 2e-10
MODEL_CONSTANT FloatType	l_max_m = 5e-6
MODEL_CONSTANT FloatType	l_min_m = 0.9e-6
MODEL_CONSTANT FloatType	d_m = 0.6e-6
MODEL_CONSTANT FloatType	k_s = 1e-3
MODEL_CONSTANT FloatType	lin_density = c_linear_density(static_cast<FloatType>(1000), d_m)
MODEL_CONSTANT FloatType	phi_s_max = _get_phi_s_max<FloatType>(lin_density, l_dot_max)
MODEL_CONSTANT auto	l_dist
MODEL_CONSTANT auto	t_div_dist

Detailed Description

Rod-shaped cell growing on glucose, dividing on a timer.

Elongation follows a Monod law on glucose. Division is not triggered by length but by an age threshold drawn per cell, so the population spreads even with a deterministic growth rate.

Member Typedef Documentation

Config

using Models::SimpleModel::Config = std::nullopt_t

FloatType

using Models::SimpleModel::FloatType = float

Self

using Models::SimpleModel::Self = SimpleModel

SelfContribs

using Models::SimpleModel::SelfContribs = MC::ParticlesContribs<Self::n_c, Self::FloatType>

SelfParticle

using Models::SimpleModel::SelfParticle = MC::ParticlesModel<Self::n_var, Self::FloatType>

uniform_weight

using Models::SimpleModel::uniform_weight = std::true_type

Member Enumeration Documentation

particle_var

enum class Models::SimpleModel::particle_var : int

strong

Enumerator
length
age
t_div
phi_s
__COUNT__

Member Function Documentation

division()

KOKKOS_INLINE_FUNCTION void Models::SimpleModel::division ( const MC::pool_type & random_pool, std::size_t idx, std::size_t idx2, const SelfParticle & arr, const SelfParticle & buffer_arr )

static

get_number()

std::vector< std::size_t > Models::SimpleModel::get_number ( )

inlinestatic

init()

KOKKOS_INLINE_FUNCTION void Models::SimpleModel::init ( const MC::pool_type & random_pool, std::size_t idx, const SelfParticle & arr )

static

mass()

KOKKOS_INLINE_FUNCTION double Models::SimpleModel::mass ( std::size_t idx, const SelfParticle & arr )

inlinestatic

names()

std::vector< std::string_view > Models::SimpleModel::names ( )

inlinestatic

species()

std::vector< std::string_view > Models::SimpleModel::species ( )

inlinestatic

update()

KOKKOS_INLINE_FUNCTION MC::Status Models::SimpleModel::update ( const MC::pool_type & random_pool, FloatType d_t, std::size_t idx, const SelfParticle & arr, const SelfContribs & arr_contribs, std::size_t position_index, const MC::LocalConcentration & c )

static

Member Data Documentation

d_m

MODEL_CONSTANT FloatType Models::SimpleModel::d_m = 0.6e-6

k_s

MODEL_CONSTANT FloatType Models::SimpleModel::k_s = 1e-3

l_dist

MODEL_CONSTANT auto Models::SimpleModel::l_dist

Initial value:

= MC::Distributions::TruncatedNormal<FloatType>(
        l_min_m, l_min_m / 5., l_min_m * 0.5, l_max_m)

l_dot_max

MODEL_CONSTANT FloatType Models::SimpleModel::l_dot_max = 8 * 2e-10

l_max_m

MODEL_CONSTANT FloatType Models::SimpleModel::l_max_m = 5e-6

l_min_m

MODEL_CONSTANT FloatType Models::SimpleModel::l_min_m = 0.9e-6

lin_density

MODEL_CONSTANT FloatType Models::SimpleModel::lin_density = c_linear_density(static_cast<FloatType>(1000), d_m)

n_c

MODEL_CONSTANT std::size_t Models::SimpleModel::n_c = 1

n_var

MODEL_CONSTANT std::size_t Models::SimpleModel::n_var = INDEX_FROM_ENUM(particle_var::__COUNT__)

name

MODEL_CONSTANT std::string_view Models::SimpleModel::name = "simple"

phi_s_max

MODEL_CONSTANT FloatType Models::SimpleModel::phi_s_max = _get_phi_s_max<FloatType>(lin_density, l_dot_max)

t_div_dist

MODEL_CONSTANT auto Models::SimpleModel::t_div_dist

Initial value:

= MC::Distributions::TruncatedNormal<FloatType>(500.,
                                                        500. / 2.,
                                                        10.,
                                                        1200.)

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

• apps/libs/models/public/models/simple_model.hpp