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/uptake_dyn.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 = 0.5e-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; // TODO should be /y
    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 adder_dist
        = MC::Distributions::TruncatedNormal<FloatType>(
            1.567e-6, 0.24e-6, 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::pool_type& random_pool,
                                            std::size_t idx,
                                            const SelfParticle& arr);
 
    KOKKOS_INLINE_FUNCTION static MC::Status
    update(const MC::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::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::ap_2),
               INDEX_FROM_ENUM(Uptakeparticle_var::ap_1),
               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::pool_type& random_pool,
                std::size_t idx,
                const SelfParticle& arr)
  {
    constexpr auto local_adder = adder_dist;
 
    constexpr auto length_dist = MC::Distributions::TruncatedNormal<FloatType>(
        1.5e-6, 0.19e-6, 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();
    const auto l0 = length_dist.draw(gen);
    const auto dl = local_adder.draw(gen);
    GET_PROPERTY(Self::particle_var::length) = l0;
    GET_PROPERTY(Self::particle_var::l_cp) = l0 + dl;
    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<UptakeDefault<typename Self::FloatType>, Self>::init(
        random_pool, idx, arr);
  }
 
  KOKKOS_INLINE_FUNCTION MC::Status
  TwoMeta::update(const MC::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<UptakeDefault<typename Self::FloatType>, Self>::uptake_step(
            phi_s_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::pool_type& random_pool,
                    std::size_t idx,
                    std::size_t idx2,
                    const SelfParticle& arr,
                    const SelfParticle& child_buffer_arr)
  {
    constexpr auto local_adder = adder_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)
        = new_current_length + local_adder.draw(gen);
 
    GET_PROPERTY_FROM(idx2, child_buffer_arr, Self::particle_var::nu1) = nu_1_o;
    GET_PROPERTY_FROM(idx2, child_buffer_arr, Self::particle_var::nu2) = nu_2_o;
    // 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)
        = new_current_length + local_adder.draw(gen);
    random_pool.free_state(gen);
 
    Uptake<UptakeDefault<typename Self::FloatType>, 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