Problem in compiling Athena with code modifications agn_triggering

[epanini]

Error: ```
/home/elyon/athenapk/src/pgen/cluster/agn_triggering.cpp(428): error: no instance of function template "cluster::AGNTriggering::ReduceColdMass" matches the argument list and object (the object has type qualifiers that prevent a match)
argument types are: (parthenon::Real, parthenon::Real, parthenon::MeshDataparthenon::Real *, const parthenon::Real, const AdiabaticGLMMHDEOS)
object type is: const cluster::AGNTriggering
agn_triggering.ReduceColdMass(cold_mass, total_mass,md, dt,
^

/home/elyon/athenapk/src/pgen/cluster/agn_triggering.cpp(532): error: expression must be a modifiable lvalue
agn_triggering.inflow_cold_ = (cold_mass - hydro_pkg->Param("agn_triggering_prev_cold_mass")) / tm.dt;
^

/home/elyon/athenapk/src/pgen/cluster/agn_triggering.cpp(533): error: expression must be a modifiable lvalue
agn_triggering.inflow_tot_ = (total_mass - hydro_pkg->Param("agn_triggering_prev_total_mass")) / tm.dt;
^

4 errors detected in the compilation of "/home/elyon/athenapk/src/pgen/cluster/agn_triggering.cpp".
make[2]: *** [src/CMakeFiles/athenaPK.dir/build.make:342: src/CMakeFiles/athenaPK.dir/pgen/cluster/agn_triggering.cpp.o] Error 2

```//! \file agn_triggering.cpp
//  \brief  Class for computing AGN triggering from Bondi-like and cold gas accretion

#include <cmath>
#include <fstream> // for ofstream
#include <limits>

// Parthenon headers
#include <coordinates/uniform_cartesian.hpp>
#include <globals.hpp>
#include <interface/params.hpp>
#include <interface/state_descriptor.hpp>
#include <mesh/domain.hpp>
#include <parameter_input.hpp>
#include <parthenon/package.hpp>

// Athena headers
#include "../../eos/adiabatic_glmmhd.hpp"
#include "../../eos/adiabatic_hydro.hpp"
#include "../../main.hpp"
#include "../../units.hpp"
#include "agn_feedback.hpp"
#include "agn_triggering.hpp"
#include "cluster_utils.hpp"

namespace cluster {
using namespace parthenon;

AGNTriggeringMode ParseAGNTriggeringMode(const std::string &mode_str) {

  if (mode_str == "COLD_GAS") {
    return AGNTriggeringMode::COLD_GAS;
  } else if (mode_str == "BOOSTED_BONDI") {
    return AGNTriggeringMode::BOOSTED_BONDI;
  } else if (mode_str == "BOOTH_SCHAYE") {
    return AGNTriggeringMode::BOOTH_SCHAYE;
  } else if (mode_str == "NONE") {
    return AGNTriggeringMode::NONE;
  } else {
    std::stringstream msg;
    msg << "### FATAL ERROR in function [ParseAGNTriggeringMode]" << std::endl
        << "Unrecognized AGNTriggeringMode: \"" << mode_str << "\"" << std::endl;
    PARTHENON_FAIL(msg);
  }
  return AGNTriggeringMode::NONE;
}

AGNTriggering::AGNTriggering(parthenon::ParameterInput *pin,
                             parthenon::StateDescriptor *hydro_pkg,
                             const std::string &block)
    : gamma_(pin->GetReal("hydro", "gamma")),
      triggering_mode_(
          ParseAGNTriggeringMode(pin->GetOrAddString(block, "triggering_mode", "NONE"))),
      accretion_radius_(pin->GetOrAddReal(block, "accretion_radius", 0)),
      cold_temp_thresh_(pin->GetOrAddReal(block, "cold_temp_thresh", 0)),
      cold_t_acc_(pin->GetOrAddReal(block, "cold_t_acc", 0)),
      bondi_alpha_(pin->GetOrAddReal(block, "bondi_alpha", 0)),
      bondi_M_smbh_(pin->GetOrAddReal("problem/cluster/gravity", "m_smbh", 0)),
      bondi_n0_(pin->GetOrAddReal(block, "bondi_n0", 0)),
      bondi_beta_(pin->GetOrAddReal(block, "bondi_beta", 0)),
      accretion_cfl_(pin->GetOrAddReal(block, "accretion_cfl", 1e-1)),
      remove_accreted_mass_(pin->GetOrAddBoolean(block, "removed_accreted_mass", true)),
      write_to_file_(pin->GetOrAddBoolean(block, "write_to_file", false)),

      triggering_filename_(
          pin->GetOrAddString(block, "triggering_filename", "agn_triggering.dat")) {

 
  const auto units = hydro_pkg->Param<Units>("units");
  const parthenon::Real He_mass_fraction = pin->GetReal("hydro", "He_mass_fraction");
  const parthenon::Real H_mass_fraction = 1.0 - He_mass_fraction;
  const parthenon::Real mu =
      1 / (He_mass_fraction * 3. / 4. + (1 - He_mass_fraction) * 2);

  mean_molecular_mass_ = mu * units.atomic_mass_unit();

  if (triggering_mode_ == AGNTriggeringMode::NONE) {
    hydro_pkg->AddParam<bool>("agn_triggering_reduce_accretion_rate", false);
  } else {
    hydro_pkg->AddParam<bool>("agn_triggering_reduce_accretion_rate", true);
  }
  switch (triggering_mode_) {
  case AGNTriggeringMode::COLD_GAS: {
    hydro_pkg->AddParam<Real>("agn_triggering_cold_mass", 0, Params::Mutability::Restart);
    
