Chimie.cpp

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#include <Chimie.h>
#include <Probleme_base.h>
#include <Motcle.h>
#include <Param.h>
#include <Parser_U.h>
#include <Domaine_VF.h>
#include <Discretisation_base.h>
#include <Convection_Diffusion_Concentration.h>
#include <dlsinterf.h>
#include <Constituant.h>
 
// XD reactions listobj nul BRACE reaction COMMA list of reactions
 
Implemente_instanciable(Chimie,"Chimie",Objet_U_With_Params);
// XD chimie objet_u chimie BRACE Keyword to describe the chmical reactions
 
 
Sortie& Chimie::printOn(Sortie& os) const
{
  os<<(*this).le_nom()<<finl;
  os<<reactions_<<finl;
  return os;
}
 
void Chimie::set_param(Param& param) const
{
  param.ajouter("reactions",&reactions_,Param::REQUIRED);                           // XD attr reactions reactions reactions REQ list of reactions
  param.ajouter("modele_micro_melange",&modele_micro_melange_);                     // XD attr modele_micro_melange entier modele_micro_melange OPT modele_micro_melange (0 by default)
  param.ajouter("constante_modele_micro_melange",&constante_modele_micro_melange_); // XD attr constante_modele_micro_melange floattant constante_modele_micro_melange OPT constante of modele (1 by default)
  param.ajouter("espece_en_competition_micro_melange",&espece_en_competition_micro_melange_);  // XD attr espece_en_competition_micro_melange chaine espece_en_competition_micro_melange OPT espece in competition in reactions
}
 
double Chimie::calculer_pas_de_temps() const
{
  double dt=1e30;
  double dt_reaction;
  for (int i=0; i<reactions_.size(); i++) // loop over all reactions
    {
      dt_reaction=reactions_[i].calculer_pas_de_temps();
      if(i==0) Cout<<"Pour le(s) reaction(s), dt_max = ";
      Cout<<dt_reaction<<" ";
      if (i==(reactions_.size()-1)) Cout<<finl;
      dt=std::min(dt,dt_reaction);
    }
  // double dt_n=pb_->schema_temps().pas_de_temps();
  // Butterworth filter:
  //        alpha=1    -> no filter
  //        alpha->0   -> heavily filtered
  // double alpha_Butterworth=1.;
  // return (dt_n*(1.-alpha_Butterworth)+alpha_Butterworth*dt);
  return dt;
}
 
 
 
void  Chimie::completer(const Probleme_base& pb)
{
  // if no reaction, do nothing
  if (reactions_.size()==0)
    return;
  pb_=pb;
  // 1) determine the number of FM
  int nb_fm=0;
  int nb_grains=0;
  int nb_concentration=0;
  //  Motcles alias;
  ArrOfDouble masses_molaires;
  for (int n=0; n<pb.nombre_d_equations(); n ++)
    {
 
      if (sub_type(Convection_Diffusion_Concentration,pb.equation(n)))
        nb_concentration++;
 
