parse_optimize.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 */
/*ParseOptimize parse the optimize command lines */
/*GetOptColDen read observed column densities & errors for optimizer */
/*GetOptLineInt parse observed line intensities for optimization routines */
/*GetOptTemp read observed temperatures & errors for optimizer */
#include "cddefines.h"
#include "trace.h"
#include "optimize.h"
#include "prt.h"
#include "flux.h"
#include "predcont.h"
#include "parser.h"
#include "lines_service.h"
#include "lines.h"

static const realnum DEFERR = 0.05f;

/*GetOptLineInt parse observed line intensities for optimization routines */
STATIC void GetOptLineInt(Parser &p );

/*GetOptColDen read observed column densities & errors for optimizer */
STATIC void GetOptColDen(Parser &p );

/*GetOptTemp read observed temperatures & errors for optimizer */
STATIC void GetOptTemp(Parser &p );

/* ParseOptimize - called from ParseCommands if OPTIMIZE command found */
void ParseOptimize(
        /* command line, which was changed to all caps in main parsing routine */
        Parser &p)
{
        DEBUG_ENTRY( "ParseOptimize()" );

        /* this must come first so that contents of filename do not trigger wrong command */
        if( p.nMatch("FILE") )
        {
                /* option to send final set of parameters to an input file 
                 * get name within double quotes, 
                 * and set to blanks in chCard and OrgCard */
                /* chCard is all caps at this point.  GetQuote will work with 
                 * original version of command line, which preserves case of
                 * characters.  Also removes string between quotes */
                /* GetQuote will abort if it fails, so we can ignore the return value */
                string str;
                if (p.GetQuote( str ))
                        p.StringError();
                strcpy(chOptimFileName, str.c_str());
        }

        else if( p.nMatch("COLU") )
        {
                /* optimize column density */
                /* read column densities to match */
                GetOptColDen(p);

                optimize.lgOptimize = true;
        }

        else if( p.nMatch("CONT") && p.nMatch("FLUX") )
        {
                /* optimize continuum flux at arbitrary wavelength */
                double energy = p.FFmtRead();
                if( p.lgEOL() )
                        p.NoNumb("energy");
                const char* unit = p.StandardEnergyUnit();
                long ind = t_PredCont::Inst().add( energy, unit );
                Energy E( energy, unit );

                double flux = p.FFmtRead();
                if( p.lgEOL() )
                        p.NoNumb("flux");
                if( flux <= 0. || p.nMatch( " LOG" ) )
                        flux = exp10(flux);
                Flux F( E, flux, p.StandardFluxUnit() );

                double relerr = p.FFmtRead();
                if( p.lgEOL() )
                        relerr = DEFERR;
                /* value is an upper limit only, use negative error to flag */
                if( p.nMatch("<" ) )
                        relerr = -relerr;

                optimize.ContIndex.push_back( ind );
                optimize.ContEner.push_back( E );
                optimize.ContNFnu.push_back( F );
                optimize.ContNFnuErr.push_back( chi2_type(relerr) );
                optimize.lgOptimize = true;
        }

        else if( p.nMatch("CONT") )
        {
                /* set flag saying that optimization should start from continue file */
                optimize.lgOptCont = true;
                optimize.lgOptimize = true;
        }

        else if( p.nMatch("DIAM") )
        {
                /* optimize angular diameter */
                optimize.optDiam = chi2_type( p.FFmtRead() );
                optimize.optDiamErr = chi2_type( p.FFmtRead() );
                if( p.lgEOL() )
                        optimize.optDiamErr = chi2_type( DEFERR );
                /* value is an upper limit only, use negative error to flag */
                if( p.nMatch( "<" ) )
                        optimize.optDiamErr = -optimize.optDiamErr;

                if( p.nMatch( " LOG" ) )
                        optimize.optDiam = exp10(optimize.optDiam);