    hydro_pkg->AddParam<Real>("agn_triggering_total_mass", 0,
                              Params::Mutability::Restart);
    break;
  }
  case AGNTriggeringMode::BOOSTED_BONDI:
  case AGNTriggeringMode::BOOTH_SCHAYE: {
    hydro_pkg->AddParam<Real>("agn_triggering_total_mass", 0,
                              Params::Mutability::Restart);
    hydro_pkg->AddParam<Real>("agn_triggering_mass_weighted_density", 0,
                              Params::Mutability::Restart);
    hydro_pkg->AddParam<Real>("agn_triggering_mass_weighted_velocity", 0,
                              Params::Mutability::Restart);
    hydro_pkg->AddParam<Real>("agn_triggering_mass_weighted_cs", 0,
                              Params::Mutability::Restart);
    break;
  }
  case AGNTriggeringMode::NONE: {
    break;
  }
  }

  // Set up writing the triggering to file, used for debugging and regression
  // testing. Note that this is written every timestep, which is more
  // frequently than history outputs. It is also not reduced across ranks and
  // so is only valid without MPI
  if (write_to_file_ && parthenon::Globals::my_rank == 0) {
    // Clear the triggering_file
    std::ofstream triggering_file;
    triggering_file.open(triggering_filename_, std::ofstream::out | std::ofstream::trunc);
    triggering_file.close();
  }

  hydro_pkg->AddParam<AGNTriggering>("agn_triggering", *this);
}

// Compute Cold gas accretion rate within the accretion radius for cold gas triggering
// and simultaneously remove cold gas (updating conserveds and primitives)
template <typename EOS>
void AGNTriggering::ReduceColdMass(parthenon::Real &cold_mass,
                                   parthenon::Real &total_mass,
                                   parthenon::MeshData<parthenon::Real> *md,
                                   const parthenon::Real dt, const EOS eos)  {
  using parthenon::IndexDomain;
  using parthenon::IndexRange;
  using parthenon::Real;
  Real md_cold_mass = 0;
  Real md_total_mass = 0;

  auto hydro_pkg = md->GetBlockData(0)->GetBlockPointer()->packages.Get("Hydro");

  // Grab some necessary variables
  const auto &prim_pack = md->PackVariables(std::vector<std::string>{"prim"});
  const auto &cons_pack = md->PackVariables(std::vector<std::string>{"cons"});
  IndexRange ib = md->GetBlockData(0)->GetBoundsI(IndexDomain::entire);
  IndexRange jb = md->GetBlockData(0)->GetBoundsJ(IndexDomain::entire);
  IndexRange kb = md->GetBlockData(0)->GetBoundsK(IndexDomain::entire);
  IndexRange int_ib = md->GetBlockData(0)->GetBoundsI(IndexDomain::interior);
  IndexRange int_jb = md->GetBlockData(0)->GetBoundsJ(IndexDomain::interior);
  IndexRange int_kb = md->GetBlockData(0)->GetBoundsK(IndexDomain::interior);
  const auto nhydro = hydro_pkg->Param<int>("nhydro");
  const auto nscalars = hydro_pkg->Param<int>("nscalars");

  const Real accretion_radius2 = pow(accretion_radius_, 2);

  // Reduce just the cold gas
  const auto units = hydro_pkg->Param<Units>("units");
  const Real mean_molecular_mass_by_kb = mean_molecular_mass_ / units.k_boltzmann();

  const Real cold_temp_thresh = cold_temp_thresh_;
  const Real cold_t_acc = cold_t_acc_;

  const bool remove_accreted_mass = remove_accreted_mass_;

  

  parthenon::par_reduce(
      parthenon::loop_pattern_mdrange_tag, "AGNTriggering::ReduceColdGas",
      parthenon::DevExecSpace(), 0, cons_pack.GetDim(5) - 1, kb.s, kb.e, jb.s, jb.e, ib.s,
      ib.e,
      KOKKOS_LAMBDA(const int &b, const int &k, const int &j, const int &i,
                    Real &team_cold_mass, Real &team_total_mass) {
        auto &cons = cons_pack(b);
        auto &prim = prim_pack(b);
        const auto &coords = cons_pack.GetCoords(b);

        const parthenon::Real r2 =
            pow(coords.Xc<1>(i), 2) + pow(coords.Xc<2>(j), 2) + pow(coords.Xc<3>(k), 2);
        if (r2 < accretion_radius2) {
          const Real cell_total_mass = prim(IDN, k, j, i) * coords.CellVolume(k, j, i);
          team_total_mass += cell_total_mass;
          const Real temp =
              mean_molecular_mass_by_kb * prim(IPR, k, j, i) / prim(IDN, k, j, i);
          
          if (temp <= cold_temp_thresh) {

            const Real cell_cold_mass = prim(IDN, k, j, i) * coords.CellVolume(k, j, i);

            if (k >= int_kb.s && k <= int_kb.e && j >= int_jb.s && j <= int_jb.e &&
                i >= int_ib.s && i <= int_ib.e) {
              // Only reduce the cold gas that exists on the interior grid
              team_cold_mass += cell_cold_mass;
