cont_createpointers.cpp

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/* This file is part of Cloudy and is copyright (C)1978-2017 by Gary J. Ferland and
 * others.  For conditions of distribution and use see copyright notice in license.txt */
/*ContCreatePointers set up pointers for lines and continua called by cloudy after input read in 
 * and continuum mesh has been set */
/*ipShells assign continuum energy pointers to shells for all atoms,
 * called by ContCreatePointers */
/*LimitSh sets upper energy limit to subshell integrations */
/*ContBandsCreate - read set of continuum bands to enter total emission into line stack*/
#include "cddefines.h"
#include "iso.h"
#include "secondaries.h"
#include "taulines.h"
#include "elementnames.h"
#include "ionbal.h"
#include "rt.h"
#include "opacity.h"
#include "yield.h"
#include "he.h"
#include "fe.h"
#include "rfield.h"
#include "oxy.h"
#include "trace.h"
#include "hmi.h"
#include "heavy.h"
#include "atmdat_adfa.h"
#include "ipoint.h"
#include "h2.h"
#include "continuum.h"
#include "freebound.h"
#include "two_photon.h"
#include "dense.h"
#include "lines_service.h"

/*LimitSh sets upper energy limit to subshell integrations */
STATIC long LimitSh(long int ion, 
  long int nshell, 
  long int nelem);

STATIC void ipShells(
        /* nelem is the atomic number on the C scale, Li is 2 */
        long int nelem);

/*ContBandsCreate - read set of continuum bands to enter total emission into line*/
STATIC void ContBandsCreate(
        /* chFile is optional filename, if void then use default bands,
         * if not void then use file specified,
         * return value is 0 for success, 1 for failure */
         const char chFile[] );

STATIC inline void print_emline_fine( const char *LineGroup, const TransitionProxy &tr )
{
        fprintf( ioQQQ, "%-10s -> '%s'\t Energy Ang= %.4e\t Ryd= %.4e\t Fine= %ld\t fine_ener= %.4e\n",
                        LineGroup,
                        tr.chLabel().c_str(),
                        tr.EnergyAng(),
                        tr.EnergyRyd(),
                        tr.Emis().ipFine(),
                        rfield.fine_anu[ tr.Emis().ipFine() ] );
}

void ContCreatePointers(void)
{
        /* counter to say whether pointers have ever been evaluated */
        static int nCalled = 0;

        DEBUG_ENTRY( "ContCreatePointers()" );

        /* create the hydrogen atom for this core load, routine creates space then zeros it out
         * on first call, on second and later calls it only zeros things out */
        iso_create();

        /* create internal static variables needed to do the H2 molecule */
        for( diatom_iter diatom = diatoms.begin(); diatom != diatoms.end(); ++diatom )
                (*diatom)->init();

        /* nCalled is local static variable defined 0 when defined. 
         * it is incremented below, so that space only allocated one time per coreload. */
        if( nCalled > 0 )
        {
                if( trace.lgTrace )
                        fprintf( ioQQQ, " ContCreatePointers called, not evaluating.\n" );
                return;
        }
        else
        {
                if( trace.lgTrace )
                        fprintf( ioQQQ, " ContCreatePointers called first time.\n" );
                ++nCalled;
        }

        for( long i=0; i < rfield.nflux_with_check; i++ )
        {
                /* this is array of labels for lines and continua, set to blanks at first */
                rfield.chContLabel[i] = "    ";
                rfield.chLineLabel[i] = "    ";
        }

        /* we will generate a set of array indices to ionization edges for
         * the first thirty elements.  First set all array indices to
         * totally bogus values so we will crash if misused */
        for( long nelem=0; nelem<LIMELM; ++nelem )
        {
                if( dense.lgElmtOn[nelem] )
                {
                        for( long ion=0; ion<LIMELM; ++ion )
                        {
                                for( long nshells=0; nshells<7; ++nshells )
                                {
                                        for( long j=0; j<3; ++j )
                                        {
                                                opac.ipElement[nelem][ion][nshells][j] = INT_MIN;
                                        }
                                }
                        }
                }
        }

        /* pointer to excited state of O+2 */
        opac.o3exc = 3.855;
        opac.ipo3exc[0] = ipContEnergy(opac.o3exc,"O3ex");

        /* main hydrogenic arrays - THIS OCCURS TWICE!! H and He here, then the
         * remaining hydrogenic species near the bottom.  This is so that H and HeII get
         * their labels stuffed into the arrays, and the rest of the hydrogenic series 
         * get whatever is left over after the level 1 lines.
         * to find second block, search on "ipZ=2" */
        /* NB note that no test for H or He being on exists here - we will always
         * define the H and He arrays even when He is off, since we need to
         * know where the he edges are for the bookkeeping that occurs in continuum
         * binning routines */
        /* this loop is over H, He-like only - DO NOT CHANGE TO NISO */
        for( long ipISO=ipH_LIKE; ipISO<=ipHE_LIKE; ++ipISO )
        {
                /* this will be over HI, HeII, then HeI only */
                for( long nelem=ipISO; nelem < 2; nelem++ )
                {
                        /* generate label for this ion */
                        string chLab = chIonLbl( nelem+1, nelem+1-ipISO );

                        /* array index for continuum edges for ground */
                        iso_sp[ipISO][nelem].fb[0].ipIsoLevNIonCon = ipContEnergy(iso_sp[ipISO][nelem].fb[0].xIsoLevNIonRyd, chLab.c_str());
                        for( long ipHi=1; ipHi < iso_sp[ipISO][nelem].numLevels_max; ipHi++ )
                        {
                                /* array index for continuum edges for excited levels */
                                iso_sp[ipISO][nelem].fb[ipHi].ipIsoLevNIonCon = ipContEnergy(iso_sp[ipISO][nelem].fb[ipHi].xIsoLevNIonRyd, chLab.c_str());

                                /* define all line array indices */
                                for( long ipLo=0; ipLo < ipHi; ipLo++ )
                                {
                                        if( iso_sp[ipISO][nelem].trans(ipHi,ipLo).Emis().Aul() <= iso_ctrl.SmallA )
                                                continue;

                                        /* some lines have negative or zero energy */
                                        /* >>chng 03 apr 22, this check was if less than or equal to zero,
                                         * changed to lowest energy point so that ultra low energy transitions are
                                         * not considered.      */
                                        if( iso_sp[ipISO][nelem].trans(ipHi,ipLo).EnergyRyd() < rfield.emm() )
                                                continue;

                                        /* some energies are negative for inverted levels */
                                        iso_sp[ipISO][nelem].trans(ipHi,ipLo).ipCont() = 
                                                ipLineEnergy(iso_sp[ipISO][nelem].trans(ipHi,ipLo).EnergyRyd(), chLab.c_str(),
                                                iso_sp[ipISO][nelem].fb[ipLo].ipIsoLevNIonCon);
                                        iso_sp[ipISO][nelem].trans(ipHi,ipLo).Emis().ipFine() = 
                                                ipFineCont(iso_sp[ipISO][nelem].trans(ipHi,ipLo).EnergyRyd() );
                                        /* check that energy scales are the same, to within energy resolution of arrays */
#                                       ifndef NDEBUG
                                        if( iso_sp[ipISO][nelem].trans(ipHi,ipLo).Emis().ipFine() > 0 )
                                        {
                                                realnum anuCoarse = rfield.anu(iso_sp[ipISO][nelem].trans(ipHi,ipLo).ipCont()-1);
                                                realnum anuFine = rfield.fine_anu[iso_sp[ipISO][nelem].trans(ipHi,ipLo).Emis().ipFine()];
                                                realnum widCoarse = rfield.widflx(iso_sp[ipISO][nelem].trans(ipHi,ipLo).ipCont()-1);
                                                realnum widFine = anuFine - rfield.fine_anu[iso_sp[ipISO][nelem].trans(ipHi,ipLo).Emis().ipFine()-1];
                                                realnum width = MAX2( widFine , widCoarse );
                                                /* NB - can only assert more than width of coarse cell 
                                                 * since close to ionization limit, coarse index is 
                                                 * kept below next ionization edge 
                                                 * >>chng 05 mar 02, pre factor below had been 1.5, chng to 2
                                                 * tripped near H grnd photo threshold */
                                                ASSERT( fabs(anuCoarse - anuFine) / anuCoarse < 
                                                        2.*width/anuCoarse);
                                        }
#                                       endif
                                }
                        }/* ipHi loop */
                }/* nelem loop */
        }/* ipISO */

