rt_tau_init.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 */
/*RT_tau_init set initial outward optical depths at start of first iteration,
 * it is only called by cloudy one time per complete calculation, just after
 * continuum set up and before start of convergence attempts. 
 * 
 * RT_tau_reset after first iteration, updates the optical depths, mirroring this
 * routine but with the previous iteration's variables */
#include "cddefines.h"
#define TAULIM  1e8
#include "taulines.h"
#include "doppvel.h"
#include "iso.h"
#include "h2.h"
#include "lines_service.h"
#include "rfield.h"
#include "dense.h"
#include "opacity.h"
#include "thermal.h"
#include "geometry.h"
#include "stopcalc.h"
#include "ipoint.h"
#include "abund.h"
#include "conv.h"
#include "atomfeii.h"
#include "rt.h"
#include "trace.h"
 
void RT_tau_init(void)
{
        long int i, 
          nelem,
          ipISO,
          ipHi, 
          ipLo,
          nHi;
        long lgHit; /* used for logic check */
 
        double AbunRatio, 
          balc, 
          coleff;
 
        realnum f, BalmerTauOn;
 
        DEBUG_ENTRY( "RT_tau_init()" );
 
        ASSERT( dense.eden > 0. );
 
        /* Zero lines first */
        for( ipISO=ipH_LIKE; ipISO<NISO; ++ipISO )
        {
                for( nelem=ipISO; nelem < LIMELM; nelem++ )
                {
                        if( dense.lgElmtOn[nelem] )
                        {
                                if( iso_ctrl.lgDielRecom[ipISO] )
                                {
                                        // SatelliteLines are indexed by lower level
                                        for( ipLo=0; ipLo < iso_sp[ipISO][nelem].numLevels_max; ipLo++ )
                                        {
                                                SatelliteLines[ipISO][nelem][ipSatelliteLines[ipISO][nelem][ipLo]].Zero();
                                        }
                                }
 
                                for( ipHi=1; ipHi < iso_sp[ipISO][nelem].numLevels_max; ipHi++ )
                                {
                                        for( ipLo=0; ipLo < ipHi; ipLo++ )
                                        {
                                                iso_sp[ipISO][nelem].trans(ipHi,ipLo).Zero();
                                        }
                                }
                                for( ipHi=2; ipHi <iso_ctrl.nLyman[ipISO]; ipHi++ )
                                {
                                        ExtraLymanLines[ipISO][nelem][ipExtraLymanLines[ipISO][nelem][ipHi]].Zero();
                                }
                        }
                }
        }
 
        /* initialize heavy element line array */
        for( i=1; i <= nLevel1; i++ )
        {
                TauLines[i].Zero();
        }
        /* this is a dummy optical depth array for non-existant lines 
         * when this goes over to struc, make sure all are set to zero here since
         * init in grid may depend on it */
        (*TauDummy).Zero();
 
        /* lines in cooling function with Mewe approximate collision strengths */
        for( i=0; i < nWindLine; i++ )
        {
                if( (*TauLine2[i].Hi()).IonStg() < (*TauLine2[i].Hi()).nelem()+1-NISO )
                {
                        /* inward optical depth */
                        TauLine2[i].Zero();
                }
        }
 
        /* inner shell lines */
        for( i=0; i < nUTA; i++ )
        {
                /* these are line optical depth arrays
                 * inward optical depth */
                /* heat is special for this array - it is heat per pump */
                double hsave = UTALines[i].Coll().heat();
                UTALines[i].Zero();
                UTALines[i].Coll().heat() = hsave;
        }
 
        /* hyperfine structure lines */
        for( i=0; i < nHFLines; i++ )
        {
                HFLines[i].Zero();
        }
 
        /* external database lines */
        for( long ipSpecies=0; ipSpecies<nSpecies; ipSpecies++ )
        {
                // can't filter by lgActive, must do all to properly reset in grids
                //if( dBaseSpecies[ipSpecies].lgActive )
                {
                        for (TransitionList::iterator tr=dBaseTrans[ipSpecies].begin(); 
                                  tr != dBaseTrans[ipSpecies].end(); ++tr)
                        {
                                (*tr).Zero();
                        }
                }
        }
 
        /* initialize optical depths in H2 */
        for( diatom_iter diatom = diatoms.begin(); diatom != diatoms.end(); ++diatom )
                (*diatom)->H2_LineZero();
 
        /* initialize large atom FeII arrays */
        FeII_LineZero();
 
        /* ==================================================================*/
        /* end setting lines to zero */
 
