baryons.h

#pragma once
#include <string_view>
 
#include "../species/base_species.h"
#include "background.h"
#include "perturbations.h"
#include "species_build_context.h"
 
class BaryonsSpecies : public BaseSpecies {
 public:
  static constexpr std::string_view kTypeName = "baryons";
 
  explicit BaryonsSpecies(const background& pba)
      : BaseSpecies("Baryons", EnergyType::Matter), pba_(pba) {}
 
  // ── PerturbLayout ──────────────────────────────────────────────────────────
 
  struct PerturbLayout : BaseSpecies::PerturbLayout {
    int idx_delta = -1;  
    int idx_theta = -1;  
  };
 
  std::unique_ptr<BaseSpecies::PerturbLayout> CreatePerturbLayout() const override {
    return std::make_unique<PerturbLayout>();
  }
 
  static std::vector<Named> CreateAll(const SpeciesBuildContext& ctx);
 
  double GetOmega0() const override {
    return pba_.Omega0_b;
  }
 
  void RegisterBackgroundIndices(int& index_bg) override {
    index_bg_rho_ = index_bg++;
  }
 
  void ComputeBackground(double a, const double* /*pvecback_B*/, double* pvecback) override {
    pvecback[index_bg_rho_] = pba_.Omega0_b * pba_.H0 * pba_.H0 / (a * a * a);
  }
 
  double Rho(const double* pvecback) const override {
    return pvecback[index_bg_rho_];
  }
  double P(const double* /*pvecback*/) const override {
    return 0.;
  }
 
  void WriteBackgroundColumnTitles(BackgroundColumnWriter& w) const override {
    w.Add("(.)rho_b", 0.);
  }
  void WriteBackgroundData(const double* pvecback, BackgroundColumnWriter& w) const override {
    w.Add("(.)rho_b", pvecback[index_bg_rho_]);
  }
 
  // ── Perturbation index registration ────────────────────────────────────────
 
  void RegisterTransferSourceIndices(int& index_tp, const SourceRequestContext& ctx) override;
 
  void RegisterPerturbationIndices(BaseSpecies::PerturbLayout& layout,
                                   perturb_vector* pv,
                                   const precision* ppr,
                                   int& index_pt,
                                   const perturb_workspace* ppw,
                                   int gauge) override;
 
  void RegisterVectorPerturbationIndices(BaseSpecies::PerturbLayout& layout,
                                         perturb_vector* pv,
                                         const precision* ppr,
                                         int& index_pt,
                                         const perturb_workspace* ppw,
                                         int gauge) override;
 
  // ── PerturbDerivs ──────────────────────────────────────────────────────────
 
  void PerturbDerivs(const BaseSpecies::PerturbLayout& layout,
                     double tau,
                     const double* y,
                     double* dy,
                     const perturb_parameters_and_workspace& ppaw) const override;
 
  // ── Source filling and initial conditions ──────────────────────────────────
 
  void FillSources(const BaseSpecies::PerturbLayout& layout,
                   const double* y,
                   const double* dy,
                   PerturbSourceContext& ctx) const override;
 
  void ApplyInitialConditions(const BaseSpecies::PerturbLayout& layout,
                              double* y,
                              const PerturbIcContext& ctx) override;
 
  void PerturbSynchronousToNewtonian(const BaseSpecies::PerturbLayout& layout,
                                     double* y,
                                     const PerturbIcContext& ctx) override;
 
  void CopyPerturbationsAcrossSwitch(const BaseSpecies::PerturbLayout& old_layout,
                                     const BaseSpecies::PerturbLayout& new_layout,
                                     const double* old_y,
                                     double* new_y,
                                     const PerturbSwitchContext& ctx) const override;
 
  void WriteOutputColumns(
      PerturbColumnWriter& writer,
      const PerturbationsModule& mod,
      file_format fmt,
      TransferColumnSection section = TransferColumnSection::all) const override;
  void PrintVariables(PerturbColumnWriter& writer,
                      double tau,
                      const double* y,
                      const PerturbationsModule& mod,
                      const perturb_workspace* ppw) const override;
 
  // ── Stress-energy observables ───────────────────────────────────────────────
 
  StressEnergyContribution StressEnergy(const BaseSpecies::PerturbLayout& layout,
                                        const perturb_vector* pv,
                                        const double* y,
                                        const double* pvecback,
                                        const perturb_workspace* ppw) const override;
 
  void SetThermodynamicsModule(const ThermodynamicsModule* thm) override {
    thm_ = thm;
  }
  void SetPerturbs(const perturbs* ppt) override {
    ppt_ = ppt;
  }
 
 private:
  const background& pba_;
  const ThermodynamicsModule* thm_ = nullptr;
  const perturbs* ppt_             = nullptr;
 
  int index_tp_delta_ = -1;  // #309 transfer-source slot
  int index_tp_theta_ = -1;
};