pyEQL 1.4.0rc9__cp311-cp311-win_amd64.whl

pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/Phreeqc.cpp

@@ -0,0 +1,2087 @@
+#include "Phreeqc.h"
+#include <algorithm>			// std::replace
+
+#include "NameDouble.h"
+#include "Solution.h"
+#include "Reaction.h"
+#include "PPassemblage.h"
+#include "Exchange.h"
+#include "Surface.h"
+#include "GasPhase.h"
+#include "SSassemblage.h"
+#include "cxxKinetics.h"
+#include "phqalloc.h"
+#include "PBasic.h"
+#include "Temperature.h"
+#include "SSassemblage.h"
+#include "Utils.h"
+
+#if defined(PHREEQCI_GUI)
+#ifdef _DEBUG
+#define new DEBUG_NEW
+#undef THIS_FILE
+static char THIS_FILE[] = __FILE__;
+#endif
+#endif
+
+//const const_iso Phreeqc::iso_defaults[] = {
+//	{"13C", -10, 1},
+//	{"13C(4)", -10, 1},
+//	{"13C(-4)", -50, 5},
+//	{"34S", 10, 1},
+//	{"34S(6)", 10, 1},
+//	{"34S(-2)", -30, 5},
+//	{"2H", -28, 1},
+//	{"2H(1)", -28, 1},
+//	{"2H(0)", -28, 1},
+//	{"18O", -5, .1},
+//	{"18O(-2)", -5, .1},
+//	{"18O(0)", -5, .1},
+//	{"87Sr", .71, .01},
+//	{"11B", 20, 5}
+//};
+const const_iso Phreeqc::iso_defaults[] = {
+	const_iso("13C", -10, 1),
+	const_iso("13C(4)", -10, 1),
+	const_iso("13C(-4)", -50, 5),
+	const_iso("34S", 10, 1),
+	const_iso("34S(6)", 10, 1),
+	const_iso("34S(-2)", -30, 5),
+	const_iso("2H", -28, 1),
+	const_iso("2H(1)", -28, 1),
+	const_iso("2H(0)", -28, 1),
+	const_iso("18O", -5, .1),
+	const_iso("18O(-2)", -5, .1),
+	const_iso("18O(0)", -5, .1),
+	const_iso("87Sr", .71, .01),
+	const_iso("11B", 20, 5)
+};
+
+const int Phreeqc::count_iso_defaults = (sizeof(iso_defaults) / sizeof(class const_iso));
+
+Phreeqc::~Phreeqc(void)
+{
+
+	clean_up();
+	
+	PHRQ_free_all();
+	if (phrq_io == &ioInstance)
+	{
+		this->phrq_io->clear_istream();
+		this->phrq_io->close_ostreams();
+	}
+}
+
+void Phreeqc::set_phast(int tf)
+{
+	this->phast = tf;
+}
+size_t Phreeqc::list_components(std::list<std::string> &list_c)
+/*
+ *	 Find all elements in any class definition
+ */
+{
+	cxxNameDouble accumulator;
+	//accumulator.add("H", 1);
+	//accumulator.add("O", 1);
+
+	// solutions
+	{
+		std::map<int, cxxSolution>::const_iterator cit = Rxn_solution_map.begin();
+		for (; cit !=  Rxn_solution_map.end(); cit++)
+		{
+			cxxSolution entity(cit->second);
+			accumulator.add_extensive(entity.Get_totals(), 1.0);
+		}
+	}
+
+	// irreversible reactions
+	{
+		std::map<int, cxxReaction>::const_iterator cit = Rxn_reaction_map.begin();
+		for (; cit !=  Rxn_reaction_map.end(); cit++)
+		{
+			cxxReaction r_ptr(cit->second);
+			reaction_calc(&r_ptr);
+			accumulator.add_extensive(r_ptr.Get_elementList(), 1.0);
+		}
+	}
+
+	// pure phases
+	{
+		std::map<int, cxxPPassemblage>::const_iterator cit = Rxn_pp_assemblage_map.begin();
+		for (; cit !=  Rxn_pp_assemblage_map.end(); cit++)
+		{
+			cxxPPassemblage entity = cit->second;
+			entity.totalize(this);
+			accumulator.add_extensive(entity.Get_eltList(), 1.0);
+		}
+	}
+	// exchangers
+	{
+		std::map<int, cxxExchange>::const_iterator cit = Rxn_exchange_map.begin();
+		for (; cit !=  Rxn_exchange_map.end(); cit++)
+		{
+			cxxExchange entity = cit->second;
+			entity.totalize();
+			accumulator.add_extensive(entity.Get_totals(), 1.0);
+		}
+	}
+
+	// surfaces
+	{
+		std::map<int, cxxSurface>::const_iterator cit = Rxn_surface_map.begin();
+		for (; cit !=  Rxn_surface_map.end(); cit++)
+		{
+			cxxSurface entity = cit->second;
+			entity.totalize();
+			accumulator.add_extensive(entity.Get_totals(), 1.0);
+		}
+	}
+	// gas phases
+	{
+		std::map<int, cxxGasPhase>::const_iterator cit = Rxn_gas_phase_map.begin();
+		for (; cit !=  Rxn_gas_phase_map.end(); cit++)
+		{
+			cxxGasPhase entity = cit->second;
+			entity.totalize(this);
+			accumulator.add_extensive(entity.Get_totals(), 1.0);
+		}
+	}
+
+	// solid-solutions
+	{
+		std::map<int, cxxSSassemblage>::const_iterator cit = Rxn_ss_assemblage_map.begin();
+		for (; cit !=  Rxn_ss_assemblage_map.end(); cit++)
+		{
+			cxxSSassemblage entity = cit->second;
+			entity.totalize(this);
+			accumulator.add_extensive(entity.Get_totals(), 1.0);
+		}
+	}
+	// kinetics
+	{
+		std::map<int, cxxKinetics>::iterator it = Rxn_kinetics_map.begin();
+		for (; it !=  Rxn_kinetics_map.end(); it++)
+		{
+			calc_dummy_kinetic_reaction_tally(&(it->second));
+			cxxKinetics entity = it->second;
+			accumulator.add_extensive(entity.Get_totals(), 1.0);
+		}
+	}
+	// Put in all primaries
+	cxxNameDouble::iterator it;
+	for (it = accumulator.begin(); it != accumulator.end(); it++)
+	{
+		if (it->first == "Charge") continue;
+		char string[MAX_LENGTH];
+		Utilities::strcpy_safe(string, MAX_LENGTH, it->first.c_str());
+		class master *master_ptr = master_bsearch_primary(string);
+		if (master_ptr == NULL) continue;
+		if (master_ptr->type != AQ) continue;
+		accumulator.add(master_ptr->elt->name, 1);
+	}
+	// print list
+	for (it = accumulator.begin(); it != accumulator.end(); it++)
+	{
+		class master *master_ptr = master_bsearch(it->first.c_str());
+		if (master_ptr == NULL) continue;
+		if (master_ptr->type != AQ) continue;
+		if (master_ptr->primary == 0) continue;
+		if (it->first == "Charge") continue;
+		if (it->first == "O") continue;
+		if (it->first == "H") continue;
+		list_c.push_back(it->first);
+	}
+	return(list_c.size());
+}
+size_t Phreeqc::list_EquilibriumPhases(std::list<std::string> &list_pp)
+/*
+*	 Find all elements in any class definition
+*/
+{
+	std::set<std::string> accumulator;
+	// pure phases
+	{
+		std::map<int, cxxPPassemblage>::const_iterator cit = Rxn_pp_assemblage_map.begin();
+		for (; cit != Rxn_pp_assemblage_map.end(); cit++)
+		{
+			cxxPPassemblage entity = cit->second;
+			std::set<std::string> pp = entity.GetPhases(this);
+			std::set<std::string>::iterator ppit = pp.begin();
+			for (; ppit != pp.end(); ppit++)
+			{ 
+				accumulator.insert(*ppit);
+			}
+		}
+	}
+	list_pp.clear();
+	std::set<std::string>::iterator it = accumulator.begin();
+	for (; it != accumulator.end(); it++)
+	{
+		list_pp.insert(list_pp.end(),*it);
+	}
+	return(list_pp.size());
+}
+size_t Phreeqc::list_GasComponents(std::list<std::string> &list_gc)
+/*
+*	 Find all elements in any class definition
+*/
+{
+	std::set<std::string> accumulator;
+	// pure phases
+	{
+		std::map<int, cxxGasPhase>::const_iterator cit = Rxn_gas_phase_map.begin();
+		for (; cit != Rxn_gas_phase_map.end(); cit++)
+		{
+			cxxGasPhase entity = cit->second;
+			std::vector<cxxGasComp> &gc = entity.Get_gas_comps();
+			for (size_t i = 0; i < gc.size(); i++)
+			{
+				int j;
+				phase * p = phase_bsearch(gc[i].Get_phase_name().c_str(), &j, 0);
+				accumulator.insert(p->name);
+			}
+		}
+	}
+	list_gc.clear();
+	std::set<std::string>::iterator it = accumulator.begin();
+	for (; it != accumulator.end(); it++)
+	{
+		list_gc.insert(list_gc.end(), *it);
+	}
+	return(list_gc.size());
+}
+size_t Phreeqc::list_KineticReactions(std::list<std::string> &list_kr)
+/*
+*	 Find all kinetic reactions
+*/
+{
+	std::set<std::string> accumulator;
+	// Kinetics
+	{
+		std::map<int, cxxKinetics>::const_iterator cit = Rxn_kinetics_map.begin();
+		for (; cit != Rxn_kinetics_map.end(); cit++)
+		{
+			cxxKinetics entity = cit->second;
+			for (size_t i = 0; i < entity.Get_kinetics_comps().size(); i++)
+			{
+				std::string ratename = entity.Get_kinetics_comps()[i].Get_rate_name();
+				int j;
+				rate *r = rate_search(ratename.c_str(), &j);
+				if (r != NULL)
+				{
+					accumulator.insert(r->name);
+				}
+			}
+		}
+	}
+	list_kr.clear();
+	std::set<std::string>::iterator it = accumulator.begin();
+	for (; it != accumulator.end(); it++)
+	{
+		list_kr.insert(list_kr.end(), *it);
+	}
+	return(list_kr.size());
+}
+size_t Phreeqc::list_SolidSolutions(std::list<std::string> &list_comps, std::list<std::string> &list_names)
+/*
+*	 Find all elements in any class definition
+*/
+{
+	std::vector< std::set<std::string> > ss_sets;
+	std::vector<std::string> ss_names;
+	// solid solutions
+	std::map<int, cxxSSassemblage>::const_iterator cit = Rxn_ss_assemblage_map.begin();
+	// Fill vectors, ss names and related set of component names
+	for (; cit != Rxn_ss_assemblage_map.end(); cit++)
+	{
+		cxxSSassemblage entity = cit->second;
+		std::map<std::string, cxxSS> &SSs = entity.Get_SSs();
+		std::map<std::string, cxxSS>::iterator ssit = SSs.begin();
+		for (; ssit != SSs.end(); ssit++)
+		{
+			std::string ssname = ssit->second.Get_name();
+			std::set<std::string> accumulator_phases;
+			for (size_t i = 0; i < ssit->second.Get_ss_comps().size(); i++)