        /* >>chng 02 feb 08, moved to here from opacitycreateall, which was called later.
         * bug inhibited convergence in some models.  Caught by PvH */
        /* this is option to stop at certain optical depth */
        if( StopCalc.taunu > 0. )
        {
                StopCalc.iptnu = ipoint(StopCalc.taunu);
                StopCalc.iptnu = MIN2(StopCalc.iptnu,rfield.nupper-1);
        }
        else
        {
                StopCalc.iptnu = rfield.nupper;
                /* >>chng 04 dec 21, remove from here and init to 1e30 in zero */
                /*StopCalc.tauend = 1e30f;*/
        }
 
        /* if taunu was set with a stop optical depth command, then iptnu must
         * have also been set to a continuum index before this code is reaced */
        ASSERT( StopCalc.taunu == 0. || StopCalc.iptnu >= 0 );
 
        /* set initial and total optical depths in arrays
         * TAUNU is set when lines read in, sets stopping radius */
        if( StopCalc.taunu > 0. )
        {
                /*  an optical depth has been specified */
                if( StopCalc.iptnu >= iso_sp[ipH_LIKE][ipHYDROGEN].fb[ipH1s].ipIsoLevNIonCon )
                {
                        /* at ionizing energies */
                        for( i=0; i < (iso_sp[ipH_LIKE][ipHYDROGEN].fb[ipH1s].ipIsoLevNIonCon - 1); i++ )
                        {
                                /* taumin set to 1e-20, can be reset with taumin command */
                                opac.TauAbsGeo[1][i] = opac.taumin;
                                opac.TauScatGeo[1][i] = opac.taumin;
                                opac.TauTotalGeo[1][i] = opac.taumin;
                        }
 
                        for( i=iso_sp[ipH_LIKE][ipHYDROGEN].fb[ipH1s].ipIsoLevNIonCon-1; i < rfield.nupper; i++ )
                        {
                                /* TauAbsGeo(i,2) = tauend * (anu(i)/anu(iptnu))**(-2.43) */
                                opac.TauAbsGeo[1][i] = StopCalc.tauend;
                                opac.TauScatGeo[1][i] = opac.taumin;
                                opac.TauTotalGeo[1][i] = opac.TauAbsGeo[1][i] + opac.TauScatGeo[1][i];
                        }
                }
 
                else
                {
                        /* not specified at ionizing energies */
                        for( i=0; i < (iso_sp[ipH_LIKE][ipHYDROGEN].fb[ipH1s].ipIsoLevNIonCon - 1); i++ )
                        {
                                opac.TauAbsGeo[1][i] = StopCalc.tauend;
                                opac.TauScatGeo[1][i] = StopCalc.tauend;
                                opac.TauTotalGeo[1][i] = StopCalc.tauend;
                        }
 
                        for( i=iso_sp[ipH_LIKE][ipHYDROGEN].fb[ipH1s].ipIsoLevNIonCon-1; i < rfield.nupper; i++ )
                        {
                                opac.TauAbsGeo[1][i] = (realnum)(TAULIM*pow(rfield.anu[i],-2.43));
                                opac.TauScatGeo[1][i] = opac.taumin;
                                opac.TauTotalGeo[1][i] = opac.TauAbsGeo[1][i] + opac.TauScatGeo[1][i];
                        }
 
                }
        }
 
        else
        {
                /*  ending optical depth not specified, assume 1E8 at 1 Ryd */
                for( i=0; i < (iso_sp[ipH_LIKE][ipHYDROGEN].fb[ipH1s].ipIsoLevNIonCon - 1); i++ )
                {
                        opac.TauAbsGeo[1][i] = opac.taumin;
                        opac.TauScatGeo[1][i] = opac.taumin;
                        opac.TauTotalGeo[1][i] = opac.taumin;
                }
 
                for( i=iso_sp[ipH_LIKE][ipHYDROGEN].fb[ipH1s].ipIsoLevNIonCon-1; i < rfield.nupper; i++ )
                {
                        opac.TauAbsGeo[1][i] = (realnum)(TAULIM*pow(rfield.anu[i],-2.43));
                        opac.TauScatGeo[1][i] = opac.taumin;
                        opac.TauTotalGeo[1][i] = opac.TauAbsGeo[1][i] + opac.TauScatGeo[1][i];
                }
        }
 