        /* make sure the HeII Balmer pointers are above the HI Lyman pointer
         *
         * H and He are special because of their large abundances -
         * the OTS fields they produce are very important in establishing the ionization in the gas.
         * The OTS fields are placed in a single cell at an element's threshold.
         * When that shell's photoionization rate is evaluated the first cell,
         * with the OTS field, is not included - that would be double counting.
         * The self-OTS is taken into account with changes to the recombination coefficient.
         *
         * Note that this code makes implicit assumptions about the abundance pattern, which is a bug
         *
         * The edges in the frequency mesh (in mesh.cpp) are chosen such that the test below should
         * always pass. If these ASSERTs trip, update the energies of the H end He edges in mesh.cpp
         * to be the same as the ones used here (i.e. iso_sp[][].fb[].xIsoLevNIonRyd). */
        ASSERT( iso_sp[ipH_LIKE][ipHELIUM].fb[ipH2s].ipIsoLevNIonCon > iso_sp[ipH_LIKE][ipHYDROGEN].fb[ipH1s].ipIsoLevNIonCon );
        ASSERT( iso_sp[ipH_LIKE][ipHELIUM].fb[ipH2p].ipIsoLevNIonCon > iso_sp[ipH_LIKE][ipHYDROGEN].fb[ipH1s].ipIsoLevNIonCon );

        /* we will define an array of either 1 or 0 to show whether photooelectron
         * energy is large enough to produce secondary ionizations
         * below 100eV no secondary ionization - this is the threshold*/
        secondaries.ipSecIon = ipoint(7.353);

        /* this is highest energy where k-shell opacities are counted
         * can be adjusted with "set kshell" command */
        continuum.KshellLimit = ipoint(continuum.EnergyKshell);

        /* pointers for molecules
         * H2+ dissociation energy 2.647 eV but cs small below 0.638 Ryd */
        opac.ih2pnt[0] = ipContEnergy(0.502,"H2+ ");
        opac.ih2pnt[1] = ipoint(1.03);
        // Excited state H2+
        opac.ih2pnt_ex[0] = ipContEnergy(0.052,"H2+*");
        opac.ih2pnt_ex[1] = ipoint(1.03);

        //pointers for most prominent PAH features
        {
                /* energies given to ipContEnergy are only to put lave in the right place
                 * wavelengths are rough observed values of blends
                 * 7.6 microns */
                (void) ipContEnergy(0.0117, "PAH " );

                /* feature near 6.2 microns */
                (void) ipContEnergy(0.0147, "PAH " );

                /* 3.3 microns */
                (void) ipContEnergy(0.028, "PAH " );

                /* 11.2 microns */
                (void) ipContEnergy(0.0080, "PAH " );

                /* 12.3 microns */
                (void) ipContEnergy(0.0077, "PAH " );

                /* 13.5 microns */
                (void) ipContEnergy(0.0069, "PAH " );
        }

        /* fix pointers for hydrogen and helium */

        /* pointer to Bowen 374A resonance line */
        he.ip660 = ipLineEnergy(1.38,"He 2",0);

        /* pointer to energy defining effect x-ray column */
        rt.ipxry = ipoint(73.5);

        /* pointer to Hminus edge at 0.754eV */
        hmi.iphmin = ipContEnergy(HMINUSIONPOT,"H-  ");

        /* pointer to threshold for H2 photoionization at 15.4 eV */
        fixit("need to generalize ionization energy and label!");
        for( diatom_iter diatom = diatoms.begin(); diatom != diatoms.end(); ++diatom )
                (*diatom)->ip_photo_opac_thresh = ipContEnergy( 15.4/EVRYD , "H2  ");

        hmi.iheh1 = ipoint(1.6);
        hmi.iheh2 = ipoint(2.3);

        /* pointer to carbon k-shell ionization */
        opac.ipCKshell = ipoint(20.6);

        /* pointer to threshold for pair production */
        opac.ippr = ipoint(7.51155e4) + 1;

        /* pointer to x-ray - gamma ray bound; 100 kev */
        rfield.ipEnerGammaRay = ipoint(rfield.EnerGammaRay);

        /* confirm that labels are in correct location */
        ASSERT( strcmp( rfield.chContLabel[iso_sp[ipH_LIKE][ipHYDROGEN].fb[ipH1s].ipIsoLevNIonCon-1].c_str(), "H  1" ) ==0 );
        ASSERT( strcmp( rfield.chContLabel[iso_sp[ipH_LIKE][ipHYDROGEN].fb[ipH2p].ipIsoLevNIonCon-1].c_str(), "H  1" ) ==0 );

        ASSERT( strcmp( rfield.chContLabel[iso_sp[ipH_LIKE][ipHELIUM].fb[ipH1s].ipIsoLevNIonCon-1].c_str(), "He 2" ) ==0 );

        /* these are indices for centers of B and V filters,
         * taken from table on page 202 of Allen, AQ, 3rd ed */
        /* the B filter array offset */
        rfield.ipB_filter = ipoint( RYDLAM / WL_B_FILT );
        /* the V filter array offset */
        rfield.ipV_filter = ipoint( RYDLAM / WL_V_FILT );

        /* these are the lower and upper bounds for the G0 radiation field
         * used by Tielens & Hollenbach in their PDR work */
        rfield.ipG0_TH85_lo =  ipoint(  6.0 / EVRYD );
        rfield.ipG0_TH85_hi =  ipoint( 13.6 / EVRYD );

        /* this is the limits for Draine & Bertoldi Habing field */
        rfield.ipG0_DB96_lo =  ipoint(  RYDLAM / 1110. );
        rfield.ipG0_DB96_hi =  ipoint( RYDLAM / 912. );

        /* this is special form of G0 that could be used in some future version, for now,
         * use default, TH85 */
        rfield.ipG0_spec_lo = ipoint(  6.0 / EVRYD );
        rfield.ipG0_spec_hi = ipoint( RYDLAM / 912. );

        /* this index is to 1000A to obtain the extinction at 1000A */
        rfield.ip1000A = ipoint( RYDLAM / 1000. );

        /* following order of elements is in roughly decreasing abundance
         * when ipShells gets a cell for the valence IP it does so through
         * ipContEnergy, which makes sure that no two ions get the same cell
         * earliest elements have most precise ip mapping */

        /* set up shell pointers for hydrogen */
        {
                long nelem = ipHYDROGEN;
                long ion = 0;

                /* the number of shells */
                Heavy.nsShells[nelem][0] = 1;

                /*pointer to ionization threshold in energy array*/
                Heavy.ipHeavy[nelem][ion] = iso_sp[ipH_LIKE][nelem].fb[ipH1s].ipIsoLevNIonCon;
                opac.ipElement[nelem][ion][0][0] = iso_sp[ipH_LIKE][nelem].fb[ipH1s].ipIsoLevNIonCon;

                /* upper limit to energy integration */
                opac.ipElement[nelem][ion][0][1] = rfield.nflux_with_check;
        }

        if( dense.lgElmtOn[ipHELIUM] )
        {
                /* set up shell pointers for helium */
                long nelem = ipHELIUM;
                long ion = 0;

                /* the number of shells */
                Heavy.nsShells[nelem][0] = 1;

                /*pointer to ionization threshold in energy array*/
                Heavy.ipHeavy[nelem][ion] = iso_sp[ipHE_LIKE][ipHELIUM].fb[0].ipIsoLevNIonCon;
                opac.ipElement[nelem][ion][0][0] = iso_sp[ipHE_LIKE][ipHELIUM].fb[0].ipIsoLevNIonCon;

                /* upper limit to energy integration */
                opac.ipElement[nelem][ion][0][1] = rfield.nflux_with_check;

                /* (hydrogenic) helium ion */
                ion = 1;
                /* the number of shells */
                Heavy.nsShells[nelem][1] = 1;

                /*pointer to ionization threshold in energy array*/
                Heavy.ipHeavy[nelem][ion] = iso_sp[ipH_LIKE][nelem].fb[ipH1s].ipIsoLevNIonCon;
                opac.ipElement[nelem][ion][0][0] = iso_sp[ipH_LIKE][nelem].fb[ipH1s].ipIsoLevNIonCon;

                /* upper limit to energy integration */
                opac.ipElement[nelem][ion][0][1] = rfield.nflux_with_check;
        }

        /* check that ionization potential of neutral carbon valence shell is
         * positive */
        ASSERT( t_ADfA::Inst().ph1(2,5,5,0) > 0. );

