iphreeqc/System.cxx

#include <algorithm>			// std::replace 

#if !defined(PHREEQC_CLASS)
#define EXTERNAL extern
#include "global.h"
#else
#include "Phreeqc.h"
#endif
#include "System.h"
#include "SSassemblage.h"
#include "Solution.h"
#include "Exchange.h"
#include "GasPhase.h"
#include "cxxKinetics.h"
#include "PPassemblage.h"
#include "SSassemblageSS.h"
#include "SSassemblage.h"
#include "Surface.h"
#include "cxxMix.h"
#include "Reaction.h"
#include "Temperature.h"


extern void ORCH_write_chemistry_species(std::ostream & chemistry_dat);
cxxSystem::cxxSystem(void) 
{
	this->solution = NULL;
	this->exchange = NULL;
	this->ppassemblage = NULL;
	this->gasphase = NULL;
	this->ssassemblage = NULL;
	this->kinetics = NULL;
	this->surface = NULL;
	this->mix = NULL;
	this->reaction = NULL;
	this->temperature = NULL;
} 
cxxSystem::~cxxSystem(void) 
{
} 
void
cxxSystem::Initialize(void) 
{
	this->solution = NULL;
	this->exchange = NULL;
	this->ppassemblage = NULL;
	this->gasphase = NULL;
	this->ssassemblage = NULL;
	this->kinetics = NULL;
	this->surface = NULL;
	this->mix = NULL;
	this->reaction = NULL;
	this->temperature = NULL;
} 
void
cxxSystem::totalize(void) 
{
	//initialize
	this->totals.clear();
	//add solution
	if (this->solution != NULL)
	{
		char token[MAX_LENGTH];
		strcpy(token, "O");
		this->totals[token] = this->solution->get_total_o();
		strcpy(token, "H");
		this->totals[token] = this->solution->get_total_h();
		strcpy(token, "Charge");
		this->totals[token] = this->solution->get_cb();
		this->totals.add_extensive(this->solution->get_totals(), 1.0);
	}
	if (this->exchange != NULL)
	{
		this->exchange->totalize();
		this->totals.add_extensive(this->exchange->get_totals(), 1.0);
	}
	if (this->ppassemblage != NULL)
	{
		this->ppassemblage->totalize();
		this->totals.add_extensive(this->ppassemblage->get_totals(), 1.0);
	}
	if (this->gasphase != NULL)
	{
		this->gasphase->totalize();
		this->totals.add_extensive(this->gasphase->get_totals(), 1.0);
	}
	if (this->ssassemblage != NULL)
	{
		this->ssassemblage->totalize();
		this->totals.add_extensive(this->ssassemblage->get_totals(), 1.0);
	}
	if (this->surface != NULL)
	{
		this->ssassemblage->totalize();
		this->totals.add_extensive(this->surface->get_totals(), 1.0);
	}
	//Need to handle the following 3 reactions:
	//
	//this->kinetics = NULL;
	//this->mix = NULL;
	//this->reaction = NULL;
	//this->temperature = NULL;
	//this->totals.dump_raw(std::cerr, 1);
	return;
}
#ifdef ORCHESTRA
void
cxxSystem::ORCH_write(std::ostream & chemistry_dat, std::ostream & input_dat,
					  std::ostream & output_dat) 
{
	//
	// chemistry file
	//
	this->totalize();
	// calculate orchestra components from PHREEQC totals
	this->ORCH_components();
	// write definitions for chemistry
	chemistry_dat << std::
		endl << "@class: species_reactions () {" << std::endl;
	this->ORCH_write_chemistry_water(chemistry_dat);
	this->ORCH_write_chemistry_primary(chemistry_dat);
	this->ORCH_write_chemistry_total_O_H(chemistry_dat);
	ORCH_write_chemistry_species(chemistry_dat);
	// add definitions for pure phases
	if (this->ppassemblage != NULL)
		this->ppassemblage->ORCH_write_chemistry(chemistry_dat);
	// add definitions for other PHREEQC entities here
	// finish up
	chemistry_dat << std::endl << "}" << std::endl;
	//
	// input file
	//
	input_dat << std::endl << "@class: input_file_data () {" << std::endl;
	this->ORCH_write_input(input_dat);
	input_dat << std::endl << "}" << std::endl;
	//
	// output file
	//
	output_dat << std::endl << "Output_every: 1" << std::endl;
	output_dat << "Var:";
	this->ORCH_write_output_vars(output_dat);
	// add definitions for pure phases
	if (this->ppassemblage != NULL)
		this->ppassemblage->ORCH_write_output_vars(output_dat);
	//finish up
	output_dat << std::endl;
};
void
cxxSystem::ORCH_write_chemistry_water(std::ostream & chemistry_dat) 
{
	//
	//  Write water entities
	//
	chemistry_dat << std::
		endl << "//********* The water entities" << std::endl;
	//  e-, total hydrogen
	chemistry_dat << "@entity(e-, diss, 0)" << std::endl;
	chemistry_dat << "@Calc: (1, \"e-.act = 10.^(-pe)\")" << std::endl;
	chemistry_dat << "@solve (pe, 1e-6, lin, 1, e-.liter,  1e-14)" << std::
		endl;
	//  H+, charge balance
	chemistry_dat << "@Calc: (1, \"H+.act = 10.^(-pH)\")" << std::endl;
	chemistry_dat << "@solve (pH, 1e-6, lin, 1, H+.liter,  1e-14)" << std::
		endl;
	// H2O
	chemistry_dat << "@entity(" << s_h2o->
		name << ", diss, 55.506)" << std::endl;
	chemistry_dat << std::endl;
} 
void
cxxSystem::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
	//
	chemistry_dat << "@species(H+, 1)" << std::endl;
	for (cxxNameDouble::iterator iter = this->totals.begin();
		iter != this->totals.end(); ++iter)
	{
		std::string name(iter->first);
		if (name == "H(1)" || name == "E" || name == "H" || name == "O"