        /* if lgSphere then double outer, set inner to half
         * assume will be optically thin at sub-ionizing energies */
        if( geometry.lgSphere || opac.lgCaseB )
        {
                for( i=0; i < (iso_sp[ipH_LIKE][ipHYDROGEN].fb[ipH1s].ipIsoLevNIonCon - 1); i++ )
                {
                        opac.TauAbsGeo[0][i] = opac.taumin;
                        opac.TauAbsGeo[1][i] = opac.taumin*2.f;
                        opac.TauScatGeo[0][i] = opac.taumin;
                        opac.TauScatGeo[1][i] = opac.taumin*2.f;
                        opac.TauTotalGeo[0][i] = 2.f*opac.taumin;
                        opac.TauTotalGeo[1][i] = 4.f*opac.taumin;
                }
 
                for( i=iso_sp[ipH_LIKE][ipHYDROGEN].fb[ipH1s].ipIsoLevNIonCon-1; i < rfield.nupper; i++ )
                {
                        opac.TauAbsGeo[0][i] = opac.TauAbsGeo[1][i];
                        opac.TauAbsGeo[1][i] *= 2.;
                        opac.TauScatGeo[0][i] = opac.TauScatGeo[1][i];
                        opac.TauScatGeo[1][i] *= 2.;
                        opac.TauTotalGeo[0][i] = opac.TauTotalGeo[1][i];
                        opac.TauTotalGeo[1][i] *= 2.;
                }
 
                if( StopCalc.taunu > 0. )
                {
                        /* ending optical depth specified, and lgSphere also */
                        StopCalc.tauend *= 2.;
                }
        }
 
        /* fix escape prob for He, metals, first set log of Te, needed by RECEFF
         * do not do this if temperature has been set by command */
        if( !thermal.lgTemperatureConstant )
        {
                double TeNew;
                /* this is a typical temperature for the H+ zone, and will use it is
                 * the line widths & opt depth in the following.  this is not meant to be the first
                 * temperature during the search phase. */
                TeNew = 2e4;
                /* >>chng 05 jul 19, in PDR models the guess of the optical depth in Lya could
                 * be very good since often limiting column density is set, but must use
                 * the temperature of H0 gas.  in a dense BLR this is roughly 7000K and
                 * closer to 100K for a low-density PDR - use these guesses */
                if( dense.gas_phase[ipHYDROGEN] >= 1e9 )
                {
                        /* this is a typical BLR H0 temp */
                        TeNew = 7000.;
                }
                else if( dense.gas_phase[ipHYDROGEN] <= 1e5 )
                {
                        /* this is a typical PDR H0 temp */
                        TeNew = 100.;
                }
                else
                {
                        /* power law interpolation between them */
                        TeNew = 0.5012 * pow( (double)dense.gas_phase[ipHYDROGEN], 0.46 );
                }
 
                /* propagate this temperature through the code */
                /* must not call tfidle at this stage since not all vectors have been allocated */
                TempChange( TeNew );
        }
 
        SumDensities();
        ASSERT( dense.xNucleiTotal > 0. );      
        /* set inward optical depths for hydrogenic ions to small number proportional to abundance */
        for( nelem=0; nelem < LIMELM; nelem++ )
        {
                if( dense.lgElmtOn[nelem] )
                {
                        /* now get actual optical depths */
                        AbunRatio = dense.gas_phase[nelem]/dense.xNucleiTotal;
                        for( ipLo=ipH1s; ipLo < (iso_sp[ipH_LIKE][nelem].numLevels_max - 1); ipLo++ )
                        {
                                for( ipHi=ipLo + 1; ipHi < iso_sp[ipH_LIKE][nelem].numLevels_max; ipHi++ )
                                {
                                        /* set all inward optical depths to taumin, regardless of abundance
                                         * this is a very small number, 1e-20 */
                                        iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().TauIn() = opac.taumin;
                                        iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().TauTot() = 2.f*opac.taumin;
                                }
                        }
 
                        /* La may be case B, tlamin set to 1e-20 and reset with Case B
                         * command to 1e5.  Case A and C set it to 1e-5 */
                        iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().TauIn() = opac.tlamin;
 
                        /* scale factor so that all other Lyman lines are appropriate for this Lya optical depth*/
                        f = opac.tlamin/iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().opacity();
                        fixit(); /* this appears to be redundant to code below. */
 
                        for( nHi=3; nHi<=iso_sp[ipH_LIKE][nelem].n_HighestResolved_max; nHi++ )
                        {
                                ipHi = iso_sp[ipH_LIKE][nelem].QuantumNumbers2Index[nHi][1][2];
                                iso_sp[ipH_LIKE][nelem].trans(ipHi,ipH1s).Emis().TauIn() = MAX2( opac.taumin, 
                                        f*iso_sp[ipH_LIKE][nelem].trans(ipHi,ipH1s).Emis().opacity() );
                        }
                        for( ipHi=iso_sp[ipH_LIKE][nelem].numLevels_max - iso_sp[ipH_LIKE][nelem].nCollapsed_max; ipHi < iso_sp[ipH_LIKE][nelem].numLevels_max; ipHi++ )
                        {
                                iso_sp[ipH_LIKE][nelem].trans(ipHi,ipH1s).Emis().TauIn() = MAX2( opac.taumin, 
                                        f*iso_sp[ipH_LIKE][nelem].trans(ipHi,ipH1s).Emis().opacity() );
                        }
 