        /* now fill in all sub-shell ionization array indices for elements heavier than He,
         * this must be done after previous loop on iso.ipIsoLevNIonCon[ipH_LIKE] since hydrogenic species use
         * iso.ipIsoLevNIonCon[ipH_LIKE] rather than ipoint in getting array index within continuum array */
        for( long i=NISO; i<LIMELM; ++i )
        {
                /* i is the atomic number on the c scale, 2 for Li */
                ipShells(i);
        }

        /* most of these are set in ipShells, but not h-like or he-like, so do these here */
        Heavy.Valence_IP_Ryd[ipHYDROGEN][0] = t_ADfA::Inst().ph1(0,0,ipHYDROGEN,0)/EVRYD* 0.9998787;
        Heavy.Valence_IP_Ryd[ipHELIUM][0] = t_ADfA::Inst().ph1(0,1,ipHELIUM,0)/EVRYD* 0.9998787;
        Heavy.Valence_IP_Ryd[ipHELIUM][1] = t_ADfA::Inst().ph1(0,0,ipHELIUM,0)/EVRYD* 0.9998787;
        for( long nelem=2; nelem<LIMELM; ++nelem )
        {
                Heavy.Valence_IP_Ryd[nelem][nelem-1] = t_ADfA::Inst().ph1(0,1,nelem,0)/EVRYD* 0.9998787;
                Heavy.Valence_IP_Ryd[nelem][nelem] = t_ADfA::Inst().ph1(0,0,nelem,0)/EVRYD* 0.9998787;
                if( dense.lgElmtOn[nelem])
                {
                        /* now confirm that all are properly set */
                        for( long j=0; j<=nelem; ++j )
                        {
                                ASSERT( Heavy.Valence_IP_Ryd[nelem][j] > 0.05 );
                        }
                        for( long j=0; j<nelem; ++j )
                        {
                                ASSERT( Heavy.Valence_IP_Ryd[nelem][j] < Heavy.Valence_IP_Ryd[nelem][j+1]);
                        }
                }
        }

        /* array indices to bound Compton electron recoil ionization of all elements */
        for( long nelem=0; nelem<LIMELM; ++nelem )
        {
                if( dense.lgElmtOn[nelem])
                {
                        for( long ion=0; ion<nelem+1; ++ion )
                        {
                                /* this is the threshold energy to Compton ionize valence shell electrons */
                                double energy = sqrt( Heavy.Valence_IP_Ryd[nelem][ion] * EN1RYD * ELECTRON_MASS * SPEEDLIGHT * SPEEDLIGHT ) / EN1RYD;
                                /* the array index for this energy */
                                ionbal.ipCompRecoil[nelem][ion] = ipoint( energy );
                        }
                }
        }

        /* oxygen pointers for excited states
         * IO3 is pointer to O++ exc state, is set above */
        oxy.i2d = ipoint(1.242);
        oxy.i2p = ipoint(1.367);
        opac.ipo1exc[0] = ipContEnergy(0.856,"O1ex");//2s^2 2p^4, ^1D level, J=2, energy relative to ground level is ~0.1446 Ry
        opac.ipo1exc[1] = ipoint(2.0);// upper limit to range of energies where opacity for 1D absorption is defined

        /* upper limit for excited state photoionization
         * do not use ipContEnergy since only upper limit */
        opac.ipo3exc[1] = ipoint(5.0);

        /* upper level of 4363 */
        opac.o3exc3 = 3.646;
        opac.ipo3exc3[0] = ipContEnergy(opac.o3exc3,"O3ex");
        opac.ipo3exc3[1] = ipoint(5.0);

        /* >>chng 97 jan 27, move nitrogen after oxygen so that O gets the
         * most accurate pointers
         * Nitrogen
         * in1(1) is thresh for photo from excited state */
        opac.in1[0] = ipContEnergy(0.893,"N1ex");

        /* upper limit */
        opac.in1[1] = ipoint(2.);

        if( (trace.lgTrace && trace.lgConBug) || (trace.lgTrace && trace.lgPointBug) )
        {
                fprintf( ioQQQ, "   ContCreatePointers:%ld energy cells used. N(1R):%4ld N(1.8):%4ld  N(4Ryd):%4ld N(O3)%4ld  N(x-ray):%5ld N(rcoil)%5ld\n", 
                  rfield.nflux_with_check, 
                  iso_sp[ipH_LIKE][ipHYDROGEN].fb[ipH1s].ipIsoLevNIonCon, 
                  iso_sp[ipHE_LIKE][ipHELIUM].fb[ipH1s].ipIsoLevNIonCon, 
                  iso_sp[ipH_LIKE][ipHELIUM].fb[ipH1s].ipIsoLevNIonCon, 
                  opac.ipo3exc[0], 
                  opac.ipCKshell, 
                  ionbal.ipCompRecoil[ipHYDROGEN][0] );


                fprintf( ioQQQ, "   ContCreatePointers: ipEnerGammaRay: %5ld IPPRpari produc%5ld\n", 
                  rfield.ipEnerGammaRay, opac.ippr );

                fprintf( ioQQQ, "   ContCreatePointers: H pointers;" );
                for( long i=0; i <= 6; i++ )
                {
                        fprintf( ioQQQ, "%4ld%4ld", i, iso_sp[ipH_LIKE][ipHYDROGEN].fb[i].ipIsoLevNIonCon );
                }
                fprintf( ioQQQ, "\n" );

                fprintf( ioQQQ, "   ContCreatePointers: Oxy pnters;" );

                for( long i=1; i <= 8; i++ )
                {
                        fprintf( ioQQQ, "%4ld%4ld", i, Heavy.ipHeavy[ipOXYGEN][i-1] );
                }
                fprintf( ioQQQ, "\n" );

        }

        /* Magnesium
         * following is energy for phot of MG+ from exc state producing 2798 */
        opac.ipmgex = ipoint(0.779);

        /* lower, upper edges of Ca+ excited term photoionizaiton */
        opac.ica2ex[0] = ipContEnergy(0.72,"Ca2x");
        opac.ica2ex[1] = ipoint(1.);

        /* set up factors and pointers for Fe continuum fluorescence */
        fe.ipfe10 = ipoint(2.605);

        /* following is WL(CM)**2/(8PI) * conv fac for RYD to NU *A21 */
        fe.pfe10 = (realnum)(2.00e-18/rfield.widflx(fe.ipfe10-1));

        /* this is 353 pump, f=0.032 */
        fe.pfe11a = (realnum)(4.54e-19/rfield.widflx(fe.ipfe10-1));

        /* this is 341.1 f=0.012 */
        fe.pfe11b = (realnum)(2.75e-19/rfield.widflx(fe.ipfe10-1));
        fe.pfe14 = (realnum)(1.15e-18/rfield.widflx(fe.ipfe10-1));

        /* set up energy pointers for line optical depth arrays
         * this also increments flux, sets other parameters for lines */

        /*Beginning of the dBaseLines*/
        for (int ipSpecies=0; ipSpecies < nSpecies; ++ipSpecies)
        {
                /*Put null terminated line label into chLab*/
                char chLab[NCHLAB];
                strncpy(chLab,dBaseSpecies[ipSpecies].chLabel,NCHLAB-1);
                chLab[NCHLAB-1]='\0';

                for( EmissionList::iterator em=dBaseTrans[ipSpecies].Emis().begin();
                          em != dBaseTrans[ipSpecies].Emis().end(); ++em)
                {
                        /* upper level lifetime to calculate the damping parameter.*/
                        (*em).dampXvel() = (realnum)(1./
                                        dBaseStates[ipSpecies][em->Tran().ipHi()].lifetime()/em->Tran().EnergyWN()/PI4);
                        (*em).damp() = -1000.0;

                        // Data intended for ADAS have a large number of transitions with Aul = 1e-30 - these are
                        // not real, but are there to keep the ADAS codes happy.  We do not want to transfer them.
                        static const double minAul = 1e-29;
                        if( (*em).Aul() > minAul )
                        {
                                (*em).Tran().ipCont() = ipLineEnergy((*em).Tran().EnergyRyd(), chLab ,0);
                                (*em).ipFine() = ipFineCont((*em).Tran().EnergyRyd() );
                        }
                        else
                        {
                                (*em).Tran().ipCont() = -1;
                                (*em).ipFine() = -1;
                        }

