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37b1add946
Added lines at end of files. Ran test cases, a few had changes from format and Tony. git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2182 1feff8c3-07ed-0310-ac33-dd36852eb9cd
931 lines
31 KiB
C++
931 lines
31 KiB
C++
// ISolution.cxx: implementation of the cxxSolutionxx class.
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//
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//////////////////////////////////////////////////////////////////////
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#ifdef _DEBUG
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#pragma warning(disable : 4786) // disable truncation warning (Only used by debugger)
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#endif
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#include "ISolution.h"
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#include "ISolutionComp.h"
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#define EXTERNAL extern
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#include "global.h"
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#include "phqalloc.h"
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#include "phrqproto.h"
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#include "output.h"
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#include <cassert> // assert
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#include <algorithm> // std::sort
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#include <sstream>
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#ifdef ORCHESTRA
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extern void ORCH_write_chemistry_species(std::ostream &chemistry_dat);
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#endif
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//////////////////////////////////////////////////////////////////////
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// Construction/Destruction
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//////////////////////////////////////////////////////////////////////
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//static std::map<int, cxxISolution> ss_map;
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//std::map<int, cxxISolution>& cxxISolution::s_map = ss_map;
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cxxISolution::cxxISolution()
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:
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units("mMol/kgw")
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{
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density = 1.0;
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default_pe = -1;
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pes = NULL;
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}
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cxxISolution::cxxISolution(struct solution *solution_ptr)
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: cxxSolution(solution_ptr)
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//, pe(cxxPe_Data::alloc())
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{
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density = solution_ptr->density;
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units = solution_ptr->units;
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// totals
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for (int i = 0; solution_ptr->totals[i].description != NULL; i++) {
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cxxISolutionComp c(&(solution_ptr->totals[i]));
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//comps.insert(solution_ptr->totals[i].description, c);
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comps[solution_ptr->totals[i].description] = c;
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}
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default_pe = solution_ptr->default_pe;
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// pe_data
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pes = pe_data_dup(solution_ptr->pe);
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}
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cxxISolution::~cxxISolution()
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{
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pe_data_free(this->pes);
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}
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struct solution *cxxISolution::cxxISolution2solution()
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//
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// Builds a solution structure from instance of cxxISolution
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//
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{
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struct solution *soln_ptr = this->cxxSolution2solution();
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soln_ptr->new_def = TRUE;
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soln_ptr->density = this->density;
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soln_ptr->units = string_hsave(this->units.c_str());
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soln_ptr->default_pe = this->default_pe;
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// pe
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soln_ptr->pe = (struct pe_data *) pe_data_free(soln_ptr->pe);
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soln_ptr->pe = pe_data_dup(this->pes);
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// totals
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soln_ptr->totals = (struct conc *) free_check_null(soln_ptr->totals);
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soln_ptr->totals = cxxISolutionComp::cxxISolutionComp2conc(this->comps);
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return(soln_ptr);
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}
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void cxxISolution::ConvertUnits()
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//