                optimize.lgOptDiam = true;
                /* angular diameter is default in arcsec, or in cm of keyword present */
                optimize.lgDiamInCM = ( p.nMatch( " CM " ) != 0 );
                optimize.lgOptimize = true;
        }

        else if( p.nMatch("INCR") )
        {
                /* scan off increments for the previously selected parameter */
                if( optimize.nparm > 0 )
                {
                        /* also called during optimization process, ignore then */
                        optimize.OptIncrm[optimize.nparm-1] = 
                                (realnum)p.FFmtRead();
                }
                else
                {
                        if( optimize.lgInitialParse && optimize.lgVaryOn )
                        {
                                fprintf( ioQQQ, " The OPTIMIZE INCREMENT command needs to follow the"
                                         " command being varied.\n None was found. Bailing out...\n" );
                                cdEXIT(EXIT_FAILURE);
                        }
                }
        }

        else if( p.nMatch("LUMI") || p.nMatch("INTE") )
        {
                /* scan off intensity or luminosity of normalization line */
                optimize.optint = (realnum)p.FFmtRead();
                optimize.optier = (realnum)p.FFmtRead();
                if( p.lgEOL() )
                        optimize.optier = DEFERR;

                // default intrinsic intensity, accept emergent
                optimize.nOptLum = p.nMatch("EMER") ? 1 : 0;

                /* set flag to say that intensity or luminosity of line set */
                optimize.lgOptLum = true;
                optimize.lgOptimize = true;
        }

        else if( p.nMatch("ITER") )
        {
                /* scan off number of iterations */
                optimize.nIterOptim = (long)p.FFmtRead();
        }

        else if( p.nMatch("LINE") )
        {
                /* read lines to match */
                GetOptLineInt(p);

                optimize.lgOptimize = true;
        }

        else if( p.nMatch("PHYM") )
        {
                /* use PvH's PHYMIR to optimize parameters */
                strcpy( optimize.chOptRtn, "PHYM" );
#               if defined(__unix) || defined(__APPLE__)
                // turn parallel mode off if explicitly requested or if we are in single rank mode
                // the latter means that each rank runs its own model in single-CPU mode
                optimize.lgParallel = ! ( p.nMatch("SEQU") || cpu.i().lgMPISingleRankMode() );
#               else
                optimize.lgParallel = false;
#               endif
                if( optimize.lgParallel ) 
                {
                        long dum = (long)p.FFmtRead();
                        /* default is the total number of available CPUs */
                        optimize.useCPU = p.lgEOL() ? cpu.i().nCPU() : dum;
                }
                else 
                {
                        optimize.useCPU = 1;
                }
        }

        else if( p.nMatch("RANG") )
        {
                /* scan off range for the previously selected variable */
                if( optimize.nparm > 0 )
                {
                        bool lgFirstOneReal = false;

                        optimize.varang[optimize.nparm-1][0] = 
                                (realnum)p.FFmtRead();
                        if( p.lgEOL() )
                        {
                                optimize.varang[optimize.nparm-1][0] = -FLT_MAX;
                        }
                        else
                        {
                                lgFirstOneReal = true;
                        }

                        optimize.varang[optimize.nparm-1][1] = 
                                (realnum)p.FFmtRead();
                        if( p.lgEOL() )
                        {
                                optimize.varang[optimize.nparm-1][1] = FLT_MAX;
                        }
                        else if( lgFirstOneReal )
                        {
                                /* >>chng 06 aug 22, swap if second range parameter is less than the first,
                                 * and always increment optimize.nRangeSet */
                                ++optimize.nRangeSet;
                                if( optimize.varang[optimize.nparm-1][1] < optimize.varang[optimize.nparm-1][0] )
                                {
                                        realnum temp = optimize.varang[optimize.nparm-1][0];
                                        optimize.varang[optimize.nparm-1][0] = optimize.varang[optimize.nparm-1][1];
                                        optimize.varang[optimize.nparm-1][1] = temp;
                                }
                        }
                }
        }

        else if( p.nMatch("SUBP") )
        {
                /* use subplex to optimize parameters */
                strcpy( optimize.chOptRtn, "SUBP" );
        }

