/home66/gary/public_html/cloudy/c13_branch/source/transition.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 */

#include "cddefines.h"
#include "transition.h"
#include "version.h"
#include "dense.h"
#include "elementnames.h"
#include "lines.h"
#include "lines_service.h"
#include "opacity.h"
#include "phycon.h"
#include "radius.h"
#include "rfield.h"
#include "rt.h"
#include "taulines.h"
#include "conv.h"

/*outline - adds line photons to reflin and outlin */
/*PutLine enter local line intensity into the intensity stack for eventual printout */
/*PutExtra enter and 'extra' intensity source for some line */
/*DumpLine print various information about an emission line vector, 
 * used in debugging, print to std out, ioQQQ */
/*TexcLine derive excitation temperature of line from contents of line array */
/*transition::Zero zeros out transition */
/*LineConvRate2CS convert down coll rate back into electron cs in case other parts of code need this for reference */
/*OccupationNumberLine - derive the photon occupation number at line center for any line */
/*MakeCS compute collision strength by g-bar approximations */
/*gbar1 compute g-bar collision strength using Mewe approximations */
/*gbar0 compute g-bar gaunt factor for neutrals */
/*emit_frac returns fraction of populations the produce emission */
/*chIonLbl use information in line array to generate a null terminated ion label in "Fe 2" */
/*chLineLbl use information in line transfer arrays to generate a line label */
/*PutCS enter a collision strength into an individual line vector */

/*outline - adds line photons to reflin and outlin */
void TransitionProxy::outline_resonance( ) const
{
        bool lgDoChecks = true;
        outline(Emis().ColOvTot(), lgDoChecks);
}

/*outline - adds line photons to reflin and outlin */
void TransitionProxy::outline( double nonScatteredFraction, 
                                                                                 bool lgDoChecks  ) const
{
        long int ip = ipCont()-1;

        DEBUG_ENTRY( "TransitionProxy::outline()" );

        if ( 0 && lgDoChecks)
        {
                // nothing to do if very small photon flux or below plasma frequency
                ASSERT( Emis().phots() >= 0. );
                if( Emis().phots() < SMALLFLOAT || EnergyErg() / EN1RYD <= rfield.plsfrq )
                        return;

                ASSERT( Emis().FracInwd() >= 0. );
                ASSERT( radius.BeamInIn >= 0. );
                ASSERT( radius.BeamInOut >= 0. );
                double Ptot = Emis().Pesc() + Emis().Pelec_esc();
                double PhotEmit = Emis().Aul()*Ptot*(*Hi()).Pop();
                // do not assert accuracy if close to bounds of fp precision
                double error = MAX2( SMALLFLOAT*1e3 , 3e-1*PhotEmit );
                // do not assert if do not have valid solution
                bool lgGoodSolution = conv.lgConvEden && conv.lgConvIoniz() &&
                        conv.lgConvPops && conv.lgConvPres && conv.lgConvTemp;
                // see ticket #135 rt inconsistent results
                // this assert trips on a regular basis.  The fix is to rewrite
                // the RT and level population solvers so that the level population
                // and OTS rates are done simultaneously rather than sequentially
                // For now do not throw the assert on a release version - we know
                // about this problem
                ASSERT( t_version::Inst().lgRelease || !lgGoodSolution || 
                        Ptot < 1e-3 ||  fp_equal_tol( Emis().phots(), PhotEmit , error ));
        }

        bool lgTransStackLine = true;
        outline_base(Emis().dampXvel(), Emis().damp(), lgTransStackLine, ip, Emis().phots(), Emis().FracInwd(),
                                         nonScatteredFraction);
}

/*emit_frac returns fraction of populations the produce emission */
double emit_frac(const TransitionProxy& t)
{
        DEBUG_ENTRY( "emit_frac()" );

        ASSERT( t.ipCont() > 0 );