            }

            const Real cell_delta_rho = -prim(IDN, k, j, i) / cold_t_acc * dt;

            if (remove_accreted_mass) {
              AddDensityToConsAtFixedVelTemp(cell_delta_rho, cons, prim, eos.GetGamma(),
                                             k, j, i);
              // Update the Primitives
              eos.ConsToPrim(cons, prim, nhydro, nscalars, k, j, i);
            }
          }
        }
      },
     
      Kokkos::Sum<Real>(md_cold_mass), Kokkos::Sum<Real>(md_total_mass)); 
  cold_mass += md_cold_mass;
  total_mass += md_total_mass;
  
}

// Compute Mass-weighted total density, velocity, and sound speed and total mass
// for Bondi accretion
void AGNTriggering::ReduceBondiTriggeringQuantities(
    parthenon::Real &total_mass, parthenon::Real &mass_weighted_density,
    parthenon::Real &mass_weighted_velocity, parthenon::Real &mass_weighted_cs,
    parthenon::MeshData<parthenon::Real> *md) const {
  using parthenon::IndexDomain;
  using parthenon::IndexRange;
  using parthenon::Real;

  auto hydro_pkg = md->GetBlockData(0)->GetBlockPointer()->packages.Get("Hydro");

  // Grab some necessary variables
  const auto &prim_pack = md->PackVariables(std::vector<std::string>{"prim"});
  IndexRange ib = md->GetBlockData(0)->GetBoundsI(IndexDomain::interior);
  IndexRange jb = md->GetBlockData(0)->GetBoundsJ(IndexDomain::interior);
  IndexRange kb = md->GetBlockData(0)->GetBoundsK(IndexDomain::interior);

  const Real accretion_radius2 = pow(accretion_radius_, 2);

  // Reduce Mass-weighted total density, velocity, and sound speed and total
  // mass (in that order). Will need to divide the three latter quantities by
  // total mass in order to get their mass-weighted averaged values
  Real total_mass_red, mass_weighted_density_red, mass_weighted_velocity_red,
      mass_weighted_cs_red;

  const parthenon::Real gamma = gamma_;

  Kokkos::parallel_reduce(
      "AGNTriggering::ReduceBondi",
      Kokkos::MDRangePolicy<Kokkos::Rank<4>>(
          DevExecSpace(), {0, kb.s, jb.s, ib.s},
          {prim_pack.GetDim(5), kb.e + 1, jb.e + 1, ib.e + 1},
          {1, 1, 1, ib.e + 1 - ib.s}),
      KOKKOS_LAMBDA(const int &b, const int &k, const int &j, const int &i,
                    Real &ltotal_mass_red, Real &lmass_weighted_density_red,
                    Real &lmass_weighted_velocity_red, Real &lmass_weighted_cs_red) {
        if (k >= kb.s && k <= kb.e && j >= jb.s && j <= jb.e && i >= ib.s && i <= ib.e) {                
          auto &prim = prim_pack(b);
          const auto &coords = prim_pack.GetCoords(b);
          const parthenon::Real r2 =
            pow(coords.Xc<1>(i), 2) + pow(coords.Xc<2>(j), 2) + pow(coords.Xc<3>(k), 2);
          if (r2 < accretion_radius2) {
            const Real cell_mass = prim(IDN, k, j, i) * coords.CellVolume(k, j, i);

            const Real cell_mass_weighted_density = cell_mass * prim(IDN, k, j, i);
            const Real cell_mass_weighted_velocity =
              cell_mass * sqrt(pow(prim(IV1, k, j, i), 2) + pow(prim(IV2, k, j, i), 2) +
                               pow(prim(IV3, k, j, i), 2));
            const Real cell_mass_weighted_cs =
              cell_mass * sqrt(gamma * prim(IPR, k, j, i) / prim(IDN, k, j, i));

            ltotal_mass_red += cell_mass;
            lmass_weighted_density_red += cell_mass_weighted_density;
            lmass_weighted_velocity_red += cell_mass_weighted_velocity;
            lmass_weighted_cs_red += cell_mass_weighted_cs;
          }
        }  
      },
      total_mass_red, mass_weighted_density_red, mass_weighted_velocity_red,
      mass_weighted_cs_red);
  // Save the reduction results to triggering_quantities
  total_mass += total_mass_red;
  mass_weighted_density += mass_weighted_density_red;
  mass_weighted_velocity += mass_weighted_velocity_red;
  mass_weighted_cs += mass_weighted_cs_red;
}

// Remove gas consistent with Bondi accretion
/// i.e. proportional to the accretion rate, weighted by the local gas mass
template <typename EOS>
void AGNTriggering::RemoveBondiAccretedGas(parthenon::MeshData<parthenon::Real> *md,
                                           const parthenon::Real dt,
                                           const EOS eos) const {
  using parthenon::IndexDomain;
  using parthenon::IndexRange;
  using parthenon::Real;

  auto hydro_pkg = md->GetBlockData(0)->GetBlockPointer()->packages.Get("Hydro");
 
  // Grab some necessary variables
  // FIXME(forrestglines) When reductions are called, is `prim` up to date?
