two_meta.hpp

#ifndef __TWOMETA_MODEL_HPP__
#define __TWOMETA_MODEL_HPP__
 
#include "Kokkos_Printf.hpp"
#include "common/traits.hpp"
#include "mc/macros.hpp"
#include "models/utils.hpp"
#include <mc/prng/prng_extension.hpp>
#include <mc/traits.hpp>
#include <models/uptake.hpp>
#include <string_view>
 
namespace
{
  // template <FloatingPointType F> static F consteval get_phi_s_max(F density, F dl)
  // {
  //   // dl and density must be same unit, dl*density -> mass and y is mass yield
  //   return (dl * density) * 0.5;
  // }
} // namespace
 
namespace Models
{
 
  struct TwoMeta
  {
    using uniform_weight = std::true_type; // Using type alias
    using Self = TwoMeta;
    using FloatType = float;
    using Config = std::nullopt_t;
 
    enum class particle_var : int
    {
      age = INDEX_FROM_ENUM(Uptakeparticle_var::COUNT),
      length,
      nu1,
      nu2,
      l_cp,
      nu_eff_1, // This is not itself a model property but stored to be exported
      nu_eff_2, // This is not itself a model property but stored to be exported
      // TODO FIND BETTER WAY TO STORE/GET CONTRIBUTIONS
      contrib_phi_s,
      contrib_phi_o2,
      contrib_phi_ac,
      COUNT
    };
 
    static constexpr std::size_t n_var = INDEX_FROM_ENUM(particle_var::COUNT);
    static constexpr std::string_view name = "simple";
    using SelfParticle = MC::ParticlesModel<Self::n_var, Self::FloatType>;
 
    MODEL_CONSTANT FloatType l_max_m = 5e-6;   // m
    MODEL_CONSTANT FloatType l_c_m = 3e-6;     // m
    MODEL_CONSTANT FloatType d_m = 0.6e-6;     // m
    MODEL_CONSTANT FloatType l_min_m = 0.9e-6; // m
    MODEL_CONSTANT FloatType lin_density = c_linear_density(static_cast<FloatType>(1000), d_m);
    MODEL_CONSTANT FloatType MolarMassG = Models::MolarMass::GramPerMole::glucose<float>;
    MODEL_CONSTANT FloatType MolarMassO2 = Models::MolarMass::GramPerMole::dioxygen<float>; // g/mol
 
    MODEL_CONSTANT FloatType y_sx_1 = 1. / 2.217737e+00; // Mode 1 S to X yield (mass)
    MODEL_CONSTANT FloatType y_sx_2 = y_sx_1 / 3.;       // Mode 2 S to X yield (mass)
    MODEL_CONSTANT FloatType y_sa = 0.8;                 // S to A yield (mass)
    MODEL_CONSTANT FloatType y_os_molar = 3;             // 3 mol o2 per mol for glucose
    MODEL_CONSTANT FloatType k_o = 0.0001; // g/L: Anane et. al 2017 (Biochem. Eng. J) (g/g)
    MODEL_CONSTANT FloatType dl_max_ms = 8 * 2e-10; // m/s  https://doi.org/10.7554/eLife.67495;
    MODEL_CONSTANT FloatType tau_1 = 1000.;         // s
    MODEL_CONSTANT FloatType tau_2 = 1000.;         // s
 
    MODEL_CONSTANT FloatType phi_s_max = (dl_max_ms * lin_density) * y_sx_1;
    MODEL_CONSTANT FloatType phi_perm_max = phi_s_max / 40.; // kgS/
    MODEL_CONSTANT FloatType phi_o2_max =
        10 * phi_s_max / MolarMassG * y_os_molar * MolarMassO2; // kgS/s
    MODEL_CONSTANT float nu_max_kg_s = dl_max_ms * lin_density;
 
    // MODEL_CONSTANT auto length_c_dist =
    //     MC::Distributions::TruncatedNormal<FloatType>(l_c_m, l_c_m / 7., l_min_m, l_max_m); use
    //     in out_str_l2
 
    MODEL_CONSTANT auto length_c_dist = MC::Distributions::TruncatedNormal<FloatType>(
        l_c_m, l_c_m / 2., l_min_m, l_max_m); // use in out_str_l3
 
    // MODEL_CONSTANT auto length_c_dist =
    // MC::Distributions::TruncatedNormal<FloatType>(1.5*l_c_m, l_c_m / 7., 3*l_min_m, l_max_m);
 
    KOKKOS_INLINE_FUNCTION static void
    init(const MC::KPRNG::pool_type& random_pool, std::size_t idx, const SelfParticle& arr);
 
    KOKKOS_INLINE_FUNCTION static MC::Status update(const MC::KPRNG::pool_type& random_pool,
                                                    FloatType d_t,
                                                    std::size_t idx,
                                                    const SelfParticle& arr,
                                                    const MC::LocalConcentration& c);
 