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// Converts from input units to moles per kilogram water
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//
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{
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double sum_solutes = 0;
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// foreach conc
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std::map<char *, cxxISolutionComp, CHARSTAR_LESS>::iterator iter = this->comps.begin();
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for(; iter != this->comps.end(); ++iter)
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{
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struct master *master_ptr = master_bsearch (iter->first);
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if (master_ptr != NULL && (master_ptr->minor_isotope == TRUE)) continue;
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if (iter->second.get_description() == "H(1)" || iter->second.get_description() == "E") continue;
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if (iter->second.get_input_conc() <= 0.0) continue;
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/*
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* Convert liters to kg solution
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*/
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double moles = iter->second.get_input_conc();
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if (this->units.find("/l") != std::string::npos )
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{
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moles /= this->density;
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}
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/*
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* Convert to moles
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*/
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//set gfw for element
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iter->second.set_gfw();
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// convert to moles
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if (iter->second.get_units().find("g/") != std::string::npos)
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{
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if (iter->second.get_gfw() != 0)
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{
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moles /= iter->second.get_gfw();
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}
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else
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{
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std::ostringstream oss;
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oss << "Could not find gfw, " << iter->second.get_description();
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error_msg(oss.str().c_str(), CONTINUE);
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input_error++;
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}
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}
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/*
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* Convert milli or micro
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*/
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char c = iter->second.get_units().c_str()[0];
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if (c == 'm')
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{
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moles *= 1e-3;
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}
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else if (c == 'u')
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{
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moles *= 1e-6;
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}
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iter->second.set_moles(moles);
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/*
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* Sum grams of solute, convert from moles necessary
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*/
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sum_solutes += moles * (iter->second.get_gfw());
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}
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/*
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* Convert /kgs to /kgw
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*/
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double mass_water;
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if ((this->units.find("kgs") != std::string::npos) ||
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(this->units.find("/l") != std::string::npos))
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{
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mass_water = 1.0 - 1e-3 * sum_solutes;
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for(; iter != this->comps.end(); ++iter)
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{
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iter->second.set_moles(iter->second.get_moles() / mass_water);
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}
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}
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/*
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* Scale by mass of water in solution
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*/
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mass_water = this->mass_water;
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for(; iter != this->comps.end(); ++iter)
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{
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iter->second.set_moles(iter->second.get_moles() * mass_water);
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}
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}
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#ifdef SKIP
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cxxISolution& cxxISolution::read(CParser& parser)
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{
