mole_eval_balance.cpp

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/* This file is part of Cloudy and is copyright (C)1978-2013 by Gary J. Ferland and
 * others.  For conditions of distribution and use see copyright notice in license.txt */
/*CO_step fills in matrix for heavy elements molecular routines */
#include "cddefines.h"
#include "mole.h"
#include "mole_priv.h"
#include "save.h"
#include "dense.h"
#include "atmdat.h"
#include "trace.h"
/* Nick Abel between July and October of 2003 assisted Dr. Ferland in improving the heavy element 
 * molecular network in Cloudy. Before this routine would predict negative abundances if 
 * the fraction of carbon in the form of molecules came close to 100%. A reorganizing of 
 * the reaction network detected several bugs.  Treatment of "coupled reactions",
 * in which both densities in the reaction rate were being predicted by Cloudy, were also 
 * added.  Due to these improvements, Cloudy can now perform calculations
 * where 100% of the carbon is in the form of CO without predicting negative abundances
 *
 * Additional changes were made in November of 2003 so that our reaction 
 * network would include all reactions from the TH85 paper.  This involved 
 * adding silicon to the chemical network.  Also the reaction rates were
 * labeled to make identification with the reaction easier and the matrix 
 * elements of atomic C, O, and Si are now done in a loop, which makes 
 * the addition of future chemical species (like N or S) easy.
 * */
/* Robin Williams in August 2006 onwards reorganized the coding to cut down repetitions.  
 * This isolated several further bugs, and allows a sigificant number of lines of
 * code to be eliminated.  The balance of S2/S2+ amd ClO/ClO+ seems highly sensitive
 * (with small log scale results varying significantly if the order of arithmetic
 * operations is changed) -- I suspect this may imply a bug somewhere.
 * */
/*lint -e778 constant expression evaluatess to 0 in operation '-' */
/*=================================================================*/
 
STATIC bool lgNucleiConserved(const multi_arr<double,2> &c);
 
void mole_eval_balance(long int num_total, double *b, bool lgJac, multi_arr<double,2> &c)
{
        long int i, j;
        mole_reaction *rate;
        double rate_tot, rate_deriv[MAXREACTANTS], rk;
        molecule *sp;
 
        DEBUG_ENTRY("mole_eval_balance()");
        /* zero out array used for formation rates */
        for( i=0; i < num_total; i++ )
        {
                b[i] = 0.;
        }
        if (lgJac)
                c.zero();
 
        if (trace.lgTrace)
        {
                for(long mol=0;mol<mole_global.num_calc;mol++) 
                {
                        fprintf(ioQQQ," TrChemSp %20.13g %s\n",mole.species[mol].den,
                                          mole_global.list[mol]->label.c_str());
                }
                for(mole_reaction_i p=mole_priv::reactab.begin(); 
                         p != mole_priv::reactab.end(); ++p) 
                {
                        rate = &(*p->second);
                        rk = mole.reaction_rks[ rate->index ];
                        fprintf(ioQQQ," TrChem %20.13g %s\n",rk,rate->label.c_str());
                }
        }
 
 
        for(mole_reaction_i p=mole_priv::reactab.begin(); 
                        p != mole_priv::reactab.end(); ++p) 
        {
                rate = &(*p->second);
                rk = mole.reaction_rks[ rate->index ];
 
                rate_tot = rk;
                for(i=0;i<rate->nreactants;i++)
                {
                        rate_tot *= mole.species[ rate->reactants[i]->index ].den;
                }               
                
                if (trace.lgTrace)
                {
                        fprintf(ioQQQ," TrChemTot %20.13g %20.13g %s\n",rate_tot,rk,rate->label.c_str());                       
                        for(i=0;i<rate->nreactants;i++)
                        {
                                fprintf(ioQQQ, " %20.13g", mole.species[ rate->reactants[i]->index ].den);
                        }
                        fprintf(ioQQQ,"\n");
                }
                for(i=0;i<rate->nreactants;i++)
                {       
                        sp = rate->reactants[i];
                        if (rate->rvector[i] == NULL)
                        {
                                b[sp->index] -= rate_tot;
                        }
                }
                
                for(i=0;i<rate->nproducts;i++)
                {
                        sp = rate->products[i];
                        if (rate->pvector[i] == NULL)
                        {
                                b[sp->index] += rate_tot;
                        }
                }
                
                if (lgJac)
                {
                        for(i=0;i<rate->nreactants;i++)
                        {
                                rate_deriv[i] = rk;
                                for(j=0;j<rate->nreactants;j++)
                                {
                                        if(i!=j)
                                        {
                                                rate_deriv[i] *= mole.species[ rate->reactants[j]->index ].den;
                                        }
                                }
                        }
                        for(j=0;j<rate->nreactants;j++)
                        {
                                sp = rate->reactants[j];
                                const double rated = rate_deriv[j];
                                for(i=0;i<rate->nreactants;i++)
                                {
                                        if (rate->rvector[i] == NULL)
                                                c[sp->index][rate->reactants[i]->index] -= rated;
                                }
                                for(i=0;i<rate->nproducts;i++)
                                {
                                        if (rate->pvector[i] == NULL)
                                                c[sp->index][rate->products[i]->index] += rated;
                                }
                        }
                }
        }
 
        if (lgJac)
        {
                ASSERT( lgNucleiConserved(c) );
        }
 
        //mole_dominant_rates(findspecies("H+"),ioQQQ);
        return;
}
 
void mole_eval_sources(long int num_total)
{
        long int i, j, nelem, ion, ion2;
        mole_reaction *rate;
        double rate_tot, rate_deriv[MAXREACTANTS], rk;
        molecule *sp;
 