    }
 
  // 2) store aliases and molar masses
  masses_molaires.resize_array(nb_grains+nb_fm+nb_concentration);
  alias.dimensionner(nb_grains+nb_fm+nb_concentration);
  nb_grains_=nb_grains;
  int nb=0;
  for (int n=0; n<pb.nombre_d_equations(); n ++)
    {
      if (sub_type(Convection_Diffusion_Concentration,pb.equation(n)))
        {
          const Convection_Diffusion_Concentration& eq= ref_cast(Convection_Diffusion_Concentration,pb.equation(n));
          masses_molaires[nb]=eq.masse_molaire();
          alias[nb]=eq.inconnue().le_nom();
          OBS_PTR(Champ_Inc_base) inco;
          inco = eq.inconnue();
          liste_C_.add(inco);
          nb++;
        }
    }
  assert(liste_ai_.size()==nb_grains_);
  // check uniqueness of aliases
  marqueur_espece_en_competition_micro_melange_=-1;
  {
    LIST(Nom) test;
    for (int n=0; n<alias.size(); n++)
      {
        int deja=test.contient(alias[n]);
        if (!deja)
          test.add(alias[n]);
        else
          {
            Cerr<<alias[n] <<" defini plusieurs fois !!!!!"<<finl;
            //Cerr<<test<< " "<<alias<<finl;
            exit();
          }
        if (espece_en_competition_micro_melange_!=Nom())
          {
            if (espece_en_competition_micro_melange_==alias[n])
              marqueur_espece_en_competition_micro_melange_=n;
          }
      }
    assert(test.size()==nb_fm+nb_grains_+nb_concentration);
  }
  if (espece_en_competition_micro_melange_!=Nom())
    {
      if (marqueur_espece_en_competition_micro_melange_==-1)
        {
          Cerr<<" espece_en_competition_micro_melange not found: "<< espece_en_competition_micro_melange_<<finl;
          exit();
        }
      else
        Cerr<<" marqueur_espece_en_competition_micro_melange "<<marqueur_espece_en_competition_micro_melange_<<finl;
    }
  if(min_array(masses_molaires)<0)
    {
      Cerr<< "problem with masses_molaires "<<masses_molaires<<finl;
      exit();
    }
  if (liste_Y_.size()>0)
    {
      Puissance_volumique_=(liste_Y_[0]->valeurs()); // array sizing...
      Puissance_volumique_=0.;
    }
  else
    {
      assert(liste_C_.size()!=0);
    }
  //alias_=alias;
  for (int i=0; i<reactions_.size(); i++)
    {
      reactions_[i].completer(alias,masses_molaires);
    }
}
 
void Chimie::discretiser(const Probleme_base& pb)
{
  for (int i=0; i<reactions_.size(); i++)
    {
      Nom test("omega_");
      test+=Nom(i);
      reactions_[i].discretiser_omega(pb,test);
    }
}
 
int Chimie::preparer_calcul()
{
  return 1;
}
 
 
 
void  Chimie::mettre_a_jour(double temps)
{
  if (reactions_.size()==0) // no reaction
    return;
 
  double dt=pb_->schema_temps().pas_de_temps();
 
  if (liste_C_.size())
    {
      // We assume there is no temperature for now...
      int old=0;
      int nbr=reactions_.size();
      if (old)
        {
          for (int i=0; i<nbr; i++)
            {
              Reaction& reaction=reactions_[i];
              int nb_sous_pas_de_temps_reaction=reaction.nb_sous_pas_de_temps_reaction();
 
              const double dt_chimie=dt/nb_sous_pas_de_temps_reaction;
              for (int n=0; n<nb_sous_pas_de_temps_reaction; n++)
                reaction.reagir(liste_C_,dt_chimie);
            }
 
          for (int i=0; i<liste_C_.size(); i++)
            liste_C_[i]->valeurs().echange_espace_virtuel();
          return;
        }
      const int vef = (int)pb_->discretisation().is_vef();
      Domaine_VF& zvf = ref_cast(Domaine_VF,liste_C_[0]->equation().domaine_dis());
 
      const IntTab& face_voisins = zvf.face_voisins();
      const ArrOfDouble& volume=zvf.volumes();
      int newd=1;
      if (newd)
        {
          int nbrtot=0;
          ArrOfInt marq_contre(2*nbr);
          for (int i=0; i<nbr; i++)
            {
              Reaction& reaction=reactions_[i];
              marq_contre[nbrtot++]=i+1;
              if (reaction.contre_reaction_>0)
                marq_contre[nbrtot++]=-(i+1);
 
              if ((reaction.beta_!=0)||(reaction.Ea_!=0)||((reaction.c_r_Ea_!=0)&&(reaction.contre_reaction_>0)))
                {
                  Cerr<<"Reaction:  Data incompatible with the fact that there is no temperature"<<finl;
                  Cerr<<reaction<<finl;
                  exit();
                }
            }
          marq_contre.resize_array(nbrtot);
 
          int nbc=liste_C_.size();
 