  const auto &prim_pack = md->PackVariables(std::vector<std::string>{"prim"});
  const auto &cons_pack = md->PackVariables(std::vector<std::string>{"cons"});
  IndexRange ib = md->GetBlockData(0)->GetBoundsI(IndexDomain::entire);
  IndexRange jb = md->GetBlockData(0)->GetBoundsJ(IndexDomain::entire);
  IndexRange kb = md->GetBlockData(0)->GetBoundsK(IndexDomain::entire);
  const auto nhydro = hydro_pkg->Param<int>("nhydro");
  const auto nscalars = hydro_pkg->Param<int>("nscalars");

  const Real accretion_radius2 = pow(accretion_radius_, 2);

  const Real accretion_rate = GetAccretionRate(hydro_pkg.get());
  const Real total_mass = hydro_pkg->Param<Real>("agn_triggering_total_mass");

  parthenon::par_for(
      parthenon::loop_pattern_mdrange_tag, "AGNTriggering::RemoveBondiAccretedGas",
      parthenon::DevExecSpace(), 0, cons_pack.GetDim(5) - 1, kb.s, kb.e, jb.s, jb.e, ib.s,
      ib.e, KOKKOS_LAMBDA(const int &b, const int &k, const int &j, const int &i) {
        auto &cons = cons_pack(b);
        auto &prim = prim_pack(b);
        const auto &coords = cons_pack.GetCoords(b);

        const parthenon::Real r2 =
            pow(coords.Xc<1>(i), 2) + pow(coords.Xc<2>(j), 2) + pow(coords.Xc<3>(k), 2);
        if (r2 < accretion_radius2) {

          const Real cell_delta_rho =
              -prim(IDN, k, j, i) / total_mass * accretion_rate * dt;

          AddDensityToConsAtFixedVelTemp(cell_delta_rho, cons, prim, eos.GetGamma(), k, j,
                                         i);

          // Update the Primitives
          eos.ConsToPrim(cons, prim, nhydro, nscalars, k, j, i);
        }
      });
}

// Compute and return the current AGN accretion rate from already globally
// reduced quantities
parthenon::Real
AGNTriggering::GetAccretionRate(parthenon::StateDescriptor *hydro_pkg) const {
  switch (triggering_mode_) {
  case AGNTriggeringMode::COLD_GAS: {
    // Test the Cold-Gas-like triggering methods
    const parthenon::Real cold_mass = hydro_pkg->Param<Real>("agn_triggering_cold_mass");

    return cold_mass / cold_t_acc_;
  }
  case AGNTriggeringMode::BOOSTED_BONDI:
  case AGNTriggeringMode::BOOTH_SCHAYE: {
    // Test the Bondi-like triggering methods
    auto units = hydro_pkg->Param<Units>("units");
    const Real total_mass = hydro_pkg->Param<Real>("agn_triggering_total_mass");
    const Real mean_mass_weighted_density =
        hydro_pkg->Param<Real>("agn_triggering_mass_weighted_density") / total_mass;
    const Real mean_mass_weighted_velocity =
        hydro_pkg->Param<Real>("agn_triggering_mass_weighted_velocity") / total_mass;
    const Real mean_mass_weighted_cs =
        hydro_pkg->Param<Real>("agn_triggering_mass_weighted_cs") / total_mass;

    Real alpha = 0;
    if (triggering_mode_ == AGNTriggeringMode::BOOSTED_BONDI) {
      alpha = bondi_alpha_;
    } else if (triggering_mode_ == AGNTriggeringMode::BOOTH_SCHAYE) {
      const Real mean_mass_weighted_n = mean_mass_weighted_density / mean_molecular_mass_;
      alpha = (mean_mass_weighted_n <= bondi_n0_)
                  ? 1
                  : pow(mean_mass_weighted_n / bondi_n0_, bondi_beta_);
    } else {
      PARTHENON_FAIL("### FATAL ERROR in AGNTriggering::AccretionRate unsupported "
                     "Bondi-like triggering");
    }
    const Real mdot =
        alpha * 2 * M_PI * pow(units.gravitational_constant(), 2) *
        pow(bondi_M_smbh_, 2) * mean_mass_weighted_density /
        (pow(pow(mean_mass_weighted_velocity, 2) + pow(mean_mass_weighted_cs, 2),
             3. / 2.));

    return mdot;
  }
  case AGNTriggeringMode::NONE: {
    return 0;
  }
  }
  //return 0;
}

parthenon::TaskStatus
AGNTriggeringResetTriggering(parthenon::StateDescriptor *hydro_pkg) {
  auto &agn_triggering = hydro_pkg->Param<AGNTriggering>("agn_triggering");
  hydro_pkg->UpdateParam<Real>("agn_triggering_prev_cold_mass", hydro_pkg->Param<Real>("agn_triggering_cold_mass"));
  hydro_pkg->UpdateParam<Real>("agn_triggering_prev_total_mass", hydro_pkg->Param<Real>("agn_triggering_total_mass"));
  switch (agn_triggering.triggering_mode_) {
  case AGNTriggeringMode::COLD_GAS: {
    hydro_pkg->UpdateParam<Real>("agn_triggering_cold_mass", 0);
    hydro_pkg->UpdateParam<Real>("agn_triggering_total_mass", 0);
    
    
    break;
  }
  case AGNTriggeringMode::BOOSTED_BONDI:
  case AGNTriggeringMode::BOOTH_SCHAYE: {
