sanity_check.cpp

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/* This file is part of Cloudy and is copyright (C)1978-2022 by Gary J. Ferland and
 * others.  For conditions of distribution and use see copyright notice in license.txt */
/*SanityCheck, check that various parts of the code still work, called by Cloudy after continuum
 * and optical depth arrays are set up, but before initial temperature and ionization */
#include "cddefines.h"
#include "dense.h"
#include "elementnames.h"
#include "continuum.h"
#include "rfield.h"
#include "iso.h"
#include "opacity.h"
#include "hydro_bauman.h"
#include "heavy.h"
#include "trace.h"
#include "freebound.h"
#include "integrate.h"
#include "atmdat_gaunt.h"
#include "cloudy.h"

#ifndef NDEBUG
namespace {
        class my_Integrand: public std::unary_function<double, double>
        {
        public:
                double operator() (double x) const
                {
                        return sin(x);
                }
                // the constructor is needed to avoid warnings by the Sun Studio compiler
                my_Integrand() {}
        };

        // create a version of sin with C++ linkage
        // this is done because we need a C++ pointer to this routine below
        double mySin(double x)
        {
                return sin(x);
        }
}
#endif

/* NB - this routine must not change any global variables - any that are changed as part of
 * a test must be reset, so that the code retains state */

STATIC void SanityCheckBegin();
STATIC void SanityCheckFinal();
STATIC void SanityCheckGaunt(long Z, double loggam2, double logu, double refval, double relerr);

/* chJob is either "begin" or "final" 
 * "begin is before code starts up
 * "final is after model is complete */
void SanityCheck( const char *chJob )
{
        DEBUG_ENTRY( "SanityCheck()" );

        if( strcmp(chJob,"begin") == 0 )
        {
                SanityCheckBegin();
        }
        else if( strcmp(chJob,"final") == 0 )
        {
                SanityCheckFinal();
        }
        else
        {
                fprintf(ioQQQ,"SanityCheck called with insane argument.\n");
                cdEXIT(EXIT_FAILURE);
        }
}

STATIC void SanityCheckFinal()
{
        /* PrtComment also has some ending checks on sanity */
}

STATIC void SanityCheckBegin()
{
        bool lgOK=true;
        int lgFlag;// error return for spsort, 0 success, >=1 for errors
        int32 ner, ipiv[3];
        long    i , 
                j , 
                nelem , 
                ion ,
                nshells;
        double *A;

        /* this will be charge to the 4th power */
        double Aul ,
                error,
                Z4;

        long n;

        const int NDIM = 10;
        double xMatrix[NDIM][NDIM] , yVector[NDIM] ,
                rcond;
        realnum *fvector;
        long int *ipvector;

        DEBUG_ENTRY( "SanityCheck()" );

        /*********************************************************
         *                                                       *
         * confirm that various part of cloudy still work        *
         *                                                       *
         *********************************************************/

        /* if this is no longer true at end, we have a problem */
        lgOK = true;

        /*********************************************************
         *                                                       *
         * check that all the Lyas As are ok                     *
         *                                                       *
         *********************************************************/
        for( nelem=0; nelem<LIMELM; ++nelem )
        {
                /* this element may be turned off */
                if( dense.lgElmtOn[nelem] )
                { 
                        /* H_Einstein_A( n, l, np, lp, iz ) - all are on physics scale */
                        Aul = H_Einstein_A( 2, 1, 1, 0, nelem+1 );
                        /*fprintf(ioQQQ,"%li\t%.4e\n", nelem+1, iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().Aul() );*/
                        if( fabs(Aul - iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().Aul() ) /Aul > 0.01 )
                        {
                                fprintf(ioQQQ," SanityCheck found insane H-like As.\n");
                                lgOK = false;
                        }
                }
        }

        /*********************************************************
         *                                                       *
         * check that gaunt factors are good                     *
         *                                                       *
         *********************************************************/
        // our Gaunt factors are merged relativistic and non-relativistic data
        // for high gamma^2 we have non-relativistic data, these are compared to Sutherland (1998)
        // for low gamma^2 we have relativistic data, these are compared to Nozawa+ (1998)
        // more elaborate checks are done in the unit test suite