			|| name == "Charge")
			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;
		// regular mole balance
		chemistry_dat << "@primary_entity(" << s_ptr->
			name << ", 1e-9, liter, 1.0e-9)" << std::endl;
	} 
	chemistry_dat << std::endl;
} 
void
cxxSystem::ORCH_write_chemistry_total_O_H(std::ostream & chemistry_dat) 
{
	chemistry_dat << std::
		endl << "//********* Define total hydrogen and 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 << ".liter}";
			}
		}
	}
	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 << ".liter}";
			}
		}
	}
	chemistry_dat << "\")" << std::endl;
	chemistry_dat << std::endl;
}
void
cxxSystem::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:  ";
	headings << "tempc\t";
	data << this->solution->get_tc() << "\t";
	headings << "pH\t";
	data << this->solution->get_ph() << "\t";
	headings << "pe\t";
	data << this->solution->get_pe() << "\t";
	headings << "H2O.act\t";
	data << 1 << "\t";
	headings << "I\t";
	data << this->solution->get_mu() << "\t";
	for (cxxNameDouble::iterator iter = this->orch_totals.begin();
		iter != this->orch_totals.end(); ++iter)
	{
		headings << iter->first << ".liter" << "\t";
		data << iter->second << "\t";
	}
	//  activity estimate
	for (cxxNameDouble::iterator iter = this->totals.begin();
		iter != this->totals.end(); ++iter)
	{
		if (iter->first == "O" || iter->first == "Charge")
			continue;
		std::string master_name;
		struct master *master_ptr;
		master_ptr = master_bsearch(iter->first);
		assert(master_ptr != NULL);
		cxxNameDouble ma = this->solution->get_master_activity();
		cxxNameDouble::iterator it = ma.find(iter->first);
		if (it == ma.end())
		{
			it = ma.find(master_ptr->s->secondary->elt->name);
		}
		headings << master_ptr->s->name << ".act\t";
		if (it != ma.end())
		{
			data << pow(10., it->second) << "\t";
		}
		else
		{
			data << 1e-9 << "\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
cxxSystem::ORCH_components(void) 
{
	// translate from H, O, charge to H+tot, e-tot, and H2Otot
	cxxNameDouble::iterator it;
	cxxNameDouble temp_totals;
	//
	// Set names in orch_totals to master species names
	//
	this->orch_totals.clear();
	temp_totals = this->totals;
	temp_totals.erase("H");
	temp_totals.erase("O");
	temp_totals.erase("Charge");
	//temp_totals.dump_raw(std::cerr, 1);
	for (it = temp_totals.begin(); it != temp_totals.end(); it++)
	{
		struct element *elt_ptr;
		elt_ptr = element_store(it->first);
		assert(elt_ptr != NULL);
		struct master *master_ptr;
		master_ptr = elt_ptr->primary;
		assert(master_ptr != NULL);
		double coef = master_ptr->coef;
		if (master_ptr->coef == 0)
		{
			coef = 1;
		}
		this->orch_totals[master_ptr->s->name] = it->second / coef;
	}
	//
	// Calculate h2otot
	//
	it = this->totals.find("O");
	assert(it != this->totals.end());
	double h2otot = it->second;
	// subtract O in master species
	for (it = temp_totals.begin(); it != temp_totals.end(); it++)
	{
		struct element *elt_ptr;
		elt_ptr = element_store(it->first);
		struct master *master_ptr;
		master_ptr = elt_ptr->primary;
		h2otot -= it->second * master_ptr->s->o;
	} 
	//
	// Calculate htot
	//
	it = this->totals.find("H");
	assert(it != this->totals.end());
	double htot = it->second - 2 * h2otot;
	// subtract O in master species
	for (it = temp_totals.begin(); it != temp_totals.end(); it++)
	{
		struct element *elt_ptr;
		elt_ptr = element_store(it->first);
		struct master *master_ptr;
		master_ptr = elt_ptr->primary;
		htot -= it->second * master_ptr->s->h;
	} 
	//
	// Calculate etot
	//
	it = this->totals.find("Charge");
	assert(it != this->totals.end());
	double etot = -it->second + htot;
	// subtract O in master species
	for (it = temp_totals.begin(); it != temp_totals.end(); it++)
	{
		struct element *elt_ptr;
		elt_ptr = element_store(it->first);
		struct master *master_ptr;
		master_ptr = elt_ptr->primary;
		etot += it->second * master_ptr->s->z;
	} 
	//
	// store h2otot, htot, etot in orch_totals
	//
	this->orch_totals["H2O"] = h2otot;
	this->orch_totals["H+"] = htot;
	this->orch_totals["e-"] = etot;
	this->orch_totals.dump_raw(std::cerr, 1);
} 
void
cxxSystem::ORCH_write_output_vars(std::ostream & outstream) 
{
	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";
	//
	// Write totals
	for (cxxNameDouble::iterator it = this->orch_totals.begin();
		it != this->orch_totals.end(); it++)
	{
		if (it->first == "H+" || it->first == "H2O" || it->first == "e-")
			continue;
		outstream << "\t" << it->first << ".diss";
	}
	outstream << "\tend_totals";
	for (cxxNameDouble::iterator it = this->orch_totals.begin();
		it != this->orch_totals.end(); it++)
	{
		if (it->first == "H+" || it->first == "H2O" || it->first == "e-")
			continue;
		outstream << "\t" << it->first << ".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";
}
#endif	/* */