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static std::vector<std::string> vopts;
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if (vopts.empty()) {
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vopts.reserve(11);
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vopts.push_back("temp"); // 0
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vopts.push_back("temperature"); // 1
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vopts.push_back("dens"); // 2
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vopts.push_back("density"); // 3
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vopts.push_back("units"); // 4
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vopts.push_back("redox"); // 5
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vopts.push_back("ph"); // 6
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vopts.push_back("pe"); // 7
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vopts.push_back("unit"); // 8
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vopts.push_back("isotope"); // 9
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vopts.push_back("water"); // 10
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}
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// const int count_opt_list = vopts.size();
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cxxISolution numkey;
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// Read solution number and description
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numkey.read_number_description(parser);
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// Malloc space for solution data
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//// g_solution_map[numkey.n_user()] = numkey;
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s_map[numkey.n_user()] = numkey;
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std::istream::pos_type ptr;
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std::istream::pos_type next_char;
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std::string token;
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CParser::TOKEN_TYPE j;
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cxxISolution& sol = s_map[numkey.n_user()];
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int default_pe = 0;
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for (;;)
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{
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int opt = parser.get_option(vopts, next_char);
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if (opt == CParser::OPTION_DEFAULT)
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{
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ptr = next_char;
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if (parser.copy_token(token, ptr) == CParser::TT_DIGIT) {
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opt = 9;
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}
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}
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switch (opt)
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{
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case CParser::OPTION_EOF:
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break;
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case CParser::OPTION_KEYWORD:
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break;
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case CParser::OPTION_ERROR:
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opt = CParser::OPTION_EOF;
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CParser::error_msg("Unknown input in SOLUTION keyword.", CParser::OT_CONTINUE);
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CParser::error_msg(parser.line().c_str(), CParser::OT_CONTINUE);
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break;
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case 0: // temp
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case 1: // temperature
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if (!(parser.get_iss() >> sol.tc))
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{
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sol.tc = 25;
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}
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break;
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case 2: // dens
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case 3: // density
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parser.get_iss() >> sol.density;
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break;
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case 4: // units
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case 8: // unit
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if (parser.copy_token(token, next_char) == CParser::TT_EMPTY) break;
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if (parser.check_units(token, false, false, sol.units, true) == CParser::OK) {
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sol.units = token;
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} else {
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parser.incr_input_error();
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}
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break;
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case 5: // redox
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if (parser.copy_token(token, next_char) == CParser::TT_EMPTY) break;
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if (parser.parse_couple(token) == CParser::OK) {
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default_pe = cxxPe_Data::store(sol.pe, token);
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} else {
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parser.incr_input_error();
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}
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break;
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case 6: // ph
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{
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cxxISolutionComp conc;