        /* match a temperature */
        else if( p.nMatch("TEMP") )
        {
                /* read temperatures to match */
                GetOptTemp(p);

                optimize.lgOptimize = true;
        }

        else if( p.nMatch("TOLE") )
        {
                /* scan off tolerance of fit, sum of residuals must be smaller than this
                 * default is 0.10 */
                optimize.OptGlobalErr = (realnum)p.FFmtRead();
        }

        else if( p.nMatch("TRAC") )
        {
                if( p.nMatch("STAR") )
                {
                        /* trace start iteration number
                         * turn on trace printout starting on nth call to cloudy */
                        optimize.nTrOpt = (long)p.FFmtRead();
                        if( p.lgEOL() )
                        {
                                fprintf( ioQQQ, " optimize trace start command:\n" );
                                fprintf( ioQQQ, " The iteration number must appear.\n" );
                                cdEXIT(EXIT_FAILURE);
                        }
                        optimize.lgTrOpt = true;
                }
                else if( p.nMatch("FLOW") )
                {
                        /* trace flow
                         * follow logical flow within code */
                        optimize.lgOptimFlow = true;
                }
                else
                {
                        fprintf( ioQQQ, " optimize trace flow command:\n" );
                        fprintf( ioQQQ, " One of the sub keys START or FLOW must appear.\n" );
                        cdEXIT(EXIT_FAILURE);
                }
        }

        else
        {
                p.PrintLine(ioQQQ);
                fprintf( ioQQQ, " is unrecognized keyword, consult HAZY.\n" );
                cdEXIT(EXIT_FAILURE);
        }
        return;
}

/*GetOptColDen read observed column densities & errors for optimizer */
STATIC void GetOptColDen(Parser &p )
{

        DEBUG_ENTRY( "GetOptColDen()" );

        /* read observed column densities & errors */

        /* get first line */
        p.getline();
        if( p.m_lgEOF )
        {
                fprintf( ioQQQ, " Hit EOF while reading column density list; use END to end list.\n" );
                cdEXIT(EXIT_FAILURE);
        }

        while( !p.m_lgEOF )
        {
                /* order on line is element label (col 1-4), ionization stage, column density, err */
                /* copy cap'd version of first 4 char of chCard to chColDen_label */
                optimize.chColDen_label.push_back(p.getFirstChunk(4));

                /* now get the ion stage, this should be 1 for atom, up to element
                 * number plus one */
                long ion = nint(p.FFmtRead());
                if( p.lgEOL() )
                {
                        p.PrintLine( ioQQQ );
                        fprintf( ioQQQ, " The ionization stage MUST appear on this line.  Sorry.\n" );
                        cdEXIT(EXIT_FAILURE);
                }

                /* the ion must be 1 or greater unless requesting a special,
                 * like a molecule or excited state population, in which
                 * case ion = 0
                 * can't check on upper limit yet since have not resolved element name */
                if( ion < 0 )
                {
                        p.PrintLine( ioQQQ );
                        fprintf( ioQQQ, " An ionization stage of %ld does not make sense.  Sorry.\n", ion );
                        cdEXIT(EXIT_FAILURE);
                }
                optimize.ion_ColDen.push_back(ion);

                optimize.ColDen_Obs.push_back( realnum(exp10(p.FFmtRead())) );
                if( p.lgEOL() )
                {
                        p.PrintLine( ioQQQ );
                        fprintf( ioQQQ, " An observed column density MUST be entered.  Sorry.\n" );
                        cdEXIT(EXIT_FAILURE);
                }

                realnum err = realnum(p.FFmtRead());
                if( err <= 0.0 )
                {
                        /* this is the relative error allowed */
                        err = realnum(DEFERR);
                }

