Models::Monod Struct Reference

Simplified Monod model for glucose consumption and biomass growth. More...

#include <monod.hpp>

Public Types
enum class	particle_var : int {   l = 0 , l_max , mu_p , mue ,   _init_only_cell_lenghtening , phi_s_c , __COUNT__ }
	Enumeration for the Monod model variables. More...
using	uniform_weight = std::true_type
using	Self = Monod
using	FloatType = float
using	SelfParticle = MC::ParticlesModel<Self::n_var, Self::FloatType>
using	Config = std::nullopt_t

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 double	mass (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 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 MC::ContribIndexBounds	get_bounds ()
static std::vector< std::string_view >	names ()
static std::vector< std::size_t >	get_number ()

Public Attributes
MODEL_CONSTANT FloatType	y_s_x = 2
	Model constants used in biomass growth and cell elongation.
MODEL_CONSTANT FloatType	mu_max = 0.77 / 3600.
	Maximum specific growth rate (1/s), converted from per hour.
MODEL_CONSTANT FloatType	tau_meta = 1. / mu_max
	Metabolic time constant (s), inverse of max growth rate.
MODEL_CONSTANT FloatType	l_max_m = 2e-6
	Maximum cell length (m)
MODEL_CONSTANT FloatType	l_min_m = l_max_m / 2.
	Minimum cell length (m), half of maximum length.
MODEL_CONSTANT FloatType	k_s = 1e-3
	Monod constant for substrate concentration (m)
MODEL_CONSTANT FloatType	d_m = 0.6e-6
	Cell diameter (m)
MODEL_CONSTANT FloatType	lin_density
	Linear density of the biomass (kg/m), calculated from cell diameter.
MODEL_CONSTANT auto	initial_length_dist

Static Public Attributes
static constexpr std::size_t	n_var = INDEX_FROM_ENUM(particle_var::__COUNT__)
static constexpr std::string_view	name = "monod"

Detailed Description

Simplified Monod model for glucose consumption and biomass growth.

This model links glucose consumption and biomass growth using the Monod equation. It models biomass growth through cell elongation for rod-shaped strains, and cell division is assumed to be deterministic. The primary purpose of this model is for validation and to demonstrate how the framework operates without requiring the typical formation. Instead, it focuses on the core dynamics of glucose consumption and biomass growth through the Monod law.

Member Typedef Documentation

Config

using Models::Monod::Config = std::nullopt_t

FloatType

using Models::Monod::FloatType = float

Self

using Models::Monod::Self = Monod

SelfParticle

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

uniform_weight

using Models::Monod::uniform_weight = std::true_type

Member Enumeration Documentation

particle_var

enum class Models::Monod::particle_var : int

strong

Enumeration for the Monod model variables.

This enum represents the different variables used in the Monod model. These variables do not strictly correspond to the state vector (xi), as some are auxiliary variables (e.g., phi_s_c) not part of the primary state. The Monod factor is used to convert the growth rate into elongation rates.

Enumerator
l	Length of the cell.
l_max	Maximum cell length (assumed constant for all cells)
mu_p	Maximum specific growth rate (potential growth rate)
mue	Effective growth rate (used for export purposes only)
_init_only_cell_lenghtening	Factor for converting growth rate into elongation rate
phi_s_c	Instantaneous glucose consumption rate.
__COUNT__	Helper for determining the size of the variable list.

Member Function Documentation

division()

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

inlinestatic

Note

Important to note that new_current_length is not l_max/2 but l/2 This is completly different but as growth is slow and time step has to be small it's ok

get_bounds()

MC::ContribIndexBounds Models::Monod::get_bounds ( )

inlinestatic

get_number()

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

inlinestatic

init()

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

inlinestatic

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mass()

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

inlinestatic

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names()

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

inlinestatic

update()

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

inlinestatic

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Member Data Documentation

d_m

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

Cell diameter (m)

initial_length_dist

MODEL_CONSTANT auto Models::Monod::initial_length_dist

Initial value:

= MC::Distributions::TruncatedNormal<FloatType>(
            l_max_m * 0.75, l_max_m * 0.75 / 4, l_min_m, l_max_m)

k_s

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

Monod constant for substrate concentration (m)

l_max_m

MODEL_CONSTANT FloatType Models::Monod::l_max_m = 2e-6

Maximum cell length (m)

l_min_m

MODEL_CONSTANT FloatType Models::Monod::l_min_m = l_max_m / 2.

Minimum cell length (m), half of maximum length.

lin_density

MODEL_CONSTANT FloatType Models::Monod::lin_density

Initial value:

= 
        c_linear_density(static_cast<FloatType>(1000), d_m)

Linear density of the biomass (kg/m), calculated from cell diameter.

mu_max

MODEL_CONSTANT FloatType Models::Monod::mu_max = 0.77 / 3600.

Maximum specific growth rate (1/s), converted from per hour.

n_var

std::size_t Models::Monod::n_var = INDEX_FROM_ENUM(particle_var::__COUNT__)

staticconstexpr

name

std::string_view Models::Monod::name = "monod"

staticconstexpr

tau_meta

MODEL_CONSTANT FloatType Models::Monod::tau_meta = 1. / mu_max

Metabolic time constant (s), inverse of max growth rate.

y_s_x

MODEL_CONSTANT FloatType Models::Monod::y_s_x = 2

Model constants used in biomass growth and cell elongation.

These constants define various parameters for the model, including maximum growth rates, cell size, and other metabolic factors. The units are specified in meters (m) unless otherwise indicated. Specific yield of biomass per unit substrate (m)

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

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