        // these data were taken from
        // >>refer      HI      gff     Sutherland R.S., 1998, MNRAS, 300, 321
        SanityCheckGaunt( 1, 4., -4., 2.7008, 0.0004 );
        SanityCheckGaunt( 1, 4., 4., 1.1040, 0.0004 );
        SanityCheckGaunt( 1, 4., 0., 1.0237, 0.0004 );
        SanityCheckGaunt( 2, 3., -3., 2.2126, 0.0004 );
        SanityCheckGaunt( 2, 1., -1., 1.5088, 0.0004 );
        // these data were taken from
        // >>refer      gff     Nozawa S., Itoh N., Kohyama Y., 1998, ApJ, 507, 530
        SanityCheckGaunt( 1, -4., -4., 6.120, 0.005 );
        SanityCheckGaunt( 2, -4., -4., 8.934, 0.005 );
        SanityCheckGaunt( 1, -3., -1., 1.852, 0.005 );
        SanityCheckGaunt( 2, -3., -1., 1.921, 0.005 );
        SanityCheckGaunt( 1, 0., 3., 0.2001, 0.005 );
        SanityCheckGaunt( 2, 0., 3., 0.2041, 0.005 );

        /*********************************************************
         *                                                       *
         * check some transition probabililties for he-like ions *
         *                                                       *
         *********************************************************/
        for( nelem=1; nelem<LIMELM; ++nelem )
        {
                /* the helike 9-1 transition, A(3^3P to 2^3S) */
                double as[]={
                 /* updated with Johnson values */
                 0.       ,9.47e+006 ,3.44e+008 ,1.74e+009 ,5.51e+009 ,1.34e+010 ,
                2.79e+010 ,5.32E+010 ,8.81e+010 ,1.46E+011 ,2.15e+011 ,3.15e+011 ,
                4.46e+011 ,6.39E+011 ,8.26e+011 ,1.09e+012 ,1.41e+012 ,1.86E+012 ,
                2.26e+012 ,2.80e+012 ,3.44e+012 ,4.18e+012 ,5.04e+012 ,6.02e+012 ,
                7.14e+012 ,8.40e+012 ,9.83e+012 ,1.14e+013 ,1.32e+013 ,1.52e+013
                };

                if( iso_sp[ipHE_LIKE][nelem].numLevels_max > 8 && dense.lgElmtOn[nelem])
                {       
                        /* following used to print current values of As */
                        if( fabs( as[nelem] - iso_sp[ipHE_LIKE][nelem].trans(9,1).Emis().Aul() ) /as[nelem] > 0.025 )
                        {
                                fprintf(ioQQQ,
                                        " SanityCheck found insane He-like As: expected, nelem=%li found: %.2e %.2e.\n",
                                        nelem,
                                        as[nelem] , 
                                        iso_sp[ipHE_LIKE][nelem].trans(9,1).Emis().Aul() );
                                lgOK = false;
                        }
                }
        }

        /* only do this test if case b is not in effect */
        if( !opac.lgCaseB )
        {

                for( i = 0; i <=110; i++ )
                {
                        double DrakeTotalAuls[111] = {
                                -1.0000E+00, -1.0000E+00, -1.0000E+00, 1.02160E+07,
                                1.02160E+07, 1.02160E+07, 1.80090E+09, 2.78530E+07,
                                1.82990E+07, 1.05480E+07, 7.07210E+07, 6.37210E+07,
                                5.79960E+08, 1.60330E+07, 1.13640E+07, 7.21900E+06,
                                3.11920E+07, 2.69830E+07, 1.38380E+07, 1.38330E+07,
                                2.52270E+08, 9.20720E+06, 6.82220E+06, 4.56010E+06,
                                1.64120E+07, 1.39290E+07, 7.16030E+06, 7.15560E+06,
                                4.25840E+06, 4.25830E+06, 1.31150E+08, 5.62960E+06,
                                4.29430E+06, 2.95570E+06, 9.66980E+06, 8.12340E+06,
                                4.19010E+06, 4.18650E+06, 2.48120E+06, 2.48120E+06,
                                1.64590E+06, 1.64590E+06, 7.65750E+07, 3.65330E+06,
                                2.84420E+06, 1.99470E+06, 6.16640E+06, 5.14950E+06,
                                2.66460E+06, 2.66200E+06, 1.57560E+06, 1.57560E+06,
                                1.04170E+06, 1.04170E+06, 7.41210E+05, 7.41210E+05,
                                4.84990E+07, 2.49130E+06, 1.96890E+06, 1.39900E+06,
                                4.16900E+06, 3.46850E+06, 1.79980E+06, 1.79790E+06,
                                1.06410E+06, 1.06410E+06, 7.02480E+05, 7.02480E+05,
                                4.98460E+05, 4.98460E+05, -1.0000E+00, -1.0000E+00,
                                3.26190E+07, 1.76920E+06, 1.41440E+06, 1.01460E+06,
                                2.94830E+06, 2.44680E+06, 1.27280E+06, 1.27140E+06,
                                7.52800E+05, 7.52790E+05, 4.96740E+05, 4.96740E+05,
                                3.51970E+05, 3.51970E+05, -1.0000E+00, -1.0000E+00,
                                -1.0000E+00, -1.0000E+00, 2.29740E+07, 1.29900E+06,
                                1.04800E+06, 7.57160E+05, 2.16090E+06, 1.79030E+06,
                                9.33210E+05, 9.32120E+05, 5.52310E+05, 5.52310E+05,
                                3.64460E+05, 3.64460E+05, 2.58070E+05, 2.58070E+05,
                                -1.0000E+00, -1.0000E+00, -1.0000E+00, -1.0000E+00,
                                -1.0000E+00, -1.0000E+00, 1.67840E+07};