                /* check if number is a limit - if '<' appears on the line then it is */
                if( p.nMatch( "<" ) )
                {
                        /* value is an upper limit only, use negative error to flag */
                        err = -err;
                }
                optimize.ColDen_error.push_back(err);

                p.getline();
                if( p.m_lgEOF )
                {
                        fprintf( ioQQQ, " Hit EOF while reading column density list; use END to end list.\n" );
                        cdEXIT(EXIT_FAILURE);
                }

                if( p.hasCommand( "END" ) )
                {
                        p.m_lgEOF = true;
                }
        }

        if( trace.lgTrace && optimize.lgTrOpt )
        {
                fprintf( ioQQQ, "%ld columns were entered, they were;\n", 
                                        (long int) optimize.ColDen_Obs.size() );
                for( long i=0; i < long(optimize.ColDen_Obs.size()); i++ )
                {
                        fprintf( ioQQQ, " %4.4s ion=%5ld%10.2e%10.2e\n", 
                                 optimize.chColDen_label[i].c_str(), optimize.ion_ColDen[i],
                                 optimize.ColDen_Obs[i], optimize.ColDen_error[i] );
                }
        }
        return;
}

/*GetOptLineInt parse observed line intensities for optimization routines */
STATIC void GetOptLineInt(Parser &p )
{
        DEBUG_ENTRY( "GetOptLineInt()" );

        // default intrinsic intensity, accept emergent
        optimize.nEmergent = p.nMatch("EMER") ? 1 : 0;

        /* read observed line fluxes & errors */
        p.getline();
        if( p.m_lgEOF )
        {
                fprintf( ioQQQ, " Hit EOF while reading line list; use END to end list.\n" );
                cdEXIT(EXIT_FAILURE);
        }

        while( !p.m_lgEOF )
        {
                LineID line=p.getLineID();
                /* order on line is label (col 1-4), wavelength, flux, error */
                optimize.chLineLabel.push_back( line.chLabel.c_str() );
                optimize.wavelength.push_back( line.wave );

                /* get the error associated with specified significant figures */
                optimize.errorwave.push_back( WavlenErrorGet(line.wave, LineSave.sig_figs ) );

                /* next get the observed intensity */
                realnum xLineInt = realnum(p.FFmtRead());
                if( p.lgEOL() )
                {
                        fprintf( ioQQQ, " The wavelength and relative intensity MUST be entered on this line.  Sorry.\n" );
                        fprintf( ioQQQ, " The command line is the following:\n " );
                        p.PrintLine(ioQQQ);
                        cdEXIT(EXIT_FAILURE);
                }

                if( xLineInt <= 0. )
                {
                        fprintf( ioQQQ, " An observed intensity of %.2e is not allowed.  Sorry.\n", 
                                 xLineInt );
                        fprintf( ioQQQ, " The command line is the following:\n" );
                        p.PrintLine(ioQQQ);
                        cdEXIT(EXIT_FAILURE);
                }
                optimize.xLineInt_Obs.push_back(xLineInt);

                /* finally the optional error */
                realnum err = realnum(p.FFmtRead());
                /* most often will use the default */
                if( err <= 0.0 )
                        err = realnum(DEFERR);

                /* check if number is a limit - if '<' appears on the line then it is */
                if( p.nMatch( "<" ) )
                {
                        /* value is an upper limit only, use negative error to flag */
                        err = -err;
                }
                optimize.xLineInt_error.push_back(err);

                if( !p.lgReachedEnd() )
                {
                        fprintf( ioQQQ, "GetOptLineInt: found junk at end of input line:\n" );
                        p.showLocation();
                        cdEXIT(EXIT_FAILURE);
                }

                /* get next line */
                p.getline();
                if( p.m_lgEOF )
                {
                        fprintf( ioQQQ, " Hit EOF while reading line list for optimize command; use END to end list.\n" );
                        cdEXIT(EXIT_FAILURE);
                }

                if( p.hasCommand( "END" ) )
                        p.m_lgEOF = true;
        }

        if( trace.lgTrace && trace.lgTrOptm )
        {
                fprintf( ioQQQ, "%ld lines were entered, they were:\n", 
                         (long int) optimize.xLineInt_Obs.size() );

                for( long i=0; i < long(optimize.xLineInt_Obs.size()); i++ )
                {
                        fprintf( ioQQQ, " %4.4s ", optimize.chLineLabel[i].c_str() );
                        prt_wl( ioQQQ, optimize.wavelength[i] );