    hydro_pkg->UpdateParam<Real>("agn_triggering_total_mass", 0);
    hydro_pkg->UpdateParam<Real>("agn_triggering_mass_weighted_density", 0);
    hydro_pkg->UpdateParam<Real>("agn_triggering_mass_weighted_velocity", 0);
    hydro_pkg->UpdateParam<Real>("agn_triggering_mass_weighted_cs", 0);
    break;
  }
  case AGNTriggeringMode::NONE: {
    break;
  }
  }
  return TaskStatus::complete;
}

parthenon::TaskStatus
AGNTriggeringReduceTriggering(parthenon::MeshData<parthenon::Real> *md,
                              const parthenon::Real dt) {

  auto hydro_pkg = md->GetBlockData(0)->GetBlockPointer()->packages.Get("Hydro");
  auto &agn_triggering = hydro_pkg->Param<AGNTriggering>("agn_triggering");
  const parthenon::Real pre_accretion_cold_mass = hydro_pkg->Param<Real>("agn_triggering_cold_mass");
  const parthenon::Real pre_accretion_total_mass = hydro_pkg->Param<Real>("agn_triggering_total_mass");
  switch (agn_triggering.triggering_mode_) {
  case AGNTriggeringMode::COLD_GAS: {
    Real cold_mass = hydro_pkg->Param<parthenon::Real>("agn_triggering_cold_mass");
    Real total_mass = hydro_pkg->Param<parthenon::Real>("agn_triggering_total_mass");
   

    auto fluid = hydro_pkg->Param<Fluid>("fluid");
    if (fluid == Fluid::euler) {
      agn_triggering.ReduceColdMass(cold_mass, total_mass,md, dt,
                                    hydro_pkg->Param<AdiabaticHydroEOS>("eos"));
    } else if (fluid == Fluid::glmmhd) {
      agn_triggering.ReduceColdMass(cold_mass, total_mass,md, dt,
                                    hydro_pkg->Param<AdiabaticGLMMHDEOS>("eos"));
    } else {
      PARTHENON_FAIL("AGNTriggeringReduceTriggeringQuantities: Unknown EOS");
    }

    hydro_pkg->UpdateParam("agn_triggering_cold_mass", cold_mass);
    hydro_pkg->UpdateParam("agn_triggering_total_mass", total_mass);
    break;
  }
  case AGNTriggeringMode::BOOSTED_BONDI:
  case AGNTriggeringMode::BOOTH_SCHAYE: {
    Real total_mass = hydro_pkg->Param<parthenon::Real>("agn_triggering_total_mass");
    Real mass_weighted_density =
        hydro_pkg->Param<parthenon::Real>("agn_triggering_mass_weighted_density");
    Real mass_weighted_velocity =
        hydro_pkg->Param<parthenon::Real>("agn_triggering_mass_weighted_velocity");
    Real mass_weighted_cs =
        hydro_pkg->Param<parthenon::Real>("agn_triggering_mass_weighted_cs");

    agn_triggering.ReduceBondiTriggeringQuantities(
        total_mass, mass_weighted_density, mass_weighted_velocity, mass_weighted_cs, md);

    hydro_pkg->UpdateParam("agn_triggering_total_mass", total_mass);
    hydro_pkg->UpdateParam("agn_triggering_mass_weighted_density", mass_weighted_density);
    hydro_pkg->UpdateParam("agn_triggering_mass_weighted_velocity",
                           mass_weighted_velocity);
    hydro_pkg->UpdateParam("agn_triggering_mass_weighted_cs", mass_weighted_cs);
    break;
  }
  case AGNTriggeringMode::NONE: {
    break;
  }
  }
  if (agn_triggering.triggering_mode_ == AGNTriggeringMode::COLD_GAS) {
    auto &agn_triggering = hydro_pkg->Param<AGNTriggering>("agn_triggering"); // Make it non-const
    const parthenon::Real cold_mass = hydro_pkg->Param<Real>("agn_triggering_cold_mass");
    const parthenon::Real total_mass = hydro_pkg->Param<Real>("agn_triggering_total_mass");

    hydro_pkg->UpdateParam<Real>("agn_triggering_prev_cold_mass", cold_mass); //Move from AGNTriggeringFinalizeTriggering
    hydro_pkg->UpdateParam<Real>("agn_triggering_prev_total_mass", total_mass);
  }
  hydro_pkg->UpdateParam<AGNTriggering>("agn_triggering", agn_triggering);
  return TaskStatus::complete;
}

parthenon::TaskStatus
AGNTriggeringMPIReduceTriggering(parthenon::StateDescriptor *hydro_pkg) {
#ifdef MPI_PARALLEL
  auto &agn_triggering = hydro_pkg->Param<AGNTriggering>("agn_triggering");
  switch (agn_triggering.triggering_mode_) {
  case AGNTriggeringMode::COLD_GAS: {

    Real accretion_rate = hydro_pkg->Param<Real>("agn_triggering_cold_mass");
    PARTHENON_MPI_CHECK(MPI_Allreduce(MPI_IN_PLACE, &accretion_rate, 1,
                                      MPI_PARTHENON_REAL, MPI_SUM, MPI_COMM_WORLD));
    hydro_pkg->UpdateParam("agn_triggering_cold_mass", accretion_rate);

    Real total_mass = hydro_pkg->Param<Real>("agn_triggering_total_mass");
    PARTHENON_MPI_CHECK(MPI_Allreduce(MPI_IN_PLACE, &total_mass, 1,
                                          MPI_PARTHENON_REAL, MPI_SUM, MPI_COMM_WORLD));
