parse_species.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 */

#include "cddefines.h"
#include "parse_species.h"

#include "parser.h"
#include "mole.h"
#include "species.h"

// This file groups the handler for the species command with the
// routines which interpret the options.  It would be better if this
// were done in just one routine, to allow the code to warn on invalid
// options rather than just ignore them

void ParseSpecies(Parser &p)
{
        DEBUG_ENTRY( "ParseSpecies()" );
        string chString_quotes_original;
        bool lgQuotesFound = true;
        if (p.GetQuote(chString_quotes_original))
                lgQuotesFound = false;

        if( ! lgQuotesFound )
        {
                fprintf(ioQQQ,"Need to provide species name to SPECIES command.\n"
                                  "The previous SPECIES command has been renamed DATABASE -- did you mean to use that?\n");
                cdEXIT(EXIT_FAILURE);
        }

        // Break up the remainder of the input line into options and (optionally) values
        // String or numeric values can be given without an '=', named options require '='
        Symbol s=p.getSymbol();
        while(1)
        {
                if (s.toktype == Symbol::EOSTAT)
                {
                        break;
                }
                if ( s.toktype != Symbol::NAME )
                {
                        fprintf(ioQQQ,"Value %s not understood\n",s.value.c_str());
                        cdEXIT(EXIT_FAILURE);
                }
                Symbol t=p.getSymbol();
                if (t.toktype == Symbol::EOSTAT || t.toktype == Symbol::NAME)
                {
                        mole_global.speciesProperties[chString_quotes_original].p.push_back(
                                pair<string,count_ptr<Option> >(s.value,count_ptr<Option>(new Option(true))));
                        s = t;
                }
                else if (t.toktype == Symbol::NUMBER)
                {
                        long num = strtol(t.value.c_str(),NULL,10);
                        mole_global.speciesProperties[chString_quotes_original].p.push_back(
                                pair<string,count_ptr<Option> >(s.value,count_ptr<Option>(new Option(num))));
                        s = p.getSymbol();
                }
                else if (t.toktype == Symbol::STRING)
                {
                        mole_global.speciesProperties[chString_quotes_original].p.push_back(
                                pair<string,count_ptr<Option> >(s.value,count_ptr<Option>(new Option(t.value,Option::QUOTED))));
                        s = p.getSymbol();
                }
                else if (t.toktype == Symbol::OPERATOR && t.value == "=")
                {
                        t = p.getSymbol();
                        if (t.toktype == Symbol::NAME)
                        {
                                mole_global.speciesProperties[chString_quotes_original].p.push_back(
                                pair<string,count_ptr<Option> >(s.value,count_ptr<Option>(new Option(t.value,Option::NOTQUOTED))));
                        }
                        else if (t.toktype == Symbol::STRING)
                        {
                                mole_global.speciesProperties[chString_quotes_original].p.push_back(
                                pair<string,count_ptr<Option> >(s.value,count_ptr<Option>(new Option(t.value,Option::QUOTED))));
                        }
                        else if (t.toktype == Symbol::NUMBER)
                        {
                                long num = strtol(t.value.c_str(),NULL,10);
                                mole_global.speciesProperties[chString_quotes_original].p.push_back(
                                pair<string,count_ptr<Option> >(s.value,count_ptr<Option>(new Option(num))));
                        }
                        else
                        {
                                fprintf(ioQQQ,"Option '%s' value '%s' not understood\n",s.value.c_str(),t.value.c_str());
                                fprintf(ioQQQ,"WARNING: This usage of the SPECIES command was not understood.\n"
                                                  "The previous SPECIES command has been renamed DATABASE -- did you mean to use that?\n");
                                cdEXIT(EXIT_FAILURE);
                        }
                        s = p.getSymbol();
                }
                else
                {
                        fprintf(ioQQQ,"Option '%s' not understood\n",s.value.c_str());
                        fprintf(ioQQQ,"WARNING: This usage of the SPECIES command was not understood.\n"
                                          "The previous SPECIES command has been renamed DATABASE -- did you mean to use that?\n");
                        cdEXIT(EXIT_FAILURE);
                }
        }
}