                        if( DrakeTotalAuls[i] > 0. && 
                                i < iso_sp[ipHE_LIKE][ipHELIUM].numLevels_max - iso_sp[ipHE_LIKE][ipHELIUM].nCollapsed_max)
                        {
                                if( fabs( DrakeTotalAuls[i] - (1./iso_sp[ipHE_LIKE][ipHELIUM].st[i].lifetime()) ) /DrakeTotalAuls[i] > 0.001 )
                                {
                                        fprintf(ioQQQ,
                                                " SanityCheck found helium lifetime outside 0.1 pct of Drake values: index, expected, found: %li %.4e %.4e\n",
                                                i,
                                                DrakeTotalAuls[i], 
                                                (1./iso_sp[ipHE_LIKE][ipHELIUM].st[i].lifetime()) );
                                        lgOK = false;
                                }
                        }
                }
        }

        /*********************************************************
         *                                                       *
         * check the threshold photoionization cs for He I       *
         *                                                       *
         *********************************************************/
        if( dense.lgElmtOn[ipHELIUM] )
        {
                /* HeI photoionization cross sections at threshold for lowest 20 levels */
                const int NHE1CS = 20;
                double he1cs[NHE1CS] = 
                {
                        5.480E-18 , 9.253E-18 , 1.598E-17 , 1.598E-17 , 1.598E-17 , 1.348E-17 , 
                        8.025E-18 , 1.449E-17 , 2.852E-17 , 1.848E-17 , 1.813E-17 , 2.699E-17 , 
                        1.077E-17 , 2.038E-17 , 4.159E-17 , 3.670E-17 , 3.575E-17 , 1.900E-17 , 
                        1.900E-17 , 4.175E-17 
                };

                /* loop over levels and check on photo cross section */
                j = MIN2( NHE1CS+1 , iso_sp[ipHE_LIKE][ipHELIUM].numLevels_max -iso_sp[ipHE_LIKE][ipHELIUM].nCollapsed_max );
                for( n=1; n<j; ++n )
                {
                        /* above list of levels does not include the ground */
                        i = iso_sp[ipHE_LIKE][ipHELIUM].fb[n].ipOpac;
                        ASSERT( i>0 );
                        /*fprintf(ioQQQ,"%li\t%lin", n , i );*/
                        /* >>chng 02 apr 10, from 0.01 to 0.02, values stored
                         * where taken from calc at low contin resolution, when continuum
                         * resolution changed this changes too */
                        /*fprintf(ioQQQ,"%li %.2e\n", n,( he1cs[n-1] - opac.OpacStack[i - 1] ) /he1cs[n-1] );*/
                        /* >>chng 02 jul 16, limt from 0.02 to 0.04, so that "set resolution 4" will work */
                        /* >>chng 04 may 18, levels 10 and 11 are about 12% off - because of energy binning, chng from 0.08 to 0.15 */ 
                        if( fabs( he1cs[n-1] - opac.OpacStack[i - 1] ) /he1cs[n-1] > 0.15 )
                        {
                                fprintf(ioQQQ,
                                        " SanityCheck found insane HeI photo cs: expected, n=%li found: %.3e %.3e.\n",
                                        n,
                                        he1cs[n-1] , 
                                        opac.OpacStack[i - 1]);
                                fprintf(ioQQQ,
                                        " n=%li, l=%li, s=%li\n",
                                        iso_sp[ipHE_LIKE][ipHELIUM].st[n].n() ,
                                        iso_sp[ipHE_LIKE][ipHELIUM].st[n].l() ,
                                        iso_sp[ipHE_LIKE][ipHELIUM].st[n].S());
                                lgOK = false;
                        }
                }
        }

