Merge commit '1d5c59a175fa4bcc9d525f1feda2cd4b9415143e'

src/phreeqcpp/ChartHandler.cpp

@@ -0,0 +1,227 @@
+// ChartHandler.cpp: implementation of the ChartHandler class.
+//
+//////////////////////////////////////////////////////////////////////
+#if defined MULTICHART
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include "ChartHandler.h"
+#include "phreeqc.h"
+#include <iostream>
+
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+ChartHandler::ChartHandler(PHRQ_io *io)
+:
+PHRQ_base(io)
+	//
+	// default constructor for ChartHandler
+	//
+{
+	current_chart = NULL;
+	current_chart_n_user = -1000;
+	u_g_defined = false;
+	timer = true;
+	active_charts = 0;
+}
+
+ChartHandler::~ChartHandler()
+{
+	std::map<int, ChartObject *>::iterator it;
+	for (it = this->chart_map.begin(); it != chart_map.end(); it++)
+	{
+		delete it->second;
+	}
+}
+void
+ChartHandler::Punch_user_graph(Phreeqc * phreeqc_ptr)
+{
+	std::map<int, ChartObject *>::iterator it = this->chart_map.begin();
+	for ( ; it != chart_map.end(); it++)
+	{
+		if (it->second->Get_active())
+		{
+#if defined(__cplusplus_cli)
+			while (0 != System::Threading::Interlocked::CompareExchange(it->second->usingResource, 4, 0))
+			{
+				System::Threading::Thread::Sleep(5);
+			}
+#endif
+			try
+			{
+				this->current_chart = it->second;
+				phreeqc_ptr-> punch_user_graph();
+			}
+			catch (...)
+			{
+#if defined(__cplusplus_cli)
+				int n = System::Threading::Interlocked::Exchange(it->second->usingResource, 0);
+				assert(n == 4);
+#endif
+				throw;
+			}
+#if defined(__cplusplus_cli)
+			System::Threading::Interlocked::Exchange(it->second->usingResource, 0);
+#endif
+		}
+	}
+}
+
+bool
+ChartHandler::Read(Phreeqc * phreeqc_ptr, CParser &parser)
+{
+	int n_user;
+	std::string token;
+
+	// reads line, next character is after keyword
+	parser.check_line("ChartHandler", true, false, true, false);
+
+	std::istringstream iss(parser.line());
+	// keyword
+	iss >> token;
+	// number
+	if (!(iss >> n_user))
+	{
+		n_user = 1;
+	}
+
+	// makes new ChartObject if necessary
+	std::map<int, ChartObject *>::iterator it = this->chart_map.find(n_user);
+	if (it == this->chart_map.end())
+	{
+		chart_map[n_user] = new ChartObject(this->Get_io());
+		it = this->chart_map.find(n_user);
+		it->second->Set_phreeqc(phreeqc_ptr);
+	}
+
+	// Read/update ChartObject
+#if defined(__cplusplus_cli)
+	while (0 != System::Threading::Interlocked::CompareExchange(it->second->usingResource, 5, 0))
+	{
+		System::Threading::Thread::Sleep(5);
+	}
+#endif
+	try
+	{
+		{
+			it->second->Read(parser);
+			current_chart_n_user = n_user;
+			current_chart = it->second;
+			u_g_defined = true;
+		}
+
+		// if detached, set timer_end and free
+		if (it->second->Get_detach() && it->second->Get_form_started())
+		{
+			it->second->Set_end_timer(true);
+			it->second->Rate_free();
+		}
+	}
+	catch(...)
+	{
+#if defined(__cplusplus_cli)
+		// Release lock
+		int n = System::Threading::Interlocked::Exchange(it->second->usingResource, 0);
+		assert(n == 5);
+		throw;
+#endif
+	}
+#if defined(__cplusplus_cli)
+	// Release lock
+	int n = System::Threading::Interlocked::Exchange(it->second->usingResource, 0);
+	assert(n == 5);
+#endif
+
+	// if detached, wait for thread to acknowledge and then erase chart
+	if (it->second->Get_detach())
+	{
+		while (it->second->Get_form_started() && it->second->Get_done() != true) 
+		{
+#if defined(__cplusplus_cli)
+			System::Threading::Thread::Sleep(5);
+#endif
+		}
+		delete it->second;
+		this->chart_map.erase(it);
+	}	
+	return true;
+}
+bool
+ChartHandler::End_timer()
+{
+	
+	size_t max_tries = 6000; // 1 h, but not used
+	std::map<int, ChartObject *>::iterator it = this->chart_map.begin();
+	if (chart_map.size() > 0) 
+	{
+		screen_msg("Detaching charts...");
+		if (io != NULL)
+		{
+			io->error_flush();
+		}
+	}
+	size_t i(0), i2(0);
+	for  ( ; it != chart_map.end(); it++)
+	{
+		i = 0;
+		it->second->Rate_free();
+		if (it->second->Get_form_started())
+		{
+#if defined(__cplusplus_cli)
+			while (0 != System::Threading::Interlocked::CompareExchange(it->second->usingResource, 6, 0))
+			{
+				//if (i > max_tries) break;
+				i++;
+				System::Threading::Thread::Sleep(60);
+			}
+#endif
+			it->second->Set_end_timer(true);
+			//it->second->Set_phreeqc(NULL);
+#if defined(__cplusplus_cli)
+			int n = System::Threading::Interlocked::Exchange(it->second->usingResource, 0);
+			assert(n == 6);
+#endif
+
+			i2 = 0;
+			while (it->second->Get_done() != true) 
+			{
+				//if (i2 > max_tries) break;
+				i2++;
+#if defined(__cplusplus_cli)
+				System::Threading::Thread::Sleep(60);
+#endif
+			}
+			//if (i >= max_tries || i2 >= max_tries)
+			//{
+			//	error_msg("\nChart did not respond.", CONTINUE);
+			//}
+		}
+	}
+	if (chart_map.size() > 0)
+	{
+		screen_msg("\rCharts detached.         \n");
+		if (io != NULL)
+		{
+			io->error_flush();
+		}
+	}
+	this->timer = false;
+
+	return true;
+}
+bool
+ChartHandler::dump(std::ostream & oss, unsigned int indent)
+{
+	std::map<int, ChartObject *>::iterator it = this->chart_map.begin();
+	for  ( ; it != chart_map.end(); it++)
+	{
+		size_t i = 0;
+		it->second->dump(oss, indent);
+	}
+	return true;
+}
+#endif
+

src/phreeqcpp/ChartHandler.h

@@ -0,0 +1,59 @@
+#if !defined(CHARTHANDLER_H_INCLUDED)
+#define CHARTHANDLER_H_INCLUDED
+#if defined MULTICHART
+#include <vector>
+#include <map>
+#include <string>
+#include "Parser.h"
+#include "ChartObject.h"
+#include "PHRQ_base.h"
+
+class ChartHandler: public PHRQ_base
+{
+
+public:
+	ChartHandler(PHRQ_io *io = NULL);
+	virtual ~ChartHandler();
+
+	size_t Get_chart_count()const
+	{
+		return this->chart_map.size();
+	}
+	ChartObject * Get_current_chart()
+	{
+		return this->current_chart;
+	}
+	const ChartObject * Get_current_chart()const
+	{
+		return this->current_chart;
+	}
+	bool Get_timer()
+	{
+		return timer;
+	}
+	int Get_active_charts() {return this->active_charts;}
+	void Increment_active_charts()
+	{
+		System::Threading::Interlocked::Increment(this->active_charts);
+	}
+	void Decrement_active_charts()
+	{
+		System::Threading::Interlocked::Decrement(this->active_charts);
+	}
+	bool Read(Phreeqc * phreeqc_ptr, CParser &parser);
+	void Punch_user_graph(Phreeqc * phreeqc_ptr);
+	bool End_timer();
+	bool dump(std::ostream & oss, unsigned int indent);
+protected:
+	std::map<int, ChartObject *> chart_map;
+	int current_chart_n_user;
+	ChartObject * current_chart;
+	bool u_g_defined;
+	bool timer;
+	int active_charts;
+
+public:
+
+};
+#endif // MULTICHART
+#endif // !defined(CHARTHANDLER_H_INCLUDED)

src/phreeqcpp/ChartObject.h

@@ -0,0 +1,444 @@
+#if !defined(CHARTOBJECT_H_INCLUDED)
+#define CHARTOBJECT_H_INCLUDED
+#if defined MULTICHART
+#include <vector>
+#include <list>
+#include <string>
+#include <sstream>
+#include "CurveObject.h"
+#include "NumKeyword.h"
+
+#include <float.h>
+class Phreeqc;
+
+class ChartObject:public cxxNumKeyword
+{
+
+  public:
+	ChartObject(PHRQ_io *io=NULL);
+	ChartObject(int i, PHRQ_io *io=NULL);
+	~ChartObject();
+
+	enum chart_batch_type
+	{ ChO_NO_BATCH   = -1, 
+	  ChO_BATCH_ONLY = 0,
+	  ChO_EMF        = 1,
+	  ChO_PNG        = 2, 
+	  ChO_JPG        = 3,
+	  ChO_GIF        = 4,
+	  ChO_TIFF       = 5, 
+	  ChO_BMP        = 6
+	};
+
+	bool Get_new_ug()const
+	{
+		return this->new_ug;
+	}
+	void Set_new_ug(bool b)
+	{
+		this->new_ug = b;
+	}
+	void Set_FirstCallToUSER_GRAPH(bool b)
+	{
+		this->FirstCallToUSER_GRAPH = b;
+	}
+	bool Get_FirstCallToUSER_GRAPH()const
+	{
+		return this->FirstCallToUSER_GRAPH;
+	}
+	int Get_update_time_chart()const
+	{
+		return (this->update_time_chart);
+	}
+	int Get_PanelHeight()const
+	{
+		return (this->PanelHeight);
+	}
+	int Get_PanelWidth()const
+	{
+		return (this->PanelWidth);
+	}
+	std::string &Get_chart_title()
+	{
+		return this->chart_title;
+	}
+	const std::string &Get_chart_title()const
+	{
+		return this->chart_title;
+	}
+	std::string Get_batch_fn()
+	{
+		return this->batch_fn;
+	}
+	void Set_batch_fn(std::string fn)
+	{
+		this->batch_fn = fn;
+	}
+	std::vector<std::string> &Get_axis_titles()
+	{
+		return this->axis_titles;
+	}
+	const std::vector<std::string> &Get_axis_titles()const
+	{
+		return this->axis_titles;
+	}
+	LDBLE *Get_axis_scale_x()
+	{
+		return this->axis_scale_x;
+	}
+	const LDBLE *Get_axis_scale_x()const
+	{
+		return this->axis_scale_x;
+	}
+	LDBLE *Get_axis_scale_y()
+	{
+		return this->axis_scale_y;
+	}
+	const LDBLE *Get_axis_scale_y()const
+	{
+		return this->axis_scale_y;
+	}
+	LDBLE *Get_axis_scale_y2()
+	{
+		return this->axis_scale_y2;
+	}
+	const LDBLE *Get_axis_scale_y2()const
+	{
+		return this->axis_scale_y2;
+	}
+	int Get_chart_type()const
+	{
+		return this->chart_type;
+	}
+	bool Get_graph_initial_solutions()const
+	{
+		return this->graph_initial_solutions;
+	}
+	void Set_graph_initial_solutions(bool val)
+	{
+		this->graph_initial_solutions = val;
+	}
+	bool Get_connect_simulations()const
+	{
+		return this->connect_simulations;
+	}
+	void Set_connect_simulations(bool val)
+	{
+		this->connect_simulations = val;
+	}
+	void Set_colnr(int i)
+	{
+		this->colnr = i;
+	}
+	int Get_colnr()const
+	{
+		return (this->colnr);
+	}
+	void Set_ColumnOffset(int i)
+	{
+		this->ColumnOffset = i;
+	}
+	int Get_ColumnOffset()const
+	{
+		return (this->ColumnOffset);
+	}	
+	void Set_AddSeries(bool b)
+	{
+		this->AddSeries = b;
+	}
+	bool Get_AddSeries()const
+	{
+		return this->AddSeries;
+	}
+	std::vector< std::string > Get_csv_file_names()const
+	{
+		return this->csv_file_names;
+	}
+	void Get_csv_file_names(std::vector< std::string > names)
+	{
+		this->csv_file_names = names;
+	}
+	void Set_prev_advection_step(int i)
+	{
+		this->prev_advection_step = i;
+	}
+	int Get_prev_advection_step()const
+	{
+		return (this->prev_advection_step);
+	}
+	void Set_prev_transport_step(int i)
+	{
+		this->prev_transport_step = i;
+	}
+	int Get_prev_transport_step()const
+	{
+		return (this->prev_transport_step);
+	}
+	void Set_prev_sim_no(int i)
+	{
+		this->prev_sim_no = i;
+	}
+	int Get_prev_sim_no(void)const
+	{
+		return this->prev_sim_no;
+	}
+	void Set_end_timer(bool b)
+	{
+		this->end_timer = b;
+	}
+	bool Get_end_timer()const
+	{
+		return this->end_timer;
+	}
+	void Set_done(bool b)
+	{
+		this->done = b;
+	}
+	bool Get_done()const
+	{
+		return this->done;
+	}
+	std::vector<CurveObject *> &Get_CurvesCSV()
+	{
+		return this->CurvesCSV;
+	}
+	const std::vector<CurveObject *> &Get_CurvesCSV()const
+	{
+		return this->CurvesCSV;
+	}
+	std::vector<CurveObject *> &Get_Curves()
+	{
+		return this->Curves;
+	}
+	const std::vector<CurveObject *> &Get_Curves()const
+	{
+		return this->Curves;
+	}
+	void Set_curve_added(bool tf)
+	{
+		this->curve_added = tf;
+	}
+	bool Get_curve_added()const
+	{
+		return this->curve_added;
+	}
+	void Set_point_added(bool tf)
+	{
+		this->point_added = tf;
+	}
+	bool Get_point_added()const
+	{
+		return this->point_added;
+	}
+	struct rate *Get_user_graph()
+	{
+		return this->user_graph;
+	}
+	const struct rate *Get_user_graph()const
+	{
+		return this->user_graph;
+	}
+	std::list<std::string> &Get_rate_command_list()
+	{
+		return this->rate_command_list;
+	}
+	const std::list<std::string> &Get_rate_command_list()const
+	{
+		return this->rate_command_list;
+	}
+	void Set_rate_new_def(bool tf);
+
+	bool Get_rate_new_def()const
+	{
+		return this->rate_new_def;
+	}
+	void Set_graph_x(LDBLE d)
+	{
+		this->graph_x = d;
+	}
+	LDBLE Get_graph_x()const
+	{
+		return this->graph_x;
+	}
+	std::map<int, LDBLE> &Get_graph_y()
+	{
+		return this->graph_y;
+	}
+	const std::map<int, LDBLE> &Get_graph_y()const
+	{
+		return this->graph_y;
+	}
+	std::map<int, bool> &Get_secondary_y()
+	{
+		return this->secondary_y;
+	}
+	const std::map<int, bool> &Get_secondary_y()const
+	{
+		return this->secondary_y;
+	}
+	std::vector<CurveObject> &Get_new_plotxy_curves()
+	{
+		return this->new_plotxy_curves;
+	}
+	const std::vector<CurveObject> &Get_new_plotxy_curves()const
+	{
+		return this->new_plotxy_curves;
+	}
+	std::vector<std::string> &Get_new_headings()
+	{
+		return this->new_headings;
+	}
+	const std::vector<std::string> &Get_new_headings()const
+	{
+		return this->new_headings;
+	}
+	void Set_active(bool tf)
+	{
+		this->active = tf;
+	}
+	bool Get_active()const
+	{
+		return this->active;
+	}
+	void Set_detach(bool tf)
+	{
+		this->detach = tf;
+	}
+	bool Get_detach()const
+	{
+		return this->detach;
+	}
+	bool Get_form_started()const
+	{
+		return this->form_started;
+	}
+	void Set_phreeqc(Phreeqc * ptr)
+	{
+		this->phreeqc_ptr = ptr;
+	}
+	Phreeqc * Get_phreeqc()
+	{
+		return this->phreeqc_ptr;
+	}
+	const Phreeqc * Get_phreeqc()const
+	{
+		return this->phreeqc_ptr;
+	}
+	const std::list<std::string>& Get_rate_command_list_original()const
+	{
+		return this->rate_command_list_original;
+	}
+	bool Set_axis_scale(std::vector<std::string>, std::vector<int> types, std::ostringstream &);
+	bool Set_axis_scale(CParser & parser);
+	bool Read(CParser & parser);
+	bool OpenCSVFile(std::string fn);
+	static CurveObject ExtractCurveInfo(std::string & str_line);
+	void Set_rate_struct(void);
+	void PlotXY(std::string x, std::string y);
+    bool start_chart(void);
+	ZedGraph::SymbolType Return_SymbolType(std::string);
+	void SaveCurvesToFile(std::string &);
+	void Rate_free(void);
+	void Initialize_graph_pts(void);
+	void Finalize_graph_pts(void);
+	void Get_legal_symbol(std::string &sym);
+	void Get_legal_symbol_csv(std::string &sym);
+	void Get_color_string(std::string &color);
+	void Get_color_string_csv(std::string &color);
+	void Add_new_series(void);
+	void Add_curve(bool plotxy, std::string id = "", 
+					   LDBLE line_width = 1.0, 
+					   std::string symbol = "",
+					   LDBLE symbol_size = 6.0, 
+					   int y_axis = 1,
+					   std::string color = "");
+	void dump(std::ostream & s_oss, unsigned int indent);
+
+	chart_batch_type Get_batch(void) {return this->batch;}
+	void Set_batch(chart_batch_type bt) {this->batch = bt;}
+	bool Get_batch_background(void) {return this->batch_background;}
+	void Set_batch_background(bool tf) {this->batch_background = tf;}
+
+	bool Get_batch_grid(void) {return this->batch_grid;}
+	void Set_batch_grid(bool tf) {this->batch_grid = tf;}
+  protected:
+
+	bool new_ug;
+	bool FirstCallToUSER_GRAPH;
+
+	int update_time_chart;			/* milliseconds, maybe read */
+	int PanelHeight;
+	int PanelWidth;
+	std::map<std::string, int> Symbol_map;
+	std::vector<std::string> Color_vector; 
+	std::string chart_title;
+	std::vector<std::string> axis_titles;
+	LDBLE axis_scale_x[5];
+	LDBLE axis_scale_y[5];
+	LDBLE axis_scale_y2[5];
+
+	int chart_type;
+	bool graph_initial_solutions;
+	bool connect_simulations;
+	int shifts_as_points;
+	int colnr;
+	int ColumnOffset;
+	bool AddSeries;
+	
+	int prev_advection_step;
+	int prev_transport_step;
+
+	int prev_sim_no;
+
+	bool end_timer;
+	bool done;
+
+	std::vector<std::string> csv_file_names;
+	std::vector<CurveObject *> CurvesCSV;
+	std::vector<CurveObject *> Curves;
+	bool curve_added;
+	bool point_added;
+	
+	struct rate *user_graph;
+	// C++ for rate struct
+	std::string rate_name;
+	std::list<std::string> rate_command_list;
+	std::list<std::string> rate_command_list_original;
+	bool rate_new_def;
+
+	int default_symbol;
+	int default_symbol_csv;
+	int default_color;
+	int default_color_csv;
+
+	// temporary storage before stored graph_x/y/sy data are stored in curves
+	// Initialize_graph_pts and Finalize_graph_pts use this storage.
+	LDBLE graph_x;
+	std::map<int, LDBLE> graph_y;
+	std::map<int, bool> secondary_y;
+
+	// temporary plotxy curve definitions before stored in curves
+	// a plotxy curve is copied to Curves when cmdplotxy is encountered
+	// this keeps order correct between plotxy and graph_x/y/sy
+	std::vector<CurveObject> new_plotxy_curves;
+
+	// temporary headings until stored during basic_run
+	std::vector<std::string> new_headings;
+	std::vector<std::string> headings_original;
+	bool active;
+	bool detach;
+	bool form_started;
+	class Phreeqc * phreeqc_ptr;
+
+	bool batch_background;
+	bool batch_grid;
+	std::string batch_fn;
+	chart_batch_type batch;
+	const static std::vector < std::string > vopts;
+
+  public:
+	int usingResource;
+
+};
+#endif // MULTICHART
+#endif // !defined(CHARTOBJECT_H_INCLUDED)

src/phreeqcpp/CurveObject.cpp

@@ -0,0 +1,35 @@
+// CurveObject.cpp: implementation of the CurveObject class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef MULTICHART
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include "CurveObject.h"
+
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+CurveObject::CurveObject()
+	//
+	// default constructor for cxxExchComp
+	//
+{
+	x.clear();
+	y.clear();
+	this->id = "";
+	this->symbol = "";
+	this->color = "";
+	this->y_axis = 1;
+	this->line_w = 1.0;
+	this->symbol_size = 6.0;
+}
+
+
+CurveObject::~CurveObject()
+{
+}
+
+#endif // MULTICHART

src/phreeqcpp/CurveObject.h

@@ -0,0 +1,79 @@
+#if !defined(CURVEOBJECT_H_INCLUDED)
+#define CURVEOBJECT_H_INCLUDED
+#include <vector>
+#include <string>
+#include "phrqtype.h"
+class CurveObject
+{
+
+public:
+	CurveObject();
+	~CurveObject();
+	void Set_id(std::string s)
+	{
+		this->id = s;
+	}
+	std::string &Get_id(void)
+	{
+		return this->id;
+	}
+	void Set_color(std::string s)
+	{
+		this->color = s;
+	}
+	std::string &Get_color(void)
+	{
+		return this->color;
+	}
+	void Set_symbol(std::string s)
+	{
+		this->symbol = s;
+	}
+	std::string &Get_symbol(void)
+	{
+		return this->symbol;
+	}
+	void Set_symbol_size(LDBLE f)
+	{
+		this->symbol_size = f;
+	}
+	LDBLE Get_symbol_size(void)
+	{
+		return this->symbol_size;
+	}
+	void Set_line_w(LDBLE f)
+	{
+		this->line_w = f;
+	}
+	LDBLE Get_line_w(void)
+	{
+		return this->line_w;
+	}
+	void Set_y_axis(int f)
+	{
+		this->y_axis = f;
+	}
+	std::vector<LDBLE> & Get_x()
+	{
+		return this->x;
+	}
+	std::vector<LDBLE> & Get_y()
+	{
+		return this->y;
+	}
+	int Get_y_axis()
+	{
+		return this->y_axis;
+	}
+
+protected:
+	std::vector<LDBLE> x, y;
+	std::string id, color, symbol;
+	int y_axis; 
+	LDBLE line_w, symbol_size;
+
+public:
+
+};
+
+#endif // !defined(CURVEOBJECT_H_INCLUDED)

src/phreeqcpp/Dictionary.cpp

@@ -0,0 +1,32 @@
+#include "Dictionary.h"
+Dictionary::Dictionary(void)
+{
+}
+
+Dictionary::Dictionary(std::string & words_string)
+{
+	std::istringstream words_stream(words_string);
+	char str[256];
+	while (words_stream.getline(str,256))
+	{
+		this->Find(str);
+	}
+}
+Dictionary::~Dictionary(void)
+{
+}
+
+int 
+Dictionary::Find(std::string str)
+{
+	std::map<std::string, int>::iterator it = this->dictionary_map.find(str);
+	if (it != this->dictionary_map.end()) 
+	{
+		return it->second;
+	}
+	int i = this->MapSize();
+	this->dictionary_map[str] = i;
+	this->words.push_back(str);
+	this->dictionary_oss << str << "\n";
+	return i;
+}

src/phreeqcpp/Dictionary.h

@@ -0,0 +1,28 @@
+#if !defined(DICTIONARY_H_INCLUDED)
+#define DICTIONARY_H_INCLUDED
+#include <iostream>
+#include <map>
+#include <vector>
+#include <sstream>
+class Phreeqc;
+class Dictionary
+{
+public:
+	Dictionary(void);
+	Dictionary(std::string & words_string);
+	~Dictionary(void);
+	int Find(std::string str);
+	int MapSize() {return (int) this->dictionary_map.size();}
+	int OssSize() {return (int) this->dictionary_oss.str().size();}
+	std::ostringstream &GetDictionaryOss() {return this->dictionary_oss;}
+	std::vector<std::string> &GetWords() {return this->words;}
+
+protected:
+	std::map<std::string, int> dictionary_map;
+	std::vector<std::string> words;
+	std::ostringstream dictionary_oss;
+
+};
+
+#endif // !defined(DICTIONARY_H_INCLUDED)
+

src/phreeqcpp/ExchComp.cxx

@@ -0,0 +1,450 @@
+// ExchComp.cxx: implementation of the cxxExchComp class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <iostream>				// std::cout std::cerr
+#include <cassert>				// assert
+#include <algorithm>			// std::sort
+#include <float.h>
+
+#include "Utils.h"				// define first
+#include "Phreeqc.h"
+#include "ExchComp.h"
+#include "phqalloc.h"
+#include "Dictionary.h"
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+cxxExchComp::cxxExchComp(PHRQ_io *io)
+	//
+	// default constructor for cxxExchComp 
+	//
+	: PHRQ_base(io)
+{
+	totals.type = cxxNameDouble::ND_ELT_MOLES;
+	la = 0.0;
+	charge_balance = 0.0;
+	phase_proportion = 0.0;
+	formula_z = 0.0;
+}
+#ifdef SKIP
+cxxExchComp::cxxExchComp(std::vector < cxxExchComp > &ec_vector,
+						 std::vector < LDBLE >&f_vector)
+		//
+		// constructor for cxxExchComp from mixing 
+		//
+{
+	if (ec_vector.size() <= 0)
+		return;
+	//
+	//  check consistency
+	//
+	std::vector < LDBLE >::iterator it_f;
+	std::vector < cxxExchComp >::iterator it_ec;
+	// set fixed variables
+	it_ec = ec_vector.begin();
+	this->formula = it_ec->formula;
+	this->formula_totals = it_ec->formula_totals;
+	this->formula_z = it_ec->formula_z;
+	this->phase_name = it_ec->phase_name;
+	this->rate_name = it_ec->rate_name;
+	it_ec++;
+	for (; it_ec != ec_vector.end(); it_ec++)
+	{
+		if (it_ec->formula != this->formula ||
+			it_ec->formula_z != this->formula_z ||
+			it_ec->phase_name != this->phase_name ||
+			this->rate_name != this->rate_name)
+		{
+			error_msg
+				("Mixing exchange components. Formula, z, phase_name, or rate_name did not match",
+				 STOP);
+		}
+	}
+	// calculate sum of extensive factors
+	LDBLE sum_extensive = 0;
+	for (it_f = f_vector.begin(); it_f != f_vector.end(); it_f++)
+	{
+		sum_extensive += *it_f;
+	}
+	this->moles = 0;
+	this->la = 0;
+	this->charge_balance = 0;
+	this->phase_proportion = 0;
+	this->totals.clear();
+	this->totals.type = cxxNameDouble::ND_ELT_MOLES;
+	it_ec = ec_vector.begin();
+	it_f = f_vector.begin();
+	for (; it_ec != ec_vector.end();)
+	{
+		LDBLE extensive = *it_f;
+		LDBLE intensive = extensive / sum_extensive;
+		this->moles += it_ec->moles * extensive;
+		this->la += it_ec->la * intensive;
+		this->charge_balance += it_ec->charge_balance * extensive;
+		this->phase_proportion += it_ec->phase_proportion * intensive;
+		this->totals.add_extensive(it_ec->totals, extensive);
+		it_ec++;
+		it_f++;
+	}
+}
+#endif
+cxxExchComp::~cxxExchComp()
+{
+}
+
+void
+cxxExchComp::dump_xml(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// Exch_Comp element and attributes
+
+	s_oss << indent0 << "formula=\"" << this->formula << "\"" << "\n";
+	s_oss << indent0 << "formula_z=\"" << this->
+		formula_z << "\"" << "\n";
+	s_oss << indent0 << "la=\"" << this->la << "\"" << "\n";
+	s_oss << indent0 << "charge_balance=\"" << this->
+		charge_balance << "\"" << "\n";
+	if (this->phase_name.size() != 0)
+	{
+		s_oss << indent0 << "phase_name=\"" << this->phase_name << "\"" << "\n";
+	}
+	if (this->rate_name.size() != 0)
+	{
+		s_oss << indent0 << "rate_name=\"" << this->
+			rate_name << "\"" << "\n";
+	}
+	s_oss << indent0 << "phase_proportion=\"" << this->
+		phase_proportion << "\"" << "\n";
+
+	// totals
+	s_oss << indent0;
+	s_oss << "<totals " << "\n";
+	this->totals.dump_xml(s_oss, indent + 1);
+}
+
+void
+cxxExchComp::dump_raw(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// Exch_Comp element and attributes
+	//s_oss << indent1 << "# critical values" << "\n";
+
+	// totals
+	s_oss << indent0 << "# EXCHANGE_MODIFY candidate identifiers #\n";
+	s_oss << indent0;
+	s_oss << "-totals" << "\n";
+	this->totals.dump_raw(s_oss, indent + 1);
+
+	s_oss << indent0 << "-charge_balance          " << this->charge_balance << "\n";
+
+	//s_oss << indent1 << "# Noncritical values" << "\n";
+	s_oss << indent0 << "-la                      " << this->la << "\n";
+
+	if (this->phase_name.size() != 0)
+	{
+		s_oss << indent0 << "-phase_name              " << this->phase_name << "\n";
+	}
+	if (this->rate_name.size() != 0)
+	{
+		s_oss << indent0 << "-rate_name               " << this->rate_name << "\n";
+	}
+	s_oss << indent0 << "-phase_proportion        " << this->phase_proportion << "\n";
+	s_oss << indent0 << "-formula_z               " << this->formula_z << "\n";
+}
+
+void
+cxxExchComp::read_raw(CParser & parser, bool check)
+{
+	std::string str;
+
+	std::istream::pos_type ptr;
+	std::istream::pos_type next_char;
+	std::string token;
+	int opt_save;
+
+	opt_save = CParser::OPT_ERROR;
+	bool la_defined(false);
+	bool charge_balance_defined(false);
+	bool formula_z_defined(false);
+
+	for (;;)
+	{
+		int opt = parser.get_option(vopts, next_char);
+		if (opt == CParser::OPT_DEFAULT)
+		{
+			opt = opt_save;
+		}
+
+		switch (opt)
+		{
+		case CParser::OPT_EOF:
+			break;
+		case CParser::OPT_KEYWORD:
+			break;
+		case CParser::OPT_DEFAULT:
+		case CParser::OPT_ERROR:
+			opt = CParser::OPT_KEYWORD;
+			// Allow return to Exchange for more processing
+			break;
+
+		case 0:				// formula
+			warning_msg("-formula ignored. Defined with -component.");
+			break;
+
+		case 1:				// moles
+			parser.warning_msg("-moles is an obsolete identifier");
+			break;
+
+		case 2:				// la
+			if (!(parser.get_iss() >> this->la))
+			{
+				this->la = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for la.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			la_defined = true;
+			break;
+
+		case 3:				// charge_balance
+			if (!(parser.get_iss() >> this->charge_balance))
+			{
+				this->charge_balance = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for charge_balance.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			charge_balance_defined = true;
+			break;
+
+		case 4:				// phase_name
+			if (!(parser.get_iss() >> str))
+			{
+				this->phase_name.clear();
+				parser.incr_input_error();
+				parser.error_msg("Expected string value for phase_name.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			else
+			{
+				this->phase_name = str;
+			}
+			break;
+
+		case 5:				// rate_name
+			if (!(parser.get_iss() >> str))
+			{
+				this->rate_name.clear();
+				parser.incr_input_error();
+				parser.error_msg("Expected string value for rate_name.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			else
+			{
+				this->rate_name = str;
+			}
+			break;
+
+		case 6:				// formula_z
+			if (!(parser.get_iss() >> this->formula_z))
+			{
+				this->formula_z = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for formula_z.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			formula_z_defined = true;
+			break;
+
+		case 7:				// phase_proportion
+			if (!(parser.get_iss() >> this->phase_proportion))
+			{
+				this->phase_proportion = 0;
+				parser.incr_input_error();
+				parser.
+					error_msg("Expected numeric value for phase_proportion.",
+							  PHRQ_io::OT_CONTINUE);
+			}
+			break;
+
+		case 8:				// totals
+			if (this->totals.read_raw(parser, next_char) !=
+				CParser::PARSER_OK)
+			{
+				parser.incr_input_error();
+				parser.
+					error_msg
+					("Expected element name and molality for ExchComp totals.",
+					 PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = 8;
+			break;
+
+		case 9:				// formula_totals
+			parser.warning_msg("-formula_totals is an obsolete identifier");
+			break;
+		}
+		if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
+			break;
+	}
+	if (check)
+	{
+		// members that must be defined
+		if (la_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("La not defined for ExchComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (charge_balance_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Charge_balance not defined for ExchComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (formula_z_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Formula_z not defined for ExchComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+	}
+}
+void
+cxxExchComp::add(const cxxExchComp & addee, LDBLE extensive)
+{
+	LDBLE f1, f2;
+	if (extensive == 0.0)
+		return;
+	if (addee.formula.size() == 0)
+		return;
+	// this and addee must have same formula
+	// otherwise generate a new exchcomp with multiply
+	f1 = 0.5;
+	f2 = 0.5;
+
+	if (this->formula.size() == 0 && addee.formula.size() == 0)
+	{
+		return;
+	}
+	assert(this->formula == addee.formula);
+	assert(this->formula_z == addee.formula_z);
+	if (this->formula.size() == 0 && addee.formula.size() != 0)
+	{
+		this->formula = addee.formula;
+	}
+	this->totals.add_extensive(addee.totals, extensive);
+	this->la = f1 * this->la + f2 * addee.la;
+	this->charge_balance += addee.charge_balance * extensive;
+
+	if (this->phase_name != addee.phase_name)
+	{
+		std::ostringstream oss;
+		oss <<
+			"Cannot mix two exchange components with same formula and different related phases, "
+			<< this->formula;
+		error_msg(oss.str().c_str(), CONTINUE);
+		return;
+	}
+	else if (this->phase_name.size() != 0)
+	{
+		this->phase_proportion =
+			this->phase_proportion * f1 + addee.phase_proportion * f2;
+	}
+	if (this->rate_name != addee.rate_name)
+	{
+		std::ostringstream oss;
+		oss <<
+			"Cannot mix two exchange components with same formula and different related kinetics, "
+			<< this->formula;
+		error_msg(oss.str().c_str(), CONTINUE);
+		return;
+	}
+	else if (this->rate_name.size() != 0)
+	{
+		this->phase_proportion =
+			this->phase_proportion * f1 + addee.phase_proportion * f2;
+	}
+	if ((this->rate_name.size() != 0 && addee.phase_name.size() != 0) ||
+		(this->phase_name.size() != 0 && addee.rate_name.size() != 0))
+	{
+		std::ostringstream oss;
+		oss <<
+			"Cannot mix exchange components related to phase with exchange components related to kinetics, "
+			<< this->formula;
+		error_msg(oss.str().c_str(), CONTINUE);
+		return;
+	}
+}
+void
+cxxExchComp::multiply(LDBLE extensive)
+{ 
+	this->totals.multiply(extensive);
+	this->charge_balance *= extensive;  
+	this->phase_proportion *= extensive;
+}
+
+void
+cxxExchComp::Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles)
+{
+	ints.push_back(dictionary.Find(this->formula));
+	this->totals.Serialize(dictionary, ints, doubles);
+	doubles.push_back(this->la);
+	doubles.push_back(this->charge_balance);
+	ints.push_back(dictionary.Find(this->phase_name));
+	doubles.push_back(this->phase_proportion);
+	ints.push_back(dictionary.Find(this->rate_name));
+	doubles.push_back(this->formula_z);
+}
+
+void
+cxxExchComp::Deserialize(Dictionary & dictionary, std::vector < int >&ints, 
+	std::vector < double >&doubles, int &ii, int &dd)
+{
+	this->formula = dictionary.GetWords()[ints[ii++]];
+	this->totals.Deserialize(dictionary, ints, doubles, ii, dd);
+	this->la = doubles[dd++];
+	this->charge_balance = doubles[dd++];
+	this->phase_name = dictionary.GetWords()[ints[ii++]];
+	this->phase_proportion = doubles[dd++];
+	this->rate_name = dictionary.GetWords()[ints[ii++]];
+	this->formula_z = doubles[dd++];
+}
+
+
+const std::vector< std::string >::value_type temp_vopts[] = {
+	std::vector< std::string >::value_type("formula"),	            // 0 
+	std::vector< std::string >::value_type("moles"),	            // 1
+	std::vector< std::string >::value_type("la"),	                // 2 
+	std::vector< std::string >::value_type("charge_balance"),	    // 3 
+	std::vector< std::string >::value_type("phase_name"),	        // 4 
+	std::vector< std::string >::value_type("rate_name"),	        // 5 
+	std::vector< std::string >::value_type("formula_z"),	        // 6
+	std::vector< std::string >::value_type("phase_proportion"),	    // 7 
+	std::vector< std::string >::value_type("totals"),	            // 8
+	std::vector< std::string >::value_type("formula_totals")	    // 9	
+};									   
+const std::vector< std::string > cxxExchComp::vopts(temp_vopts, temp_vopts + sizeof temp_vopts / sizeof temp_vopts[0]);