                        /* after this set of if's the total Lya optical depth will be known,
                         * common code later on will set rest of Lyman lines
                         * if case b then set total Lyman to twice inner */
                        if( opac.lgCaseB )
                        {
                                /* force outer optical depth to twice inner if case B */
                                iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().TauTot() = 
                                        (realnum)(2.*iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().TauIn());
                                /* force off Balmer et al optical depths */
                                BalmerTauOn = 0.f;
                        }
 
                        else
                        {
                                /* usual case for H LyA; try to guess outer optical depth */
                                if( StopCalc.colnut < 6e29 )
                                {
                                        /* neutral column is defined */
                                        iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().TauTot() = (realnum)(StopCalc.colnut*
                                          rt.DoubleTau*iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().opacity()/
                                          GetDopplerWidth(dense.AtomicWeight[nelem])*AbunRatio);
                                        ASSERT( iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().TauTot() > 0. );
                                }
                                /* has optical depth at some energy where we want to stop been specified?
                                 * taunu is energy where
                                 * this has been specified - this checks on Lyman continuum, taunu = 1 */
                                else if( StopCalc.taunu < 3. && StopCalc.taunu >= 0.99 )
                                {
                                        /* Lyman continuum optical depth defined */
                                        iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().TauTot() = (realnum)(StopCalc.tauend*
                                          1.2e4*1.28e6/GetDopplerWidth(dense.AtomicWeight[nelem])*rt.DoubleTau*AbunRatio);
                                        ASSERT( iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().TauTot() > 0. );
                                }
                                else if( StopCalc.HColStop < 6e29 )
                                {
                                        /* neutral column not defined, guess from total col and U */
                                        coleff = StopCalc.HColStop - 
                                                MIN2(MIN2(rfield.qhtot/dense.eden,1e24)/2.6e-13,0.6*StopCalc.HColStop);
 
                                        iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().TauTot() = (realnum)(coleff*
                                          7.6e-14*AbunRatio);
                                        ASSERT( iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().TauTot() > 0. );
                                }
                                else
                                {
                                        /* no way to estimate 912 optical depth, set to large number */
                                        iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().TauTot() = (realnum)(1e20*
                                          AbunRatio);
                                        ASSERT( iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().TauTot() > 0. );
                                }
                                /* allow Balmer et al. optical depths */
                                BalmerTauOn = 1.f;
                        }
 
                        /* Lya total optical depth now known, is it optically thick?*/
                        if( iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().TauTot() > 1. )
                        {
                                rt.TAddHLya = (realnum)MIN2(1.,iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().TauTot()/
                                  1e4);
                                iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().TauIn() += rt.TAddHLya;
                        }
 
                        else
                        {
                                rt.TAddHLya = opac.tlamin;
                        }
 
                        /* this scale factor is to set other lyman lines, given the Lya optical depth */
                        f = iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().TauTot()/
                                iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().opacity();
 
                        ipISO = ipH_LIKE;
                        ASSERT( ipISO<NISO && nelem < LIMELM );
                        for( nHi=3; nHi<=iso_sp[ipISO][nelem].n_HighestResolved_max; nHi++ )
                        {
                                ipHi = iso_sp[ipISO][nelem].QuantumNumbers2Index[nHi][1][2];
                                iso_sp[ipH_LIKE][nelem].trans(ipHi,ipH1s).Emis().TauTot() = MAX2( opac.taumin, 
                                        iso_sp[ipH_LIKE][nelem].trans(ipHi,ipH1s).Emis().opacity() * f );
 
                                /* increment inward optical depths by rt all lyman lines, inward
                                 * optical depth was set above, this adds to it.  this was originally
                                 * set some place above */
                                iso_sp[ipH_LIKE][nelem].trans(ipHi,ipH1s).Emis().TauIn() += rt.TAddHLya*
                                  iso_sp[ipH_LIKE][nelem].trans(ipHi,ipH1s).Emis().opacity()/
                                  iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().opacity();
 
