radius_increment.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 */
/*radius_increment do work associated with geometry increments of this zone, called before RT_tau_inc */
#include "cddefines.h"
#include "physconst.h"
#include "iso.h"
#include "hydrogenic.h"
#include "rfield.h"
#include "colden.h"
#include "geometry.h"
#include "opacity.h"
#include "thermal.h"
#include "doppvel.h"
#include "dense.h"
#include "mole.h"
#include "h2.h"
#include "timesc.h"
#include "hmi.h"
#include "lines_service.h"
#include "taulines.h"
#include "trace.h"
#include "wind.h"
#include "phycon.h"
#include "pressure.h"
#include "grainvar.h"
#include "molcol.h"
#include "conv.h"
#include "hyperfine.h"
#include "mean.h"
#include "struc.h"
#include "radius.h"
#include "gravity.h"

void radius_increment(void)
{

        long int nelem,
          i, 
          ion,
          nzone_minus_1 , 
          mol;
        double 
          avWeight,
          t;

        double ajmass, 
                Error,
          rjeans;

        DEBUG_ENTRY( "radius_increment()" );

        /* when this sub is called radius is the outer edge of zone */

        /* save information about structure of model
         * first zone is 1 but array starts at 0 - nzone_minus_1 is current zone
         * max nzone because abort during search phase gets here with nzone = -1 */
        nzone_minus_1 = MAX2( 0, nzone-1 );
        ASSERT(nzone_minus_1>=0 && nzone_minus_1 < struc.nzlim );

        struc.heatstr[nzone_minus_1] = thermal.htot;
        struc.coolstr[nzone_minus_1] = thermal.ctot;
        struc.testr[nzone_minus_1] = (realnum)phycon.te;

        /* number of particles per unit vol */
        struc.DenParticles[nzone_minus_1] = dense.pden;
        /* rjrw: add hden for dilution */
        struc.hden[nzone_minus_1] = (realnum)dense.gas_phase[ipHYDROGEN];
        /* total grams per unit vol */
        struc.DenMass[nzone_minus_1] = dense.xMassDensity;
        struc.volstr[nzone_minus_1] = (realnum)radius.dVeffAper;
        struc.drad[nzone_minus_1] = (realnum)radius.drad;
        struc.drad_x_fillfac[nzone_minus_1] = (realnum)radius.drad_x_fillfac;
        struc.histr[nzone_minus_1] = dense.xIonDense[ipHYDROGEN][0];
        struc.hiistr[nzone_minus_1] = dense.xIonDense[ipHYDROGEN][1];
        struc.ednstr[nzone_minus_1] = (realnum)dense.eden;
        struc.o3str[nzone_minus_1] = dense.xIonDense[ipOXYGEN][2];
        struc.pressure[nzone_minus_1] = (realnum)pressure.PresTotlCurr;
        struc.windv[nzone_minus_1] = (realnum)wind.windv;
        struc.AccelTotalOutward[nzone_minus_1] = wind.AccelTotalOutward;
        struc.AccelGravity[nzone_minus_1] = wind.AccelGravity;
        struc.pres_radiation_lines_curr[nzone_minus_1] = (realnum)pressure.pres_radiation_lines_curr;
        struc.GasPressure[nzone_minus_1] = (realnum)pressure.PresGasCurr;
        struc.depth[nzone_minus_1] = (realnum)radius.depth;
        /* save absorption optical depth from illuminated face to current position */
        struc.xLyman_depth[nzone_minus_1] = opac.TauAbsFace[iso_sp[ipH_LIKE][ipHYDROGEN].fb[ipH1s].ipIsoLevNIonCon];
        for( nelem=ipHYDROGEN; nelem<LIMELM; ++nelem)
        {
                struc.gas_phase[nelem][nzone_minus_1] = dense.gas_phase[nelem];
                for( ion=0; ion<nelem+2; ++ion )
                {
                        struc.xIonDense[nelem][ion][nzone_minus_1] = dense.xIonDense[nelem][ion];
                }
        }
        for( long ipISO=ipH_LIKE; ipISO<NISO; ++ipISO )
        {
                for( nelem=ipISO; nelem<LIMELM; ++nelem)
                {
                        if( dense.lgElmtOn[nelem] )
                        {
                                for( long level=0; level < iso_sp[ipISO][nelem].numLevels_max; ++level )
                                {
                                        struc.StatesElem[nelem][nelem-ipISO][level][nzone_minus_1] = (realnum)iso_sp[ipISO][nelem].st[level].Pop();
                                }
                        }
                }
        }