+			{
+				std::string pname = ssit->second.Get_ss_comps()[i].Get_name();
+				int j;
+				phase * p = phase_bsearch(pname.c_str(), &j, 0);
+				accumulator_phases.insert(p->name);
+			}
+			ss_names.push_back(ssname);
+			ss_sets.push_back(accumulator_phases);
+		}
+	}
+	// need to merge into exclusive sets of solid solution components
+	bool repeat = true;
+	while (repeat)
+	{
+		repeat = false;
+		for (int i = 0; i < (int) ss_sets.size() - 1; i++)
+		{
+			for (int j = i + 1; j < (int) ss_sets.size(); j++)
+			{
+				// locate any common component
+				std::set<std::string>::iterator it = ss_sets[j].begin();
+				for (; it != ss_sets[j].end(); it++)
+				{
+					if (ss_sets[i].find(*it) != ss_sets[i].end())
+					{
+						repeat = true;
+						break;
+					}
+				}
+				// merge sets and clear second set
+				if (repeat)
+				{
+					for (it = ss_sets[j].begin(); it != ss_sets[j].end(); it++)
+					{
+						ss_sets[i].insert(*it);
+					}
+					ss_sets[j].clear();
+					break;
+				}
+			}
+			if (repeat) break;
+		}
+	}
+	list_comps.clear();
+	list_names.clear();
+	// Write lists
+	for (size_t i = 0; i < ss_sets.size(); i++)
+	{
+		std::set<std::string>::iterator it = ss_sets[i].begin();
+		for (; it != ss_sets[i].end(); it++)
+		{
+			list_names.push_back(ss_names[i]);
+			list_comps.push_back(*it);
+		}
+	}
+	return(list_comps.size());
+}
+size_t Phreeqc::list_Surfaces(std::list<std::string> &list_surftype, std::list<std::string> &list_surfname)
+/*
+*	 Find all surface types and surfaces
+*/
+{
+	std::set<std::pair<std::string,std::string> > accumulator;
+	// Surfaces
+	{
+		std::map<int, cxxSurface>::const_iterator cit = Rxn_surface_map.begin();
+		for (; cit != Rxn_surface_map.end(); cit++)
+		{
+			cxxSurface entity = cit->second;
+			std::vector<cxxSurfaceComp> &scomps = entity.Get_surface_comps();
+			//std::vector<cxxSurfaceCharge> &scharges = entity.Get_surface_charges();
+			for (size_t i = 0; i < scomps.size(); i++)
+			{
+				std::pair<std::string, std::string> p(scomps[i].Get_master_element(), scomps[i].Get_charge_name());
+				accumulator.insert(p);
+			}
+		}
+	}
+	list_surftype.clear();
+	list_surfname.clear();
+	std::set<std::pair<std::string, std::string> >::iterator it = accumulator.begin();
+	for (; it != accumulator.end(); it++)
+	{
+		list_surftype.push_back(it->first);
+		list_surfname.push_back(it->second);
+	}
+	return(list_surfname.size());
+}
+size_t Phreeqc::list_Exchangers(std::list<std::string> &list_exname)
+/*
+*	 Find all exchangers
+*/
+{
+	std::set<std::string> accumulator;
+	// Exchangers
+	std::map<int, cxxExchange>::const_iterator cit = Rxn_exchange_map.begin();
+	for (; cit != Rxn_exchange_map.end(); cit++)
+	{
+		cxxExchange entity = cit->second;
+		std::vector<cxxExchComp> &ecomps = entity.Get_exchange_comps();
+		for (size_t i = 0; i < ecomps.size(); i++)
+		{
+			std::string exname = "";
+			cxxNameDouble nd = ecomps[i].Get_totals();
+			cxxNameDouble::iterator it = nd.begin();
+			for (; it != nd.end(); it++)
+			{
+				class master *m = master_bsearch(it->first.c_str());
+				if (m != NULL)
+				{
+					if (m->type == EX)
+					{
+						exname = it->first;
+						break;
+					}
+				}
+			}
+			if (exname != "")
+			{
+				accumulator.insert(exname);
+			}
+		}
+	}
+	list_exname.clear();
+	std::set< std::string>::iterator it = accumulator.begin();
+	for (; it != accumulator.end(); it++)
+	{
+		list_exname.push_back(*it);
+	}
+	return(list_exname.size());
+}
+Phreeqc::Phreeqc(PHRQ_io *io)
+{
+	user_print = NULL;
+	sformatf_buffer = NULL;
+	basic_interpreter = NULL;
+	count_elts = 0;
+	aphi = NULL;
+	// phrq_io
+	if (io)
+	{
+		this->phrq_io = io;
+	}
+	else
+	{
+		this->phrq_io = &this->ioInstance;
+	}
+	// auto PHRQ_io ioInstance;
+
+	// initialize data members
+	init();
+
+#if defined(SWIG) || defined(SWIG_IPHREEQC)
+	basicCallback = NULL;
+#endif
+}
+void Phreeqc::init(void)
+{
+	same_model                      = FALSE;
+	current_tc                      = NAN;
+	current_pa                      = NAN;
+	current_mu                      = NAN;
+	mu_terms_in_logk                = true;
+	current_A                       = 0.0;
+	current_x                       = 0.0;
+	fix_current                     = 0.0;
+	/* ----------------------------------------------------------------------
+	*   STRUCTURES
+	* ---------------------------------------------------------------------- */
+/*
+ *	 last model
+ */
+	last_model.force_prep           = true;
+	last_model.gas_phase_type       = cxxGasPhase::GP_UNKNOWN;
+	last_model.gas_phase.clear();
+	last_model.ss_assemblage.clear();
+	last_model.pp_assemblage.clear();
+	last_model.add_formula.clear();
+	last_model.si.clear();
+	last_model.dl_type              = cxxSurface::NO_DL;
+	last_model.surface_type         = cxxSurface::UNKNOWN_DL;
+
+	current_selected_output         = NULL;
+	current_user_punch              = NULL;
+	high_precision                  = false;
+	MIN_LM = -30.0;			    /* minimum log molality allowed before molality set to zero */
+	LOG_ZERO_MOLALITY = -30;	/* molalities <= LOG_ZERO_MOLALITY are considered equal to zero */
+	MIN_RELATED_LOG_ACTIVITY = -30;
+	MIN_TOTAL = 1e-25;
+	MIN_TOTAL_SS = MIN_TOTAL/100;
+	MIN_RELATED_SURFACE = MIN_TOTAL*100;
+	// auto Rxn_temperature_map;
+	// auto Rxn_pressure_map;
+
+	/* ----------------------------------------------------------------------
+	*   Surface
+	* --------------------------------------------------------------------- */
+	g_iterations               = -1;
+	G_TOL                      = 1e-8;
+	// auto Rxn_surface_map;
+	// auto charge_group_map;
+	change_surf_count          = 0;
+	change_surf                = NULL;
+	/* ----------------------------------------------------------------------
+	*   Exchange
+	* ---------------------------------------------------------------------- */
+	// auto Rxn_exchange_map;
+
+	/* ----------------------------------------------------------------------
+	*   Kinetics
+	* ---------------------------------------------------------------------- */
+	// auto Rxn_kinetics_map;
+
+	/*----------------------------------------------------------------------
+	*   Save
+	*---------------------------------------------------------------------- */
+	save_init(-1);             // set initial save values
+
+	/*----------------------------------------------------------------------
+	*   Inverse
+	*---------------------------------------------------------------------- */
+	count_inverse			= 0;
+	/*----------------------------------------------------------------------
+	*   Mix
+	*---------------------------------------------------------------------- */
+	// auto Rxn_mix_map;
+	// auto Dispersion_mix_map;
+	// auto Rxn_solution_mix_map;
+	// auto Rxn_exchange_mix_map;
+	// auto Rxn_gas_phase_mix_map;
+	// auto Rxn_kinetics_mix_map;
+	// auto Rxn_pp_assemblage_mix_map;
+	// auto Rxn_ss_assemblage_mix_map;
+	// auto Rxn_surface_mix_map;
+	/*----------------------------------------------------------------------
+	*   Irreversible reaction
+	*---------------------------------------------------------------------- */
+	run_cells_one_step = false;
+	// auto Rxn_reaction_map;
+	/*----------------------------------------------------------------------
+	*   Gas phase
+	*---------------------------------------------------------------------- */
+	// auto Rxn_gas_phase_map;
+	/*----------------------------------------------------------------------
+	*   Solid solution
+	*---------------------------------------------------------------------- */
+	// auto Rxn_ss_assemblage_map;
+	/*----------------------------------------------------------------------
+	*   Pure-phase assemblage
+	*---------------------------------------------------------------------- */
+	// auto Rxn_pp_assemblage_map;
+	/*----------------------------------------------------------------------
+	*   Species_list
+	*---------------------------------------------------------------------- */
+	/*----------------------------------------------------------------------
+	*   Jacobian and Mass balance lists
+	*---------------------------------------------------------------------- */
+
+	/*----------------------------------------------------------------------
+	*   Solution
+	*---------------------------------------------------------------------- */
+	// auto Rxn_solution_map;
+	// auto unnumbered_solutions;
+	save_species = false;
+	/*----------------------------------------------------------------------