                                iso_sp[ipH_LIKE][nelem].trans(ipHi,ipH1s).Emis().TauIn() = MAX2( 
                                        opac.taumin, iso_sp[ipH_LIKE][nelem].trans(ipHi,ipH1s).Emis().TauIn() );
                        }
                        for( ipHi=iso_sp[ipH_LIKE][nelem].numLevels_max - iso_sp[ipH_LIKE][nelem].nCollapsed_max; ipHi < iso_sp[ipH_LIKE][nelem].numLevels_max; ipHi++ )
                        {
                                /* set total optical depth for higher lyman lines */
                                iso_sp[ipH_LIKE][nelem].trans(ipHi,ipH1s).Emis().TauTot() = MAX2( opac.taumin, 
                                        iso_sp[ipH_LIKE][nelem].trans(ipHi,ipH1s).Emis().opacity() * f );
 
                                /* increment inward optical depths by rt all lyman lines, inward
                                 * optical depth was set above, this adds to it.  this was originally
                                 * set some place above */
                                iso_sp[ipH_LIKE][nelem].trans(ipHi,ipH1s).Emis().TauIn() += rt.TAddHLya*
                                  iso_sp[ipH_LIKE][nelem].trans(ipHi,ipH1s).Emis().opacity()/
                                  iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().opacity();
 
                                iso_sp[ipH_LIKE][nelem].trans(ipHi,ipH1s).Emis().TauIn() = MAX2( 
                                        opac.taumin, iso_sp[ipH_LIKE][nelem].trans(ipHi,ipH1s).Emis().TauIn() );
                        }
 
                        /* try to guess what Balmer cont optical guess,
                         * first branch is case where we will stop at a balmer continuum optical
                         * depth - taunu is energy where tauend was set */
                        if( StopCalc.taunu > 0.24 && StopCalc.taunu < 0.7 )
                        {
                                iso_sp[ipH_LIKE][nelem].trans(ipH3p,ipH2s).Emis().TauTot() = (realnum)(StopCalc.tauend*
                                  3.7e4*BalmerTauOn*AbunRatio + 1e-20);
 
                                iso_sp[ipH_LIKE][nelem].trans(ipH3s,ipH2p).Emis().TauTot() = (realnum)(StopCalc.tauend*
                                  3.7e4*BalmerTauOn*AbunRatio + 1e-20);
 
                                iso_sp[ipH_LIKE][nelem].trans(ipH3d,ipH2p).Emis().TauTot() = (realnum)(StopCalc.tauend*
                                  3.7e4*BalmerTauOn*AbunRatio + 1e-20);
                        }
 
                        else
                        {
                                /* this is a guess based on Ferland&Netzer 1979, but it gets very large */
                                balc = rfield.qhtot*2.1e-19*BalmerTauOn*AbunRatio + 1e-20;
 
                                iso_sp[ipH_LIKE][nelem].trans(ipH3p,ipH2s).Emis().TauTot() = 
                                        (realnum)(MIN2(2e5, balc*3.7e4*BalmerTauOn+1e-20));
 
                                iso_sp[ipH_LIKE][nelem].trans(ipH3s,ipH2p).Emis().TauTot() = 
                                        (realnum)(MIN2(2e5, balc*3.7e4*BalmerTauOn+1e-20));
 
                                iso_sp[ipH_LIKE][nelem].trans(ipH3d,ipH2p).Emis().TauTot() = 
                                        (realnum)(MIN2(2e5, balc*3.7e4*BalmerTauOn+1e-20));
 
                                ASSERT( iso_sp[ipH_LIKE][nelem].trans(ipH3p,ipH2s).Emis().TauTot() > 0.);
                                ASSERT( iso_sp[ipH_LIKE][nelem].trans(ipH3s,ipH2p).Emis().TauTot() > 0.);
                                ASSERT( iso_sp[ipH_LIKE][nelem].trans(ipH3d,ipH2p).Emis().TauTot() > 0.);
                        }
 
                        /* transitions down to 2s are special since 'alpha' (2s-2p) has
                         * small optical depth, so use 3 to 2p instead */
                        f = iso_sp[ipH_LIKE][nelem].trans(ipH3s,ipH2p).Emis().TauTot()/
                                iso_sp[ipH_LIKE][nelem].trans(ipH3s,ipH2p).Emis().opacity()* BalmerTauOn;
 
                        ipLo = ipH2s;
                        for( ipHi=ipLo + 1; ipHi < iso_sp[ipH_LIKE][nelem].numLevels_max; ipHi++ )
                        {
                                if( iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).ipCont() <= 0 )
                                        continue;
 
                                iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().TauTot() = opac.taumin +
                                        f* iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().opacity();
                                ASSERT(iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().TauTot() > 0.);
                        }
 