        /* collisional deexcitation and destruction by background opacities
         * are loss of photons without net emission */
        double deexcit_loss = t.Coll().col_str() * dense.cdsqte + t.Emis().Aul()*t.Emis().Pdest();
        /* this is what is observed */
        double rad_deexcit = t.Emis().Aul()*(t.Emis().Pelec_esc() + t.Emis().Pesc());
        return rad_deexcit/(deexcit_loss + rad_deexcit);
}

/*DumpLine print various information about an emission line vector, 
 * used in debugging, print to std out, ioQQQ */
void DumpLine(const TransitionProxy& t)
{
        char chLbl[110];

        DEBUG_ENTRY( "DumpLine()" );

        ASSERT( t.ipCont() > 0 );

        /* routine to print contents of line arrays */
        strcpy( chLbl, "DEBUG ");
        strcat( chLbl, chLineLbl(t) );

        fprintf( ioQQQ, 
                "%10.10s Te%.2e eden%.1e CS%.2e Aul%.1e Tex%.2e cool%.1e het%.1e conopc%.1e albdo%.2e\n", 
          chLbl, 
          phycon.te, 
          dense.eden, 
          t.Coll().col_str(), 
          t.Emis().Aul(), 
          TexcLine(t), 
          t.Coll().cool(), 
          t.Coll().heat() ,
          opac.opacity_abs[t.ipCont()-1],
          opac.albedo[t.ipCont()-1]);

        fprintf( ioQQQ, 
                "Tin%.1e Tout%.1e Esc%.1e eEsc%.1e DesP%.1e Pump%.1e OTS%.1e PopL,U %.1e %.1e PopOpc%.1e\n", 
          t.Emis().TauIn(), 
          t.Emis().TauTot(), 
          t.Emis().Pesc(), 
          t.Emis().Pelec_esc(), 
          t.Emis().Pdest(), 
          t.Emis().pump(), 
          t.Emis().ots(), 
          (*t.Lo()).Pop(), 
          (*t.Hi()).Pop() ,
          t.Emis().PopOpc() );
        return;
}


/*OccupationNumberLine - derive the photon occupation number at line center for any line */
double OccupationNumberLine(const TransitionProxy& t)
{
        double OccupationNumberLine_v;

        DEBUG_ENTRY( "OccupationNumberLine()" );

        ASSERT( t.ipCont() > 0 );

        /* routine to evaluate line photon occupation number - 
         * return negative number if line is maser */
        if( fabs(t.Emis().PopOpc()) > SMALLFLOAT )
        {
                /* the lower population with correction for stimulated emission */
                OccupationNumberLine_v = ( (*t.Hi()).Pop() / (*t.Hi()).g() ) /
                        ( t.Emis().PopOpc() / (*t.Lo()).g() )  *
                        (1. - t.Emis().Pesc());
        }
        else
        {
                OccupationNumberLine_v = 0.;
        }
        /* return value is not guaranteed to be positive - negative if
         * line mases */
        return( OccupationNumberLine_v );
}

/*TexcLine derive excitation temperature of line from contents of line array */
double TexcLine(const TransitionProxy& t)
{
        double TexcLine_v;

        DEBUG_ENTRY( "TexcLine()" );

        /* routine to evaluate line excitation temp using contents of line array
         * */
        if( (*t.Hi()).Pop() * (*t.Lo()).Pop() > 0. )
        {
                TexcLine_v = ( (*t.Hi()).Pop() / (*t.Hi()).g() )/( (*t.Lo()).Pop() / (*t.Lo()).g() );
                TexcLine_v = log(TexcLine_v);
                /* protect against infinite temp limit */
                if( fabs(TexcLine_v) > SMALLFLOAT )
                {
                        TexcLine_v = - t.EnergyK() / TexcLine_v;
                }
        }
        else
        {
                TexcLine_v = 0.;
        }
        return( TexcLine_v );
}

/*chIonLbl use information in line array to generate a null terminated ion label in "Fe 2" */
void chIonLbl(char *chIonLbl_v, const TransitionProxy& t)
{
        DEBUG_ENTRY( "chIonLbl()" );