                        // these are edge cases which did pass the minAul above, but still underflowed
                        // when converted to (real)gf - conversion depends on energy of transition so
                        // Aul - gf mapping is not linear
                        if ((*em).gf() <= 0.0)
                        {
                                (*em).Tran().ipCont() = -1;
                                (*em).ipFine() = -1;
                        }

                        /* derive the abs coefficient, call to function is gf, wl (A), g_low */
                        (*em).opacity() = 
                                (realnum)(abscf((*em).gf(),(*em).Tran().EnergyWN(),
                                                                         (*(*em).Tran().Lo()).g()));
                }
        }
        /*end of the dBaseLines*/

        /* set the ipCont struc element for the H2 molecule */
        for( diatom_iter diatom = diatoms.begin(); diatom != diatoms.end(); ++diatom )
                (*diatom)->H2_ContPoint();

        for( long ipISO=ipH_LIKE; ipISO<NISO; ++ipISO )
        {
                /* do remaining part of the iso sequences */
                for( long nelem=2; nelem < LIMELM; nelem++ )
                {
                        if( dense.lgElmtOn[nelem])
                        {
                                string chLab = chIonLbl( nelem+1, nelem+1-ipISO );

                                /* array index for continuum edges */
                                iso_sp[ipISO][nelem].fb[0].ipIsoLevNIonCon = 
                                        ipContEnergy(iso_sp[ipISO][nelem].fb[0].xIsoLevNIonRyd, chLab.c_str());

                                for( long ipHi=1; ipHi < iso_sp[ipISO][nelem].numLevels_max; ipHi++ )
                                {
                                        /* array index for continuum edges */
                                        iso_sp[ipISO][nelem].fb[ipHi].ipIsoLevNIonCon = ipContEnergy(iso_sp[ipISO][nelem].fb[ipHi].xIsoLevNIonRyd, chLab.c_str());

                                        /* define all line pointers */
                                        for( long ipLo=0; ipLo < ipHi; ipLo++ )
                                        {

                                                if( iso_sp[ipISO][nelem].trans(ipHi,ipLo).Emis().Aul() <= iso_ctrl.SmallA )
                                                        continue;

                                                /* some lines have negative or zero energy */
                                                /* >>chng 03 apr 22, this check was if less than or equal to zero,
                                                 * changed to lowest energy point so that ultra low energy transitions are
                                                 * not considered.      */
                                                if( iso_sp[ipISO][nelem].trans(ipHi,ipLo).EnergyRyd() < rfield.emm() )
                                                        continue;

                                                iso_sp[ipISO][nelem].trans(ipHi,ipLo).ipCont() = 
                                                        ipLineEnergy(iso_sp[ipISO][nelem].trans(ipHi,ipLo).EnergyRyd(), chLab.c_str(),
                                                        iso_sp[ipISO][nelem].fb[ipLo].ipIsoLevNIonCon);
                                                iso_sp[ipISO][nelem].trans(ipHi,ipLo).Emis().ipFine() = 
                                                        ipFineCont(iso_sp[ipISO][nelem].trans(ipHi,ipLo).EnergyRyd() );
                                        }
                                }
                                iso_sp[ipISO][nelem].fb[0].ipIsoLevNIonCon = ipContEnergy(iso_sp[ipISO][nelem].fb[0].xIsoLevNIonRyd, chLab.c_str());
                        }
                }
        }
        for( long ipISO=ipH_LIKE; ipISO<NISO; ++ipISO )
        {
                /* this will be over HI, HeII, then HeI only */
                for( long nelem=ipISO; nelem < LIMELM; nelem++ )
                {
                        if( dense.lgElmtOn[nelem])
                        {
                                /* these are the extra Lyman lines */
                                for( long ipHi=2; ipHi < iso_ctrl.nLyman_malloc[ipISO]; ipHi++ )
                                {
                                        long ipLo = 0;
                                        /* some energies are negative for inverted levels */
                                        char chLab[NCHLAB];
                                        strncpy(chLab,"LyEx",NCHLAB-1);
                                        chLab[NCHLAB-1]='\0';
                                        TransitionList::iterator tr = ExtraLymanLines[ipISO][nelem].begin()+ipExtraLymanLines[ipISO][nelem][ipHi];
                                        (*tr).ipCont() = 
                                                ipLineEnergy((*tr).EnergyRyd() , chLab ,
                                                iso_sp[ipISO][nelem].fb[ipLo].ipIsoLevNIonCon);

                                        (*tr).Emis().ipFine() = 
                                                ipFineCont((*tr).EnergyRyd() );
                                }

                                if( iso_ctrl.lgDielRecom[ipISO] )
                                {
                                        ASSERT( ipISO>ipH_LIKE );
                                        for( long ipLo=0; ipLo<iso_sp[ipISO][nelem].numLevels_max; ipLo++ )
                                        {
                                                char chLab[NCHLAB];
                                                strncpy(chLab,"SatL",NCHLAB-1);
                                                chLab[NCHLAB-1]='\0';
                                                SatelliteLines[ipISO][nelem][ipSatelliteLines[ipISO][nelem][ipLo]].ipCont() = ipLineEnergy(
                                                        SatelliteLines[ipISO][nelem][ipSatelliteLines[ipISO][nelem][ipLo]].EnergyRyd() , chLab , 
                                                        0);

                                                SatelliteLines[ipISO][nelem][ipSatelliteLines[ipISO][nelem][ipLo]].Emis().ipFine() =  
                                                        ipFineCont(SatelliteLines[ipISO][nelem][ipSatelliteLines[ipISO][nelem][ipLo]].EnergyRyd() );
                                        }
                                }
                        }
                }
        }

        fixit("is this redundant?");
        /* for He-like sequence the majority of the transitions are bogus - A set to special value in this case */
        {
                long ipISO = ipHE_LIKE;
                /* do remaining part of the he iso sequence */
                for( long nelem=ipISO; nelem < LIMELM; nelem++ )
                {
                        if( dense.lgElmtOn[nelem])
                        {
                                for( long ipHi=1; ipHi < iso_sp[ipISO][nelem].numLevels_max; ipHi++ )
                                {
                                        for( long ipLo=0; ipLo < ipHi; ipLo++ )
                                        {
                                                TransitionProxy tr = iso_sp[ipISO][nelem].trans(ipHi,ipLo);
                                                if( tr.ipCont() <= 0 )
                                                        continue;
                                        
                                                if( fabs(tr.Emis().Aul() - iso_ctrl.SmallA) < SMALLFLOAT )
                                                {
                                                        /* iso_ctrl.SmallA is value assigned to bogus transitions */
                                                        tr.ipCont() = -1;
                                                        tr.Emis().ipFine() = -1;
                                                }
                                        }
                                }
                        }
                }
        }

        /* inner shell transitions */
        for( size_t i=0; i<UTALines.size(); ++i )
        {
                if( UTALines[i].Emis().Aul() > 0. )
                {

                        // dampXvel is derived in atmdat_readin because autoionization rates
                        // must be included in the total rate for the damping constant
                        ASSERT( UTALines[i].Emis().dampXvel() >0. );

                        /* derive the abs coefficient, call to function is gf, wl (A), g_low */
                        UTALines[i].Emis().opacity() = 
                                (realnum)(abscf( UTALines[i].Emis().gf(), UTALines[i].EnergyWN(), (*UTALines[i].Lo()).g()));

                        /* get pointer to energy in continuum mesh */
                        UTALines[i].ipCont() = ipLineEnergy(UTALines[i].EnergyRyd(), chIonLbl(UTALines[i]).c_str(),0 );
                        UTALines[i].Emis().ipFine() = ipFineCont(UTALines[i].EnergyRyd() );
                        {
                                enum{ DEBUG_LOC = false };
                                if( DEBUG_LOC && UTALines[i].chLabel() == "Ar 7 43.5239A" )
                                {
                                        print_emline_fine( "UTA", UTALines[i] );
                                }
                        }

                        /* find heating per absorption,
                         * first find threshold for this shell in ergs */
                        /* ionization threshold in erg */
                        double thresh = Heavy.Valence_IP_Ryd[(*UTALines[i].Hi()).nelem()-1][(*UTALines[i].Hi()).IonStg()-1] *EN1RYD;
                        UTALines[i].Coll().heat() = (UTALines[i].EnergyErg()-thresh);
                        ASSERT( UTALines[i].Coll().heat()> 0. );
                }
        }

        /* level 2 heavy element lines */
        for( long i=0; i < nWindLine; i++ )
        {
                /* derive the A, call to function is gf, wl (A), g_up */
                TauLine2[i].Emis().Aul() = 
                        (realnum)(eina(TauLine2[i].Emis().gf(),
                  TauLine2[i].EnergyWN(),(*TauLine2[i].Hi()).g()));