src/phreeqcpp/ExchComp.h

@@ -0,0 +1,125 @@
+#if !defined(EXCHCOMP_H_INCLUDED)
+#define EXCHCOMP_H_INCLUDED
+
+#include <cassert>				// assert
+#include <map>					// std::map
+#include <string>				// std::string
+#include <list>					// std::list
+#include <vector>				// std::vector
+
+#include "NameDouble.h"
+
+class cxxExchComp: public PHRQ_base
+{
+
+  public:
+	cxxExchComp(PHRQ_io *io=NULL);
+	virtual ~cxxExchComp();
+
+	void dump_xml(std::ostream & os, unsigned int indent = 0) const;
+
+	void dump_raw(std::ostream & s_oss, unsigned int indent) const;
+
+	void read_raw(CParser & parser, bool check=true);
+
+	const std::string &Get_formula() const
+	{
+		return this->formula;
+	}
+	void Set_formula(const char *cstring)
+	{
+		if (cstring != NULL)
+			this->formula = std::string(cstring);
+		else
+			this->formula.clear();
+	}
+	LDBLE Get_la() const
+	{
+		return this->la;
+	}
+	void Set_la(LDBLE d)
+	{
+		this->la = d;
+	}
+	LDBLE Get_charge_balance() const
+	{
+		return this->charge_balance;
+	}
+	void Set_charge_balance(LDBLE d)
+	{
+		this->charge_balance = d;
+	}
+	const std::string &Get_phase_name() const
+	{
+		return this->phase_name;
+	}
+	void Set_phase_name(const char *cstring)
+	{
+		if (cstring != NULL)
+			this->phase_name = std::string(cstring);
+		else
+			this->phase_name.clear();
+	}
+	LDBLE Get_phase_proportion() const
+	{
+		return this->phase_proportion;
+	}
+	void Set_phase_proportion(LDBLE d)
+	{
+		this->phase_proportion = d;
+	}
+	const std::string &Get_rate_name() const
+	{
+		return this->rate_name;
+	}
+	void Set_rate_name(const char *cstring)
+	{
+		if (cstring != NULL)
+			this->rate_name = std::string(cstring);
+		else
+			this->rate_name.clear();
+	}
+	LDBLE Get_formula_z() const
+	{
+		return this->formula_z;
+	}
+	void Set_formula_z(LDBLE d)
+	{
+		this->formula_z = d;
+	}
+	void Set_totals(struct elt_list *e_l, int count)
+	{
+		this->totals = cxxNameDouble(e_l, count);
+	}
+	void Set_totals(struct elt_list *e_l)
+	{
+		this->totals = cxxNameDouble(e_l);
+	}
+	void Set_totals(cxxNameDouble nd)
+	{
+		this->totals = nd;
+	}
+	cxxNameDouble & Get_totals() {return (this->totals);}
+	const cxxNameDouble & Get_totals()const {return (this->totals);}
+
+	void add(const cxxExchComp & comp, LDBLE extensive);
+	void multiply(LDBLE extensive);
+	void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
+	void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
+
+protected:
+	std::string formula;
+	// EXCHANGE_MODIFY candidates
+	cxxNameDouble totals;
+	LDBLE la;
+	LDBLE charge_balance;
+	std::string phase_name;
+	LDBLE phase_proportion;
+	std::string rate_name;
+	LDBLE formula_z;			// charge on formula
+	const static std::vector < std::string > vopts;
+  public:
+
+};
+
+#endif // !defined(EXCHCOMP_H_INCLUDED)

src/phreeqcpp/Exchange.cxx

@@ -0,0 +1,492 @@
+// Exchange.cxx: implementation of the cxxExchange class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <iostream>				// std::cout std::cerr
+#include <cassert>				// assert
+#include <algorithm>			// std::sort
+
+#include "Utils.h" // define first
+
+#include "Phreeqc.h"
+#include "cxxMix.h"
+#include "Exchange.h"
+#include "phqalloc.h"
+
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+cxxExchange::cxxExchange(PHRQ_io *io)
+	//
+	// default constructor for cxxExchange
+	//
+:	cxxNumKeyword(io)
+{
+	new_def = false;
+	solution_equilibria = false;
+	n_solution = -999;
+	pitzer_exchange_gammas = true;
+}
+cxxExchange::cxxExchange(const std::map < int, cxxExchange > &entities,
+						 cxxMix & mix, int l_n_user, PHRQ_io *io):
+cxxNumKeyword(io)
+{
+	this->n_user = this->n_user_end = l_n_user;
+	this->pitzer_exchange_gammas = true;
+	this->new_def = false;
+	this->n_solution = -999;
+//
+//   Mix exchangers
+//
+	const std::map < int, LDBLE >&mixcomps = mix.Get_mixComps();
+	std::map < int, LDBLE >::const_iterator it;
+	for (it = mixcomps.begin(); it != mixcomps.end(); it++)
+	{
+		if (entities.find(it->first) != entities.end())
+		{
+			const cxxExchange *entity_ptr =
+				&(entities.find(it->first)->second);
+			this->add(*entity_ptr, it->second);
+			this->pitzer_exchange_gammas = entity_ptr->pitzer_exchange_gammas;
+		}
+	}
+}
+
+
+cxxExchange::~cxxExchange()
+{
+}
+bool
+cxxExchange::Get_related_phases() const
+{
+	for (size_t i = 0; i < this->exchange_comps.size(); i++)
+	{
+		if (this->exchange_comps[i].Get_phase_name().size() > 0)
+		{
+			return (true);
+		}
+	}
+	return (false);
+}
+
+bool
+cxxExchange::Get_related_rate() const
+{
+	for (size_t i = 0; i < this->exchange_comps.size(); i++)
+	{
+		if (this->exchange_comps[i].Get_rate_name().size() > 0)
+		{
+			return (true);
+		}
+	}
+	return (false);
+}
+
+void
+cxxExchange::dump_xml(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// Exchange element and attributes
+	s_oss << indent0;
+	s_oss << "<exchange " << "\n";
+
+	s_oss << indent1;
+	s_oss << "pitzer_exchange_gammas=\"" << this->
+		pitzer_exchange_gammas << "\"" << "\n";
+
+	// components
+	s_oss << indent1;
+	s_oss << "<component " << "\n";
+	for (size_t j = 0; j < this->exchange_comps.size(); j++)
+	{
+		this->exchange_comps[j].dump_xml(s_oss, indent + 2);
+	}
+
+	return;
+}
+#ifdef SKIP
+void
+cxxExchange::dump_xml(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// Exchange element and attributes
+	s_oss << indent0;
+	s_oss << "<exchange " << "\n";
+
+	s_oss << indent1;
+	s_oss << "pitzer_exchange_gammas=\"" << this->
+		pitzer_exchange_gammas << "\"" << "\n";
+
+	// components
+	s_oss << indent1;
+	s_oss << "<component " << "\n";
+	for (std::map < std::string, cxxExchComp >::const_iterator it = exchComps.begin();
+		 it != exchComps.end(); ++it)
+	{
+		(*it).second.dump_xml(s_oss, indent + 2);
+	}
+
+	return;
+}
+#endif
+void
+cxxExchange::dump_raw(std::ostream & s_oss, unsigned int indent, int *n_out) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// Exchange element and attributes
+	s_oss << indent0;
+	int n_user_local = (n_out != NULL) ? *n_out : this->n_user;
+	s_oss << "EXCHANGE_RAW                 " << n_user_local << " " << this->description << "\n";
+
+	s_oss << indent1 << "# EXCHANGE_MODIFY candidate identifiers #\n";
+	s_oss << indent1;
+	s_oss << "-exchange_gammas           " << (this->pitzer_exchange_gammas ? 1 : 0) << "\n";
+	// exchComps 
+	for (size_t i = 0; i < this->exchange_comps.size(); i++)
+	{
+		s_oss << indent1;
+		s_oss << "-component                 " << this->exchange_comps[i].Get_formula() << "\n";
+		this->exchange_comps[i].dump_raw(s_oss, indent + 2);
+	}
+
+	s_oss << indent1 << "# EXCHANGE_MODIFY candidates with new_def=true #\n";
+	s_oss << indent1;
+	s_oss << "-new_def                   " << 0 << "\n";
+	s_oss << indent1;
+	s_oss << "-solution_equilibria       " << 0 << "\n";
+	s_oss << indent1;
+	s_oss << "-n_solution                " << this->n_solution << "\n";
+
+	s_oss << indent1 << "# Exchange workspace variables #\n";
+	s_oss << indent1;
+	s_oss << "-totals" << "\n";
+	this->totals.dump_raw(s_oss, indent + 1);
+
+	return;
+}
+void
+cxxExchange::read_raw(CParser & parser, bool check)
+{
+	std::istream::pos_type ptr;
+	std::istream::pos_type next_char;
+	std::string token;
+	bool useLastLine(false);
+
+	// Read exchange number and description
+	this->read_number_description(parser);
+	this->Set_new_def(false);
+	
+	bool pitzer_exchange_gammas_defined(false);
+
+	for (;;)
+	{
+		int opt;
+		if (useLastLine == false)
+		{
+			opt = parser.get_option(vopts, next_char);
+		}
+		else
+		{
+			opt = parser.getOptionFromLastLine(vopts, next_char, true);
+		}
+		useLastLine = false;
+		switch (opt)
+		{
+		case CParser::OPT_EOF:
+			break;
+		case CParser::OPT_KEYWORD:
+			break;
+		case CParser::OPT_DEFAULT:
+		case CParser::OPT_ERROR:
+			opt = CParser::OPT_EOF;
+			parser.error_msg("Unknown input in EXCH_COMP_RAW keyword.",
+							 PHRQ_io::OT_CONTINUE);
+			parser.error_msg(parser.line().c_str(), PHRQ_io::OT_CONTINUE);
+			break;
+
+		case 0:				// pitzer_exchange_gammas
+		case 2:				// exchange_gammas
+			if (!(parser.get_iss() >> this->pitzer_exchange_gammas))
+			{
+				this->pitzer_exchange_gammas = false;
+				parser.incr_input_error();
+				parser.
+					error_msg
+					("Expected boolean value for pitzer_exchange_gammas.",
+					 PHRQ_io::OT_CONTINUE);
+			}
+			pitzer_exchange_gammas_defined = true;
+			break;
+		case 1:				// component
+			{
+				std::string str;
+				if (!(parser.get_iss() >> str))
+				{
+					parser.incr_input_error();
+					parser.error_msg("Expected string value for component name.",
+									 PHRQ_io::OT_CONTINUE);
+				}
+				else
+				{
+					cxxExchComp temp_comp(this->io);
+					temp_comp.Set_formula(str.c_str());
+					cxxExchComp *comp_ptr = this->Find_comp(str);
+					if (comp_ptr)
+					{
+						temp_comp = *comp_ptr;
+					}
+					temp_comp.read_raw(parser, check);
+					if (comp_ptr)
+					{
+						for (size_t j = 0; j < this->exchange_comps.size(); j++)
+						{
+							if (Utilities::strcmp_nocase(this->exchange_comps[j].Get_formula().c_str(), str.c_str()) == 0)
+							{
+								this->exchange_comps[j] = temp_comp;
+							}
+						}
+					}
+					else
+					{
+						this->exchange_comps.push_back(temp_comp);
+					}
+					useLastLine = true;
+				}
+			}
+			break;
+		case 3:				// new_def
+			if (!(parser.get_iss() >> this->new_def))
+			{
+				this->new_def = false;
+				parser.incr_input_error();
+				parser.
+					error_msg
+					("Expected boolean value for new_def.",
+					 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+		case 4:				// solution_equilibria
+			if (!(parser.get_iss() >> this->solution_equilibria))
+			{
+				this->solution_equilibria = false;
+				parser.incr_input_error();
+				parser.
+					error_msg
+					("Expected boolean value for solution_equilibria.",
+					 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+		case 5:				// n_solution
+			if (!(parser.get_iss() >> this->n_solution))
+			{
+				this->n_solution = -999;
+				parser.incr_input_error();
+				parser.
+					error_msg
+					("Expected integer value for n_solution.",
+					 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+		case 6:				// totals
+			if (this->totals.read_raw(parser, next_char) !=
+				CParser::PARSER_OK)
+			{
+				parser.incr_input_error();
+				parser.
+					error_msg
+					("Expected element name and molality for Exchange totals.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			break;
+		}
+		if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
+			break;
+	}
+	// members that must be defined
+	if (check)
+	{
+		if (pitzer_exchange_gammas_defined == false)
+		{
+			parser.incr_input_error();
+			parser.
+				error_msg
+				("Pitzer_exchange_gammsa not defined for EXCHANGE_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+	}
+	this->Sort_comps();
+}
+void
+cxxExchange::add(const cxxExchange & addee, LDBLE extensive)
+		//
+		// Add existing exchange to "this" exchange
+		//
+{
+	// exchComps
+	if (extensive == 0.0)
+		return;
+	for (size_t i = 0; i < addee.exchange_comps.size(); i++)
+	{
+		size_t j;
+		for (j = 0; j < this->Get_exchange_comps().size(); j++)
+		if (addee.exchange_comps[i].Get_formula() == this->exchange_comps[j].Get_formula())
+		{
+			this->exchange_comps[j].add(addee.exchange_comps[i], extensive);
+			break;
+		}
+		if (j == this->exchange_comps.size())
+		{
+			cxxExchComp exc = addee.exchange_comps[i];
+			exc.multiply(extensive);
+			this->exchange_comps.push_back(exc);
+		}
+	}
+	this->pitzer_exchange_gammas = addee.pitzer_exchange_gammas;
+}
+void
+cxxExchange::totalize()
+{
+	this->totals.clear();
+	// component structures
+	for (size_t i = 0; i < this->exchange_comps.size(); i++)
+	{
+		this->totals.add_extensive(this->exchange_comps[i].Get_totals(), 1.0);
+		this->totals.add("Charge", this->exchange_comps[i].Get_charge_balance());
+	}
+	return;
+}
+bool 
+cxxExchange::Get_pitzer_exchange_gammas() const
+{
+	return this->pitzer_exchange_gammas;
+}
+void 
+cxxExchange::Set_pitzer_exchange_gammas(bool b)
+{
+	this->pitzer_exchange_gammas = b;
+}
+const cxxNameDouble & 
+cxxExchange::Get_totals() const
+{
+	return totals;
+}
+cxxExchComp *cxxExchange::Find_comp(std::string s)
+{
+	for (size_t i = 0; i < this->exchange_comps.size(); i++)
+	{
+		cxxNameDouble nd(this->exchange_comps[i].Get_totals());
+		cxxNameDouble::iterator nd_it;
+		for (nd_it = nd.begin(); nd_it != nd.end(); nd_it++)
+		{
+			if(nd_it->first == s)
+			{
+				return (&(this->exchange_comps[i]));
+			}
+		}
+	}
+	return NULL;
+}
+void cxxExchange::
+Sort_comps(void)
+{
+	// sort comps
+	{
+		std::map<std::string, cxxExchComp> comp_map;
+		for (size_t i = 0; i < this->exchange_comps.size(); i++)
+		{
+			comp_map[this->exchange_comps[i].Get_formula()] = this->exchange_comps[i];
+		}
+		this->exchange_comps.clear();
+		std::map<std::string, cxxExchComp>::iterator it;
+		for (it = comp_map.begin(); it != comp_map.end(); it++)
+		{
+			this->exchange_comps.push_back(it->second);
+		}
+	}
+}
+/* ---------------------------------------------------------------------- */
+void
+cxxExchange::Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles)
+/* ---------------------------------------------------------------------- */
+{
+	ints.push_back(this->n_user);
+	ints.push_back((int) this->exchange_comps.size());
+	for (size_t i = 0; i < this->exchange_comps.size(); i++)
+	{
+		exchange_comps[i].Serialize(dictionary, ints, doubles);
+	}
+	ints.push_back(this->pitzer_exchange_gammas ? 1 : 0);
+	ints.push_back(this->new_def ? 1 : 0);
+	ints.push_back(this->solution_equilibria ? 1 : 0);
+	ints.push_back(this->n_solution);
+	this->totals.Serialize(dictionary, ints, doubles);
+
+}
+
+/* ---------------------------------------------------------------------- */
+void
+cxxExchange::Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd)
+/* ---------------------------------------------------------------------- */
+{
+	this->n_user = ints[ii++];
+	this->n_user_end = this->n_user;
+	this->description = " ";
+
+	int count = ints[ii++];
+	this->exchange_comps.clear();
+	for (int n = 0; n < count; n++)
+	{
+		cxxExchComp ec;
+		ec.Deserialize(dictionary, ints, doubles, ii, dd);
+		this->exchange_comps.push_back(ec);
+	}
+	this->pitzer_exchange_gammas = (ints[ii++] != 0);
+	this->new_def = (ints[ii++] != 0);
+	this->solution_equilibria = (ints[ii++] != 0);
+	this->n_solution = ints[ii++];
+	this->totals.Deserialize(dictionary, ints, doubles, ii, dd);
+
+}
+
+
+const std::vector< std::string >::value_type temp_vopts[] = {
+	std::vector< std::string >::value_type("pitzer_exchange_gammas"),   // 0
+	std::vector< std::string >::value_type("component"),		        // 1
+	std::vector< std::string >::value_type("exchange_gammas"),	        // 2
+	std::vector< std::string >::value_type("new_def"),		            // 3
+	std::vector< std::string >::value_type("solution_equilibria"),	    // 4
+	std::vector< std::string >::value_type("n_solution"),		        // 5
+	std::vector< std::string >::value_type("totals")		            // 6
+};									   
+const std::vector< std::string > cxxExchange::vopts(temp_vopts, temp_vopts + sizeof temp_vopts / sizeof temp_vopts[0]);

src/phreeqcpp/Exchange.h

@@ -0,0 +1,74 @@
+#if !defined(EXCHANGE_H_INCLUDED)
+#define EXCHANGE_H_INCLUDED
+
+#include <cassert>				// assert
+#include <map>					// std::map
+#include <string>				// std::string
+#include <list>					// std::list
+#include "NumKeyword.h"
+#include "ExchComp.h"
+#include "NameDouble.h"
+#include "PHRQ_base.h"
+class cxxMix;
+
+class cxxExchange:public cxxNumKeyword
+{
+
+public:
+	cxxExchange(PHRQ_io *io=NULL);
+	cxxExchange(const std::map < int, cxxExchange > &exchange_map,
+		cxxMix & mx, int n_user, PHRQ_io *io=NULL);
+	~cxxExchange();
+
+	void dump_raw(std::ostream & s_oss, unsigned int indent, int *n_out=NULL) const;
+
+	void read_raw(CParser & parser, bool check = true);
+
+	bool Get_related_phases(void) const;
+
+	bool Get_related_rate(void) const;
+
+	bool Get_pitzer_exchange_gammas() const;
+	void Set_pitzer_exchange_gammas(bool b);
+
+	bool Get_new_def(void) const {return this->new_def;}
+	void Set_new_def(bool tf) {this->new_def = tf;}
+	bool Get_solution_equilibria(void) const {return this->solution_equilibria;}
+	void Set_solution_equilibria(bool tf) {this->solution_equilibria = tf;}
+	int Get_n_solution(void) const {return this->n_solution;}
+	void Set_n_solution(int i) {this->n_solution = i;}
+	cxxExchComp *Find_comp(std::string s);
+	std::vector<cxxExchComp> & Get_exchange_comps(void) {return this->exchange_comps;}
+	const std::vector<cxxExchComp> & Get_exchange_comps(void)const {return this->exchange_comps;}
+	void Set_exchange_comps(std::vector<cxxExchComp> &c) {this->exchange_comps = c;}
+
+	void Sort_comps(void);
+	void totalize();
+
+	const cxxNameDouble & Get_totals() const;
+	void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
+	void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
+
+protected:
+	void add(const cxxExchange & addee, LDBLE extensive);
+	// not written
+	void dump_xml(std::ostream & os, unsigned int indent = 0) const;
+
+protected:
+	// EXCHANGE_MODIFY candidates
+	std::vector<cxxExchComp> exchange_comps;
+	bool pitzer_exchange_gammas;
+
+	// EXCHANGE_MODIFY candidates with new_def=true
+	bool new_def;
+	bool solution_equilibria;
+	int n_solution;
+
+	// exchange workspace variables
+	cxxNameDouble totals;
+	const static std::vector < std::string > vopts;
+public:
+
+};
+
+#endif // !defined(EXCHANGE_H_INCLUDED)

src/phreeqcpp/Form1.2005.resX

@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="utf-8"?>
+<root>
+  <!-- In Managed Resources,
+       set Resource File Name:
+          $(IntDir)\zdg_ui2.$(InputName).resources
+    -->
+  <resheader name="resmimetype">
+    <value>text/microsoft-resx</value>
+  </resheader>
+  <resheader name="version">
+    <value>2.0</value>
+  </resheader>
+  <resheader name="reader">
+    <value>System.Resources.ResXResourceReader, System.Windows.Forms, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089</value>
+  </resheader>
+  <resheader name="writer">
+    <value>System.Resources.ResXResourceWriter, System.Windows.Forms, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089</value>
+  </resheader>
+  <metadata name="imageList1.TrayLocation" type="System.Drawing.Point, System.Drawing, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a">
+    <value>17, 17</value>
+  </metadata>
+  <assembly alias="System.Drawing" name="System.Drawing, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a" />
+  <data name="$this.Icon" type="System.Drawing.Icon, System.Drawing" mimetype="application/x-microsoft.net.object.bytearray.base64">
+    <value>
+        AAABAAEAEBAQAAEABAAoAQAAFgAAACgAAAAQAAAAIAAAAAEABAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+        AAAAAP8AMzOaAGgymgA0Mc0AmWVoAGdlmwBjZssAy5kvAP+ZNQDLmmMAzpmVAP/MLQDLzWUA/8xjAP3/
+        mAAAAAAAiIiIiIiIiIiIgAAIhIiIhHAAAAB3KXcXcAeQAAeTk5fQDd0ADdoK3b27uwALugm7u7u7AAtz
+        k9vbuwAAu2u7Xbu7AAva29u5zMzAAMzMzMzu7u4ADu7szOAO7gAO7u7u4ADuAA7u7u7uAAAA7u7u7u7g
+        AA7u7u7u7u7u7u7u7u4AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+        AAAAAAAAAAAAAAAAAAAAAAAA
+</value>
+  </data>
+</root>

src/phreeqcpp/Form1.resX

@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="utf-8"?>
+<root>
+  <!-- In Managed Resources,
+       set Resource File Name:
+          $(IntDir)\zdg_ui2.$(InputName).resources
+          in VS2012: compile with resgen.exe:
+          click Start, All Programs, Visual Studio 20**, Visual Studio Tools, Visual Studio Command Prompt
+          resgen path**.Form1.resX
+    -->
+  <resheader name="resmimetype">
+    <value>text/microsoft-resx</value>
+  </resheader>
+  <resheader name="version">
+    <value>2.0</value>
+  </resheader>
+  <resheader name="reader">
+    <value>System.Resources.ResXResourceReader, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089</value>
+  </resheader>
+  <resheader name="writer">
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src/phreeqcpp/GasComp.cxx

@@ -0,0 +1,208 @@
+// GasComp.cxx: implementation of the cxxGasComp class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <iostream>				// std::cout std::cerr
+#include <cassert>				// assert
+#include <algorithm>			// std::sort
+#include <float.h>
+
+#include "Utils.h"				// define first
+#include "Phreeqc.h"
+#include "GasComp.h"
+#include "phqalloc.h"
+#include "Dictionary.h"
+
+
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+cxxGasComp::cxxGasComp(PHRQ_io *io)
+	//
+	// default constructor for cxxExchComp 
+	//
+	: PHRQ_base(io)
+{
+	p_read = 0.0;
+	moles = 0.0;
+	initial_moles = 0.0;
+}
+
+cxxGasComp::~cxxGasComp()
+{
+}
+
+void
+cxxGasComp::dump_raw(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+	s_oss << indent0 << "# GAS_PHASE_MODIFY candidate identifiers #\n";
+	s_oss << indent0 << "-moles                   " << this->moles << "\n";
+
+	s_oss << indent0 << "# GAS_PHASE_MODIFY candidate identifiers with new_def=true #\n";
+	s_oss << indent0 << "-p_read                  " << this->p_read << "\n";
+
+	s_oss << indent0 << "# GasComp workspace variables #\n";
+	s_oss << indent0 << "-initial_moles           " << this->initial_moles << "\n";
+}
+
+bool
+cxxGasComp::read_raw(CParser & parser, bool check)
+{
+	std::string str;
+
+	int errors = parser.get_input_error();
+
+	std::istream::pos_type ptr;
+	std::istream::pos_type next_char;
+	std::string token;
+
+	bool moles_defined(false);
+	int opt;
+	for (;;)
+	{
+		opt = parser.get_option(vopts, next_char);
+
+		switch (opt)
+		{
+		case CParser::OPT_EOF:
+			break;
+		case CParser::OPT_KEYWORD:
+			break;
+		case CParser::OPT_DEFAULT:
+		case CParser::OPT_ERROR:
+			opt = CParser::OPT_KEYWORD;
+			// Allow return to Exchange for more processing
+			break;
+
+		case 0:				// phase_name
+			output_msg("-phase_name is obsolete. Define with -component\n");
+			break;
+
+		case 1:				// name
+			output_msg("-name is obsolete. Define with -component\n");
+			break;
+
+		case 2:				// p_read
+			if (!(parser.get_iss() >> this->p_read))
+			{
+				this->p_read = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for initial partial pressure.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+
+		case 3:				// moles
+			if (!(parser.get_iss() >> this->moles))
+			{
+				this->moles = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for moles.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			moles_defined = true;
+			break;
+
+		case 4:				// initial_moles
+			if (!(parser.get_iss() >> this->initial_moles))
+			{
+				this->initial_moles = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for initial_moles.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+		}
+		if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
+			break;
+	}
+	if (check)
+	{
+		// members that must be defined
+		if (moles_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Moles not defined for GasComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+	}
+	return (parser.get_input_error() == errors);
+}
+void
+cxxGasComp::add(const cxxGasComp & addee, LDBLE extensive)
+{
+	//LDBLE ext1, ext2;
+	if (extensive == 0.0)
+		return;
+	if (addee.phase_name.size() == 0)
+		return;
+
+	/*
+	ext1 = this->moles;
+	ext2 = addee.moles * extensive;
+	if (ext1 + ext2 != 0)
+	{
+		f1 = ext1 / (ext1 + ext2);
+		f2 = ext2 / (ext1 + ext2);
+	}
+	else
+	{
+		f1 = 0.5;
+		f2 = 0.5;
+	}
+	*/
+
+	assert(this->phase_name == addee.phase_name);
+
+	this->p_read += addee.p_read * extensive;
+	this->moles += addee.moles * extensive;
+	this->initial_moles += addee.initial_moles * extensive;
+}
+
+void
+cxxGasComp::multiply(LDBLE extensive)
+{
+	this->p_read *= extensive;
+	this->moles *= extensive;
+	this->initial_moles *= extensive;
+}
+void
+cxxGasComp::Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles)
+{
+	ints.push_back(dictionary.Find(this->phase_name));
+	doubles.push_back(this->moles);
+	doubles.push_back(this->p_read);
+	doubles.push_back(this->initial_moles);
+}
+
+void
+cxxGasComp::Deserialize(Dictionary & dictionary, std::vector < int >&ints, 
+	std::vector < double >&doubles, int &ii, int &dd)
+{
+	this->phase_name = dictionary.GetWords()[ints[ii++]];
+	this->moles = doubles[dd++];
+	this->p_read = doubles[dd++];
+	this->initial_moles = doubles[dd++];
+}
+
+const std::vector< std::string >::value_type temp_vopts[] = {
+	std::vector< std::string >::value_type("phase_name"),	// 0 
+	std::vector< std::string >::value_type("name"),	        // 1
+	std::vector< std::string >::value_type("p_read"),	    // 2 
+	std::vector< std::string >::value_type("moles"),	    // 3 
+	std::vector< std::string >::value_type("initial_moles")	// 4 
+};									   
+const std::vector< std::string > cxxGasComp::vopts(temp_vopts, temp_vopts + sizeof temp_vopts / sizeof temp_vopts[0]);	

src/phreeqcpp/GasComp.h

@@ -0,0 +1,50 @@
+#if !defined(GASCOMP_H_INCLUDED)
+#define GASCOMP_H_INCLUDED
+
+#include <cassert>				// assert
+#include <map>					// std::map
+#include <string>				// std::string
+#include <list>					// std::list
+#include <vector>				// std::vector
+
+#include "NameDouble.h"
+
+class cxxGasComp: public PHRQ_base
+{
+
+  public:
+	cxxGasComp(PHRQ_io *io=NULL);
+
+	virtual ~cxxGasComp();
+
+
+	void dump_raw(std::ostream & s_oss, unsigned int indent) const;
+
+	bool read_raw(CParser & parser, bool check=true);
+
+	std::string Get_phase_name(void) const {return this->phase_name;}
+	void Set_phase_name(std::string s) {this->phase_name = s;}
+	LDBLE Get_p_read() const {return this->p_read;}
+	void Set_p_read(LDBLE t) {this->p_read = t;}
+	LDBLE Get_moles() const {return this->moles;}
+	void Set_moles(LDBLE t) {this->moles = t;}
+	LDBLE Get_initial_moles() const {return this->initial_moles;}
+	void Set_initial_moles(LDBLE t) {this->initial_moles = t;}
+
+	void add(const cxxGasComp & addee, LDBLE extensive);
+	void multiply(LDBLE extensive);
+	void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
+	void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
+	
+  protected:
+	std::string phase_name;
+	// GAS_PHASE_MODIFY candidates
+	LDBLE moles;
+	// GAS_PHASE_MODIFY candidates with new_def=true
+	LDBLE p_read;
+	// internal workspace
+	LDBLE initial_moles;
+	const static std::vector < std::string > vopts;
+};
+
+#endif // !defined(GASCOMP_H_INCLUDED)