                        fprintf( ioQQQ, " %10.2e%10.2e\n", 
                                optimize.xLineInt_Obs[i], 
                                optimize.xLineInt_error[i] );
                }
        }
        return;
}

/*GetOptTemp parse observed line intensities for optimization routines */
STATIC void GetOptTemp(Parser &p )
{
        DEBUG_ENTRY( "GetOptTemp()" );

        /* read observed line fluxes & errors - first set total number of observe temps */
        p.getline();
        if( p.m_lgEOF )
        {
                fprintf( ioQQQ, " Hit EOF while reading line list; use END to end list.\n" );
                cdEXIT(EXIT_FAILURE);
        }

        /* make line caps so we can parse it */
        while( !p.m_lgEOF )
        {
                /* order on line is label (col 1-4), ion, temperature, error */
                optimize.chTempLab.push_back( p.getFirstChunk(4) );

                /* next get the ion stage */
                optimize.ionTemp.push_back( nint(p.FFmtRead()) );

                /* next get the observed temperature */
                realnum temp_obs = realnum(p.FFmtRead());
                if( p.lgEOL() )
                {
                        fprintf( ioQQQ, " The ion stage and temperature MUST be entered on this line.  Sorry.\n" );
                        fprintf( ioQQQ, " The command line is the following:\n " );
                        p.PrintLine(ioQQQ);
                        cdEXIT(EXIT_FAILURE);
                }
                /* temperatures less than or equal to 10 are logs */
                if( temp_obs <= 10. )
                        temp_obs = realnum(exp10(  (double)temp_obs ) );
                optimize.temp_obs.push_back(temp_obs);

                /* finally the optional error */
                realnum temp_error = realnum(p.FFmtRead());
                /* most often will use the default */
                if( temp_error <= 0.f )
                        temp_error = realnum(DEFERR);
                /* check if number is a limit - if '<' appears on the line then it is */
                if( p.nMatch( "<" ) )
                        temp_error = -temp_error;
                optimize.temp_error.push_back(temp_error);

                /* check for radius or volume for how to weight the mean temp 
                 * this will be the default */
                /* >>chng 05 dec 29, from chCard to chCap, unlike much of code in this file,
                 * chCard has been read in by this routine and contains the original form of 
                 * the command line.  It was converted to caps and stored in chCap above.
                 * As it was written only VOLUME was matched, would not match volume.
                 * Bug caught and corrected by Bohdan Melekh */
                if( p.nMatch( "VOLUME" ) )
                        optimize.chTempWeight.push_back("volume");
                else
                        optimize.chTempWeight.push_back("radius");

                /* get next line */
                p.getline();
                if( p.m_lgEOF )
                {
                        fprintf( ioQQQ, " Hit EOF while reading line list for optimize command; use END to end list.\n" );
                        cdEXIT(EXIT_FAILURE);
                }

                if( p.hasCommand( "END" ) )
                        p.m_lgEOF = true;
        }

        if( trace.lgTrace && trace.lgTrOptm )
        {
                fprintf( ioQQQ, "%ld temperatures were entered, they were;\n", 
                         (long int) optimize.temp_obs.size() );

                for( long i=0; i < long(optimize.temp_obs.size()); i++ )
                {
                        fprintf( ioQQQ, " %4.4s ", optimize.chTempLab[i].c_str() );
                        fprintf( ioQQQ, " %li " , optimize.ionTemp[i] );

                        fprintf( ioQQQ, " %.2e %.2e\n", 
                                optimize.temp_obs[i], 
                                optimize.temp_error[i] );
                }
        }
        return;
}