    hydro_pkg->UpdateParam("agn_triggering_total_mass", total_mass);
    break;
  }
  case AGNTriggeringMode::BOOSTED_BONDI:
  case AGNTriggeringMode::BOOTH_SCHAYE: {
    Real triggering_quantities[] = {
        hydro_pkg->Param<Real>("agn_triggering_total_mass"),
        hydro_pkg->Param<Real>("agn_triggering_mass_weighted_density"),
        hydro_pkg->Param<Real>("agn_triggering_mass_weighted_velocity"),
        hydro_pkg->Param<Real>("agn_triggering_mass_weighted_cs"),
    };

    PARTHENON_MPI_CHECK(MPI_Allreduce(MPI_IN_PLACE, &triggering_quantities, 4,
                                      MPI_PARTHENON_REAL, MPI_SUM, MPI_COMM_WORLD));

    hydro_pkg->UpdateParam("agn_triggering_total_mass", triggering_quantities[0]);
    hydro_pkg->UpdateParam("agn_triggering_mass_weighted_density",
                           triggering_quantities[1]);
    hydro_pkg->UpdateParam("agn_triggering_mass_weighted_velocity",
                           triggering_quantities[2]);
    hydro_pkg->UpdateParam("agn_triggering_mass_weighted_cs", triggering_quantities[3]);
    break;
  }
  case AGNTriggeringMode::NONE: {
    break;
  }
  }
#endif
  return TaskStatus::complete;
}

parthenon::TaskStatus
AGNTriggeringFinalizeTriggering(parthenon::MeshData<parthenon::Real> *md,
                                const parthenon::SimTime &tm) {
  auto hydro_pkg = md->GetBlockData(0)->GetBlockPointer()->packages.Get("Hydro");
  auto &agn_triggering = hydro_pkg->Param<AGNTriggering>("agn_triggering");
  parthenon::Real cold_mass = 0.0; // Declare outside the if block
  parthenon::Real total_mass = 0.0; // Declare outside the if block
  if (agn_triggering.triggering_mode_ == AGNTriggeringMode::COLD_GAS) {
    cold_mass = hydro_pkg->Param<Real>("agn_triggering_cold_mass"); // Assign here
    total_mass = hydro_pkg->Param<Real>("agn_triggering_total_mass"); 


    agn_triggering.inflow_cold_ = (cold_mass - hydro_pkg->Param<Real>("agn_triggering_prev_cold_mass")) / tm.dt; //Now this is the only place to calculate inflow rates
    agn_triggering.inflow_tot_ = (total_mass - hydro_pkg->Param<Real>("agn_triggering_prev_total_mass")) / tm.dt; //Now this is the only place to calculate inflow rates

  }
  hydro_pkg->UpdateParam<AGNTriggering>("agn_triggering", agn_triggering); 

  hydro_pkg->UpdateParam<Real>("agn_triggering_prev_cold_mass", cold_mass);
  hydro_pkg->UpdateParam<Real>("agn_triggering_prev_total_mass", total_mass);

  // Append quantities to file if applicable
  if (agn_triggering.write_to_file_ && parthenon::Globals::my_rank == 0) {
    std::ofstream triggering_file;
    triggering_file.open(agn_triggering.triggering_filename_, std::ofstream::app);

    triggering_file << tm.time << " | " << tm.dt << " | "
                    << agn_triggering.GetAccretionRate(hydro_pkg.get()) << " | "
                    << cold_mass << " | " 
                    << total_mass  << " | " 
                    << agn_triggering.inflow_cold_ << " | " 
                    << agn_triggering.inflow_tot_ << " ";

    switch (agn_triggering.triggering_mode_) {
    case AGNTriggeringMode::COLD_GAS: {

      triggering_file << hydro_pkg->Param<Real>("agn_triggering_cold_mass");
      break;
    }
    case AGNTriggeringMode::BOOSTED_BONDI:
    case AGNTriggeringMode::BOOTH_SCHAYE: {
      const auto &total_mass = hydro_pkg->Param<Real>("agn_triggering_total_mass");
      const auto &avg_density =
          hydro_pkg->Param<Real>("agn_triggering_mass_weighted_density") / total_mass;
      const auto &avg_velocity =
          hydro_pkg->Param<Real>("agn_triggering_mass_weighted_velocity") / total_mass;
      const auto &avg_cs =
          hydro_pkg->Param<Real>("agn_triggering_mass_weighted_cs") / total_mass;
      triggering_file << total_mass << " " << avg_density << " " << avg_velocity << " "
                      << avg_cs;
      break;
    }
    case AGNTriggeringMode::NONE: {
      break;
    }
    }

    triggering_file << std::endl;
    triggering_file.close();
  }

  // Remove accreted gas if using a Bondi-like mode
  if (agn_triggering.remove_accreted_mass_) {
    switch (agn_triggering.triggering_mode_) {
    case AGNTriggeringMode::BOOSTED_BONDI:
    case AGNTriggeringMode::BOOTH_SCHAYE: {
      auto fluid = hydro_pkg->Param<Fluid>("fluid");
      if (fluid == Fluid::euler) {
        agn_triggering.RemoveBondiAccretedGas(md, tm.dt,