src/phreeqcpp/GasPhase.cxx

@@ -0,0 +1,729 @@
+// GasPhase.cxx: implementation of the cxxGasPhase class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <cassert>				// assert
+#include <algorithm>			// std::sort
+#include <float.h>
+
+#include "Utils.h"				// define first
+#include "Phreeqc.h"
+#include "GasPhase.h"
+#include "cxxMix.h"
+#include "phqalloc.h"
+
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+cxxGasPhase::cxxGasPhase(PHRQ_io * io)
+	//
+	// default constructor for cxxGasPhase 
+	//
+:	cxxNumKeyword(io)
+{
+	new_def = false;
+	solution_equilibria = false;
+	n_solution = -999;
+	type = cxxGasPhase::GP_PRESSURE;
+	total_p = 1.0;
+	total_moles = 0.0;
+	volume = 1.0;
+	v_m = 0;
+	pr_in = false;
+	temperature = 298.15;
+}
+#ifdef SKIP
+cxxGasPhase::cxxGasPhase(std::map < int, cxxGasPhase > &entity_map,
+		cxxMix & mx, int l_n_user, PHRQ_io * io)
+: cxxNumKeyword(io)
+{
+	this->n_user = this->n_user_end = l_n_user;
+	total_p = 0;
+	volume = 0;
+	v_m = 0;
+	pr_in = false;
+	bool first = true;
+//
+//   Mix
+//
+	// accumulate in map
+	std::map<std::string, cxxGasComp> comp_map;
+	std::map<std::string, cxxGasComp>::iterator comp_it;
+
+	const std::map < int, LDBLE > & mixcomps = mx.Get_mixComps();
+	std::map < int, LDBLE >::const_iterator it;
+	for (it = mixcomps.begin(); it != mixcomps.end(); it++)
+	{
+		const cxxGasPhase *entity_ptr =	&(entity_map.find(it->first)->second);
+		if (first)
+		{
+			this->new_def = entity_ptr->new_def;
+			this->solution_equilibria = entity_ptr->solution_equilibria;
+			this->n_solution = entity_ptr->n_solution;
+			this->type = entity_ptr->type;
+			this->total_p = entity_ptr->total_p * it->second;
+			this->total_moles = entity_ptr->total_moles * it->second;
+			this->volume = entity_ptr->volume * it->second;
+			this->v_m = entity_ptr->v_m * it->second;
+			this->pr_in = entity_ptr->pr_in;
+			this->temperature = entity_ptr->temperature;
+			first = false;
+		}
+		else
+		{
+			if (this->type != entity_ptr->type)
+			{
+				std::ostringstream oss;
+				oss << "Cannot mix two gas_phases with differing types.";
+				error_msg(oss.str().c_str(), CONTINUE);
+				return;
+			}
+
+			this->total_p += entity_ptr->total_p * it->second;
+			this->volume += entity_ptr->volume * it->second;
+			this->v_m += entity_ptr->v_m * it->second;
+		}
+		cxxGasPhase *gas_phase_ptr = Utilities::Rxn_find(entity_map, it->first);
+		if (gas_phase_ptr)
+		{
+			std::vector<cxxGasComp> add_comps = gas_phase_ptr->Get_gas_comps();
+			for (size_t i = 0; i < add_comps.size(); i++)
+			{
+				comp_it = comp_map.find(add_comps[i].Get_phase_name());
+				if (comp_it != comp_map.end())
+				{
+					comp_it->second.add(add_comps[i], it->second);
+				}
+				else
+				{
+					cxxGasComp gc(add_comps[i]);
+					gc.multiply(it->second);
+					comp_map[add_comps[i].Get_phase_name()] = gc;
+				}
+			}
+
+		}
+	}
+
+	// put map into vector
+	this->gas_comps.clear();
+	std::vector<cxxGasComp> gc;
+	for (comp_it = comp_map.begin(); comp_it != comp_map.end(); comp_it++)
+	{
+		this->gas_comps.push_back(comp_it->second);
+	}
+}
+#endif
+cxxGasPhase::cxxGasPhase(std::map < int, cxxGasPhase > &entity_map,
+		cxxMix & mx, int l_n_user, PHRQ_io * io)
+: cxxNumKeyword(io)
+{
+	this->n_user = this->n_user_end = l_n_user;
+	total_p = 0;
+	volume = 0;
+	v_m = 0;
+	pr_in = false;
+	bool first = true;
+//
+//   Mix
+//
+	// accumulate in map
+	std::map<std::string, cxxGasComp> comp_map;
+	std::map<std::string, cxxGasComp>::iterator comp_it;
+
+	const std::map < int, LDBLE > & mixcomps = mx.Get_mixComps();
+	std::map < int, LDBLE >::const_iterator it;
+	this->total_p  = 0;
+	double sum_fractions = 0.0;
+	for (it = mixcomps.begin(); it != mixcomps.end(); it++)
+	{
+		sum_fractions += it->second;
+	}
+	for (it = mixcomps.begin(); it != mixcomps.end(); it++)
+	{
+		if (entity_map.find(it->first) != entity_map.end())
+		{
+			const cxxGasPhase *entity_ptr =	&(entity_map.find(it->first)->second);
+			if (first)
+			{
+				this->new_def = entity_ptr->new_def;
+				this->solution_equilibria = entity_ptr->solution_equilibria;
+				this->n_solution = entity_ptr->n_solution;
+				this->type = entity_ptr->type;
+				this->total_moles = entity_ptr->total_moles * it->second;
+				this->volume = entity_ptr->volume * it->second;
+				if (sum_fractions > 0.0)
+				{
+					this->v_m = entity_ptr->v_m * it->second / sum_fractions;
+					this->total_p += entity_ptr->total_p  * it->second / sum_fractions;
+				}
+				else
+				{
+					this->v_m = 0.0;
+					this->total_p = 0.0;
+				}
+				this->pr_in = entity_ptr->pr_in;
+				this->temperature = entity_ptr->temperature;
+				first = false;
+				}
+				else
+				{
+				if (this->type != entity_ptr->type)
+				{
+					std::ostringstream oss;
+					oss << "Cannot mix two gas_phases with differing types.";
+					error_msg(oss.str().c_str(), CONTINUE);
+					return;
+				}
+
+				this->total_p += entity_ptr->total_p * it->second;
+				this->volume += entity_ptr->volume * it->second;
+				this->v_m += entity_ptr->v_m * it->second;
+			}
+		}
+		cxxGasPhase *gas_phase_ptr = Utilities::Rxn_find(entity_map, it->first);
+		if (gas_phase_ptr)
+		{
+			std::vector<cxxGasComp> add_comps = gas_phase_ptr->Get_gas_comps();
+			for (size_t i = 0; i < add_comps.size(); i++)
+			{
+				comp_it = comp_map.find(add_comps[i].Get_phase_name());
+				if (comp_it != comp_map.end())
+				{
+					comp_it->second.add(add_comps[i], it->second);
+				}
+				else
+				{
+					cxxGasComp gc(add_comps[i]);
+					gc.multiply(it->second);
+					comp_map[add_comps[i].Get_phase_name()] = gc;
+				}
+			}
+
+		}
+	}
+
+	// put map into vector
+	this->gas_comps.clear();
+	std::vector<cxxGasComp> gc;
+	for (comp_it = comp_map.begin(); comp_it != comp_map.end(); comp_it++)
+	{
+		this->gas_comps.push_back(comp_it->second);
+	}
+}
+#ifdef SKIP
+cxxGasPhase::cxxGasPhase(const std::map < int, cxxGasPhase > &entities,
+						 cxxMix & mix, int l_n_user, PHRQ_io * io):
+cxxNumKeyword(io)
+{
+	this->n_user = this->n_user_end = l_n_user;
+	gasPhaseComps.type = cxxNameDouble::ND_NAME_COEF;
+	total_p = 0;
+	volume = 0;
+	v_m = 0;
+	pr_in = false;
+	bool first = true;
+//
+//   Mix
+//
+	//cxxNameDouble gasPhaseComps;
+	const std::map < int, LDBLE > & mixcomps = mix.Get_mixComps();
+	std::map < int, LDBLE >::const_iterator it;
+	for (it = mixcomps.begin(); it != mixcomps.end(); it++)
+	{
+		if (entities.find(it->first) != entities.end())
+		{
+			const cxxGasPhase *entity_ptr =
+				&(entities.find(it->first)->second);
+			this->gasPhaseComps.add_extensive(entity_ptr->gasPhaseComps,
+											  it->second);
+			//GP_TYPE type;
+			//LDBLE total_p;
+			//LDBLE volume;
+			if (first)
+			{
+				this->type = entity_ptr->type;
+				this->total_p = entity_ptr->total_p * it->second;
+				this->volume = entity_ptr->volume * it->second;
+				this->v_m = entity_ptr->v_m * it->second;
+				this->pr_in = entity_ptr->pr_in;
+				first = false;
+			}
+			else
+			{
+				if (this->type != entity_ptr->type)
+				{
+					std::ostringstream oss;
+					oss << "Cannot mix two gas_phases with differing types.";
+					error_msg(oss.str().c_str(), CONTINUE);
+					//input_error++;
+					return;
+				}
+
+				this->total_p += entity_ptr->total_p * it->second;
+				this->volume += entity_ptr->volume * it->second;
+				this->v_m += entity_ptr->v_m * it->second;
+			}
+		}
+	}
+}
+#endif
+cxxGasPhase::~cxxGasPhase()
+{
+}
+
+#ifdef SKIP
+void
+cxxGasPhase::dump_xml(std::ostream & s_oss, unsigned int indent) const const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// GasPhase element and attributes
+	s_oss << indent0;
+	s_oss << "<gas_phase " << "\n";
+
+	s_oss << indent1;
+	s_oss << "pitzer_gas_phase_gammas=\"" << this->
+		pitzer_gas_phase_gammas << "\"" << "\n";
+
+	// components
+	s_oss << indent1;
+	s_oss << "<component " << "\n";
+	for (std::list < cxxGasPhaseComp >::const_iterator it =
+		 gas_phaseComps.begin(); it != gas_phaseComps.end(); ++it)
+	{
+		it->dump_xml(s_oss, indent + 2);
+	}
+
+	return;
+}
+#endif
+
+void
+cxxGasPhase::dump_raw(std::ostream & s_oss, unsigned int indent, int *n_out) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// GasPhase element and attributes
+	s_oss << indent0;
+	int n_user_local = (n_out != NULL) ? *n_out : this->n_user;
+	s_oss << "GAS_PHASE_RAW                " << n_user_local << " " << this->description << "\n";
+
+	s_oss << indent1 << "# GAS_PHASE_MODIFY candidate identifiers #\n";
+	s_oss << indent1;
+	s_oss << "-type                      " << this->type << "\n";
+	s_oss << indent1;
+	s_oss << "-total_p                   " << this->total_p << "\n";
+	s_oss << indent1;
+	s_oss << "-volume                    " << this->volume << "\n";
+	// gasPhaseComps 
+	for (size_t i = 0 ; i < this->gas_comps.size(); i++)
+	{
+		s_oss << indent1;
+		s_oss << "-component                 " << this->gas_comps[i].Get_phase_name() << "\n";
+		this->gas_comps[i].dump_raw(s_oss, indent + 2);
+	}
+
+	s_oss << indent1 << "# GAS_PHASE_MODIFY candidate identifiers with new_def=true #\n";
+	s_oss << indent1;
+	s_oss << "-new_def                   " << this->new_def << "\n";
+	s_oss << indent1;
+	s_oss << "-solution_equilibria       " << this->solution_equilibria << "\n";
+	s_oss << indent1;
+	s_oss << "-n_solution                " << this->n_solution << "\n";
+	s_oss << indent1;
+	s_oss << "-temperature               " << this->temperature << "\n";
+
+	s_oss << indent1 << "# GasPhase workspace variables #\n";
+	s_oss << indent1;
+	s_oss << "-total_moles               " << this->total_moles << "\n";
+	s_oss << indent1;
+	s_oss << "-v_m                       " << this->v_m << "\n";
+	s_oss << indent1;
+	s_oss << "-pr_in                     " << (this->pr_in ? 1 : 0) << "\n";
+	s_oss << indent1;
+	s_oss << "-totals                    " << "\n";
+	this->totals.dump_raw(s_oss, indent + 2);
+}
+
+void
+cxxGasPhase::read_raw(CParser & parser, bool check)
+{
+
+	int i;
+
+	std::istream::pos_type ptr;
+	std::istream::pos_type next_char;
+	std::string token;
+	int opt_save;
+	bool useLastLine(false);
+
+	// Read gas_phase number and description
+	this->read_number_description(parser);
+	this->Set_new_def(false);
+
+	opt_save = CParser::OPT_ERROR;
+	bool type_defined(false);
+	bool total_p_defined(false);
+	bool volume_defined(false);
+
+	for (;;)
+	{
+		int opt;
+		if (useLastLine == false)
+		{
+			opt = parser.get_option(vopts, next_char);
+		}
+		else
+		{
+			CParser::ECHO_OPTION eo = parser.get_echo_file();
+			parser.set_echo_file(CParser::EO_NONE);
+			opt = parser.getOptionFromLastLine(vopts, next_char, true);
+			parser.set_echo_file(eo);
+		}
+		if (opt == CParser::OPT_DEFAULT)
+		{
+			opt = opt_save;
+		}
+		switch (opt)
+		{
+		case CParser::OPT_EOF:
+			break;
+		case CParser::OPT_KEYWORD:
+			break;
+		case CParser::OPT_DEFAULT:
+		case CParser::OPT_ERROR:
+			opt = CParser::OPT_EOF;
+			parser.error_msg("Unknown input in GAS_PHASE_COMP_RAW keyword.",
+							 PHRQ_io::OT_CONTINUE);
+			parser.error_msg(parser.line().c_str(), PHRQ_io::OT_CONTINUE);
+			useLastLine = false;
+			break;
+
+		case 0:				// type
+			if (!(parser.get_iss() >> i))
+			{
+				this->type = cxxGasPhase::GP_PRESSURE;
+				parser.incr_input_error();
+				parser.error_msg("Expected enum for type.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			else
+			{
+				this->type = (cxxGasPhase::GP_TYPE) i;
+			}
+			type_defined = true;
+			useLastLine = false;
+			break;
+
+		case 1:				// total_p
+		case 5:				// pressure
+			if (!(parser.get_iss() >> this->total_p))
+			{
+				this->total_p = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for total_p.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			total_p_defined = true;
+			useLastLine = false;
+			break;
+
+		case 2:				// volume
+			if (!(parser.get_iss() >> this->volume))
+			{
+				this->volume = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for volume.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			volume_defined = true;
+			useLastLine = false;
+			break;
+
+		case 3:				// v_m
+			if (!(parser.get_iss() >> this->v_m))
+			{
+				this->v_m = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for v_m.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			useLastLine = false;
+			break;
+		case 4:				// component
+			{
+				std::string str;
+				if (!(parser.get_iss() >> str))
+				{
+					parser.incr_input_error();
+					parser.error_msg("Expected string value for component name.",
+									 PHRQ_io::OT_CONTINUE);
+				}
+				else
+				{
+					cxxGasComp temp_comp(io);
+					temp_comp.Set_phase_name(str);
+					cxxGasComp * comp_ptr = this->Find_comp(str.c_str());
+					if (comp_ptr)
+					{
+						temp_comp = *comp_ptr;	
+					}
+					temp_comp.read_raw(parser, false);
+					if (comp_ptr)
+					{
+						for (size_t j = 0; j < this->gas_comps.size(); j++)
+						{
+							if (Utilities::strcmp_nocase(this->gas_comps[j].Get_phase_name().c_str(), str.c_str()) == 0)
+							{
+								this->gas_comps[j] = temp_comp;
+							}
+						}
+					}
+					else
+					{
+						this->gas_comps.push_back(temp_comp);
+					}
+					useLastLine = true;
+				}
+			}
+			
+			opt_save = CParser::OPT_DEFAULT;
+			break;
+		case 6:				// pr_in
+			if (!(parser.get_iss() >> i))
+			{
+				parser.incr_input_error();
+				parser.error_msg("Expected 0/1 for pr_in.", PHRQ_io::OT_CONTINUE);
+			}
+			else
+			{
+				this->pr_in = (i == 0) ? false : true;
+			}
+			useLastLine = false;
+			break;
+		case 7:				// new_def
+			if (!(parser.get_iss() >> i))
+			{
+				parser.incr_input_error();
+				parser.error_msg("Expected 0/1 for new_def.", PHRQ_io::OT_CONTINUE);
+			}
+			else
+			{
+				this->new_def = (i == 0) ? false : true;
+			}
+			useLastLine = false;
+			break;
+		case 8:				// solution_equilibria
+			if (!(parser.get_iss() >> i))
+			{
+				parser.incr_input_error();
+				parser.error_msg("Expected 0/1 for solution_equilibria.", PHRQ_io::OT_CONTINUE);
+			}
+			else
+			{
+				this->solution_equilibria = (i == 0) ? false : true;
+			}
+			useLastLine = false;
+			break;
+		case 9:				// n_solution
+			if (!(parser.get_iss() >> this->n_solution))
+			{
+				parser.incr_input_error();
+				parser.error_msg("Expected integer for n_solution.", PHRQ_io::OT_CONTINUE);
+			}
+			useLastLine = false;
+			break;
+		case 10:				// total_moles
+			if (!(parser.get_iss() >> this->total_moles))
+			{
+				this->total_moles = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for total_moles.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			useLastLine = false;
+			break;
+		case 11:				// temperature
+			if (!(parser.get_iss() >> this->temperature))
+			{
+				this->temperature = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for temperature.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			useLastLine = false;
+			break;
+		case 12:				// totals
+			if (this->totals.read_raw(parser, next_char) !=
+				CParser::PARSER_OK)
+			{
+				parser.incr_input_error();
+				parser.
+					error_msg
+					("Expected element name and molality for GasPhase totals.",
+					 PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = 12;
+			break;
+		}
+		if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
+			break;
+	}
+	if (check)
+	{
+		// members that must be defined
+		if (type_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Type not defined for GAS_PHASE_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (total_p_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Total_p not defined for GAS_PHASE_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (volume_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Volume not defined for GAS_PHASE_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+	}
+}
+
+void
+cxxGasPhase::totalize(Phreeqc * phreeqc_ptr)
+{
+	this->totals.clear();
+	// component structures
+	for (size_t i = 0; i < this->gas_comps.size(); i++)
+	{
+		struct phase *phase_ptr;
+		int l;
+		phase_ptr = phreeqc_ptr-> phase_bsearch(this->gas_comps[i].Get_phase_name().c_str(), &l, FALSE);
+		if (phase_ptr != NULL)
+		{
+			cxxNameDouble phase_formula(phase_ptr->next_elt);
+			this->totals.add_extensive(phase_formula, this->gas_comps[i].Get_moles());
+		}
+		else
+		{
+			assert(false);
+		}
+	}
+	return;
+}
+LDBLE cxxGasPhase::Calc_total_moles(void)const
+{
+	LDBLE tot = 0.0;
+	for (size_t i = 0; i < this->gas_comps.size(); i++)
+	{
+		tot += gas_comps[i].Get_moles();
+	}
+	return tot;
+}
+cxxGasComp *
+cxxGasPhase::Find_comp(const char * comp_name)
+{
+	for (size_t i = 0; i < this->gas_comps.size(); i++)
+	{
+		if (Utilities::strcmp_nocase(this->gas_comps[i].Get_phase_name().c_str(), comp_name) == 0)
+		{
+			return &(this->gas_comps[i]);
+		}
+	}
+	return NULL;
+}
+void
+cxxGasPhase::Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles)
+{
+	ints.push_back(this->n_user);
+	ints.push_back((this->type == cxxGasPhase::GP_PRESSURE) ? 0 : 1);
+	doubles.push_back(this->total_p);
+	doubles.push_back(this->volume);
+	ints.push_back((int) this->gas_comps.size());
+	for (size_t i = 0; i < this->gas_comps.size(); i++)
+	{
+		this->gas_comps[i].Serialize(dictionary, ints, doubles);
+	}
+	ints.push_back(this->new_def ? 1 : 0);
+	ints.push_back(this->solution_equilibria ? 1 : 0);
+	ints.push_back(this->n_solution);
+	doubles.push_back(this->temperature);
+	doubles.push_back(this->total_moles);
+	doubles.push_back(this->v_m);
+	ints.push_back(this->pr_in ? 1 : 0);
+	this->totals.Serialize(dictionary, ints, doubles);
+
+}
+
+void
+cxxGasPhase::Deserialize(Dictionary & dictionary, std::vector < int >&ints, 
+	std::vector < double >&doubles, int &ii, int &dd)
+{
+	this->n_user = ints[ii++];
+	this->n_user_end = this->n_user;
+	this->description = " ";
+
+	this->type = (ints[ii++] == 0) ? cxxGasPhase::GP_PRESSURE : cxxGasPhase::GP_VOLUME;
+	this->total_p = doubles[dd++];
+	this->volume = doubles[dd++];
+	int count = ints[ii++];
+	this->gas_comps.clear();
+	for (int i = 0; i < count; i++)
+	{
+		cxxGasComp gc;
+		gc.Deserialize(dictionary, ints, doubles, ii, dd);
+		this->gas_comps.push_back(gc);
+	}
+	this->new_def = (ints[ii++] != 0) ? 1 : 0;
+	this->solution_equilibria = (ints[ii++] != 0) ? 1 : 0;
+	this->n_solution = ints[ii++];
+	this->temperature = doubles[dd++];
+	this->total_moles = doubles[dd++];
+	this->v_m = doubles[dd++];
+	this->pr_in = (ints[ii++] != 0);
+	this->totals.Deserialize(dictionary, ints, doubles, ii, dd);
+
+}
+
+
+const std::vector< std::string >::value_type temp_vopts[] = {
+	std::vector< std::string >::value_type("type"),				    //0
+	std::vector< std::string >::value_type("total_p"),				//1
+	std::vector< std::string >::value_type("volume"),				//2
+	std::vector< std::string >::value_type("v_m"),					//3
+	std::vector< std::string >::value_type("component"),			//4
+	std::vector< std::string >::value_type("pressure"),			    //5
+	std::vector< std::string >::value_type("pr_in"),				//6
+	std::vector< std::string >::value_type("new_def"),				//7
+	std::vector< std::string >::value_type("solution_equilibria"),	//8
+	std::vector< std::string >::value_type("n_solution"),			//9
+	std::vector< std::string >::value_type("total_moles"),			//10
+	std::vector< std::string >::value_type("temperature"),			//11
+	std::vector< std::string >::value_type("totals")                //12
+};									   
+const std::vector< std::string > cxxGasPhase::vopts(temp_vopts, temp_vopts + sizeof temp_vopts / sizeof temp_vopts[0]);

src/phreeqcpp/GasPhase.h

@@ -0,0 +1,97 @@
+#if !defined(GASPHASE_H_INCLUDED)
+#define GASPHASE_H_INCLUDED
+
+#include <cassert>				// assert
+#include <map>					// std::map
+#include <string>				// std::string
+#include <list>					// std::list
+#include <vector>				// std::vector
+#include "phrqtype.h"
+#include "NumKeyword.h"
+#include "NameDouble.h"
+#include "GasComp.h"
+class cxxMix;
+
+class cxxGasPhase:public cxxNumKeyword
+{
+
+  public:
+	cxxGasPhase(PHRQ_io * io=NULL);
+	cxxGasPhase(std::map < int, cxxGasPhase > &entity_map,
+		cxxMix & mx, int n_user, PHRQ_io * io=NULL);
+	 ~cxxGasPhase();
+
+	enum GP_TYPE
+	{
+		GP_PRESSURE = 0,
+		GP_VOLUME = 1
+	};
+
+	//void dump_xml(std::ostream& os, unsigned int indent = 0)const;
+
+	void dump_raw(std::ostream & s_oss, unsigned int indent, int *n_out=NULL) const;
+
+	void read_raw(CParser & parser, bool check = true);
+
+	void totalize(Phreeqc * phreeqc_ptr);
+
+	const cxxNameDouble & Get_totals() const
+	{
+		return this->totals;
+	};
+	std::vector<cxxGasComp> & Get_gas_comps(void) {return gas_comps;};
+	const std::vector<cxxGasComp> & Get_gas_comps(void)const {return gas_comps;};
+	void Set_gas_comps(const std::vector<cxxGasComp> v) {gas_comps = v;};
+
+	GP_TYPE Get_type(void) const {return type;};
+	void Set_type(GP_TYPE t) {type = t;};
+	LDBLE Get_total_p(void) const {return total_p;};
+	void Set_total_p(LDBLE t) {total_p = t;};
+	LDBLE Get_volume(void) const {return volume;};
+	void Set_volume(LDBLE v) {volume = v;};
+	LDBLE Get_v_m(void) const {return v_m;};
+	void Set_v_m(LDBLE v) {v_m = v;};
+	bool Get_pr_in(void) const {return pr_in;};
+	void Set_pr_in(bool tf) {pr_in = tf;};
+	cxxNameDouble & Get_totals(void) {return totals;};
+
+	bool Get_new_def(void) const {return this->new_def;};
+	void Set_new_def(bool tf) {this->new_def = tf;};
+	bool Get_solution_equilibria(void) const {return this->solution_equilibria;};
+	void Set_solution_equilibria(bool tf) {this->solution_equilibria = tf;};
+	int Get_n_solution(void) const {return this->n_solution;};
+	void Set_n_solution(int i) {this->n_solution = i;};
+	LDBLE Get_total_moles(void)const {return total_moles;};
+	void Set_total_moles(LDBLE t) {total_moles = t;};
+	LDBLE Get_temperature(void)const {return temperature;};
+	void Set_temperature(LDBLE t) {temperature = t;};
+	LDBLE Calc_total_moles(void)const;
+	cxxGasComp *Find_comp(const char * comp_name);
+	void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
+	void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
+
+protected:
+	void add(const cxxGasPhase & addee, LDBLE extensive);
+
+protected:
+	// candidate variables for GAS_PHASE_MODIFY
+	GP_TYPE type;
+	LDBLE total_p;
+	LDBLE volume;
+	std::vector<cxxGasComp> gas_comps;
+
+	// GAS_PHASE_MODIFY with new_def=true variables
+	bool new_def;
+	bool solution_equilibria;
+	int n_solution;
+	LDBLE temperature;
+
+	// internal variables
+	LDBLE total_moles;
+	LDBLE v_m;
+	bool pr_in;
+	cxxNameDouble totals;
+	const static std::vector < std::string > vopts;
+};
+
+#endif // !defined(GASPHASE_H_INCLUDED)

src/phreeqcpp/ISolution.cxx

@@ -0,0 +1,209 @@
+// ISolution.cxx: implementation of the cxxSolutionxx class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <cassert>				// assert
+#include <algorithm>			// std::sort
+#include <sstream>
+
+#include "Utils.h" // define first
+#include "Phreeqc.h"
+#include "ISolution.h"
+#include "phqalloc.h"
+
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+cxxISolution::cxxISolution(PHRQ_io *io)
+:
+units("mMol/kgw")
+{
+	default_pe = "pe";
+	cxxChemRxn temp_pe_reactions;
+	pe_reactions[default_pe] = temp_pe_reactions;
+	this->calc_density = false;
+
+}
+cxxISolution::~cxxISolution()
+{
+}
+
+#ifdef SKIP_OR_MOVE_TO_STRUCTURES
+void
+cxxISolution::ConvertUnits(Phreeqc * phreeqc_ptr)
+  //
+  // Converts from input units to moles per kilogram water
+  //
+{
+	LDBLE sum_solutes = 0;
+	// foreach conc
+	std::map < std::string, cxxISolutionComp >::iterator iter =
+		this->comps.begin();
+	for (; iter != this->comps.end(); ++iter)
+	{
+		struct master *master_ptr = phreeqc_ptr-> master_bsearch(iter->first.c_str());
+		if (master_ptr != NULL && (master_ptr->minor_isotope == TRUE))
+			continue;
+		//if (iter->second.Get_description() == "H(1)" || iter->second.Get_description() == "E") continue;
+		if (strcmp(iter->second.Get_description().c_str(), "H(1)") == 0
+			|| strcmp(iter->second.Get_description().c_str(), "E"))
+			continue;
+		if (iter->second.get_input_conc() <= 0.0)
+			continue;
+/*
+*   Convert liters to kg solution
+*/
+		LDBLE moles = iter->second.get_input_conc();
+		if (this->units.find("/l") != std::string::npos)
+		{
+			moles /= this->density;
+		}
+/*
+* Convert to moles
+*/
+		//set gfw for element
+		iter->second.set_gfw(phreeqc_ptr);
+		// convert to moles
+		if (iter->second.get_units().find("g/") != std::string::npos)
+		{
+			if (iter->second.get_gfw() != 0)
+			{
+				moles /= iter->second.get_gfw();
+			}
+			else
+			{
+				std::ostringstream oss;
+				oss << "Could not find gfw, " << iter->second.
+					Get_description();
+				error_msg(oss.str().c_str(), CONTINUE);
+			}
+		}
+/*
+*   Convert milli or micro
+*/
+		char c = iter->second.get_units().c_str()[0];
+		if (c == 'm')
+		{
+			moles *= 1e-3;
+		}
+		else if (c == 'u')
+		{
+			moles *= 1e-6;
+		}
+		iter->second.set_moles(moles);
+/*
+*   Sum grams of solute, convert from moles necessary
+*/
+		sum_solutes += moles * (iter->second.get_gfw());
+	}
+/*
+ *   Convert /kgs to /kgw
+ */
+	LDBLE l_mass_water;
+	if ((this->units.find("kgs") != std::string::npos) ||
+		(this->units.find("/l") != std::string::npos))
+	{
+		l_mass_water = 1.0 - 1e-3 * sum_solutes;
+		for (; iter != this->comps.end(); ++iter)
+		{
+			iter->second.set_moles(iter->second.get_moles() / l_mass_water);
+		}
+	}
+/*
+ *   Scale by mass of water in solution
+ */
+	l_mass_water = this->mass_water;
+	for (; iter != this->comps.end(); ++iter)
+	{
+		iter->second.set_moles(iter->second.get_moles() * l_mass_water);
+	}
+}
+#endif
+
+#ifdef SKIP
+void
+cxxISolution::dump_xml(std::ostream & os, unsigned int indent) const const
+{
+	unsigned int i;
+
+	for (i = 0; i < indent; ++i)
+		os << Utilities::INDENT;
+	os << "<solution>\n";
+
+	cxxNumKeyword::dump_xml(os, indent);
+
+	for (i = 0; i < indent + 1; ++i)
+		os << Utilities::INDENT;
+	os << "<temp>" << this->get_tc() << "</temp>" << "\n";
+
+	for (i = 0; i < indent + 1; ++i)
+		os << Utilities::INDENT;
+	os << "<pH>" << this->get_ph() << "</pH>" << "\n";
+
+	for (i = 0; i < indent + 1; ++i)
+		os << Utilities::INDENT;
+	os << "<pe>" << this->get_solution_pe() << "</pe>" << "\n";
+
+	assert(this->pe.size() > 0);
+	assert(this->default_pe >= 0);
+	assert(this->pe.size() > (unsigned int) this->default_pe);
+
+	for (i = 0; i < indent + 1; ++i)
+		os << Utilities::INDENT;
+	os << "<units>" << this->get_units() << "</units>" << "\n";
+
+	for (i = 0; i < indent + 1; ++i)
+		os << Utilities::INDENT;
+	os << "<density>" << this->get_density() << "</density>" << "\n";
+
+	// foreach conc
+	if (!this->totals.empty())
+	{
+		for (i = 0; i < indent + 1; ++i)
+			os << Utilities::INDENT;
+		os << "<totals>\n";
+
+		std::vector < cxxISolutionComp >::const_iterator iter =
+			this->totals.begin();
+		for (; iter != this->totals.end(); ++iter)
+		{
+			(*iter).dump_xml(*this, os, indent + 2);
+		}
+
+		for (i = 0; i < indent + 1; ++i)
+			os << Utilities::INDENT;
+		os << "</totals>\n";
+	}
+
+	// foreach isotope
+	if (!this->isotopes.empty())
+	{
+		for (i = 0; i < indent + 1; ++i)
+			os << Utilities::INDENT;
+		os << "<isotopes>\n";
+
+		std::list < cxxIsotope >::const_iterator iter =
+			this->isotopes.begin();
+		for (; iter != this->isotopes.end(); ++iter)
+		{
+			(*iter).dump_xml(os, indent + 2);
+		}
+
+		for (i = 0; i < indent + 1; ++i)
+			os << Utilities::INDENT;
+		os << "</isotopes>\n";
+	}
+
+	for (i = 0; i < indent + 1; ++i)
+		os << Utilities::INDENT;
+	os << "<water>" << this->get_mass_water() << "</water>" << "\n";
+
+	for (i = 0; i < indent; ++i)
+		os << Utilities::INDENT;
+	os << "</solution>" << "\n";
+}
+#endif

src/phreeqcpp/ISolution.h

@@ -0,0 +1,55 @@
+#if !defined(ISOLUTION_H_INCLUDED)
+#define ISOLUTION_H_INCLUDED
+
+#include <cassert>				// assert
+#include <map>					// std::map
+#include <string>				// std::string
+#include <list>					// std::list
+#include <vector>				// std::vector
+#include <set>					// std::set
+#include <iostream>
+#include <sstream>
+#include <fstream>
+
+#include "ISolutionComp.h"
+#include "PHRQ_base.h"
+#include "NameDouble.h"
+#include "global_structures.h"
+class cxxISolution: public PHRQ_base
+{
+
+  public:
+	cxxISolution(PHRQ_io *io=NULL);
+	cxxISolution(const cxxISolution *is);
+	virtual ~cxxISolution();
+	std::string Get_units() const                     {return units;}
+	void Set_units(std::string l_units)               {units = l_units;}
+	void Set_units(const char * l_units)
+	{
+		if (l_units != NULL)
+			this->units = std::string(l_units);
+		else
+			this->units.clear();
+	}
+	const char * Get_default_pe() const                {return default_pe;}
+	void Set_default_pe(const char * pe)               {default_pe = pe;}
+	bool Get_calc_density(void)                        {return this->calc_density;}
+	void Set_calc_density(bool calc)                   {this->calc_density = calc;}
+	std::map < std::string, cxxISolutionComp > &Get_comps(void) {return this->comps;}
+	const std::map < std::string, cxxISolutionComp > &Get_comps(void)const {return this->comps;}
+	void Set_comps(std::map < std::string, cxxISolutionComp > &c) {this->comps = c;}
+	std::map < std::string, cxxChemRxn >  &Get_pe_reactions(void) {return this->pe_reactions;}
+	void Set_pe_reactions(std::map < std::string, cxxChemRxn >  &pe) {this->pe_reactions = pe;}
+	//void dump_xml(std::ostream& os, unsigned int indent = 0)const;
+	//void ConvertUnits(Phreeqc * phreeqc_ptr);
+
+  protected:
+	friend class cxxISolutionComp;	// for this->pe access
+	std::string units;
+	bool calc_density;
+	std::map < std::string, cxxISolutionComp > comps;
+	std::map <std::string, cxxChemRxn > pe_reactions;
+	const char * default_pe;
+};
+
+#endif // !defined(ISOLUTION_H_INCLUDED)