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if (conc.read(parser, sol) == cxxISolutionComp::ERROR) {
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parser.incr_input_error();
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break;
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}
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sol.ph = conc.get_input_conc();
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if (conc.get_equation_name().empty()) {
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break;
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}
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conc.set_description("H(1)");
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sol.add(conc);
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}
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break;
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case 7: // pe
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{
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cxxISolutionComp conc;
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if (conc.read(parser, sol) == cxxISolutionComp::ERROR) {
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parser.incr_input_error();
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break;
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}
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sol.solution_pe = conc.get_input_conc();
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if (conc.get_equation_name().empty()) {
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break;
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}
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conc.set_description("E");
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sol.add(conc);
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}
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break;
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case 9: // isotope
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{
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cxxIsotope isotope;
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if (isotope.read(parser) == cxxIsotope::OK) {
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sol.add(isotope);
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}
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}
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break;
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case 10: // water
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j = parser.copy_token(token, next_char);
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if (j == CParser::TT_EMPTY) {
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sol.mass_water = 1.0;
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} else if (j != CParser::TT_DIGIT) {
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parser.incr_input_error();
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parser.error_msg("Expected numeric value for mass of water in solution.", CParser::OT_CONTINUE);
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} else {
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std::istringstream(token) >> sol.mass_water;
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}
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break;
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case CParser::OPTION_DEFAULT:
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{
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// Read concentration
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cxxISolutionComp conc;
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if (conc.read(parser, sol) == cxxISolutionComp::ERROR) {
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parser.incr_input_error();
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} else {
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sol.add(conc);
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}
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}
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break;
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}
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if (opt == CParser::OPTION_EOF || opt == CParser::OPTION_KEYWORD) break;
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}
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#ifdef SKIP
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//
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// Sort totals by description
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//
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std::sort(sol.totals.begin(), sol.totals.end());
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#endif
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//
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// fix up default units and default pe
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//
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std::string token1;
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std::vector<cxxISolutionComp>::iterator iter = sol.totals.begin();
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for (; iter != sol.totals.end(); ++iter)
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{
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token = (*iter).get_description();
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Utilities::str_tolower(token);
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if ((*iter).get_units().empty()) {
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(*iter).set_units(sol.units);
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} else {
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bool alk = false;
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if (token.find("alk") == 0) alk = true;
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token1 = (*iter).get_units();
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if (parser.check_units(token1, alk, true, sol.get_units(), true) == CParser::ERROR) {
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parser.incr_input_error();
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} else {
