// Solution.cxx: implementation of the cxxSolution class.
//
//////////////////////////////////////////////////////////////////////
#ifdef _DEBUG
#pragma warning(disable : 4786)   // disable truncation warning (Only used by debugger)
#endif

#include "Utils.h"   // define first
#include "Solution.h"
#define EXTERNAL extern
#include "global.h"
#include "phqalloc.h"
#include "phrqproto.h"
#include "output.h"
#include <cassert>     // assert
#include <algorithm>   // std::sort 


//////////////////////////////////////////////////////////////////////
// Construction/Destruction
//////////////////////////////////////////////////////////////////////


cxxSolution::cxxSolution()
        //
        // default constructor for cxxSolution 
        //
: cxxNumKeyword()
{
        tc          = 25.0;
        ph          = 7.0;
        pe          = 4.0;
        mu          = 1e-7;
        ah2o        = 1.0;
        total_h     = 111.1;
        total_o     = 55.55;
        cb          = 0.0;
        mass_water  = 1.0;
        total_alkalinity = 0.0;
        totals.type = cxxNameDouble::ND_ELT_MOLES;
        master_activity.type = cxxNameDouble::ND_SPECIES_LA;
        species_gamma.type = cxxNameDouble::ND_SPECIES_GAMMA;
}
cxxSolution::cxxSolution(double zero)
        //
        // empty cxxSolution constructor
        //
: cxxNumKeyword()
{
	assert (zero == 0.0);
        tc          = 0.0;
        ph          = 0.0;
        pe          = 0.0;
        mu          = 0.0;
        ah2o        = 0.0;
        total_h     = 0.0;
        total_o     = 0.0;
        cb          = 0.0;
        mass_water  = 0.0;
        total_alkalinity = 0.0;
        totals.type = cxxNameDouble::ND_ELT_MOLES;
        master_activity.type = cxxNameDouble::ND_SPECIES_LA;
        species_gamma.type = cxxNameDouble::ND_SPECIES_GAMMA;
}
cxxSolution::cxxSolution(struct solution *solution_ptr)
        //
        // constructor for cxxSolution from struct solution
        //
: 
cxxNumKeyword(),
totals(solution_ptr->totals),
master_activity(solution_ptr->master_activity, solution_ptr->count_master_activity, cxxNameDouble::ND_SPECIES_LA),
species_gamma(solution_ptr->species_gamma, solution_ptr->count_species_gamma, cxxNameDouble::ND_SPECIES_GAMMA),
isotopes(solution_ptr)
{

        this->set_description(solution_ptr->description);
        n_user      = solution_ptr->n_user;
        n_user_end  = solution_ptr->n_user_end;
        tc          = solution_ptr->tc;
        ph          = solution_ptr->ph;
        pe          = solution_ptr->solution_pe;
        mu          = solution_ptr->mu;
        ah2o        = solution_ptr->ah2o;
        total_h     = solution_ptr->total_h;
        total_o     = solution_ptr->total_o;
        cb          = solution_ptr->cb;
        mass_water  = solution_ptr->mass_water;
        total_alkalinity     = solution_ptr->total_alkalinity;

        // Totals filled in constructor, just save description and moles 

        // Isotopes
	/*
        for (i = 0; i < solution_ptr->count_isotopes; i++) {
                cxxSolutionIsotope iso(&solution_ptr->isotopes[i]);
                isotopes.push_back(iso);
        }
	*/
        // Master_activity in constructor
        // Species_gamma in constructor
}

#ifdef SKIP
cxxSolution::cxxSolution(const cxxSolution &old, double intensive, double extensive)
        //
        // constructor for cxxSolution from struct solution
        //
: 
cxxNumKeyword(),
totals(old.totals, extensive),
master_activity(old.master_activity, intensive),
species_gamma(old.species_gamma, intensive)
{

        this->set_description(old.description);
        this->n_user                   = old.n_user;
        this->n_user_end               = old.n_user_end;
	this->tc                       = old.tc * intensive;
	this->ph                       = old.ph * intensive;
	this->pe                       = old.pe * intensive;
	this->mu                       = old.mu * intensive;
	this->ah2o                     = old.ah2o * intensive;
	this->total_h                  = old.total_h * extensive;
	this->total_o                  = old.total_o * extensive;
	this->cb                       = old.cb * extensive;
	this->mass_water               = old.mass_water * extensive;
	this->total_alkalinity         = old.total_alkalinity * extensive;
	/*
        cxxNameDouble totals;
        std::list<cxxSolutionIsotope> isotopes;
        cxxNameDouble master_activity;
        cxxNameDouble species_gamma;
	*/
	for (std::list<cxxSolutionIsotope>::const_iterator it = old.isotopes.begin(); it != old.isotopes.end(); it++) {
		this->isotopes.push_back(cxxSolutionIsotope((*it), intensive, extensive));
	}
}
#endif

cxxSolution::~cxxSolution()
{
}


struct solution *cxxSolution::cxxSolution2solution()
        //
        // Builds a solution structure from instance of cxxSolution 
        //
{

        struct solution *solution_ptr = solution_alloc();
        
        solution_ptr->description        = this->get_description();
        solution_ptr->n_user             = this->n_user;
        solution_ptr->n_user_end         = this->n_user_end;
        solution_ptr->new_def            = FALSE;
        solution_ptr->tc                 = this->tc;
        solution_ptr->ph                 = this->ph;
        solution_ptr->solution_pe        = this->pe;
        solution_ptr->mu                 = this->mu;
        solution_ptr->ah2o               = this->ah2o;
        solution_ptr->total_h            = this->total_h;
        solution_ptr->total_o            = this->total_o;
        solution_ptr->cb                 = this->cb;
        solution_ptr->mass_water         = this->mass_water;
        solution_ptr->total_alkalinity   = this->total_alkalinity;
        solution_ptr->density            = 1.0;
        solution_ptr->units              = moles_per_kilogram_string;
        solution_ptr->default_pe         = 0;
        // pe_data

        // totals
        solution_ptr->totals = (struct conc *) free_check_null(solution_ptr->totals);
        solution_ptr->totals = this->totals.conc();