        /* the hydrogen molecules */
        for(mol=0;mol<mole_global.num_calc;mol++) 
        {
                struc.molecules[mol][nzone_minus_1] = (realnum) mole.species[mol].den;
        }
        struc.H2_abund[nzone_minus_1] = hmi.H2_total;

        // during abort many quantities used in this routine are in ill-defined
        // state - safer to do nothing here
        if( lgAbort )
        {
                return;
        }

        if( trace.lgTrace )
        {
                fprintf( ioQQQ, 
                        " radius_increment called; radius=%10.3e rinner=%10.3e DRAD=%10.3e drNext=%10.3e ROUTER=%10.3e DEPTH=%10.3e\n", 
                  radius.Radius, radius.rinner, radius.drad, radius.drNext, 
                  radius.StopThickness[iteration-1], radius.depth );
        }

        /* remember mean and largest errors on electron density */
        Error = fabs(dense.eden - dense.EdenTrue)/SDIV(dense.EdenTrue);
        if( Error > conv.BigEdenError )
        {
                conv.BigEdenError = (realnum)Error;
                dense.nzEdenBad = nzone;
        }
        conv.AverEdenError += (realnum)Error;

        dense.EdenMax = MAX2( dense.eden , dense.EdenMax);
        dense.EdenMin = MIN2( dense.eden , dense.EdenMin);

        /* remember mean and largest errors between heating and cooling */
        Error = fabs(thermal.ctot - thermal.htot) / thermal.ctot;
        conv.BigHeatCoolError = MAX2((realnum)Error , conv.BigHeatCoolError );
        conv.AverHeatCoolError += (realnum)Error;

        /* remember mean and largest pressure errors */
        Error = fabs(pressure.PresTotlError);
        conv.BigPressError = MAX2((realnum)Error , conv.BigPressError );
        conv.AverPressError += (realnum)Error;

        /* integrate total mass over model (relative to 4pi rinner^2) */
        dense.xMassTotal += (realnum)(dense.xMassDensity * radius.dVeffVol);

        /* check cooling time for this zone, remember longest */
        timesc.time_therm_long = MAX2(timesc.time_therm_long,1.5*dense.pden*BOLTZMANN*phycon.te/
          thermal.ctot);

        /* H 21 cm equilibrium timescale, H21cm returns H (not e) collisional 
         * deexcitation rate (not cs) */
        t = H21cm_H_atom( phycon.te )* dense.xIonDense[ipHYDROGEN][0] +
                /* >>chng 02 feb 14, add electron term as per discussion in */
                /* >>refer      H1      21cm    Liszt, H., 2001, A&A, 371, 698 */
                H21cm_electron( phycon.te )*dense.eden;

        /* only update time scale if t is significant */
        if( t > SMALLFLOAT )
                timesc.TimeH21cm = MAX2( 1./t, timesc.TimeH21cm );

        /* remember longest CO timescale */
        if( (double)dense.xIonDense[ipCARBON][0]*(double)dense.xIonDense[ipOXYGEN][0] > SMALLFLOAT )
        {
                int ipCO = findspecies("CO")->index;
                /* this is rate CO is destroyed, equal to formation rate in equilibrium */
                if (ipCO != -1)
                        timesc.BigCOMoleForm = MAX2( timesc.BigCOMoleForm, 1./SDIV(mole.species[ipCO].snk ));
        }