        for( long ipISO=ipH_LIKE; ipISO<NISO; ipISO++ )
        {
                long nelem = ipISO;
                /* Check for agreement between on-the-fly and interpolation calculations
                 * of recombination, but only if interpolation is turned on. */
                if( !iso_ctrl.lgNoRecombInterp[ipISO] )
                {
                        /* check the recombination coefficients for ground state */
                        error = fabs( iso_recomb_check( ipISO, nelem , 0 , 7500. ) );
                        if( error > 0.01 )
                        {
                                fprintf(ioQQQ,
                                        " SanityCheck found insane1 %s %s recom coef: expected, n=%i error: %.2e \n",
                                        iso_ctrl.chISO[ipISO],
                                        elementnames.chElementSym[nelem],
                                        0,
                                        error );
                                lgOK = false;
                        }

                        /* check the recombination coefficients for ground state of the root of each iso sequence */
                        error = fabs( iso_recomb_check( ipISO, nelem , 1 , 12500. ) );
                        if( error > 0.01 )
                        {
                                fprintf(ioQQQ,
                                        " SanityCheck found insane2 %s %s recom coef: expected, n=%i error: %.2e \n",
                                        iso_ctrl.chISO[ipISO],
                                        elementnames.chElementSym[nelem],
                                        1,
                                        error );
                                lgOK = false;
                        }
                }
        }

        /*********************************************************
         *                                                       *
         * check out the sorting routine                         *
         *                                                       *
         *********************************************************/

        const int NSORT = 100 ;

        fvector = (realnum *)MALLOC((NSORT)*sizeof(realnum) );

        ipvector = (long *)MALLOC((NSORT)*sizeof(long int) );

        nelem = 1;
        /* make up some unsorted values */
        for( i=0; i<NSORT; ++i )
        {
                nelem *= -1;
                fvector[i] = (realnum)nelem * ((realnum)NSORT-i);
        }

        /*spsort netlib routine to sort array returning sorted indices */
        spsort(fvector, 
                   NSORT, 
                  ipvector, 
                  /* flag saying what to do - 1 sorts into increasing order, not changing
                   * the original routine */
                  1, 
                  &lgFlag);

        if( lgFlag ) lgOK = false;

        for( i=1; i<NSORT; ++i )
        {
                /*fprintf(ioQQQ," %li %li %.0f\n", 
                        i, ipvector[i],fvector[ipvector[i]] );*/
                if( fvector[ipvector[i]] <= fvector[ipvector[i-1]] )
                {
                        fprintf(ioQQQ," SanityCheck found insane sort\n");
                        lgOK = false;
                }
        }

        free( fvector );
        free( ipvector);

#       if 0
        ttemp = (realnum)sqrt(phycon.te);
        /* check that the temperatures make sense */
        if( fabs(ttemp - phycon.sqrte )/ttemp > 1e-5 )
        {
                fprintf(ioQQQ , "SanityCheck finds insane te %e sqrt te %e sqrte %e dif %e\n",
                        phycon.te , 
                        sqrt(phycon.te) , 
                        phycon.sqrte , 
                        fabs(sqrt(phycon.te) - phycon.sqrte ) );
                lgOK = false;
        }
#       endif

        /*********************************************************
         *                                                       *
         * confirm the validity of the mesh                      *
         *                                                       *
         *********************************************************/

        rfield.ValidateEdges();
        rfield.CheckMesh();