        // master_activity
        solution_ptr->master_activity = (struct master_activity *) free_check_null(solution_ptr->master_activity);
        solution_ptr->master_activity = this->master_activity.master_activity();
        solution_ptr->count_master_activity = (int) this->master_activity.size() + 1;

        // species_gamma
        solution_ptr->species_gamma = this->species_gamma.master_activity();
        solution_ptr->count_species_gamma = (int) this->species_gamma.size();

        // isotopes
        solution_ptr->isotopes = (struct isotope *) free_check_null(solution_ptr->isotopes);
        //solution_ptr->isotopes = cxxSolutionIsotope::list2isotope(this->isotopes);
	solution_ptr->isotopes = this->isotopes.cxxSolutionIsotopeList2isotope();
        solution_ptr->count_isotopes = (int) this->isotopes.size();

        return(solution_ptr);
}
void cxxSolution::dump_xml(std::ostream& s_oss, unsigned int indent)const
{
        //const char    ERR_MESSAGE[] = "Packing solution message: %s, element not found\n";
        unsigned int i;
        s_oss.precision(DBL_DIG - 1);
        std::string indent0(""), indent1("");
        for(i = 0; i < indent; ++i) indent0.append(Utilities::INDENT);
        for(i = 0; i < indent + 1; ++i) indent1.append(Utilities::INDENT);

        // Solution element and attributes
        s_oss << indent0;
        s_oss << "<solution " << std::endl;

        //s_oss << indent1;
        //s_oss << "soln_new_def=\"" << this->new_def << "\"" << std::endl;

        s_oss << indent1;
        s_oss << "soln_n_user=\"" << this->n_user << "\" " << std::endl;

        s_oss << indent1;
        s_oss << "soln_description=\"" << this->description << "\"" << std::endl;

        s_oss << indent1;
        s_oss << "soln_tc=\"" << this->tc << "\"" << std::endl;

        s_oss << indent1;
        s_oss << "soln_ph=\"" << this->ph << "\"" << std::endl;

        s_oss << indent1;
        s_oss << "soln_solution_pe=\"" << this->pe << "\"" << std::endl;

        s_oss << indent1;
        s_oss << "soln_mu=\"" << this->mu << "\"" << std::endl;

        s_oss << indent1;
        s_oss << "soln_ah2o=\""  << this->ah2o << "\"" << std::endl;

        s_oss << indent1;
        s_oss << "soln_total_h=\"" << this->total_h << "\"" << std::endl;

        s_oss << indent1;
        s_oss << "soln_total_o=\"" << this->total_o << "\"" << std::endl;

        s_oss << indent1;
        s_oss << "soln_cb=\"" << this->cb << "\"" << std::endl;

        s_oss << indent1;
        s_oss << "soln_mass_water=\"" << this->mass_water << "\"" << std::endl;

        s_oss << indent1;
        s_oss << "soln_total_alkalinity=\"" << this->total_alkalinity << "\"" << std::endl;

        s_oss << indent1;
        s_oss << "\">" << std::endl;

        // soln_total conc structures
        this->totals.dump_xml(s_oss, indent + 1);
        /*
        {
        for (std::map <char *, double, CHARSTAR_LESS>::const_iterator it = totals.begin(); it != totals.end(); ++it) {
                s_oss << indent1;
                s_oss << "<soln_total";
                s_oss << " conc_desc=\"" << it->first << "\"";
                s_oss << " conc_moles=\"" << it->second << "\"" ;
                s_oss << "\">" << std::endl;
        }
        }
        */
        // master_activity map
        this->master_activity.dump_xml(s_oss, indent + 1);
        /*
        {
        for (std::map <char *, double>::const_iterator it = master_activity.begin(); it != master_activity.end(); ++it) {
                s_oss << indent1;
                s_oss << "<soln_m_a";
                s_oss << " m_a_desc=\"" << it->first << "\"" ;
                s_oss << " m_a_la=\"" << it->second << "\"" ;
                s_oss << "\">" << std::endl;
        }
        }
        */
        // species_gamma map
        this->species_gamma.dump_xml(s_oss, indent + 1);
        /*
        {
        for (std::map <char *, double>::const_iterator it = species_gamma.begin(); it != species_gamma.end(); ++it) {
                s_oss << indent1;
                s_oss << "<soln_s_g";
                s_oss << " m_a_desc=\"" << it->first << "\"" ;
                s_oss << " m_a_la=\"" << it->second << "\"" ;
                s_oss << "\">" << std::endl;
        }
        }
        */

        for (std::list<cxxSolutionIsotope>::const_iterator it = this->isotopes.begin(); it != isotopes.end(); ++it) {
                it->dump_xml(s_oss, indent + 1);
        }

        // End of solution
        s_oss << indent0;
        s_oss << "</solution>" << std::endl;

        return;
}

void cxxSolution::dump_raw(std::ostream& s_oss, unsigned int indent)const
{
        //const char    ERR_MESSAGE[] = "Packing solution message: %s, element not found\n";
        unsigned int i;
        s_oss.precision(DBL_DIG - 1);
        std::string indent0(""), indent1(""), indent2("");
        for(i = 0; i < indent; ++i) indent0.append(Utilities::INDENT);
        for(i = 0; i < indent + 1; ++i) indent1.append(Utilities::INDENT);
        for(i = 0; i < indent + 2; ++i) indent2.append(Utilities::INDENT);

        // Solution element and attributes
        s_oss << indent0;
        s_oss << "SOLUTION_RAW       " << this->n_user  << " " << this->description << std::endl;

        s_oss << indent1;
        s_oss << "-temp              " << this->tc << std::endl;

        s_oss << indent1;
        s_oss << "-pH                " << this->ph << std::endl;

        s_oss << indent1;
        s_oss << "-pe                " << this->pe << std::endl;

        // new identifier
        s_oss << indent1;
        s_oss << "-mu                " << this->mu << std::endl;

        // new identifier
        s_oss << indent1;
        s_oss << "-ah2o              " << this->ah2o << std::endl;

        // new identifier
        s_oss << indent1;
        s_oss << "-total_h           " << this->total_h << std::endl;