        DEBUG_ENTRY("mole_eval_sources()");
        /* zero out array used for formation rates */
        for( i=0; i < num_total; i++ )
        {
                mole.species[i].src = mole.species[i].snk = 0.;
        }
 
        for( nelem=0; nelem< LIMELM; ++nelem )
        {
                /* these have one more ion than above */
                for( ion=0; ion<nelem+2; ++ion )
                {
                        /* zero out the transfer array */
                        for( ion2=0; ion2<nelem+2; ++ion2 )
                        {
                                mole.xMoleChTrRate[nelem][ion][ion2] = 0.;
                        }
                }
        }
 
        for(mole_reaction_i p=mole_priv::reactab.begin(); 
                        p != mole_priv::reactab.end(); ++p) 
        {
                rate = &(*p->second);
                rk = mole.reaction_rks[ rate->index ];
                
                for(i=0;i<rate->nreactants;i++)
                {
                        rate_deriv[i] = rk;
                        for(j=0;j<rate->nreactants;j++)
                        {
                                if(i!=j)
                                {
                                        rate_deriv[i] *= mole.species[ rate->reactants[j]->index ].den;
                                }
                        }
                }
                
                rate_tot = rate_deriv[0] * mole.species[ rate->reactants[0]->index ].den;
                
                for(i=0;i<rate->nreactants;i++)
                {       
                        sp = rate->reactants[i];
                        if (rate->rvector[i] == NULL)
                        {
                                mole.species[sp->index].snk += rate_deriv[i];
                        }
                        else
                        {
                                // exclude charge exchange with isotopes of same element 
                                if( rate->nreactants==2 )
                                {
                                        long otherIndex = 1-i;
                                        molecule *sp2 = rate->reactants[otherIndex];
                                        if( sp->isMonatomic() && sp2->isMonatomic() && sp->nAtom.begin()->first->el == sp2->nAtom.begin()->first->el )
                                                continue;
                                }
 
                                if ( atmdat.lgCTOn )
                                {
                                        for( ChemAtomList::iterator atom = unresolved_atom_list.begin(); atom != unresolved_atom_list.end(); ++atom)
                                        {
                                                nelem = (*atom)->el->Z-1;
                                                if (sp->nAtom.find(*atom) != sp->nAtom.end() && sp->nAtom[*atom] != 0 && rate->rvector[i]->charge != sp->charge)
                                                {
                                                        mole.xMoleChTrRate[nelem][sp->charge][rate->rvector[i]->charge] +=
                                                                (realnum) rate_deriv[i];
                                                        break;
                                                }
                                        }
                                }
                        }
                }
                
                for(i=0;i<rate->nproducts;i++)
                {
                        sp = rate->products[i];
                        if (rate->pvector[i] == NULL)
                        {
                                mole.species[sp->index].src += rate_tot;
                        }
                }
        }
 
        for (ChemAtomList::iterator atom = unresolved_atom_list.begin();
                  atom != unresolved_atom_list.end(); ++atom)
        {
                const long int nelem=(*atom)->el->Z-1;
                if( !dense.lgElmtOn[nelem] )
                        continue;
 
                for (long int ion=0;ion<nelem+2;ion++) 
                {
                        if ((*atom)->ipMl[ion] != -1)
                        {
                                mole.source[nelem][ion] = mole.species[(*atom)->ipMl[ion]].src;
                                mole.sink[nelem][ion] = mole.species[(*atom)->ipMl[ion]].snk;
                        }
                        else
                        {
                                mole.source[nelem][ion] = 0.0;
                                mole.sink[nelem][ion] = 0.0;
                        }
                }
        }
 
        //mole_dominant_rates(findspecies("H+"),ioQQQ);
        return;
}
 
STATIC bool lgNucleiConserved(const multi_arr<double,2> &c)
{
        DEBUG_ENTRY ("lgNucleiConserved()");
        bool checkAllOK = true;
        multi_arr<double,2> test(atom_list.size(),mole_global.num_calc),
                tot(atom_list.size(),mole_global.num_calc);
        vector<double> ccache(mole_global.num_calc);
        vector<long> ncache(mole_global.num_calc);
        test.zero();
        tot.zero();
 