                        /* this is for rest of lines, scale from opacity */
                        for( ipLo=ipH2p; ipLo < (iso_sp[ipH_LIKE][nelem].numLevels_max - 1); ipLo++ )
                        {
                                long ipISO = ipH_LIKE, ipNS, ipNPlusOneP;
 
                                /* scale everything with same factor we use for n+1 P -> nS */
                                ipNS = iso_sp[ipH_LIKE][nelem].QuantumNumbers2Index[ N_(ipLo) ][0][2];
                                if( ( N_(ipLo) + 1 ) <= 
                                        (iso_sp[ipH_LIKE][nelem].n_HighestResolved_max + iso_sp[ipH_LIKE][nelem].nCollapsed_max ) )
                                {
                                        ipNPlusOneP = iso_sp[ipH_LIKE][nelem].QuantumNumbers2Index[ N_(ipLo)+1 ][1][2];
                                }
                                else
                                {
                                        ipNPlusOneP = ipNS + 1;
                                }
 
#if     1                       /* old way */
                                ipNS = ipLo;
                                ipNPlusOneP = ipNS + 1;
#endif
 
                                if( iso_sp[ipH_LIKE][nelem].trans(ipNPlusOneP,ipNS).ipCont() <= 0 )
                                {       
                                        f = SMALLFLOAT;
                                }
                                else
                                {
                                        f = iso_sp[ipH_LIKE][nelem].trans(ipNPlusOneP,ipNS).Emis().TauTot()/
                                          iso_sp[ipH_LIKE][nelem].trans(ipNPlusOneP,ipNS).Emis().opacity()*
                                          BalmerTauOn;
                                }
 
                                for( ipHi=ipLo + 1; ipHi < iso_sp[ipH_LIKE][nelem].numLevels_max; ipHi++ )
                                {
                                        if( iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).ipCont() <= 0 )
                                                continue;
 
                                        iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().TauTot() = opac.taumin +
                                                f* iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().opacity();
                                        ASSERT(iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().TauTot() > 0.);
                                }
                        }
 
                        /* this loop is over all possible H lines, do some final cleanup */
                        for( ipLo=ipH1s; ipLo < (iso_sp[ipH_LIKE][nelem].numLevels_max - 1); ipLo++ )
                        {
                                for( ipHi=ipLo + 1; ipHi < iso_sp[ipH_LIKE][nelem].numLevels_max; ipHi++ )
                                {
                                        if( iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).ipCont() <= 0 )
                                                continue;
 
                                        /* TauCon is line optical depth to inner face used for continuum pumping rate,
                                         * not equal to TauIn in case of static sphere since TauCon will never
                                         * count the far side line optical depth */
                                        iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().TauCon() = 
                                                iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().TauIn();
 
                                        /* make sure inward optical depth is not larger than half total */
                                        iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().TauIn() = 
                                                MIN2(   iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().TauIn() ,
                                                iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().TauTot()/2.f );
                                        ASSERT(iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().TauIn() > 0.f);
 
                                        /* this is fraction of line that goes inward, not known until second iteration*/
                                        iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().FracInwd() = 0.5;
                                }
                        }
                }
        }
 
        /* initialize all he-like optical depths */
        for( nelem=ipHELIUM; nelem < LIMELM; nelem++ )
        {
                if( dense.lgElmtOn[nelem] )
                {
                        for( ipLo=0; ipLo < (iso_sp[ipHE_LIKE][nelem].numLevels_max - 1); ipLo++ )
                        {
                                for( ipHi=ipLo + 1; ipHi < iso_sp[ipHE_LIKE][nelem].numLevels_max; ipHi++ )
                                {
                                        /* set all inward optical depths to taumin, regardless of abundance
                                         * this is a very small number, 1e-20 */
                                        iso_sp[ipHE_LIKE][nelem].trans(ipHi,ipLo).Emis().TauIn() = opac.taumin;
                                        iso_sp[ipHE_LIKE][nelem].trans(ipHi,ipLo).Emis().TauTot() = 2.f*opac.taumin;
                                }
                        }
                }
        }
 
        /* now do helium like sequence if case b */
        if( opac.lgCaseB )
        {
                for( nelem=1; nelem < LIMELM; nelem++ )
                {
                        if( dense.lgElmtOn[nelem] )
                        {
                                double Aprev;
                                realnum ratio;
                                /* La may be case B, tlamin set to 1e9 by default with case b command */
                                iso_sp[ipHE_LIKE][nelem].trans(ipHe2p1P,ipHe1s1S).Emis().TauIn() = opac.tlamin;
 
                                iso_sp[ipHE_LIKE][nelem].trans(ipHe2p1P,ipHe1s1S).Emis().TauCon() = 
                                        iso_sp[ipHE_LIKE][nelem].trans(ipHe2p1P,ipHe1s1S).Emis().TauIn();
 