        // new identifier
        s_oss << indent1;
        s_oss << "-total_o           " << this->total_o << std::endl;

        // new identifier
        s_oss << indent1;
        s_oss << "-cb                " << this->cb << std::endl;

        // new identifier
        s_oss << indent1;
        s_oss << "-mass_water        " << this->mass_water << std::endl;

        // new identifier
        s_oss << indent1;
        s_oss << "-total_alkalinity  " << this->total_alkalinity << std::endl;

        // soln_total conc structures
        s_oss << indent1;
        s_oss << "-totals" << std::endl;
        this->totals.dump_raw(s_oss, indent + 2);
        /*
        for (std::map <char *, double, CHARSTAR_LESS>::const_iterator it = totals.begin(); it != totals.end(); ++it) {
                s_oss << indent2;
                s_oss << it->first << "   " <<  it->second << std::endl;
        }
        */

        // master_activity map
        s_oss << indent1;
        s_oss << "-activities" << std::endl;
        this->master_activity.dump_raw(s_oss, indent + 2);
        /*
        {
                for (std::map <char *, double>::const_iterator it = master_activity.begin(); it != master_activity.end(); ++it) {
                        s_oss << indent2;
                        s_oss << it->first << "   " << it->second << std::endl;
                }
        }
        */
        // species_gamma map
        s_oss << indent1;
        s_oss << "-gammas" << std::endl;
        this->species_gamma.dump_raw(s_oss, indent + 2);
        /*
        {
                {
                        for (std::map <char *, double>::const_iterator it = species_gamma.begin(); it != species_gamma.end(); ++it) {
                                s_oss << indent2;
                                s_oss << it->first << "   " << it->second << std::endl;
                        }
                }
        }
        */
        // Isotopes
        s_oss << indent1;
        s_oss << "-Isotopes" << std::endl;
        {
                for (std::list<cxxSolutionIsotope>::const_iterator it = this->isotopes.begin(); it != isotopes.end(); ++it) {
                        it->dump_raw(s_oss, indent + 2);
                }
        }

        return;
}

void cxxSolution::read_raw(CParser& parser)
{
        static std::vector<std::string> vopts;
        if (vopts.empty()) {
                vopts.reserve(21);
                vopts.push_back("totals");                    // 0 
                vopts.push_back("activities");                // 1 
                vopts.push_back("gammas");                    // 2 
                vopts.push_back("isotopes");                  // 3 
                vopts.push_back("temp");                      // 4 
                vopts.push_back("tc");                        // 5 
                vopts.push_back("temperature");               // 6 
                vopts.push_back("ph");                        // 7 
                vopts.push_back("pe");                        // 8 
                vopts.push_back("mu");                        // 9 
                vopts.push_back("ionic_strength");            // 10
                vopts.push_back("ah2o");                      // 11
                vopts.push_back("activity_water");            // 12
                vopts.push_back("total_h");                   // 13
                vopts.push_back("total_o");                   // 14
                vopts.push_back("mass_water");                // 15
                vopts.push_back("mass_h2o");                  // 16
                vopts.push_back("total_alkalinity");          // 17
                vopts.push_back("total_alk");                 // 18
                vopts.push_back("cb");                        // 19
                vopts.push_back("charge_balance");            // 20
        }

        std::istream::pos_type ptr;
        std::istream::pos_type next_char;
        std::string token;
        int opt_save;

        // Read solution number and description
        this->read_number_description(parser);

        opt_save = CParser::OPT_ERROR;
        bool tc_defined(false); 
        bool ph_defined(false); 
        bool pe_defined(false); 
        bool mu_defined(false); 
        bool ah2o_defined(false); 
        bool total_h_defined(false); 
        bool total_o_defined(false); 
        bool cb_defined(false); 
        bool mass_water_defined(false); 
        bool total_alkalinity_defined(false);

        for (;;)
        {
                int opt = parser.get_option(vopts, next_char);
                if (opt == CParser::OPT_DEFAULT)
                {
                        opt = opt_save;
                }

                switch (opt)
                {
                case CParser::OPT_EOF:
                        break;
                case CParser::OPT_KEYWORD:
                        break;
                case CParser::OPT_DEFAULT:
                case CParser::OPT_ERROR:
                        opt = CParser::OPT_EOF;
                        parser.error_msg("Unknown input in SOLUTION_RAW keyword.", CParser::OT_CONTINUE);
                        parser.error_msg(parser.line().c_str(), CParser::OT_CONTINUE);
                        break;

                case 0: // totals
                        if ( this->totals.read_raw(parser, next_char) != CParser::PARSER_OK) {
                                parser.incr_input_error();
                                parser.error_msg("Expected element name and moles for totals.", CParser::OT_CONTINUE);
                        }                       
                        opt_save = 0;
                        break;

                case 1: // activities
                        if ( this->master_activity.read_raw(parser, next_char) != CParser::PARSER_OK) {
                                parser.incr_input_error();
                                parser.error_msg("Expected species name and log activity for activities.", CParser::OT_CONTINUE);
                        }                               
                        opt_save = 1;
                        break;

                case 2: // gammas
                        if ( this->species_gamma.read_raw(parser, next_char) != CParser::PARSER_OK) {
                                parser.incr_input_error();
                                parser.error_msg("Expected species name and activity coefficient for gammas.", CParser::OT_CONTINUE);
                        }                               
                        opt_save = 2;
                        break;

                case 3: // isotopes
                        {
                                cxxSolutionIsotope iso;
                                if ( iso.read_raw(parser) != CParser::PARSER_OK) {
                                        parser.incr_input_error();
                                        parser.error_msg("Expected data for isotopes.", CParser::OT_CONTINUE);
                                } else {
                                        if (iso.get_isotope_name() != NULL) {
                                                this->isotopes.push_back(iso);
                                        }
                                }
                        }
                        opt_save = 3;
                        break;