                                              hydro_pkg->Param<AdiabaticHydroEOS>("eos"));
      } else if (fluid == Fluid::glmmhd) {
        agn_triggering.RemoveBondiAccretedGas(
            md, tm.dt, hydro_pkg->Param<AdiabaticGLMMHDEOS>("eos"));
      } else {
        PARTHENON_FAIL("AGNTriggeringFinalizeTriggering: Unknown EOS");
      }
      break;
    }
    case AGNTriggeringMode::COLD_GAS: // Already removed during reduction
    case AGNTriggeringMode::NONE: {
      break;
    }
    }
  }

  return TaskStatus::complete;
}

// Limit timestep to a factor of the cold gas accretion time for Cold Gas
// triggered cooling, or a factor of the time to accrete the total mass for
// Bondi-like accretion
parthenon::Real
AGNTriggering::EstimateTimeStep(parthenon::MeshData<parthenon::Real> *md) const {
  auto hydro_pkg = md->GetBlockData(0)->GetBlockPointer()->packages.Get("Hydro");

  switch (triggering_mode_) {
  case AGNTriggeringMode::COLD_GAS: {
    return accretion_cfl_ * cold_t_acc_;
  }
  case AGNTriggeringMode::BOOSTED_BONDI:
  case AGNTriggeringMode::BOOTH_SCHAYE: {
    // Test the Bondi-like triggering methods
    const Real total_mass = hydro_pkg->Param<Real>("agn_triggering_total_mass");
    if (total_mass == 0) {
      // TODO(forrestglines)During the first timestep, the total mass and
      // accretion rate has not yet been reduced. However, since accreted mass is
      // removed during that reduction, the timestep is needed to execute that
      // reduction. As a compromise, we ignore the timestep constraint during the
      // first timestep, assuming that accretion is slow initially
      return std::numeric_limits<Real>::max();
    }
    const Real mdot = GetAccretionRate(hydro_pkg.get());
    return accretion_cfl_ * total_mass / mdot;
  }
  case AGNTriggeringMode::NONE: {
    return std::numeric_limits<Real>::max();
  }
  }
  //return std::numeric_limits<Real>::max();
}

} // namespace cluster

#define CLUSTER_AGN_TRIGGERING_HPP_
//========================================================================================
// AthenaPK - a performance portable block structured AMR astrophysical MHD code.
// Copyright (c) 2021-2023, Athena-Parthenon Collaboration. All rights reserved.
// Licensed under the 3-clause BSD License, see LICENSE file for details
//========================================================================================
//! \file agn_triggering.hpp
//  \brief  Class for computing AGN triggering from Bondi-like and cold gas accretion

// parthenon headers
#include <basic_types.hpp>
#include <interface/state_descriptor.hpp>
#include <mesh/domain.hpp>
#include <mesh/mesh.hpp>
#include <parameter_input.hpp>
#include <parthenon/package.hpp>
#include <string> 
// AthenaPK headers
#include "../../units.hpp"
#include "jet_coords.hpp"
#include "utils/error_checking.hpp"

namespace cluster {

enum class AGNTriggeringMode { NONE, COLD_GAS, BOOSTED_BONDI, BOOTH_SCHAYE };

AGNTriggeringMode ParseAGNTriggeringMode(const std::string &mode_str);

/************************************************************
 * AGN Triggering class : For computing the mass triggering the AGN
 ************************************************************/
class AGNTriggering {
 private:
  const parthenon::Real gamma_;
  parthenon::Real mean_molecular_mass_;
  
 public:
  const AGNTriggeringMode triggering_mode_;
 
  parthenon::Real inflow_cold_=0.0;         // Cold mass inflow rate
  parthenon::Real inflow_tot_=0.0;          // Total gas mass inflow rate

  const parthenon::Real accretion_radius_;

  // Parameters for cold-gas triggering
  const parthenon::Real cold_temp_thresh_;
  const parthenon::Real cold_t_acc_;

  // Parameters necessary for Boosted Bondi accretion
  const parthenon::Real bondi_alpha_; //(Only for boosted Bondi)
  const parthenon::Real bondi_M_smbh_;

  // Additional parameters for Booth Schaye
  const parthenon::Real bondi_n0_;
  const parthenon::Real bondi_beta_;

  // Used in timestep estimation
  const parthenon::Real accretion_cfl_;

  // Useful for debugging
  const bool remove_accreted_mass_;

  // Write triggering quantities (accretion rate or Bondi quantities) to file at
  // every timestep.  Intended for testing quantities at every timestep, since
  // this file does not work across restarts, and since these quantities are
  // included in Parthenon phdf outputs.