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(*iter).set_units(token1);
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}
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}
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if ((*iter).get_n_pe() < 0) {
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(*iter).set_n_pe(default_pe);
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}
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}
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sol.default_pe = default_pe;
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return sol;
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}
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#endif
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#ifdef SKIP
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void cxxISolution::dump_xml(std::ostream& os, unsigned int indent)const
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{
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unsigned int i;
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for(i = 0; i < indent; ++i) os << Utilities::INDENT;
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os << "<solution>\n";
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cxxNumKeyword::dump_xml(os, indent);
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for(i = 0; i < indent + 1; ++i) os << Utilities::INDENT;
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os << "<temp>" << this->get_tc() << "</temp>" << "\n";
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for(i = 0; i < indent + 1; ++i) os << Utilities::INDENT;
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os << "<pH>" << this->get_ph() << "</pH>" << "\n";
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for(i = 0; i < indent + 1; ++i) os << Utilities::INDENT;
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os << "<pe>" << this->get_solution_pe() << "</pe>" << "\n";
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assert(this->pe.size() > 0);
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assert(this->default_pe >= 0);
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assert(this->pe.size() > (unsigned int) this->default_pe);
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//this->pe[this->default_pe].dump_xml(os, indent + 1);
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for(i = 0; i < indent + 1; ++i) os << Utilities::INDENT;
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os << "<units>" << this->get_units() << "</units>" << "\n";
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for(i = 0; i < indent + 1; ++i) os << Utilities::INDENT;
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os << "<density>" << this->get_density() << "</density>" << "\n";
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// foreach conc
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if (!this->totals.empty())
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{
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for(i = 0; i < indent + 1; ++i) os << Utilities::INDENT;
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os << "<totals>\n";
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std::vector<cxxISolutionComp>::const_iterator iter = this->totals.begin();
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for(; iter != this->totals.end(); ++iter)
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{
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(*iter).dump_xml(*this, os, indent + 2);
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}
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for(i = 0; i < indent + 1; ++i) os << Utilities::INDENT;
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os << "</totals>\n";
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}
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// foreach isotope
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if (!this->isotopes.empty())
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{
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for(i = 0; i < indent + 1; ++i) os << Utilities::INDENT;
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os << "<isotopes>\n";
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std::list<cxxIsotope>::const_iterator iter = this->isotopes.begin();
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for(; iter != this->isotopes.end(); ++iter)
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{
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(*iter).dump_xml(os, indent + 2);
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}
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for(i = 0; i < indent + 1; ++i) os << Utilities::INDENT;
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os << "</isotopes>\n";
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}
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for(i = 0; i < indent + 1; ++i) os << Utilities::INDENT;
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os << "<water>" << this->get_mass_water() << "</water>" << "\n";
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for(i = 0; i < indent; ++i) os << Utilities::INDENT;
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os << "</solution>" << "\n";
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}
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#endif
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#ifdef ORCHESTRA
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void cxxISolution::ORCH_write_chemistry(std::ostream &chemistry_dat)
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{
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this->ORCH_write_chemistry_water(chemistry_dat);
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this->ORCH_write_chemistry_primary(chemistry_dat);
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this->ORCH_write_chemistry_total_O_H(chemistry_dat);
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this->ORCH_write_chemistry_alkalinity(chemistry_dat);
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ORCH_write_chemistry_species(chemistry_dat);