+	*   Global solution
+	*---------------------------------------------------------------------- */
+	new_x                   = FALSE;
+	tc_x                    = 0;
+	tk_x                    = 0;
+	patm_x                  = 1;
+	last_patm_x             = 1;
+	potV_x                  = 0;
+	numerical_fixed_volume  = false;
+	force_numerical_fixed_volume = false;
+	//switch_numerical        = false;
+	ph_x                    = 0;
+	solution_pe_x           = 0;
+	mu_x                    = 0;
+	ah2o_x                  = 1.0;
+	total_h_x               = 0;
+	total_o_x               = 0;
+	cb_x                    = 0;
+	total_ions_x            = 0;
+	mass_water_aq_x         = 0;
+	mass_water_surfaces_x   = 0;
+	mass_water_bulk_x       = 0;
+	// auto pe_x
+	// auto isotopes_x
+	// auto default_pe_x
+	dl_type_x                = cxxSurface::NO_DL;
+	total_carbon             = 0;
+	total_co2                = 0;
+	total_alkalinity         = 0;
+	gfw_water                = 0;
+	step_x                   = 0;
+	kin_time_x               = 0;
+	/*----------------------------------------------------------------------
+	*   Transport data
+	*---------------------------------------------------------------------- */
+	count_cells              = 1;
+	count_shifts             = 1;
+	ishift                   = 1;
+	bcon_first = bcon_last   = 3;
+	correct_disp             = FALSE;
+	tempr                    = 2.0;
+	timest                   = 0.0;
+	simul_tr                 = 0;
+	diffc                    = 0.3e-9;
+	heat_diffc               = -0.1;
+	cell                     = 0;
+	mcd_substeps             = 1.0;
+	print_modulus            = 1;
+	punch_modulus            = 1;
+	dump_in                  = FALSE;
+	dump_modulus             = 0;
+	transport_warnings       = TRUE;
+	old_cells                = 0;
+	max_cells                = 0;
+	all_cells                = 0;
+	multi_Dflag              = FALSE;
+	interlayer_Dflag         = FALSE;
+	implicit                 = FALSE;
+	max_mixf                 = 1.0;
+	min_dif_LM               = -30.0;
+	default_Dw               = 0;
+	correct_Dw               = 0;
+	multi_Dpor               = 0;
+	interlayer_Dpor          = 0.1;
+	multi_Dpor_lim           = 0;
+	interlayer_Dpor_lim      = 0;
+	multi_Dn                 = 0;
+	interlayer_tortf         = 100.0;
+	cell_no                  = 0;
+	fix_current              = 0.0;
+	/*----------------------------------------------------------------------
+	*   Advection data
+	*---------------------------------------------------------------------- */
+	count_ad_cells           = 1;
+	count_ad_shifts          = 1;
+	print_ad_modulus         = 1;
+	punch_ad_modulus         = 1;
+	advection_kin_time       = 0.0;
+	advection_kin_time_defined = FALSE;
+	advection_warnings       = TRUE;
+	/*----------------------------------------------------------------------
+	*   Tidy data
+	*---------------------------------------------------------------------- */
+	new_model                = TRUE;
+	new_exchange             = FALSE;
+	new_pp_assemblage        = FALSE;
+	new_surface              = FALSE;
+	new_reaction             = FALSE;
+	new_temperature          = FALSE;
+	new_mix                  = FALSE;
+	new_solution             = FALSE;
+	new_gas_phase            = FALSE;
+	new_inverse              = FALSE;
+	new_punch                = FALSE;
+	new_ss_assemblage        = FALSE;
+	new_kinetics             = FALSE;
+	new_copy                 = FALSE;
+	new_pitzer               = FALSE;
+	/*----------------------------------------------------------------------
+	*   Elements
+	*---------------------------------------------------------------------- */
+	element_h_one            = NULL;
+	/*----------------------------------------------------------------------
+	*   Element List
+	*---------------------------------------------------------------------- */
+	count_elts               = 0;
+	/*----------------------------------------------------------------------
+	*   Species
+	*---------------------------------------------------------------------- */
+	s_h2o					= NULL;
+	s_hplus					= NULL;
+	s_h3oplus				= NULL;
+	s_eminus				= NULL;
+	s_co3					= NULL;
+	s_h2					= NULL;
+	s_o2					= NULL;
+	/*----------------------------------------------------------------------
+	*   Phases
+	*---------------------------------------------------------------------- */
+
+	/*----------------------------------------------------------------------
+	*   Master species
+	*---------------------------------------------------------------------- */
+
+	/*----------------------------------------------------------------------
+	*   Unknowns
+	*---------------------------------------------------------------------- */
+	count_unknowns          = 0;
+	max_unknowns            = 0;
+	ah2o_unknown            = NULL;
+	alkalinity_unknown      = NULL;
+	carbon_unknown          = NULL;
+	charge_balance_unknown  = NULL;
+	exchange_unknown        = NULL;
+	mass_hydrogen_unknown   = NULL;
+	mass_oxygen_unknown     = NULL;
+	mb_unknown              = NULL;
+	mu_unknown              = NULL;
+	pe_unknown              = NULL;
+	ph_unknown              = NULL;
+	pure_phase_unknown      = NULL;
+	solution_phase_boundary_unknown = NULL;
+	surface_unknown         = NULL;
+	gas_unknown             = NULL;
+	ss_unknown              = NULL;
+	// auto gas_unknowns;
+	/*----------------------------------------------------------------------
+	*   Reaction work space
+	*---------------------------------------------------------------------- */
+	// struct trxn;	
+	for (int i = 0; i < MAX_LOG_K_INDICES; i++)
+	{
+		trxn.logk[i] = 0;
+	}
+	for (int i = 0; i < 3; i++)
+	{
+		trxn.dz[i] = 0;
+	}
+	count_trxn              = 0;
+
+	/* ----------------------------------------------------------------------
+	*   Print
+	* ---------------------------------------------------------------------- */
+	pr.all                  = TRUE;
+	pr.initial_solutions    = TRUE;
+	pr.initial_exchangers   = TRUE;
+	pr.reactions            = TRUE;
+	pr.gas_phase            = TRUE;
+	pr.ss_assemblage        = TRUE;
+	pr.pp_assemblage        = TRUE;
+	pr.surface              = TRUE;
+	pr.exchange             = TRUE;
+	pr.kinetics             = TRUE;
+	pr.totals               = TRUE;
+	pr.eh                   = TRUE;
+	pr.species              = TRUE;
+	pr.saturation_indices   = TRUE;
+	pr.irrev                = TRUE;
+	pr.mix                  = TRUE;
+	pr.reaction             = TRUE;
+	pr.use                  = TRUE;
+	pr.logfile              = FALSE;
+	pr.punch                = TRUE;
+	pr.status               = TRUE;
+	pr.inverse              = TRUE;
+	pr.dump                 = TRUE;
+	pr.user_print           = TRUE;
+	pr.headings             = TRUE;
+	pr.user_graph           = TRUE;
+	pr.echo_input           = TRUE;
+	pr.warnings             = 100;
+	pr.initial_isotopes     = TRUE;
+	pr.isotope_ratios       = TRUE;
+	pr.isotope_alphas       = TRUE;
+	pr.hdf                  = FALSE;
+	pr.alkalinity           = FALSE;
+	status_on               = true;
+#ifdef NPP
+	status_interval         = 40;
+#else
+	status_interval         = 250;
+#endif
+	status_timer            = clock();
+	count_warnings          = 0;
+	/* ----------------------------------------------------------------------
+	*   RATES
+	* ---------------------------------------------------------------------- */
+	rate_m					= 0;
+	rate_m0					= 0;
+	rate_time				= 0;
+	rate_kin_time           = 1.0;
+	rate_sim_time_start		= 0;
+	rate_sim_time_end		= 0;
+	rate_sim_time			= 0;
+	rate_moles				= 0;
+	initial_total_time		= 0;
+	// auto rate_p
+	count_rate_p            = 0;
+	/* ----------------------------------------------------------------------
+	*   USER PRINT COMMANDS
+	* ---------------------------------------------------------------------- */
+	//user_print				= NULL;
+	n_user_punch_index      = 0;
+	fpunchf_user_s_warning  = 0;
+	fpunchf_user_buffer[0]  = 0;
+
+#if defined PHREEQ98 
+	class rate *user_graph;
+	char **user_graph_headings;
+	int user_graph_count_headings;
+#endif
+#if defined MULTICHART
+	// auto chart_handler;
+	chart_handler.Set_io(phrq_io);
+#endif
+	/* ----------------------------------------------------------------------
+	*   GLOBAL DECLARATIONS
+	* ---------------------------------------------------------------------- */
+	error_string            = NULL;
+	simulation				= 0;
+	state                   = INITIALIZE;
+	reaction_step           = 0;