src/phreeqcpp/ISolutionComp.cxx

@@ -0,0 +1,447 @@
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <cassert>
+
+#include "Utils.h"
+#include "ISolutionComp.h"
+#include "Parser.h"
+#include "Solution.h"
+#include "phqalloc.h"
+
+cxxISolutionComp::cxxISolutionComp(PHRQ_io *io):
+PHRQ_base(io),
+moles(0.0), 
+input_conc(0.0), 
+phase_si(0.0),
+gfw(0.0)
+{
+}
+cxxISolutionComp::~cxxISolutionComp(void)
+{
+}
+
+#ifdef SKIP_OR_MOVE_TO_STRUCTURES
+struct conc *
+cxxISolutionComp::cxxISolutionComp2conc(Phreeqc * phreeqc_ptr, const std::map < std::string,
+										cxxISolutionComp > &totals)
+		// for ISolutions
+		// takes a std::vector cxxISolutionComp structures
+		// returns list of conc structures
+{
+	struct conc *c;
+	c = (struct conc *)
+		phreeqc_ptr-> PHRQ_malloc((size_t) ((totals.size() + 1) * sizeof(struct conc)));
+	if (c == NULL)
+		phreeqc_ptr-> malloc_error();
+	int i = 0;
+	for (std::map < std::string, cxxISolutionComp >::const_iterator it = totals.begin();
+		 it != totals.end(); ++it)
+	{
+		c[i].description = phreeqc_ptr-> string_duplicate(it->second.description.c_str());
+		c[i].moles = it->second.moles;
+		c[i].input_conc = it->second.input_conc;
+		if (it->second.units.size() == 0)
+			c[i].units = NULL;
+		else
+			c[i].units = phreeqc_ptr-> string_hsave(it->second.units.c_str());
+		if (it->second.equation_name.size() == 0)
+			c[i].equation_name = NULL;
+		else
+			c[i].equation_name = phreeqc_ptr-> string_hsave(it->second.equation_name.c_str());
+		c[i].phase_si = it->second.phase_si;
+		c[i].n_pe = it->second.n_pe;
+		c[i].as = phreeqc_ptr-> string_hsave(it->second.as.c_str());
+		c[i].gfw = it->second.gfw;
+		//c[i].skip                = 0;
+		c[i].phase = NULL;
+		i++;
+	}
+	c[i].description = NULL;
+	return (c);
+}
+#endif
+
+#ifdef SKIP_OR_MOVE_TO_STRUCTURES
+void
+cxxISolutionComp::set_gfw(Phreeqc * phreeqc_ptr)
+{
+// return gfw
+	if (this->gfw > 0.0)
+		return;
+// calculate gfw from as or from master species gfw
+	if (this->as.size() != 0)
+	{
+		/* use given chemical formula to calculate gfw */
+		LDBLE l_gfw;
+		if (phreeqc_ptr-> compute_gfw(this->as.c_str(), &l_gfw) == ERROR)
+		{
+			std::ostringstream oss;
+			oss << "Could not compute gfw, " << this->as;
+			error_msg(oss.str().c_str(), CONTINUE);
+			return;
+		}
+		//if (this->description == "Alkalinity" && this->as == "CaCO3") 
+		if (strcmp(this->description.c_str(), "Alkalinity") == 0
+			&& strcmp(this->as.c_str(), "CaCO3"))
+		{
+			l_gfw /= 2.;
+		}
+		this->gfw = l_gfw;
+		return;
+	}
+	/* use gfw of master species */
+	std::string str(this->description);
+	struct master *master_ptr = phreeqc_ptr-> master_bsearch(str.c_str());
+	if (master_ptr != NULL)
+	{
+		/* use gfw for element redox state */
+		this->gfw = master_ptr->gfw;
+		return;
+	}
+	std::ostringstream oss;
+	oss << "Could not find gfw, " << this->description;
+	error_msg(oss.str().c_str(), CONTINUE);
+	return;
+}
+#endif
+#ifdef SKIP
+cxxISolutionComp::STATUS_TYPE cxxISolutionComp::read(CParser & parser,
+													 cxxISolution & solution)
+{
+	// std::string& str = parser.line(); 
+	std::string str = parser.line();
+
+	// defaults set in ctor
+
+	// Remove space between "kg" and "solution" or "water" in units
+	Utilities::replace("Kg", "kg", str);
+	Utilities::replace("KG", "kg", str);
+	while (Utilities::replace("kg ", "kg", str));
+
+	std::istream::pos_type ptr = 0;
+
+	//
+	// Read master species list for mass balance equation
+	//
+	std::string token;
+	std::string token1;
+	int
+		count_redox_states = 0;
+	CParser::TOKEN_TYPE j;
+	while (((j = parser.copy_token(token, ptr)) == CParser::TT_UPPER) ||
+		   (token[0] == '[') ||
+		   (Utilities::strcmp_nocase_arg1(token.c_str(), "ph") == 0) ||
+		   (Utilities::strcmp_nocase_arg1(token.c_str(), "pe") == 0))
+	{
+		++count_redox_states;
+		Utilities::replace("(+", "(", token);
+		if (count_redox_states > 1)
+			token1 += " ";
+		token1 += token;
+	}
+	if (count_redox_states == 0)
+	{
+		parser.incr_input_error();
+		parser.
+			error_msg
+			("No element or master species given for concentration input.",
+			 PHRQ_io::OT_CONTINUE);
+		return cxxISolutionComp::ERROR;
+	}
+	description = token1;
+
+	// Determine if reading alkalinity, allow equivalents for units
+	Utilities::str_tolower(token1);
+	bool
+		alk = false;
+	if (token1.find("alk") == 0)
+	{
+		alk = true;
+	}
+
+	// Read concentration
+	if (!(std::istringstream(token) >> this->input_conc))
+	{
+		std::ostringstream err;
+		err << "Concentration data error for " << token1 <<
+			" in solution input.";
+		parser.error_msg(err, PHRQ_io::OT_CONTINUE);
+		return cxxISolutionComp::ERROR;
+	}
+	if ((j = parser.copy_token(token, ptr)) == CParser::TT_EMPTY)
+		return cxxISolutionComp::OK;
+
+	// Read optional data
+	token1 = token;
+
+	// Check for units info
+	if (parser.check_units(token1, alk, false, solution.get_units(), false) ==
+		CParser::OK)
+	{
+		if (parser.
+			check_units(token1, alk, false, solution.get_units(),
+						true) == CParser::OK)
+		{
+			this->units = token1;
+			if ((j = parser.copy_token(token, ptr)) == CParser::TT_EMPTY)
+				return cxxISolutionComp::OK;
+		}
+		else
+		{
+			return cxxISolutionComp::ERROR;
+		}
+	}
+
+	// Check for "as" followed by formula to be used for gfw
+	token1 = token;
+	Utilities::str_tolower(token1);
+	if (token1.compare("as") == 0)
+	{
+		parser.copy_token(token, ptr);
+		this->as = token;
+		if ((j = parser.copy_token(token, ptr)) == CParser::TT_EMPTY)
+			return cxxISolutionComp::OK;
+	}
+	// Check for "gfw" followed by gram formula weight
+	else if (token1.compare("gfw") == 0)
+	{
+		if (parser.copy_token(token, ptr) != CParser::TT_DIGIT)
+		{
+			parser.error_msg("Expecting gram formula weight.",
+							 PHRQ_io::OT_CONTINUE);
+			return cxxISolutionComp::ERROR;
+		}
+		else
+		{
+			parser.get_iss() >> this->gfw;
+			if ((j = parser.copy_token(token, ptr)) == CParser::TT_EMPTY)
+				return cxxISolutionComp::OK;
+		}
+	}
+
+	// Check for redox couple for pe
+	if (Utilities::strcmp_nocase_arg1(token.c_str(), "pe") == 0)
+	{
+		this->n_pe = cxxPe_Data::store(solution.pe, token);
+		if ((j = parser.copy_token(token, ptr)) == CParser::TT_EMPTY)
+			return cxxISolutionComp::OK;
+	}
+	else if (token.find("/") != std::string::npos)
+	{
+		if (parser.parse_couple(token) == CParser::OK)
+		{
+			this->n_pe = cxxPe_Data::store(solution.pe, token);
+			if ((j = parser.copy_token(token, ptr)) == CParser::TT_EMPTY)
+				return cxxISolutionComp::OK;
+		}
+		else
+		{
+			return cxxISolutionComp::ERROR;
+		}
+	}
+
+	// Must have phase
+	this->equation_name = token;
+	if ((j = parser.copy_token(token, ptr)) == CParser::TT_EMPTY)
+		return cxxISolutionComp::OK;
+
+	// Check for saturation index
+	if (!(std::istringstream(token) >> this->phase_si))
+	{
+		parser.error_msg("Expected saturation index.", PHRQ_io::OT_CONTINUE);
+		return cxxISolutionComp::ERROR;
+	}
+	return cxxISolutionComp::OK;
+}
+#endif
+#ifdef SKIP
+void
+cxxISolutionComp::dump_xml(std::ostream & s_oss, unsigned int indent) const const
+{
+	unsigned int i;
+	std::string indent0("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+
+	s_oss << indent0;
+	s_oss << "<soln_total";
+
+	s_oss << " conc_desc=\"" << this->description << "\"";
+
+	s_oss << " conc_moles=\"" << this->moles << "\"";
+
+	s_oss << "\">" << "\n";
+}
+#endif
+/* ---------------------------------------------------------------------- */
+CParser::STATUS_TYPE cxxISolutionComp::
+read(const char *line_in, cxxSolution *solution_ptr)
+/* ---------------------------------------------------------------------- */
+{
+/*
+ *   Remove space between "kg" and "solution" or "water" in units
+ */
+	std::string line = line_in;
+	Utilities::replace("Kg", "kg", line);
+	Utilities::replace("KG", "kg", line);
+	while (Utilities::replace("kg ", "kg", line) == TRUE);
+/*
+ *   Read master species list for mass balance equation
+ */
+	std::string master_list;
+	std::string token;
+	std::string::iterator b = line.begin(); 
+	std::string::iterator e = line.end(); 
+	{
+		int j;
+		while (((j = CParser::copy_token(token, b, e)) == CParser::TT_UPPER) ||
+			(token[0] == '[') ||
+			(Utilities::strcmp_nocase(token.c_str(), "ph") == 0) ||
+			(Utilities::strcmp_nocase(token.c_str(), "pe") == 0))
+		{
+			Utilities::replace("(+", "(", token);
+			if (master_list.size() > 0)
+				master_list.append(" ");
+			master_list.append(token);
+		}
+	}
+	if (master_list.size() == 0)
+	{
+		error_msg
+			("No element or master species given for concentration input.",
+			  PHRQ_io::OT_CONTINUE);
+		return (CParser::PARSER_ERROR);
+	}
+	this->Set_description(master_list.c_str());
+/*
+ *   Determine if reading alkalinity, allow equivalents for units
+ */
+	bool alk;
+	Utilities::str_tolower(master_list);
+	if (strstr(master_list.c_str(), "alk") == master_list.c_str())
+	{
+		alk = true;
+	}
+	else
+	{
+		alk = false;
+	}
+/*
+ *   Read concentration
+ */
+	{
+		LDBLE dummy;
+		int j = sscanf(token.c_str(), SCANFORMAT, &dummy);
+		if (j == 0)
+		{
+			std::ostringstream errstr;
+			errstr << "Concentration data error for " << master_list << " in solution input.";
+			error_msg(errstr.str().c_str(),  PHRQ_io::OT_CONTINUE);
+			return (CParser::PARSER_ERROR);
+		}
+		else
+		{
+			this->Set_input_conc(dummy);
+		}
+		if ((j = CParser::copy_token(token, b, e)) == CParser::TT_EMPTY)
+			return (CParser::PARSER_OK);
+	}
+/*
+ *   Read optional data
+ */
+	std::string token1 = token;
+
+/*
+ *   Check for units info
+ */
+	CParser parser(this->io);
+	if (solution_ptr->Get_initial_data() == NULL)
+	{
+		error_msg("Initial_data instance not defined in cxxISolutionComp::read", 1);
+	}
+	if (parser.check_units(token1, alk, false, solution_ptr->Get_initial_data()->Get_units().c_str(), false) == CParser::PARSER_OK)
+	{
+		if (parser.check_units(token1, alk, false, solution_ptr->Get_initial_data()->Get_units().c_str(), true) == CParser::PARSER_OK)
+		{
+			this->units = token1;
+			if ((CParser::copy_token(token, b, e)) == CParser::TT_EMPTY)
+				return (CParser::PARSER_OK);
+		}
+		else
+		{
+			return (CParser::PARSER_ERROR);
+		}
+	}
+/*
+ *   Check for "as" followed by formula to be used for gfw
+ */
+	token1 = token;
+	Utilities::str_tolower(token1);
+	if (strcmp(token1.c_str(), "as") == 0)
+	{
+		CParser::copy_token(token, b, e);
+		this->as = token;
+		if ((CParser::copy_token(token, b, e)) == CParser::TT_EMPTY)
+			return (CParser::PARSER_OK);
+/*
+ *   Check for "gfw" followed by gram formula weight
+ */
+	}
+	else if (strcmp(token1.c_str(), "gfw") == 0 || strcmp(token1.c_str(), "gfm") == 0)
+	{
+		if (CParser::copy_token(token, b, e) != DIGIT)
+		{
+			error_msg("Expecting gram formula weight.",  PHRQ_io::OT_CONTINUE);
+			return (CParser::PARSER_ERROR);
+		}
+		else
+		{
+			sscanf(token.c_str(), SCANFORMAT, &this->gfw);
+			if ((CParser::copy_token(token, b, e)) == CParser::TT_EMPTY)
+				return (CParser::PARSER_OK);
+		}
+	}
+/*
+ *   Check for redox couple for pe
+ */
+	if (Utilities::strcmp_nocase(token.c_str(), "pe") == 0)
+	{
+		this->pe_reaction = token;
+		if ((CParser::copy_token(token, b, e)) == CParser::TT_EMPTY)
+			return (CParser::PARSER_OK);
+	}
+	else if (strstr(token.c_str(), "/") != NULL)
+	{
+		if (parser.parse_couple(token) == CParser::PARSER_OK)
+		{
+			this->pe_reaction = token;
+			if ((CParser::copy_token(token, b, e)) == CParser::TT_EMPTY)
+				return (CParser::PARSER_OK);
+		}
+		else
+		{
+			return (CParser::PARSER_ERROR);
+		}
+	}
+/*
+ *   Must have phase
+ */
+	this->equation_name = token;
+	if (CParser::copy_token(token, b, e) == CParser::TT_EMPTY)
+		return (CParser::PARSER_OK);
+/*
+ *   Check for saturation index
+ */
+	{
+		int j = sscanf(token.c_str(), SCANFORMAT,
+			&(this->phase_si));
+		if (j != 1)
+		{
+			error_msg("Expected saturation index.",  PHRQ_io::OT_CONTINUE);
+			return (CParser::PARSER_ERROR);
+		}
+	}
+	return (CParser::PARSER_OK);
+
+}

src/phreeqcpp/ISolutionComp.h

@@ -0,0 +1,138 @@
+#if !defined(ISOLUTIONCOMP_H_INCLUDED)
+#define ISOLUTIONCOMP_H_INCLUDED
+
+#include <string.h>             // ::strcmp
+#include <string>
+#include <map>                  // std::map
+#include <vector>
+#include <set>
+#include "phrqtype.h"           // LDBLE
+#include "Parser.h"             // CParser
+#include "PHRQ_base.h"          // PHRQ_base
+
+// forward declarations
+class cxxSolution;
+class cxxISolution;             // reqd for read and dump_xml
+class PHRQ_io;
+
+class cxxISolutionComp: public PHRQ_base
+{
+  public:
+	cxxISolutionComp(PHRQ_io *io=NULL);
+	virtual ~cxxISolutionComp(void);
+
+  public:
+
+	CParser::STATUS_TYPE read(const char *line, cxxSolution *solution_ptr);
+
+	void dump_xml(std::ostream & os, unsigned int indent = 0) const;
+
+	const std::string &Get_description() const
+	{
+		return this->description;
+	}
+	void Set_description(const char *l_description)
+	{
+		if (l_description != NULL)
+			this->description = std::string(l_description);
+		else
+			this->description.clear();
+	}
+
+	LDBLE Get_moles() const
+	{
+		return this->moles;
+	}
+	void Set_moles(LDBLE l_moles)
+	{
+		this->moles = l_moles;
+	}
+
+	LDBLE Get_input_conc() const
+	{
+		return this->input_conc;
+	}
+	void Set_input_conc(LDBLE l_input_conc)
+	{
+		this->input_conc = l_input_conc;
+	}
+
+	std::string Get_units()const
+	{
+		return this->units;
+	}
+	void Set_units(const char *l_units)
+	{
+		if (l_units != NULL)
+			this->units = std::string(l_units);
+		else
+			this->units.clear();
+	}
+
+	const std::string &Get_equation_name() const
+	{
+		return this->equation_name;
+	}
+	void Set_equation_name(const char *l_equation_name)
+	{
+		if (l_equation_name != NULL)
+			this->equation_name = std::string(l_equation_name);
+		else
+			this->equation_name.clear();
+
+	}
+
+	LDBLE Get_phase_si() const
+	{
+		return this->phase_si;
+	}
+	void Set_phase_si(int l_phase_si)
+	{
+		this->phase_si = l_phase_si;
+	}
+	std::string Get_pe_reaction() const
+	{
+		return this->pe_reaction;
+	}
+	void Set_pe_reaction(const std::string & pe_r)
+	{
+		this->pe_reaction = pe_r;
+	}
+	const std::string &Get_as() const
+	{
+		return this->as;
+	}
+	void Set_as(const char *l_as)
+	{
+		if (l_as != NULL)
+			this->as = std::string(l_as);
+		else
+			this->as.clear();
+	}
+	LDBLE Get_gfw() const
+	{
+		return this->gfw;
+	};
+	void Set_gfw(LDBLE l_gfw)
+	{
+		this->gfw = l_gfw;
+	}
+
+	bool operator<(const cxxISolutionComp & conc) const
+	{
+		return ::strcmp(this->description.c_str(), conc.description.c_str()) < 0;
+	}
+
+  protected:
+	  std::string description;
+	  LDBLE moles;
+	  LDBLE input_conc;
+	  std::string units;
+	  std::string equation_name;
+	  LDBLE phase_si;
+	  std::string pe_reaction;
+	  std::string as;
+	  LDBLE gfw;
+};
+
+#endif // ISOLUTIONCOMP_H_INCLUDED

src/phreeqcpp/KineticsComp.cxx

@@ -0,0 +1,355 @@
+// KineticsComp.cxx: implementation of the cxxKineticsComp class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <cassert>				// assert
+#include <algorithm>			// std::sort
+
+#include "Utils.h"				// define first
+#include "Phreeqc.h"
+#include "KineticsComp.h"
+//#include "Dictionary.h"
+#include "phqalloc.h"
+#include "Dictionary.h"
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+cxxKineticsComp::cxxKineticsComp(PHRQ_io *io)
+:
+PHRQ_base(io)
+	//
+	// default constructor for cxxKineticsComp 
+	//
+{
+	tol = 1e-8;
+	m = -1;
+	m0 = -1;
+	moles = 0.0;
+	initial_moles = 0;
+	namecoef.type = cxxNameDouble::ND_NAME_COEF;
+}
+cxxKineticsComp::~cxxKineticsComp()
+{
+}
+
+#ifdef SKIP
+void
+cxxKineticsComp::dump_xml(std::ostream & s_oss, unsigned int indent) const const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// Kinetics_Comp element and attributes
+
+	s_oss << indent0 << "formula=\"" << this->formula << "\"" << "\n";
+	s_oss << indent0 << "moles=\"" << this->moles << "\"" << "\n";
+	s_oss << indent0 << "la=\"" << this->la << "\"" << "\n";
+	s_oss << indent0 << "charge_balance=\"" << this->
+		charge_balance << "\"" << "\n";
+	if (this->phase_name != NULL)
+	{
+		s_oss << indent0 << "phase_name=\"" << this->
+			phase_name << "\"" << "\n";
+	}
+	if (this->rate_name != NULL)
+	{
+		s_oss << indent0 << "rate_name=\"" << this->
+			rate_name << "\"" << "\n";
+	}
+	s_oss << indent0 << "phase_proportion=\"" << this->
+		phase_proportion << "\"" << "\n";
+
+	// totals
+	s_oss << indent0;
+	s_oss << "<totals " << "\n";
+	this->totals.dump_xml(s_oss, indent + 1);
+
+	// formula_totals
+	s_oss << indent0;
+	s_oss << "<formula_totals " << "\n";
+	this->formula_totals.dump_xml(s_oss, indent + 1);
+}
+#endif
+void
+cxxKineticsComp::dump_raw(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// Kinetics_Comp element and attributes
+	s_oss << indent1 << "# KINETICS_MODIFY candidate identifiers #\n";
+	s_oss << indent1 << "-tol                   " << this->tol << "\n";
+	s_oss << indent1 << "-m                     " << this->m << "\n";
+	s_oss << indent1 << "-m0                    " << this->m0 << "\n";
+
+	// namecoef
+	s_oss << indent1;
+	s_oss << "-namecoef" << "\n";
+	this->namecoef.dump_raw(s_oss, indent + 2);
+
+	// d_params
+	s_oss << indent1;
+	s_oss << "-d_params" << "\n";
+	{
+		int i = 0;
+		s_oss << indent2;
+		for (std::vector < LDBLE >::const_iterator it = d_params.begin();
+			 it != d_params.end(); it++)
+		{
+			if (i++ == 5)
+			{
+				s_oss << "\n";
+				s_oss << indent2;
+				i = 0;
+			}
+			s_oss << *it << " ";
+		}
+		s_oss << "\n";
+	}
+
+	s_oss << indent1 << "# KineticsComp workspace variables #\n";
+	s_oss << indent1 << "-moles                 " << this->moles << "\n";
+	s_oss << indent1 << "-initial_moles         " << this->initial_moles << "\n";
+}
+
+void
+cxxKineticsComp::read_raw(CParser & parser, bool check)
+{
+	std::string str;
+
+
+	std::istream::pos_type ptr;
+	std::istream::pos_type next_char;
+	std::string token;
+	int opt_save;
+
+	std::vector < LDBLE > temp_d_params;
+	opt_save = CParser::OPT_ERROR;
+	bool tol_defined(false);
+	bool m_defined(false);
+	bool m0_defined(false);
+	bool d_params_defined(false);
+
+	for (;;)
+	{
+		int opt = parser.get_option(vopts, next_char);
+		if (opt == CParser::OPT_DEFAULT)
+		{
+			opt = opt_save;
+		}
+
+		switch (opt)
+		{
+		case CParser::OPT_EOF:
+			break;
+		case CParser::OPT_KEYWORD:
+			break;
+		case CParser::OPT_DEFAULT:
+		case CParser::OPT_ERROR:
+			opt = CParser::OPT_KEYWORD;
+			// Allow return to Kinetics for more processing
+			break;
+
+		case 0:				// rate_name not used
+			parser.warning_msg("Rate_name ignored. Define in -comp.");
+			break;
+
+		case 1:				// tol
+			if (!(parser.get_iss() >> this->tol))
+			{
+				this->tol = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for tol.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			tol_defined = true;
+			break;
+
+		case 2:				// m
+			if (!(parser.get_iss() >> this->m))
+			{
+				this->m = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for m.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			m_defined = true;
+			break;
+
+		case 3:				// m0
+			if (!(parser.get_iss() >> this->m0))
+			{
+				this->m0 = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for m0.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			m0_defined = true;
+			break;
+
+
+		case 4:				// moles
+			if (!(parser.get_iss() >> this->moles))
+			{
+				this->moles = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for moles.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+
+		case 5:				// namecoef
+			if (this->namecoef.read_raw(parser, next_char) !=
+				CParser::PARSER_OK)
+			{
+				parser.incr_input_error();
+				parser.
+					error_msg
+					("Expected element name and molality for namecoef.",
+					 PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = 5;
+			break;
+
+		case 6:				// d_params
+			while (parser.copy_token(token, next_char) == CParser::TT_DIGIT)
+			{
+				double dd;
+				sscanf(token.c_str(), "%lf", &dd);
+				temp_d_params.push_back((LDBLE) dd);
+				d_params_defined = true;
+			}
+			opt_save = 6;
+			break;
+		case 7:				// initial_moles
+			if (!(parser.get_iss() >> this->initial_moles))
+			{
+				this->moles = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for initial_moles.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+		}
+		if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
+			break;
+	}
+
+	if (d_params_defined)
+	{
+		this->d_params = temp_d_params;
+	}
+	if (check)
+	{
+		// members that must be defined
+		if (tol_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Tol not defined for KineticsComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (m_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("M not defined for KineticsComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (m0_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("M0 not defined for KineticsComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+	}
+}
+
+void
+cxxKineticsComp::add(const cxxKineticsComp & addee, LDBLE extensive)
+{
+	if (extensive == 0.0)
+		return;
+	if (addee.rate_name.size() == 0)
+		return;
+	// this and addee must have same name
+	// otherwise generate a new KineticsComp with multiply
+	if (this->rate_name.size() == 0 && addee.rate_name.size() == 0)
+	{
+		return;
+	}
+	assert(this->rate_name == addee.rate_name);
+	this->m += addee.m * extensive;
+	this->m0 += addee.m0 * extensive;
+	this->moles += addee.moles * extensive;
+}
+
+void
+cxxKineticsComp::multiply(LDBLE extensive)
+{
+	this->m *= extensive;
+	this->m0 *= extensive;
+	this->moles *= extensive;
+}
+void
+cxxKineticsComp::Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles)
+{
+	ints.push_back(dictionary.Find(this->rate_name));
+	this->namecoef.Serialize(dictionary, ints, doubles);
+	doubles.push_back(this->tol);
+	doubles.push_back(this->m);
+	doubles.push_back(this->m0);
+	ints.push_back((int) this->d_params.size());
+	for (size_t i = 0; i < this->d_params.size(); i++)
+	{
+		doubles.push_back(d_params[i]);
+	}
+	doubles.push_back(this->moles);
+	doubles.push_back(this->initial_moles);
+	this->moles_of_reaction.Serialize(dictionary, ints, doubles);
+}
+void
+cxxKineticsComp::Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd)
+{
+	this->rate_name = dictionary.GetWords()[ints[ii++]];
+	this->namecoef.Deserialize(dictionary, ints, doubles, ii, dd);
+	this->tol = doubles[dd++];
+	this->m = doubles[dd++];
+	this->m0 = doubles[dd++];
+	int n = ints[ii++];
+	this->d_params.clear();
+	for (int j = 0; j < n; j++)
+	{
+		this->d_params.push_back(doubles[dd++]);
+	}
+	this->moles = doubles[dd++];
+	this->initial_moles = doubles[dd++];
+	this->moles_of_reaction.Deserialize(dictionary, ints, doubles, ii, dd);
+}
+const std::vector< std::string >::value_type temp_vopts[] = {
+	std::vector< std::string >::value_type("rate_name_not_used"),	// 0
+	std::vector< std::string >::value_type("tol"),	                // 1
+	std::vector< std::string >::value_type("m"),	                // 2
+	std::vector< std::string >::value_type("m0"),	                // 3
+	std::vector< std::string >::value_type("moles"),	            // 4
+	std::vector< std::string >::value_type("namecoef"),	            // 5
+	std::vector< std::string >::value_type("d_params"),	            // 6
+	std::vector< std::string >::value_type("initial_moles") 	    // 7
+};									   
+const std::vector< std::string > cxxKineticsComp::vopts(temp_vopts, temp_vopts + sizeof temp_vopts / sizeof temp_vopts[0]);

src/phreeqcpp/KineticsComp.h

@@ -0,0 +1,81 @@
+#if !defined(KINETICSCOMP_H_INCLUDED)
+#define KINETICSCOMP_H_INCLUDED
+
+#include <cassert>				// assert
+#include <map>					// std::map
+#include <string>				// std::string
+#include <list>					// std::list
+#include <vector>				// std::vector
+
+#include "NameDouble.h"
+
+class cxxKineticsComp: public PHRQ_base
+{
+
+public:
+	cxxKineticsComp(PHRQ_io *io=NULL);
+	cxxKineticsComp(struct kinetics_comp *, PHRQ_io *io=NULL);
+	virtual ~cxxKineticsComp();
+
+	void dump_xml(std::ostream & os, unsigned int indent = 0) const;
+
+	void dump_raw(std::ostream & s_oss, unsigned int indent) const;
+
+	void read_raw(CParser & parser, bool check = true);
+
+	const std::string &Get_rate_name() const
+	{
+		return this->rate_name;
+	}
+	void Set_rate_name(const char * s)
+	{
+		if (s != NULL)
+			this->rate_name = std::string(s);
+		else
+			this->rate_name.clear();
+	}
+
+	cxxNameDouble &Get_namecoef(void) {return namecoef;}
+	const cxxNameDouble &Get_namecoef(void)const {return namecoef;}
+	void Set_namecoef(const cxxNameDouble nd) {namecoef = nd;}
+	LDBLE Get_tol(void) const {return tol;}	
+	void Set_tol(LDBLE t) {tol = t;}	
+	LDBLE Get_m(void) const {return m;}	
+	void Set_m(LDBLE t) {m = t;}	
+	LDBLE Get_m0(void) const {return m0;}
+	void Set_m0(LDBLE t) {m0 = t;}	
+	LDBLE Get_moles(void) const {return moles;}
+	void Set_moles(LDBLE t) {moles = t;}
+	LDBLE Get_initial_moles(void) const {return initial_moles;}
+	void Set_initial_moles(LDBLE t) {initial_moles = t;}	
+	std::vector < LDBLE > &Get_d_params(void) {return d_params;};
+	const std::vector < LDBLE > &Get_d_params(void)const {return d_params;};
+	std::vector < std::string > &Get_c_params(void) {return c_params;};
+	cxxNameDouble &Get_moles_of_reaction(void) {return moles_of_reaction;}
+	const cxxNameDouble &Get_moles_of_reaction(void)const {return moles_of_reaction;}
+	void Set_moles_of_reaction(const cxxNameDouble nd) {moles_of_reaction = nd;}
+
+	void add(const cxxKineticsComp & comp, LDBLE extensive);
+	void multiply(LDBLE extensive);
+	void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
+	void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
+
+  protected:
+	  std::string rate_name;
+	  // KINETICS_MODIFY candidates
+	  cxxNameDouble namecoef;		//stoichiometry of reaction
+	  LDBLE tol;
+	  LDBLE m;
+	  LDBLE m0;
+	  std::vector< LDBLE > d_params;
+	  std::vector< std::string > c_params;  // Not used
+	  // kinetics workspace variables
+	  LDBLE moles;
+	  LDBLE initial_moles;
+	  cxxNameDouble moles_of_reaction;
+	  const static std::vector < std::string > vopts;
+  public:
+
+};
+
+#endif // !defined(KINETICSCOMP_H_INCLUDED)