          F77NAME(INITTAILLECOMMON)(&nbrtot,&nbc);
          ArrOfDouble pstochio(nbc);
          ArrOfInt pactivite(nbc);
          F77NAME(SETMARQUEUR)(&marqueur_espece_en_competition_micro_melange_);
          for (int i=0; i<nbrtot; i++)
            {
              int ir=marq_contre[i];
              int ir2=ir;
              if (ir<0) ir2=-ir2;
              ir2-=1;
              Reaction& reaction=reactions_[ir2];
              pstochio=reaction.coeff_stoechio_;
              pactivite=0;
 
              double cw=reaction.constante_taux_reaction_;
              if (ir<0)
                {
                  pstochio*=-1;
                  assert(reaction.contre_reaction_>0);
                  cw/=reaction.contre_reaction_;
                }
              for (int ic=0; ic<nbc; ic++)
                {
                  if (pstochio[ic]>0)
                    pactivite[ic]=(int)reaction.coeff_activite_[ic];
                }
              int ii=i+1;
              int avec_contre_reaction=(reaction.contre_reaction_>0);
              F77NAME(INITREACTIONCOMMON)(&(ii), pstochio.addr(), pactivite.addr(),&avec_contre_reaction) ;
              F77NAME(SETCWREACTION)(&(ii), &cw);
 
            }
          // F77NAME(PRINT_COMMON)();
          // abort();
          int mf=21;
          int lrw;
          int liw;
          if (mf==21)
            {
              liw=20+nbc;
              lrw=22+9*nbc+nbc*nbc;
            }
          else
            throw;
          assert(mf==21);
 
 
          ArrOfDouble rwork(lrw);
          ArrOfInt iwork(liw);
 
 
          DoubleTab tau_mel;
          if (modele_micro_melange_>0)
            {
 
              const DoubleTab& visc_turb=liste_C_[0]->equation().probleme().get_champ("viscosite_turbulente").valeurs();
              tau_mel=visc_turb;
              const DoubleTab& D_moleculaire = ref_cast(Convection_Diffusion_Concentration,liste_C_[0]->equation()).constituant().diffusivite_constituant().valeurs();
              double D_mol=0.;
              if (D_moleculaire.dimension(0) == 1)
                D_mol = D_moleculaire(0, 0);
              else
                {
                  Cerr << "D_mol not implemented for non-uniform field" << finl;
                  exit();
                }
              double invsct=1./0.9;
              for (int element=0; element<visc_turb.dimension(0); element++)
                {
                  double delta=exp(log(volume[element])/double(dimension));
                  //  Cerr<<" iii "<<delta<<" "<<D_mol<<finl;
                  tau_mel(element)=constante_modele_micro_melange_*delta*delta/(D_mol+visc_turb(element)*invsct);
                }
              tau_mel.echange_espace_virtuel();
            }
          int nb_elem=liste_C_[0]->valeurs().size();
          ArrOfDouble C(nbc);
 
          for (int elem=0; elem<nb_elem; elem++)
            {
 
              double tau_melange=-1;
              if (modele_micro_melange_>0)
                {
                  if (vef==0)
                    tau_melange=tau_mel(elem);
                  else
                    {
                      if (face_voisins(elem,1)!=-1)
                        tau_melange = 0.5*(tau_mel(face_voisins(elem,0))+tau_mel(face_voisins(elem,1)));
                      else
                        tau_melange = (tau_mel(face_voisins(elem,0)));
                    }
                }
              // tau_melange <0 not taken into account
              // retrieval of initial values
              for (int i=0; i<nbc; i++)
                {
                  C[i]=liste_C_[i]->valeurs()(elem);
 
                }
              for (int i=0; i<nbc; i++)
                {
                  if (C[i]<0)
                    {
                      if (C[i]<-1e-5)
                        {
                          Cerr<<" clipping C_"<<i<<" in cell "<<elem<<" in the chemistry !!!!!! "<<C[i]<<finl;
                          exit();
                        }
                      C[i]=0;
                    }
                }
              int init=1;
              if (init)
                {
 