        /*********************************************************
         *                                                       *
         * confirm that hydrogen einstein As are still valid     *
         *                                                       *
         *********************************************************/
        for( nelem=0; nelem<2; ++nelem )
        {
                /* this element may be turned off */
                if( dense.lgElmtOn[nelem] )
                { 
                        /*Z4 = (double)(POW2(nelem+1)*POW2(nelem+1));*/
                        /* form charge to the 4th power */
                        Z4 = (double)(nelem+1);
                        Z4 *= Z4;
                        Z4 *= Z4;
                        /* H Lya */
                        double ans1 = iso_sp[ipH_LIKE][nelem].trans(ipH2p,ipH1s).Emis().Aul();
                        double ans2 = 6.265e8*Z4;
                        if( fabs(ans1-ans2)/ans2 > 1e-3 )
                        {
                                fprintf(ioQQQ , "SanityCheck finds insane A for H Lya %g %g nelem=%li\n",
                                        ans1 , ans2 , nelem );
                                lgOK = false;
                        }
                }
        }

        /* check that hydrogenic branching ratios add up to unity */
        for( nelem=0; nelem<LIMELM; ++nelem )
        {
                if( dense.lgElmtOn[nelem] )
                {
                        int ipHi, ipLo;
                        for( ipHi=4; ipHi< iso_sp[ipH_LIKE][nelem].numLevels_max-iso_sp[ipH_LIKE][nelem].nCollapsed_max; ++ipHi )
                        {
                                double sum = 0.;
                                for( ipLo=0; ipLo<ipHi; ++ipLo )
                                {
                                        sum += iso_sp[ipH_LIKE][nelem].BranchRatio[ipHi][ipLo];
                                }
                                if( fabs(sum-1.)>0.01 ) 
                                {
                                        fprintf(ioQQQ , 
                                                "SanityCheck H branching ratio sum not unity for nelem=%li upper level=%i sum=%.3e\n",
                                                nelem, ipHi, sum );
                                        lgOK = false;
                                }
                        }
                }
        }

        /* check that hydrogenic lifetimes are sane (compare inverse sum of As with closed form of lifetime) */
        for( nelem=0; nelem<LIMELM; ++nelem )
        {
                if( dense.lgElmtOn[nelem] )
                {
                        int ipHi, ipLo;
                        for( ipHi=1; ipHi< iso_sp[ipH_LIKE][nelem].numLevels_max-iso_sp[ipH_LIKE][nelem].nCollapsed_max; ++ipHi )
                        {
                                double inverse_sum = 0.;
                                double sum = 0.;
                                long ipISO = ipH_LIKE;
                                
                                /* we do not have an accurate closed form for l=0 lifetimes.  Everything else should be very accurate. */
                                if( L_(ipHi)==0 )
                                        continue;

                                for( ipLo=0; ipLo<ipHi; ++ipLo )
                                {
                                        sum += iso_sp[ipH_LIKE][nelem].trans(ipHi,ipLo).Emis().Aul();
                                }

                                inverse_sum = 1./sum;

                                double lifetime = iso_state_lifetime( ipH_LIKE, nelem, N_(ipHi), L_(ipHi) );
                                double percent_error = (1. - inverse_sum/lifetime)*100;
                                /* The closed form seems to consistently yield lifetimes roughly 0.2% smaller than the inverse sum
                                 * Transition probabilities go like energy cubed.  The cube of the finite mass rydberg is about 0.16% less than unity.  
                                 * is that the difference? */
                                /* for now enforce to better than 0.5% */
                                if( fabs(percent_error) > 0.5 ) 
                                {
                                        fprintf(ioQQQ , 
                                                "SanityCheck hydrogenic lifetime not consistent with closed form for nelem=%2li upper level=%2i inverse-sum= %.3e lifetime= %.3e error= %.2f%%\n",
                                                nelem, ipHi, inverse_sum, lifetime, percent_error );
                                        lgOK = false;
                                }
                        }
                }
        }

        /* check photo cross sections for H */
        long ipISO = ipH_LIKE;
        nelem = 0;
        for( long n=1; n <= iso_sp[ipISO][nelem].n_HighestResolved_max; ++n )
        {
                // This sanity check is of little value, as the cross-section is calculated 
                // with the same routine here as when populating the opacity stack.  
                // Make sure to use the cell mid-point energy which was also used in populating OpacStack
                // as it can be greater than the threshold energy (especially if the freq mesh is coarse)
                // For very Rydberg, very yrare levels, the cross-section can fall off fast 
                // enough over that energy difference to fail this check otherwise.
                // Will reported a sim that failed the check for some levels with n >= 71. 
                // So just don't bother checking above 60.    
                if( n > 60 )
                        break;

                for( long l=0; l < n; l++ )
                {
                        long index = iso_sp[ipISO][nelem].QuantumNumbers2Index[n][l][2];