                /* coefficient needed for damping constant - units cm s-1 */
                TauLine2[i].Emis().dampXvel() = 
                        (realnum)(TauLine2[i].Emis().Aul()/
                  TauLine2[i].EnergyWN()/PI4);

                /* derive the abs coefficient, call to function is gf, wl (A), g_low */
                TauLine2[i].Emis().opacity() = 
                        (realnum)(abscf(TauLine2[i].Emis().gf(),
                  TauLine2[i].EnergyWN(),(*TauLine2[i].Lo()).g()));

                /* get pointer to energy in continuum mesh */
                TauLine2[i].ipCont() = ipLineEnergy(TauLine2[i].EnergyRyd(), chIonLbl(TauLine2[i]).c_str(),0 );
                TauLine2[i].Emis().ipFine() = ipFineCont(TauLine2[i].EnergyRyd() );
                /*if( TauLine2[i].ipCont()==751 )
                        fprintf(ioQQQ,"( atom_level2 %s\n", chLab);*/
        }

        /* hyperfine structure lines */
        for( size_t i=0; i < HFLines.size(); i++ )
        {
                ASSERT( HFLines[i].Emis().Aul() > 0. );
                /* coefficient needed for damping constant */
                HFLines[i].Emis().dampXvel() = 
                        (realnum)(HFLines[i].Emis().Aul()/
                        HFLines[i].EnergyWN()/PI4);
                HFLines[i].Emis().damp() = 1e-20f;

                /* derive the abs coefficient, call to function is gf, wl (A), g_low */
                HFLines[i].Emis().opacity() = 
                        (realnum)(abscf(HFLines[i].Emis().gf(),
                        HFLines[i].EnergyWN(),
                        (*HFLines[i].Lo()).g()));
                /* gf from this and 21 cm do not agree, A for HFS is 10x larger than level1 dat */
                /*fprintf(ioQQQ,"HFLinesss\t%li\t%.2e\t%.2e\t%.2e\t%.2e\t%.2e\n",
                        i,HFLines[i].Emis().opacity() , HFLines[i].Emis().gf() , HFLines[i].Emis().Aul() , HFLines[i].EnergyWN(),(*HFLines[i].Lo()).g());*/

                /* get pointer to energy in continuum mesh */
                HFLines[i].ipCont() = ipLineEnergy(HFLines[i].EnergyRyd() , chIonLbl(HFLines[i]).c_str(),0 );
                HFLines[i].Emis().ipFine() = ipFineCont(HFLines[i].EnergyRyd() );
        }

        /* the group of inner shell fluorescent lines */
        for( long i=0; i < t_yield::Inst().nlines(); ++i )
        {
                string chLab = chIonLbl( t_yield::Inst().nelem(i)+1, t_yield::Inst().ion_emit(i)+1 );
                t_yield::Inst().set_ipoint( i, ipLineEnergy( t_yield::Inst().energy(i) , chLab.c_str() , 0 ) );
        }

        /* ================================================================================== */
        /*        two photon two-photon 2-nu 2 nu 2 photon 2-photon                           */

        /* now loop over the two iso-sequences with two photon continua */
        for( long ipISO=ipH_LIKE; ipISO<NISO; ++ipISO )
        {
                /* set up two photon emission */
                for( long nelem=ipISO; nelem<LIMELM; ++nelem )
                {
                        if( dense.lgElmtOn[nelem] )
                        {
                                // upper level for two-photon emission in H and He iso sequences 
                                // The 1+ipISO is not rigorous, it just works for H- and He-like 
                                const int TwoS = (1+ipISO);
                                double Aul;
                                /* 2s two photon */
                                if( ipISO==ipH_LIKE )
                                        Aul =  8.226*powi((double)(nelem+1.),6);
                                else 
                                {
                                        ASSERT( ipISO==ipHE_LIKE );
                                        /* >>refer      Helike  2pho    Derevianko, A., & Johnson, W. R. 1997, Phys. Rev. A, 56, 1288
                                         * numbers are not explicitly given in this paper for Z=21-24,26,27,and 29.
                                         * So numbers given here are interpolated.      */
                                        fixit("where is 51.02 from? Value is 51.3 from the Derevianko & Johnson paper cited above.");
                                        const double As2nuFrom1S[29] = {51.02,1940.,1.82E+04,9.21E+04,3.30E+05,9.44E+05,2.31E+06,5.03E+06,1.00E+07,
                                        1.86E+07,3.25E+07,5.42E+07,8.69E+07,1.34E+08,2.02E+08,2.96E+08,4.23E+08,5.93E+08,8.16E+08,
                                        1.08E+09,1.43E+09,1.88E+09,2.43E+09,3.25E+09,3.95E+09,4.96E+09,6.52E+09,7.62E+09,9.94E+09};
                                        Aul =  As2nuFrom1S[nelem-1];
                                }
        
                                TwoPhotonSetup( iso_sp[ipISO][nelem].TwoNu, TwoS, 0, 
                                        Aul,
                                        iso_sp[ipISO][nelem].trans(TwoS,0),
                                        ipISO, nelem );
                        }
                }
        }

        // add He-like 2nu 2^3S - 1^1S
        {
                const long ipISO = ipHE_LIKE;
                for( long nelem=ipISO; nelem<LIMELM; ++nelem )
                {
                        if( dense.lgElmtOn[nelem] )
                        {
                                /* Important clarification, according to Derevianko & Johnson (see ref above), 2^3S can decay
                                 * to ground in one of two ways: through a two-photon process, or through a single-photon M1 decay,
                                 * but the M1 rates are about 10^4 greater that the two-photon decays throughout the entire
                                 * sequence.  Thus these numbers, are much weaker than the effective decay rate, but should probably
                                 * be treated in as a two-photon decay at some point    */
                                // >> refer     He      As      Drake, G. W. F., Victor, G. A., & Dalgarno, A. 1969, Physical Review, 180, 25                   
                                const double As2nuFrom3S[29] = {4.09e-9,1.25E-06,5.53E-05,8.93E-04,8.05E-03,4.95E-02,2.33E-01,8.94E-01,2.95E+00,
                                        8.59E+00,2.26E+01,5.49E+01,1.24E+02,2.64E+02,5.33E+02,1.03E+03,1.91E+03,3.41E+03,5.91E+03,
                                        9.20E+03,1.50E+04,2.39E+04,3.72E+04,6.27E+04,8.57E+04,1.27E+05,2.04E+05,2.66E+05,4.17E+05};
                
                                TwoPhotonSetup( iso_sp[ipISO][nelem].TwoNu, ipHe2s3S, ipHe1s1S,
                                        As2nuFrom3S[nelem-1],
                                        iso_sp[ipISO][nelem].trans(ipHe2s3S,ipHe1s1S),
                                        ipISO, nelem );
                        }
                }
        }

        {
                /* this is an option to print out one of the two photon continua */
                enum {DEBUG_LOC=false};
                if( DEBUG_LOC )
                {       
                        const int nCRS = 21;
                        double ener[nCRS]={
                          0.,     0.03738,  0.07506,  0.1124,  0.1498,  0.1875,
                          0.225,  0.263,    0.300,    0.3373,  0.375,   0.4127,
                          0.4500, 0.487,    0.525,    0.5625,  0.6002,  0.6376,
                          0.6749, 0.7126,   0.75};

                        long nelem = ipHYDROGEN;
                        long ipISO = ipHYDROGEN;
                        two_photon& tnu = iso_sp[ipISO][nelem].TwoNu[0];

                        double limit = tnu.ipTwoPhoE;

                        for( long i=0; i < nCRS; i++ )
                        {
                                fprintf(ioQQQ,"%.3e\t%.3e\n", ener[i] , 
                                        atmdat_2phot_shapefunction( ener[i]/0.75, ipISO, nelem ) );
                        }

                        double xnew = 0.;
                        for( long i=0; i < limit; i++ )
                        {
                                double fach = tnu.As2nu[i]/2.*rfield.anu2(i)/rfield.widflx(i)*EN1RYD;
                                fprintf(ioQQQ,"%.3e\t%.3e\t%.3e\n", 
                                        rfield.anu(i) , 
                                        tnu.As2nu[i] / rfield.widflx(i) , 
                                        fach );
                                xnew += tnu.As2nu[i];
                        }
                        fprintf(ioQQQ," sum is %.3e\n", xnew );
                        cdEXIT(EXIT_FAILURE);
                }
        }