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this->ORCH_write_chemistry_minerals(chemistry_dat);
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}
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void cxxISolution::ORCH_write_chemistry_water(std::ostream &chemistry_dat)
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{
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//
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// Write water entities
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//
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chemistry_dat << std::endl << "//********* The water entities" << std::endl;
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// e-
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chemistry_dat << "@entity(e-, diss, 0)" << std::endl;
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if (this->comps.find("E") == this->comps.end() || this->comps.find("E")->second.get_equation_name() == NULL)
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{
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// fixed pe
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chemistry_dat << "@Calc: (1, \"e-.act = 10^-pe\")" << std::endl;
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} else if (this->comps.find("E")->second.get_equation_name() == string_hsave("charge"))
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{
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// charge balance
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chemistry_dat << "@Calc: (1, \"pe = -log10({e-.act})\")" << std::endl;
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chemistry_dat << "@solve (e-.act, 1e-6, log, 1, chargebalance, 1e-14)" << std::endl;
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} else
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{
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// adjust to equilbirium with a phase
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chemistry_dat << "@Calc: (1, \"pe = -log10({e-.act})\")" << std::endl;
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int n;
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struct phase *phase_ptr = phase_bsearch(this->comps.find("E)")->second.get_equation_name(), &n, FALSE);
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assert (phase_ptr != NULL);
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std::string phase_name(phase_ptr->name);
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std::replace(phase_name.begin(), phase_name.end(), '(', '[');
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std::replace(phase_name.begin(), phase_name.end(), ')', ']');
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chemistry_dat << "@solve (e-.act, 1e-6, log, 1, " << phase_name.c_str() << ".si_raw, 1e-9)" << std::endl;
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}
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// H+
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if (this->comps.find("H(1)") == this->comps.end() || this->comps.find("H(1)")->second.get_equation_name() == NULL)
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{
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// fixed pH
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chemistry_dat << "@Calc: (1, \"H+.act = 10^-pH\")" << std::endl;
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} else if (this->comps.find("H(1)")->second.get_equation_name() == string_hsave("charge"))
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{
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// charge balance
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chemistry_dat << "@Calc: (1, \"pH = -log10({H+.act})\")" << std::endl;
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chemistry_dat << "@solve (H+.act, 1e-6, log, 1, chargebalance, 1e-14)" << std::endl;
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} else
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{
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// adjust to equilbirium with a phase
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chemistry_dat << "@Calc: (1, \"pH = -log10({H+.act})\")" << std::endl;
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int n;
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struct phase *phase_ptr = phase_bsearch(this->comps.find("H(1)")->second.get_equation_name(), &n, FALSE);
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assert (phase_ptr != NULL);
|
|
chemistry_dat << "@solve (H+.act, 1e-6, log, 1, " << phase_ptr->name << ".si_raw, 1e-9)" << std::endl;
|
|
}
|
|
|
|
// H2O
|
|
chemistry_dat << "@entity(" << s_h2o->name << ", diss, 55.506)" << std::endl;
|
|
chemistry_dat << std::endl;
|
|
}
|
|
|
|
void cxxISolution::ORCH_write_chemistry_primary(std::ostream &chemistry_dat)
|
|
{
|
|
chemistry_dat << std::endl << "//********* The primary species" << std::endl;
|
|
//
|
|
// Write other master species definitions, i.e. primary entities
|
|
//
|
|
std::map<char *, cxxISolutionComp, CHARSTAR_LESS>::iterator iter = this->comps.begin();
|
|
chemistry_dat << "@species(H+, 1)" << std::endl;
|
|
for(; iter != this->comps.end(); ++iter)
|
|
{
|
|
std::string name(iter->second.get_description());
|
|
if (name == "H(1)" || name == "E" || name == "Alkalinity") continue;
|
|
struct element *elt;
|
|
char *element_name = string_hsave(name.c_str());
|
|
elt = element_store(element_name);
|
|
assert(elt != NULL);
|
|
struct species *s_ptr;
|
|
s_ptr = elt->master->s;
|
|
assert(s_ptr != NULL);
|
|
chemistry_dat << "@species(" << s_ptr->name << ", " << s_ptr->z << ")" << std::endl;
|
|
if (iter->second.get_equation_name() == NULL)
|
|
{
|
|
// regular mole balance
|
|
chemistry_dat << "@primary_entity(" << s_ptr->name << ", 1e-9, diss, 1.0e-9)" << std::endl;
|
|
} else
|
|
{
|
|
std::string eqn(iter->second.get_equation_name());
|
|
if (eqn == "charge")
|
|
{
|
|
// charge balance
|
|
chemistry_dat << "@solve (" << s_ptr->name << ".act, 1e-6, log, 1, chargebalance, 1e-9)" << std::endl;
|
|
} else
|
|
{
|
|
// adjust to phase equilibrium
|
|
int n;
|
|
struct phase *phase_ptr = phase_bsearch(eqn.c_str(), &n, FALSE);
|
|
assert (phase_ptr != NULL);
|
|