                        double anu = rfield.anu(iso_sp[ipISO][nelem].fb[index].ipIsoLevNIonCon-1);
                        double rel_photon_energy = max(anu/iso_sp[ipISO][nelem].fb[index].xIsoLevNIonRyd, 1. + FLT_EPSILON*2.);
                        double cs = H_photo_cs( rel_photon_energy, n, l, nelem+1 );

                        error = fabs(cs - opac.OpacStack[iso_sp[ipISO][nelem].fb[index].ipOpac-1] )/
                                ( (cs + opac.OpacStack[iso_sp[ipISO][nelem].fb[index].ipOpac-1] )/2.);

                        if( error > 0.05 )
                        {
                                fprintf(ioQQQ , "SanityCheck finds insane H photo cs, n,l = %li, %li, expected, found = %e, %e, error = %e\n",
                                        n, l, opac.OpacStack[iso_sp[ipISO][nelem].fb[index].ipOpac-1], cs, error );
                                lgOK = false;
                        }
                }
        }
        
        /*********************************************************
         *                                                       *
         * confirm that Gaussian integration routines still work *
         *                                                       *
         *********************************************************/
        ASSERT( fp_equal( qg32( 0., PI, mySin ) , 2. ) );

#ifndef NDEBUG
        /* And again with the new structure */
        my_Integrand func;
        Integrator<my_Integrand,Gaussian32> mySine(func);
#endif
        ASSERT( fp_equal( mySine.sum( 0., PI ), 2. ) );

        /*********************************************************
         *                                                       *
         * confirm that exponential integral routines still work *
         *                                                       *
         *********************************************************/

        /* check that first and second exponential integrals are ok,
         * step through range of values, beginning with following */
        double x = 1e-3;
        do
        {
                {
                        /* check that fast e1 routine is ok */
                        double ans1 = e1(x);
                        double ans2 = expn( 1 , x );
                        error = safe_div(ans1-ans2,ans1+ans2,0.);
                        if( fabs(error) > 3e-7 )
                        {
                                fprintf(ioQQQ , "SanityCheck finds insane E1 %g %g %g error %g\n",
                                                  x , ans1 , ans2, error );
                                lgOK = false;
                        }
                }
                {
                        /* check that e2 is ok */
                        double ans1 = e2(x);
                        double ans2 = expn( 2 , x );
                        error = safe_div(ans1-ans2,ans1+ans2,0.);
                        if( fabs(error) > 1e-8 )
                        {
                                fprintf(ioQQQ , "SanityCheck finds insane E2 %g %g %g error %g\n",
                                                  x , ans1 , ans2, error );
                                lgOK = false;
                        }
                }
                /* now increment x */
                x *= 2.;
                /* following limit set by values not underflowing to zero */
        } while( x < 700. );

        /*********************************************************
         *                                                       *
         * confirm that matrix inversion routine still works     *
         *                                                       *
         *********************************************************/

        /* these are the answer, chosen to get xvec 1,2,3 */
        yVector[0] = 1.;
        yVector[1] = 3.;
        yVector[2] = 3.;

        /* zero out the main matrix */
        for(i=0;i<3;++i)
        {
                for( j=0;j<3;++j )
                {
                        xMatrix[i][j] = 0.;
                }
        }

        /* remember that order is column, row, alphabetical order, rc */
        xMatrix[0][0] = 1.;
        xMatrix[0][1] = 1.;
        xMatrix[1][1] = 1.;
        xMatrix[2][2] = 1.;

        /* this is the default matrix solver */
        /* this test is the 1-d matrix with 2-d macro simulation */
        /* LDA is right dimension of matrix */

        /* MALLOC space for the  1-d array */
        A = (double*)MALLOC( sizeof(double)*NDIM*NDIM );

        /* copy over the main matrix */
        for( i=0; i < 3; ++i )
        {
                for( j=0; j < 3; ++j )
                {
                        A[i*NDIM+j] = xMatrix[i][j];
                }
        }

        ner = 0;