                case 4: // temp
                case 5: // tc
                case 6: // temperature                  
                        if (!(parser.get_iss() >> this->tc))
                        {
                                this->tc = 25.0;
                                parser.incr_input_error();
                                parser.error_msg("Expected numeric value for temperature.", CParser::OT_CONTINUE);
                        }
                        tc_defined = true;
                        opt_save = CParser::OPT_DEFAULT;
                        break;

                case 7: // ph
                        if (!(parser.get_iss() >> this->ph))
                        {
                                this->ph = 7.0;
                                parser.incr_input_error();
                                parser.error_msg("Expected numeric value for pH.", CParser::OT_CONTINUE);
                        }
                        ph_defined = true;
                        opt_save = CParser::OPT_DEFAULT;
                        break;

                case 8: // pe
                        if (!(parser.get_iss() >> this->pe))
                        {
                                this->pe = 4.0;
                                parser.incr_input_error();
                                parser.error_msg("Expected numeric value for pe.", CParser::OT_CONTINUE);
                        }
                        pe_defined = true;
                        opt_save = CParser::OPT_DEFAULT;
                        break;

                case 9: // mu
                case 10: // ionic_strength
                        if (!(parser.get_iss() >> this->mu))
                        {
                                this->mu = 1e-7;
                                parser.incr_input_error();
                                parser.error_msg("Expected numeric value for ionic strength.", CParser::OT_CONTINUE);
                        }
                        mu_defined = true;
                        opt_save = CParser::OPT_DEFAULT;
                        break;

                case 11: // ah2o
                case 12: // activity_water
                        if (!(parser.get_iss() >> this->ah2o))
                        {
                                this->ah2o = 1.0;
                                parser.incr_input_error();
                                parser.error_msg("Expected numeric value for activity of water.", CParser::OT_CONTINUE);
                        }
                        ah2o_defined = true;
                        opt_save = CParser::OPT_DEFAULT;
                        break;

                case 13: // total_h
                        if (!(parser.get_iss() >> this->total_h))
                        {
                                this->total_h = 111.1;
                                parser.incr_input_error();
                                parser.error_msg("Expected numeric value for total hydrogen.", CParser::OT_CONTINUE);
                        }
                        total_h_defined = true;
                        opt_save = CParser::OPT_DEFAULT;
                        break;

                case 14: // total_o
                        if (!(parser.get_iss() >> this->total_o))
                        {
                                this->total_o = 55.55;
                                parser.incr_input_error();
                                parser.error_msg("Expected numeric value for total oxygen.", CParser::OT_CONTINUE);
                        }
                        total_o_defined = true;
                        opt_save = CParser::OPT_DEFAULT;
                        break;

                case 15: // mass_water
                case 16: // mass_h2o
                        if (!(parser.get_iss() >> this->mass_water))
                        {
                                this->mass_water = 1.0;
                                parser.incr_input_error();
                                parser.error_msg("Expected numeric value for mass of water.", CParser::OT_CONTINUE);
                        }
                        mass_water_defined = true;
                        opt_save = CParser::OPT_DEFAULT;
                        break;

                case 17: // total_alkalinity
                case 18: // total_alk
                        if (!(parser.get_iss() >> this->total_alkalinity))
                        {
                                this->total_alkalinity = 0;
                                parser.incr_input_error();
                                parser.error_msg("Expected numeric value for total_alkalinity.", CParser::OT_CONTINUE);
                        }
                        total_alkalinity_defined = true;
                        opt_save = CParser::OPT_DEFAULT;
                        break;

                case 19: // cb
                case 20: // charge_balance
                        if (!(parser.get_iss() >> this->cb))
                        {
                                this->cb = 0;
                                parser.incr_input_error();
                                parser.error_msg("Expected numeric value for charge balance.", CParser::OT_CONTINUE);
                        }
                        cb_defined = true;
                        opt_save = CParser::OPT_DEFAULT;
                        break;

                }
                if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD) break;
        }
        // all members must be defined
        if (tc_defined == false) {
                parser.incr_input_error();
                parser.error_msg("Temp not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
        }
        if (ph_defined == false) {
                parser.incr_input_error();
                parser.error_msg("pH not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
        }
        if (pe_defined == false) {
                parser.incr_input_error();
                parser.error_msg("pe not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
        }
        if (mu_defined == false) {
                parser.incr_input_error();
                parser.error_msg("Ionic strength not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
        }
        if (ah2o_defined == false) {
                parser.incr_input_error();
                parser.error_msg("Activity of water not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
        }
        if (total_h_defined == false) {
                parser.incr_input_error();
                parser.error_msg("Total hydrogen not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
        }
        if (total_o_defined == false) {
                parser.incr_input_error();
                parser.error_msg("Total oxygen not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
        }
        if (cb_defined == false) {
                parser.incr_input_error();
                parser.error_msg("Charge balance not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
        }
        if (mass_water_defined == false) {
                parser.incr_input_error();
                parser.error_msg("Temp not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
        }
        if (total_alkalinity_defined == false) {
                parser.incr_input_error();
                parser.error_msg("Total alkalinity not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
        }
        return;
}

void cxxSolution::add(const cxxSolution &old, double intensive, double extensive)
        //
        // Add existing solution to "this" solution
        //
{

	this->tc                       += old.tc * intensive;
	this->ph                       += old.ph * intensive;
	this->pe                       += old.pe * intensive;
	this->mu                       += old.mu * intensive;
	this->ah2o                     += old.ah2o * intensive;
	this->total_h                  += old.total_h * extensive;
	this->total_o                  += old.total_o * extensive;
	this->cb                       += old.cb * extensive;
	this->mass_water               += old.mass_water * extensive;
	this->total_alkalinity         += old.total_alkalinity * extensive;

	this->totals.add(old.totals, extensive);
	this->master_activity.add(old.master_activity, intensive);
	this->species_gamma.add(old.species_gamma, intensive);
	this->isotopes.add(old.isotopes, intensive, extensive);