                                iso_sp[ipHE_LIKE][nelem].trans(ipHe2p1P,ipHe1s1S).Emis().TauTot() = 
                                        2.f*iso_sp[ipHE_LIKE][nelem].trans(ipHe2p1P,ipHe1s1S).Emis().TauIn();
 
                                ratio = opac.tlamin/iso_sp[ipHE_LIKE][nelem].trans(ipHe2p1P,ipHe1s1S).Emis().opacity();
 
                                /* this will be the trans prob of the previous lyman line, will use this to 
                                 * find the next one up in the series */
                                Aprev = iso_sp[ipHE_LIKE][nelem].trans(ipHe2p1P,ipHe1s1S).Emis().Aul();
 
                                i = ipHe2p1P+1;
                                /* >>chng 02 jan 05, remove explicit list of lyman lines, use As to guess
                                 * which are which - this will work for any number of levels */
                                for( i=ipHe2p1P+1; i < iso_sp[ipHE_LIKE][nelem].numLevels_max; i++ )
                                {
                                        if( iso_sp[ipHE_LIKE][nelem].trans(i,ipHe1s1S).ipCont() <= 0 )
                                                continue;
 
                                        /* >>chng 02 mar 15, add test for collapsed levels - As are very much
                                         * smaller at boundary between collapsed/resolved so this test is needed*/
                                        if( iso_sp[ipHE_LIKE][nelem].trans(i,ipHe1s1S).Emis().Aul()> Aprev/10. ||
                                                iso_sp[ipHE_LIKE][nelem].st[i].S() < 0 )
                                        {
                                                Aprev = iso_sp[ipHE_LIKE][nelem].trans(i,ipHe1s1S).Emis().Aul();
 
                                                iso_sp[ipHE_LIKE][nelem].trans(i,ipHe1s1S).Emis().TauIn() = 
                                                        ratio*iso_sp[ipHE_LIKE][nelem].trans(i,ipHe1s1S).Emis().opacity();
                                                /* reset line optical depth to continuum source */
                                                iso_sp[ipHE_LIKE][nelem].trans(i,ipHe1s1S).Emis().TauCon() = 
                                                        iso_sp[ipHE_LIKE][nelem].trans(i,ipHe1s1S).Emis().TauIn();
                                                iso_sp[ipHE_LIKE][nelem].trans(i,ipHe1s1S).Emis().TauTot() = 
                                                        2.f*iso_sp[ipHE_LIKE][nelem].trans(i,ipHe1s1S).Emis().TauIn();
                                        }
                                }
                        }
                }
        }
 
        /* begin sanity check, total greater than 1/0.9 time inward */
        lgHit = false;
        for( nelem=0; nelem < LIMELM; nelem++ )
        {
                if( dense.lgElmtOn[nelem] )
                {
                        for( ipLo=ipH1s; ipLo < (iso_sp[ipH_LIKE][nelem].numLevels_max - 1); ipLo++ )
                        {
                                for( ipHi=ipLo + 1; ipHi < iso_sp[ipH_LIKE][nelem].numLevels_max; ipHi++ )
                                {
                                        if( iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).ipCont() <= 0 )
                                                continue;
 
                                        if( iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().TauTot() < 
                                                0.9f*iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().TauIn() )
                                        {
                                                fprintf(ioQQQ,
                                                        "RT_tau_init insanity for h line, Z=%li lo=%li hi=%li tot=%g in=%g \n",
                                                        nelem , ipLo, ipHi , iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().TauTot() , 
                                                        iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().TauIn() );
                                                lgHit = true;
                                        }
                                }
                        }
                }
        }
        if( lgHit )
        {
                fprintf( ioQQQ," stopping due to insanity in RT_tau_init\n");
                ShowMe();
                cdEXIT(EXIT_FAILURE);
        }
        /*end sanity check */
 
        /* fix offset for effective column density optical depth */
        rt.tauxry = opac.TauAbsGeo[0][rt.ipxry-1];
 
        /* this is flag detected by dest prob routines to see whether ots rates are
         * oscillating - damp them out if so */
        conv.lgOscilOTS = false;
 
        /* now that optical depths have been incremented, do escape prob, this
         * is located here instead on in cloudy.c (where it belongs) because
         * information generated by RT_line_all is needed for the following printout */
        conv.lgFirstSweepThisZone = true;
        RT_line_all( );
 