src/phreeqcpp/Makefile

@@ -0,0 +1,639 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# src/Makefile.  Generated from Makefile.in by configure.
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+
+
+
+pkgdatadir = $(datadir)/phreeqc
+pkgincludedir = $(includedir)/phreeqc
+pkglibdir = $(libdir)/phreeqc
+pkglibexecdir = $(libexecdir)/phreeqc
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+bin_PROGRAMS = phreeqc$(EXEEXT)
+am__append_1 = \
+	cl1mp.cpp
+
+subdir = src
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+	$(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+am__installdirs = "$(DESTDIR)$(bindir)"
+PROGRAMS = $(bin_PROGRAMS)
+am__phreeqc_SOURCES_DIST = class_main.cpp cxxKinetics.cxx \
+	cxxKinetics.h cxxMix.cxx cxxMix.h dumper.cpp dumper.h \
+	Exchange.cxx Exchange.h ExchComp.cxx ExchComp.h GasComp.cxx \
+	GasComp.h GasPhase.cxx GasPhase.h ISolution.cxx ISolution.h \
+	ISolutionComp.cxx ISolutionComp.h Keywords.cpp Keywords.h \
+	KineticsComp.cxx KineticsComp.h NameDouble.cxx NameDouble.h \
+	NumKeyword.cxx NumKeyword.h Parser.cxx Parser.h PBasic.cpp \
+	PBasic.h Phreeqc.cpp Phreeqc.h PHRQ_base.cxx PHRQ_base.h \
+	PHRQ_io.cpp PHRQ_io.h PPassemblage.cxx PPassemblage.h \
+	PPassemblageComp.cxx PPassemblageComp.h Pressure.cxx \
+	Pressure.h Reaction.cxx Reaction.h ReadClass.cxx runner.cpp \
+	runner.h SelectedOutput.cpp SelectedOutput.h Solution.cxx \
+	Solution.h SolutionIsotope.cxx SolutionIsotope.h \
+	SSassemblage.cxx SSassemblage.h SS.cxx SS.h SScomp.cxx \
+	SScomp.h StorageBin.cxx StorageBin.h StorageBinList.cpp \
+	StorageBinList.h Surface.cxx Surface.h SurfaceCharge.cxx \
+	SurfaceCharge.h SurfaceComp.cxx SurfaceComp.h System.cxx \
+	System.h Temperature.cxx Temperature.h Use.cpp Use.h \
+	UserPunch.cpp UserPunch.h Utils.cxx Utils.h advection.cpp \
+	basicsubs.cpp cl1.cpp cvdense.cpp cvdense.h cvode.cpp cvode.h \
+	dense.cpp dense.h dw.cpp gases.cpp global_structures.h \
+	input.cpp integrate.cpp inverse.cpp isotopes.cpp kinetics.cpp \
+	mainsubs.cpp model.cpp NA.h nvector.cpp nvector.h \
+	nvector_serial.cpp nvector_serial.h parse.cpp phqalloc.cpp \
+	phqalloc.h PHRQ_io_output.cpp phrqtype.h pitzer.cpp \
+	pitzer_structures.cpp prep.cpp print.cpp read.cpp readtr.cpp \
+	sit.cpp smalldense.cpp smalldense.h spread.cpp step.cpp \
+	structures.cpp sundialsmath.cpp sundialsmath.h sundialstypes.h \
+	tally.cpp tidy.cpp transport.cpp utilities.cpp cl1mp.cpp
+am__objects_1 = cl1mp.$(OBJEXT)
+am_phreeqc_OBJECTS = class_main.$(OBJEXT) cxxKinetics.$(OBJEXT) \
+	cxxMix.$(OBJEXT) dumper.$(OBJEXT) Exchange.$(OBJEXT) \
+	ExchComp.$(OBJEXT) GasComp.$(OBJEXT) GasPhase.$(OBJEXT) \
+	ISolution.$(OBJEXT) ISolutionComp.$(OBJEXT) Keywords.$(OBJEXT) \
+	KineticsComp.$(OBJEXT) NameDouble.$(OBJEXT) \
+	NumKeyword.$(OBJEXT) Parser.$(OBJEXT) PBasic.$(OBJEXT) \
+	Phreeqc.$(OBJEXT) PHRQ_base.$(OBJEXT) PHRQ_io.$(OBJEXT) \
+	PPassemblage.$(OBJEXT) PPassemblageComp.$(OBJEXT) \
+	Pressure.$(OBJEXT) Reaction.$(OBJEXT) ReadClass.$(OBJEXT) \
+	runner.$(OBJEXT) SelectedOutput.$(OBJEXT) Solution.$(OBJEXT) \
+	SolutionIsotope.$(OBJEXT) SSassemblage.$(OBJEXT) SS.$(OBJEXT) \
+	SScomp.$(OBJEXT) StorageBin.$(OBJEXT) StorageBinList.$(OBJEXT) \
+	Surface.$(OBJEXT) SurfaceCharge.$(OBJEXT) \
+	SurfaceComp.$(OBJEXT) System.$(OBJEXT) Temperature.$(OBJEXT) \
+	Use.$(OBJEXT) UserPunch.$(OBJEXT) Utils.$(OBJEXT) \
+	advection.$(OBJEXT) basicsubs.$(OBJEXT) cl1.$(OBJEXT) \
+	cvdense.$(OBJEXT) cvode.$(OBJEXT) dense.$(OBJEXT) dw.$(OBJEXT) \
+	gases.$(OBJEXT) input.$(OBJEXT) integrate.$(OBJEXT) \
+	inverse.$(OBJEXT) isotopes.$(OBJEXT) kinetics.$(OBJEXT) \
+	mainsubs.$(OBJEXT) model.$(OBJEXT) nvector.$(OBJEXT) \
+	nvector_serial.$(OBJEXT) parse.$(OBJEXT) phqalloc.$(OBJEXT) \
+	PHRQ_io_output.$(OBJEXT) pitzer.$(OBJEXT) \
+	pitzer_structures.$(OBJEXT) prep.$(OBJEXT) print.$(OBJEXT) \
+	read.$(OBJEXT) readtr.$(OBJEXT) sit.$(OBJEXT) \
+	smalldense.$(OBJEXT) spread.$(OBJEXT) step.$(OBJEXT) \
+	structures.$(OBJEXT) sundialsmath.$(OBJEXT) tally.$(OBJEXT) \
+	tidy.$(OBJEXT) transport.$(OBJEXT) utilities.$(OBJEXT) \
+	$(am__objects_1)
+phreeqc_OBJECTS = $(am_phreeqc_OBJECTS)
+phreeqc_LDADD = $(LDADD)
+am__DEPENDENCIES_1 =
+phreeqc_DEPENDENCIES = $(am__DEPENDENCIES_1)
+DEFAULT_INCLUDES = -I.
+depcomp = $(SHELL) $(top_srcdir)/config/depcomp
+am__depfiles_maybe = depfiles
+am__mv = mv -f
+CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
+	$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+CXXLD = $(CXX)
+CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
+	-o $@
+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
+	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+CCLD = $(CC)
+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+SOURCES = $(phreeqc_SOURCES)
+DIST_SOURCES = $(am__phreeqc_SOURCES_DIST)
+ETAGS = etags
+CTAGS = ctags
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = ${SHELL} /raid/home/dlpark/programs/phreeqc3-trunk/config/missing --run aclocal-1.11
+AMTAR = ${SHELL} /raid/home/dlpark/programs/phreeqc3-trunk/config/missing --run tar
+AUTOCONF = ${SHELL} /raid/home/dlpark/programs/phreeqc3-trunk/config/missing --run autoconf
+AUTOHEADER = ${SHELL} /raid/home/dlpark/programs/phreeqc3-trunk/config/missing --run autoheader
+AUTOMAKE = ${SHELL} /raid/home/dlpark/programs/phreeqc3-trunk/config/missing --run automake-1.11
+AWK = gawk
+CPPFLAGS = 
+CXX = g++
+CXXCPP = g++ -E
+CXXDEPMODE = depmode=gcc3
+CXXFLAGS = -g -O2
+CYGPATH_W = echo
+DEFS = -DPACKAGE_NAME=\"phreeqc\" -DPACKAGE_TARNAME=\"phreeqc\" -DPACKAGE_VERSION=\"3.0.0-7109\" -DPACKAGE_STRING=\"phreeqc\ 3.0.0-7109\" -DPACKAGE_BUGREPORT=\"dlpark@usgs.gov\" -DPACKAGE=\"phreeqc\" -DVERSION=\"3.0.0-7109\" -DNDEBUG=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_FLOAT_H=1 -DHAVE_LIMITS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STDDEF_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DHAVE_MEMMOVE=1 -DHAVE_MEMSET=1 -DHAVE_STRCHR=1 -DHAVE_STRCSPN=1 -DHAVE_STRTOL=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_ISFINITE=/\*\*/ -DHAVE_FINITE=/\*\*/ -DHAVE_ISNAN=1 -DINVERSE_CL1MP=1
+DEPDIR = .deps
+ECHO_C = 
+ECHO_N = -n
+ECHO_T = 
+EGREP = /bin/grep -E
+EXEEXT = 
+GREP = /bin/grep
+INSTALL = /usr/bin/install -c
+INSTALL_DATA = ${INSTALL} -m 644
+INSTALL_PROGRAM = ${INSTALL}
+INSTALL_SCRIPT = ${INSTALL}
+INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
+LDFLAGS = 
+LIBGMP = -lgmp
+LIBOBJS = 
+LIBS = 
+LTLIBOBJS = 
+MAKEINFO = ${SHELL} /raid/home/dlpark/programs/phreeqc3-trunk/config/missing --run makeinfo
+MKDIR_P = /bin/mkdir -p
+OBJEXT = o
+PACKAGE = phreeqc
+PACKAGE_BUGREPORT = dlpark@usgs.gov
+PACKAGE_NAME = phreeqc
+PACKAGE_STRING = phreeqc 3.0.0-7109
+PACKAGE_TARNAME = phreeqc
+PACKAGE_VERSION = 3.0.0-7109
+PATH_SEPARATOR = :
+POW_LIB = 
+SET_MAKE = 
+SHELL = /bin/sh
+STRIP = 
+VERSION = 3.0.0-7109
+abs_builddir = /raid/home/dlpark/programs/phreeqc3-trunk/src
+abs_srcdir = /raid/home/dlpark/programs/phreeqc3-trunk/src
+abs_top_builddir = /raid/home/dlpark/programs/phreeqc3-trunk
+abs_top_srcdir = /raid/home/dlpark/programs/phreeqc3-trunk
+ac_ct_CXX = g++
+am__include = include
+am__leading_dot = .
+am__quote = 
+am__tar = ${AMTAR} chof - "$$tardir"
+am__untar = ${AMTAR} xf -
+bindir = ${exec_prefix}/bin
+build_alias = 
+builddir = .
+datadir = ${datarootdir}
+datarootdir = ${prefix}/share
+docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
+dvidir = ${docdir}
+exec_prefix = ${prefix}
+host_alias = 
+htmldir = ${docdir}
+includedir = ${prefix}/include
+infodir = ${datarootdir}/info
+install_sh = ${SHELL} /raid/home/dlpark/programs/phreeqc3-trunk/config/install-sh
+libdir = ${exec_prefix}/lib
+libexecdir = ${exec_prefix}/libexec
+localedir = ${datarootdir}/locale
+localstatedir = ${prefix}/var
+mandir = ${datarootdir}/man
+mkdir_p = /bin/mkdir -p
+oldincludedir = /usr/include
+pdfdir = ${docdir}
+prefix = /usr/local
+program_transform_name = s,x,x,
+psdir = ${docdir}
+sbindir = ${exec_prefix}/sbin
+sharedstatedir = ${prefix}/com
+srcdir = .
+sysconfdir = ${prefix}/etc
+target_alias = 
+top_build_prefix = ../
+top_builddir = ..
+top_srcdir = ..
+AM_CPPFLAGS = -I$(top_srcdir)/src -I$(top_srcdir)/src/phreeqc
+
+# sources for phreeqc
+phreeqc_SOURCES = class_main.cpp cxxKinetics.cxx cxxKinetics.h \
+	cxxMix.cxx cxxMix.h dumper.cpp dumper.h Exchange.cxx \
+	Exchange.h ExchComp.cxx ExchComp.h GasComp.cxx GasComp.h \
+	GasPhase.cxx GasPhase.h ISolution.cxx ISolution.h \
+	ISolutionComp.cxx ISolutionComp.h Keywords.cpp Keywords.h \
+	KineticsComp.cxx KineticsComp.h NameDouble.cxx NameDouble.h \
+	NumKeyword.cxx NumKeyword.h Parser.cxx Parser.h PBasic.cpp \
+	PBasic.h Phreeqc.cpp Phreeqc.h PHRQ_base.cxx PHRQ_base.h \
+	PHRQ_io.cpp PHRQ_io.h PPassemblage.cxx PPassemblage.h \
+	PPassemblageComp.cxx PPassemblageComp.h Pressure.cxx \
+	Pressure.h Reaction.cxx Reaction.h ReadClass.cxx runner.cpp \
+	runner.h SelectedOutput.cpp SelectedOutput.h Solution.cxx \
+	Solution.h SolutionIsotope.cxx SolutionIsotope.h \
+	SSassemblage.cxx SSassemblage.h SS.cxx SS.h SScomp.cxx \
+	SScomp.h StorageBin.cxx StorageBin.h StorageBinList.cpp \
+	StorageBinList.h Surface.cxx Surface.h SurfaceCharge.cxx \
+	SurfaceCharge.h SurfaceComp.cxx SurfaceComp.h System.cxx \
+	System.h Temperature.cxx Temperature.h Use.cpp Use.h \
+	UserPunch.cpp UserPunch.h Utils.cxx Utils.h advection.cpp \
+	basicsubs.cpp cl1.cpp cvdense.cpp cvdense.h cvode.cpp cvode.h \
+	dense.cpp dense.h dw.cpp gases.cpp global_structures.h \
+	input.cpp integrate.cpp inverse.cpp isotopes.cpp kinetics.cpp \
+	mainsubs.cpp model.cpp NA.h nvector.cpp nvector.h \
+	nvector_serial.cpp nvector_serial.h parse.cpp phqalloc.cpp \
+	phqalloc.h PHRQ_io_output.cpp phrqtype.h pitzer.cpp \
+	pitzer_structures.cpp prep.cpp print.cpp read.cpp readtr.cpp \
+	sit.cpp smalldense.cpp smalldense.h spread.cpp step.cpp \
+	structures.cpp sundialsmath.cpp sundialsmath.h sundialstypes.h \
+	tally.cpp tidy.cpp transport.cpp utilities.cpp $(am__append_1)
+LDADD = $(LIBGMP)
+all: all-am
+
+.SUFFIXES:
+.SUFFIXES: .cpp .cxx .o .obj
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+	@for dep in $?; do \
+	  case '$(am__configure_deps)' in \
+	    *$$dep*) \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
+	      exit 1;; \
+	  esac; \
+	done; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign src/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --foreign src/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+	@case '$?' in \
+	  *config.status*) \
+	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+	  *) \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+	esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+install-binPROGRAMS: $(bin_PROGRAMS)
+	@$(NORMAL_INSTALL)
+	test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
+	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
+	for p in $$list; do echo "$$p $$p"; done | \
+	sed 's/$(EXEEXT)$$//' | \
+	while read p p1; do if test -f $$p; \
+	  then echo "$$p"; echo "$$p"; else :; fi; \
+	done | \
+	sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+	    -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
+	sed 'N;N;N;s,\n, ,g' | \
+	$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
+	  { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
+	    if ($$2 == $$4) files[d] = files[d] " " $$1; \
+	    else { print "f", $$3 "/" $$4, $$1; } } \
+	  END { for (d in files) print "f", d, files[d] }' | \
+	while read type dir files; do \
+	    if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
+	    test -z "$$files" || { \
+	      echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
+	      $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
+	    } \
+	; done
+
+uninstall-binPROGRAMS:
+	@$(NORMAL_UNINSTALL)
+	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
+	files=`for p in $$list; do echo "$$p"; done | \
+	  sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
+	      -e 's/$$/$(EXEEXT)/' `; \
+	test -n "$$list" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(bindir)" && rm -f $$files
+
+clean-binPROGRAMS:
+	-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+phreeqc$(EXEEXT): $(phreeqc_OBJECTS) $(phreeqc_DEPENDENCIES) 
+	@rm -f phreeqc$(EXEEXT)
+	$(CXXLINK) $(phreeqc_OBJECTS) $(phreeqc_LDADD) $(LIBS)
+
+mostlyclean-compile:
+	-rm -f *.$(OBJEXT)
+
+distclean-compile:
+	-rm -f *.tab.c
+
+include ./$(DEPDIR)/ExchComp.Po
+include ./$(DEPDIR)/Exchange.Po
+include ./$(DEPDIR)/GasComp.Po
+include ./$(DEPDIR)/GasPhase.Po
+include ./$(DEPDIR)/ISolution.Po
+include ./$(DEPDIR)/ISolutionComp.Po
+include ./$(DEPDIR)/Keywords.Po
+include ./$(DEPDIR)/KineticsComp.Po
+include ./$(DEPDIR)/NameDouble.Po
+include ./$(DEPDIR)/NumKeyword.Po
+include ./$(DEPDIR)/PBasic.Po
+include ./$(DEPDIR)/PHRQ_base.Po
+include ./$(DEPDIR)/PHRQ_io.Po
+include ./$(DEPDIR)/PHRQ_io_output.Po
+include ./$(DEPDIR)/PPassemblage.Po
+include ./$(DEPDIR)/PPassemblageComp.Po
+include ./$(DEPDIR)/Parser.Po
+include ./$(DEPDIR)/Phreeqc.Po
+include ./$(DEPDIR)/Pressure.Po
+include ./$(DEPDIR)/Reaction.Po
+include ./$(DEPDIR)/ReadClass.Po
+include ./$(DEPDIR)/SS.Po
+include ./$(DEPDIR)/SSassemblage.Po
+include ./$(DEPDIR)/SScomp.Po
+include ./$(DEPDIR)/SelectedOutput.Po
+include ./$(DEPDIR)/Solution.Po
+include ./$(DEPDIR)/SolutionIsotope.Po
+include ./$(DEPDIR)/StorageBin.Po
+include ./$(DEPDIR)/StorageBinList.Po
+include ./$(DEPDIR)/Surface.Po
+include ./$(DEPDIR)/SurfaceCharge.Po
+include ./$(DEPDIR)/SurfaceComp.Po
+include ./$(DEPDIR)/System.Po
+include ./$(DEPDIR)/Temperature.Po
+include ./$(DEPDIR)/Use.Po
+include ./$(DEPDIR)/UserPunch.Po
+include ./$(DEPDIR)/Utils.Po
+include ./$(DEPDIR)/advection.Po
+include ./$(DEPDIR)/basicsubs.Po
+include ./$(DEPDIR)/cl1.Po
+include ./$(DEPDIR)/cl1mp.Po
+include ./$(DEPDIR)/class_main.Po
+include ./$(DEPDIR)/cvdense.Po
+include ./$(DEPDIR)/cvode.Po
+include ./$(DEPDIR)/cxxKinetics.Po
+include ./$(DEPDIR)/cxxMix.Po
+include ./$(DEPDIR)/dense.Po
+include ./$(DEPDIR)/dumper.Po
+include ./$(DEPDIR)/dw.Po
+include ./$(DEPDIR)/gases.Po
+include ./$(DEPDIR)/input.Po
+include ./$(DEPDIR)/integrate.Po
+include ./$(DEPDIR)/inverse.Po
+include ./$(DEPDIR)/isotopes.Po
+include ./$(DEPDIR)/kinetics.Po
+include ./$(DEPDIR)/mainsubs.Po
+include ./$(DEPDIR)/model.Po
+include ./$(DEPDIR)/nvector.Po
+include ./$(DEPDIR)/nvector_serial.Po
+include ./$(DEPDIR)/parse.Po
+include ./$(DEPDIR)/phqalloc.Po
+include ./$(DEPDIR)/pitzer.Po
+include ./$(DEPDIR)/pitzer_structures.Po
+include ./$(DEPDIR)/prep.Po
+include ./$(DEPDIR)/print.Po
+include ./$(DEPDIR)/read.Po
+include ./$(DEPDIR)/readtr.Po
+include ./$(DEPDIR)/runner.Po
+include ./$(DEPDIR)/sit.Po
+include ./$(DEPDIR)/smalldense.Po
+include ./$(DEPDIR)/spread.Po
+include ./$(DEPDIR)/step.Po
+include ./$(DEPDIR)/structures.Po
+include ./$(DEPDIR)/sundialsmath.Po
+include ./$(DEPDIR)/tally.Po
+include ./$(DEPDIR)/tidy.Po
+include ./$(DEPDIR)/transport.Po
+include ./$(DEPDIR)/utilities.Po
+
+.cpp.o:
+	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+#	source='$<' object='$@' libtool=no \
+#	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
+#	$(CXXCOMPILE) -c -o $@ $<
+
+.cpp.obj:
+	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+#	source='$<' object='$@' libtool=no \
+#	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
+#	$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+
+.cxx.o:
+	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+#	source='$<' object='$@' libtool=no \
+#	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
+#	$(CXXCOMPILE) -c -o $@ $<
+
+.cxx.obj:
+	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+#	source='$<' object='$@' libtool=no \
+#	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
+#	$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+
+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
+	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	mkid -fID $$unique
+tags: TAGS
+
+TAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
+		$(TAGS_FILES) $(LISP)
+	set x; \
+	here=`pwd`; \
+	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	shift; \
+	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
+	  test -n "$$unique" || unique=$$empty_fix; \
+	  if test $$# -gt 0; then \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      "$$@" $$unique; \
+	  else \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      $$unique; \
+	  fi; \
+	fi
+ctags: CTAGS
+CTAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
+		$(TAGS_FILES) $(LISP)
+	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	test -z "$(CTAGS_ARGS)$$unique" \
+	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+	     $$unique
+
+GTAGS:
+	here=`$(am__cd) $(top_builddir) && pwd` \
+	  && $(am__cd) $(top_srcdir) \
+	  && gtags -i $(GTAGS_ARGS) "$$here"
+
+distclean-tags:
+	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+
+distdir: $(DISTFILES)
+	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	list='$(DISTFILES)'; \
+	  dist_files=`for file in $$list; do echo $$file; done | \
+	  sed -e "s|^$$srcdirstrip/||;t" \
+	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+	case $$dist_files in \
+	  */*) $(MKDIR_P) `echo "$$dist_files" | \
+			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+			   sort -u` ;; \
+	esac; \
+	for file in $$dist_files; do \
+	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+	  if test -d $$d/$$file; then \
+	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+	  else \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
+	    || exit 1; \
+	  fi; \
+	done
+check-am: all-am
+check: check-am
+all-am: Makefile $(PROGRAMS)
+installdirs:
+	for dir in "$(DESTDIR)$(bindir)"; do \
+	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+	done
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	  `test -z '$(STRIP)' || \
+	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
+
+distclean: distclean-am
+	-rm -rf ./$(DEPDIR)
+	-rm -f Makefile
+distclean-am: clean-am distclean-compile distclean-generic \
+	distclean-tags
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am:
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am: install-binPROGRAMS
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+	-rm -rf ./$(DEPDIR)
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-compile mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-binPROGRAMS
+
+.MAKE: install-am install-strip
+
+.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
+	clean-generic ctags distclean distclean-compile \
+	distclean-generic distclean-tags distdir dvi dvi-am html \
+	html-am info info-am install install-am install-binPROGRAMS \
+	install-data install-data-am install-dvi install-dvi-am \
+	install-exec install-exec-am install-html install-html-am \
+	install-info install-info-am install-man install-pdf \
+	install-pdf-am install-ps install-ps-am install-strip \
+	installcheck installcheck-am installdirs maintainer-clean \
+	maintainer-clean-generic mostlyclean mostlyclean-compile \
+	mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
+	uninstall-am uninstall-binPROGRAMS
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:

src/phreeqcpp/Makefile.am

@@ -0,0 +1,159 @@
+EXTRA_DIST=\
+	ChartHandler.cpp\
+	ChartHandler.h\
+	ChartObject.cpp\
+	ChartObject.h\
+	CurveObject.cpp\
+	CurveObject.h\
+	Form1.h\
+	Form1.2005.resX\
+	Form1.resX\
+	ZedGraph.dll	
+
+AM_CPPFLAGS=-I$(top_srcdir)/src -I$(top_srcdir)/src/common -I$(top_srcdir)/src/PhreeqcKeywords
+
+bin_PROGRAMS = phreeqc
+
+# sources for phreeqc
+phreeqc_SOURCES=\
+	advection.cpp\
+	basicsubs.cpp\
+	cl1.cpp\
+	class_main.cpp\
+	common/Parser.cxx\
+	common/Parser.h\
+	common/PHRQ_base.cxx\
+	common/PHRQ_base.h\
+	common/PHRQ_io.cpp\
+	common/PHRQ_io.h\
+	common/phrqtype.h\
+	common/Utils.cxx\
+	common/Utils.h\
+	cvdense.cpp\
+	cvdense.h\
+	cvode.cpp\
+	cvode.h\
+	cxxKinetics.cxx\
+	cxxKinetics.h\
+	cxxMix.cxx\
+	cxxMix.h\
+	dense.cpp\
+	dense.h\
+	Dictionary.cpp\
+	Dictionary.h\
+	dumper.cpp\
+	dumper.h\
+	Exchange.cxx\
+	Exchange.h\
+	ExchComp.cxx\
+	ExchComp.h\
+	GasComp.cxx\
+	GasComp.h\
+	gases.cpp\
+	GasPhase.cxx\
+	GasPhase.h\
+	global_structures.h\
+	input.cpp\
+	integrate.cpp\
+	inverse.cpp\
+	ISolution.cxx\
+	ISolution.h\
+	ISolutionComp.cxx\
+	ISolutionComp.h\
+	isotopes.cpp\
+	kinetics.cpp\
+	KineticsComp.cxx\
+	KineticsComp.h\
+	mainsubs.cpp\
+	model.cpp\
+	NA.h\
+	NameDouble.cxx\
+	NameDouble.h\
+	NumKeyword.cxx\
+	NumKeyword.h\
+	nvector.cpp\
+	nvector.h\
+	nvector_serial.cpp\
+	nvector_serial.h\
+	parse.cpp\
+	PBasic.cpp\
+	PBasic.h\
+	phqalloc.cpp\
+	phqalloc.h\
+	Phreeqc.cpp\
+	Phreeqc.h\
+	PhreeqcKeywords/Keywords.cpp\
+	PhreeqcKeywords/Keywords.h\
+	PHRQ_io_output.cpp\
+	pitzer.cpp\
+	pitzer_structures.cpp\
+	PPassemblage.cxx\
+	PPassemblage.h\
+	PPassemblageComp.cxx\
+	PPassemblageComp.h\
+	prep.cpp\
+	Pressure.cxx\
+	Pressure.h\
+	print.cpp\
+	Reaction.cxx\
+	Reaction.h\
+	read.cpp\
+	ReadClass.cxx\
+	readtr.cpp\
+	runner.cpp\
+	runner.h\
+	SelectedOutput.cpp\
+	SelectedOutput.h\
+	Serializer.cxx\
+	Serializer.h\
+	sit.cpp\
+	smalldense.cpp\
+	smalldense.h\
+	Solution.cxx\
+	Solution.h\
+	SolutionIsotope.cxx\
+	SolutionIsotope.h\
+	spread.cpp\
+	SS.cxx\
+	SS.h\
+	SSassemblage.cxx\
+	SSassemblage.h\
+	SScomp.cxx\
+	SScomp.h\
+	step.cpp\
+	StorageBin.cxx\
+	StorageBin.h\
+	StorageBinList.cpp\
+	StorageBinList.h\
+	structures.cpp\
+	sundialsmath.cpp\
+	sundialsmath.h\
+	sundialstypes.h\
+	Surface.cxx\
+	Surface.h\
+	SurfaceCharge.cxx\
+	SurfaceCharge.h\
+	SurfaceComp.cxx\
+	SurfaceComp.h\
+	System.cxx\
+	System.h\
+	tally.cpp\
+	Temperature.cxx\
+	Temperature.h\
+	tidy.cpp\
+	transport.cpp\
+	Use.cpp\
+	Use.h\
+	UserPunch.cpp\
+	UserPunch.h\
+	utilities.cpp
+
+if BUILD_GMP
+
+phreeqc_SOURCES+=\
+	cl1mp.cpp
+
+endif
+
+
+LDADD = $(LIBGMP)