        /*void DGETRF(long,long,double*,long,long[],long*);*/
        /*void DGETRF(int,int,double*,int,int[],int*);*/
        getrf_wrapper(3, 3, A, NDIM, ipiv, &ner);
        if( ner != 0 )
        {
                fprintf( ioQQQ, " SanityCheck DGETRF error\n" );
                cdEXIT(EXIT_FAILURE);
        }

        /* usage DGETRS, 'N' = no transpose
                * order of matrix,
                * number of cols in bvec, =1
                * array
                * leading dim of array */
        /*void DGETRS(char,int,int,double*,int,int[],double*,int,int*);*/
        getrs_wrapper('N', 3, 1, A, NDIM, ipiv, yVector, 3, &ner);

        if( ner != 0 )
        {
                fprintf( ioQQQ, " SanityCheck DGETRS error\n" );
                cdEXIT(EXIT_FAILURE);
        }
        /* release the vector */
        free( A );

        /* now check on validity of the solution, demand that this
         * simple problem have come within a few epsilons of the
         * correct answer */

        /* find largest deviation */
        rcond = 0.;
        for(i=0;i<3;++i)
        {
                x = fabs( yVector[i]-i-1.);
                rcond = MAX2( rcond, x );
                /*printf(" %g ", yVector[i]);*/
        }

        if( rcond>DBL_EPSILON)
        {
                fprintf(ioQQQ,
                        "SanityCheck found too large a deviation in matrix solver = %g \n", 
                        rcond);
                /* set flag saying that things are not ok */
                lgOK = false;
        }
        /* end matrix inversion check */

        /* these pointers were set to INT_MIN in ContCreatePointers,
         * then set to valid numbers in ipShells and OpacityCreate1Element
         * this checks that all values have been properly filled */
        for( nelem=0; nelem<LIMELM; ++nelem )
        {
                /* must reset state of code after tests performed, remember state here */
                realnum xIonF[NISO][LIMELM];
                double hbn[NISO][LIMELM], hn[NISO][LIMELM];

                if( dense.lgElmtOn[nelem] )
                {
                        /* set these abundances so that opacities can be checked below */
                        hbn[ipH_LIKE][nelem] = iso_sp[ipH_LIKE][nelem].st[0].DepartCoef();
                        hn[ipH_LIKE][nelem] = iso_sp[ipH_LIKE][nelem].st[0].Pop();
                        xIonF[ipH_LIKE][nelem] = dense.xIonDense[nelem][nelem+1-ipH_LIKE];

                        iso_sp[ipH_LIKE][nelem].st[0].DepartCoef() = 0.;
                        iso_sp[ipH_LIKE][nelem].st[0].Pop() = 1.;
                        dense.xIonDense[nelem][nelem+1-ipH_LIKE] = 1.;

                        if( nelem > ipHYDROGEN )
                        {

                                hbn[ipHE_LIKE][nelem] = iso_sp[ipHE_LIKE][nelem].st[0].DepartCoef();
                                hn[ipHE_LIKE][nelem] = iso_sp[ipHE_LIKE][nelem].st[0].Pop();
                                xIonF[ipHE_LIKE][nelem] = dense.xIonDense[nelem][nelem+1-ipHE_LIKE];

                                /* this does not exist for hydrogen itself */
                                iso_sp[ipHE_LIKE][nelem].st[0].DepartCoef() = 0.;
                                iso_sp[ipHE_LIKE][nelem].st[0].Pop() = 1.;
                                dense.xIonDense[nelem][nelem+1-ipHE_LIKE] = 1.;
                        }

                        for( ion=0; ion<=nelem; ++ion )
                        {
                                /* loop over all shells that are defined */
                                for( nshells=0; nshells<Heavy.nsShells[nelem][ion]; ++nshells )
                                {
                                        for( j=0; j<3; ++j )
                                        {
                                                /* >>chng 00 apr 05, array index is on fortran scale so must be
                                                 * >= 1.  This test had been <0, correct for C.  Caught by Peter van Hoof */
                                                if( opac.ipElement[nelem][ion][nshells][j] <=0 )
                                                {
                                                        /* this is not possible */
                                                        fprintf(ioQQQ,
                                                                "SanityCheck found insane ipElement for nelem=%li ion=%li nshells=%li j=%li \n", 
                                                                nelem , ion , nshells, j );
                                                        fprintf(ioQQQ,
                                                                "value was %li  \n", opac.ipElement[nelem][ion][nshells][j] );
                                                        /* set flag saying that things are not ok */
                                                        lgOK = false;
                                                }
                                        }
                                }