#ifdef SKIP
	//
	//  isotopes
	//  go through old list, update or add to current list 
	//
	for (std::list <cxxSolutionIsotope>::const_iterator itold = old.isotopes.begin(); itold != old.isotopes.end(); ++itold) {
		bool found = false;
		for (std::list <cxxSolutionIsotope>::iterator it = this->isotopes.begin(); it != this->isotopes.end(); ++it) {
			if ((it->isotope_number == itold->isotope_number) &&
			    (it->elt_name       == itold->elt_name) &&
			    (it->isotope_name   == itold->isotope_name)) {
				it->total                   += itold->total * extensive;
				it->ratio                   += itold->ratio * intensive;
				it->ratio_uncertainty       += itold->ratio_uncertainty * intensive;
				it->ratio_uncertainty_defined = (it->ratio_uncertainty_defined || itold->ratio_uncertainty_defined);
				found = true;
				break;
			}
		}
		if (!found) {
			this->isotopes.push_back(*itold);
		}
        }
#endif
	/*
        cxxNameDouble totals;
        std::list<cxxSolutionIsotope> isotopes;
        cxxNameDouble master_activity;
        cxxNameDouble species_gamma;
	*/
}

double cxxSolution::get_total(char *string)const
{
	cxxNameDouble::const_iterator it = this->totals.find(string);
	if (it == this->totals.end()) {
		return(0.0);
	} else {
		return(it->second);
	}
}

void cxxSolution::set_total(char *string, double d)
{
	this->totals[string] = d;
}

double cxxSolution::get_master_activity(char *string)const
{
	cxxNameDouble::const_iterator it = this->master_activity.find(string);
	if (it == this->master_activity.end()) {
		return(0.0);
	} else {
		return(it->second);
	}
}
#ifdef USE_MPI
#include <mpi.h>
/* ---------------------------------------------------------------------- */
void cxxSolution::mpi_pack(std::vector<int>& ints, std::vector<double>& doubles)
/* ---------------------------------------------------------------------- */
{
/*
 *   Make list of list of ints and doubles from solution structure
 *   This list is not the complete structure, but only enough
 *   for batch-reaction, advection, and transport calculations
 */
	ints.push_back(this->n_user);
	doubles.push_back(this->tc);
	doubles.push_back(this->ph);
	doubles.push_back(this->pe);
	doubles.push_back(this->mu);
	doubles.push_back(this->ah2o);
	doubles.push_back(this->total_h);
	doubles.push_back(this->total_o);
	doubles.push_back(this->cb);
	doubles.push_back(this->mass_water);
	doubles.push_back(this->total_alkalinity);
/*
 *	struct conc *totals;
*/
	this->totals.mpi_pack(ints, doubles);
/*
 *	struct master_activity *master_activity;
 */
	this->master_activity.mpi_pack(ints, doubles);
/*
 *	struct master_activity *species_gamma
 */
	this->species_gamma.mpi_pack(ints, doubles);

	/*
	position = 0;
	int i = ints.size();
	int int_array[i];
	int d = doubles.size();
	double double_array[d];
	for (int j = 0; j < i; j++) {
		int_array[j] = ints[j];
	}
	for (int j = 0; j < d; j++) {
		double_array[j] = ints[j];
	}
	MPI_Send(&max_size, 1, MPI_INT, task_number, 0, MPI_COMM_WORLD);
	MPI_Pack(&i, 1, MPI_INT, buffer, max_size, &position, MPI_COMM_WORLD);
	MPI_Pack(&int_array, i, MPI_INT, buffer, max_size, &position, MPI_COMM_WORLD);
	MPI_Pack(&d, 1, MPI_INT, buffer, max_size, &position, MPI_COMM_WORLD);
	MPI_Pack(&double_array, d, MPI_DOUBLE, buffer, max_size, &position, MPI_COMM_WORLD);
	MPI_Send(buffer, position, MPI_PACKED, task_number, 0, MPI_COMM_WORLD);

	buffer = (void *) free_check_null(buffer);
	*/
}
/* ---------------------------------------------------------------------- */
void cxxSolution::mpi_unpack(int *ints, int *ii, double *doubles, int *dd)
/* ---------------------------------------------------------------------- */
{
	int i = *ii;
	int d = *dd;
	this->n_user = ints[i++];
	this->n_user_end = this->n_user;
	this->description = "  ";
	this->tc = doubles[d++];
	this->ph = doubles[d++];
	this->pe = doubles[d++];
	this->mu = doubles[d++];
	this->ah2o = doubles[d++];
	this->total_h = doubles[d++];
	this->total_o = doubles[d++];
	this->cb = doubles[d++];
	this->mass_water = doubles[d++];
	this->total_alkalinity = doubles[d++];
/*
 *	struct conc *totals;
*/
	this->totals.mpi_unpack(ints, &i, doubles, &d);
/*
 *	struct master_activity *master_activity;
 */
	this->master_activity.mpi_unpack(ints, &i, doubles, &d);
/*
 *	struct master_activity *species_gamma;
 */
	this->species_gamma.mpi_unpack(ints, &i, doubles, &d);

	*ii = i;
	*dd = d;
}
/* ---------------------------------------------------------------------- */
void cxxSolution::mpi_send(int task_number)
/* ---------------------------------------------------------------------- */
{
	//int count_totals, count_totals_position, count_activity, count_activity_position;
	int max_size, member_size, position;
	//int ints[MESSAGE_MAX_NUMBERS];
	//double doubles[MESSAGE_MAX_NUMBERS];
	void *buffer;
	std::vector<int> ints;
	std::vector<double> doubles;
/*
 *   Make list of list of ints and doubles from solution structure
 *   This list is not the complete structure, but only enough
 *   for batch-reaction, advection, and transport calculations
 */
	ints.push_back(this->n_user);
	/*	int n_user_end; */
	/*	char *description; */
	doubles.push_back(this->tc);
	doubles.push_back(this->ph);
	doubles.push_back(this->pe);
	doubles.push_back(this->mu);
	doubles.push_back(this->ah2o);
	doubles.push_back(this->total_h);
	doubles.push_back(this->total_o);
	doubles.push_back(this->cb);
	doubles.push_back(this->mass_water);
	doubles.push_back(this->total_alkalinity);
/*
 *	struct conc *totals;
*/
	this->totals.mpi_pack(ints, doubles);
/*
 *	struct master_activity *master_activity;
 */
	this->master_activity.mpi_pack(ints, doubles);
/*
 *	struct master_activity *species_gamma
 */
	this->species_gamma.mpi_pack(ints, doubles);

