two_meta_nb.hpp

#ifndef __TWOMETA_MODEL_NB_HPP__
#define __TWOMETA_MODEL_NB_HPP__
 
#include <common/traits.hpp>
#include <mc/macros.hpp>
#include <mc/prng/prng_extension.hpp>
#include <mc/traits.hpp>
#include <models/uptake_dyn.hpp>
#include <models/utils.hpp>
#include <string_view>
 
namespace Models
{
 
  struct TwoMetaNb
  {
    using uniform_weight = std::true_type; // Using type alias
    using Self = TwoMetaNb;
    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
      phi_pts,
      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 = "two_mode_nb";
    using SelfParticle = MC::ParticlesModel<Self::n_var, Self::FloatType>;
 
    // Constants BEGIN
    MODEL_CONSTANT FloatType MolarMassG
        = Models::MolarMass::GramPerMole::glucose<FloatType>;
    MODEL_CONSTANT FloatType MolarMassO2
        = Models::MolarMass::GramPerMole::dioxygen<FloatType>; // g/mol
 
    MODEL_CONSTANT FloatType l_max_m = 5e-6;   // m
    MODEL_CONSTANT FloatType l_c_m = 3e-6;     // m
    MODEL_CONSTANT FloatType d_m = 0.3e-6;     // m
    MODEL_CONSTANT FloatType l_min_m = 0.9e-6; // m
 
    MODEL_CONSTANT FloatType dl_max_ms
        = 10 * 2e-10; // m/s  https://doi.org/10.7554/eLife.67495;
 
    MODEL_CONSTANT FloatType lin_density
        = c_linear_density(static_cast<FloatType>(1000), d_m);
 
    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 tau_1 = 1000.; // s
    MODEL_CONSTANT FloatType tau_2 = 1000.; // s
 
    MODEL_CONSTANT FloatType phi_max = (dl_max_ms * lin_density) * y_sx_1;
    MODEL_CONSTANT FloatType phi_o2_max
        = 10 * phi_max / MolarMassG * y_os_molar * MolarMassO2; // kgS/s
    MODEL_CONSTANT FloatType nu_max_kg_s = dl_max_ms * lin_density;
 
    MODEL_CONSTANT FloatType k_o
        = 0.0001; // g/L: Anane et. al 2017 (Biochem. Eng. J) (g/g)
    MODEL_CONSTANT FloatType k = 1e-2;
    MODEL_CONSTANT FloatType k_perm = 1e-3;
    MODEL_CONSTANT FloatType beta = 7;
    MODEL_CONSTANT FloatType tau_ap_1 = 300;
    MODEL_CONSTANT FloatType tau_ap_2 = 200;
    MODEL_CONSTANT FloatType tau_ap_3 = 1000;
 
    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 FloatType adder_mean = 1.5e-6; // m
    MODEL_CONSTANT auto adder_dist
        = MC::Distributions::TruncatedNormal<FloatType>(
            adder_mean,
            adder_mean / 2.,
            adder_mean / 20.,
            adder_mean * 10); // use in out_str_l3
    // Constants END
 
    static MC::ContribIndexBounds get_bounds();
 
    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_p1", "a_p2",   "a_p3", "phi_o2", "phi_g",    "phi_pts" };
    }
 
    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_1),
               INDEX_FROM_ENUM(Uptakeparticle_var::ap_2),
               INDEX_FROM_ENUM(Uptakeparticle_var::ap_3),
               INDEX_FROM_ENUM(particle_var::contrib_phi_o2),
               INDEX_FROM_ENUM(particle_var::contrib_phi_s),
               INDEX_FROM_ENUM(particle_var::phi_pts) };
    }
 
    static KOKKOS_INLINE_FUNCTION void
    preinit()
    {
      Kokkos::printf("[Model]: PRENINIT:BEGIN\r\n");
      //      Kokkos::printf("[Model]: phi_max:%.12f\r\n", phi_pts_max * 1e12);
      //      Kokkos::printf("[Model]: PRENINIT:END\r\n");
    }
 
    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);
  };
 
  CHECK_MODEL(TwoMetaNb)
 
  KOKKOS_INLINE_FUNCTION void
  TwoMetaNb::init([[maybe_unused]] const MC::pool_type& random_pool,
                  std::size_t idx,
                  const SelfParticle& arr)
  {
 
    // auto& v = init_uptake_cst;
    constexpr auto local_ac = adder_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<FloatType>(
            mu_nu_dist, mu_nu_dist / 7., 0., static_cast<double>(nu_max_kg_s));
 
    auto gen = random_pool.get_state();
    auto l = length_dist.draw(gen);
 