                }
              double t=0,tout=dt;
              int itol=1;
              double rtol=0;
              double atol=1e-10;
              F77NAME(DLSODECHIMIES)(&nbc, C.addr(),&t, &tout,&tau_melange, &itol, &rtol, &atol, rwork.addr(), &lrw, iwork.addr(), &liw);
              // update unknowns
              for (int i=0; i<liste_C_.size(); i++)
                liste_C_[i]->valeurs()(elem)=C[i];
            }
          for (int i=0; i<liste_C_.size(); i++)
            liste_C_[i]->valeurs().echange_espace_virtuel();
          return;
        }
      // compute nb_sous_pas_temps_max
      int nb_sous_pas_de_temps_reaction_max=1;
      int nbr_directe=0;
 
      ArrOfInt marq_directe(nbr);
      for (int i=0; i<nbr; i++)
        {
          Reaction& reaction=reactions_[i];
          int nb_sous_pas_de_temps_reaction=reaction.nb_sous_pas_de_temps_reaction();
          if (nb_sous_pas_de_temps_reaction>nb_sous_pas_de_temps_reaction_max)
            nb_sous_pas_de_temps_reaction_max=nb_sous_pas_de_temps_reaction;
          if (reaction.contre_reaction_<=0)
            marq_directe[nbr_directe++]=i;
 
          if ((reaction.beta_!=0)||(reaction.Ea_!=0)||((reaction.c_r_Ea_!=0)&&(reaction.contre_reaction_>0)))
            {
              Cerr<<"Reaction:  Data incompatible with the fact that there is no temperature"<<finl;
              Cerr<<reaction<<finl;
              exit();
            }
        }
      const double dt_chimie=dt/nb_sous_pas_de_temps_reaction_max;
 
      int nbc=liste_C_.size();
 
 
      //      double R_gaz_parfait=8.3143;
 
      ArrOfDouble C(nbc),C_tmp(nbc), proportion_eq(nbr_directe);
 
      int nb_elem=liste_C_[0]->valeurs().size();
      for (int elem=0; elem<nb_elem; elem++)
        {
 
 
          // retrieval of initial values
          for (int i=0; i<nbc; i++)
            {
              C[i]=liste_C_[i]->valeurs()(elem);
            }
          for (int n=0; n<nb_sous_pas_de_temps_reaction_max; n++)
            {
              // clamp negative values if any
              for (int i=0; i<nbc; i++)
                if (C[i]<0)
                  {
                    if (C[i]<-1e-5)
                      {
                        Cerr<<" clipping C_"<<i<<" in cell "<<elem<<" in the chemistry !!!!!! "<<C[i]<<finl;
                        exit();
                      }
                    C[i]=0;
                  }
              // compute initial proportions for non-equilibrium reactions
 
              for (int i=0; i<nbr_directe; i++)
                {
                  Reaction& reaction=reactions_[marq_directe[i]];
                  assert(reaction.contre_reaction_<=0);
 
                  double proportion_directe;
                  reaction.calcul_proportion_implicite(C_tmp,C,dt_chimie,1e-7,proportion_directe);
                  if (0)
                    {
                      double proportion_directe2;
                      reaction.calcul_proportion_implicite(C_tmp,C,dt_chimie,1e9,proportion_directe2);
                      if (proportion_directe==proportion_directe2)
 
                        {
                          exit();
                        }
                    }
                  // use proportion_directe to avoid the security limitation
                  proportion_eq[i]=proportion_directe;
 
 
                }
              // for each constituent, check whether limiting is needed...
              double securite=1-1e-6;
              for (int c=0; c<nbc; c++)
                {
                  double St=0;
                  for (int i=0; i<nbr_directe; i++)
                    {
                      Reaction& reaction=reactions_[marq_directe[i]];
                      assert(reaction.contre_reaction_<=0);
                      if (reaction.coeff_Y_[c]>0.)
                        St+=proportion_eq[i]*reaction.coeff_stoechio_[c];
                    }
 
                  double rapport=St/(securite);
                  //  Cerr<< c<<" ici0b "<< rapport <<" st "<<St<<" "<<C(c)<<finl;
 
                  if (rapport>C[c])
                    {
                      // risk of consuming too much... limiting.
                      Cerr<< c<<" limite ici0 "<< rapport <<" st "<<St<<" "<<C[c]<<" "<<C[c]/rapport<<finl;
                      // exit();
                      for (int i=0; i<nbr_directe; i++)
                        {
                          Reaction& reaction=reactions_[marq_directe[i]];
                          assert(reaction.contre_reaction_<=0);
 