        /* function to use information within the line array
         * to generate an ion label, giving element and
         * ionization stage
         * */
        if( (*t.Hi()).nelem() < 0 )
        {
                /* this line is to be ignored */
                if( (*t.Hi()).chLabel()[0]=='\0' )
                        strcpy( chIonLbl_v, "Dumy" );
                else 
                        strcpy( chIonLbl_v, (*t.Hi()).chLabel() );
        }
        else
        {
                chIonLbl( chIonLbl_v, (*t.Hi()).nelem(), (*t.Hi()).IonStg() );
        }
        /* chIonLbl is four char null terminated string */
        return/*( chIonLbl_v )*/;
}

void chIonLbl(char *chIonLbl_v, const long& nelem, const long& IonStg)
{
        DEBUG_ENTRY( "chIonLbl()" );

        // NB - nelem passed here is expected to be on the physical scale, not C (so hydrogen = 1).
        ASSERT( nelem >= 1 );
        ASSERT( nelem <= LIMELM );
        /* ElmntSym.chElementSym is null terminated, 2 ch + null, string giving very
         * short form of element name */
        strcpy( chIonLbl_v , elementnames.chElementSym[nelem-1] );
        /* chIonStage is four char null terminated string, starting with "_1__" */
        strcat( chIonLbl_v, elementnames.chIonStage[IonStg-1] );
        return;
}

/*chLineLbl use information in line transfer arrays to generate a line label */
/* this label is null terminated */
/* ContCreatePointers has test this with full range of wavelengths */
char* chLineLbl(const TransitionProxy& t)
{
        static char chLineLbl_v[11];
        static char chSpecies[5];

        DEBUG_ENTRY( "chLineLbl()" );

        if( (*t.Hi()).nelem() < 1 && (*t.Hi()).IonStg() < 1 )
        {
                sprintf( chSpecies, "%4.4s", (*t.Hi()).chLabel() );
        }
        else
        {
                ASSERT( (*t.Hi()).nelem() >= 1 );
                ASSERT( (*t.Hi()).IonStg() >= 1 && (*t.Hi()).IonStg() <= (*t.Hi()).nelem() + 1 );
                sprintf( chSpecies, "%2.2s%2.2s",
                        elementnames.chElementSym[(*t.Hi()).nelem() -1], 
                        elementnames.chIonStage[(*t.Hi()).IonStg()-1] ); 
        }

        /* function to use information within the line array
         * to generate a line label, giving element and
         * ionization stage
         * rhs are set in large block data */

        /* NB this function is profoundly slow due to sprintf statement
         * also - it cannot be evaluated within a write statement itself*/

        if( t.WLAng() > (realnum)INT_MAX )
        {
                sprintf( chLineLbl_v, "%4.4s%5i%c", chSpecies, 
                   (int)(t.WLAng()/1e8), 'c' );
        }
        else if( t.WLAng() > 9999999. )
        {
                /* wavelength is very large, convert to centimeters */
                sprintf( chLineLbl_v, "%4.4s%5.2f%c", chSpecies, 
                        t.WLAng()/1e8, 'c' );
        }
        else if( t.WLAng() > 999999. )
        {
                /* wavelength is very large, convert to microns */
                sprintf( chLineLbl_v, "%4.4s%5i%c", chSpecies, 
                        (int)(t.WLAng()/1e4), 'm' );
        }
        else if( t.WLAng() > 99999. )
        {
                /* wavelength is very large, convert to microns */
                sprintf( chLineLbl_v, "%4.4s%5.1f%c", chSpecies, 
                        t.WLAng()/1e4, 'm' );
        }
        else if( t.WLAng() > 9999. )
        {
                sprintf( chLineLbl_v, "%4.4s%5.2f%c", chSpecies, 
                   t.WLAng()/1e4, 'm' );
        }
        else if( t.WLAng() >= 100. )
        {
                sprintf( chLineLbl_v, "%4.4s%5i%c", chSpecies, 
                   (int)t.WLAng(), 'A' );
        }
        /* the following two formats should be changed for the
         * wavelength to get more precision */
        else if( t.WLAng() >= 10. )
        {
                sprintf( chLineLbl_v, "%4.4s%5.1f%c", chSpecies, 
                   t.WLAng(), 'A' );
        }
        else
        {
                sprintf( chLineLbl_v, "%4.4s%5.2f%c", chSpecies, 
                   t.WLAng(), 'A' );
        }
        /* make sure that string ends with null character - this should
         * be redundant */
        ASSERT( chLineLbl_v[10]=='\0' );
        return( chLineLbl_v );
}