+	transport_step          = 0;
+	transport_start         = 0;
+	advection_step          = 0;
+	stop_program            = FALSE;
+	incremental_reactions   = FALSE;
+	count_strings           = 0;
+	input_error             = 0;
+	next_keyword            = Keywords::KEY_NONE;
+	parse_error             = 0;
+	paren_count             = 0;
+	iterations              = 0;
+	gamma_iterations        = 0;
+	density_iterations = 0;
+	run_reactions_iterations= 0;
+	overall_iterations      = 0;
+	max_line				= MAX_LINE;
+	line                    = NULL;
+	line_save				= NULL;
+	LOG_10                  = log(10.0);
+	debug_model             = FALSE;
+	debug_prep              = FALSE;
+	debug_set               = FALSE;
+	debug_mass_action       = FALSE;
+	debug_mass_balance      = FALSE;
+	debug_diffuse_layer     = FALSE;
+	debug_inverse           = FALSE;
+#ifdef USE_LONG_DOUBLE
+	/* from float.h, sets tolerance for cl1 routine */
+	inv_tol_default         = pow((long double) 10, (long double) -LDBL_DIG + 5);
+#else
+	inv_tol_default         = pow((double) 10, (double) -DBL_DIG + 5);
+#endif
+	itmax                   = 100;
+	max_tries               = 1000;
+#ifdef USE_LONG_DOUBLE
+	/* from float.h, sets tolerance for cl1 routine */
+	ineq_tol                = pow((long double) 10, (long double) -LDBL_DIG);
+#elif NPP
+// appt:
+	ineq_tol                = pow((double) 10, (double) -DBL_DIG + 2);
+#else
+	ineq_tol                = pow((double) 10, (double) -DBL_DIG);
+#endif
+	convergence_tolerance   = 1e-8;	
+	step_size				= 100.;
+	pe_step_size			= 10.;
+	step_size_now           = step_size;
+	pe_step_size_now        = pe_step_size;
+	pp_scale				= 1.0;
+	pp_column_scale			= 1.0;
+	diagonal_scale			= FALSE;
+	mass_water_switch		= FALSE;
+	delay_mass_water		= FALSE;
+	equi_delay      		= 0;
+	dampen_ah2o             = false;
+	censor					= 0.0;
+	aqueous_only			= 0;
+	negative_concentrations = FALSE;
+	calculating_deriv		= FALSE;
+	numerical_deriv			= FALSE;
+	count_total_steps       = 0;
+	phast                   = FALSE;
+	output_newline          = true;
+	//selected_output_file_name = NULL;
+	dump_file_name			= NULL;
+	remove_unstable_phases  = FALSE;
+	// auto screen_string;
+	spread_length           = 10;
+	/* ----------------------------------------------------------------------
+	*   ISOTOPES
+	* ---------------------------------------------------------------------- */
+	initial_solution_isotopes = FALSE;
+
+	phreeqc_mpi_myself		= 0;
+	first_read_input		= TRUE;
+	print_density		    = 0;
+	print_viscosity		    = 0;
+	cell_pore_volume	    = 0;
+	cell_volume			    = 0;
+	cell_porosity		    = 0;
+	cell_saturation		    = 0;
+	sys_tot                 = 0;
+
+	V_solutes               = 0.0;
+	viscos                  = 0.0;
+	viscos_0                = 0.0;
+	viscos_0_25             = 0.0;
+	density_x               = 0.0;
+	rho_0                   = 0.0;
+	kappa_0                 = 0.0;
+	p_sat                   = 0.0;
+	eps_r                   = EPSILON;
+	DH_A                    = 0.0;
+	DH_B                    = 0.0;
+	DH_Av                   = 0.0;
+	QBrn                    = 0.0;
+	ZBrn                    = 0.0;
+	dgdP                    = 0.0;
+
+	need_temp_msg           = 0;
+	solution_mass           = 0;
+	solution_volume         = 0;
+	/* phqalloc.cpp ------------------------------- */
+	s_pTail                 = NULL;
+	/* Basic */
+	//basic_interpreter       = NULL;
+	basic_callback_ptr      = NULL;
+	basic_callback_cookie   = NULL;
+	basic_fortran_callback_ptr  = NULL;
+
+#ifdef SKIP
+	/* dw.cpp ------------------------------- */
+	/* COMMON /QQQQ/ */	
+	Q0                      = 0;
+	Q5                      = 0;
+	GASCON                  = 0.461522e0;
+	TZ                      = 647.073e0;
+	AA                      = 1.e0;
+	Z                       = 0;
+	DZ                      = 0;
+	Y                       = 0;
+	G1                      = 11.e0;
+	G2                      = 44.333333333333e0;
+	GF                      = 3.5e0;
+	B1                      = 0;
+	B2                      = 0;
+	B1T                     = 0;
+	B2T                     = 0;
+	B1TT                    = 0;
+	B2TT                    = 0;
+#endif
+	/* gases.cpp ------------------------------- */
+	a_aa_sum                = 0;
+	b2                      = 0;
+	b_sum                   = 0;
+	R_TK                    = 0;
+	/* input.cpp ------------------------------- */
+	check_line_return       = 0;  
+	reading_db              = FALSE;
+	/* integrate.cpp ------------------------------- */
+	midpoint_sv             = 0;
+	z_global                = 0;
+	xd_global               = 0;
+	alpha_global            = 0;
+	/* integrate.cpp ------------------------------- */
+	max_row_count           = 50;
+	max_column_count        = 50;
+	carbon                  = FALSE;
+	count_rows              = 0;
+	count_optimize          = 0;
+	col_phases              = 0;
+	col_redox               = 0;
+	col_epsilon             = 0;
+	col_ph                  = 0;
+	col_water               = 0;
+	col_isotopes            = 0;
+	col_phase_isotopes      = 0;
+	row_mb                  = 0;
+	row_fract               = 0;
+	row_charge              = 0;
+	row_carbon              = 0;
+	row_isotopes            = 0;
+	row_epsilon             = 0;
+	row_isotope_epsilon     = 0;
+	row_water               = 0;
+	klmd                    = 0;
+	nklmd                   = 0;
+	n2d                     = 0;
+	kode                    = 0;
+	iter                    = 0;
+	toler                   = 0;
+	error                   = 0;
+	max_pct                 = 0;
+	scaled_error            = 0;
+	master_alk              = NULL;
+	max_good                = 0;
+	max_bad                 = 0;
+	max_minimal             = 0;
+	count_good              = 0;
+	count_bad               = 0;
+	count_minimal           = 0;
+	count_calls             = 0;
+	soln_bits               = 0;
+	phase_bits              = 0;
+	current_bits            = 0;
+	temp_bits               = 0;
+	netpath_file            = NULL;
+	count_inverse_models    = 0;
+	count_pat_solutions     = 0;
+	for (int i = 0; i < 32; i++)
+	{
+		min_position[i]     = 0;
+		max_position[i]     = 0;
+		now[i]              = 0;
+	}
+	/* kinetics.cpp ------------------------------- */
+	count_pp = count_pg = count_ss = 0; 
+	cvode_kinetics_ptr      = NULL;
+	cvode_test              = FALSE;
+	cvode_error             = FALSE;
+	cvode_n_user            = -99;
+	cvode_n_reactions       = -99;
+	cvode_step_fraction     = 0.0;
+	cvode_rate_sim_time     = 0.0;
+	cvode_rate_sim_time_start = 0.0;
+	cvode_last_good_time    = 0.0;
+	cvode_prev_good_time    = 0.0;
+	cvode_last_good_y       = NULL;
+	cvode_prev_good_y       = NULL;
+	kinetics_machEnv        = NULL;
+	kinetics_y              = NULL;
+	kinetics_abstol         = NULL;
+	kinetics_cvode_mem      = NULL;
+	cvode_pp_assemblage_save= NULL;
+	cvode_ss_assemblage_save= NULL;
+	set_and_run_attempt     = 0;
+	/* model.cpp ------------------------------- */
+	gas_in                  = FALSE;
+	min_value               = 1e-10;
+
+	/* phrq_io_output.cpp ------------------------------- */
+	forward_output_to_log   = 0;
+	/* phreeqc_files.cpp ------------------------------- */
+#ifdef NPP
+	default_data_base = "c:\\phreeqc\\database\\phreeqc.dat";
+#else
+	default_data_base = "phreeqc.dat";
+#endif
+	/* Pitzer  */	
+	pitzer_model			= FALSE;
+	sit_model				= FALSE;
+	pitzer_pe				= FALSE;
+	full_pitzer = FALSE;
+	always_full_pitzer = FALSE;
+	ICON					= TRUE;
+	IC                      = -1;
+	COSMOT                  = 0;
+	AW                      = 0;
+	VP                      = 0;
+	DW0                     = 0;
+	// auto pitz_param_map
+	use_etheta				= TRUE;
+	OTEMP					= -100.;
+	OPRESS					= -100.;
+	A0                      = 0;
+	cations                 = NULL;
+	anions                  = NULL;
+	neutrals                = NULL;
+	count_cations           = 0;
+	count_anions            = 0;
+	count_neutrals          = 0;
+	MAXCATIONS              = 0;
+	FIRSTANION              = 0;
+	MAXNEUTRAL              = 0;
+	mcb0                    = NULL;
+	mcb1                    = NULL;
+	mcc0                    = NULL;
+	for (int i = 0; i < 23; i++)
+	{
+		BK[i]				= 0.0;
+		DK[i]				= 0.0;
+	}
+	dummy                   = 0;
+	/* print.cpp ------------------------------- */
+	if (sformatf_buffer != NULL)
+	{
+		sformatf_buffer = (char*)free_check_null(sformatf_buffer);
+	}
+	sformatf_buffer = (char *) PHRQ_calloc(256 , sizeof(char));