	/*	int count_isotopes; */
	/*	struct isotope *isotopes; */
	if (input_error > 0) {
		std::string errstr("Stopping due to errors\n");
		error_msg(errstr.c_str(), STOP);
	}
/*
 *   Malloc space for a buffer
 */
	max_size = 0;
	//MPI_Pack_size(MESSAGE_MAX_NUMBERS, MPI_INT, MPI_COMM_WORLD, &member_size);
	MPI_Pack_size((int) ints.size(), MPI_INT, MPI_COMM_WORLD, &member_size);
	max_size += member_size;
	//MPI_Pack_size(MESSAGE_MAX_NUMBERS, MPI_DOUBLE, MPI_COMM_WORLD, &member_size);
	MPI_Pack_size((int) doubles.size(), MPI_DOUBLE, MPI_COMM_WORLD, &member_size);
	max_size += member_size + 10;
	buffer = PHRQ_malloc(max_size);
	if (buffer == NULL) malloc_error();
/*
 *   Send message to processor
 */
	position = 0;
	int i = (int) ints.size();
	int *int_array = new int[i];
	int d = (int) doubles.size();
	double *double_array = new double[d];
	for (int j = 0; j < i; j++) {
		int_array[j] = ints[j];
	}
	for (int j = 0; j < d; j++) {
		double_array[j] = doubles[j];
	}

	MPI_Send(&max_size, 1, MPI_INT, task_number, 0, MPI_COMM_WORLD);
	MPI_Pack(&i, 1, MPI_INT, buffer, max_size, &position, MPI_COMM_WORLD);
	MPI_Pack(&int_array, i, MPI_INT, buffer, max_size, &position, MPI_COMM_WORLD);
	MPI_Pack(&d, 1, MPI_INT, buffer, max_size, &position, MPI_COMM_WORLD);
	MPI_Pack(&double_array, d, MPI_DOUBLE, buffer, max_size, &position, MPI_COMM_WORLD);
	MPI_Send(buffer, position, MPI_PACKED, task_number, 0, MPI_COMM_WORLD);

	buffer = (void *) free_check_null(buffer);
	delete[] int_array;
	delete[] double_array;
}
/* ---------------------------------------------------------------------- */
void cxxSolution::mpi_recv(int task_number)
/* ---------------------------------------------------------------------- */
{
	MPI_Status mpi_status;
/*
 *   Malloc space for a buffer
 */
	int max_size;
        // buffer size

	MPI_Recv(&max_size, 1, MPI_INT, task_number, 0, MPI_COMM_WORLD, &mpi_status);
	void *buffer = PHRQ_malloc(max_size);
	if (buffer == NULL) malloc_error();
	/*
	 *   Recieve solution
	 */
	MPI_Recv(buffer, max_size, MPI_PACKED, task_number, 0, MPI_COMM_WORLD, &mpi_status);
 	int position = 0;
	int msg_size;
 	MPI_Get_count(&mpi_status, MPI_PACKED, &msg_size);

	/* Unpack ints */
	int count_ints;
 	MPI_Unpack(buffer, msg_size, &position, &count_ints, 1, MPI_INT, MPI_COMM_WORLD);
	int *ints = new int[count_ints];
 	MPI_Unpack(buffer, msg_size, &position, ints, count_ints, MPI_INT, MPI_COMM_WORLD);

	/* Unpack doubles */
	int count_doubles;
 	MPI_Unpack(buffer, msg_size, &position, &count_doubles, 1, MPI_INT, MPI_COMM_WORLD);
	double *doubles = new double[count_doubles];
 	MPI_Unpack(buffer, msg_size, &position, doubles, count_doubles, MPI_DOUBLE, MPI_COMM_WORLD);
	buffer = free_check_null(buffer);
/*
 *   Make list of list of ints and doubles from solution structure
 *   This list is not the complete structure, but only enough
 *   for batch-reaction, advection, and transport calculations
 */
	int i = 0;
	int d = 0;
	/*	int new_def; */
	/* solution_ptr->new_def = FALSE; */
	/*	int n_user; */
	this->n_user = ints[i++];
	/*	int n_user_end; */
	this->n_user_end = this->n_user;

	/*debugging*/
	//this->description = (char *) free_check_null(this->description);
	//this->description = string_duplicate(" ");
	this->description = " ";
	this->tc = doubles[d++];
	this->ph = doubles[d++];
	this->pe = doubles[d++];
	this->mu = doubles[d++];
	this->ah2o = doubles[d++];
	this->total_h = doubles[d++];
	this->total_o = doubles[d++];
	this->cb = doubles[d++];
	this->mass_water = doubles[d++];
	this->total_alkalinity = 0;
/*
 *	struct conc *totals;
*/
	this->totals.mpi_unpack(ints, &i, doubles, &d);
/*
 *	struct master_activity *master_activity;
 */
	this->master_activity.mpi_unpack(ints, &i, doubles, &d);
/*
 *	struct master_activity *species_gamma;
 */
	this->species_gamma.mpi_unpack(ints, &i, doubles, &d);
	delete[] ints;
	delete[] doubles;
}
#endif
void cxxSolution::set_master_activity(char *string, double d)
{
	this->master_activity[string] = d;
}
#ifdef SKIP
#include "../hst.h"
/* ---------------------------------------------------------------------- */
void cxxSolution::xsolution_save(int n)
/* ---------------------------------------------------------------------- */
{
/*
 *   Save solution composition into Solution class
 *
 *   input:  n is pointer number in solution
 */
        this->set_description(" ");
        this->n_user      = n;
        this->n_user_end  = n;
        this->tc          = tc_x;
        this->ph          = ph_x;
        this->pe          = solution_pe_x;
        this->mu          = mu_x;
        this->ah2o        = ah2o_x;
        this->total_h     = total_h_x;
        this->total_o     = total_o_x;
        this->cb          = cb_x;
        this->mass_water  = mass_water_aq_x;
        this->total_alkalinity = total_alkalinity;
/*
 *   Copy totals data
 */
	for (int j = 2; j < count_total; j++) {
		this->totals.insert(buffer[j].master->elt->name, buffer[j].master->total_primary);
	}

	for (int j = 0; j < count_activity_list; j++) {
		this->master_activity.insert(activity_list[j].master->elt->name, activity_list[j].master->s->la);
	}
	if (pitzer_model == TRUE) {
		for (int j= 0; j < count_s; j++) {
			if (s[j]->lg != 0.0) {
				this->species_gamma.insert(s[j]->name, s[j]->lg);
			}
		}
	} 
}
#endif