        {
                enum {DEBUG_LOC=false};
                if( DEBUG_LOC )
                {       
                        for( long i=0; i<11; ++i )
                        {
                                (*TauDummy).WLAng() = (realnum)(PI * exp10((double)i));
                                fprintf(ioQQQ,"%.2f\t%s\n", (*TauDummy).WLAng() , chLineLbl(*TauDummy).c_str());
                        }
                        cdEXIT(EXIT_FAILURE);
                }
        }

        /* option to print out whole thing with "trace lines" command */
        if( trace.lgTrLine )
        {
                fprintf( ioQQQ, "       WL(Ang)   E(RYD)   IP   gl  gu      gf       A        damp     abs K\n" );

                /*Atomic Or Molecular lines*/
                for (int ipSpecies=0; ipSpecies < nSpecies; ++ipSpecies)
                {
                        for( EmissionList::iterator em=dBaseTrans[ipSpecies].Emis().begin();
                                  em != dBaseTrans[ipSpecies].Emis().end(); ++em)
                        {
                                long iWL_Ang = (long)(*em).Tran().WLAng();
                                
                                if( iWL_Ang > 1000000 )
                                {
                                        iWL_Ang /= 10000;
                                }
                                else if( iWL_Ang > 10000 )
                                {
                                        iWL_Ang /= 1000;
                                }
                                fprintf( ioQQQ, " %10.10s%5ld%10.3e %4li%4ld%4ld%10.2e%10.2e%10.2e%10.2e\n", 
                                                        chLineLbl((*em).Tran()).c_str(), iWL_Ang, RYDLAM/(*em).Tran().WLAng(), 
                                                        (*em).Tran().ipCont(), (long)((*(*em).Tran().Lo()).g()), 
                                                        (long)((*(*em).Tran().Hi()).g()),(*em).gf(), 
                                                        (*em).Aul(),(*em).dampXvel(), 
                                                        (*em).opacity());
                        }
                }

                for( long i=0; i < nWindLine; i++ )
                {
                        long iWL_Ang = (long)TauLine2[i].WLAng();

                        if( iWL_Ang > 1000000 )
                        {
                                iWL_Ang /= 10000;
                        }
                        else if( iWL_Ang > 10000 )
                        {
                                iWL_Ang /= 1000;
                        }
                        fprintf( ioQQQ, " %10.10s%5ld%10.3e %4li%4ld%4ld%10.2e%10.2e%10.2e%10.2e\n", 
                          chLineLbl(TauLine2[i]).c_str(), iWL_Ang, RYDLAM/TauLine2[i].WLAng(), 
                          TauLine2[i].ipCont(), (long)((*TauLine2[i].Lo()).g()), 
                          (long)((*TauLine2[i].Hi()).g()), TauLine2[i].Emis().gf(), 
                          TauLine2[i].Emis().Aul(), TauLine2[i].Emis().dampXvel(), 
                          TauLine2[i].Emis().opacity() );
                }
                for( size_t i=0; i < HFLines.size(); i++ )
                {
                        long iWL_Ang = (long)HFLines[i].WLAng();

                        if( iWL_Ang > 1000000 )
                        {
                                iWL_Ang /= 10000;
                        }
                        else if( iWL_Ang > 10000 )
                        {
                                iWL_Ang /= 1000;
                        }
                        fprintf( ioQQQ, " %10.10s%5ld%10.3e %4li%4ld%4ld%10.2e%10.2e%10.2e%10.2e\n", 
                          chLineLbl(HFLines[i]).c_str(), iWL_Ang, RYDLAM/HFLines[i].WLAng(), 
                          HFLines[i].ipCont(), (long)((*HFLines[i].Lo()).g()), 
                          (long)((*HFLines[i].Hi()).g()), HFLines[i].Emis().gf(), 
                          HFLines[i].Emis().Aul(), HFLines[i].Emis().dampXvel(), 
                          HFLines[i].Emis().opacity() );
                }
        }

        /* this is an option to kill fine structure line optical depths */
        if( !rt.lgFstOn )
        {
                /*Atomic or Molecular Lines-Humeshkar Nemala*/
                for (int ipSpecies=0; ipSpecies < nSpecies; ++ipSpecies)
                {
                        for( EmissionList::iterator em=dBaseTrans[ipSpecies].Emis().begin();
                                  em != dBaseTrans[ipSpecies].Emis().end(); ++em)
                        {
                                if((*em).Tran().EnergyWN() < 10000. )
                                {
                                        (*em).opacity() = 0.;
                                }
                        }
                }
        }

        /* read in continuum bands data set */
        ContBandsCreate( "" );

        /* we're done adding lines and states to the stacks.  
         * This flag is used to make sure we never add them again in this coreload. */
        lgLinesAdded = true;
        lgStatesAdded = true;
        
        checkTransitionListOfLists(AllTransitions);

        return;
}

/*ipShells assign continuum energy pointers to shells for all atoms,
 * called by ContCreatePointers */
STATIC void ipShells(
        /* nelem is the atomic number on the C scale, Li is 2 */
        long int nelem)
{
        long int 
          imax, 
          ion, 
          nelec, 
          ns, 
          nshell;
        /* following value cannot be used - will be set to proper threshold */
        double thresh=-DBL_MAX;

        DEBUG_ENTRY( "ipShells()" );

        ASSERT( nelem >= NISO);
        ASSERT( nelem < LIMELM );

        /* fills in pointers to valence shell ionization threshold
         * PH1(a,b,c,d)
         * a=1 => thresh, others fitting parameters
         * b atomic number
         * c number of electrons
         * d shell number 7-1 */

        /* threshold in Ryd
         * ion=0 for atom, up to nelem-1 for helium like, hydrogenic is elsewhere */
        for( ion=0; ion < nelem; ion++ )
        {
                string chLab = chIonLbl( nelem+1, ion+1 );

                /* this is the iso sequence - must not redo sequence if done as iso */
                long int ipISO = nelem-ion;

                /* number of bound electrons */
                nelec = ipISO+1;

                /* nsShells(nelem,ion) is the number of shells for ion with nelec electrons,
                 * physical not c scale */
                imax = Heavy.nsShells[nelem][ion];

                /* loop on all inner shells, valence shell */
                for( nshell=0; nshell < imax; nshell++ )
                {
                        /* ionization potential of this shell in rydbergs */
                        thresh = (double)(t_ADfA::Inst().ph1(nshell,nelec-1,nelem,0)/EVRYD* 0.9998787);
                        if( thresh <= 0.1 )
                        {
                                /* negative ip shell does not exist, set upper limit
                                 * to less than lower limit so this never looped upon
                                 * these are used as flags by LimitSh to check whether
                                 * this is a real shell - if 1 or 2 is changed - change LimitSh!! */
                                opac.ipElement[nelem][ion][nshell][0] = 2;
                                opac.ipElement[nelem][ion][nshell][1] = 1;
                        }
                        else
                        {
                                /* this is lower bound to energy range for this shell */
                                /* >>chng 02 may 27, change to version of ip with label, so that
                                 * inner shell edges will appear */
                                /*opac.ipElement[nelem][ion][nshell][0] = ipoint(thresh);*/
                                opac.ipElement[nelem][ion][nshell][0] = 
                                        ipContEnergy( thresh , chLab.c_str() );

                                /* this is upper bound to energy range for this shell 
                                 * LimitSh is an integer function, returns pointer
                                 * to threshold of next major shell.  For k-shell it
                                 * returns the values KshellLimit, default=7.35e4
                                 * >>chng 96 sep 26, had been below, result zero cross sec at 
                                 * many energies where opacity project did not produce state specific 
                                 * cross section */
                                opac.ipElement[nelem][ion][nshell][1] = 
                                        LimitSh(ion+1,  nshell+1,nelem+1);
                                ASSERT( opac.ipElement[nelem][ion][nshell][1] > 0);
                        }
                }

                ASSERT( imax > 0 && imax <= 7 );

                /* this will be index pointing to valence edge */
                /* [0] is pointer to threshold in energy array */
                opac.ipElement[nelem][ion][imax-1][0] = 
                        ipContEnergy(thresh, chLab.c_str());

                /* pointer to valence electron ionization potential */
                Heavy.ipHeavy[nelem][ion] = opac.ipElement[nelem][ion][imax-1][0];
                ASSERT( Heavy.ipHeavy[nelem][ion]>0 );