        /* remember longest H2  destruction timescale timescale */
        timesc.time_H2_Dest_longest = MAX2(timesc.time_H2_Dest_longest, timesc.time_H2_Dest_here );

        /* remember longest H2 formation timescale timescale */
        timesc.time_H2_Form_longest = MAX2( timesc.time_H2_Form_longest , timesc.time_H2_Form_here );

        /* increment counter if this zone possibly thermally unstable
         * this flag was set in conv_temp_eden_ioniz.cpp, 
         * derivative of heating and cooling negative */
        if( thermal.lgUnstable )
                thermal.nUnstable += 1;

        /* remember Stromgren radius - where hydrogen ionization falls below half */
        if( !rfield.lgUSphON && dense.xIonDense[ipHYDROGEN][0]/dense.gas_phase[ipHYDROGEN] > 0.49 )
        {
                rfield.rstrom = (realnum)radius.Radius;
                rfield.lgUSphON = true;
        }

        /* remember the largest value */
        wind.AccelMax = (realnum)MAX2(wind.AccelMax,wind.AccelTotalOutward);

        /* keep track of average acceleration */
        wind.AccelAver += wind.AccelTotalOutward*(realnum)radius.drad_x_fillfac;
        wind.acldr += (realnum)radius.drad_x_fillfac;

        /* following is integral of radiative force */
        pressure.pinzon = (realnum)(wind.AccelTotalOutward*dense.xMassDensity*
                radius.drad_x_fillfac*geometry.DirectionalCosin);
        /*fprintf(ioQQQ," debuggg pinzon %.2f %.2e %.2e %.2e\n", 
                fnzone,pressure.pinzon,dense.xMassDensity,wind.AccelTotalOutward);*/
        pressure.PresInteg += pressure.pinzon;

        // the integrated acceleration due to electron scattering, neglecting
        // absorption
        static realnum AccelElecScatZone1;
        if( nzone == 1 )
                AccelElecScatZone1 = wind.AccelElectron;
        pressure.pinzon_PresIntegElecThin = (realnum)(AccelElecScatZone1*dense.xMassDensity/radius.r1r0sq*
                radius.drad_x_fillfac*geometry.DirectionalCosin);
        pressure.PresIntegElecThin += pressure.pinzon_PresIntegElecThin;

        /* integrate gravitational pressure term */
        GravitationalPressure();
        pressure.IntegRhoGravity += pressure.RhoGravity;

        /* sound is sound travel time, sqrt term is sound speed */
        timesc.sound_speed_isothermal = sqrt(pressure.PresGasCurr/dense.xMassDensity);
        /* adiabatic sound speed assuming mono-atomic gas - gamma is 5/3*/
        timesc.sound_speed_adiabatic = sqrt(5.*pressure.PresGasCurr/(3.*dense.xMassDensity) );
        timesc.sound += radius.drad_x_fillfac / timesc.sound_speed_isothermal;

        /* save largest relative change in heating or cooling between this 
         * iteration and previous iteration at this zone
         * may be used to set time step in time dependent sims 
         * nzonePreviousIteration is number of zones in previous iteration,
         * 1 if only 1 done, while nzone_minus_1 is 1 on first zone */
        if( iteration > 1 && nzone_minus_1 < struc.nzonePreviousIteration )
        {
                /* set largest relative changes in heating/cooling between current
                 * and previous zones */
                realnum TempChange = (realnum)
                        fabs( (phycon.te-struc.testr[nzone_minus_1])/phycon.te);

                struc.TempChangeMax = MAX2( struc.TempChangeMax , TempChange );
        }
        else
        {
                /* zero out on first iteration */
                struc.TempChangeMax = 0.;
        }
        /*fprintf(ioQQQ,"DEBUG radius_increment iteration %li Heat %.2e Cool %.2e change max \n",
                iteration , struc.HeatChangeMax , struc.CoolChangeMax);*/

        colden.dlnenp += dense.eden*(double)(dense.xIonDense[ipHYDROGEN][1])*radius.drad_x_fillfac;
        colden.dlnenHep += dense.eden*(double)(dense.xIonDense[ipHELIUM][1])*radius.drad_x_fillfac;
        colden.dlnenHepp += dense.eden*(double)(dense.xIonDense[ipHELIUM][2])*radius.drad_x_fillfac;
        colden.dlnenCp += dense.eden*(double)(dense.xIonDense[ipCARBON][1])*radius.drad_x_fillfac;