    GET_PROPERTY(Self::particle_var::length) = l;
    GET_PROPERTY(Self::particle_var::l_cp) = l + local_ac.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
  TwoMetaNb::update([[maybe_unused]] const MC::pool_type& random_pool,
                    FloatType d_t,
                    std::size_t idx,
                    const SelfParticle& arr,
                    const MC::LocalConcentration& concentrations)
  {
    const auto phi_s
        = Uptake<Self>::uptake_step(phi_max,
                                    d_t,
                                    idx,
                                    arr,
                                    concentrations,
                                    &GET_PROPERTY(Self::particle_var::phi_pts));
 
    const auto o = Kokkos::max(static_cast<FloatType>(concentrations(1)), 0.F);
 
    const auto phi_o2 = (phi_o2_max)*o / (o + k_o); // gO2/s
 
    const auto nu_1_star
        = y_sx_1 * MolarMassG
          * Kokkos::min(phi_s / MolarMassG,
                        phi_o2 / MolarMassO2 / y_os_molar); // gX/s
 
    const auto s_1_star = (1.F / y_sx_1 * nu_1_star);
 
    const auto phi_s_residual_1_star = Kokkos::max(phi_s - s_1_star, 0.F);
    KOKKOS_ASSERT(phi_s_residual_1_star >= 0.F);
 
    const auto nu_2_star = y_sx_2 * phi_s_residual_1_star; // gX/s
 
    auto& nu_eff_1 = GET_PROPERTY(Self::particle_var::nu_eff_1);
    auto& nu_eff_2 = GET_PROPERTY(Self::particle_var::nu_eff_2);
    auto& nu_1 = GET_PROPERTY(Self::particle_var::nu1);
    auto& nu_2 = GET_PROPERTY(Self::particle_var::nu2);
 
    nu_eff_1 = Kokkos::min(nu_1_star, nu_1); // gX/s
 
    const auto s_1 = (1.F / y_sx_1 * nu_eff_1);
    const auto phi_s_residual_1 = Kokkos::max(phi_s - s_1, 0.F);
 
    nu_eff_2 = Kokkos::min(y_sx_2 * phi_s_residual_1,
                           nu_2); // gX/s
 
    const auto sum_nu = (nu_eff_1 + nu_eff_2);
 
    const auto s_growth = s_1 + (1 / y_sx_2 * nu_eff_2);
 
    const auto s_overflow = phi_s - s_growth;
 
    KOKKOS_ASSERT(nu_eff_1 >= 0.F);
    KOKKOS_ASSERT(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.F
          * ((1.F / y_sx_1 / MolarMassG * y_os_molar * MolarMassO2 * nu_eff_1)
             + 0.F * nu_eff_2);
 
    GET_PROPERTY(Self::particle_var::contrib_phi_ac)
        = nu_eff_2 / y_sx_2 * y_sa
          + (s_overflow > 0. ? y_sa * (s_overflow) : 0);
 
    // ODE
    nu_1 += d_t * ((nu_1_star - nu_1) / tau_1);
 
    nu_2 += d_t * ((nu_2_star - nu_2) / tau_2);
 
    GET_PROPERTY(Self::particle_var::length) += 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
  TwoMetaNb::division(const MC::pool_type& random_pool,
                      std::size_t idx,
                      std::size_t idx2,
                      const SelfParticle& arr,
                      const SelfParticle& child_buffer_arr)
  {
    constexpr FloatType half = 0.5;
    constexpr auto local_ac = 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;
 
    const auto nu_1_o
        = GET_PROPERTY_FROM(idx, arr, Self::particle_var::nu_eff_1);
    const 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_ac.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 * half, 0.F, 1.F);
    }
 
    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 * half, 0.F, 1.F);
    }
 
    GET_PROPERTY_FROM(idx2, child_buffer_arr, Self::particle_var::l_cp)
        = new_current_length + local_ac.draw(gen);
    random_pool.free_state(gen);
 
    Uptake<Self>::division(random_pool, idx, idx2, arr, child_buffer_arr);
  }
 
  inline MC::ContribIndexBounds
  TwoMetaNb::get_bounds()
  {
    const int begin = INDEX_FROM_ENUM(Self::particle_var::contrib_phi_s);
    const int end = INDEX_FROM_ENUM(Self::particle_var::contrib_phi_ac);
    assert(begin < end);
    return { .begin = begin, .end = end };
  }
  // KOKKOS_INLINE_FUNCTION void
  // TwoMetaNb::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<TwoMetaNb>, "ee");
 
} // namespace Models
 
#endif //__TWOMETA_MODEL_NB_HPP__