        /* rest of routine is printout in case of trace */
        if( trace.lgTrace )
        {
                /* default is h-like */
                ipISO = ipH_LIKE;
                if( trace.lgIsoTraceFull[ipHE_LIKE] )
                        ipISO = ipHE_LIKE;
 
                if( trace.lgIsoTraceFull[ipISO] )
                {
                        t_iso_sp *sp= &iso_sp[ipISO][trace.ipIsoTrace[ipISO]];
                        fprintf( ioQQQ, "\n\n   up TauTot array as set in RT_tau_init ipZTrace (nelem)= %ld\n",
                                trace.ipIsoTrace[ipH_LIKE] );
                        long upper_limit = iso_sp[ipISO][ trace.ipIsoTrace[ipISO] ].numLevels_local;
                        for( ipHi=2; ipHi < upper_limit; ipHi++ )
                        {
                                fprintf( ioQQQ, " %3ld", ipHi );
                                for( ipLo=ipH1s; ipLo < ipHi; ipLo++ )
                                {
                                        if( sp->trans(ipHi,ipLo).Emis().Aul() <= iso_ctrl.SmallA )
                                                continue;
 
                                        fprintf( ioQQQ,PrintEfmt("%9.2e",
                                                sp->trans(ipHi,ipLo).Emis().TauTot() ));
                                }
                                fprintf( ioQQQ, "\n" );
                        }
 
                        fprintf( ioQQQ, "\n\n TauIn array\n" );
                        for( ipHi=1; ipHi < upper_limit; ipHi++ )
                        {
                                fprintf( ioQQQ, " %3ld", ipHi );
                                for( ipLo=ipH1s; ipLo < ipHi; ipLo++ )
                                {
                                        if( sp->trans(ipHi,ipLo).Emis().Aul() <= iso_ctrl.SmallA )
                                                continue;
 
                                        fprintf( ioQQQ,PrintEfmt("%9.2e", 
                                                sp->trans(ipHi,ipLo).Emis().TauIn() ));
                                }
                                fprintf( ioQQQ, "\n" );
                        }
 
                        fprintf( ioQQQ, "\n\n Aul As array\n" );
                        for( ipHi=1; ipHi < upper_limit; ipHi++ )
                        {
                                fprintf( ioQQQ, " %3ld", ipHi );
                                for( ipLo=ipH1s; ipLo < ipHi; ipLo++ )
                                {
                                        if( sp->trans(ipHi,ipLo).Emis().Aul() <= iso_ctrl.SmallA )
                                                continue;
 
                                        fprintf( ioQQQ,PrintEfmt("%9.2e", 
                                                sp->trans(ipHi,ipLo).Emis().Aul()) );
                                }
                                fprintf( ioQQQ, "\n" );
                        }
 
                        fprintf( ioQQQ, "\n\n Aul*esc array\n" );
                        for( ipHi=1; ipHi < upper_limit; ipHi++ )
                        {
                                fprintf( ioQQQ, " %3ld", ipHi );
                                for( ipLo=ipH1s; ipLo < ipHi; ipLo++ )
                                {
                                        if( sp->trans(ipHi,ipLo).Emis().Aul() <= iso_ctrl.SmallA )
                                                continue;
 
                                        fprintf( ioQQQ,PrintEfmt("%9.2e", 
                                                sp->trans(ipHi,ipLo).Emis().Aul()*
                                                (sp->trans(ipHi,ipLo).Emis().Pdest()+
                                                sp->trans(ipHi,ipLo).Emis().Pelec_esc() +
                                                sp->trans(ipHi,ipLo).Emis().Pesc()) ));
                                }
                                fprintf( ioQQQ, "\n" );
                        }
 
                        fprintf( ioQQQ, "\n\n H opac array\n" );
                        for( ipHi=1; ipHi < upper_limit; ipHi++ )
                        {
                                fprintf( ioQQQ, " %3ld", ipHi );
                                for( ipLo=ipH1s; ipLo < ipHi; ipLo++ )
                                {
                                        if( sp->trans(ipHi,ipLo).Emis().Aul() <= iso_ctrl.SmallA )
                                                continue;
 
                                        fprintf( ioQQQ,PrintEfmt("%9.2e", 
                                                sp->trans(ipHi,ipLo).Emis().opacity() ));
                                }
                                fprintf( ioQQQ, "\n" );
                        }
                }
 
                else
                {
                        fprintf( ioQQQ, " RT_tau_init called.\n" );
                }
        }
 
        ASSERT( iso_sp[ipH_LIKE][ipHYDROGEN].trans(ipH2p,ipH1s).Emis().TauIn()> 0. );
        ASSERT( iso_sp[ipH_LIKE][ipHYDROGEN].trans(ipH2p,ipH1s).Emis().PopOpc()>= 0. );
        return;
}