        // column densities of all states 
        for( unsigned i = 0; i < mole.species.size(); ++i )
        {
                if( mole.species[i].levels != NULL )
                {
                        for( qList::iterator st = mole.species[i].levels->begin(); st != mole.species[i].levels->end(); ++st )
                        {
                                (*st).ColDen() += radius.drad_x_fillfac * (*st).Pop();
                        }
                }
        }

        /* integral of n(H0) / Tspin - related to 21 cm optical depth*/
        if( hyperfine.Tspin21cm > SMALLFLOAT )
                colden.H0_ov_Tspin += (double)(dense.xIonDense[ipHYDROGEN][0]) / hyperfine.Tspin21cm*radius.drad_x_fillfac;

        /* >>chng 05 Mar 07, add integral of n(OH) / Tspin */
        colden.OH_ov_Tspin += (double)(findspecieslocal("OH")->den) / phycon.te*radius.drad_x_fillfac;

        /* this is Lya excitation temperature */
        hydro.TexcLya = (realnum)TexcLine( iso_sp[ipH_LIKE][ipHYDROGEN].trans(ipH2p,ipH1s) );

        /* count number of times Lya excitation temp hotter than gas */
        if( hydro.TexcLya > phycon.te )
        {
                hydro.nLyaHot += 1;
                if( hydro.TexcLya > hydro.TLyaMax )
                {
                        hydro.TLyaMax = hydro.TexcLya;
                        hydro.TeLyaMax = (realnum)phycon.te;
                        hydro.nZTLaMax = nzone;
                }
        }

        /* column densities in various species */
        colden.colden[ipCOL_HTOT] += (realnum)(dense.gas_phase[ipHYDROGEN]*radius.drad_x_fillfac);
        ASSERT( colden.colden[ipCOL_HTOT] >SMALLFLOAT );
        colden.colden[ipCOL_HMIN] += (realnum)(findspecieslocal("H-")->den*radius.drad_x_fillfac);
        /* >>chng 02 sep 20, from htwo to H2_total */
        /* >>chng 05 mar 14, rather than H2_total, give H2g and H2s */
        colden.colden[ipCOL_H2g] += (realnum)(findspecieslocal("H2")->den*(realnum)radius.drad_x_fillfac);
        colden.colden[ipCOL_H2s] += (realnum)(findspecieslocal("H2*")->den*(realnum)radius.drad_x_fillfac);
        /* this is a special form of column density - should be proportional to total shielding */
        colden.coldenH2_ov_vel += hmi.H2_total*(realnum)radius.drad_x_fillfac / GetDopplerWidth(2.f*dense.AtomicWeight[ipHYDROGEN]);
        colden.colden[ipCOL_HeHp] += (realnum)(findspecieslocal("HeH+")->den*(realnum)radius.drad_x_fillfac);
        colden.colden[ipCOL_H2p] += (realnum)(findspecieslocal("H2+")->den*(realnum)radius.drad_x_fillfac);
        colden.colden[ipCOL_H3p] += (realnum)(findspecieslocal("H3+")->den*(realnum)radius.drad_x_fillfac);
        colden.colden[ipCOL_Hp] += dense.xIonDense[ipHYDROGEN][1]*(realnum)radius.drad_x_fillfac;
        colden.colden[ipCOL_H0] += dense.xIonDense[ipHYDROGEN][0]*(realnum)radius.drad_x_fillfac;

        colden.colden[ipCOL_elec] += (realnum)(dense.eden*radius.drad_x_fillfac);
        /* He I t2S column density*/
        colden.He123S += iso_sp[ipHE_LIKE][ipHELIUM].st[ipHe2s3S].Pop()*(realnum)radius.drad_x_fillfac;