    KOKKOS_INLINE_FUNCTION static void division(const MC::KPRNG::pool_type& random_pool,
                                                std::size_t idx,
                                                std::size_t idx2,
                                                const SelfParticle& arr,
                                                const SelfParticle& buffer_arr);
 
    KOKKOS_INLINE_FUNCTION static void contribution(std::size_t idx,
                                                    std::size_t position,
                                                    double weight,
                                                    const SelfParticle& arr,
                                                    const MC::ContributionView& contributions);
 
    KOKKOS_INLINE_FUNCTION static double mass(std::size_t idx, const SelfParticle& arr)
    {
      return GET_PROPERTY(Self::particle_var::length) * lin_density;
    }
 
    static std::vector<std::string_view> names()
    {
      return {"age",
              "length",
              "nu1",
              "nu2",
              "nu_eff_1",
              "nu_eff_2",
              "a_perm",
              "a_pts",
              "phi_o2",
              "phi_g"};
    }
 
    static std::vector<std::size_t> get_number()
    {
      return {INDEX_FROM_ENUM(particle_var::age),
              INDEX_FROM_ENUM(particle_var::length),
              INDEX_FROM_ENUM(particle_var::nu1),
              INDEX_FROM_ENUM(particle_var::nu2),
              INDEX_FROM_ENUM(particle_var::nu_eff_1),
              INDEX_FROM_ENUM(particle_var::nu_eff_2),
              INDEX_FROM_ENUM(Uptakeparticle_var::a_permease),
              INDEX_FROM_ENUM(Uptakeparticle_var::a_pts),
              INDEX_FROM_ENUM(particle_var::contrib_phi_o2),
              INDEX_FROM_ENUM(particle_var::contrib_phi_s)};
    }
  };
 
  CHECK_MODEL(TwoMeta)
 
  KOKKOS_INLINE_FUNCTION void
  TwoMeta::init([[maybe_unused]] const MC::KPRNG::pool_type& random_pool,
                std::size_t idx,
                const SelfParticle& arr)
  {
    constexpr auto local_lc = length_c_dist;
    constexpr auto length_dist =
        MC::Distributions::TruncatedNormal<FloatType>(l_c_m / 2, l_c_m / 5., l_min_m, l_max_m);
 
    constexpr auto mu_nu_dist = nu_max_kg_s * 0.1;
    constexpr auto nu_1_initial_dist = MC::Distributions::TruncatedNormal<float>(
        mu_nu_dist, mu_nu_dist / 7., 0., static_cast<double>(nu_max_kg_s));
 
    auto gen = random_pool.get_state();
    GET_PROPERTY(Self::particle_var::length) = length_dist.draw(gen);
    GET_PROPERTY(Self::particle_var::l_cp) = local_lc.draw(gen);
    GET_PROPERTY(particle_var::nu1) = nu_1_initial_dist.draw(gen);
    random_pool.free_state(gen);
    GET_PROPERTY(particle_var::contrib_phi_s) = 0;
    Uptake<Self>::init(random_pool, idx, arr);
  }
 
  KOKKOS_INLINE_FUNCTION MC::Status TwoMeta::update(const MC::KPRNG::pool_type& random_pool,
                                                    FloatType d_t,
                                                    std::size_t idx,
                                                    const SelfParticle& arr,
                                                    const MC::LocalConcentration& concentrations)
  {
    (void)random_pool;
    const auto phi_s =
        Uptake<Self>::uptake_step(phi_s_max, phi_perm_max, d_t, idx, arr, concentrations);
 
    const auto o = Kokkos::max(static_cast<float>(concentrations(1)), 0.F);
 
    const float phi_o2 = (phi_o2_max)*o / (o + k_o); // gO2/s
 
    const float nu_1_star = y_sx_1 * MolarMassG *
                            Kokkos::min(phi_s / MolarMassG,
                                        phi_o2 / MolarMassO2 / y_os_molar); // gX/s
 
    const float s_1_star = (1 / y_sx_1 * nu_1_star);
 
    const float phi_s_residual_1_star = Kokkos::max(phi_s - s_1_star, 0.F);
    KOKKOS_ASSERT(phi_s_residual_1_star >= 0.F);
 
    const float nu_2_star = y_sx_2 * phi_s_residual_1_star; // gX/s
 
    GET_PROPERTY(Self::particle_var::nu_eff_1) =
        Kokkos::min(nu_1_star, GET_PROPERTY(Self::particle_var::nu1)); // gX/s
 
    const float s_1 = (1 / y_sx_1 * GET_PROPERTY(Self::particle_var::nu_eff_1));
    const float phi_s_residual_1 = Kokkos::max(phi_s - s_1, 0.F);
    GET_PROPERTY(Self::particle_var::nu_eff_2) =
        Kokkos::min(y_sx_2 * phi_s_residual_1, GET_PROPERTY(Self::particle_var::nu2)); // gX/s
 
    const float s_growth = s_1 + (1 / y_sx_2 * GET_PROPERTY(Self::particle_var::nu_eff_2));
 
    const float s_overflow = phi_s - s_growth;
 