/*PutCS enter a collision strength into an individual line vector */
void PutCS(double cs, 
  const TransitionProxy& t)
{
        DEBUG_ENTRY( "PutCS()" );

        /* collision strength must be non-negative */
        ASSERT( cs > 0. );

        t.Coll().col_str() = (realnum)cs;

        return;
}

void GenerateTransitionConfiguration( const TransitionProxy &t, char *chComment )
{
        strcpy( chComment, (*t.Lo()).chConfig() );
        strcat( chComment, " - " );
        strcat( chComment, (*t.Hi()).chConfig() );
        return;
}

static realnum ExtraInten;

/*PutLine enter local line intensity into the intensity stack for eventual printout */
STATIC void PutLine_base(const TransitionProxy& t, const char *chComment, const char *chLabelTemp, bool lgLabel)
{
        DEBUG_ENTRY( "PutLine_base()" );

        char chLabel[5];
        double xIntensity,
                other,
                xIntensity_in;
                
        /* routine to use line array data to generate input
         * for emission line array */
        ASSERT( t.ipCont() > 0. );
                
        if (lgLabel == true)
        {
                strncpy( chLabel, chLabelTemp, 4 );
                chLabel[4] = '\0';
        }

        /* if ipass=0 then we must generate label info since first pass
         * gt.0 then only need line intensity data */
        if( LineSave.ipass == 0 )
        {
                if (lgLabel == false)
                {
                        /* these variables not used by linadd if ipass ne 0 */
                        /* chIonLbl is function that generates a null terminated 4 char string, of form "C  2" */
                        chIonLbl(chLabel, t);
                }
                xIntensity = 0.;
        }
        else
        {
                /* both the counting and integrating modes comes here */
                /* not actually used so set to safe value */
                chLabel[0] = '\0';
                /* total line intensity or luminosity 
                 * these may not be defined in initial calls so define here */
                xIntensity = t.Emis().xIntensity() + ExtraInten;
        }

        /* initial counting case, where ipass == -1, just ignored above, call linadd below */
        
        /* ExtraInten is option that allows extra intensity (i.e., recomb)
         * to be added to this line  with Call PutExtra( exta )
         * in main lines this extra
         * contribution must be identified explicitly */
        ExtraInten = 0.;
        /*linadd(xIntensity,wl,chLabel,'i');*/
        /*lindst add line with destruction and outward */
        rt.fracin = t.Emis().FracInwd();
        lindst(xIntensity, 
                         t.WLAng(), 
                         chLabel, 
                         t.ipCont(), 
                         /* this is information only - has been counted in cooling already */
                         'i', 
                         /* do not add to outward beam, also done separately */
                         false,
                         chComment);
        rt.fracin = 0.5;
                
        /* inward part of line - do not move this away from previous lines
         * since xIntensity is used here */
        xIntensity_in = xIntensity*t.Emis().FracInwd();
        ASSERT( xIntensity_in>=0. );
        linadd(xIntensity_in,t.WLAng(),"Inwd",'i',chComment);
        
        /* cooling part of line */
        other = t.Coll().cool();
        linadd(other,t.WLAng(),"Coll",'i',chComment);
        