        /* the ortho and para column densities */
        h2.ortho_colden += h2.ortho_density*radius.drad_x_fillfac;
        h2.para_colden += h2.para_density*radius.drad_x_fillfac;
        if( hmi.H2_total > SMALLFLOAT )
                ASSERT( fabs( h2.ortho_density + h2.para_density - hmi.H2_total ) / hmi.H2_total < 1e-4 );
        /*fprintf(ioQQQ,"DEBUG ortho para\t%.3e\t%.3e\ttot\t%.3e\t or pa colden\t%.3e\t%.3e\n", 
                h2.ortho_density, h2.para_density,hmi.H2_total,
                h2.ortho_colden , h2.para_colden);*/

        /*>>chng 27mar, GS, Column density of F=0 and F=1 levels of H0*/
        colden.H0_21cm_upper += ((*HFLines[0].Hi()).Pop()*radius.drad_x_fillfac);
        colden.H0_21cm_lower += ((*HFLines[0].Lo()).Pop()*radius.drad_x_fillfac);
        /*fprintf(ioQQQ,"DEBUG pophi-poplo\t%.3e\t%.3e\radius\t%.3e\t col_hi\t%.3e\t%.3e\n", 
                HFLines[0].PopHi, HFLines[0].PopLo, radius.drad_x_fillfac,
                 HFLines[0].PopHi*radius.drad_x_fillfac,colden.H0_21cm_upper );*/

        /* the CII and SiII atoms are resolved */
        for( i=0; i < 5; i++ )
        {
                /* pops and column density for C II atom */
                colden.C2Colden[i] += colden.C2Pops[i]*(realnum)radius.drad_x_fillfac;
                /* pops and column density for SiII atom */
                colden.Si2Colden[i] += colden.Si2Pops[i]*(realnum)radius.drad_x_fillfac;
        }
        for( i=0; i < 3; i++ )
        {
                /* pops and column density for CI atom */
                colden.C1Colden[i] += colden.C1Pops[i]*(realnum)radius.drad_x_fillfac;
                /* pops and column density for OI atom */
                colden.O1Colden[i] += colden.O1Pops[i]*(realnum)radius.drad_x_fillfac;
        }
        for( i=0; i < 4; i++ )
        {
                /* pops and column density for CIII atom */
                colden.C3Colden[i] += colden.C3Pops[i]*(realnum)radius.drad_x_fillfac;
        }

        /* now add total molecular column densities */
        molcol("ADD ",ioQQQ);

        /* increment forming the mean ionization and temperature */
        mean.MeanInc();

        /*-----------------------------------------------------------------------*/

        /* calculate average atomic weight per hydrogen of the plasma */
        avWeight = 0.;
        for( nelem=0; nelem < LIMELM; nelem++ ) 
        {
                avWeight += dense.gas_phase[nelem]*dense.AtomicWeight[nelem];
        }
        avWeight /= dense.gas_phase[ipHYDROGEN];

        /* compute some average grain properties */
        rfield.opac_mag_B_point = 0.;
        rfield.opac_mag_V_point = 0.;
        rfield.opac_mag_B_extended = 0.;
        rfield.opac_mag_V_extended = 0.;
        for( size_t nd=0; nd < gv.bin.size(); nd++ )
        {
                /* this is total extinction in magnitudes at V and B, for a point source 
                 * total absorption and scattering,
                 * does not discount forward scattering to be similar to stellar extinction
                 * measurements made within ism */
                rfield.opac_mag_B_point += (gv.bin[nd]->dstab1[rfield.ipB_filter-1] +
                        gv.bin[nd]->pure_sc1[rfield.ipB_filter-1])*double(gv.bin[nd]->dstAbund)*
                        double(dense.gas_phase[ipHYDROGEN]) * OPTDEP2EXTIN;

                rfield.opac_mag_V_point += (gv.bin[nd]->dstab1[rfield.ipV_filter-1] +
                        gv.bin[nd]->pure_sc1[rfield.ipV_filter-1])*double(gv.bin[nd]->dstAbund)*
                        double(dense.gas_phase[ipHYDROGEN]) * OPTDEP2EXTIN;