+	if (sformatf_buffer == NULL) 
+			malloc_error();
+	sformatf_buffer_size = 256;
+	/* read.cpp */
+	prev_next_char          = NULL;
+#if defined PHREEQ98 
+	int shifts_as_points;
+#endif
+	/* read_class.cxx */
+	// auto dump_info
+	// auto delete_info
+	// auto run_info
+	run_info.Set_io(phrq_io);
+	/* readtr.cpp */
+	// auto dump_file_name_cpp;
+	/* sit.cpp ------------------------------- */
+
+	sit_A0                  = 0;
+	sit_count_cations       = 0;
+	sit_count_anions        = 0;
+	sit_count_neutrals      = 0;
+	sit_MAXCATIONS          = 0;
+	sit_FIRSTANION          = 0;
+	sit_MAXNEUTRAL          = 0;
+	/* tidy.cpp ------------------------------- */
+	a0                      = 0;
+	a1                      = 0;
+	kc                      = 0;
+	kb                      = 0;
+	/* tally.cpp ------------------------------- */
+	t_buffer                = NULL;
+	tally_count_component   = 0;
+	//tally_table             = NULL;
+	count_tally_table_columns = 0;
+	count_tally_table_rows  = 0;
+	/* transport.cpp ------------------------------- */
+	sol_D                   = NULL;
+	sol_D_dbg               = NULL;
+	J_ij                    = NULL;
+	J_ij_il                 = NULL;
+	J_ij_count_spec         = 0;
+	m_s                     = NULL;
+	count_m_s               = 0;
+	tot1_h                  = 0;
+	tot1_o                  = 0;
+	tot2_h                  = 0;
+	tot2_o                  = 0;
+	diffc_max               = 0;
+	diffc_tr                = 0;
+	J_ij_sum                = 0;
+	transp_surf             = FALSE;
+	heat_mix_array          = NULL;
+	temp1                   = NULL;
+	temp2                   = NULL;
+	nmix                    = 0;
+	heat_nmix               = 0;
+	heat_mix_f_imm          = 0;
+	heat_mix_f_m            = 0;
+	warn_MCD_X              = 0;
+	warn_fixed_Surf         = 0;
+	/* utilities.cpp ------------------------------- */
+	spinner                 = 0;
+	// keycount;
+	keycount.resize(Keywords::KEY_COUNT_KEYWORDS);
+	for (int i = 0; i < Keywords::KEY_COUNT_KEYWORDS; i++)
+	{
+		keycount[i] = 0;
+	}
+
+	return;
+}
+/*-----------------------------------------------------*/
+Phreeqc::Phreeqc(const Phreeqc &src)
+{
+	user_print = NULL;
+	sformatf_buffer = NULL;
+	basic_interpreter = NULL;
+	count_elts = 0;
+	aphi = NULL;
+	//this->phrq_io = src.phrq_io;
+	this->phrq_io = &this->ioInstance;
+	this->init();
+	this->initialize();
+	InternalCopy(&src);
+}
+void
+Phreeqc::InternalCopy(const Phreeqc* pSrc)
+{
+	// phrq_io
+	//this->phrq_io = new PHRQ_io;
+	same_model = FALSE;
+	current_tc = pSrc->current_tc;
+	current_pa = pSrc->current_pa;
+	current_mu = pSrc->current_mu;
+	mu_terms_in_logk = pSrc->mu_terms_in_logk;
+
+	/* ----------------------------------------------------------------------
+	*   STRUCTURES
+	* ---------------------------------------------------------------------- */
+	//last_model, accept init
+	high_precision = pSrc->high_precision;
+	// Maps
+	Rxn_temperature_map = pSrc->Rxn_temperature_map;
+	Rxn_pressure_map = pSrc->Rxn_pressure_map;
+	g_iterations = -1;
+	G_TOL = pSrc->G_TOL;
+	Rxn_surface_map = pSrc->Rxn_surface_map;
+	change_surf_count = pSrc->change_surf_count;
+	change_surf = change_surf_alloc(change_surf_count + 1);
+	for (int ii = 0; ii < change_surf_count; ii++)
+	{
+		change_surf[ii].comp_name = string_hsave(pSrc->change_surf[ii].comp_name);
+		change_surf[ii].fraction = pSrc->change_surf[ii].fraction;
+		change_surf[ii].new_comp_name = string_hsave(pSrc->change_surf[ii].new_comp_name);
+		change_surf[ii].new_Dw = pSrc->change_surf[ii].new_Dw;
+		change_surf[ii].cell_no = pSrc->change_surf[ii].cell_no;
+		change_surf[ii].next = pSrc->change_surf[ii].next;
+	}
+	Rxn_exchange_map = pSrc->Rxn_exchange_map;
+	Rxn_kinetics_map = pSrc->Rxn_kinetics_map;
+	use_kinetics_limiter = pSrc->use_kinetics_limiter;
+	save_values = pSrc->save_values;
+	save_strings = pSrc->save_strings;
+	save = pSrc->save;
+	//class copier copy_solution;
+	//class copier copy_pp_assemblage;
+	//class copier copy_exchange;
+	//class copier copy_surface;
+	//class copier copy_ss_assemblage;
+	//class copier copy_gas_phase;
+	//class copier copy_kinetics;
+	//class copier copy_mix;
+	//class copier copy_reaction;
+	//class copier copy_temperature;
+	//class copier copy_pressure;
+	//	Inverse not implemented
+	//std::vector<class inverse> inverse;
+	count_inverse = 0;
+	/* rate parameters */
+	rate_parameters_pk = pSrc->rate_parameters_pk;
+	rate_parameters_svd = pSrc->rate_parameters_svd;
+	rate_parameters_hermanska = pSrc->rate_parameters_hermanska;
+	// Mean gammas
+	mean_gammas = pSrc->mean_gammas;
+	//   Mix
+	Rxn_mix_map = pSrc->Rxn_mix_map;
+	Dispersion_mix_map = pSrc->Dispersion_mix_map;
+	Rxn_solution_mix_map = pSrc->Rxn_solution_mix_map;
+	Rxn_exchange_mix_map = pSrc->Rxn_exchange_mix_map;
+	Rxn_gas_phase_mix_map = pSrc->Rxn_gas_phase_mix_map;
+	Rxn_kinetics_mix_map = pSrc->Rxn_kinetics_mix_map;
+	Rxn_pp_assemblage_mix_map = pSrc->Rxn_pp_assemblage_mix_map;
+	Rxn_ss_assemblage_mix_map = pSrc->Rxn_ss_assemblage_mix_map;
+	Rxn_surface_mix_map = pSrc->Rxn_surface_mix_map;
+	//List new definitions
+	//std::set<int> Rxn_new_exchange;
+	//std::set<int> Rxn_new_gas_phase;
+	//std::set<int> Rxn_new_kinetics;     // not used
+	//std::set<int> Rxn_new_mix;          // not used
+	//std::set<int> Rxn_new_pp_assemblage;
+	//std::set<int> Rxn_new_pressure;     // not used
+	//std::set<int> Rxn_new_reaction;     // not used
+	//std::set<int> Rxn_new_solution;
+	//std::set<int> Rxn_new_ss_assemblage;
+	//std::set<int> Rxn_new_surface;
+	//std::set<int> Rxn_new_temperature;  // not used
+	Rxn_reaction_map = pSrc->Rxn_reaction_map;
+	Rxn_gas_phase_map = pSrc->Rxn_gas_phase_map;
+	Rxn_ss_assemblage_map = pSrc->Rxn_ss_assemblage_map;
+	Rxn_pp_assemblage_map = pSrc->Rxn_pp_assemblage_map;
+
+	std::vector<class species_list> species_list;
+	// will be rebuilt
+	//std::vector<class list0> sum_jacob0;	
+	//std::vector<class list1> sum_mb1; 
+	//std::vector<class list1> sum_jacob1;	
+	//std::vector<class list2> sum_mb2; 
+	//std::vector<class list2> sum_jacob2; 
+	//std::vector<class list2> sum_delta; 
+	// Solution
+	Rxn_solution_map = pSrc->Rxn_solution_map;
+	unnumbered_solutions = pSrc->unnumbered_solutions;
+	save_species = pSrc->save_species;
+	// Global solution
+	title_x = pSrc->title_x;
+	last_title_x = pSrc->last_title_x;
+	//new_x                   = FALSE;
+	description_x = pSrc->description_x;
+	//new_x                   = FALSE;
+	description_x = pSrc->description_x;
+	//tc_x                    = 0;
+	//tk_x                    = 0;
+	//patm_x                  = 1;
+	//last_patm_x             = 1;
+	//numerical_fixed_volume  = false;
+	//force_numerical_fixed_volume = false;
+	//ph_x                    = 0;
+	//solution_pe_x           = 0;
+	//mu_x                    = 0;
+	//ah2o_x                  = 1.0;
+	//density_x               = 0;
+	//total_h_x               = 0;
+	//total_o_x               = 0;
+	//cb_x                    = 0;
+	//total_ions_x            = 0;
+	//mass_water_aq_x         = 0;
+	//mass_water_surfaces_x   = 0;
+	//mass_water_bulk_x       = 0;
+	//units_x
+	//pe_x
+	//isotopes_x
+	//default_pe_x
+	//dl_type_x                = cxxSurface::NO_DL;
+	//total_carbon             = 0;
+	//total_co2                = 0;
+	//total_alkalinity         = 0;
+	gfw_water = pSrc->gfw_water;
+	//step_x                   = 0;
+	//kin_time_x               = 0;
+	//   Transport data
+	count_cells = pSrc->count_cells;
+	count_shifts = pSrc->count_shifts;
+	ishift = pSrc->ishift;
+	bcon_first = pSrc->bcon_first;
+	bcon_last = pSrc->bcon_last;
+	correct_disp = pSrc->correct_disp;
+	tempr = pSrc->tempr;
+	timest = pSrc->timest;
+	simul_tr = pSrc->simul_tr;
+	diffc = pSrc->diffc;
+	heat_diffc = pSrc->heat_diffc;
+	cell = pSrc->cell;
+	mcd_substeps = pSrc->mcd_substeps;
+	stag_data = pSrc->stag_data;
+	print_modulus = pSrc->print_modulus;
+	punch_modulus = pSrc->punch_modulus;
+	dump_in = pSrc->dump_in;
+	dump_modulus = pSrc->dump_modulus;
+	transport_warnings = pSrc->transport_warnings;
+	// cell_data 
+	cell_data = pSrc->cell_data;
+	old_cells = pSrc->old_cells;
+	max_cells = pSrc->max_cells;
+	if (stag_data.count_stag > 0)
+	{
+		max_cells = (max_cells - 2) / (1 + stag_data.count_stag);
+	}
+	all_cells = pSrc->all_cells;
+	max_cells = pSrc->max_cells;
+	multi_Dflag = pSrc->multi_Dflag;
+	interlayer_Dflag = pSrc->interlayer_Dflag;
+	implicit = pSrc->implicit;