src/phreeqcpp/Makefile.old

@@ -0,0 +1,986 @@
+# Makefile for PHREEQCPP
+#
+# Generates object files and executables for 2 versions of PHREEQCPP
+#	    Release
+#           Debug
+#
+# Serial verisons:   Release Debug
+#
+# Makefile sets CFG variable, cd's to appropriate directory, runs Makefile recursively
+# Recursive make sets appropriate compiler, objects, options, libraries, and compiles PHREEQC
+#
+
+PROGRAM = phreeqc
+
+CFG1 :=`uname`
+CFG :=$(shell echo $(CFG1) | sed "s/Linux.*/Linux/")
+ifeq ($(CFG), Linux)
+	SPOOL=>&
+	SPOOL2=
+	CONCAT=;
+else
+	SPOOL=>
+	SPOOL2=2>&1
+	CONCAT=&
+endif
+all: class_release class_debug
+
+Debug: class_debug
+debug: class_debug
+Class_debug: class_debug
+
+Release: class_release
+release: class_release
+Class_release: class_release
+
+Debug_64: class_debug_64
+debug_64: class_debug_64
+Class_debug_64: class_debug_64
+
+Release_64: class_release_64
+release_64: class_release_64
+Class_release_64: class_release_64
+
+
+CLASS_DEBUG_DIR        = Class_debug
+CLASS_DIR              = Class_release
+CLASS_DEBUG_64_DIR     = Class_debug_64
+CLASS_64_DIR           = Class_release_64
+MAKEFILE               = Makefile.old
+
+# -----------------------------------------------------------------------------
+# fixes shared object lookup error(SIGFPE floating point exception)
+HASH_STYLE=$(call ld-option, -Wl$(comma)--hash-style=sysv)
+
+
+#########################
+#### Serial Versions ####
+#########################
+.PHONY : Class_debug
+class_debug:
+	mkdir -p $(CLASS_DEBUG_DIR) 
+	cd $(CLASS_DEBUG_DIR); $(MAKE) -r -f ../$(MAKEFILE) CFG=CLASS_DEBUG $(PROGRAM)
+
+.PHONY : Class_release
+class_release:
+	mkdir -p $(CLASS_DIR) 
+	cd $(CLASS_DIR); $(MAKE) -r -f ../$(MAKEFILE) CFG=CLASS_RELEASE $(PROGRAM)
+.PHONY : Class_debug_64
+class_debug_64:
+	mkdir -p $(CLASS_DEBUG_64_DIR) 
+	cd $(CLASS_DEBUG_64_DIR); $(MAKE) -r -f ../$(MAKEFILE) CFG=CLASS_DEBUG_64 $(PROGRAM)
+
+.PHONY : Class_release_64
+class_release_64:
+	mkdir -p $(CLASS_64_DIR) 
+	cd $(CLASS_64_DIR); $(MAKE) -r -f ../$(MAKEFILE) CFG=CLASS_RELEASE_64 $(PROGRAM)
+
+# Recursive make begins here
+#
+# =============================================================================
+# Significant suffixes [assuming Fortran 90 (.f90)  source code]:
+# Significant suffixes [assuming Fortran 90 (.F90)  source code, needs to be preprocessed ]:
+# =============================================================================
+
+#SRC     = ../phreeqc
+.SUFFIXES : .o .c .cxx .cpp
+
+# compilers
+
+# -----------------------------------------------------------------------------
+.c.o :
+	${CXX} ${CXXFLAGS} -c -o $@ $<
+
+.cxx.o :
+	${CXX} ${CXXFLAGS} -c -o $@ $<
+
+.cpp.o :
+	${CXX} ${CXXFLAGS} -c -o $@ $<
+
+# -----------------------------------------------------------------------------
+#hdf options
+#HDF5_ROOT=$(HOME)/../../usr
+#HDF5_INCLUDES=-I$(HDF5_ROOT)/src
+#HDF5_LIBS=${HDF5_ROOT}/lib/libhdf5.a -lz -lpthread  
+
+# -----------------------------------------------------------------------------
+# #define compile options
+
+# -----------------------------------------------------------------------------
+# #define gmp for inverse modeling
+# comment the following lines to remove multiprecision option
+
+# -----------------------------------------------------------------------------
+#efence for debugging
+EFENCE_LIB=-L$(HOME)/packages/efence
+
+# -----------------------------------------------------------------------------
+# 4 Versions
+# -----------------------------------------------------------------------------
+ifeq ($(CFG), CLASS_DEBUG)
+  INVERSE_CL1MP=
+  ifdef INVERSE_CL1MP
+	DEFINE_INVERSE_CL1MP=-DINVERSE_CL1MP
+	CL1MP_OBJS=cl1mp.o
+#	CL1MP_LIB=-lgmp
+	CL1MP_LIB=/z/parkplace/usr/lib/libgmp.a 
+  endif
+  DEFINES      = -DUSE_PHRQ_ALLOC $(DEFINE_INVERSE_CL1MP) # -DPHREEQC2
+  VPATH        = ..:../PhreeqcKeywords:../common
+  INCLUDES     = -I.. -I../PhreeqcKeywords -I../common
+  CXX          = g++
+  CXXFLAGS     = -Wall -g $(DEFINES) $(INCLUDES) 
+  OBJECT_FILES = $(CLASS_FILES) $(COMMON_COBJS) $(COMMON_CXXOBJS) $(CL1MP_OBJS)
+  LD_FLAGS     = -lm ${CL1MP_LIB} ${HASH_STYLE}
+endif
+
+ifeq ($(CFG), CLASS_RELEASE)
+  INVERSE_CL1MP=
+  ifdef INVERSE_CL1MP
+	DEFINE_INVERSE_CL1MP=-DINVERSE_CL1MP
+	CL1MP_OBJS=cl1mp.o
+#	CL1MP_LIB=-lgmp
+	CL1MP_LIB=/z/parkplace/usr/lib/libgmp.a 
+  endif
+  DEFINES      = -DNDEBUG $(DEFINE_INVERSE_CL1MP) # -DPHREEQC2
+  VPATH        = ..:../PhreeqcKeywords:../common
+  INCLUDES     = -I.. -I../PhreeqcKeywords -I../common
+  CXX          = g++
+  CXXFLAGS     = -Wall -pedantic -O3 $(DEFINES) $(INCLUDES)
+  OBJECT_FILES = $(CLASS_FILES) $(COMMON_COBJS) $(COMMON_CXXOBJS) $(CL1MP_OBJS)
+  LD_FLAGS     = -lm ${CL1MP_LIB} ${HASH_STYLE}
+endif
+
+ifeq ($(CFG), CLASS_DEBUG_64)
+#  INVERSE_CL1MP=
+  ifdef INVERSE_CL1MP
+	DEFINE_INVERSE_CL1MP=-DINVERSE_CL1MP
+	CL1MP_OBJS=cl1mp.o
+	CL1MP_LIB=libgmp.a 
+  endif
+  DEFINES      = -DUSE_PHRQ_ALLOC $(DEFINE_INVERSE_CL1MP) # -DPHREEQC2
+  VPATH        = ..:../PhreeqcKeywords:../common
+  INCLUDES     = -I.. -I../PhreeqcKeywords -I../common
+  CXX          = g++
+  CXXFLAGS     = -Wall -g $(DEFINES) $(INCLUDES) 
+  OBJECT_FILES = $(CLASS_FILES) $(COMMON_COBJS) $(COMMON_CXXOBJS) $(CL1MP_OBJS)
+  LD_FLAGS     = -lm ${CL1MP_LIB} ${HASH_STYLE}
+endif
+
+ifeq ($(CFG), CLASS_RELEASE_64)
+  INVERSE_CL1MP=
+  ifdef INVERSE_CL1MP
+	DEFINE_INVERSE_CL1MP=-DINVERSE_CL1MP
+	CL1MP_OBJS=cl1mp.o
+	CL1MP_LIB=/usr/lib64/libgmp.a 
+  endif
+  DEFINES      = -DNDEBUG $(DEFINE_INVERSE_CL1MP) # -DUSE_PHRQ_ALLOC # -DR_SO 
+  VPATH        = ..:../PhreeqcKeywords:../common
+  INCLUDES     = -I.. -I../PhreeqcKeywords -I../common
+  CXX          = g++
+  PROFILE      = 
+  CXXFLAGS     = $(PROFILE) -Wall -pedantic -O3 $(DEFINES) $(INCLUDES) # -g 
+#  CXXFLAGS     = -fprofile-arcs -ftest-coverage  $(DEFINES) $(INCLUDES) # -g 
+  OBJECT_FILES = $(CLASS_FILES) $(COMMON_COBJS) $(COMMON_CXXOBJS) $(CL1MP_OBJS)
+  LD_FLAGS     = $(PROFILE) -lm ${CL1MP_LIB} ${HASH_STYLE} # -L/usr/lib/gcc/x86_64-redhat-linux/4.4.4 -lgcov
+endif
+
+# -----------------------------------------------------------------------------
+#
+
+COMMON_COBJS =  \
+               advection.o \
+	       basicsubs.o \
+	       cl1.o \
+	       cvdense.o \
+	       cvode.o \
+	       dense.o \
+	       gases.o \
+	       input.o \
+	       integrate.o \
+	       inverse.o \
+	       isotopes.o \
+	       kinetics.o \
+	       mainsubs.o \
+	       model.o \
+	       nvector.o \
+	       nvector_serial.o \
+	       parse.o \
+	       PHRQ_io_output.o \
+	       phqalloc.o \
+	       pitzer.o \
+	       pitzer_structures.o \
+	       prep.o \
+	       print.o \
+	       read.o \
+	       readtr.o \
+	       sit.o \
+	       smalldense.o \
+	       spread.o \
+	       step.o \
+	       structures.o \
+	       sundialsmath.o \
+	       tally.o \
+	       tidy.o \
+	       transport.o \
+	       utilities.o 	                
+
+MAIN_FILE      = main.o 
+
+CLASS_FILES = \
+		class_main.o \
+		Phreeqc.o
+
+
+COMMON_CXXOBJS = \
+	       dumper.o \
+	       Dictionary.o \
+	       Exchange.o \
+	       ExchComp.o \
+	       GasPhase.o \
+	       GasComp.o \
+	       ISolution.o \
+	       ISolutionComp.o \
+	       Keywords.o \
+	       KineticsComp.o \
+	       cxxKinetics.o \
+	       cxxMix.o \
+	       NameDouble.o \
+	       NumKeyword.o \
+	       Parser.o \
+	       PBasic.o \
+	       PHRQ_base.o \
+	       PHRQ_io.o \
+	       PPassemblageComp.o \
+	       PPassemblage.o \
+	       Pressure.o \
+	       Reaction.o \
+	       ReadClass.o \
+	       runner.o \
+	       SelectedOutput.o \
+	       Serializer.o \
+	       Solution.o \
+	       SolutionIsotope.o \
+	       SSassemblage.o \
+	       SScomp.o \
+	       SS.o \
+               StorageBin.o \
+               StorageBinList.o \
+	       Surface.o \
+	       SurfaceCharge.o \
+	       SurfaceComp.o \
+	       System.o \
+	       Temperature.o \
+	       Use.o \
+	       UserPunch.o \
+	       Utils.o 
+
+# -----------------------------------------------------------------------------
+#  Assign dependents to target on dependency line & link options on command 
+#  line. Command line is initiated with a tab. ($@ is an internal macro for 
+#  the current target.) 
+
+${PROGRAM} : ${OBJECT_FILES}
+#	${CXX} -p -o $@ ${OBJECT_FILES}  ${LD_FLAGS} 
+	${CXX} -o $@ ${OBJECT_FILES}  ${LD_FLAGS} 
+	@echo; echo Done making for phreeqcpp
+# -----------------------------------------------------------------------------
+# Module dependency list
+# -----------------------------------------------------------------------------
+#
+#  CXX files
+#
+
+cxxKinetics.o: ../cxxKinetics.cxx ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../cxxKinetics.h ../KineticsComp.h \
+ ../phqalloc.h ../Dictionary.h
+cxxMix.o: ../cxxMix.cxx ../common/Utils.h ../common/phrqtype.h \
+ ../common/Parser.h ../common/PHRQ_base.h ../PhreeqcKeywords/Keywords.h \
+ ../common/PHRQ_io.h ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../SelectedOutput.h ../NumKeyword.h ../UserPunch.h \
+ ../Pressure.h ../cxxMix.h ../Use.h ../Surface.h ../SurfaceComp.h \
+ ../NameDouble.h ../SurfaceCharge.h ../global_structures.h ../NA.h \
+ ../phqalloc.h
+Exchange.o: ../Exchange.cxx ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../Exchange.h ../ExchComp.h ../phqalloc.h
+ExchComp.o: ../ExchComp.cxx ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../ExchComp.h ../phqalloc.h \
+ ../Dictionary.h
+GasComp.o: ../GasComp.cxx ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../GasComp.h ../phqalloc.h \
+ ../Dictionary.h
+GasPhase.o: ../GasPhase.cxx ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../GasPhase.h ../GasComp.h ../phqalloc.h
+ISolutionComp.o: ../ISolutionComp.cxx ../common/Utils.h \
+ ../common/phrqtype.h ../ISolutionComp.h ../common/phrqtype.h \
+ ../common/Parser.h ../common/PHRQ_base.h ../PhreeqcKeywords/Keywords.h \
+ ../common/PHRQ_io.h ../common/PHRQ_base.h ../Solution.h ../NumKeyword.h \
+ ../SolutionIsotope.h ../NameDouble.h ../common/PHRQ_io.h ../ISolution.h \
+ ../global_structures.h ../Surface.h ../SurfaceComp.h ../SurfaceCharge.h \
+ ../NA.h ../phqalloc.h
+ISolution.o: ../ISolution.cxx ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../ISolution.h ../ISolutionComp.h \
+ ../phqalloc.h
+KineticsComp.o: ../KineticsComp.cxx ../common/Utils.h \
+ ../common/phrqtype.h ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../KineticsComp.h ../phqalloc.h \
+ ../Dictionary.h
+NameDouble.o: ../NameDouble.cxx ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../Dictionary.h ../phqalloc.h \
+ ../ISolutionComp.h
+NumKeyword.o: ../NumKeyword.cxx ../NumKeyword.h ../common/PHRQ_base.h \
+ ../common/Parser.h ../common/PHRQ_base.h ../PhreeqcKeywords/Keywords.h \
+ ../common/PHRQ_io.h ../common/Utils.h ../common/phrqtype.h
+PPassemblageComp.o: ../PPassemblageComp.cxx ../common/Utils.h \
+ ../common/phrqtype.h ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../PPassemblageComp.h ../Dictionary.h \
+ ../phqalloc.h
+PPassemblage.o: ../PPassemblage.cxx ../common/Utils.h \
+ ../common/phrqtype.h ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../PPassemblage.h ../PPassemblageComp.h \
+ ../phqalloc.h
+Pressure.o: ../Pressure.cxx ../common/Utils.h ../common/phrqtype.h \
+ ../common/Parser.h ../common/PHRQ_base.h ../PhreeqcKeywords/Keywords.h \
+ ../common/PHRQ_io.h ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../SelectedOutput.h ../NumKeyword.h ../UserPunch.h \
+ ../Pressure.h ../cxxMix.h ../Use.h ../Surface.h ../SurfaceComp.h \
+ ../NameDouble.h ../SurfaceCharge.h ../global_structures.h ../NA.h \
+ ../phqalloc.h
+Reaction.o: ../Reaction.cxx ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../Reaction.h ../phqalloc.h
+ReadClass.o: ../ReadClass.cxx ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../Solution.h ../SolutionIsotope.h \
+ ../ISolution.h ../ISolutionComp.h ../Exchange.h ../ExchComp.h \
+ ../PPassemblage.h ../PPassemblageComp.h ../cxxKinetics.h \
+ ../KineticsComp.h ../SSassemblage.h ../SS.h ../SScomp.h ../GasPhase.h \
+ ../GasComp.h ../Reaction.h ../Temperature.h ../phqalloc.h
+Serializer.o: ../Serializer.cxx ../Serializer.h ../common/PHRQ_base.h \
+ ../Dictionary.h ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../dumper.h ../common/PHRQ_io.h \
+ ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h ../NumKeyword.h \
+ ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h ../Surface.h \
+ ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../common/Utils.h ../common/phrqtype.h \
+ ../Solution.h ../SolutionIsotope.h ../ISolution.h ../ISolutionComp.h \
+ ../Exchange.h ../ExchComp.h ../Temperature.h ../GasPhase.h ../GasComp.h \
+ ../cxxKinetics.h ../KineticsComp.h ../PPassemblage.h \
+ ../PPassemblageComp.h ../SSassemblage.h ../SS.h ../SScomp.h
+Solution.o: ../Solution.cxx ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../Solution.h ../SolutionIsotope.h \
+ ../ISolution.h ../ISolutionComp.h ../phqalloc.h ../Dictionary.h
+SolutionIsotope.o: ../SolutionIsotope.cxx ../common/Utils.h \
+ ../common/phrqtype.h ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../SolutionIsotope.h ../phqalloc.h \
+ ../Dictionary.h
+SSassemblage.o: ../SSassemblage.cxx ../common/Utils.h \
+ ../common/phrqtype.h ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../SSassemblage.h ../SS.h ../SScomp.h \
+ ../phqalloc.h ../Dictionary.h
+SScomp.o: ../SScomp.cxx ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../SScomp.h ../phqalloc.h ../Dictionary.h
+SS.o: ../SS.cxx ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../common/Utils.h ../common/phrqtype.h \
+ ../SS.h ../SScomp.h ../Dictionary.h ../phqalloc.h
+StorageBin.o: ../StorageBin.cxx ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../StorageBin.h ../System.h \
+ ../SSassemblage.h ../SS.h ../SScomp.h ../Solution.h ../SolutionIsotope.h \
+ ../ISolution.h ../ISolutionComp.h ../Exchange.h ../ExchComp.h \
+ ../GasPhase.h ../GasComp.h ../cxxKinetics.h ../KineticsComp.h \
+ ../PPassemblage.h ../PPassemblageComp.h ../Reaction.h ../Temperature.h \
+ ../phqalloc.h
+SurfaceCharge.o: ../SurfaceCharge.cxx ../common/Utils.h \
+ ../common/phrqtype.h ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h ../Dictionary.h
+SurfaceComp.o: ../SurfaceComp.cxx ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h ../Dictionary.h
+Surface.o: ../Surface.cxx ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h
+System.o: ../System.cxx ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../System.h ../SSassemblage.h ../SS.h \
+ ../SScomp.h ../Solution.h ../SolutionIsotope.h ../ISolution.h \
+ ../ISolutionComp.h ../Exchange.h ../ExchComp.h ../GasPhase.h \
+ ../GasComp.h ../cxxKinetics.h ../KineticsComp.h ../PPassemblage.h \
+ ../PPassemblageComp.h ../Reaction.h ../Temperature.h
+Temperature.o: ../Temperature.cxx ../common/Utils.h ../common/phrqtype.h \
+ ../common/Parser.h ../common/PHRQ_base.h ../PhreeqcKeywords/Keywords.h \
+ ../common/PHRQ_io.h ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../SelectedOutput.h ../NumKeyword.h ../UserPunch.h \
+ ../Pressure.h ../cxxMix.h ../Use.h ../Surface.h ../SurfaceComp.h \
+ ../NameDouble.h ../SurfaceCharge.h ../global_structures.h ../NA.h \
+ ../Temperature.h ../phqalloc.h
+advection.o: ../advection.cpp ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h ../cxxKinetics.h \
+ ../KineticsComp.h ../Solution.h ../SolutionIsotope.h ../ISolution.h \
+ ../ISolutionComp.h
+basicsubs.o: ../basicsubs.cpp ../Phreeqc.h ../common/phrqtype.h \
+ ../cvdense.h ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h \
+ ../smalldense.h ../runner.h ../StorageBinList.h ../common/PHRQ_base.h \
+ ../dumper.h ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h \
+ ../SelectedOutput.h ../NumKeyword.h ../UserPunch.h ../Pressure.h \
+ ../cxxMix.h ../Use.h ../Surface.h ../SurfaceComp.h ../NameDouble.h \
+ ../common/Parser.h ../common/PHRQ_base.h ../common/PHRQ_io.h \
+ ../SurfaceCharge.h ../global_structures.h ../NA.h ../phqalloc.h \
+ ../common/Utils.h ../common/phrqtype.h ../PBasic.h ../Exchange.h \
+ ../ExchComp.h ../GasPhase.h ../GasComp.h ../PPassemblage.h \
+ ../PPassemblageComp.h ../SSassemblage.h ../SS.h ../SScomp.h \
+ ../cxxKinetics.h ../KineticsComp.h ../Solution.h ../SolutionIsotope.h \
+ ../ISolution.h ../ISolutionComp.h
+ChartHandler.o: ../ChartHandler.cpp
+ChartObject.o: ../ChartObject.cpp
+cl1.o: ../cl1.cpp ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h
+cl1mp.o: ../cl1mp.cpp
+class_main.o: ../class_main.cpp ../Phreeqc.h ../common/phrqtype.h \
+ ../cvdense.h ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h \
+ ../smalldense.h ../runner.h ../StorageBinList.h ../common/PHRQ_base.h \
+ ../dumper.h ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h \
+ ../SelectedOutput.h ../NumKeyword.h ../UserPunch.h ../Pressure.h \
+ ../cxxMix.h ../Use.h ../Surface.h ../SurfaceComp.h ../NameDouble.h \
+ ../common/Parser.h ../common/PHRQ_base.h ../common/PHRQ_io.h \
+ ../SurfaceCharge.h ../global_structures.h ../NA.h ../Solution.h \
+ ../SolutionIsotope.h ../ISolution.h ../ISolutionComp.h ../Reaction.h \
+ ../PPassemblage.h ../PPassemblageComp.h ../Exchange.h ../ExchComp.h \
+ ../GasPhase.h ../GasComp.h ../SSassemblage.h ../SS.h ../SScomp.h \
+ ../cxxKinetics.h ../KineticsComp.h
+CurveObject.o: ../CurveObject.cpp
+cvdense.o: ../cvdense.cpp ../cvdense.h ../cvode.h ../sundialstypes.h \
+ ../common/phrqtype.h ../nvector.h ../dense.h ../smalldense.h \
+ ../sundialsmath.h ../Phreeqc.h ../runner.h ../StorageBinList.h \
+ ../common/PHRQ_base.h ../dumper.h ../common/PHRQ_io.h \
+ ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h ../NumKeyword.h \
+ ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h ../Surface.h \
+ ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h
+cvode.o: ../cvode.cpp ../nvector_serial.h ../nvector.h ../sundialstypes.h \
+ ../common/phrqtype.h ../cvode.h ../sundialsmath.h ../Phreeqc.h \
+ ../cvdense.h ../dense.h ../smalldense.h ../runner.h ../StorageBinList.h \
+ ../common/PHRQ_base.h ../dumper.h ../common/PHRQ_io.h \
+ ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h ../NumKeyword.h \
+ ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h ../Surface.h \
+ ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h
+dense.o: ../dense.cpp ../sundialstypes.h ../common/phrqtype.h \
+ ../sundialsmath.h ../dense.h ../smalldense.h
+Dictionary.o: ../Dictionary.cpp ../Dictionary.h
+dumper.o: ../dumper.cpp ../dumper.h ../StorageBinList.h \
+ ../common/PHRQ_base.h ../common/Parser.h ../common/PHRQ_base.h \
+ ../PhreeqcKeywords/Keywords.h ../common/PHRQ_io.h ../common/PHRQ_io.h
+gases.o: ../gases.cpp ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../GasPhase.h ../GasComp.h
+input.o: ../input.cpp ../common/Utils.h ../common/phrqtype.h ../Phreeqc.h \
+ ../common/phrqtype.h ../cvdense.h ../cvode.h ../sundialstypes.h \
+ ../nvector.h ../dense.h ../smalldense.h ../runner.h ../StorageBinList.h \
+ ../common/PHRQ_base.h ../dumper.h ../common/PHRQ_io.h \
+ ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h ../NumKeyword.h \
+ ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h ../Surface.h \
+ ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h
+integrate.o: ../integrate.cpp ../Phreeqc.h ../common/phrqtype.h \
+ ../cvdense.h ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h \
+ ../smalldense.h ../runner.h ../StorageBinList.h ../common/PHRQ_base.h \
+ ../dumper.h ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h \
+ ../SelectedOutput.h ../NumKeyword.h ../UserPunch.h ../Pressure.h \
+ ../cxxMix.h ../Use.h ../Surface.h ../SurfaceComp.h ../NameDouble.h \
+ ../common/Parser.h ../common/PHRQ_base.h ../common/PHRQ_io.h \
+ ../SurfaceCharge.h ../global_structures.h ../NA.h ../phqalloc.h \
+ ../common/Utils.h ../common/phrqtype.h ../Solution.h \
+ ../SolutionIsotope.h ../ISolution.h ../ISolutionComp.h
+inverse.o: ../inverse.cpp ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h ../common/Utils.h \
+ ../common/phrqtype.h ../Solution.h ../SolutionIsotope.h ../ISolution.h \
+ ../ISolutionComp.h
+isotopes.o: ../isotopes.cpp ../Phreeqc.h ../common/phrqtype.h \
+ ../cvdense.h ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h \
+ ../smalldense.h ../runner.h ../StorageBinList.h ../common/PHRQ_base.h \
+ ../dumper.h ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h \
+ ../SelectedOutput.h ../NumKeyword.h ../UserPunch.h ../Pressure.h \
+ ../cxxMix.h ../Use.h ../Surface.h ../SurfaceComp.h ../NameDouble.h \
+ ../common/Parser.h ../common/PHRQ_base.h ../common/PHRQ_io.h \
+ ../SurfaceCharge.h ../global_structures.h ../NA.h ../phqalloc.h \
+ ../Solution.h ../SolutionIsotope.h ../ISolution.h ../ISolutionComp.h
+kinetics.o: ../kinetics.cpp ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h ../StorageBin.h ../System.h \
+ ../Reaction.h ../cxxKinetics.h ../KineticsComp.h ../Solution.h \
+ ../SolutionIsotope.h ../ISolution.h ../ISolutionComp.h ../PPassemblage.h \
+ ../PPassemblageComp.h ../Exchange.h ../ExchComp.h ../GasPhase.h \
+ ../GasComp.h ../SSassemblage.h ../SS.h ../SScomp.h ../Temperature.h \
+ ../nvector_serial.h
+mainsubs.o: ../mainsubs.cpp ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h ../PBasic.h \
+ ../Temperature.h ../Exchange.h ../ExchComp.h ../GasPhase.h ../GasComp.h \
+ ../Reaction.h ../PPassemblage.h ../PPassemblageComp.h ../SSassemblage.h \
+ ../SS.h ../SScomp.h ../cxxKinetics.h ../KineticsComp.h ../Solution.h \
+ ../SolutionIsotope.h ../ISolution.h ../ISolutionComp.h
+model.o: ../model.cpp ../common/Utils.h ../common/phrqtype.h ../Phreeqc.h \
+ ../common/phrqtype.h ../cvdense.h ../cvode.h ../sundialstypes.h \
+ ../nvector.h ../dense.h ../smalldense.h ../runner.h ../StorageBinList.h \
+ ../common/PHRQ_base.h ../dumper.h ../common/PHRQ_io.h \
+ ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h ../NumKeyword.h \
+ ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h ../Surface.h \
+ ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h ../Exchange.h ../ExchComp.h \
+ ../GasPhase.h ../GasComp.h ../PPassemblage.h ../PPassemblageComp.h \
+ ../SSassemblage.h ../SS.h ../SScomp.h ../Solution.h ../SolutionIsotope.h \
+ ../ISolution.h ../ISolutionComp.h
+nvector.o: ../nvector.cpp ../nvector.h ../sundialstypes.h \
+ ../common/phrqtype.h
+nvector_serial.o: ../nvector_serial.cpp ../nvector_serial.h ../nvector.h \
+ ../sundialstypes.h ../common/phrqtype.h ../sundialsmath.h
+parse.o: ../parse.cpp ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h
+PBasic.o: ../PBasic.cpp ../PBasic.h ../common/phrqtype.h \
+ ../common/PHRQ_base.h ../global_structures.h ../Surface.h \
+ ../NumKeyword.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../PhreeqcKeywords/Keywords.h ../common/PHRQ_io.h \
+ ../SurfaceCharge.h ../NA.h ../Phreeqc.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../dumper.h ../common/PHRQ_io.h ../SelectedOutput.h \
+ ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h ../phqalloc.h \
+ ../common/Utils.h ../common/phrqtype.h ../Solution.h \
+ ../SolutionIsotope.h ../ISolution.h ../ISolutionComp.h
+phqalloc.o: ../phqalloc.cpp ../Phreeqc.h ../common/phrqtype.h \
+ ../cvdense.h ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h \
+ ../smalldense.h ../runner.h ../StorageBinList.h ../common/PHRQ_base.h \
+ ../dumper.h ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h \
+ ../SelectedOutput.h ../NumKeyword.h ../UserPunch.h ../Pressure.h \
+ ../cxxMix.h ../Use.h ../Surface.h ../SurfaceComp.h ../NameDouble.h \
+ ../common/Parser.h ../common/PHRQ_base.h ../common/PHRQ_io.h \
+ ../SurfaceCharge.h ../global_structures.h ../NA.h
+Phreeqc.o: ../Phreeqc.cpp ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../Solution.h ../SolutionIsotope.h \
+ ../ISolution.h ../ISolutionComp.h ../Reaction.h ../PPassemblage.h \
+ ../PPassemblageComp.h ../Exchange.h ../ExchComp.h ../GasPhase.h \
+ ../GasComp.h ../SSassemblage.h ../SS.h ../SScomp.h ../cxxKinetics.h \
+ ../KineticsComp.h ../phqalloc.h ../PBasic.h ../Temperature.h
+PHRQ_io_output.o: ../PHRQ_io_output.cpp ../Phreeqc.h ../common/phrqtype.h \
+ ../cvdense.h ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h \
+ ../smalldense.h ../runner.h ../StorageBinList.h ../common/PHRQ_base.h \
+ ../dumper.h ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h \
+ ../SelectedOutput.h ../NumKeyword.h ../UserPunch.h ../Pressure.h \
+ ../cxxMix.h ../Use.h ../Surface.h ../SurfaceComp.h ../NameDouble.h \
+ ../common/Parser.h ../common/PHRQ_base.h ../common/PHRQ_io.h \
+ ../SurfaceCharge.h ../global_structures.h ../NA.h ../phqalloc.h
+pitzer.o: ../pitzer.cpp ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h ../Exchange.h ../ExchComp.h \
+ ../Solution.h ../SolutionIsotope.h ../ISolution.h ../ISolutionComp.h
+pitzer_structures.o: ../pitzer_structures.cpp ../Phreeqc.h \
+ ../common/phrqtype.h ../cvdense.h ../cvode.h ../sundialstypes.h \
+ ../nvector.h ../dense.h ../smalldense.h ../runner.h ../StorageBinList.h \
+ ../common/PHRQ_base.h ../dumper.h ../common/PHRQ_io.h \
+ ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h ../NumKeyword.h \
+ ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h ../Surface.h \
+ ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h
+prep.o: ../prep.cpp ../common/Utils.h ../common/phrqtype.h ../Phreeqc.h \
+ ../common/phrqtype.h ../cvdense.h ../cvode.h ../sundialstypes.h \
+ ../nvector.h ../dense.h ../smalldense.h ../runner.h ../StorageBinList.h \
+ ../common/PHRQ_base.h ../dumper.h ../common/PHRQ_io.h \
+ ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h ../NumKeyword.h \
+ ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h ../Surface.h \
+ ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h ../Exchange.h ../ExchComp.h \
+ ../GasPhase.h ../GasComp.h ../PPassemblage.h ../PPassemblageComp.h \
+ ../SSassemblage.h ../SS.h ../SScomp.h ../Solution.h ../SolutionIsotope.h \
+ ../ISolution.h ../ISolutionComp.h ../cxxKinetics.h ../KineticsComp.h
+print.o: ../print.cpp ../common/Utils.h ../common/phrqtype.h ../Phreeqc.h \
+ ../common/phrqtype.h ../cvdense.h ../cvode.h ../sundialstypes.h \
+ ../nvector.h ../dense.h ../smalldense.h ../runner.h ../StorageBinList.h \
+ ../common/PHRQ_base.h ../dumper.h ../common/PHRQ_io.h \
+ ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h ../NumKeyword.h \
+ ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h ../Surface.h \
+ ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h ../Temperature.h \
+ ../Exchange.h ../ExchComp.h ../GasPhase.h ../GasComp.h ../Reaction.h \
+ ../PPassemblage.h ../PPassemblageComp.h ../SSassemblage.h ../SS.h \
+ ../SScomp.h ../cxxKinetics.h ../KineticsComp.h ../Solution.h \
+ ../SolutionIsotope.h ../ISolution.h ../ISolutionComp.h
+read.o: ../read.cpp ../common/Utils.h ../common/phrqtype.h ../Phreeqc.h \
+ ../common/phrqtype.h ../cvdense.h ../cvode.h ../sundialstypes.h \
+ ../nvector.h ../dense.h ../smalldense.h ../runner.h ../StorageBinList.h \
+ ../common/PHRQ_base.h ../dumper.h ../common/PHRQ_io.h \
+ ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h ../NumKeyword.h \
+ ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h ../Surface.h \
+ ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h ../Temperature.h \
+ ../Exchange.h ../ExchComp.h ../GasPhase.h ../GasComp.h ../Reaction.h \
+ ../PPassemblage.h ../PPassemblageComp.h ../SSassemblage.h ../SS.h \
+ ../SScomp.h ../cxxKinetics.h ../KineticsComp.h ../Solution.h \
+ ../SolutionIsotope.h ../ISolution.h ../ISolutionComp.h
+readtr.o: ../readtr.cpp ../StorageBin.h ../System.h ../NameDouble.h \
+ ../common/Parser.h ../common/PHRQ_base.h ../PhreeqcKeywords/Keywords.h \
+ ../common/PHRQ_io.h ../common/phrqtype.h ../common/PHRQ_base.h \
+ ../common/PHRQ_io.h ../SS.h ../SScomp.h ../Phreeqc.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../dumper.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../SurfaceCharge.h ../global_structures.h \
+ ../NA.h ../phqalloc.h ../common/Utils.h ../common/phrqtype.h
+runner.o: ../runner.cpp ../runner.h ../common/phrqtype.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../PhreeqcKeywords/Keywords.h ../common/PHRQ_io.h \
+ ../NA.h ../common/Utils.h ../common/phrqtype.h
+SelectedOutput.o: ../SelectedOutput.cpp ../SelectedOutput.h \
+ ../NumKeyword.h ../common/PHRQ_base.h
+sit.o: ../sit.cpp ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h ../Exchange.h ../ExchComp.h \
+ ../Solution.h ../SolutionIsotope.h ../ISolution.h ../ISolutionComp.h
+smalldense.o: ../smalldense.cpp ../smalldense.h ../sundialstypes.h \
+ ../common/phrqtype.h ../sundialsmath.h
+spread.o: ../spread.cpp ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h ../Solution.h \
+ ../SolutionIsotope.h ../ISolution.h ../ISolutionComp.h ../common/Utils.h \
+ ../common/phrqtype.h
+step.o: ../step.cpp ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h ../common/Utils.h \
+ ../common/phrqtype.h ../StorageBin.h ../System.h ../Solution.h \
+ ../SolutionIsotope.h ../ISolution.h ../ISolutionComp.h ../PPassemblage.h \
+ ../PPassemblageComp.h ../SSassemblage.h ../SS.h ../SScomp.h \
+ ../Temperature.h ../Exchange.h ../ExchComp.h ../GasPhase.h ../GasComp.h \
+ ../Reaction.h ../cxxKinetics.h ../KineticsComp.h
+StorageBinList.o: ../StorageBinList.cpp ../StorageBinList.h \
+ ../common/PHRQ_base.h ../common/Parser.h ../common/PHRQ_base.h \
+ ../PhreeqcKeywords/Keywords.h ../common/PHRQ_io.h
+structures.o: ../structures.cpp ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h ../Temperature.h \
+ ../Exchange.h ../ExchComp.h ../GasPhase.h ../GasComp.h ../Reaction.h \
+ ../PPassemblage.h ../PPassemblageComp.h ../SSassemblage.h ../SS.h \
+ ../SScomp.h ../cxxKinetics.h ../KineticsComp.h ../Solution.h \
+ ../SolutionIsotope.h ../ISolution.h ../ISolutionComp.h ../StorageBin.h \
+ ../System.h
+sundialsmath.o: ../sundialsmath.cpp ../sundialsmath.h ../sundialstypes.h \
+ ../common/phrqtype.h
+tally.o: ../tally.cpp ../common/Utils.h ../common/phrqtype.h ../Phreeqc.h \
+ ../common/phrqtype.h ../cvdense.h ../cvode.h ../sundialstypes.h \
+ ../nvector.h ../dense.h ../smalldense.h ../runner.h ../StorageBinList.h \
+ ../common/PHRQ_base.h ../dumper.h ../common/PHRQ_io.h \
+ ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h ../NumKeyword.h \
+ ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h ../Surface.h \
+ ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h ../Temperature.h \
+ ../Exchange.h ../ExchComp.h ../GasPhase.h ../GasComp.h ../Reaction.h \
+ ../PPassemblage.h ../PPassemblageComp.h ../SSassemblage.h ../SS.h \
+ ../SScomp.h ../cxxKinetics.h ../KineticsComp.h ../Solution.h \
+ ../SolutionIsotope.h ../ISolution.h ../ISolutionComp.h
+tidy.o: ../tidy.cpp ../common/Utils.h ../common/phrqtype.h ../Phreeqc.h \
+ ../common/phrqtype.h ../cvdense.h ../cvode.h ../sundialstypes.h \
+ ../nvector.h ../dense.h ../smalldense.h ../runner.h ../StorageBinList.h \
+ ../common/PHRQ_base.h ../dumper.h ../common/PHRQ_io.h \
+ ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h ../NumKeyword.h \
+ ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h ../Surface.h \
+ ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h ../Exchange.h ../ExchComp.h \
+ ../GasPhase.h ../GasComp.h ../PPassemblage.h ../PPassemblageComp.h \
+ ../SSassemblage.h ../SS.h ../SScomp.h ../cxxKinetics.h ../KineticsComp.h \
+ ../Solution.h ../SolutionIsotope.h ../ISolution.h ../ISolutionComp.h
+transport.o: ../transport.cpp ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h ../Exchange.h ../ExchComp.h \
+ ../GasPhase.h ../GasComp.h ../PPassemblage.h ../PPassemblageComp.h \
+ ../SSassemblage.h ../SS.h ../SScomp.h ../cxxKinetics.h ../KineticsComp.h \
+ ../Solution.h ../SolutionIsotope.h ../ISolution.h ../ISolutionComp.h
+Use.o: ../Use.cpp ../Use.h
+UserPunch.o: ../UserPunch.cpp ../UserPunch.h ../NumKeyword.h \
+ ../common/PHRQ_base.h ../Phreeqc.h ../common/phrqtype.h ../cvdense.h \
+ ../cvode.h ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h \
+ ../runner.h ../StorageBinList.h ../dumper.h ../common/PHRQ_io.h \
+ ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h ../Pressure.h \
+ ../cxxMix.h ../Use.h ../Surface.h ../SurfaceComp.h ../NameDouble.h \
+ ../common/Parser.h ../common/PHRQ_base.h ../common/PHRQ_io.h \
+ ../SurfaceCharge.h ../global_structures.h ../NA.h
+utilities.o: ../utilities.cpp ../common/Utils.h ../common/phrqtype.h \
+ ../Phreeqc.h ../common/phrqtype.h ../cvdense.h ../cvode.h \
+ ../sundialstypes.h ../nvector.h ../dense.h ../smalldense.h ../runner.h \
+ ../StorageBinList.h ../common/PHRQ_base.h ../dumper.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h ../SelectedOutput.h \
+ ../NumKeyword.h ../UserPunch.h ../Pressure.h ../cxxMix.h ../Use.h \
+ ../Surface.h ../SurfaceComp.h ../NameDouble.h ../common/Parser.h \
+ ../common/PHRQ_base.h ../common/PHRQ_io.h ../SurfaceCharge.h \
+ ../global_structures.h ../NA.h ../phqalloc.h ../Exchange.h ../ExchComp.h \
+ ../Solution.h ../SolutionIsotope.h ../ISolution.h ../ISolutionComp.h
+Keywords.o: ../PhreeqcKeywords/Keywords.cpp ../PhreeqcKeywords/Keywords.h
+Parser.o: ../common/Parser.cxx ../common/Utils.h ../common/phrqtype.h \
+ ../common/Parser.h ../common/PHRQ_base.h ../PhreeqcKeywords/Keywords.h \
+ ../common/PHRQ_io.h
+PHRQ_base.o: ../common/PHRQ_base.cxx ../common/PHRQ_base.h \
+ ../common/PHRQ_io.h ../PhreeqcKeywords/Keywords.h
+Utils.o: ../common/Utils.cxx ../common/Utils.h ../common/phrqtype.h \
+ ../common/Parser.h ../common/PHRQ_base.h ../PhreeqcKeywords/Keywords.h \
+ ../common/PHRQ_io.h
+
+# -----------------------------------------------------------------------------
+clean:
+	rm -rf Class_release Class_debug Class_release_64 Class_debug_64
+
+dependencies:
+	mkdir -p $(CLASS_DEBUG_DIR) 
+	cd $(CLASS_DEBUG_DIR); gcc -MM -I.. -I../PhreeqcKeywords -I../common ../*.cxx ../*.cpp ../PhreeqcKeywords/*.cpp ../common/*.cxx
+
+tester:
+#	cd ../mytest; make clean; make -k -j 1 $(SPOOL) make.out $(SPOOL2); make diff $(SPOOL) diff.out $(SPOOL2)
+	cd ../mytest $(CONCAT) make clean $(CONCAT) make -k -j 1 $(SPOOL) make.out $(SPOOL2) $(CONCAT) make diff $(SPOOL) diff.out $(SPOOL2)
+	cd ../examples $(CONCAT) make -f Makefile.old clean $(CONCAT) make -f Makefile.old -k -j 1 $(SPOOL) make.out $(SPOOL2) $(CONCAT) make -f Makefile.old diff $(SPOOL) diff.out $(SPOOL2)
+	svn status -q ../mytest 
+	svn status -q ../examples
+
+#ld-option
+# Usage: ldflags += $(call ld-option, -Wl$(comma)--hash-style=sysv)
+comma=,
+ld-option = $(shell if $(CC) $(1) \
+              -nostdlib -o /dev/null -xc /dev/null \
+              > /dev/null 2>&1 ; then echo "$(1)" ; else echo "$(2)"; fi)
+
+# =============================================================================
+# End of makefile.
+# =============================================================================

src/phreeqcpp/NA.h

@@ -0,0 +1 @@
+#define NA -98.7654321

src/phreeqcpp/NameDouble.cxx

@@ -0,0 +1,628 @@
+// NameDouble.cxx: implementation of the cxxNameDouble class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <cassert>				// assert
+#include <algorithm>			// std::sort
+#include <map>					// std::sort
+#include <iostream>				// std::cout std::cerr
+
+#include "Utils.h"				// define first
+#include "Phreeqc.h"
+#include "NameDouble.h"
+#include "Dictionary.h"
+//#include "Dictionary.h"
+#include "phqalloc.h"
+#include "ISolutionComp.h"
+
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+cxxNameDouble::cxxNameDouble()
+	//
+	// default constructor for cxxNameDouble 
+	//
+{
+	this->type = ND_ELT_MOLES;
+}
+
+cxxNameDouble::cxxNameDouble(struct elt_list *elt_list_ptr)
+		//
+		// constructor for cxxNameDouble from list of elt_list
+		//
+{
+	int i;
+	if (elt_list_ptr != NULL)
+	{
+		for (i = 0; elt_list_ptr[i].elt != NULL; i++)
+		{
+			(*this)[elt_list_ptr[i].elt->name] = elt_list_ptr[i].coef;
+		}
+	}
+	this->type = ND_ELT_MOLES;
+}
+
+cxxNameDouble::cxxNameDouble(struct elt_list *elt_list_ptr, int count)
+		//
+		// constructor for cxxNameDouble from list of elt_list with known count
+		//
+{
+	int i;
+	if (elt_list_ptr != NULL)
+	{
+		for (i = 0; i < count; i++)
+		{
+			(*this)[elt_list_ptr[i].elt->name] = elt_list_ptr[i].coef;
+		}
+	}
+	this->type = ND_ELT_MOLES;
+}
+
+cxxNameDouble::cxxNameDouble(const cxxNameDouble & old, LDBLE factor)
+		//
+		// constructor for cxxNameDouble from list of elt_list
+		//
+{
+	for (cxxNameDouble::const_iterator it = old.begin(); it != old.end();
+		 it++)
+	{
+		if (old.type == ND_ELT_MOLES)
+		{
+			if (it->second * factor > 0)
+			{
+				(*this)[(it->first)] = it->second * factor;
+			}
+		}
+		else
+		{
+			(*this)[(it->first)] = it->second * factor;
+		}
+	}
+	this->type = old.type;
+}
+cxxNameDouble::cxxNameDouble(std::map < std::string, cxxISolutionComp > &comps)
+		//
+		// constructor for cxxNameDouble from map of cxxISolutionComp
+		//
+{
+	std::map < std::string, cxxISolutionComp >::iterator it;
+	for (it = comps.begin(); it != comps.end(); it++)
+	{
+		(*this)[it->first] = it->second.Get_moles();
+	}
+	this->type = ND_ELT_MOLES;
+}
+#ifdef SKIP
+cxxNameDouble::cxxNameDouble(struct master_activity *ma, int count,
+							 cxxNameDouble::ND_TYPE l_type)
+		//
+		// constructor for cxxNameDouble from list of elt_list
+		//
+{
+	int i;
+	for (i = 0; i < count; i++)
+	{
+		if (ma[i].description == NULL)
+			continue;
+		(*this)[ma[i].description] = ma[i].la;
+	}
+	this->type = l_type;
+}
+#endif
+cxxNameDouble::cxxNameDouble(struct name_coef *nc, int count)
+		//
+		// constructor for cxxNameDouble from list of elt_list
+		//
+{
+	int i;
+	for (i = 0; i < count; i++)
+	{
+		if (nc[i].name == NULL)
+			continue;
+
+		if ((*this).find(nc[i].name) == (*this).end())
+		{
+			(*this)[nc[i].name] = nc[i].coef;
+		}
+		else
+		{
+			(*this)[nc[i].name] = (*this).find(nc[i].name)->second + nc[i].coef;
+		}
+
+	}
+	this->type = ND_NAME_COEF;
+}
+
+cxxNameDouble::~cxxNameDouble()
+{
+}
+
+void
+cxxNameDouble::dump_xml(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	std::string xmlElement, xmlAtt1, xmlAtt2;
+
+	switch ((*this).type)
+	{
+	case cxxNameDouble::ND_SPECIES_LA:
+		xmlElement = "<soln_m_a ";
+		xmlAtt1 = " m_a_desc=\"";
+		xmlAtt1 = " m_a_la=\"";
+		break;
+	case cxxNameDouble::ND_SPECIES_GAMMA:
+		xmlElement = "<soln_s_g ";
+		xmlAtt1 = " m_a_desc=\"";
+		xmlAtt1 = " m_a_la=\"";
+		break;
+	case cxxNameDouble::ND_ELT_MOLES:
+		xmlElement = "<soln_total ";
+		xmlAtt1 = " conc_desc=\"";
+		xmlAtt1 = " conc_moles=\"";
+		break;
+	case cxxNameDouble::ND_NAME_COEF:
+		xmlElement = "<NameCoef ";
+		xmlAtt1 = " name=\"";
+		xmlAtt1 = " coef=\"";
+		break;
+	}
+
+	for (const_iterator it = (*this).begin(); it != (*this).end(); it++)
+	{
+		s_oss << indent0;
+		s_oss << xmlElement << xmlAtt1 << it->first << xmlAtt2 << it->
+			second << "/>" << "\n";
+	}
+}
+
+void
+cxxNameDouble::dump_raw(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+
+	for (const_iterator it = (*this).begin(); it != (*this).end(); it++)
+	{
+		s_oss << indent0;
+		if (it->first.size() < 29 - indent0.size())
+		{
+			s_oss << Utilities::pad_right(it->first, 29 - indent0.size())  << it->second << "\n";
+		}
+		else
+		{
+			s_oss << Utilities::pad_right(it->first, it->first.size()  + indent0.size())  << " " << it->second << "\n";
+		}
+	}
+}
+
+CParser::STATUS_TYPE cxxNameDouble::read_raw(CParser & parser,
+											 std::istream::pos_type & pos)
+{
+	std::string token;
+	LDBLE
+		d;
+
+	CParser::TOKEN_TYPE j;
+	j = parser.copy_token(token, pos);
+
+	if (j == CParser::TT_EMPTY)
+		return CParser::PARSER_OK;
+
+	if (!(parser.get_iss() >> d))
+	{
+		return CParser::PARSER_ERROR;
+	}
+	(*this)[token.c_str()] = d;
+	return CParser::PARSER_OK;
+}
+
+void
+cxxNameDouble::add_extensive(const cxxNameDouble & addee, LDBLE factor)
+//
+// Sums two name doubles, this + factor*nd2
+//
+{
+	if (factor == 0)
+		return;
+	for (cxxNameDouble::const_iterator it = addee.begin(); it != addee.end();
+		 it++)
+	{
+		cxxNameDouble::iterator current = (*this).find(it->first);
+		if (current != (*this).end())
+		{
+			(*this)[it->first] = current->second + it->second * factor;
+		}
+		else
+		{
+			(*this)[it->first] = it->second * factor;
+		}
+	}
+}
+void
+cxxNameDouble::add_intensive(const cxxNameDouble & addee, LDBLE f1,
+							 LDBLE f2)
+//
+// Sums two name doubles, this*f1 + f2*nd2
+//
+{
+	assert(f1 >= 0 && f2 >= 0);
+	for (cxxNameDouble::const_iterator it = addee.begin(); it != addee.end();
+		 it++)
+	{
+		cxxNameDouble::iterator current = (*this).find(it->first);
+		if (current != (*this).end())
+		{
+			(*this)[it->first] = f1 * current->second + f2 * it->second;
+		}
+		else
+		{
+			(*this)[it->first] = f2 * it->second;
+		}
+	}
+}
+void
+cxxNameDouble::add_log_activities(const cxxNameDouble & addee, LDBLE f1,
+								  LDBLE f2)
+//
+// Sums two name doubles, this*f1 + f2*nd2, assuming log values
+//
+{
+	assert(f1 >= 0 && f2 >= 0);
+	for (cxxNameDouble::const_iterator it = addee.begin(); it != addee.end();
+		 it++)
+	{
+		cxxNameDouble::iterator current = (*this).find(it->first);
+		if (current != (*this).end())
+		{
+			LDBLE a1 = pow((LDBLE) 10., current->second);
+			LDBLE a2 = pow((LDBLE) 10., it->second);
+			(*this)[it->first] = log10(f1 * a1 + f2 * a2);
+		}
+		else
+		{
+			(*this)[it->first] = it->second + log10(f2);
+		}
+	}
+}
+cxxNameDouble 
+cxxNameDouble::Simplify_redox(void) const
+{
+	cxxNameDouble const &nd = *this;
+	std::basic_string < char >::size_type indexCh;
+	cxxNameDouble new_totals;
+	new_totals.type = cxxNameDouble::ND_ELT_MOLES;
+	{
+		std::string current_ename;
+		std::string const *ename_ptr;
+		cxxNameDouble::const_iterator it;
+
+		// make list of elements in new_totals
+		for (it = nd.begin(); it != nd.end(); ++it)
+		{
+			current_ename = it->first;
+			if (it->first.size() < 4)
+			{
+				ename_ptr = &(it->first);
+			}
+			else
+			{
+				indexCh = it->first.find("(");
+				if (indexCh != std::string::npos)
+				{
+					current_ename = it->first.substr(0, indexCh);
+					ename_ptr = &(current_ename);
+				}
+				else
+				{
+					ename_ptr = &(it->first);
+				}
+			}
+			if (current_ename == "H" || current_ename == "O" || current_ename == "Charge")
+				continue;
+			new_totals[*ename_ptr] = 0;
+		}
+	}
+
+	// sum totals for elements
+	{
+		cxxNameDouble::const_iterator old_it = nd.begin();
+		cxxNameDouble::iterator new_it = new_totals.begin();
+		std::string old_ename;
+		std::string const *old_ename_ptr;
+		while (old_it != nd.end() && new_it != new_totals.end())
+		{
+			if (old_it->first.size() < 4)
+			{
+				old_ename_ptr = &old_it->first;
+			}
+			else
+			{
+				indexCh = old_it->first.find("(");
+				if (indexCh != std::string::npos)
+				{
+					old_ename = old_it->first.substr(0, indexCh);
+					old_ename_ptr = &old_ename;
+				}
+				else
+				{
+					old_ename_ptr = &old_it->first;
+				}
+			}
+			int j = strcmp(new_it->first.c_str(), old_ename_ptr->c_str());
+			if (j < 0)
+			{
+				new_it++;
+			}
+			else if (j == 0)
+			{
+				new_it->second += old_it->second;
+				old_it++;
+			}
+			else 
+			{
+				old_it++;
+			}
+		}
+	}
+	return new_totals;
+}
+#ifdef SKIP
+cxxNameDouble 
+cxxNameDouble::Simplify_redox(void)
+{
+	// remove individual redox states from totals
+	cxxNameDouble &nd = *this;
+	std::set<std::string> list_of_elements;
+	cxxNameDouble::const_iterator it;
+	for (it = nd.begin(); it != nd.end(); ++it)
+	{
+		std::string current_ename(it->first);
+		std::basic_string < char >::size_type indexCh;
+		indexCh = current_ename.find("(");
+		if (indexCh != std::string::npos)
+		{
+			current_ename = current_ename.substr(0, indexCh);
+		}
+		if (current_ename == "H" || current_ename == "O" || current_ename == "Charge")
+			continue;
+		list_of_elements.insert(current_ename);
+	}
+
+	cxxNameDouble new_totals;
+	new_totals.type = cxxNameDouble::ND_ELT_MOLES;
+	std::set<std::string>::iterator nt_it = list_of_elements.begin();
+	for( ; nt_it != list_of_elements.end(); nt_it++)
+	{
+		new_totals[(*nt_it).c_str()] = nd.Get_total_element((*nt_it).c_str());
+	}
+	return new_totals;
+}
+#endif
+void 
+cxxNameDouble::Multiply_activities_redox(std::string str, LDBLE f)
+{
+	// update original master_activities using just computed factors
+	cxxNameDouble::iterator it;
+	LDBLE lg_f = log10(f);
+	std::string redox_name = str;
+	redox_name.append("(");
+
+	for (it = this->begin(); it != this->end(); it++)
+	{
+		if (str[0] > it->first[0]) continue;
+		if (it->first == str)
+		{
+			// Found exact match
+			it->second += lg_f;
+		}
+		else 
+		{
+			// no exact match, current is element name, need to find all valences
+			if (strstr(it->first.c_str(), redox_name.c_str()) == it->first.c_str())
+			{
+				it->second += lg_f;
+			}
+		}
+		if (str[0] < it->first[0]) break;
+	}
+}
+#ifdef SKIP
+void 
+cxxNameDouble::Multiply_activities_redox(std::string str, LDBLE f)
+{
+	// update original master_activities using just computed factors
+	cxxNameDouble::iterator it;
+	LDBLE lg_f = log10(f);
+	std::string redox_name = str;
+	redox_name.append("(");
+
+	for (it = this->begin(); it != this->end(); it++)
+	{
+		if (it->first == str)
+		{
+			// Found exact match
+			it->second += lg_f;
+		}
+		else 
+		{
+			// no exact match, current is element name, need to find all valences
+			if (strstr(it->first.c_str(), redox_name.c_str()) == it->first.c_str())
+			{
+				it->second += lg_f;
+			}
+		}
+	}
+}
+#endif
+LDBLE
+cxxNameDouble::Get_total_element(const char *string) const
+{
+	cxxNameDouble::const_iterator it;
+	LDBLE d = 0.0;
+	for (it = this->begin(); it != this->end(); ++it)
+	{
+		// C++ way to do it
+		std::string ename(string);
+		std::string current_ename(it->first);
+		std::basic_string < char >::size_type indexCh;
+		indexCh = current_ename.find("(");
+		if (indexCh != std::string::npos)
+		{
+			current_ename = current_ename.substr(0, indexCh);
+		}
+		if (current_ename == ename)
+		{
+			d += it->second;
+		}
+	}
+	return (d);
+}
+void
+cxxNameDouble::add(const char *token, LDBLE total)
+//
+// add to total for a specified element
+//
+{
+	char key[MAX_LENGTH];
+	strcpy(key, token);
+
+	cxxNameDouble::iterator current = (*this).find(key);
+	if (current != (*this).end())
+	{
+		(*this)[key] = current->second + total;
+	}
+	else
+	{
+		(*this)[key] = total;
+	}
+}
+void
+cxxNameDouble::multiply(LDBLE extensive)
+{
+//
+// Multiplies by extensive
+//
+
+	for (cxxNameDouble::iterator it = this->begin(); it != this->end(); it++)
+	{
+		it->second *= extensive;
+	}
+}
+void
+cxxNameDouble::merge_redox(const cxxNameDouble & source)
+//
+// Merges source into this
+// Accounts for possible conflicts between redox state and
+// totals
+//
+{
+	for (cxxNameDouble::const_iterator sit = source.begin(); sit != source.end(); sit++)
+	{
+		
+		std::string redox_name = sit->first;
+		std::string elt_name;
+		size_t pos = redox_name.find("(");
+
+		bool redox;
+		if (pos != std::string::npos) 
+		{
+			redox = true;
+			elt_name = redox_name.substr(0, pos - 1);
+		}
+		else
+		{
+			redox = false;
+			elt_name = redox_name;
+		}
+		if (redox)
+		{
+			// Remove elt_name, if present
+			if ((*this).find(elt_name) != (*this).end())
+			{
+				(*this).erase((*this).find(elt_name));
+			}
+			// Put in redox name
+			(*this)[redox_name] = sit->second;
+		}
+		else
+		{
+			std::string substring;
+			substring.append(elt_name);
+			substring.append("(");
+
+			// Remove all redox
+			bool deleted = true;
+			while (deleted)
+			{
+				deleted = false;
+				cxxNameDouble::iterator current = (*this).begin();
+				for ( ; current != (*this).end(); current++)
+				{
+					if (current->first.find(substring) == 0)
+					{
+						(*this).erase(current);
+						deleted = true;
+						break;
+					}
+				}
+			}
+			// Put in elt name
+			(*this)[elt_name] = sit->second;
+		}
+	}
+}
+struct DblCmp {     
+	bool operator()(const std::pair<std::string, LDBLE> &lhs, const std::pair<std::string, LDBLE> &rhs) 
+	{         
+		return lhs.second > rhs.second;     
+	} 
+}; 
+std::vector< std::pair<std::string, LDBLE> > 
+cxxNameDouble::sort_second(void)
+{
+	std::vector< std::pair<std::string, LDBLE> > myvec(this->begin(), this->end()); 
+	std::sort(myvec.begin(), myvec.end(), DblCmp());
+
+	return myvec;
+}
+void
+cxxNameDouble::Serialize(Dictionary &dictionary, std::vector < int >&ints,
+						std::vector < double >&doubles)
+{
+	ints.push_back((int) (*this).size());
+	for (const_iterator it = (*this).begin(); it != (*this).end(); it++)
+	{
+		int n = dictionary.Find(it->first);
+		ints.push_back(n);
+		doubles.push_back(it->second);
+	}
+}
+void
+cxxNameDouble::Deserialize(Dictionary &dictionary, std::vector<int> &ints, std::vector<double> &doubles, int &ii, int &dd)
+{
+	this->clear();
+	int count = ints[ii++];
+	for (int j = 0; j < count; j++)
+	{
+		int n = ints[ii++];
+		assert(n >= 0);
+		std::string str = dictionary.GetWords()[n];
+		if (str.size() != 0)
+		{
+			(*this)[str] = doubles[dd++];
+		}
+	}
+}