std::string phase_name(phase_ptr->name);
|
|
std::replace(phase_name.begin(), phase_name.end(), '(', '[');
|
|
std::replace(phase_name.begin(), phase_name.end(), ')', ']');
|
|
chemistry_dat << "@solve (" << s_ptr->name << ".act, 1e-6, log, 1, " << phase_name << ".si_raw, 1e-9)" << std::endl;
|
|
}
|
|
}
|
|
}
|
|
chemistry_dat << std::endl;
|
|
}
|
|
|
|
void cxxISolution::ORCH_write_chemistry_total_O_H(std::ostream &chemistry_dat)
|
|
{
|
|
chemistry_dat << std::endl << "//********* Define total hydrogen and oxygen" << std::endl;
|
|
// Define total hydrogen, total oxygen, and difference
|
|
//chemistry_dat << "@var: total_diff 0" << std::endl;
|
|
//chemistry_dat << "@calc: (5, \"total_diff = total_hydrogen - 2*total_oxygen" << "\")" << std::endl;
|
|
|
|
// Write H total equation
|
|
chemistry_dat << "@var: total_hydrogen 0" << std::endl;
|
|
chemistry_dat << "@calc: (5, \"total_hydrogen = 0";
|
|
int i;
|
|
for (i = 0; i < count_s_x; i++)
|
|
{
|
|
// write in terms of orchestra components
|
|
if (s_x[i]->primary != NULL || (s_x[i]->secondary != NULL && s_x[i]->secondary->in == TRUE))
|
|
{
|
|
if (s_x[i]->h != 0)
|
|
{
|
|
chemistry_dat << "+";
|
|
if (s_x[i]->h != 1)
|
|
{
|
|
chemistry_dat << s_x[i]->h << "*";
|
|
}
|
|
chemistry_dat << "{" << s_x[i]->name << ".diss}";
|
|
}
|
|
}
|
|
}
|
|
chemistry_dat << "\")" << std::endl;
|
|
|
|
// Write O total equation
|
|
chemistry_dat << "@var: total_oxygen 0" << std::endl;
|
|
chemistry_dat << "@calc: (5, \"total_oxygen = 0";
|
|
for (i = 0; i < count_s_x; i++)
|
|
{
|
|
if (s_x[i]->o != 0)
|
|
{
|
|
// write in terms of orchestra components
|
|
if (s_x[i]->primary != NULL || (s_x[i]->secondary != NULL && s_x[i]->secondary->in == TRUE))
|
|
{
|
|
chemistry_dat << "+";
|
|
if (s_x[i]->o != 1)
|
|
{
|
|
chemistry_dat << s_x[i]->o << "*";
|
|
}
|
|
chemistry_dat << "{" << s_x[i]->name << ".diss}";
|
|
}
|
|
}
|
|
}
|
|
chemistry_dat << "\")" << std::endl;
|
|
chemistry_dat << std::endl;
|
|
}
|
|
void cxxISolution::ORCH_write_chemistry_alkalinity(std::ostream &chemistry_dat)
|
|
{
|
|
chemistry_dat << std::endl << "//********* Alkalinity definitions" << std::endl;
|
|
//
|
|
// Define alkalinity
|
|
//
|
|
chemistry_dat << "@Var: Alkalinity 0" << std::endl;
|
|
chemistry_dat << "@calc: (5, \"Alkalinity = 0";
|
|
for (int i = 0; i < count_s_x; i++)
|
|
{
|
|
if (s_x[i]->alk == 0) continue;
|
|
std::string name(s_x[i]->name);
|
|
std::replace(name.begin(), name.end(), '(', '[');
|
|
std::replace(name.begin(), name.end(), ')', ']');
|
|
if (s_x[i]->alk < 0)
|
|
{
|
|
if (s_x[i]->alk != -1)
|
|
{
|
|
chemistry_dat << s_x[i]->alk << "*{" << name << ".con}";
|
|
} else
|
|
{
|
|
chemistry_dat << "-{" << name << ".con}";
|
|
}
|
|
} else if (s_x[i]->alk > 0)
|
|
{
|
|
if (s_x[i]->alk != 1)
|
|
{
|
|
chemistry_dat << "+" << s_x[i]->alk << "*{" << name << ".con}";
|
|
} else
|
|
{
|
|
chemistry_dat << "+{" << name << ".con}";
|
|
}
|
|
}
|
|
}
|
|
chemistry_dat << "\")" << std::endl;
|
|
//
|
|
// Alkalinity (or pH) equation
|
|
//
|
|
std::map<char *, cxxISolutionComp, CHARSTAR_LESS>::iterator iter = this->comps.begin();
|
|
if ((iter = this->comps.find("Alkalinity")) != this->comps.end())
|
|
{
|
|
if ((this->comps.find("C(4)") != this->comps.end()) || (this->comps.find("C") != this->comps.end()))
|
|
{
|
|
if (this->comps.find("H(1)") != this->comps.end() )
|
|
{
|
|
std::ostringstream oss;
|
|
oss << "pH can not be adjusted to charge balance or phase equilibrium when specifying C or C(4) and Alkalinty.";
|
|
error_msg(oss.str().c_str(), CONTINUE);
|
|
input_error++;
|
|
}
|
|
chemistry_dat << "@solve (pH, 1e-6, lin, 1, Alkalinity, 7)" << std::endl;
|
|
chemistry_dat << std::endl;
|
|
} else
|
|
{
|
|
struct master *master_ptr = master_bsearch("Alkalinity");
|
|
if (master_ptr == NULL)
|
|
{
|
|
std::ostringstream oss;
|
|
oss << "Could not find Alkalinity definition in database.";
|
|
error_msg(oss.str().c_str(), CONTINUE);
|
|
input_error++;
|
|
}
|
|
chemistry_dat << "@species(" << master_ptr->s->name << ", " << master_ptr->s->z << ")" << std::endl;
|
|
chemistry_dat << "@solve (" << master_ptr->s->name << ".act, 1e-6, log, 1, Alkalinity, 1e-9)" << std::endl;
|
|
chemistry_dat << std::endl;
|
|
}
|
|
}
|
|
}
|
|
|
|
void cxxISolution::ORCH_write_chemistry_minerals(std::ostream &chemistry_dat)
|
|
{
|
|
chemistry_dat << std::endl << "//********* Adjustments to mineral equilibrium" << std::endl;
|
|
//
|
|
// Write minerals
|
|
//
|
|
std::map<char *, cxxISolutionComp, CHARSTAR_LESS>::iterator iter = this->comps.begin();
|
|
for(iter = this->comps.begin(); iter != this->comps.end(); ++iter)
|
|
{
|
|
if (iter->second.get_equation_name() != NULL)
|
|
{
|
|
std::string name(iter->second.get_equation_name());
|
|
if (name != "charge")
|
|
{
|
|
struct phase *phase_ptr;
|
|
int n;
|
|
phase_ptr = phase_bsearch(name.c_str(), &n, FALSE);
|
|
assert (phase_ptr != NULL);
|
|
std::string phase_name(phase_ptr->name);
|
|
std::replace(phase_name.begin(), phase_name.end(), '(', '[');
|
|
std::replace(phase_name.begin(), phase_name.end(), ')', ']');
|
|
chemistry_dat << "@si_mineral(" << phase_name << ")" << std::endl;
|
|
chemistry_dat << "@reaction(" << phase_name << ", " << pow(10.0, -phase_ptr->lk);
|
|
struct rxn_token *next_token = phase_ptr->rxn_x->token;
|
|
next_token++;
|
|
while (next_token->s != NULL || next_token->name != NULL)
|
|
{
|
|
chemistry_dat << ", " << next_token->coef;
|
|
if (next_token->s != NULL)
|
|
{
|
|
chemistry_dat << ", " << next_token->s->name;
|
|
} else {
|
|
chemistry_dat << ", " << next_token->name;
|
|
}
|
|
next_token++;
|
|
}
|
|
chemistry_dat << ")" << std::endl;
|
|
}
|
|
}
|
|
}
|
|
//chemistry_dat << "@mineral(Quartz)" << std::endl;
|
|
//chemistry_dat << "@sreaction(Quartz, 10139.1138573668, -2.0, H2O, 1.0, H4SiO4)" << std::endl;
|
|
}
|
|
void cxxISolution::ORCH_write_input(std::ostream &input_dat)
|
|
{
|
|
|
|
|
|
//
|
|
// Write orchestra input file info
|
|
//
|
|
std::ostringstream headings, data;
|
|
data.precision(DBL_DIG - 1);
|
|
headings << "var: ";
|
|
data << "data: ";
|
|
|
|
|
|
// Solution element and attributes
|
|
|
|
//s_oss << "SOLUTION_RAW " << this->n_user << " " << this->description << std::endl;
|
|
|
|
//s_oss << "-temp " << this->tc << std::endl;
|