  const bool write_to_file_;
  const std::string triggering_filename_;

  AGNTriggering(parthenon::ParameterInput *pin, parthenon::StateDescriptor *hydro_pkg,
                const std::string &block = "problem/cluster/agn_triggering");

  // Compute Cold gas accretion rate within the accretion radius for cold gas triggering
  // and simultaneously remove cold gas (updating conserveds and primitives)
  template <typename EOS>
  void ReduceColdMass(parthenon::Real &cold_mass,parthenon::Real &total_mass,
                      parthenon::MeshData<parthenon::Real> *md, const parthenon::Real dt,
                      const EOS eos) ;

  // Compute Mass-weighted total density, velocity, and sound speed and total mass
  // for Bondi accretion
  void ReduceBondiTriggeringQuantities(parthenon::Real &total_mass,
                                       parthenon::Real &mass_weighted_density,
                                       parthenon::Real &mass_weighted_velocity,
                                       parthenon::Real &mass_weighted_cs,
                                       parthenon::MeshData<parthenon::Real> *md) const;

  // Remove gas consistent with Bondi accretion
  /// i.e. proportional to the accretion rate, weighted by the local gas mass
  template <typename EOS>
  void RemoveBondiAccretedGas(parthenon::MeshData<parthenon::Real> *md,
                              const parthenon::Real dt, const EOS eos) const;

  // Compute and return the current AGN accretion rate from already globally
  // reduced quantities
  parthenon::Real GetAccretionRate(parthenon::StateDescriptor *hydro_pkg) const;

  friend parthenon::TaskStatus
  AGNTriggeringResetTriggering(parthenon::StateDescriptor *hydro_pkg);

  friend parthenon::TaskStatus
  AGNTriggeringReduceTriggering(parthenon::MeshData<parthenon::Real> *md,
                                const parthenon::Real dt);

  friend parthenon::TaskStatus
  AGNTriggeringMPIReduceTriggering(parthenon::StateDescriptor *hydro_pkg);

  friend parthenon::TaskStatus
  AGNTriggeringFinalizeTriggering(parthenon::MeshData<parthenon::Real> *md,
                                  const parthenon::SimTime &tm);

  // Limit timestep to a factor of the cold gas accretion time for Cold Gas
  // triggered cooling, or a factor of the time to accrete the total mass for
  // Bondi-like accretion
  parthenon::Real EstimateTimeStep(parthenon::MeshData<parthenon::Real> *md) const;
};

parthenon::TaskStatus AGNTriggeringResetTriggering(parthenon::StateDescriptor *hydro_pkg);

parthenon::TaskStatus
AGNTriggeringReduceTriggering(parthenon::MeshData<parthenon::Real> *md,
                              const parthenon::Real dt);

parthenon::TaskStatus
AGNTriggeringMPIReduceTriggering(parthenon::StateDescriptor *hydro_pkg);

parthenon::TaskStatus
AGNTriggeringFinalizeTriggering(parthenon::MeshData<parthenon::Real> *md,
                                const parthenon::SimTime &tm);

} // namespace cluster

#endif // CLUSTER_AGN_TRIGGERING_HPP_

[pgrete]

Hi @epanini
thanks for moving the discussion to github.
To make it even more easier, I'd be great if you could open a PR from your repository/branch to this repository (or to your own main branch).
This would tremendously simplify reviewing code changes as they're automatically highlighted, see, e.g., https://github.com/parthenon-hpc-lab/athenapk/pull/127/files and also allows to reply in the code directly.

Regarding the issue, I still think it's because objects in Params are non-mutable by default.
Therefore, we have separate variable (that are mutable) to save (and restore) changes, e.g., check how the "agn_triggering_cold_mass" is being added to Params and modified through UpdateParams.

[epanini]

ok thank you for the suggestions, I will open a repository with the code in order to directly solve the issue.

…

On Tue, 17 Dec 2024 at 14:55, Philipp Grete ***@***.***> wrote: Hi @epanini <https://github.com/epanini> thanks for moving the discussion to github. To make it even more easier, I'd be great if you could open a PR from your repository/branch to this repository (or to your own main branch). This would tremendously simplify reviewing code changes as they're automatically highlighted, see, e.g., https://github.com/parthenon-hpc-lab/athenapk/pull/127/files and also allows to reply in the code directly. Regarding the issue, I still think it's because objects in Params are non-mutable by default. Therefore, we have separate variable (that are mutable) to save (and restore) changes, e.g., check how the "agn_triggering_cold_mass" is being added to Params and modified through UpdateParams. — Reply to this email directly, view it on GitHub <#131 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BNYBFSYPN24FT3EM5UCLC7D2GAULJAVCNFSM6AAAAABTWT64U6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNBYGUZDINJZGI> . You are receiving this because you were mentioned.Message ID: ***@***.***>