src/phreeqcpp/NameDouble.h

@@ -0,0 +1,71 @@
+#if !defined(NAMEDOUBLE_H_INCLUDED)
+#define NAMEDOUBLE_H_INCLUDED
+
+#if defined(_WINDLL)
+#define IPQ_DLL_EXPORT __declspec(dllexport)
+#else
+#define IPQ_DLL_EXPORT
+#endif
+
+#include <cassert>				// assert
+#include <map>					// std::map
+#include <string>				// std::string
+#include <list>					// std::list
+#include <vector>				// std::vector
+class Phreeqc;
+#include "Parser.h"
+#include "phrqtype.h"
+class Dictionary;
+class cxxISolutionComp;
+
+class IPQ_DLL_EXPORT cxxNameDouble:public
+	std::map < std::string, LDBLE >
+{
+
+  public:
+	enum ND_TYPE
+	{
+		ND_ELT_MOLES = 1,
+		ND_SPECIES_LA = 2,
+		ND_SPECIES_GAMMA = 3,
+		ND_NAME_COEF = 4
+	};
+
+	cxxNameDouble();
+	cxxNameDouble(struct elt_list *);
+	cxxNameDouble(struct elt_list *, int count);
+	cxxNameDouble(std::map < std::string, cxxISolutionComp > &comps);
+
+	cxxNameDouble(struct name_coef *nc, int count);
+	cxxNameDouble(const cxxNameDouble & old, LDBLE factor);
+	 ~cxxNameDouble();
+
+	LDBLE Get_total_element(const char *string) const;
+	cxxNameDouble Simplify_redox(void) const;
+	void Multiply_activities_redox(std::string, LDBLE f);
+
+	void dump_xml(std::ostream & s_oss, unsigned int indent) const;
+	void dump_raw(std::ostream & s_oss, unsigned int indent) const;
+	CParser::STATUS_TYPE read_raw(CParser & parser, std::istream::pos_type & pos);
+	void add_extensive(const cxxNameDouble & old, LDBLE factor);
+	void add_intensive(const cxxNameDouble & addee, LDBLE fthis, LDBLE f2);
+	void add_log_activities(const cxxNameDouble & addee, LDBLE fthis, LDBLE f2);
+	void add(const char *key, LDBLE total);
+	void multiply(LDBLE factor);
+	void merge_redox(const cxxNameDouble & source);
+
+	std::vector< std::pair<std::string, LDBLE> > sort_second(void);
+
+	void
+	insert(const char *str, LDBLE d)
+	{
+		(*this)[str] = d;
+	}
+	void Serialize(Dictionary &dictionary, std::vector<int> &ints, std::vector<double> &doubles);
+	void Deserialize(Dictionary &dictionary, std::vector<int> &ints, std::vector<double> &doubles, int &ii, int &dd);
+
+	enum ND_TYPE type;
+
+};
+
+#endif // !defined(NAMEDOUBLE_H_INCLUDED)

src/phreeqcpp/NumKeyword.cxx

@@ -0,0 +1,181 @@
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+// NumKeyword.cxx: implementation of the cxxNumKeyword class.
+//
+//////////////////////////////////////////////////////////////////////
+
+#include <stdio.h>           // ::sscanf
+#include "NumKeyword.h"
+#include "Parser.h"
+#include "Utils.h"
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+cxxNumKeyword::cxxNumKeyword(PHRQ_io *io)
+{
+	this->n_user = 1;
+	this->n_user_end = 1;
+	this->Set_io(io);
+}
+
+cxxNumKeyword::~cxxNumKeyword()
+{
+}
+
+void
+cxxNumKeyword::dump_xml(std::ostream & os, unsigned int indent) const
+{
+	unsigned int i;
+
+	for (i = 0; i < indent + 1; ++i)
+		os << "  ";
+	os << "<n_user>" << this->n_user << "</n_user>" << "\n";
+
+	for (i = 0; i < indent + 1; ++i)
+		os << "  ";
+	os << "<n_user_end>" << this->n_user_end << "</n_user_end>" << "\n";
+
+	for (i = 0; i < indent + 1; ++i)
+		os << "  ";
+	os << "<Description>" << this->description << "</Description>" << "\n";
+}
+
+void
+cxxNumKeyword::read_number_description(CParser & parser)
+{
+	std::string keyword;
+	std::istream::pos_type ptr;
+
+	// skip keyword
+	parser.copy_token(keyword, ptr);
+
+	// skip whitespace
+	while (::isspace(parser.get_iss().peek()))
+		parser.get_iss().ignore();
+
+	// read number
+	if (::isdigit(parser.get_iss().peek()) || parser.get_iss().peek() == '-')
+	{
+		parser.get_iss() >> this->n_user;
+		char ch = (char)parser.get_iss().peek();
+		if (ch == '-')
+		{
+			parser.get_iss() >> ch;			// eat '-'
+			parser.get_iss() >> this->n_user_end;
+			if (this->n_user_end < this->n_user)
+			{
+				this->n_user_end = this->n_user;
+			}
+		}
+		else
+		{
+			this->n_user_end = this->n_user;
+		}
+	}
+	else
+	{
+		this->n_user = this->n_user_end = 1;
+	}
+
+	// skip whitespace
+	while (::isspace(parser.get_iss().peek()))
+		parser.get_iss().ignore();
+
+	// copy description
+	std::getline(parser.get_iss(), this->description);
+}
+
+
+void
+cxxNumKeyword::read_number_description(std::istream & is)
+{
+	// KEYWORD [[1[-20]] [This is the description]]
+
+	// eat keyword
+	std::string token;
+	is >> token;
+
+	// skip whitespace
+	while (::isspace(is.peek()))
+		is.ignore();
+
+	if (::isdigit(is.peek()))
+	{
+		is >> this->n_user;
+		char ch = (char)is.peek();
+		if (ch == '-')
+		{
+			is >> ch;			// eat '-'
+			is >> this->n_user_end;
+		}
+		else
+		{
+			this->n_user_end = this->n_user;
+		}
+	}
+	else
+	{
+		this->n_user = this->n_user_end = 1;
+	}
+
+	while (::isspace(is.peek()))
+		is.ignore();
+
+	std::getline(is, this->description);
+}
+void
+cxxNumKeyword::read_number_description(const std::string & line_in)
+{
+	std::string keyword, token;
+	//std::istream::pos_type ptr;
+
+	std::string line = line_in;
+	std::string::iterator b = line.begin();
+	std::string::iterator e = line.end();
+	// skip keyword
+	CParser::copy_token(keyword, b, e);
+
+	// read number
+	if (CParser::copy_token(token, b, e) == CParser::TT_DIGIT)
+	{
+		if (token[0] == '-') 
+		{
+			token = token.substr(1);
+			Utilities::replace("-", " ", token);
+			token = "-" + token;
+		}
+		else
+		{
+			Utilities::replace("-", " ", token);
+		}
+		int j = sscanf(token.c_str(), "%d%d", &this->n_user, &this->n_user_end);
+		if (j == 0)
+		{
+			this->n_user = this->n_user_end = 1;
+		}
+		else if (j == 1)
+		{
+			this->n_user_end = this->n_user;
+		}
+		if (this->n_user_end < this->n_user)
+		{
+			this->n_user_end = this->n_user;
+		}
+	}
+	else
+	{
+		this->n_user = this->n_user_end = 1;
+	}
+
+	// skip whitespace
+	std::string::iterator ic;
+	this->description.clear();
+	for (ic = b; ic != e; ic++)
+	{
+		this->description += *ic;
+	}
+	trim_left(this->description);
+}

src/phreeqcpp/NumKeyword.h

@@ -0,0 +1,67 @@
+#if !defined(NUMKEYWORD_H_INCLUDED)
+#define NUMKEYWORD_H_INCLUDED
+
+#include <ostream>				// std::ostream
+#include <string>				// std::string
+#include "PHRQ_base.h"
+class CParser;
+
+class cxxNumKeyword: public PHRQ_base
+{
+  public:
+	cxxNumKeyword(PHRQ_io *io=NULL);
+	virtual ~ cxxNumKeyword();
+	const std::string &Get_description() const
+	{
+		return this->description;
+	}
+	void Set_description(std::string str)
+	{
+		this->description = str;
+	}
+	void Set_description(const char *str)
+	{
+		if (str != NULL)
+			this->description = str;
+	}
+
+	int Get_n_user() const
+	{
+		return this->n_user;
+	}
+	void Set_n_user(int user)
+	{
+		this->n_user = user;
+	}
+
+	int Get_n_user_end() const
+	{
+		return this->n_user_end;
+	}
+	void Set_n_user_end(int user_end)
+	{
+		this->n_user_end = user_end;
+	}
+	void Set_n_user_both(int user_end)
+	{
+		this->n_user = this->n_user_end = user_end;
+	}
+
+	bool operator<(const cxxNumKeyword & key) const
+	{
+		return (this->n_user < key.n_user);
+	}
+
+	virtual void dump_xml(std::ostream & os, unsigned int indent = 0) const;
+
+	void read_number_description(CParser & parser);
+	void read_number_description(const std::string & line_in);
+  protected:
+	int n_user;
+	int n_user_end;
+	std::string description;
+
+  protected:
+	void read_number_description(std::istream & is);
+};
+#endif // !defined(NUMKEYWORD_H_INCLUDED)

src/phreeqcpp/PBasic.h

@@ -0,0 +1,546 @@
+#ifndef _INC_PBasic_H
+#define _INC_PBasic_H
+#if defined(PHREEQCI_GUI)
+#include <windows.h>
+#endif
+#include <map>
+#include <stdio.h>
+#include <limits.h>
+#include <ctype.h>
+#include <math.h>
+#include <setjmp.h>
+#include "phrqtype.h"
+#include "PHRQ_base.h"
+#include "global_structures.h"
+class Phreeqc;
+
+class PBasicStop : public std::exception
+{
+};
+
+#define forloop         0
+#define whileloop       1
+#define gosubloop       2
+#define checking	true
+#define varnamelen      20
+#define maxdims	 4
+#define MAX_LINE 4096
+#define FileNotFound     10
+#define FileNotOpen      13
+#define FileWriteError   38
+#define BadInputFormat   14
+#define EndOfFile        30
+#define SETBITS  32
+#define Const
+
+typedef char varnamestring[varnamelen + 1];
+
+/* Header file for code generated by "p2c", the Pascal-to-C translator */
+
+/* "p2c"  Copyright (C) 1989, 1990, 1991 Free Software Foundation.
+ * By Dave Gillespie, daveg@csvax.cs.caltech.edu.  Version 1.20.
+ * This file may be copied, modified, etc. in any way.  It is not restricted
+ * by the licence agreement accompanying p2c itself.
+ */
+
+typedef struct varrec
+{
+	varnamestring name;
+	struct varrec *next;
+	long dims[maxdims];
+	char numdims;
+	bool stringvar;
+	union
+	{
+		struct
+		{
+			LDBLE *arr;
+			LDBLE *val, rv;
+		} U0;
+		struct
+		{
+			char **sarr;
+			char **sval, *sv;
+		} U1;
+	} UU;
+} varrec;
+
+typedef struct tokenrec
+{
+	struct tokenrec *next;
+	int kind;
+	union
+	{
+		struct varrec *vp;
+		LDBLE num;
+		char *sp;
+		char snch;
+	} UU;
+//#ifdef PHREEQCI_GUI
+	size_t n_sz;
+	char *sz_num;
+//#endif
+} tokenrec;
+
+typedef struct linerec
+{
+	long num, num2;
+	tokenrec *txt;
+	char inbuf[MAX_LINE];
+	struct linerec *next;
+} linerec;
+
+class valrec
+{
+public:
+	valrec()
+	{
+		stringval = false;
+		UU.val = 0;
+	}
+	~valrec() {}
+	bool stringval;
+	union
+	{
+		LDBLE val;
+		char *sval;
+	} UU;
+};
+
+typedef struct looprec
+{
+	struct looprec *next;
+	linerec *homeline;
+	tokenrec *hometok;
+	int kind;
+	union
+	{
+		struct
+		{
+			varrec *vp;
+			LDBLE max, step;
+		} U0;
+	} UU;
+} looprec;
+
+/*  variables for exec: */
+struct LOC_exec
+{
+	bool gotoflag, elseflag;
+	tokenrec *t;
+};
+
+class PBasic: public PHRQ_base
+{
+public:
+	PBasic(Phreeqc *ptr, PHRQ_io *phrq_io=NULL);
+	virtual ~PBasic();
+
+	enum BASIC_TOKEN
+	{
+		tokvar,
+		toknum,
+		tokstr,
+		toksnerr,
+		tokplus,
+		tokminus,
+		toktimes,
+		tokdiv,
+		tokup,
+		toklp,
+		tokrp,
+		tokcomma,
+		toksemi,
+		tokcolon,
+		tokeq,
+		toklt,
+		tokgt,
+		tokle,
+		tokge,
+		tokne,
+		tokand,
+		tokor,
+		tokxor,
+		tokmod,
+		toknot,
+		toksqr,
+		toksqrt,
+		toksin,
+		tokcos,
+		toktan,
+		tokarctan,
+		toklog,
+		tokexp,
+		tokabs,
+		toksgn,
+		tokstr_,
+		tokval,
+		tokchr_,
+		tokasc,
+		toklen,
+		tokmid_,
+		tokpeek,
+		tokrem,
+		toklet,
+		tokprint,
+		tokinput,
+		tokgoto,
+		tokif,
+		tokend,
+		tokstop,
+		tokfor,
+		toknext,
+		tokwhile,
+		tokwend,
+		tokgosub,
+		tokreturn,
+		tokread,
+		tokdata,
+		tokrestore,
+		tokgotoxy,
+		tokon,
+		tokdim,
+		tokpoke,
+		toklist,
+		tokrun,
+		toknew,
+		tokload,
+		tokmerge,
+		toksave,
+		tokbye,
+		tokdel,
+		tokrenum,
+		tokthen,
+		tokelse,
+		tokto,
+		tokstep,
+		toktc,
+		tokm0,
+		tokm,
+		tokparm,
+		tokact,
+		tokmol,
+		tokla,
+		toklm,
+		toksr,
+		toksi,
+		toktot,
+		toktk,
+		toktime,
+		toklog10,
+		toksim_time,
+		tokequi,
+		tokgas,
+		tokpunch,
+		tokkin,
+		toks_s,
+		tokmu,
+		tokalk,
+		tokrxn,
+		tokdist,
+		tokmisc1,
+		tokmisc2,
+		tokedl,
+		tokstep_no,
+		toksim_no,
+		toktotal_time,
+		tokput,
+		tokget,
+		tokcharge_balance,
+		tokpercent_error,
+#if defined (PHREEQ98) || defined (MULTICHART)
+		tokgraph_x,
+		tokgraph_y,
+		tokgraph_sy,
+#endif
+		tokcell_no,
+		tokexists,
+		toksurf,
+		toklk_species,
+		toklk_named,
+		toklk_phase,
+		toksum_species,
+		toksum_gas,
+		toksum_s_s,
+		tokcalc_value,
+		tokdescription,
+		toktitle,
+		toksys,
+		tokinstr,
+		tokltrim,
+		tokrtrim,
+		toktrim,
+		tokpad,
+		tokchange_por,
+		tokget_por,
+		tokosmotic,
+		tokchange_surf,
+		tokporevolume,
+		toksc,
+		tokgamma,
+		toklg,
+		tokrho,
+		tokrho_0,
+		tokcell_volume,
+		tokcell_pore_volume,
+		tokcell_porosity,
+		tokcell_saturation,
+#if defined MULTICHART
+		tokplot_xy,
+#endif
+		toktotmole,
+		tokiso,
+		tokiso_unit,
+		toktotmol,
+		toktotmoles,
+		tokeol_,
+		tokceil,
+		tokfloor,
+		tokkinetics_formula,
+		tokkinetics_formula_,
+		tokphase_formula,
+		tokphase_formula_,
+		tokspecies_formula,
+		tokspecies_formula_,
+		toklist_s_s,
+		tokpr_p,
+		tokpr_phi,
+		tokgas_p,
+		tokgas_vm,
+		tokpressure,
+		tokerase,
+		tokeps_r,
+		tokvm,
+		tokphase_vm,
+		tokdh_a,
+		tokdh_b,
+		tokdh_av,
+		tokqbrn,
+		tokkappa,
+		tokgfw,
+		toksoln_vol,
+		tokequi_delta,
+		tokkin_delta,
+		tokkin_time,
+		tokstr_f_,
+		tokstr_e_,
+		tokeq_frac,
+		tokequiv_frac,
+		tokcallback,
+		tokdiff_c,
+		toksetdiff_c,
+		toksa_declercq,
+		tokedl_species,
+		tokviscos,
+		tokviscos_0,
+		tokcurrent_a,
+		tokpot_v,
+		tokt_sc,
+		tokaphi
+	};
+
+#if !defined(PHREEQCI_GUI)
+	enum IDErr
+	{
+		IDS_ERR_ARRAY_ALREADY,
+		IDS_ERR_BAD_SUBSCRIPT,
+		IDS_ERR_EXTRA,
+		IDS_ERR_FOR_WO_NEXT,
+		IDS_ERR_ILLEGAL,
+		IDS_ERR_INFINITE_LOOP,
+		IDS_ERR_INPUT_NOTLEGAL,
+		IDS_ERR_MISMATCH,
+		IDS_ERR_MISSING_Q,
+		IDS_ERR_MISSING_RP,
+		IDS_ERR_NEXT_WO_FOR,
+		IDS_ERR_OUT_OF_DATA,
+		IDS_ERR_RETURN_WO_GOSUB,
+		IDS_ERR_SYNTAX,
+		IDS_ERR_UNDEF_LINE,
+		IDS_ERR_WEND_WO_WHILE,
+		IDS_ERR_WHILE_WO_WEND
+	};
+#endif
+
+	// Methods
+	bool Get_phreeqci_gui(void) const {return phreeqci_gui;};
+	void Set_phreeqci_gui(bool tf) {phreeqci_gui = tf;};
+	bool Get_parse_all(void) const {return parse_all;};
+	void Set_parse_all(bool tf) {parse_all = tf;};
+	bool Get_parse_whole_program(void) const {return parse_whole_program;};
+	void Set_parse_whole_program(bool tf) {parse_whole_program = tf;};
+	int Get_nErrLineNumber(void) const {return nErrLineNumber;};
+	void Set_nErrLineNumber(int i) {nErrLineNumber = i;};
+#if defined(PHREEQCI_GUI)
+	UINT Get_nIDErrPrompt(void)const {return nIDErrPrompt;};
+	void Set_nIDErrPrompt(UINT u) {nIDErrPrompt = u;};
+	int Get_P_escapecode(void)const {return P_escapecode;};
+	void Set_P_escapecode(int code) {P_escapecode = code;};
+	HANDLE Get_hInfiniteLoop(void) const {return hInfiniteLoop;};
+	void Set_hInfiniteLoop(HANDLE h) {hInfiniteLoop = h;};
+#endif
+	int free_dim_stringvar(varrec *varbase);
+
+	void exec(void);
+	int basic_renumber(char *commands, void **lnbase, void **vbase, void **lpbase);
+	void restoredata(void);
+	void clearloops(void);
+	void clearvar(varrec * v);
+	void clearvars(void);
+	char * numtostr(char * Result, LDBLE n);
+	void parse(char * inbuf, tokenrec ** buf);
+	void listtokens(FILE * f, tokenrec * buf);
+	void disposetokens(tokenrec ** tok);
+	void parseinput(tokenrec ** buf);
+	void errormsg(const char * s);
+	void snerr(const char * s);
+	void tmerr(const char * s);
+	void badsubscr(void);
+	LDBLE realfactor(struct LOC_exec *LINK);
+	char * strfactor(struct LOC_exec * LINK);
+	char *stringfactor(char * Result, struct LOC_exec *LINK);
+	const char *stringfactor(std::string & Result, struct LOC_exec * LINK);
+	long intfactor(struct LOC_exec *LINK);
+	LDBLE realexpr(struct LOC_exec *LINK);
+	char * strexpr(struct LOC_exec * LINK);
+	char * stringexpr(char * Result, struct LOC_exec * LINK);
+	long intexpr(struct LOC_exec *LINK);
+	void require(int k, struct LOC_exec *LINK);
+	void skipparen(struct LOC_exec *LINK);
+	varrec * findvar(struct LOC_exec *LINK);
+	valrec factor(struct LOC_exec *LINK);
+	valrec upexpr(struct LOC_exec * LINK);
+	valrec term(struct LOC_exec * LINK);
+	valrec sexpr(struct LOC_exec * LINK);
+	valrec relexpr(struct LOC_exec * LINK);
+	valrec andexpr(struct LOC_exec * LINK);
+	valrec expr(struct LOC_exec *LINK);
+	void checkextra(struct LOC_exec *LINK);
+	bool iseos(struct LOC_exec *LINK);
+	void skiptoeos(struct LOC_exec *LINK);
+	linerec * findline(long n);
+	linerec * mustfindline(long n);
+	void cmdend(struct LOC_exec *LINK);
+	void cmdnew(struct LOC_exec *LINK);
+	void cmdlist(struct LOC_exec *LINK);
+	void cmdload(bool merging, char * name, struct LOC_exec *LINK);
+	void cmdrun(struct LOC_exec *LINK);
+	void cmdsave(struct LOC_exec *LINK);
+	void cmdput(struct LOC_exec *LINK);
+	void cmdchange_por(struct LOC_exec *LINK);
+	void cmdchange_surf(struct LOC_exec *LINK);
+	void cmdbye(void);
+	void cmddel(struct LOC_exec *LINK);
+	void cmdrenum(struct LOC_exec *LINK);
+	void cmdprint(struct LOC_exec *LINK);
+	void cmdpunch(struct LOC_exec *LINK);
+#if defined PHREEQ98 || defined MULTICHART
+	void cmdgraph_x(struct LOC_exec *LINK);
+	void cmdgraph_y(struct LOC_exec *LINK);
+	void cmdgraph_sy(struct LOC_exec *LINK);
+#endif
+#if defined MULTICHART
+	void cmdplot_xy(struct LOC_exec *LINK);
+#endif
+	void cmdlet(bool implied, struct LOC_exec *LINK);
+	void cmdgoto(struct LOC_exec *LINK);
+	void cmdif(struct LOC_exec *LINK);
+	void cmdelse(struct LOC_exec *LINK);
+	bool skiploop(int up, int dn, struct LOC_exec *LINK);
+	void cmdfor(struct LOC_exec *LINK);
+	void cmdnext(struct LOC_exec *LINK);
+	void cmdwhile(struct LOC_exec *LINK);
+	void cmdwend(struct LOC_exec *LINK);
+	void cmdgosub(struct LOC_exec *LINK);
+	void cmdreturn(struct LOC_exec *LINK);
+	void cmdread(struct LOC_exec *LINK);
+	void cmddata(struct LOC_exec *LINK);
+	void cmdrestore(struct LOC_exec *LINK);
+	void cmdgotoxy(struct LOC_exec *LINK);
+	void cmdon(struct LOC_exec *LINK);
+	void cmddim(struct LOC_exec *LINK);
+	void cmderase(struct LOC_exec *LINK);
+	void cmdpoke(struct LOC_exec *LINK);
+	int basic_main(char *commands);
+	int basic_compile(char *commands, void **lnbase, void **vbase, void **lpbase);
+	int basic_run(char *commands, void *lnbase, void *vbase, void *lpbase);
+	int basic_init(void);
+#ifdef PHREEQ98
+	void GridChar(char *s, char *a);
+#endif
+	int sget_logical_line(char **ptr, int *l, char *return_line);
+	long my_labs(long x);
+	void * my_memmove(void * d, Const void * s, size_t n);
+	void * my_memcpy(void * d, Const void * s, size_t n);
+	int my_memcmp(Const void * s1, Const void * s2, size_t n);
+	void * my_memset(void * d, int c, size_t n);
+	int my_toupper(int c);
+	int my_tolower(int c);
+	long ipow(long a, long b);
+	char * strsub(register char *ret, register char *s, register int pos,
+		register int len);
+	int strpos2(char *s, register char *pat, register int pos);
+	int strcicmp(register char *s1, register char *s2);
+	char * strltrim(register char *s);
+	char * strrtrim(register char *s);
+	void strmove(register int len, register char *s, register int spos,
+		register char *d, register int dpos);
+	void strinsert(register char *src, register char *dst, register int pos);
+	int P_peek(FILE * f);
+	int P_eof(void);
+	int P_eoln(FILE * f);
+	void P_readpaoc(FILE * f, char *s, int len);
+	void P_readlnpaoc(FILE * f, char *s, int len);
+	long P_maxpos(FILE * f);
+	char * P_trimname(register char * fn, register int len);
+	long memavail(void);
+	long maxavail(void);
+	long * P_setunion(register long *d, register long *s1, register long *s2);
+	long * P_setint(register long *d, register long *s1, register long *s2);
+	long * P_setdiff(register long *d, register long *s1, register long *s2);
+	long * P_setxor(register long *d, register long *s1, register long *s2);
+	long * P_addset(register long *s, register unsigned val);
+	long * P_addsetr(register long *s, register unsigned v1, register unsigned v2);
+	long * P_remset(register long *s, register unsigned val);
+	int P_setequal(register long *s1, register long *s2);
+	int P_subset(register long *s1, register long *s2);
+	long * P_setcpy(register long *d, register long *s);
+	long * P_expset(register long *d, register long s);
+	long P_packset(register long *s);	
+	int _OutMem(void);
+	int _CaseCheck(void);
+	int _NilCheck(void);
+	static char * _ShowEscape(char *buf, int code, int ior, char *prefix);
+	int _Escape(int code);
+	int _EscIO(int code);
+
+	// data members
+protected:
+	Phreeqc * PhreeqcPtr;
+	char *inbuf;
+	linerec *linebase;
+	varrec *varbase;
+	looprec *loopbase;
+	long curline;
+	linerec *stmtline, *dataline;
+	tokenrec *stmttok, *datatok, *buf;
+	bool exitflag;
+	long EXCP_LINE;
+	static std::map<const std::string, BASIC_TOKEN> command_tokens;
+	int P_escapecode;
+	int P_ioresult;
+
+	bool phreeqci_gui;
+	bool parse_all;    /* true, most function values set to 1 for testing compilation */
+	bool parse_whole_program;
+	char fnbuf[256];
+#if defined(PHREEQCI_GUI)
+	HANDLE hInfiniteLoop;
+	UINT nIDErrPrompt;
+#else
+	IDErr nIDErrPrompt;
+#endif
+	int nErrLineNumber;
+};
+
+#endif /* _INC_PBasic_H */