+	max_mixf = pSrc->max_mixf;
+	min_dif_LM = pSrc->min_dif_LM;
+	default_Dw = pSrc->default_Dw;
+	correct_Dw = pSrc->correct_Dw;
+	multi_Dpor = pSrc->multi_Dpor;
+	interlayer_Dpor = pSrc->interlayer_Dpor;
+	multi_Dpor_lim = pSrc->multi_Dpor_lim;
+	interlayer_Dpor_lim = pSrc->interlayer_Dpor_lim;
+	multi_Dn = pSrc->multi_Dn;
+	interlayer_tortf = pSrc->interlayer_tortf;
+	cell_no = pSrc->cell_no;
+	mixrun = pSrc->mixrun;
+	//  Advection data
+	count_ad_cells = pSrc->count_ad_cells;
+	count_ad_shifts = pSrc->count_ad_shifts;
+	print_ad_modulus = pSrc->print_ad_modulus;
+	punch_ad_modulus = pSrc->punch_ad_modulus;
+	advection_punch = pSrc->advection_punch;
+	advection_print = pSrc->advection_print;
+	advection_kin_time = pSrc->advection_kin_time;
+	advection_kin_time_defined = pSrc->advection_kin_time_defined;
+	advection_warnings = pSrc->advection_warnings;
+	// Tidy data
+	new_model = TRUE;
+	new_exchange = FALSE;
+	new_pp_assemblage = FALSE;
+	new_surface = FALSE;
+	new_reaction = FALSE;
+	new_temperature = FALSE;
+	new_mix = FALSE;
+	new_solution = FALSE;
+	new_gas_phase = FALSE;
+	new_inverse = FALSE;
+	new_punch = FALSE;
+	new_ss_assemblage = FALSE;
+	new_kinetics = FALSE;
+	new_copy = FALSE;
+	new_pitzer = FALSE;
+	// Elements
+	for (int i = 0; i < (int)pSrc->elements.size(); i++)
+	{
+		const char* ptr = string_hsave(pSrc->elements[i]->name);
+		class element* elt_ptr = element_store(ptr);
+		elt_ptr->gfw = pSrc->elements[i]->gfw;
+	}
+	element_h_one = element_store("H(1)");
+	// Element List
+	count_elts = 0;
+	// Reaction
+	run_cells_one_step = pSrc->run_cells_one_step;
+	//// logk
+	//logk.clear();
+	//for (size_t i = 0; i < pSrc->logk.size(); i++)
+	//{
+	//	class logk* tlk = new class logk;
+	//	*tlk = *pSrc->logk[i];
+	//	tlk->name = string_hsave(pSrc->logk[i]->name);
+	//	logk.push_back(tlk);
+	//}
+	for (int i = 0; i < (int)pSrc->logk.size(); i++)
+	{
+		class logk* logk_ptr = logk_store(pSrc->logk[i]->name, FALSE);
+		//memcpy(logk_ptr, pSrc->logk[i], sizeof(class logk));
+		*logk_ptr = *pSrc->logk[i];
+		logk_ptr->name = string_hsave(pSrc->logk[i]->name);
+		logk_ptr->add_logk.resize(pSrc->logk[i]->add_logk.size());
+		for (size_t j = 0; j < logk_ptr->add_logk.size(); j++)
+		{
+			logk_ptr->add_logk[j].coef = pSrc->logk[i]->add_logk[j].coef;
+			logk_ptr->add_logk[j].name = string_hsave(pSrc->logk[i]->add_logk[j].name);
+		}
+	}
+	// s, species
+	for (int i = 0; i < (int)pSrc->s.size(); i++)
+	{
+		class species* s_ptr = s_store(pSrc->s[i]->name, pSrc->s[i]->z, FALSE);
+		//memcpy(s_ptr, pSrc->s[i], sizeof(class species));
+		*s_ptr = *pSrc->s[i];
+		// fix up all pointers
+		s_ptr->name = string_hsave(pSrc->s[i]->name);
+		s_ptr->mole_balance = NULL;
+		if (pSrc->s[i]->mole_balance != NULL)
+		{
+			s_ptr->mole_balance = string_hsave(pSrc->s[i]->mole_balance);
+		}
+		s_ptr->primary = NULL;
+		s_ptr->secondary = NULL;
+		s_ptr->add_logk.resize(pSrc->s[i]->add_logk.size());
+		for (size_t j = 0; j < s_ptr->add_logk.size(); j++)
+		{
+			s_ptr->add_logk[j].coef = pSrc->s[i]->add_logk[j].coef;
+			s_ptr->add_logk[j].name = string_hsave(pSrc->s[i]->add_logk[j].name);
+		}
+		//next_elt
+		s_ptr->next_elt = elt_list_internal_copy(pSrc->s[i]->next_elt);
+		s_ptr->next_secondary = elt_list_internal_copy(pSrc->s[i]->next_secondary);
+		s_ptr->next_sys_total = elt_list_internal_copy(pSrc->s[i]->next_sys_total);
+		//rxn
+		s_ptr->rxn = CReaction_internal_copy(pSrc->s[i]->rxn);
+		s_ptr->rxn_s = CReaction_internal_copy(pSrc->s[i]->rxn_s);
+		s_ptr->rxn_x = CReaction_internal_copy(pSrc->s[i]->rxn_x);
+	}
+	s_diff_layer = pSrc->s_diff_layer;
+	//s_x  will be built
+	s_h2o = s_search("H2O");
+	s_hplus = s_search("H+");
+	s_h3oplus = s_search("H3O+");
+	s_eminus = s_search("e-");
+	s_co3 = s_search("CO3-2");
+	s_h2 = s_search("H2");
+	s_o2 = s_search("O2");
+	/*----------------------------------------------------------------------
+	*   Phases
+	*---------------------------------------------------------------------- */
+	for (int i = 0; i < (int)pSrc->phases.size(); i++)
+	{
+		class phase* phase_ptr = phase_store(pSrc->phases[i]->name);
+		//memcpy(phase_ptr, pSrc->phases[i], sizeof(class phase));
+		*phase_ptr = *pSrc->phases[i];
+		// clean up pointers
+		phase_ptr->name = string_hsave(pSrc->phases[i]->name);
+		phase_ptr->formula = string_hsave(pSrc->phases[i]->formula);
+		//add_logk
+		phase_ptr->add_logk.resize(pSrc->phases[i]->add_logk.size());
+		for (size_t j = 0; j < phase_ptr->add_logk.size(); j++)
+		{
+			phase_ptr->add_logk[j].coef = pSrc->phases[i]->add_logk[j].coef;
+			phase_ptr->add_logk[j].name = string_hsave(pSrc->phases[i]->add_logk[j].name);
+		}
+		//next_elt
+		phase_ptr->next_elt = elt_list_internal_copy(pSrc->phases[i]->next_elt);
+		phase_ptr->next_sys_total = elt_list_internal_copy(pSrc->phases[i]->next_sys_total);
+		//rxn
+		phase_ptr->rxn = CReaction_internal_copy(pSrc->phases[i]->rxn);
+		phase_ptr->rxn_s = CReaction_internal_copy(pSrc->phases[i]->rxn_s);
+		phase_ptr->rxn_x = CReaction_internal_copy(pSrc->phases[i]->rxn_x);
+	}
+	// Master species
+	for (size_t i = 0; i < pSrc->master.size(); i++)
+	{
+		master.resize(i + 1);
+		master[i] = new class master;
+		//memcpy(master[i], pSrc->master[i], sizeof(class master));
+		*master[i] = *pSrc->master[i];
+		// clean up pointers
+		master[i]->gfw_formula = string_hsave(pSrc->master[i]->gfw_formula);
+		master[i]->elt = element_store(pSrc->master[i]->elt->name);
+		master[i]->unknown = NULL;
+		master[i]->s = s_store(pSrc->master[i]->s->name, pSrc->master[i]->s->z, FALSE);
+		//rxn_primary
+		master[i]->rxn_primary = CReaction_internal_copy(pSrc->master[i]->rxn_primary);
+		master[i]->rxn_secondary = CReaction_internal_copy(pSrc->master[i]->rxn_secondary);
+	}
+	// Unknowns will be built
+	//x                       = NULL;
+	//count_unknowns          = 0;
+	//max_unknowns            = 0;
+	//ah2o_unknown            = NULL;
+	//alkalinity_unknown      = NULL;
+	//carbon_unknown          = NULL;
+	//charge_balance_unknown  = NULL;
+	//exchange_unknown        = NULL;
+	//mass_hydrogen_unknown   = NULL;
+	//mass_oxygen_unknown     = NULL;
+	//mb_unknown              = NULL;
+	//mu_unknown              = NULL;
+	//pe_unknown              = NULL;
+	//ph_unknown              = NULL;
+	//pure_phase_unknown      = NULL;
+	//solution_phase_boundary_unknown = NULL;
+	//surface_unknown         = NULL;
+	//gas_unknown             = NULL;
+	//ss_unknown              = NULL;
+	//gas_unknowns;
+	//mb_unknowns
+	//   Reaction work space
+	// class reaction_temp trxn;
+	count_trxn = 0;
+	// Print
+	pr = pSrc->pr;
+	status_on = pSrc->status_on;
+	status_interval = pSrc->status_interval;
+	status_timer = clock();
+	status_string.clear();
+	count_warnings = 0;
+	// RATES
+	//rates = pSrc->rates;
+	for (size_t i = 0; i < pSrc->rates.size(); i++)
+	{
+		rates.push_back(*rate_copy(&pSrc->rates[i]));
+	}
+	//rate_m					= 0;
+	//rate_m0					= 0;
+	//rate_time				= 0;
+	//rate_kin_time           = 1.0;
+	//rate_sim_time_start		= 0;
+	//rate_sim_time_end		= 0;
+	//rate_sim_time			= 0;
+	//rate_moles				= 0;
+	initial_total_time = pSrc->initial_total_time;
+	//rate_p
+	count_rate_p = 0;
+	// User print
+	user_print = rate_copy(pSrc->user_print);
+	// For now, User Punch is NOT copied
+	n_user_punch_index = pSrc->n_user_punch_index;
+	fpunchf_user_s_warning = pSrc->fpunchf_user_s_warning;
+	//fpunchf_user_buffer[0]  = 0;
+#if defined MULTICHART
+	// auto chart_handler;
+	chart_handler.Set_io(phrq_io);
+#endif
+	/* ----------------------------------------------------------------------
+	*   GLOBAL DECLARATIONS
+	* ---------------------------------------------------------------------- */
+	error_string = NULL;
+	simulation = pSrc->simulation;
+	//state                   = INITIALIZE;
+	//reaction_step           = 0;
+	//transport_step          = 0;
+	//transport_start         = 0;
+	//advection_step          = 0;
+	//stop_program            = FALSE;
+	incremental_reactions = pSrc->incremental_reactions;
+	// Constants
+	MIN_LM = pSrc->MIN_LM;			    /* minimum log molality allowed before molality set to zero */
+	LOG_ZERO_MOLALITY = pSrc->LOG_ZERO_MOLALITY;	/* molalities <= LOG_ZERO_MOLALITY are considered equal to zero */
+	MIN_RELATED_LOG_ACTIVITY = pSrc->MIN_RELATED_LOG_ACTIVITY;
+	MIN_TOTAL = pSrc->MIN_TOTAL;
+	MIN_TOTAL_SS = pSrc->MIN_TOTAL_SS;
+	MIN_RELATED_SURFACE = pSrc->MIN_RELATED_SURFACE;
+	simulation = pSrc->simulation;
+	//my_array, 
+	//delta, 