#include "ISolution.h"
#include "Exchange.h"
#include "Surface.h"
#include "PPassemblage.h"
#include "cxxKinetics.h"
#include "SSassemblage.h"
#include "GasPhase.h"
#include "Reaction.h"
#include "Temperature.h"
#include "StorageBin.h"
#include "NumKeyword.h"
#include <iostream>     // std::cout std::cerr
//#include <strstream>
#include <sstream>
#include <fstream>
void test_classes(void)
{

	

	/*
        int i;
	std::map<int, cxxSolution>      Solutions;
	cxxSolution soln(solution[0]);
	Solutions[solution[0]->n_user] = soln;
	bool b = Utilities::exists(Solutions, 1);
	*/
	/*
	cxxEntityMap x;
	cxxSolution soln(solution[0]);
	cxxNumKeyword nk;
	x[solution[0]->n_user] = soln;
	*/

#ifdef SKIP
        for (i=0; i < count_solution; i++) {
                if (solution[i]->new_def == TRUE) {
                        cxxISolution sol(solution[i]);
                        solution[i] = (struct solution *) solution_free(solution[i]);
                        solution[i] = sol.cxxISolution2solution();
                        struct solution *soln_ptr;
                        soln_ptr = solution[i];
                        soln_ptr = solution[i];
                } else {
                        std::ostringstream oss;
                        cxxSolution sol(solution[i]);
                        solution[i] = (struct solution *) solution_free(solution[i]);
                        sol.dump_raw(oss, 0);

                        //std::fstream myfile("t");
                        //CParser cparser(myfile, std::cout, std::cerr);
                        cxxSolution sol1;
                        std::string keyInput = oss.str();
                        std::istringstream iss(keyInput);

                        CParser cparser(iss, oss, std::cerr);
                        //For testing, need to read line to get started
                        std::vector<std::string> vopts;
                        std::istream::pos_type next_char;
                        cparser.get_option(vopts, next_char);


                        sol1.read_raw(cparser);

                        solution[i] = sol1.cxxSolution2solution();
                }
        }
        for (i=0; i < count_exchange; i++) {
                if (exchange[i].new_def != TRUE) {
                        std::ostringstream oss;
                        cxxExchange ex(&(exchange[i]));
                        ex.dump_raw(oss, 0);
                        std::cerr << oss.str();

                        cxxExchange ex1;
                        std::string keyInput = oss.str();
                        std::istringstream iss(keyInput);

                        CParser cparser(iss, oss, std::cerr);
                        //For testing, need to read line to get started
                        std::vector<std::string> vopts;
                        std::istream::pos_type next_char;
                        cparser.get_option(vopts, next_char);

                        ex1.read_raw(cparser);

                        struct exchange *exchange_ptr = ex1.cxxExchange2exchange();
                        exchange_free(&exchange[i]);
                        exchange_copy(exchange_ptr, &exchange[i], exchange_ptr->n_user);
                        exchange_free(exchange_ptr);
                        free_check_null(exchange_ptr);
                }
        }
        for (i=0; i < count_surface; i++) {
                if (surface[i].new_def != TRUE) {
                        std::ostringstream oss;
                        cxxSurface ex(&(surface[i]));
                        ex.dump_raw(oss, 0);
                        std::cerr << oss.str();


                        cxxSurface ex1;
                        std::string keyInput = oss.str();
                        std::istringstream iss(keyInput);

                        CParser cparser(iss, oss, std::cerr);
                        //For testing, need to read line to get started
                        std::vector<std::string> vopts;
                        std::istream::pos_type next_char;
                        cparser.get_option(vopts, next_char);

                        ex1.read_raw(cparser);

                        struct surface *surface_ptr = ex1.cxxSurface2surface();
                        surface_free(&surface[i]);
                        surface_copy(surface_ptr, &surface[i], surface_ptr->n_user);
                        surface_free(surface_ptr);
                        free_check_null(surface_ptr);

                }

        }
        for (i=0; i < count_pp_assemblage; i++) {
                if (pp_assemblage[i].new_def != TRUE) {
                        std::ostringstream oss;
                        cxxPPassemblage ex(&(pp_assemblage[i]));
                        ex.dump_raw(oss, 0);
                        std::cerr << oss.str();


                        cxxPPassemblage ex1;
                        std::string keyInput = oss.str();
                        std::istringstream iss(keyInput);

                        CParser cparser(iss, oss, std::cerr);
                        //For testing, need to read line to get started
                        std::vector<std::string> vopts;
                        std::istream::pos_type next_char;
                        cparser.get_option(vopts, next_char);

                        ex1.read_raw(cparser);

                        struct pp_assemblage *pp_assemblage_ptr = ex1.cxxPPassemblage2pp_assemblage();
                        pp_assemblage_free(&pp_assemblage[i]);
                        pp_assemblage_copy(pp_assemblage_ptr, &pp_assemblage[i], pp_assemblage_ptr->n_user);
                        pp_assemblage_free(pp_assemblage_ptr);
                        free_check_null(pp_assemblage_ptr);

                }

        }
        for (i=0; i < count_kinetics; i++) {
                        std::ostringstream oss;
                        cxxKinetics ex(&(kinetics[i]));
                        ex.dump_raw(oss, 0);
                        std::cerr << oss.str();


                        cxxKinetics ex1;
                        std::string keyInput = oss.str();
                        std::istringstream iss(keyInput);

                        CParser cparser(iss, oss, std::cerr);
                        //For testing, need to read line to get started
                        std::vector<std::string> vopts;
                        std::istream::pos_type next_char;
                        cparser.get_option(vopts, next_char);