                                if( nelem > 1 )
                                {
                                        vector<realnum> saveion;
                                        saveion.resize(nelem+2);
                                        /* check that photoionization cross sections are ok */
                                        for( j=0; j <= (nelem + 1); j++ )
                                        {
                                                saveion[j] = dense.xIonDense[nelem][j];
                                                dense.xIonDense[nelem][j] = 0.;
                                        }

                                        dense.xIonDense[nelem][ion] = 1.;

                                        OpacityZero();
                                        opac.lgRedoStatic = true;

                                        /* generate opacity with standard routine - this is the one
                                         * called in OpacityAddTotal to make opacities in usual calculations */
                                        OpacityAdd1Element(nelem);

                                        /* this starts one beyond energy of threshold since cs may be zero there */
                                        for( j=Heavy.ipHeavy[nelem][ion]; j < MIN2(rfield.nflux,continuum.KshellLimit); j++ )
                                        {
                                                if( opac.opacity_abs[j]+opac.OpacStatic[j] < FLT_MIN )
                                                {
                                                        /* this is not possible */
                                                        fprintf(ioQQQ,
                                                                "SanityCheck found non-positive photo cs for nelem=%li ion=%li \n", 
                                                                nelem , ion );
                                                        fprintf(ioQQQ,
                                                                "value was %.2e + %.2e nelem %li ion %li at energy %.2e\n", 
                                                                opac.opacity_abs[j] ,
                                                                opac.OpacStatic[j] ,
                                                                nelem , 
                                                                ion , 
                                                                rfield.anu(j));
                                                        /* set flag saying that things are not ok */
                                                        lgOK = false;
                                                        break;
                                                }
                                        }
                                        /* reset the ionization distribution */
                                        for( j=0; j <= (nelem + 1); j++ )
                                        {
                                                dense.xIonDense[nelem][j] = saveion[j];
                                        }

                                }
                        }
                        iso_sp[ipH_LIKE][nelem].st[ipH1s].DepartCoef() = hbn[ipH_LIKE][nelem];
                        iso_sp[ipH_LIKE][nelem].st[ipH1s].Pop() = hn[ipH_LIKE][nelem];
                        dense.xIonDense[nelem][nelem+1-ipH_LIKE] = xIonF[ipH_LIKE][nelem];

                        if( nelem > ipHYDROGEN )
                        {
                                iso_sp[ipHE_LIKE][nelem].st[ipHe1s1S].DepartCoef() = hbn[ipHE_LIKE][nelem];
                                iso_sp[ipHE_LIKE][nelem].st[ipHe1s1S].Pop() = hn[ipHE_LIKE][nelem];
                                dense.xIonDense[nelem][nelem+1-ipHE_LIKE] = xIonF[ipHE_LIKE][nelem];
                        }
                }
        }


        /*********************************************************
         *                                                       *
         * everything is done, all checks make, did we pass them?*
         *                                                       *
         *********************************************************/

        if( lgOK )
        {
                /*return if ok */
                if( trace.lgTrace )
                {
                        fprintf( ioQQQ, " SanityCheck returns OK\n");
                }
                return;
        }

        else
        {
                /* stop since problem encountered, lgEOF set false */
                fprintf(ioQQQ , "SanityCheck finds insanity so exiting\n");
                ShowMe();
                cdEXIT(EXIT_FAILURE);
        }
}

STATIC void SanityCheckGaunt(long Z, double loggam2, double logu, double refval, double relerr)
{
        DEBUG_ENTRY( "SanityCheckGaunt()" );
        double gam2 = exp10(loggam2);
        double u = exp10(logu);
        double ZZ = double(Z);
        double Te = TE1RYD*pow2(ZZ)/gam2;
        double anu = pow2(ZZ)*u/gam2;
        double val = t_gaunt::Inst().gauntff( Z, Te, anu );
        if( fabs(val/refval-1.) > relerr )
        {
                fprintf( ioQQQ, "Gaunt sanity check failed: log(gam2) = %e, log(u) = %e, Z = %ld, "
                         "expected gff = %e, got gff = %e\n", loggam2, logu, Z, refval, val );
                cdEXIT(EXIT_FAILURE);
        }
}