+	//residual
+	input_error = 0;
+	next_keyword = Keywords::KEY_NONE;
+	parse_error = 0;
+	paren_count = 0;
+	iterations = 0;
+	gamma_iterations = 0;
+	density_iterations = 0;
+	run_reactions_iterations = 0;
+	overall_iterations = 0;
+	free_check_null(line);
+	free_check_null(line_save);
+	max_line = pSrc->max_line;
+	line = (char*)PHRQ_malloc(max_line * sizeof(char));
+	line_save = (char*)PHRQ_malloc(max_line * sizeof(char));
+	LOG_10 = pSrc->LOG_10;
+	// Debug
+	debug_model = pSrc->debug_model;
+	debug_prep = pSrc->debug_prep;
+	debug_set = pSrc->debug_set;
+	debug_diffuse_layer = pSrc->debug_diffuse_layer;
+	debug_inverse = pSrc->debug_inverse;
+	//
+	inv_tol_default = pSrc->inv_tol_default;
+	itmax = pSrc->itmax;
+	max_tries = pSrc->max_tries;
+	ineq_tol = pSrc->ineq_tol;
+	convergence_tolerance = pSrc->convergence_tolerance;
+	step_size = pSrc->step_size;
+	pe_step_size = pSrc->pe_step_size;
+	step_size_now = step_size;
+	pe_step_size_now = pe_step_size;
+	pp_scale = pSrc->pp_scale;
+	pp_column_scale = pSrc->pp_column_scale;
+	diagonal_scale = pSrc->diagonal_scale;
+	mass_water_switch = pSrc->mass_water_switch;
+	delay_mass_water = pSrc->delay_mass_water;
+	equi_delay = pSrc->equi_delay;
+	dampen_ah2o = pSrc->dampen_ah2o;
+	censor = pSrc->censor;
+	aqueous_only = pSrc->aqueous_only;
+	negative_concentrations = pSrc->negative_concentrations;
+	calculating_deriv = pSrc->calculating_deriv;
+	numerical_deriv = pSrc->numerical_deriv;
+	count_total_steps = 0;
+	phast = FALSE;
+	output_newline = true;
+	// llnl
+	a_llnl = pSrc->a_llnl;
+	b_llnl = pSrc->b_llnl;
+	bdot_llnl = pSrc->bdot_llnl;
+	llnl_temp = pSrc->llnl_temp;
+	llnl_adh = pSrc->llnl_adh;
+	llnl_bdh = pSrc->llnl_bdh;
+	llnl_bdot = pSrc->llnl_bdot;
+	llnl_co2_coefs = pSrc->llnl_co2_coefs;
+
+	// Not implemented for now
+	SelectedOutput_map = pSrc->SelectedOutput_map;
+	{
+		std::map<int, SelectedOutput>::iterator it = SelectedOutput_map.begin();
+		for (; it != SelectedOutput_map.end(); it++)
+		{
+			//phrq_io->punch_open(it->second.Get_file_name().c_str());
+			//it->second.Set_punch_ostream(phrq_io->Get_punch_ostream());
+			//phrq_io->Set_punch_ostream(NULL);
+			it->second.Set_punch_ostream(NULL);
+		}
+	}
+	SelectedOutput_map.clear();
+
+	UserPunch_map = pSrc->UserPunch_map;
+	std::map<int, UserPunch>::iterator it = UserPunch_map.begin();
+	for (; it != UserPunch_map.end(); it++)
+	{
+		class rate* rate_new = new class rate;
+		rate_new = rate_copy(it->second.Get_rate());
+		it->second.Set_rate(rate_new);
+		it->second.Set_PhreeqcPtr(this);
+	}
+
+	remove_unstable_phases = FALSE;
+	//screen_string;
+	spread_length = pSrc->spread_length;
+	//maps set by store below
+	//std::map<std::string, std::string*> strings_map;
+	//std::map<std::string, class element*> elements_map;
+	//std::map<std::string, class species*> species_map;
+	//std::map<std::string, class phase*> phases_map;
+	//std::map<std::string, class logk*> logk_map;
+	//std::map<std::string, class master_isotope*> master_isotope_map;
+	/* ----------------------------------------------------------------------
+	*   ISOTOPES
+	* ---------------------------------------------------------------------- */
+	for (int i = 0; i < (int)pSrc->master_isotope.size(); i++)
+	{
+		class master_isotope* master_isotope_ptr = master_isotope_store(pSrc->master_isotope[i]->name, FALSE);
+		// memcpy(master_isotope_ptr, pSrc->master_isotope[i], sizeof(class master_isotope));
+		*master_isotope_ptr = *pSrc->master_isotope[i];
+		master_isotope_ptr->name = string_hsave(pSrc->master_isotope[i]->name);
+		int n;
+		master_isotope_ptr->master = NULL;
+		if (pSrc->master_isotope[i]->master)
+		{
+			master_isotope_ptr->master = master_search(pSrc->master_isotope[i]->master->elt->name, &n);
+		}
+		if (master_isotope_ptr->master == NULL)
+		{
+			//error_msg("Error in copy constructor for master_isotope.", STOP);
+		}
+		master_isotope_ptr->elt = NULL;
+		if (pSrc->master_isotope[i]->elt)
+		{
+			master_isotope_ptr->elt = element_store(pSrc->master_isotope[i]->elt->name);
+		}
+		master_isotope_ptr->units = NULL;
+		if (pSrc->master_isotope[i]->units)
+		{
+			master_isotope_ptr->units = string_hsave(pSrc->master_isotope[i]->units);
+		}
+	}
+	initial_solution_isotopes = pSrc->initial_solution_isotopes;
+	// Calculate values
+	for (int i = 0; i < pSrc->calculate_value.size(); i++)
+	{
+		class calculate_value* calculate_value_ptr = calculate_value_store(pSrc->calculate_value[i]->name, FALSE);
+		calculate_value_ptr->value = pSrc->calculate_value[i]->value;
+		calculate_value[i]->commands = pSrc->calculate_value[i]->commands;
+	}
+	// More isotopes
+	for (int i = 0; i < (int)pSrc->isotope_ratio.size(); i++)
+	{
+		class isotope_ratio* isotope_ratio_ptr = isotope_ratio_store(pSrc->isotope_ratio[i]->name, FALSE);
+		isotope_ratio_ptr->name = string_hsave(pSrc->isotope_ratio[i]->name);
+		isotope_ratio_ptr->isotope_name = string_hsave(pSrc->isotope_ratio[i]->isotope_name);
+		isotope_ratio_ptr->ratio = pSrc->isotope_ratio[i]->ratio;
+		isotope_ratio_ptr->converted_ratio = pSrc->isotope_ratio[i]->converted_ratio;
+	}
+	//std::map<std::string, class isotope_ratio*> isotope_ratio_map;
+	for (int i = 0; i < (int)pSrc->isotope_alpha.size(); i++)
+	{
+		class isotope_alpha* isotope_alpha_ptr = isotope_alpha_store(pSrc->isotope_alpha[i]->name, FALSE);
+		isotope_alpha_ptr->named_logk = string_hsave(pSrc->isotope_alpha[i]->named_logk);
+		isotope_alpha_ptr->value = pSrc->isotope_alpha[i]->value;
+	}
+	//std::map<std::string, class isotope_alpha*> isotope_alpha_map;
+	// Misc
+	phreeqc_mpi_myself = 0;
+	first_read_input = pSrc->first_read_input;
+	user_database = pSrc->user_database;
+	//have_punch_name			= pSrc->have_punch_name;
+	print_density = pSrc->print_density;
+	print_viscosity = pSrc->print_viscosity;
+	viscos = pSrc->viscos;
+	viscos_0 = pSrc->viscos_0;
+	viscos_0_25 = pSrc->viscos_0_25; // viscosity of the solution, of pure water, of pure water at 25 C
+	density_x = pSrc->density_x;
+	solution_volume_x = pSrc->solution_volume_x;
+	solution_mass_x = pSrc->solution_mass_x;
+	kgw_kgs = pSrc->kgw_kgs;
+	cell_pore_volume = pSrc->cell_pore_volume;
+	cell_porosity = pSrc->cell_porosity;
+	cell_volume = pSrc->cell_volume;
+	cell_saturation = pSrc->cell_saturation;
+	sys.clear();
+	sys_tot = pSrc->sys_tot;
+	// solution properties
+	V_solutes = pSrc->V_solutes;
+	rho_0 = pSrc->rho_0;
+	kappa_0 = pSrc->kappa_0;
+	p_sat = pSrc->p_sat;
+	eps_r = pSrc->eps_r;
+	DH_A = pSrc->DH_A;
+	DH_B = pSrc->DH_B;
+	DH_Av = pSrc->DH_Av;
+	QBrn = pSrc->QBrn;
+	ZBrn = pSrc->ZBrn;
+	dgdP = pSrc->dgdP;
+	//
+	need_temp_msg = pSrc->need_temp_msg;
+	solution_mass = pSrc->solution_mass;
+	solution_volume = pSrc->solution_volume;
+	s_pTail = NULL;
+	//basic_interpreter = NULL;
+	/* cl1.cpp ------------------------------- */
+	//std::vector<double> x_arg, res_arg, scratch;
+	// gases.cpp 
+	a_aa_sum = pSrc->a_aa_sum;
+	b2 = pSrc->b2;
+	b_sum = pSrc->b_sum;
+	R_TK = pSrc->R_TK;
+	gas_binary_parameters = pSrc->gas_binary_parameters;
+	/* input.cpp ------------------------------- */
+	check_line_return = 0;
+	reading_db = FALSE;
+	/* integrate.cpp ------------------------------- */
+	midpoint_sv = pSrc->midpoint_sv;
+	z_global = pSrc->z_global;
+	xd_global = pSrc->xd_global;
+	alpha_global = pSrc->alpha_global;
+	/* inverse.cpp ------------------------------- */	/* integrate.cpp ------------------------------- */
+	max_row_count = pSrc->max_row_count;
+	max_column_count = pSrc->max_column_count;
+	carbon = pSrc->carbon;
+	//std::vector<const char*> col_name, row_name;
+	count_rows = pSrc->count_rows;
+	count_optimize = pSrc->count_optimize;
+	col_phases = pSrc->col_phases;
+	col_redox = pSrc->col_redox;
+	col_epsilon = pSrc->col_epsilon;
+	col_ph = pSrc->col_ph;
+	col_water = pSrc->col_water;
+	col_isotopes = pSrc->col_isotopes;
+	col_phase_isotopes = pSrc->col_phase_isotopes;
+	row_mb = pSrc->row_mb;
+	row_fract = pSrc->row_fract;
+	row_charge = pSrc->row_charge;
+	row_carbon = pSrc->row_carbon;
+	row_isotopes = pSrc->row_isotopes;
+	row_epsilon = pSrc->row_epsilon;
+	row_isotope_epsilon = pSrc->row_isotope_epsilon;
+	row_water = pSrc->row_water;
+	//std::vector<double> inv_zero, array1, inv_res, inv_delta1, delta2,
+	//	delta3, inv_cu, delta_save;
+	//std::vector<double> min_delta, max_delta;
+	//std::vector<int> inv_iu, inv_is;
+	klmd = pSrc->klmd;
+	nklmd = pSrc->nklmd;
+	n2d = pSrc->n2d;
+	kode = pSrc->kode;
+	iter = pSrc->iter;
+	toler = pSrc->toler;