void setProperties(species& sp)
{
        DEBUG_ENTRY("setProperties()");
        char chLabelChemical[CHARS_SPECIES];
        if( sp.lgMolecular )
        {
                strcpy( chLabelChemical, sp.chLabel );
        }
        else
        {
                long nelem = 0, IonStg;
                parsespect(sp.chLabel,nelem,IonStg);
                makeChemical(chLabelChemical, nelem, IonStg-1);
        }

        map<string,Properties >::iterator props = 
                mole_global.speciesProperties.find(chLabelChemical);
        if (props == mole_global.speciesProperties.end())
                return;

        props->second.setDone();

        for(vector<pair<string,count_ptr<Option> > >::iterator prop=props->second.p.begin();
                 prop!=props->second.p.end();++prop)
        {
                if (prop->first == "LEVELS")
                {
                        if (prop->second->opttype == Option::LONG)
                        {
                                if (prop->second->i > sp.numLevels_max)
                                {
                                        fprintf(ioQQQ,"Species '%s', %ld levels requested, only %ld available.  Using all.\n",
                                                          chLabelChemical,prop->second->i,
                                                          sp.numLevels_max);
                                        sp.setLevels = sp.numLevels_max;
                                }
                                else
                                {
                                        sp.setLevels = prop->second->i;
                                }
                        }
                        else if (prop->second->opttype == Option::OPTION && prop->second->s == "ALL")
                        {
                                sp.setLevels = sp.numLevels_max;
                        }
                        else
                        {
                                fprintf(ioQQQ,"Incorrect type for 'LEVELS' option to species\n"
                                                  "Expecting 'LEVELS <number>', 'LEVELS=<number>' or 'LEVELS=ALL'\n");
                        }
                }
                else if (prop->first == "LTE")
                {
                        if (prop->second->opttype == Option::BOOL)
                        {
                                sp.lgLTE = prop->second->l;
                        }
                        else
                        {
                                fprintf(ioQQQ,"Incorrect type for 'LTE' option to species\n");
                        }
                }
                else if (prop->first == "OFF")
                {
                        ; // Do nothing, already handled
                }
                else
                {
                        fprintf(ioQQQ,"Option '%s' not understood for species '%s'\n",
                                          prop->first.c_str(),sp.chLabel);
                        cdEXIT(EXIT_FAILURE);
                }
        }
}

void speciesCheck()
{
        for (map<string,Properties>::iterator props = 
                          mole_global.speciesProperties.begin(); 
                  props != mole_global.speciesProperties.end();
                  ++props)
        {
                if (! props->second.isDone())
                {
                        fprintf(ioQQQ,"\n\nWarning: SPECIES \"%s\" command has no effect since species not found.\n"
                                "Is species inactive or misspelt?  Names of species are case-sensitive.  Consult species list in docs/SpeciesLabels.txt.\n\n",
                                props->first.c_str());
                }
        }
}

bool speciesOff(const string& label)
{
        map<string,Properties>::iterator props = 
                mole_global.speciesProperties.find(label);
        if (props != mole_global.speciesProperties.end())
        {
                props->second.setDone();

                for(vector<pair<string,count_ptr<Option> > >::iterator prop=props->second.p.begin();
                         prop!=props->second.p.end();++prop)
                {
                        if (prop->first == "OFF")
                        {
                                if (prop->second->opttype != Option::BOOL)
                                {
                                        fprintf(ioQQQ,"Incorrect type for 'OFF' option to species\n");
                                }
                                
                                if (prop->second->l || prop->second->opttype != Option::BOOL)
                                {
                                        return true;
                                }
                        }
                }
        }
        return false;
}