        /* fluorescent excited part of line */
        double radiative_branching;
        enum { lgNEW = true };
        if (lgNEW)
        {
                // Improved two-level version of radiative branching ratio
                const double AulEscp = t.Emis().Aul()*(t.Emis().Pesc()+t.Emis().Pelec_esc());
                // Would be better to include all outward transition processes from the
                // line, to cater for the general non-two-level case
                const double sinkrate = AulEscp + t.Emis().Aul()*t.Emis().Pdest() + t.Coll().ColUL( colliders );
                if (sinkrate > 0.0) 
                {
                        radiative_branching = AulEscp/sinkrate;
                }
                else
                {
                        radiative_branching = 0.;
                }
        }
        else
        {
                // This is the excitation ratio not the de-excitation ratio according
                // to its specification
                radiative_branching = (1.-t.Emis().ColOvTot());
        }

        other = (*t.Lo()).Pop() * t.Emis().pump() * radiative_branching * t.EnergyErg();
        linadd(other,t.WLAng(),"Pump",'i',chComment);
                

        /* heating part of line */
        other = t.Coll().heat();
        linadd(other,t.WLAng(),"Heat",'i',chComment);
}

/*PutLine enter local line intensity into the intensity stack for eventual printout */
void PutLine(const TransitionProxy& t, const char *chComment, const char *chLabelTemp)
{       
        const bool lgLabel = true;
        DEBUG_ENTRY( "PutLine()" );
        PutLine_base(t, chComment, chLabelTemp, lgLabel);
}

/*PutLine enter local line intensity into the intensity stack for eventual printout */
void PutLine(const TransitionProxy& t,
             const char *chComment)
{
        const bool lgLabel = false;
        const char *chLabelTemp = NULL;
        DEBUG_ENTRY( "PutLine()" );
        PutLine_base(t, chComment, chLabelTemp, lgLabel);
}

/* ==================================================================== */
/*PutExtra enter and 'extra' intensity source for some line */
void PutExtra(double Extra)
{

        DEBUG_ENTRY( "PutExtra()" );

        ExtraInten = (realnum)Extra;
        return;
}

void TransitionProxy::Junk( void ) const
{

        DEBUG_ENTRY( "TransitionProxy::Junk()" );

                /* wavelength, usually in A, used for printout */
        WLAng() = -FLT_MAX;

        /* transition energy in wavenumbers */
        EnergyWN() = -FLT_MAX;

        /* array offset for radiative transition within continuum array 
         * is negative if transition is non-radiative. */
        ipCont() = -10000;

        CollisionJunk( Coll() );

        /* set these equal to NULL first. That will cause the code to crash if
         * the variables are ever used before being deliberately set. */
        ipEmis() = -1;
        
        setLo(-1);
        setHi(-1);
        return;
}

/*TransitionZero zeros out transition array at start of calculation, sets
 * optical depths to initial values */
void TransitionProxy::Zero( void ) const
{

        DEBUG_ENTRY( "TransitionProxy::Zero()" );

        CollisionZero( Coll() );

	::Zero( *Lo() );
	::Zero( *Hi() );
        EmLineZero( Emis() );
        TauZero( Emis() );

        return;
}

/*LineConvRate2CS convert down coll rate back into electron cs in case other parts of code need this for reference */
void LineConvRate2CS( const TransitionProxy& t , realnum rate )
{

        DEBUG_ENTRY( "LineConvRate2CS()" );

        /* return is collision strength, convert from collision rate from 
         * upper to lower, this assumes pure electron collisions, but that will
         * also be assumed by anything that uses cs, for self-consistency */
        t.Coll().col_str() = rate * (*t.Hi()).g() / (realnum)dense.cdsqte;

        /* change assert to non-negative - there can be cases (Iin H2) where cs has
         * underflowed to 0 on some platforms */
        ASSERT( t.Coll().col_str() >= 0. );
        return;
}

/*gbar0 compute g-bar gaunt factor for neutrals */
STATIC void gbar0(double ex, 
          realnum *g)
{
        double a, 
          b, 
          c, 
          d, 
          y;