+	error = pSrc->error;
+	max_pct = pSrc->max_pct;
+	scaled_error = pSrc->scaled_error;
+	master_alk = NULL;
+	//std::vector<int> row_back, col_back;
+	//std::vector<unsigned long> good, bad, minimal;
+	max_good = pSrc->max_good;
+	max_bad = pSrc->max_bad;
+	max_minimal = pSrc->max_minimal;
+	count_good = pSrc->count_good;
+	count_bad = pSrc->count_bad;
+	count_minimal = pSrc->count_minimal;
+	count_calls = pSrc->count_calls;
+	soln_bits = pSrc->soln_bits;
+	phase_bits = pSrc->phase_bits;
+	current_bits = pSrc->current_bits;
+	temp_bits = pSrc->temp_bits;
+	netpath_file = NULL;
+	count_inverse_models = pSrc->count_inverse_models;
+	count_pat_solutions = pSrc->count_pat_solutions;
+	for (int i = 0; i < 32; i++)
+	{
+		min_position[i] = pSrc->min_position[i];
+		max_position[i] = pSrc->max_position[i];
+		now[i] = pSrc->now[i];
+	}
+	//std::vector <std::string> inverse_heading_names;
+	/* kinetics.cpp ------------------------------- */
+	count_pp = count_pg = count_ss = 0;
+	cvode_kinetics_ptr = NULL;
+	cvode_test = FALSE;
+	cvode_error = FALSE;
+	cvode_n_user = -99;
+	cvode_n_reactions = -99;
+	cvode_step_fraction = 0.0;
+	cvode_rate_sim_time = 0.0;
+	cvode_rate_sim_time_start = 0.0;
+	cvode_last_good_time = 0.0;
+	cvode_prev_good_time = 0.0;
+	cvode_last_good_y = NULL;
+	cvode_prev_good_y = NULL;
+	kinetics_machEnv = NULL;
+	kinetics_y = NULL;
+	kinetics_abstol = NULL;
+	kinetics_cvode_mem = NULL;
+	cvode_pp_assemblage_save = NULL;
+	cvode_ss_assemblage_save = NULL;
+	//std::vector<double> m_temp, m_original, rk_moles, x0_moles;
+	set_and_run_attempt = 0;
+	/* model.cpp ------------------------------- */
+	gas_in = FALSE;
+	min_value = 1e-10;
+	//std::vector<double> normal, ineq_array, res, cu, zero, delta1;
+	//std::vector<int> iu, is, back_eq;									 
+	/* phrq_io_output.cpp ------------------------------- */
+	forward_output_to_log = pSrc->forward_output_to_log;
+	/* phreeqc_files.cpp ------------------------------- */
+	default_data_base = pSrc->default_data_base;
+	// Pitzer 
+	pitzer_model = pSrc->pitzer_model;
+	sit_model = pSrc->sit_model;
+	pitzer_pe = pSrc->pitzer_pe;
+
+
+	full_pitzer = pSrc->full_pitzer;
+	always_full_pitzer = pSrc->always_full_pitzer;
+	ICON = pSrc->ICON;
+	IC = pSrc->IC;
+	COSMOT = pSrc->COSMOT;
+	AW = pSrc->AW;
+	VP = pSrc->VP;
+	DW0 = pSrc->DW0;
+	for (int i = 0; i < (int)pSrc->pitz_params.size(); i++)
+	{
+		pitz_param_store(pSrc->pitz_params[i]);
+	}
+
+	//pitz_param_map = pSrc->pitz_param_map; created by store
+	for (int i = 0; i < (int)pSrc->theta_params.size(); i++)
+	{
+		size_t count_theta_params = theta_params.size();
+		theta_params.resize(count_theta_params + 1);
+		theta_params[count_theta_params] = new class theta_param;
+		*theta_params[count_theta_params] = *pSrc->theta_params[i];
+	}
+	use_etheta = pSrc->use_etheta;
+	OTEMP = pSrc->OTEMP;
+	OPRESS = pSrc->OPRESS;
+	A0 = pSrc->A0;
+	aphi = pitz_param_copy(pSrc->aphi);
+	// will be rebuilt
+	spec = pSrc->spec;
+	cations = pSrc->cations;
+	anions = pSrc->anions;
+	neutrals = pSrc->neutrals;
+	count_cations = pSrc->count_cations;
+	count_anions = pSrc->count_anions;
+	count_neutrals = pSrc->count_neutrals;
+	MAXCATIONS = pSrc->MAXCATIONS;
+	FIRSTANION = pSrc->FIRSTANION;
+	MAXNEUTRAL = pSrc->MAXNEUTRAL;
+	mcb0 = pSrc->mcb0;
+	mcb1 = pSrc->mcb1;
+	mcc0 = pSrc->mcc0;
+	IPRSNT = pSrc->IPRSNT;
+	M = pSrc->M;
+	LGAMMA = pSrc->LGAMMA;
+	for (int i = 0; i < 23; i++)
+	{
+		BK[i] = pSrc->BK[i];
+		DK[i] = pSrc->DK[i];
+	}
+	dummy = 0;
+	/* print.cpp ------------------------------- */
+	/*
+	sformatf_buffer = (char *) PHRQ_malloc(256 * sizeof(char));
+	if (sformatf_buffer == NULL)
+		malloc_error();
+	sformatf_buffer_size = 256;
+	*/
+	/* read.cpp */
+	prev_next_char = NULL;
+#if defined PHREEQ98 
+	int shifts_as_points;
+#endif
+	/* read_class.cxx */
+	// auto dump_info
+	// auto delete_info
+	// auto run_info
+	/*
+	run_info.Set_io(phrq_io);
+	*/
+	/* readtr.cpp */
+	// auto dump_file_name_cpp;
+	/* sit.cpp ------------------------------- */
+	for (int i = 0; i < (int)pSrc->sit_params.size(); i++)
+	{
+		sit_param_store(pSrc->sit_params[i]);
+	}
+	//sit_param_map = pSrc->sit_param_map; // filled by store
+	sit_A0 = pSrc->sit_A0;
+	sit_count_cations = pSrc->sit_count_cations;
+	sit_count_anions = pSrc->sit_count_anions;
+	sit_count_neutrals = pSrc->sit_count_neutrals;
+	sit_MAXCATIONS = pSrc->sit_MAXCATIONS;
+	sit_FIRSTANION = pSrc->sit_FIRSTANION;
+	sit_MAXNEUTRAL = pSrc->sit_MAXNEUTRAL;
+	sit_IPRSNT = pSrc->sit_IPRSNT;
+	sit_M = pSrc->sit_M;
+	sit_LGAMMA = pSrc->sit_LGAMMA;
+	s_list = pSrc->s_list;
+	cation_list = pSrc->cation_list;
+	neutral_list = pSrc->neutral_list;
+	anion_list = pSrc->anion_list;
+	ion_list = pSrc->ion_list;
+	param_list = pSrc->param_list;
+
+	/* tidy.cpp ------------------------------- */
+	//a0                      = 0;
+	//a1                      = 0;
+	//kc                      = 0;
+	//kb                      = 0;
+	/* tally.cpp ------------------------------- */
+	//t_buffer                = NULL;
+	//tally_count_component   = 0;
+	//tally_table             = NULL;
+	//count_tally_table_columns = 0;
+	//count_tally_table_rows  = 0;
+
+	/* transport.cpp ------------------------------- */
+	/* storage is created and freed in transport.cpp */
+	sol_D = NULL;
+	sol_D_dbg = NULL;
+	J_ij = NULL;
+	J_ij_il = NULL;
+	J_ij_count_spec = pSrc->J_ij_count_spec;
+	m_s = NULL;
+	count_m_s = pSrc->count_m_s;
+	tot1_h = pSrc->tot1_h;
+	tot1_o = pSrc->tot1_o;
+	tot2_h = pSrc->tot2_h;
+	tot2_o = pSrc->tot2_o;
+	diffc_max = pSrc->diffc_max;
+	diffc_tr = pSrc->diffc_tr;
+	J_ij_sum = pSrc->J_ij_sum;
+	transp_surf = pSrc->transp_surf;
+	heat_mix_array = NULL;
+	temp1 = NULL;
+	temp2 = NULL;
+	nmix = pSrc->nmix;
+	heat_nmix = pSrc->heat_nmix;
+	heat_mix_f_imm = pSrc->heat_mix_f_imm;
+	heat_mix_f_m = pSrc->heat_mix_f_m;
+	warn_MCD_X = pSrc->warn_MCD_X;
+	warn_fixed_Surf = pSrc->warn_fixed_Surf;
+	current_x = pSrc->current_x;
+	current_A = pSrc->current_A;
+	fix_current = pSrc->fix_current;
+
+	/* utilities.cpp ------------------------------- */
+	//spinner                 = 0;
+	//// keycount;
+	//for (int i = 0; i < Keywords::KEY_COUNT_KEYWORDS; i++)
+	//{
+	//	keycount.push_back(0);
+	//}
+	spinner = pSrc->spinner;
+	gfw_map = pSrc->gfw_map;
+	//rates_map = pSrc->rates_map;
+	sum_species_map = pSrc->sum_species_map;
+	sum_species_map_db = pSrc->sum_species_map_db;
+
+	// make sure new_model gets set
+	this->keycount[Keywords::KEY_SOLUTION_SPECIES] = 1;
+	this->tidy_model();
+	return;
+}
+// Operator overloaded using a member function
+Phreeqc &Phreeqc::operator=(const Phreeqc &rhs) 
+{
+	if (this == &rhs)      // Same object?
+		return *this; 
+
+	// clean up this here
+	this->clean_up();
+
+	this->PHRQ_free_all();
+	if (this->phrq_io == &this->ioInstance)
+	{
+		this->phrq_io->clear_istream();
+		this->phrq_io->close_ostreams();
+	}
+
+	// copy Phreeqc object to this
+	//this->phrq_io = rhs.phrq_io;
+	//this->phrq_io = new PHRQ_io;
+#if !defined(R_SO)
+	this->phrq_io->Set_output_ostream(&std::cout);
+	this->phrq_io->Set_error_ostream(&std::cerr);
+#endif	
+	this->init();
+	this->initialize();
+	this->InternalCopy(&rhs);
+	return *this;
+}
+
+int Phreeqc::next_user_number(Keywords::KEYWORDS key)
+{
+	switch (key)
+	{
+	case Keywords::KEY_REACTION_TEMPERATURE:
+		return Utilities::Rxn_next_user_number(Rxn_temperature_map);
+		break;
+	case Keywords::KEY_REACTION_PRESSURE:
+		return Utilities::Rxn_next_user_number(Rxn_pressure_map);
+		break;
+	case Keywords::KEY_SURFACE:
+		return Utilities::Rxn_next_user_number(Rxn_surface_map);
+		break;
+	case Keywords::KEY_EXCHANGE:
+		return Utilities::Rxn_next_user_number(Rxn_exchange_map);
+		break;
+	case Keywords::KEY_KINETICS:
+		return Utilities::Rxn_next_user_number(Rxn_kinetics_map);
+		break;
+	case Keywords::KEY_MIX:
+		return Utilities::Rxn_next_user_number(Rxn_mix_map);
+		break;
+	case Keywords::KEY_REACTION:
+		return Utilities::Rxn_next_user_number(Rxn_reaction_map);
+		break;
+	case Keywords::KEY_GAS_PHASE:
+		return Utilities::Rxn_next_user_number(Rxn_gas_phase_map);
+		break;
+	case Keywords::KEY_SOLID_SOLUTIONS:
+		return Utilities::Rxn_next_user_number(Rxn_ss_assemblage_map);
+		break;
+	case Keywords::KEY_EQUILIBRIUM_PHASES:
+		return Utilities::Rxn_next_user_number(Rxn_pp_assemblage_map);
+		break;
+	case Keywords::KEY_SOLUTION:
+		return Utilities::Rxn_next_user_number(Rxn_solution_map);
+		break;
+	default:
+		assert(false);
+		return -999;
+	}
+}