                        ex1.read_raw(cparser);

                        struct kinetics *kinetics_ptr = ex1.cxxKinetics2kinetics();
                        kinetics_free(&kinetics[i]);
                        kinetics_copy(kinetics_ptr, &kinetics[i], kinetics_ptr->n_user);
                        kinetics_free(kinetics_ptr);
                        free_check_null(kinetics_ptr);
        }
        for (i=0; i < count_s_s_assemblage; i++) {
                if (s_s_assemblage[i].new_def != TRUE) {
                        std::ostringstream oss;
                        cxxSSassemblage ex(&(s_s_assemblage[i]));
                        ex.dump_raw(oss, 0);
                        std::cerr << oss.str();


                        cxxSSassemblage ex1;
                        std::string keyInput = oss.str();
                        std::istringstream iss(keyInput);

                        CParser cparser(iss, oss, std::cerr);
                        //For testing, need to read line to get started
                        std::vector<std::string> vopts;
                        std::istream::pos_type next_char;
                        cparser.get_option(vopts, next_char);

                        ex1.read_raw(cparser);

                        struct s_s_assemblage *s_s_assemblage_ptr = ex1.cxxSSassemblage2s_s_assemblage();
                        s_s_assemblage_free(&s_s_assemblage[i]);
                        s_s_assemblage_copy(s_s_assemblage_ptr, &s_s_assemblage[i], s_s_assemblage_ptr->n_user);
                        s_s_assemblage_free(s_s_assemblage_ptr);
                        free_check_null(s_s_assemblage_ptr);

                }

        }
        for (i=0; i < count_gas_phase; i++) {
                if (gas_phase[i].new_def != TRUE) {
                        std::ostringstream oss;
                        cxxGasPhase ex(&(gas_phase[i]));
                        ex.dump_raw(oss, 0);
                        std::cerr << oss.str();


                        cxxGasPhase ex1;
                        std::string keyInput = oss.str();
                        std::istringstream iss(keyInput);

                        CParser cparser(iss, oss, std::cerr);
                        //For testing, need to read line to get started
                        std::vector<std::string> vopts;
                        std::istream::pos_type next_char;
                        cparser.get_option(vopts, next_char);

                        ex1.read_raw(cparser);

                        struct gas_phase *gas_phase_ptr = ex1.cxxGasPhase2gas_phase();
                        gas_phase_free(&gas_phase[i]);
                        gas_phase_copy(gas_phase_ptr, &gas_phase[i], gas_phase_ptr->n_user);
                        gas_phase_free(gas_phase_ptr);
                        free_check_null(gas_phase_ptr);

                }

        }
        for (i=0; i < count_irrev; i++) {
                        std::ostringstream oss;
                        cxxReaction ex(&(irrev[i]));
                        ex.dump_raw(oss, 0);
                        std::cerr << oss.str();


                        cxxReaction ex1;
                        std::string keyInput = oss.str();
                        std::istringstream iss(keyInput);

                        CParser cparser(iss, oss, std::cerr);
                        //For testing, need to read line to get started
                        std::vector<std::string> vopts;
                        std::istream::pos_type next_char;
                        cparser.get_option(vopts, next_char);

                        ex1.read_raw(cparser);
                        struct irrev *irrev_ptr = ex1.cxxReaction2irrev();

                        irrev_free(&irrev[i]);
                        irrev_copy(irrev_ptr, &irrev[i], irrev_ptr->n_user);

                        irrev_free(irrev_ptr);
                        free_check_null(irrev_ptr);

        }
        for (i=0; i < count_mix; i++) {
                        std::ostringstream oss;
                        cxxMix ex(&(mix[i]));
                        ex.dump_raw(oss, 0);
                        std::cerr << oss.str();


                        cxxMix ex1;
                        std::string keyInput = oss.str();
                        std::istringstream iss(keyInput);

                        CParser cparser(iss, oss, std::cerr);
                        //For testing, need to read line to get started
                        std::vector<std::string> vopts;
                        std::istream::pos_type next_char;
                        cparser.get_option(vopts, next_char);

                        ex1.read_raw(cparser);
                        struct mix *mix_ptr = ex1.cxxMix2mix();

                        mix_free(&mix[i]);
                        mix_copy(mix_ptr, &mix[i], mix_ptr->n_user);

                        mix_free(mix_ptr);
                        free_check_null(mix_ptr);

        }
        for (i=0; i < count_temperature; i++) {
                        std::ostringstream oss;
                        cxxTemperature ex(&(temperature[i]));
                        ex.dump_raw(oss, 0);
                        std::cerr << oss.str();


                        cxxTemperature ex1;
                        std::string keyInput = oss.str();
                        std::istringstream iss(keyInput);

                        CParser cparser(iss, oss, std::cerr);
                        //For testing, need to read line to get started
                        std::vector<std::string> vopts;
                        std::istream::pos_type next_char;
                        cparser.get_option(vopts, next_char);

                        ex1.read_raw(cparser);
                        struct temperature *temperature_ptr = ex1.cxxTemperature2temperature();

                        temperature_free(&temperature[i]);
                        temperature_copy(temperature_ptr, &temperature[i], temperature_ptr->n_user);

                        temperature_free(temperature_ptr);
                        free_check_null(temperature_ptr);

        }
#endif
	{
		// get all c storage
		cxxStorageBin cstorage;
		cstorage.import_phreeqc();
		//std::ostringstream oss;
		//cstorage.dump_raw(oss, 0);
		//write it out
                std::fstream myfile;
		myfile.open("tfile", std::ios_base::out);
		cstorage.dump_raw(myfile, 0);
		myfile.close();
	}
	{
		// empty storage bin
		cxxStorageBin cstorage;
		// fstream
                std::fstream myfile;
		myfile.open("tfile", std::ios_base::in);
		// ostream
		std::ostringstream oss;
		// parser
		CParser cparser(myfile, oss, std::cerr);
		cstorage.read_raw(cparser);
		//std::cerr << oss.str();

		// read it back
	}
}