        DEBUG_ENTRY( "gbar0()" );

        /* written by Dima Verner
         *
         * Calculation of the effective Gaunt-factor by use of 
         * >>refer      gbar    cs      Van Regemorter, H., 1962, ApJ 136, 906
         * fits for neutrals
         *  Input parameters: 
         * ex - energy ryd - now K
         * t  - temperature in K
         *  Output parameter:
         * g  - effective Gaunt factor
         * */

        /* y = ex*157813.7/te */
        y = ex/phycon.te;
        if( y < 0.01 )
        {
                *g = (realnum)(0.29*(log(1.0+1.0/y) - 0.4/POW2(y + 1.0))/exp(y));
        }
        else
        {
                if( y > 10.0 )
                {
                        *g = (realnum)(0.066/sqrt(y));
                }
                else
                {
                        a = 1.5819068e-02;
                        b = 1.3018207e00;
                        c = 2.6896230e-03;
                        d = 2.5486007e00;
                        d = log(y/c)/d;
                        *g = (realnum)(a + b*exp(-0.5*POW2(d)));
                }
        }
        return;
}

/*gbar1 compute g-bar collision strength using Mewe approximations */
STATIC void gbar1(double ex, 
          realnum *g)
{
        double y;

        DEBUG_ENTRY( "gbar1()" );

        /*      *written by Dima Verner
         *
         * Calculation of the effective Gaunt-factor by use of 
         * >>refer      gbar    cs      Mewe,R., 1972, A&A 20, 215
         * fits for permitted transitions in ions MgII, CaII, FeII (delta n = 0)
         * Input parameters: 
         * ex - excitation energy in Ryd - now K
         * te  - temperature in K
         * Output parameter:
         * g  - effective Gaunt factor
         */

        /* y = ex*157813.7/te */
        y = ex/phycon.te;
        *g = (realnum)(0.6 + 0.28*(log(1.0+1.0/y) - 0.4/POW2(y + 1.0)));
        return;
}

/*MakeCS compute collision strength by g-bar approximations */
void MakeCS(const TransitionProxy& t)
{
        long int ion;
        double Abun, 
          cs;
        realnum
          gbar;

        DEBUG_ENTRY( "MakeCS()" );

        /* routine to get cs from various approximations */

        /* check if abundance greater than 0 */
        ion = (*t.Hi()).IonStg();

        Abun = dense.xIonDense[ (*t.Hi()).nelem() -1 ][ ion-1 ];
        if( Abun <= 0. )
        {
                gbar = 1.;
        }
        else
        {
                /* check if neutral or ion */
                if( ion == 1 )
                {
                        /* neutral - compute gbar for eventual cs */
                        gbar0(t.EnergyK(),&gbar);
                }
                else
                {
                        /* ion - compute gbar for eventual cs */
                        gbar1(t.EnergyK(),&gbar);
                }
        }

        /* above was g-bar, convert to cs */
        cs = gbar*(14.5104/WAVNRYD)*t.Emis().gf()/t.EnergyWN();

        /* stuff the cs in place */
        t.Coll().col_str() = (realnum)cs;
        return;
}

void TransitionProxy::AddLine2Stack() const
{
        DEBUG_ENTRY( "AddLine2Stack()" );

        ASSERT( lgLinesAdded == false );

        size_t newsize = m_list->Emis.size()+1; 
        m_list->Emis.resize(newsize);
        ipEmis() = newsize-1;
        this->resetEmis();
}

void TransitionProxy::AddLoState() const
{
        DEBUG_ENTRY( "AddLoState()" );

        ASSERT( !lgStatesAdded );

        m_list->states->resize(m_list->states->size()+1);

        setLo(m_list->states->size()-1);
}

void TransitionProxy::AddHiState() const
{
        DEBUG_ENTRY( "AddHiState()" );

        ASSERT( !lgStatesAdded );

        m_list->states->resize(m_list->states->size()+1);

        setHi(m_list->states->size()-1);
}

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