                          if (reaction.coeff_Y_[c]>0.)
                            proportion_eq[i]*=C[c]/rapport;
 
                        }
                    }
                }
              // apply direct reactions C(c)-=St;
              for (int c=0; c<nbc; c++)
                {
                  double St=0;
                  for (int i=0; i<nbr_directe; i++)
                    {
                      Reaction& reaction=reactions_[marq_directe[i]];
                      assert(reaction.contre_reaction_<=0);
                      if (reaction.coeff_Y_[c]!=0.)
                        St+=proportion_eq[i]*reaction.coeff_stoechio_[c];
                    }
 
                  // Cerr<<C(c)<<" "<< c<< " la  st "<<St<<" ";
                  //assert(St<=(C(c)*securite));
                  C[c]-=St;
                  assert(C[c]>=0);
                  // Cerr<< C(c)<<finl;
 
                }
              // now process equilibrium reactions one by one
 
              securite=0.5;
              for (int reac=0; reac<nbr; reac++)
                {
                  Reaction& reaction=reactions_[reac];
 
                  if (reaction.contre_reaction_>0)
                    {
                      double proportion_directe;
                      double proportion=reaction.calcul_proportion_implicite(C_tmp, C,dt_chimie,1e-7,proportion_directe);
                      for (int i=0; i<nbc; i++)
                        if (reaction.coeff_Y_[i]!=0.) // it is a reactant or a product
                          {
                            C[i]=C[i]-proportion*reaction.coeff_stoechio_[i];
                          }
                    }
                }
            }
          // reaction.reagir(liste_C_,dt_chimie);
          for (int i=0; i<liste_C_.size(); i++)
            liste_C_[i]->valeurs()(elem)=C[i];
 
        }
 
      for (int i=0; i<liste_C_.size(); i++)
        liste_C_[i]->valeurs().echange_espace_virtuel();
 
      return;
    }
  Cerr<<"Chimie available only with concentrations"<<finl;
  exit();
 
}
 
bool Chimie::has_champ(const Motcle& nom, OBS_PTR(Champ_base)& ref_champ) const
{
  for (int i = 0; i < reactions_.size(); i++)
    {
      Nom test("omega_");
      test += Nom(i);
      if (nom == test)
        {
          ref_champ = reactions_[i].get_omega();
          return true;
        }
    }
 
  return false; /* nothing found */
}
 
bool Chimie::has_champ(const Motcle& nom) const
{
  for (int i = 0; i < reactions_.size(); i++)
    {
      Nom test("omega_");
      test += Nom(i);
      if (nom == test)
        return true;
    }
 
  return false; /* nothing found */
}
 
const Champ_base& Chimie::get_champ(const Motcle& nom) const
{
  for (int i = 0; i < reactions_.size(); i++)
    {
      Nom test("omega_");
      test += Nom(i);
      if (nom == test)
        return reactions_[i].get_omega();
    }
 
  throw std::runtime_error(std::string("Field ") + nom.getString() + std::string(" not found !"));
}
 
void Chimie::get_noms_champs_postraitables(Noms& nom,Option opt) const
{
  if (opt==DESCRIPTION)
    Cerr<<" Chimie :";
  int nb_reac=reactions_.size();
  for (int i=0; i<nb_reac; i++)
    {
      Nom test("omega_");
      test+=Nom(i);
      if (opt==DESCRIPTION)
        Cerr<< test;
      else
        nom.add(test);
    }
  if (opt==DESCRIPTION)
    Cerr<<finl;
}
 
int Chimie::sauvegarder(Sortie& fich) const
{
  return 1;
}
 
int Chimie::reprendre(Entree& is)
{
  return 1;
}