                /* ionization potential of valence shell in Ryd 
                 * thresh was evaluated above, now has last value, the valence shell */
                Heavy.Valence_IP_Ryd[nelem][ion] = thresh;

                Heavy.xLyaHeavy[nelem][ion] = 0.;
                if( ipISO >= NISO )
                {
                        /* this is set of 3/4 of valence shell IP, this is important
                         * source of ots deep in cloud */
                        Heavy.ipLyHeavy[nelem][ion] = 
                                ipLineEnergy(thresh*0.75, chLab.c_str(), 0);

                        Heavy.ipBalHeavy[nelem][ion] = 
                                ipLineEnergy(thresh*0.25, chLab.c_str(), 0);
                }
                else
                {
                        /* do not treat this simple way since done exactly with iso 
                         * sequences */
                        Heavy.ipLyHeavy[nelem][ion] = -1;
                        Heavy.ipBalHeavy[nelem][ion] = -1;
                }
        }

        /* above loop did up to hydrogenic, now do hydrogenic - 
         * hydrogenic is special since arrays already set up */
        Heavy.nsShells[nelem][nelem] = 1;

        /* this is lower limit to range */
        /* hydrogenic photoionization set to special hydro array 
         * this is pointer to threshold energy */
        /* this statement is in ContCreatePointers but has not been done when this routine called */
        /*iso_sp[ipH_LIKE][ipZ].fb[ipLo].ipIsoLevNIonCon = ipContEnergy(iso_sp[ipH_LIKE][ipZ].fb[ipLo].xIsoLevNIonRyd,chLab);*/
        /*opac.ipElement[nelem][nelem][0][0] = iso_sp[ipH_LIKE][nelem].fb[ipH1s].ipIsoLevNIonCon;*/
        opac.ipElement[nelem][nelem][0][0] = ipoint( t_ADfA::Inst().ph1(0,0,nelem,0)/EVRYD* 0.9998787 );
        ASSERT( opac.ipElement[nelem][nelem][0][0] > 0 );

        /* this is the high-energy limit */
        opac.ipElement[nelem][nelem][0][1] = continuum.KshellLimit;

        Heavy.ipHeavy[nelem][nelem] = opac.ipElement[nelem][nelem][0][0];

        /* this is for backwards computability with Cambridge code */
        if( trace.lgTrace && trace.lgPointBug )
        {
                for( ion=0; ion < (nelem+1); ion++ )
                {
                        fprintf( ioQQQ, "Ion:%3ld%3ld %2.2s%2.2s total shells:%3ld\n", 
                          nelem, ion+1, elementnames.chElementSym[nelem], elementnames.chIonStage[ion]
                          , Heavy.nsShells[nelem][ion] );
                        for( ns=0; ns < Heavy.nsShells[nelem][ion]; ns++ )
                        {
                                fprintf( ioQQQ, " shell%3ld %2.2s range eV%10.2e-%8.2e\n", 
                                  ns+1, Heavy.chShell[ns], rfield.anu(opac.ipElement[nelem][ion][ns][0]-1)*
                                  EVRYD, rfield.anu(opac.ipElement[nelem][ion][ns][1]-1)*EVRYD );
                        }
                }
        }
        return;
}

/*LimitSh sets upper energy limit to subshell integrations */
STATIC long LimitSh(long int ion, 
  long int nshell, 
  long int nelem)
{
        long int LimitSh_v;

        DEBUG_ENTRY( "LimitSh()" );

        /* this routine returns the high-energy limit to the energy range
         * for photoionization of a given shell
         * */
        if( nshell == 1 )
        {
                /* this limit is high-energy limit to code unless changed with set kshell */
                LimitSh_v = continuum.KshellLimit;

        }
        else if( nshell == 2 )
        {
                /* this is 2s shell, upper limit is 1s
                 * >>chng 96 oct 08, up to high-energy limit
                 * LimitSh = ipElement(nelem,ion , 1,1)-1 */
                LimitSh_v = continuum.KshellLimit;

        }
        else if( nshell == 3 )
        {
                /* this is 2p shell, upper limit is 1s
                 * >>chng 96 oct 08, up to high-energy limit
                 * LimitSh = ipElement(nelem,ion , 1,1)-1 */
                LimitSh_v = continuum.KshellLimit;

        }
        else if( nshell == 4 )
        {
                /* this is 3s shell, upper limit is 2p
                 * >>chng 96 oct 08, up to K-shell edge
                 * LimitSh = ipElement(nelem,ion , 3,1)-1 */
                LimitSh_v = opac.ipElement[nelem-1][ion-1][0][0] - 1;

        }
        else if( nshell == 5 )
        {
                /* this is 3p shell, upper limit is 2p
                 * >>chng 96 oct 08, up to K-shell edge
                 * LimitSh = ipElement(nelem,ion , 3,1)-1 */
                LimitSh_v = opac.ipElement[nelem-1][ion-1][0][0] - 1;

        }
        else if( nshell == 6 )
        {
                /* this is 3d shell, upper limit is 2p
                 * >>chng 96 oct 08, up to K-shell edge
                 * LimitSh = ipElement(nelem,ion , 3,1)-1 */
                LimitSh_v = opac.ipElement[nelem-1][ion-1][0][0] - 1;

        }
        else if( nshell == 7 )
        {
                /* this is 4s shell, upper limit is 3d */
                if( opac.ipElement[nelem-1][ion-1][5][0] < 3 )
                {
                        /* this is check for empty shell 6, 3d
                         * if so then set to 3p instead */
                        LimitSh_v = opac.ipElement[nelem-1][ion-1][4][0] - 
                          1;
                }
                else
                {
                        LimitSh_v = opac.ipElement[nelem-1][ion-1][5][0] - 
                          1;
                }
                /* >>chng 96 sep 26, set upper limit down to 2s */
                LimitSh_v = opac.ipElement[nelem-1][ion-1][2][0] - 1;

        }
        else
        {
                fprintf( ioQQQ, " LimitSh cannot handle nshell as large as%4ld\n", 
                  nshell );
                cdEXIT(EXIT_FAILURE);
        }
        return( LimitSh_v );
}

/*ContBandsCreate - read set of continuum bands to enter total emission into line*/
STATIC void ContBandsCreate(
        /* chFile is optional filename, if void then use default bands,
         * if not void then use file specified,
         * return value is 0 for success, 1 for failure */
         const char chFile[] )
{
        char chLine[FILENAME_PATH_LENGTH_2];
        const char* chFilename;
        FILE *ioDATA;

        bool lgEOL;
        long int i,k;

        /* keep track of whether we have been called - want to be
         * called a total of one time */
        static bool lgCalled=false;

        DEBUG_ENTRY( "ContBandsCreate()" );

        /* do nothing if second or later call*/
        if( lgCalled )
        {
                /* success */
                return;
        }
        lgCalled = true;

        /* use default filename if void string, else use file specified */
        chFilename = ( strlen(chFile) == 0 ) ? "continuum_bands.ini" : chFile;

        /* get continuum band data  */
        if( trace.lgTrace )
        {
                fprintf( ioQQQ, " ContBandsCreate opening %s:", chFilename );
        }

        ioDATA = open_data( chFilename, "r" );

        /* now count how many bands are in the file */
        continuum.nContBand = 0;

        /* first line is a magic number and does not count as a band*/
        if( read_whole_line( chLine , (int)sizeof(chLine) , ioDATA ) == NULL )
        {
                fprintf( ioQQQ, " ContBandsCreate could not read first line of %s.\n", chFilename );
                cdEXIT(EXIT_FAILURE);
        }
        while( read_whole_line( chLine , (int)sizeof(chLine) , ioDATA ) != NULL )
        {
                /* we want to count the lines that do not start with #
                 * since these contain data */
                if( chLine[0] != '#')
                        ++continuum.nContBand;
        }

        /* now rewind the file so we can read it a second time*/
        if( fseek( ioDATA , 0 , SEEK_SET ) != 0 )
        {
                fprintf( ioQQQ, " ContBandsCreate could not rewind %s.\n", chFilename );
                cdEXIT(EXIT_FAILURE);
        }

        continuum.ContBandWavelength = (realnum *)MALLOC(sizeof(realnum)*(unsigned)(continuum.nContBand) );
        continuum.chContBandLabels = (char **)MALLOC(sizeof(char *)*(unsigned)(continuum.nContBand) );
        continuum.ipContBandLow = (long int *)MALLOC(sizeof(long int)*(unsigned)(continuum.nContBand) );
        continuum.ipContBandHi = (long int *)MALLOC(sizeof(long int)*(unsigned)(continuum.nContBand) );
        continuum.BandEdgeCorrLow = (realnum *)MALLOC(sizeof(realnum)*(unsigned)(continuum.nContBand) );
        continuum.BandEdgeCorrHi = (realnum *)MALLOC(sizeof(realnum)*(unsigned)(continuum.nContBand) );