                /* this is total extinction in magnitudes at V and B, for an extended source 
                 * total absorption and scattering,
                 * DOES discount forward scattering to apply for extended source like Orion */
                rfield.opac_mag_B_extended += (gv.bin[nd]->dstab1[rfield.ipB_filter-1] +
                        gv.bin[nd]->pure_sc1[rfield.ipB_filter-1]*gv.bin[nd]->asym[rfield.ipB_filter-1])*
                        double(gv.bin[nd]->dstAbund)*double(dense.gas_phase[ipHYDROGEN]) * OPTDEP2EXTIN;

                rfield.opac_mag_V_extended += (gv.bin[nd]->dstab1[rfield.ipV_filter-1] +
                        gv.bin[nd]->pure_sc1[rfield.ipV_filter-1]*gv.bin[nd]->asym[rfield.ipV_filter-1])*
                        double(gv.bin[nd]->dstAbund)*double(dense.gas_phase[ipHYDROGEN]) * OPTDEP2EXTIN;

                gv.bin[nd]->avdust += gv.bin[nd]->tedust*(realnum)radius.drad_x_fillfac;
                gv.bin[nd]->avdft += gv.bin[nd]->DustDftVel*(realnum)radius.drad_x_fillfac;
                gv.bin[nd]->avdpot += (realnum)(gv.bin[nd]->dstpot*EVRYD*radius.drad_x_fillfac);
                gv.bin[nd]->avDGRatio += (realnum)(gv.bin[nd]->dustp[1]*gv.bin[nd]->dustp[2]*
                        gv.bin[nd]->dustp[3]*gv.bin[nd]->dustp[4]*gv.bin[nd]->dstAbund/avWeight*
                        radius.drad_x_fillfac);
        }

        // doing the update outside the loop not only safes a few cycles, but also
        // minimizes the chance of the update getting lost in the numerical precision
        // that could lead to the sim never hitting A_V to go, and getting indefinitely
        // stuck at an epsilon distance before the requested A_V instead...
        rfield.extin_mag_B_point += rfield.opac_mag_B_point*radius.drad_x_fillfac;
        rfield.extin_mag_V_point += rfield.opac_mag_V_point*radius.drad_x_fillfac;
        rfield.extin_mag_B_extended += rfield.opac_mag_B_extended*radius.drad_x_fillfac;
        rfield.extin_mag_V_extended += rfield.opac_mag_V_extended*radius.drad_x_fillfac;

        /* there are some quantities needed to calculation the Jeans mass and radius */
        colden.TotMassColl += dense.xMassDensity*(realnum)radius.drad_x_fillfac;
        colden.tmas += (realnum)phycon.te*dense.xMassDensity*(realnum)radius.drad_x_fillfac;
        colden.wmas += dense.wmole*dense.xMassDensity*(realnum)radius.drad_x_fillfac;

        /* now find minimum Jeans length and mass; length in cm */
        rjeans = 7.79637 + (phycon.alogte - log10(dense.wmole) - log10(dense.xMassDensity*
          geometry.FillFac))/2.;

        /* minimum Jeans mass in gm */
        ajmass = 3.*(rjeans - 0.30103) + log10(4.*PI/3.*dense.xMassDensity*
          geometry.FillFac);

        /* now remember smallest */
        colden.rjnmin = MIN2(colden.rjnmin,(realnum)rjeans);
        colden.ajmmin = MIN2(colden.ajmmin,(realnum)ajmass);

        if( trace.lgTrace )
        {
                fprintf( ioQQQ, " radius_increment returns\n" );
        }
        return;
}