|
headings << "tempc\t";
|
|
data << this->tc << "\t";
|
|
|
|
//s_oss << "-pH " << this->ph << std::endl;
|
|
headings << "pH\t";
|
|
data << this->ph << "\t";
|
|
|
|
//s_oss << "-pe " << this->pe << std::endl;
|
|
headings << "pe\t";
|
|
data << this->pe << "\t";
|
|
|
|
//s_oss << "-mu " << this->mu << std::endl;
|
|
|
|
//s_oss << "-ah2o " << this->ah2o << std::endl;
|
|
headings << "H2O.act\t";
|
|
data << 1 << "\t";
|
|
//s_oss << "-total_h " << this->total_h << std::endl;
|
|
|
|
//s_oss << "-total_o " << this->total_o << std::endl;
|
|
|
|
//s_oss << "-cb " << this->cb << std::endl;
|
|
|
|
//s_oss << "-mass_water " << this->mass_water << std::endl;
|
|
|
|
//s_oss << "-total_alkalinity " << this->total_alkalinity << std::endl;
|
|
|
|
// soln_total conc structures
|
|
//this->totals.dump_raw(s_oss, indent + 2);
|
|
//this->totals.write_orchestra(headings, s_oss);
|
|
|
|
std::map<char *, cxxISolutionComp, CHARSTAR_LESS>::iterator iter = this->comps.begin();
|
|
for (; iter != this->comps.end(); ++iter)
|
|
{
|
|
std::string master_name;
|
|
struct master *master_ptr;
|
|
master_ptr = master_bsearch (iter->first);
|
|
assert (master_ptr != NULL);
|
|
std::string ename(iter->first);
|
|
double coef = master_ptr->coef;
|
|
if (master_ptr->coef == 0)
|
|
{
|
|
coef = 1;
|
|
}
|
|
if (ename != "Alkalinity")
|
|
{
|
|
ename = master_ptr->s->name;
|
|
ename.append(".diss");
|
|
}
|
|
|
|
if (iter->second.get_equation_name() == NULL)
|
|
{
|
|
headings << ename << "\t";
|
|
data << (this->totals.find(iter->first))->second / coef << "\t";
|
|
} else
|
|
{
|
|
std::string name(iter->second.get_equation_name());
|
|
if (name == "charge")
|
|
{
|
|
headings << ename << "\t";
|
|
data << (this->totals.find(iter->first))->second /coef << "\t";
|
|
} else
|
|
{
|
|
int n;
|
|
struct phase *phase_ptr = phase_bsearch(name.c_str(),&n, TRUE);
|
|
assert(phase_ptr != NULL);
|
|
std::string phase_name(phase_ptr->name);
|
|
std::replace(phase_name.begin(), phase_name.end(), '(', '[');
|
|
std::replace(phase_name.begin(), phase_name.end(), ')', ']');
|
|
headings << phase_name << ".si_raw" << "\t";
|
|
data << iter->second.get_phase_si() << "\t";
|
|
}
|
|
}
|
|
// activity estimate
|
|
if (ename == "Alkalinity")
|
|
{
|
|
if ((this->comps.find("C") == this->comps.end()) && (this->comps.find("C(4)") == this->comps.end()))
|
|
{
|
|
headings << master_ptr->s->name << ".act\t";
|
|
data << iter->second.get_moles()*1e-3 << "\t";
|
|
}
|
|
}
|
|
else
|
|
{
|
|
headings << master_ptr->s->name << ".act\t";
|
|
data << iter->second.get_moles()*1e-3 << "\t";
|
|
}
|
|
}
|
|
// Isotopes
|
|
//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);
|
|
}
|
|
}
|
|
*/
|
|
|
|
// Write data to string
|
|
input_dat << headings.str() << std::endl;
|
|
input_dat << data.str() << std::endl;
|
|
|
|
return;
|
|
}
|
|
|
|
void cxxISolution::ORCH_write_output_vars(std::ostream &outstream)
|
|
{
|
|
outstream << "Var:";
|
|
outstream << "\tnr_iter";
|
|
//
|
|
// Serialize solution
|
|
//
|
|
outstream << "\tstart_solution";
|
|
//tc
|
|
outstream << "\ttempc";
|
|
//pH
|
|
outstream << "\tpH";
|
|
//pe
|
|
outstream << "\tpe";
|
|
//mu
|
|
outstream << "\tI";
|
|
//ah2o
|
|
outstream << "\tH2O.act";
|
|
//total_h;
|
|
outstream << "\ttotal_hydrogen";
|
|
//total_o;
|
|
outstream << "\ttotal_oxygen";
|
|
//cb
|
|
outstream << "\tchargebalance";
|
|
//mass_water;
|
|
outstream << "\tH2O.con";
|
|
//total_alkalinity;
|
|
outstream << "\tAlkalinity";
|
|
//orchestra master variables
|
|
outstream << "\tH+.diss";
|
|
outstream << "\te-.diss";
|
|
outstream << "\tH2O.diss";
|
|
//totals
|
|
for(std::map<char *, cxxISolutionComp, CHARSTAR_LESS>::iterator iter = this->comps.begin(); iter != this->comps.end(); ++iter)
|
|
{
|
|
std::string name(iter->second.get_description());
|
|
if (name == "H(1)" || name == "E" || name == "Alkalinity") continue;
|
|
struct element *elt;
|
|
char *element_name = string_hsave(name.c_str());
|
|
elt = element_store(element_name);
|
|
assert(elt != NULL);
|
|
struct species *s_ptr;
|
|
s_ptr = elt->master->s;
|
|
assert(s_ptr != NULL);
|
|
outstream << "\t" << s_ptr->name << ".diss";
|
|
}
|
|
outstream << "\tend_totals";
|
|
for(std::map<char *, cxxISolutionComp, CHARSTAR_LESS>::iterator iter = this->comps.begin(); iter != this->comps.end(); ++iter)
|
|
{
|
|
std::string name(iter->second.get_description());
|
|
if (name == "H(1)" || name == "E" || name == "Alkalinity") continue;
|
|
struct element *elt;
|
|
char *element_name = string_hsave(name.c_str());
|
|
elt = element_store(element_name);
|
|
assert(elt != NULL);
|
|
struct species *s_ptr;
|
|
s_ptr = elt->master->s;
|
|
assert(s_ptr != NULL);
|
|
outstream << "\t" << s_ptr->name << ".act";
|
|
}
|
|
outstream << "\tend_master_activities";
|
|
//
|
|
// Write all species activities and concentrations
|
|
//
|
|
int i;
|
|
for (i = 0; i < count_s_x; i++) {
|
|
std::string name(s_x[i]->name);
|
|
std::replace(name.begin(), name.end(), '(', '[');
|
|
std::replace(name.begin(), name.end(), ')', ']');
|
|
outstream << "\t" << name.c_str() << ".act" << "\t" << name.c_str() << ".con";
|
|
}
|
|
outstream << "\tend_species";
|
|
outstream << std::endl;
|
|
return;
|
|
}
|
|
void cxxISolution::ORCH_write(std::ostream &chemistry_dat, std::ostream &input_dat, std::ostream &output_dat)
|
|
{
|
|
//
|
|
// Write orchestra chemistry file definition
|
|
//
|
|
chemistry_dat << std::endl << "// Write ORCHESTRA chemistry definitions" << std::endl;
|
|
// mark for Orchestra include
|
|
chemistry_dat << std::endl << "@class: species_reactions () {" << std::endl;
|
|
this->ORCH_write_chemistry(chemistry_dat);
|
|
// end orchestra include block
|
|
chemistry_dat << std::endl << "}" << std::endl;
|
|
//
|
|
// Write orchestra input file definition
|
|
//
|
|
input_dat << std::endl << "@class: input_file_data () {" << std::endl;
|
|
this->ORCH_write_input(input_dat);
|
|
input_dat << std::endl << "}" << std::endl;
|
|
|
|
//
|
|
// Write orchestra output file definition
|
|
//
|
|
output_dat << std::endl << "Output_every: 1" << std::endl;
|
|
this->ORCH_write_output_vars(output_dat);
|
|
|
|
//write data to stderr
|
|
//std::cerr << chemistry_dat.str() << input_dat.str() << output_dat.str();
|
|
|
|
}
|
|
#endif
|