        /* now make second dim, id wavelength, and lower and upper bounds */
        for( i=0; i<continuum.nContBand; ++i )
        {
                /* array of labels, each 4 long plus 0 at [4] */
                continuum.chContBandLabels[i] = (char *)MALLOC(sizeof(char)*(unsigned)(5) );
        }

        /* first line is a versioning magic number - now confirm that it is valid */
        if( read_whole_line( chLine , (int)sizeof(chLine) , ioDATA ) == NULL )
        {
                fprintf( ioQQQ, " ContBandsCreate could not read first line of %s.\n", chFilename );
                cdEXIT(EXIT_FAILURE);
        }
        /* bands_continuum magic number here <- this string is in band_continuum.dat
         * with comment to search for this to find magic number  */
        {
                long int m1 , m2 , m3,
                // the magic number at the start of the data file
                        myr = 11, mmo = 9, mdy = 10;

                i = 1;
                m1 = (long)FFmtRead(chLine,&i,sizeof(chLine),&lgEOL);
                m2 = (long)FFmtRead(chLine,&i,sizeof(chLine),&lgEOL);
                m3 = (long)FFmtRead(chLine,&i,sizeof(chLine),&lgEOL);
                if( ( m1 != myr ) ||
                    ( m2 != mmo ) ||
                    ( m3 != mdy ) )
                {
                        fprintf( ioQQQ, 
                                " ContBandsCreate: the version of the data file %s I found (%li %li %li)is not the current version (%li %li %li).\n", 
                                chFilename ,
                                m1 , m2 , m3 ,
                                myr , mmo , mdy );
                        fprintf( ioQQQ, 
                                " ContBandsCreate: you need to update this file.\n");
                        cdEXIT(EXIT_FAILURE);
                }
        }

        /* now read in data again, but save it this time */
        k = 0;
        while( read_whole_line( chLine , (int)sizeof(chLine) , ioDATA ) != NULL )
        {
                /* we want to count the lines that do not start with #
                 * since these contain data */
                if( chLine[0] != '#')
                {
                        /* copy 4 char label plus termination */
                        strncpy( continuum.chContBandLabels[k] , chLine , 4 );
                        continuum.chContBandLabels[k][4] = 0;

                        /* now get central band wavelength 
                         * >>chng 06 aug 11 from 4 to 6, the first 4 char are labels and
                         * these can contain numbers, next comes a space, then the number */
                        i = 6;
                        continuum.ContBandWavelength[k] = (realnum)FFmtRead(chLine,&i,sizeof(chLine),&lgEOL);
                        /* >>chng 06 feb 21, multiply by 1e4 to convert micron wavelength into Angstroms,
                         * which is assumed by the code.  before this correction the band centroid 
                         * wavelength was given in the output incorrectly listed as Angstroms.
                         * results were correct just label was wrong */
                        continuum.ContBandWavelength[k] *= 1e4f;

                        /* these are short and long wave limits, which are high and
                         * low energy limits - these are now wl in microns but are
                         * converted to Angstroms */
                        double xHi = FFmtRead(chLine,&i,sizeof(chLine),&lgEOL)*1e4;
                        double xLow = FFmtRead(chLine,&i,sizeof(chLine),&lgEOL)*1e4;
                        if( lgEOL )
                        {
                                fprintf( ioQQQ, " There should have been 3 numbers on this band line.   Sorry.\n" );
                                fprintf( ioQQQ, " string==%s==\n" ,chLine );
                                cdEXIT(EXIT_FAILURE);
                        }

                        {
                                enum {DEBUG_LOC=false};
                                if( DEBUG_LOC )
                                {
                                        fprintf(ioQQQ, "READ:%s\n", chLine );
                                        fprintf(ioQQQ, "GOT: %s %g %g %g\n",continuum.chContBandLabels[k],
                                        continuum.ContBandWavelength[k] , xHi , xLow );
                                }
                        }

                        /* make sure bands bounds are in correct order, shorter - longer wavelength*/
                        if( xHi >= xLow )
                        {
                                fprintf( ioQQQ, " ContBandWavelength band %li "
                                        "edges are in improper order.\n" ,k);
                                fprintf(ioQQQ,"band: %s %.3e %.3e %.3e \n",
                                        continuum.chContBandLabels[k],
                                        continuum.ContBandWavelength[k],
                                        xHi , 
                                        xLow);
                                cdEXIT(EXIT_FAILURE);
                        }

                        // check that central wavelength is indeed between the limits
                        // xHi & xLow are hi and low energy limits to band so logic reversed
                        if( continuum.ContBandWavelength[k] < xHi ||
                                continuum.ContBandWavelength[k] > xLow )
                        {
                                fprintf( ioQQQ, " ContBandWavelength band %li central "
                                        "wavelength not within band.\n" ,k);
                                fprintf(ioQQQ,"band: %s %.3e %li %li \n",
                                        continuum.chContBandLabels[k],
                                        continuum.ContBandWavelength[k],
                                        continuum.ipContBandHi[k] , 
                                        continuum.ipContBandLow[k]);
                                cdEXIT(EXIT_FAILURE);
                        }

                        /* get continuum index - RYDLAM is 911.6A = 1 Ryd so 1e4 converts 
                         * micron to Angstrom - xHi is high energy (not wavelength)
                         * edge of the band */
                        continuum.ipContBandHi[k] = ipoint( RYDLAM / xHi );
                        continuum.ipContBandLow[k] = ipoint( RYDLAM / xLow );

                        /* fraction of first and last bin to include */
                        continuum.BandEdgeCorrLow[k] = 
                                (rfield.anumax(continuum.ipContBandLow[k]-1)-
                                (realnum)(RYDLAM/xLow)) /
                                rfield.widflx(continuum.ipContBandLow[k]-1);
                        ASSERT( continuum.BandEdgeCorrLow[k]>=0. && continuum.BandEdgeCorrLow[k]<=1.);
                        continuum.BandEdgeCorrHi[k] = ((realnum)(RYDLAM/xHi) -
                                rfield.anumin(continuum.ipContBandHi[k]-1)) /
                                rfield.widflx(continuum.ipContBandHi[k]-1);
                        ASSERT( continuum.BandEdgeCorrHi[k]>=0. && continuum.BandEdgeCorrHi[k]<=1.);
                        /*fprintf(ioQQQ,"DEBUG bands_continuum %s %.3e %li %li \n",
                                continuum.chContBandLabels[k],
                                continuum.ContBandWavelength[k],
                                continuum.ipContBandHi[k] , 
                                continuum.ipContBandLow[k]);*/

                        if( trace.lgTrace && trace.lgConBug )
                        {
                                if( k==0 )
                                        fprintf( ioQQQ, "   ContCreatePointer trace bands\n");
                                fprintf( ioQQQ, 
                                        "     band %ld label %s low wl= %.3e low ipnt= %li "
                                        " hi wl= %.3e hi ipnt= %li \n", 
                                        k, 
                                        continuum.chContBandLabels[k] ,
                                        xLow,
                                        continuum.ipContBandLow[k] ,
                                        xHi,
                                        continuum.ipContBandHi[k]  );
                        }
#                       if 0
                        // hazy table giving band properties
#                       include "prt.h"
                        fprintf(ioQQQ,
                                "DEBUG %s & ", 
                                continuum.chContBandLabels[k] );
                        prt_wl( ioQQQ , continuum.ContBandWavelength[k] );
                        fprintf(ioQQQ," & ");
                        prt_wl( ioQQQ , xHi );
                        fprintf(ioQQQ," -- ");
                        prt_wl( ioQQQ , xLow );
                        fprintf(ioQQQ,"\\\\ \n");
#                       endif
                        ++k;
                }
        }
        /* now validate this incoming data */
        for( i=0; i<continuum.nContBand; ++i )
        {
                /* make sure all are positive */
                if( continuum.ContBandWavelength[i] <=0. )
                {
                        fprintf( ioQQQ, " ContBandWavelength band %li has non-positive entry.\n",i );
                        cdEXIT(EXIT_FAILURE);
                }
        }

        fclose(ioDATA);
        return;
}