        map<chem_atom*, long> atom_to_index;
        for (unsigned long j=0; j<atom_list.size(); ++j )
        {
                atom_to_index[atom_list[j].get_ptr()] = j;
        }
        for (long j=0;j<mole_global.num_calc;j++) 
        {
                long nc = 0;
                for (long i=0;i<mole_global.num_calc;i++) 
                {
                        if (c[i][j] != 0.)
                        {
                                ccache[nc] = c[i][j];
                                ncache[nc] = i;
                                ++nc;
                        }
                }
                if (nc > 0)
                {
                        for (molecule::nAtomsMap::const_iterator el = mole_global.list[j]->nAtom.begin(); 
                                  el != mole_global.list[j]->nAtom.end(); ++el)
                        {
                                long natom = atom_to_index[el->first.get_ptr()];
                                const int nAtomj = el->second;
                                for (long i=0;i<nc;i++) 
                                {
                                        const double term = ccache[i] * nAtomj;
                                        test[natom][ncache[i]] += term;
                                        tot[natom][ncache[i]] += fabs(term);
                                }
                        }
                }
        }
 
        for( unsigned long natom=0; natom < atom_list.size(); ++natom)
        {
                for (long i=0;i<mole_global.num_calc;i++) 
                {
                        const bool checkOK = 
                                ( fabs(test[natom][i]) <= MAX2(1e-10*tot[natom][i], 1e10*DBL_MIN) );
                        if ( UNLIKELY(!checkOK) )
                        {
                                chem_atom *atom = atom_list[natom].get_ptr();
                                fprintf(stdout,"Network conservation error %s %s %g %g %g %g\n",
                                                  atom->label().c_str(),
                                                  mole_global.list[i]->label.c_str(),
                                                  test[natom][i],
                                                  test[natom][i]/tot[natom][i],
                                                  mole.species[atom->ipMl[0]].den,
                                                  mole.species[atom->ipMl[1]].den);
                                //fprintf(stdout,"Problem at %s\n",rate->label);
                                checkAllOK = false;
                        }
                }
        }
        return checkAllOK;
}
 
void mole_dominant_rates( const molecule *debug_species, FILE *ioOut )
{
        long int i, j;
        mole_reaction *rate, *ratesnk=NULL, *ratesrc=NULL;
        double rate_tot, rate_deriv[MAXREACTANTS], rk;
        molecule *sp;
        double snkx=0.,srcx=0.;
 
        for(mole_reaction_i p=mole_priv::reactab.begin();
                        p != mole_priv::reactab.end(); ++p)
        {
                rate = &(*p->second);
                rk = mole.reaction_rks[ rate->index ];
 
                for(i=0;i<rate->nreactants;i++)
                {
                        rate_deriv[i] = rk;
                        for(j=0;j<rate->nreactants;j++)
                        {
                                if(i!=j)
                                {
                                        rate_deriv[i] *= mole.species[ rate->reactants[j]->index ].den;
                                }
                        }
                }
 
                rate_tot = rate_deriv[0] * mole.species[ rate->reactants[0]->index ].den;
 
                if (debug_species != null_mole)
                {
                        for(i=0;i<rate->nproducts;++i)
                        {
                                sp = rate->products[i];
                                if (sp == debug_species && rate->pvector[i] == NULL)
                                {
                                        if (fabs(rate_tot) > srcx)
                                        {
                                                srcx = rate_tot;
                                                ratesrc = rate;
                                        }
                                }
                        }
                        for(i=0;i<rate->nreactants;++i)
                        {
                                sp = rate->reactants[i];
                                if (sp == debug_species && rate->rvector[i] == NULL)
                                {
                                        if (fabs(rate_deriv[i]) > snkx)
                                        {
                                                snkx = rate_deriv[i];
                                                ratesnk = rate;
                                        }
                                }
                        }
                }
        }
 
 
        if (debug_species != null_mole)
        {
                if (ratesrc)
                {
                        fprintf( ioOut, "%20.20s src %13.7g of %13.7g [",
                                ratesrc->label.c_str(),srcx,mole.species[debug_species->index].src);
                        for (j=0;j<ratesrc->nreactants;j++)
                        {
                                if (j)
                                {
                                        fprintf( ioOut, "," );
                                }
                                fprintf( ioOut, "%-6.6s %13.7g",
                                        ratesrc->reactants[j]->label.c_str(),
                                        mole.species[ ratesrc->reactants[j]->index ].den);
                        }
                        fprintf( ioOut, "]" );
                }
                if (ratesnk)
                {
                        fprintf( ioOut, "%20.20s snk %13.7g of %13.7g [",
                                ratesnk->label.c_str(), snkx * mole.species[debug_species->index].den,
                                mole.species[debug_species->index].snk * mole.species[debug_species->index].den);
                        for (j=0;j<ratesnk->nreactants;j++)
                        {
                                if (j)
                                {
                                        fprintf( ioOut, "," );
                                }
                                fprintf( ioOut, "%-6.6s %13.7g",
                                        ratesnk->reactants[j]->label.c_str(),
                                        mole.species[ ratesnk->reactants[j]->index ].den);
                        }
                        fprintf( ioOut, "]" );
                }
        }
        fprintf( ioOut, "\n" );
 
        return;
}