    KOKKOS_ASSERT(GET_PROPERTY(Self::particle_var::nu_eff_1) >= 0.F);
    KOKKOS_ASSERT(GET_PROPERTY(Self::particle_var::nu_eff_2) >= 0.F);
 
    // CONTRIBS
    GET_PROPERTY(Self::particle_var::contrib_phi_s) = -phi_s;
    GET_PROPERTY(Self::particle_var::contrib_phi_o2) =
        -1 * ((1. / y_sx_1 / MolarMassG * y_os_molar * MolarMassO2 *
               GET_PROPERTY(Self::particle_var::nu_eff_1)) +
              0. * GET_PROPERTY(Self::particle_var::nu_eff_2));
 
    GET_PROPERTY(Self::particle_var::contrib_phi_ac) =
        GET_PROPERTY(Self::particle_var::nu_eff_2) / y_sx_2 * y_sa +
        (s_overflow > 0. ? y_sa * (s_overflow) : 0);
 
    // ODE
    GET_PROPERTY(Self::particle_var::nu1) +=
        static_cast<float>(d_t) * ((nu_1_star - GET_PROPERTY(Self::particle_var::nu1)) / tau_1);
 
    GET_PROPERTY(Self::particle_var::nu2) +=
        static_cast<float>(d_t) * ((nu_2_star - GET_PROPERTY(Self::particle_var::nu2)) / tau_2);
 
    const auto sum_nu =
        (GET_PROPERTY(Self::particle_var::nu_eff_1) + GET_PROPERTY(Self::particle_var::nu_eff_2));
 
    GET_PROPERTY(Self::particle_var::length) += static_cast<float>(d_t) * (sum_nu / lin_density);
 
    GET_PROPERTY(Self::particle_var::age) += d_t;
 
    return (GET_PROPERTY(Self::particle_var::length) > GET_PROPERTY(Self::particle_var::l_cp))
               ? MC::Status::Division
               : MC::Status::Idle;
  }
 
  KOKKOS_INLINE_FUNCTION void TwoMeta::division(const MC::KPRNG::pool_type& random_pool,
                                                std::size_t idx,
                                                std::size_t idx2,
                                                const SelfParticle& arr,
                                                const SelfParticle& child_buffer_arr)
  {
    constexpr auto local_lc = length_c_dist;
    const FloatType new_current_length =
        GET_PROPERTY(particle_var::length) / static_cast<FloatType>(2.);
 
    GET_PROPERTY(Self::particle_var::length) = new_current_length;
    GET_PROPERTY(Self::particle_var::age) = 0;
 
    GET_PROPERTY_FROM(idx2, child_buffer_arr, Self::particle_var::length) = new_current_length;
    GET_PROPERTY_FROM(idx2, child_buffer_arr, Self::particle_var::age) = 0;
 
    auto nu_1_o = GET_PROPERTY_FROM(idx, arr, Self::particle_var::nu_eff_1);
    auto nu_2_o = GET_PROPERTY_FROM(idx, arr, Self::particle_var::nu_eff_2);
    auto gen = random_pool.get_state();
    GET_PROPERTY(Self::particle_var::l_cp) = local_lc.draw(gen);
    if (nu_1_o != 0)
    {
      GET_PROPERTY_FROM(idx2, child_buffer_arr, Self::particle_var::nu1) =
          MC::Distributions::TruncatedNormal<FloatType>::draw_from(gen, nu_1_o, nu_1_o / 2., 0, 1.);
    }
    if (nu_2_o != 0)
    {
      GET_PROPERTY_FROM(idx2, child_buffer_arr, Self::particle_var::nu2) =
          MC::Distributions::TruncatedNormal<FloatType>::draw_from(gen, nu_2_o, nu_2_o / 2., 0, 1.);
    }
 
    GET_PROPERTY_FROM(idx2, child_buffer_arr, Self::particle_var::l_cp) = local_lc.draw(gen);
    random_pool.free_state(gen);
 
    Uptake<Self>::division(random_pool, idx, idx2, arr, child_buffer_arr);
  }
 
  KOKKOS_INLINE_FUNCTION void TwoMeta::contribution([[maybe_unused]] std::size_t idx,
                                                    std::size_t position,
                                                    double weight,
                                                    [[maybe_unused]] const SelfParticle& arr,
                                                    const MC::ContributionView& contributions)
  {
    auto access = contributions.access();
    access(0, position) += weight * GET_PROPERTY(Self::particle_var::contrib_phi_s);  // NOLINT
    access(1, position) += weight * GET_PROPERTY(Self::particle_var::contrib_phi_o2); // NOLINT
    access(2, position) += weight * GET_PROPERTY(Self::particle_var::contrib_phi_ac); // NOLINT
  }
 
  static_assert(HasExportProperties<TwoMeta>, "ee");
 
} // namespace Models
 
#endif