src/phreeqcpp/PHRQ_io_output.cpp

@@ -0,0 +1,401 @@
+#include <assert.h>
+#include "Phreeqc.h"
+#include "phqalloc.h"
+
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+warning_msg(const char *err_str)
+/* ---------------------------------------------------------------------- */
+{
+	if (state == TRANSPORT && transport_warnings == FALSE)
+		return (OK);
+	if (state == ADVECTION && advection_warnings == FALSE)
+		return (OK);
+	count_warnings++;
+	if (pr.warnings >= 0)
+	{
+		if (count_warnings > pr.warnings)
+			return (OK);
+	}
+	if (phrq_io)
+	{
+		if (status_on)
+		{
+			phrq_io->screen_msg("\n");
+		}
+		std::ostringstream msg;
+		msg << "WARNING: " << err_str;
+		phrq_io->warning_msg(msg.str().c_str());
+		status_on = false;
+	}
+	
+	return OK;
+}
+
+/* ---------------------------------------------------------------------- */
+void Phreeqc::
+echo_msg(const char *str)
+/* ---------------------------------------------------------------------- */
+{
+	if (pr.echo_input == TRUE)
+	{
+		if (phrq_io) phrq_io->echo_msg(str);
+	}
+}
+
+/* ---------------------------------------------------------------------- */
+void Phreeqc::
+set_forward_output_to_log(int value)
+/* ---------------------------------------------------------------------- */
+{
+	forward_output_to_log = value;
+}
+
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+get_forward_output_to_log(void)
+/* ---------------------------------------------------------------------- */
+{
+	return forward_output_to_log;
+}
+
+void Phreeqc::
+fpunchf_heading(const char *name)
+{
+	if (pr.punch == TRUE && current_selected_output != NULL)
+	{
+		punch_msg(name);
+	}
+}
+void Phreeqc::
+fpunchf(const char *name, const char *format, double d)
+{
+	try
+	{
+		if (phrq_io) phrq_io->fpunchf(name, format, d);
+	}
+	catch(std::bad_alloc)
+	{
+		malloc_error();
+	}
+}
+void Phreeqc::
+fpunchf(const char *name, const char *format, char * s)
+{
+	try
+	{
+		if (phrq_io) phrq_io->fpunchf(name, format, s);
+	}
+	catch(std::bad_alloc)
+	{
+		malloc_error();
+	}
+}
+void Phreeqc::
+fpunchf(const char *name, const char *format, int d)
+{
+	try
+	{
+		if (phrq_io) phrq_io->fpunchf(name, format, d);
+	}
+	catch(std::bad_alloc)
+	{
+		malloc_error();
+	}
+}
+
+void Phreeqc::
+fpunchf_user(int user_index, const char *format, double d)
+{
+	const char *name;
+	
+	if (current_user_punch == NULL)
+		return;
+	// check headings
+	//if (user_index < user_punch_count_headings)
+	int user_punch_count_headings = (int) current_user_punch->Get_headings().size();
+	if (user_index < user_punch_count_headings)
+	{
+		//name = user_punch_headings[user_index];
+		name = current_user_punch->Get_headings()[user_index].c_str();
+	}
+	else
+	{
+		if (fpunchf_user_s_warning == 0)
+		{
+			error_string = sformatf(
+					"USER_PUNCH: Headings count does not match number of calls to PUNCH.\n");
+			warning_msg(error_string);
+			fpunchf_user_s_warning = 1;
+		}
+		sprintf(fpunchf_user_buffer, "no_heading_%d",
+				(user_index - user_punch_count_headings) + 1);
+		name = fpunchf_user_buffer;
+	}
+	try
+	{
+		if (phrq_io) phrq_io->fpunchf(name, format, (double) d);
+	}
+	catch(std::bad_alloc)
+	{
+		malloc_error();
+	}
+}
+
+void Phreeqc::
+fpunchf_user(int user_index, const char *format, char * d)
+{
+	const char *name;
+	
+	if (current_user_punch == NULL)
+		return;
+	int user_punch_count_headings = (int) current_user_punch->Get_headings().size();
+	// check headings
+	if (user_index < user_punch_count_headings)
+	{
+		//name = user_punch_headings[user_index];
+		name = current_user_punch->Get_headings()[user_index].c_str();
+	}
+	else
+	{
+		if (fpunchf_user_s_warning == 0)
+		{
+			error_string = sformatf(
+					"USER_PUNCH: Headings count does not match number of calls to PUNCH.\n");
+			warning_msg(error_string);
+			fpunchf_user_s_warning = 1;
+		}
+		sprintf(fpunchf_user_buffer, "no_heading_%d",
+				(user_index - user_punch_count_headings) + 1);
+		name = fpunchf_user_buffer;
+	}
+	try
+	{
+		if (phrq_io) phrq_io->fpunchf(name, format, d);
+	}
+	catch(std::bad_alloc)
+	{
+		malloc_error();
+	}
+}
+
+int Phreeqc::
+fpunchf_end_row(const char *format)
+{
+	if (phrq_io) 
+	{
+		phrq_io->fpunchf_end_row(format);
+	}
+	return OK;
+}
+/* ---------------------------------------------------------------------- */
+void Phreeqc::
+screen_msg(const char *err_str)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io) phrq_io->screen_msg(err_str);
+}
+// ---------------------------------------------------------------------- */
+// dump file methods
+// ---------------------------------------------------------------------- */
+
+/* ---------------------------------------------------------------------- */
+bool Phreeqc::
+dump_open(const char *file_name)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io)
+		return this->phrq_io->dump_open(file_name);
+	return false;
+}
+/* ---------------------------------------------------------------------- */
+void Phreeqc::
+dump_flush(void)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io) this->phrq_io->dump_flush();
+}
+/* ---------------------------------------------------------------------- */
+void Phreeqc::
+dump_close(void)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io) this->phrq_io->dump_close();
+}
+
+/* ---------------------------------------------------------------------- */
+void Phreeqc::
+dump_msg(const char * str)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io) this->phrq_io->dump_msg(str);
+}
+// ---------------------------------------------------------------------- */
+// error file methods
+// ---------------------------------------------------------------------- */
+
+/* ---------------------------------------------------------------------- */
+bool Phreeqc::
+error_open(const char *file_name)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io)
+		return this->phrq_io->error_open(file_name);
+	return false;
+}
+/* ---------------------------------------------------------------------- */
+void Phreeqc::
+error_flush(void)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io) this->phrq_io->error_flush();
+}
+/* ---------------------------------------------------------------------- */
+void Phreeqc::
+error_close(void)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io) this->phrq_io->error_close();
+}
+
+/* ---------------------------------------------------------------------- */
+void Phreeqc::
+error_msg(const char *err_str, bool stop)
+/* ---------------------------------------------------------------------- */
+{
+	if (get_input_errors() <= 0)
+		input_error = 1;
+	if (phrq_io)
+	{
+		std::ostringstream msg;
+		msg << "ERROR: " << err_str << "\n";
+
+		phrq_io->output_msg(msg.str().c_str());
+		phrq_io->log_msg(msg.str().c_str());
+
+		if (status_on)
+		{
+			phrq_io->screen_msg("\n");
+		}
+		status_on = false;
+		phrq_io->error_msg(msg.str().c_str(), stop);
+	}
+
+	if (stop)
+	{
+		throw PhreeqcStop();
+	}
+}
+// ---------------------------------------------------------------------- */
+// log file methods
+// ---------------------------------------------------------------------- */
+
+/* ---------------------------------------------------------------------- */
+bool Phreeqc::
+log_open(const char *file_name)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io)
+		return this->phrq_io->log_open(file_name);
+	return false;
+}
+/* ---------------------------------------------------------------------- */
+void Phreeqc::
+log_flush(void)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io) this->phrq_io->log_flush();
+}
+/* ---------------------------------------------------------------------- */
+void Phreeqc::
+log_close(void)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io) this->phrq_io->log_close();
+}
+
+/* ---------------------------------------------------------------------- */
+void Phreeqc::
+log_msg(const char * str)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io) this->phrq_io->log_msg(str);
+}
+// ---------------------------------------------------------------------- */
+// output_temp file methods
+// ---------------------------------------------------------------------- */
+
+/* ---------------------------------------------------------------------- */
+bool Phreeqc::
+output_open(const char *file_name)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io) 
+		return this->phrq_io->output_open(file_name);
+	return false;
+}
+/* ---------------------------------------------------------------------- */
+void Phreeqc::
+output_flush(void)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io) this->phrq_io->output_flush();
+}
+/* ---------------------------------------------------------------------- */
+void Phreeqc::
+output_close(void)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io) this->phrq_io->output_close();
+}
+/* ---------------------------------------------------------------------- */
+void Phreeqc::
+output_msg(const char * str)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io)
+	{
+		if (get_forward_output_to_log())
+		{
+			phrq_io->log_msg(str);
+		}
+		else
+		{
+			phrq_io->output_msg(str);
+		}
+	}
+}
+// ---------------------------------------------------------------------- */
+// punch file methods
+// ---------------------------------------------------------------------- */
+
+/* ---------------------------------------------------------------------- */
+bool Phreeqc::
+punch_open(const char *file_name, int n_user)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io)
+		return this->phrq_io->punch_open(file_name, std::ios_base::out, n_user);
+	return false;
+}
+/* ---------------------------------------------------------------------- */
+void Phreeqc::
+punch_flush(void)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io) this->phrq_io->punch_flush();
+}
+/* ---------------------------------------------------------------------- */
+void Phreeqc::
+punch_close(void)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io) this->phrq_io->punch_close();
+}
+/* ---------------------------------------------------------------------- */
+void Phreeqc::
+punch_msg(const char * str)
+/* ---------------------------------------------------------------------- */
+{
+	if (phrq_io) this->phrq_io->punch_msg(str);
+}

src/phreeqcpp/PPassemblage.cxx

@@ -0,0 +1,373 @@
+// PPassemblage.cxx: implementation of the cxxPPassemblage class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <cassert>				// assert
+#include <algorithm>			// std::sort
+
+#include "Utils.h"				// define first
+#include "Phreeqc.h"
+#include "PPassemblage.h"
+#include "cxxMix.h"
+#include "phqalloc.h"
+
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+cxxPPassemblage::cxxPPassemblage(PHRQ_io * io)
+	//
+	// default constructor for cxxPPassemblage 
+	//
+:	cxxNumKeyword(io)
+{
+	new_def = false;
+	eltList.type = cxxNameDouble::ND_ELT_MOLES;
+}
+
+cxxPPassemblage::cxxPPassemblage(const std::map < int,
+								 cxxPPassemblage > &entities, cxxMix & mix,
+								 int l_n_user, PHRQ_io * io):
+cxxNumKeyword(io)
+{
+	this->n_user = this->n_user_end = l_n_user;
+	eltList.type = cxxNameDouble::ND_ELT_MOLES;
+//
+//   Mix
+//
+	const std::map < int, LDBLE >&mixcomps = mix.Get_mixComps();
+	std::map < int, LDBLE >::const_iterator it;
+	for (it = mixcomps.begin(); it != mixcomps.end(); it++)
+	{
+		if (entities.find(it->first) != entities.end())
+		{
+			const cxxPPassemblage *entity_ptr =
+				&(entities.find(it->first)->second);
+			this->add(*entity_ptr, it->second);
+		}
+	}
+}
+
+cxxPPassemblage::~cxxPPassemblage()
+{
+}
+
+void
+cxxPPassemblage::dump_xml(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// PPassemblage element and attributes
+	s_oss << indent0;
+	s_oss << "<EQUILIBRIUM_PHASES " << "\n";
+
+	// eltList
+	this->eltList.dump_xml(s_oss, indent + 1);
+
+	// ppAssemblageComps
+	s_oss << indent1;
+	s_oss << "<pure_phases " << "\n";
+	for (std::map < std::string, cxxPPassemblageComp >::const_iterator it =
+		 pp_assemblage_comps.begin(); it != pp_assemblage_comps.end(); ++it)
+	{
+		(*it).second.dump_xml(s_oss, indent + 2);
+	}
+}
+
+void
+cxxPPassemblage::dump_raw(std::ostream & s_oss, unsigned int indent, int *n_out) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// PPassemblage element and attributes
+	s_oss << indent0;
+	int n_user_local = (n_out != NULL) ? *n_out : this->n_user;
+	s_oss << "EQUILIBRIUM_PHASES_RAW       " << n_user_local << " " << this->
+		description << "\n";
+
+
+	s_oss << indent1 << "# EXCHANGE_MODIFY candidates; use new_def=true #\n";
+	s_oss << indent1 << "-new_def                   " << 0 << "\n";
+	for (std::map < std::string, cxxPPassemblageComp >::const_iterator it =
+		 pp_assemblage_comps.begin(); it != pp_assemblage_comps.end(); ++it)
+	{
+		s_oss << indent1;
+		s_oss << "-component                 " << (*it).second.Get_name() << "\n";
+		(*it).second.dump_raw(s_oss, indent + 2);
+	}
+	s_oss << indent1;
+	s_oss << "-eltList                   # List of all elements in phases and alternate reactions\n";
+	this->eltList.dump_raw(s_oss, indent + 2);
+
+	s_oss << indent1 << "# PPassemblage workspace variables #\n";
+	s_oss << indent1 << "-assemblage_totals" << "\n";
+	this->assemblage_totals.dump_raw(s_oss, indent + 1);
+}
+
+void
+cxxPPassemblage::read_raw(CParser & parser, bool check)
+{
+
+	std::istream::pos_type ptr;
+	std::istream::pos_type next_char;
+	std::string token;
+	int opt_save;
+	bool useLastLine(false);
+
+	// Read PPassemblage number and description
+	this->read_number_description(parser);
+	this->Set_new_def(false);
+
+	opt_save = CParser::OPT_ERROR;
+
+	for (;;)
+	{
+		int opt;
+		if (useLastLine == false)
+		{
+			opt = parser.get_option(vopts, next_char);
+		}
+		else
+		{
+			opt = parser.getOptionFromLastLine(vopts, next_char, true);
+		}
+		if (opt == CParser::OPT_DEFAULT)
+		{
+			opt = opt_save;
+		}
+		useLastLine = false;
+		switch (opt)
+		{
+		case CParser::OPT_EOF:
+			break;
+		case CParser::OPT_KEYWORD:
+			break;
+		case CParser::OPT_DEFAULT:
+		case CParser::OPT_ERROR:
+			opt = CParser::OPT_EOF;
+			parser.
+				error_msg("Unknown input in EQUILIBRIUM_PHASES_RAW keyword.",
+						  PHRQ_io::OT_CONTINUE);
+			parser.error_msg(parser.line().c_str(), PHRQ_io::OT_CONTINUE);
+			useLastLine = false;
+			break;
+
+		case 0:				// eltList
+			if (this->eltList.read_raw(parser, next_char) !=
+				CParser::PARSER_OK)
+			{
+				parser.incr_input_error();
+				parser.
+					error_msg("Expected element name and moles for totals.",
+							  PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = 0;
+			break;
+		case 1:				// component
+			{
+				std::string str;
+				if (!(parser.get_iss() >> str))
+				{
+					parser.incr_input_error();
+					parser.error_msg("Expected string value for component name.",
+									 PHRQ_io::OT_CONTINUE);
+				}
+				else
+				{
+					cxxPPassemblageComp temp_comp(this->io);
+					temp_comp.Set_name(str.c_str());
+					cxxPPassemblageComp *comp_ptr = this->Find(str);
+					if (comp_ptr)
+					{
+						temp_comp = *comp_ptr;
+					}
+					temp_comp.read_raw(parser, check);
+					this->pp_assemblage_comps[str] = temp_comp;
+					useLastLine = true;
+				}
+			}
+			break;
+		case 2:				// new_def
+			if (!(parser.get_iss() >> this->new_def))
+			{
+				this->new_def = false;
+				parser.incr_input_error();
+				parser.
+					error_msg
+					("Expected boolean value for new_def in PPassemblage.",
+					 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+		case 3:				// assemblage_totals
+			if (this->assemblage_totals.read_raw(parser, next_char) !=
+				CParser::PARSER_OK)
+			{
+				parser.incr_input_error();
+				parser.
+					error_msg
+					("Expected element name and molality for PPassemblage totals.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = 3;
+			break;
+		}
+		if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
+			break;
+	}
+}
+
+void
+cxxPPassemblage::totalize(Phreeqc * phreeqc_ptr)
+{
+	this->assemblage_totals.clear();
+	// component structures
+	for (std::map < std::string, cxxPPassemblageComp >::iterator it =
+		 pp_assemblage_comps.begin(); it != pp_assemblage_comps.end(); ++it)
+	{
+		(*it).second.totalize(phreeqc_ptr);
+		this->assemblage_totals.add_extensive((*it).second.Get_totals(), 1.0);
+	}
+	return;
+}
+void
+cxxPPassemblage::add(const cxxPPassemblage & addee, LDBLE extensive)
+		//
+		// Add to existing ppassemblage to "this" ppassemblage
+		//
+{
+	if (extensive == 0.0)
+		return;
+	for (std::map < std::string, cxxPPassemblageComp >::const_iterator itadd = addee.pp_assemblage_comps.begin();
+		 itadd != addee.pp_assemblage_comps.end(); ++itadd)
+	{
+		bool found = false;
+		for (std::map < std::string, cxxPPassemblageComp >::iterator it =
+			 this->pp_assemblage_comps.begin();
+			 it != this->pp_assemblage_comps.end(); ++it)
+		{
+			if ((*it).second.Get_name() == itadd->second.Get_name())
+			{
+				(*it).second.add((*itadd).second, extensive);
+				found = true;
+				break;
+			}
+		}
+		if (!found)
+		{
+			cxxPPassemblageComp entity = (*itadd).second;
+			entity.multiply(extensive);
+			std::string str(entity.Get_name());
+			this->pp_assemblage_comps[str] = entity;
+		}
+	}
+	//cxxNameDouble eltList;
+	this->eltList.add_extensive(addee.eltList, extensive);
+}
+#ifdef SKIP
+cxxPPassemblageComp * cxxPPassemblage::
+Find(const std::string name_in)
+{
+	std::string name(name_in);
+	Utilities::str_tolower(name);
+
+	cxxPPassemblageComp * comp = NULL;
+	std::map<std::string, cxxPPassemblageComp>::iterator it;
+	it = this->pp_assemblage_comps.begin();
+	for ( ; it != this->pp_assemblage_comps.end(); it++)
+	{
+		std::string pname(it->first);
+		Utilities::str_tolower(pname);
+		if (name == pname)
+		{
+			comp = &it->second;
+			break;
+		}
+	}
+	return comp;
+}
+#endif
+cxxPPassemblageComp * cxxPPassemblage::
+Find(const std::string name_in)
+{
+	cxxPPassemblageComp * comp = NULL;
+	std::map<std::string, cxxPPassemblageComp>::iterator it;
+	it = this->pp_assemblage_comps.begin();
+	for ( ; it != this->pp_assemblage_comps.end(); it++)
+	{
+		if (Utilities::strcmp_nocase(name_in.c_str(), it->first.c_str()) == 0)
+		{
+			comp = &it->second;
+			break;
+		}
+	}
+	return comp;
+}
+/* ---------------------------------------------------------------------- */
+void
+cxxPPassemblage::Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles)
+/* ---------------------------------------------------------------------- */
+{
+	/* int n_user; */
+	ints.push_back(this->n_user);
+	ints.push_back(this->new_def ? 1 : 0);
+	ints.push_back((int) this->pp_assemblage_comps.size());
+	for (std::map < std::string, cxxPPassemblageComp >::iterator it =
+		 this->pp_assemblage_comps.begin(); it != this->pp_assemblage_comps.end();
+		 it++)
+	{
+		(*it).second.Serialize(dictionary, ints, doubles);
+	}
+	this->eltList.Serialize(dictionary, ints, doubles);
+	this->assemblage_totals.Serialize(dictionary, ints, doubles);
+}
+
+/* ---------------------------------------------------------------------- */
+void
+cxxPPassemblage::Deserialize(Dictionary & dictionary, std::vector < int >&ints, 
+	std::vector < double >&doubles, int &ii, int &dd)
+/* ---------------------------------------------------------------------- */
+{
+	/* int n_user; */
+	this->n_user = ints[ii++];
+	this->n_user_end = this->n_user;
+	this->description = " ";
+
+	this->new_def = (ints[ii++] != 0);
+	int count = ints[ii++];
+	this->pp_assemblage_comps.clear();
+	for (int n = 0; n < count; n++)
+	{
+		cxxPPassemblageComp ppc;
+		ppc.Deserialize(dictionary, ints, doubles, ii, dd);
+		std::string str(ppc.Get_name());
+		this->pp_assemblage_comps[str] = ppc;
+	}
+	this->eltList.Deserialize(dictionary, ints, doubles, ii, dd);
+	this->assemblage_totals.Deserialize(dictionary, ints, doubles, ii, dd);
+}
+const std::vector< std::string >::value_type temp_vopts[] = {
+	std::vector< std::string >::value_type("eltlist"),	        // 0
+	std::vector< std::string >::value_type("component"),	    // 1
+	std::vector< std::string >::value_type("new_def"),          // 2
+	std::vector< std::string >::value_type("assemblage_totals") // 3
+};									   
+const std::vector< std::string > cxxPPassemblage::vopts(temp_vopts, temp_vopts + sizeof temp_vopts / sizeof temp_vopts[0]);	

src/phreeqcpp/PPassemblage.h

@@ -0,0 +1,70 @@
+#if !defined(PPASSEMBLAGE_H_INCLUDED)
+#define PPASSEMBLAGE_H_INCLUDED
+
+#include <cassert>				// assert
+#include <map>					// std::map
+#include <string>				// std::string
+#include <list>					// std::list
+#include <vector>				// std::vector
+
+#include "NumKeyword.h"
+#include "PPassemblageComp.h"
+class cxxMix;
+
+class cxxPPassemblage:public cxxNumKeyword
+{
+
+  public:
+	cxxPPassemblage(PHRQ_io * io=NULL);
+	cxxPPassemblage(const std::map < int, cxxPPassemblage > &entity_map,
+					  cxxMix & mx, int n_user, PHRQ_io * io=NULL);
+	~cxxPPassemblage();
+
+	void dump_raw(std::ostream & s_oss, unsigned int indent, int *n_out=NULL) const;
+
+	void read_raw(CParser & parser, bool check = true);
+
+	const cxxNameDouble & Get_assemblage_totals() const
+	{
+		return this->assemblage_totals;
+	};
+	const cxxNameDouble & Get_eltList() const
+	{
+		return this->eltList;
+	};
+	void Set_eltList(cxxNameDouble & nd) {this->eltList = nd;}
+	std::map <std::string, cxxPPassemblageComp > & Get_pp_assemblage_comps() 
+	{
+		return this->pp_assemblage_comps;
+	};
+	const std::map <std::string, cxxPPassemblageComp > & Get_pp_assemblage_comps() const
+	{
+		return this->pp_assemblage_comps;
+	};
+	void  Set_pp_assemblage_comps(std::map <std::string, cxxPPassemblageComp > & c) 
+	{
+		this->pp_assemblage_comps = c;
+	};
+	bool Get_new_def(void) const {return this->new_def;}
+	void Set_new_def(bool tf) {this->new_def = tf;}
+
+	cxxPPassemblageComp *Find(const std::string name);
+
+	void totalize(Phreeqc * phreeqc_ptr);
+	void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
+	void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
+
+protected:
+	void add(const cxxPPassemblage & addee, LDBLE extensive);
+	// not written
+	void dump_xml(std::ostream & os, unsigned int indent = 0) const;
+
+protected:
+	bool new_def;
+	std::map <std::string, cxxPPassemblageComp > pp_assemblage_comps;
+	cxxNameDouble eltList;              // list of elements in phases (and alternate reactions)
+	cxxNameDouble assemblage_totals;    // after totalize, total moles of elements in the PPassemblage
+	const static std::vector < std::string > vopts;
+};
+
+#endif // !defined(PPASSEMBLAGE_H_INCLUDED)

src/phreeqcpp/PPassemblageComp.cxx

@@ -0,0 +1,433 @@
+// PPassemblageComp.cxx: implementation of the cxxPPassemblageComp class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <cassert>				// assert
+#include <algorithm>			// std::sort
+
+#include "Utils.h"				// define first
+#include "Phreeqc.h"
+#include "PPassemblageComp.h"
+#include "Dictionary.h"
+#include "phqalloc.h"
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+cxxPPassemblageComp::cxxPPassemblageComp(PHRQ_io *io)
+:
+PHRQ_base(io)
+	//
+	// default constructor for cxxPPassemblageComp 
+	//
+{
+	si = 0;
+	si_org = 0;
+	moles = 10;
+	delta = 0;
+	initial_moles = 0;
+	force_equality = false;
+	dissolve_only = false;
+	precipitate_only = false;
+}
+
+cxxPPassemblageComp::~cxxPPassemblageComp()
+{
+}
+
+void
+cxxPPassemblageComp::dump_xml(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// Pure_Phase element and attributes
+
+	s_oss << indent0 << "name=\"" << this->name << "\"" << "\n";
+	s_oss << indent0 << "add_formula=\"" << this->add_formula << "\"" << "\n";
+	s_oss << indent0 << "si=\"" << this->si << "\"" << "\n";
+	s_oss << indent0 << "si_org=\"" << this->si_org << "\"" << "\n";
+	s_oss << indent0 << "moles=\"" << this->moles << "\"" << "\n";
+	s_oss << indent0 << "delta=\"" << this->delta << "\"" << "\n";
+	s_oss << indent0 << "initial_moles=\"" << this->
+		initial_moles << "\"" << "\n";
+	s_oss << indent0 << "force_equality=\"" << this->
+		force_equality << "\"" << "\n";
+	s_oss << indent0 << "dissolve_only=\"" << this->
+		dissolve_only << "\"" << "\n";
+	s_oss << indent0 << "precipitate_only=\"" << this->
+		precipitate_only << "\"" << "\n";
+
+}
+
+void
+cxxPPassemblageComp::dump_raw(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// Pure_Phase element and attributes
+	s_oss << indent1 << "# EQUILIBRIUM_PHASES_MODIFY candidate identifiers #\n";
+	if (this->add_formula.size() != 0)
+		s_oss << indent1 << "-add_formula           " << this->add_formula << "\n";
+	s_oss << indent1 << "-si                    " << this->si << "\n";
+	s_oss << indent1 << "-moles                 " << this->moles << "\n";
+	s_oss << indent1 << "-force_equality        " << this->force_equality << "\n";
+	s_oss << indent1 << "-dissolve_only         " << this->dissolve_only << "\n";
+	s_oss << indent1 << "-precipitate_only      " << this->precipitate_only << "\n";
+
+	s_oss << indent1 << "# PPassemblage workspace variables #\n";
+	s_oss << indent1 << "-si_org                " << this->si_org << "\n";
+	s_oss << indent1 << "-delta                 " << this->delta << "\n";
+	s_oss << indent1 << "-initial_moles         " << this->initial_moles << "\n";
+	s_oss << indent1 << "-totals                " << "\n";
+	this->totals.dump_raw(s_oss, indent + 2);
+}
+
+void
+cxxPPassemblageComp::read_raw(CParser & parser, bool check)
+{
+	std::string str;
+
+	std::istream::pos_type ptr;
+	std::istream::pos_type next_char;
+	std::string token;
+	int opt_save;
+
+	opt_save = CParser::OPT_ERROR;
+	bool si_defined(false);
+	bool moles_defined(false);
+	bool delta_defined(false);
+	bool initial_moles_defined(false);
+	bool dissolve_only_defined(false);
+	bool force_equality_defined(false);
+
+	for (;;)
+	{
+		int opt = parser.get_option(vopts, next_char);
+		if (opt == CParser::OPT_DEFAULT)
+		{
+			opt = opt_save;
+		}
+
+		switch (opt)
+		{
+		case CParser::OPT_EOF:
+			break;
+		case CParser::OPT_KEYWORD:
+			break;
+		case CParser::OPT_DEFAULT:
+		case CParser::OPT_ERROR:
+			opt = CParser::OPT_KEYWORD;
+			// Allow return to Exchange for more processing
+			break;
+
+		case 0:				// name
+			parser.warning_msg("-name ignored. Name is defined with -component.");
+			break;
+
+		case 1:				// add_formula
+			if (!(parser.get_iss() >> str))
+			{
+				this->add_formula.clear();
+				parser.incr_input_error();
+				parser.error_msg("Expected string value for add_formula.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			else
+			{
+				this->add_formula = str;
+			}
+			break;
+
+		case 2:				// si
+			if (!(parser.get_iss() >> this->si))
+			{
+				this->si = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for si.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			si_defined = true;
+			break;
+
+		case 3:				// moles
+			if (!(parser.get_iss() >> this->moles))
+			{
+				this->moles = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for moles.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			moles_defined = true;
+			break;
+
+		case 4:				// delta
+			if (!(parser.get_iss() >> this->delta))
+			{
+				this->delta = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for delta.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			delta_defined = true;
+			break;
+
+		case 5:				// initial_moles
+			if (!(parser.get_iss() >> this->initial_moles))
+			{
+				this->initial_moles = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for initial_moles.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			initial_moles_defined = true;
+			break;
+
+
+		case 6:				// dissolve_only
+			if (!(parser.get_iss() >> this->dissolve_only))
+			{
+				this->dissolve_only = false;
+				parser.incr_input_error();
+				parser.error_msg("Expected boolean value for dissolve_only.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			dissolve_only_defined = true;
+			if (this->dissolve_only)
+			{
+				this->precipitate_only = false;
+			}
+			break;
+
+		case 7:				// force_equality
+			if (!(parser.get_iss() >> this->force_equality))
+			{
+				this->force_equality = false;
+				parser.incr_input_error();
+				parser.error_msg("Expected boolean value for force_equality.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			force_equality_defined = true;
+			break;
+
+		case 8:				// precipitate_only
+			if (!(parser.get_iss() >> this->precipitate_only))
+			{
+				this->precipitate_only = false;
+				parser.incr_input_error();
+				parser.error_msg("Expected boolean value for precipitate_only.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			if (this->precipitate_only)
+			{
+				this->dissolve_only = false;
+			}
+			break;
+		case 9:				// si_org
+			if (!(parser.get_iss() >> this->si_org))
+			{
+				this->si_org = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for si_org.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+		case 10:				// totals
+			if (this->totals.read_raw(parser, next_char) !=	CParser::PARSER_OK)
+			{
+				parser.incr_input_error();
+				parser.
+					error_msg
+					("Expected element name and molality for Surface totals.",
+					 PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = 10;
+			break;
+		}
+		if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
+			break;
+	}
+	// members that must be defined
+	if (check)
+	{
+		if (si_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Si not defined for PPassemblageComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (moles_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Moles not defined for PPassemblageComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (delta_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Delta not defined for PPassemblageComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (initial_moles_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Initial_moles not defined for PPassemblageComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (dissolve_only_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Dissolve_only not defined for PPassemblageComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (force_equality_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg
+				("Force_equality not defined for PPassemblageComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+	}
+}
+
+void
+cxxPPassemblageComp::totalize(Phreeqc * phreeqc_ptr)
+{
+	this->totals.clear();
+	// component structures
+	if (this->add_formula.size() != 0)
+		return;
+	struct phase *phase_ptr;
+	int l;
+	phase_ptr = phreeqc_ptr-> phase_bsearch(this->name.c_str(), &l, FALSE);
+	if (phase_ptr != NULL)
+	{
+		cxxNameDouble phase_formula(phase_ptr->next_elt);
+		this->totals.add_extensive(phase_formula, this->moles);
+	}
+	else
+	{
+		assert(false);
+	}
+	return;
+}
+
+
+void
+cxxPPassemblageComp::add(const cxxPPassemblageComp & addee, LDBLE extensive)
+{
+	LDBLE ext1, ext2, f1, f2;
+	if (extensive == 0.0)
+		return;
+	if (addee.name.size() == 0)
+		return;
+	// this and addee must have same name
+	// otherwise generate a new PPassemblagComp with multiply
+
+	ext1 = this->moles;
+	ext2 = addee.moles * extensive;
+	if (ext1 + ext2 != 0)
+	{
+		f1 = ext1 / (ext1 + ext2);
+		f2 = ext2 / (ext1 + ext2);
+	}
+	else
+	{
+		f1 = 0.5;
+		f2 = 0.5;
+	}
+
+	if (this->name.size() == 0 && addee.name.size() == 0)
+	{
+		return;
+	}
+	assert(this->name == addee.name);
+	if (this->add_formula != addee.add_formula)
+	{
+		std::ostringstream oss;
+		oss <<
+			"Cannot mix two Equilibrium_phases with differing add_formulae., "
+			<< this->name;
+		error_msg(oss.str().c_str(), CONTINUE);
+		return;
+	}
+	this->si = this->si * f1 + addee.si * f2;
+	this->si_org = this->si_org * f1 + addee.si_org * f2;
+	this->moles += addee.moles * extensive;
+	this->delta += addee.delta * extensive;
+	this->initial_moles += addee.initial_moles * extensive;
+}
+
+void
+cxxPPassemblageComp::multiply(LDBLE extensive)
+{
+	this->moles *= extensive;
+	this->delta *= extensive;
+	this->initial_moles *= extensive;
+}
+void
+cxxPPassemblageComp::Serialize(Dictionary & dictionary, std::vector < int >&ints, 
+	std::vector < double >&doubles)
+{
+	ints.push_back(dictionary.Find(this->name));
+	ints.push_back(dictionary.Find(this->add_formula));
+	doubles.push_back(this->si);
+	doubles.push_back(this->si_org);
+	doubles.push_back(this->moles);
+	doubles.push_back(this->delta);
+	doubles.push_back(this->initial_moles);
+	ints.push_back( this->force_equality ? 1 : 0);
+	ints.push_back(this->dissolve_only ? 1 : 0);
+	ints.push_back(this->precipitate_only ? 1 : 0);
+	this->totals.Serialize(dictionary, ints, doubles);
+}
+
+void
+cxxPPassemblageComp::Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd)
+{
+	this->name = dictionary.GetWords()[ints[ii++]];
+	this->add_formula = dictionary.GetWords()[ints[ii++]];
+	this->si = doubles[dd++];
+	this->si_org = doubles[dd++];
+	this->moles = doubles[dd++];
+	this->delta = doubles[dd++];
+	this->initial_moles = doubles[dd++];
+	this->force_equality = (ints[ii++] != 0);
+	this->dissolve_only = (ints[ii++] != 0);
+	this->precipitate_only = (ints[ii++] != 0);
+	this->totals.Deserialize(dictionary, ints, doubles, ii, dd);
+}
+
+
+const std::vector< std::string >::value_type temp_vopts[] = {
+	std::vector< std::string >::value_type("name"),	            // 0                 
+	std::vector< std::string >::value_type("add_formula"),	    // 1
+	std::vector< std::string >::value_type("si"),	            // 2
+	std::vector< std::string >::value_type("moles"),	        // 3
+	std::vector< std::string >::value_type("delta"),	        // 4
+	std::vector< std::string >::value_type("initial_moles"),	// 5     
+	std::vector< std::string >::value_type("dissolve_only"),	// 6
+	std::vector< std::string >::value_type("force_equality"),	// 7
+	std::vector< std::string >::value_type("precipitate_only"),	// 8
+	std::vector< std::string >::value_type("si_org"),	        // 9
+	std::vector< std::string >::value_type("totals") 	        // 10
+};									   
+const std::vector< std::string > cxxPPassemblageComp::vopts(temp_vopts, temp_vopts + sizeof temp_vopts / sizeof temp_vopts[0]);	

src/phreeqcpp/PPassemblageComp.h

@@ -0,0 +1,83 @@
+#if !defined(PPASSEMBLAGECOMP_H_INCLUDED)
+#define PPASSEMBLAGECOMP_H_INCLUDED
+
+#include <cassert>				// assert
+#include <map>					// std::map
+#include <string>				// std::string
+#include <list>					// std::list
+#include <vector>				// std::vector
+
+#include "NameDouble.h"
+
+class cxxPPassemblageComp: public PHRQ_base
+{
+
+  public:
+	cxxPPassemblageComp(PHRQ_io *io=NULL);
+	virtual ~cxxPPassemblageComp();
+
+	void dump_xml(std::ostream & os, unsigned int indent = 0) const;
+	void dump_raw(std::ostream & s_oss, unsigned int indent) const;
+	void read_raw(CParser & parser, bool check = true);
+
+	const std::string &Get_name() const	{return this->name;}
+	void Set_name(const char * s)
+	{
+		if(s != NULL)
+			this->name = std::string(s);
+		else
+			this->name.clear();
+	}
+	const std::string &Get_add_formula() const {return this->add_formula;}
+	void Set_add_formula(const char * s)
+	{
+		if(s != NULL)
+			this->add_formula = std::string(s);
+		else
+			this->add_formula.clear();
+	}
+
+	void totalize(Phreeqc * phreeqc_ptr);
+	const cxxNameDouble & Get_totals() const {return (this->totals);}
+	void Get_totals(cxxNameDouble & nd) {this->totals = nd;}
+	LDBLE Get_si() const {return this->si;}
+	void Set_si(LDBLE t) {this->si = t;}
+	LDBLE Get_si_org() const {return this->si_org;}
+	void Set_si_org(LDBLE t) {this->si_org = t;}
+	LDBLE Get_moles() const {return this->moles;}
+	void Set_moles(LDBLE t) {this->moles = t;}
+	LDBLE Get_delta() const {return this->delta;}
+	void Set_delta(LDBLE t) {this->delta = t;}
+	LDBLE Get_initial_moles() const {return this->initial_moles;}
+	void Set_initial_moles(LDBLE t) {this->initial_moles = t;}
+
+	bool Get_force_equality() const {return this->force_equality;}
+	void Set_force_equality(bool tf) {this->force_equality = tf;}
+	bool Get_dissolve_only() const {return this->dissolve_only;}
+	void Set_dissolve_only(bool tf) {this->dissolve_only = tf;}
+	bool Get_precipitate_only() const {return this->precipitate_only;}
+	void Set_precipitate_only(bool tf) {this->precipitate_only = tf;}
+
+	void add(const cxxPPassemblageComp & comp, LDBLE extensive);
+	void multiply(LDBLE extensive);
+	void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
+	void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
+
+protected:
+	std::string name;
+	std::string add_formula;
+	LDBLE si;
+	LDBLE si_org;
+	LDBLE moles;
+	LDBLE delta;
+	LDBLE initial_moles;
+	bool force_equality;
+	bool dissolve_only;
+	bool precipitate_only;
+	cxxNameDouble totals;
+	const static std::vector < std::string > vopts;
+public:
+
+};
+
+#endif // !defined(PPASSEMBLAGECOMP_H_INCLUDED)

src/phreeqcpp/PhreeqcKeywords/Keywords.cpp

@@ -0,0 +1,225 @@
+#include "Keywords.h"
+
+
+Keywords::Keywords(void)
+{
+}
+
+
+Keywords::~Keywords(void)
+{
+}
+
+Keywords::KEYWORDS Keywords::Keyword_search(std::string key)
+{
+	std::map<const std::string, Keywords::KEYWORDS>::const_iterator it;
+	it = phreeqc_keywords.find(key);
+	if (it != Keywords::phreeqc_keywords.end())
+	{
+		return it->second;
+	}
+	return Keywords::KEY_NONE;
+}
+
+const std::string & Keywords::Keyword_name_search(Keywords::KEYWORDS key)
+{
+	std::map<Keywords::KEYWORDS, const std::string>::const_iterator it;
+	it = phreeqc_keyword_names.find(key);
+	if (it != Keywords::phreeqc_keyword_names.end())
+	{
+		return it->second;
+	}
+	it = phreeqc_keyword_names.find(KEY_NONE);
+	return it->second;
+}
+
+const std::map<const std::string, Keywords::KEYWORDS>::value_type temp_keywords[] = {
+std::map<const std::string, Keywords::KEYWORDS>::value_type("eof",							Keywords::KEY_END),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("end", 							Keywords::KEY_END),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("solution_species", 			Keywords::KEY_SOLUTION_SPECIES),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("solution_master_species", 		Keywords::KEY_SOLUTION_MASTER_SPECIES),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("solution", 					Keywords::KEY_SOLUTION),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("phases", 						Keywords::KEY_PHASES),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("pure_phases", 					Keywords::KEY_EQUILIBRIUM_PHASES),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("reaction", 					Keywords::KEY_REACTION),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("mix", 							Keywords::KEY_MIX),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("use", 							Keywords::KEY_USE),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("save", 						Keywords::KEY_SAVE),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("exchange_species", 			Keywords::KEY_EXCHANGE_SPECIES),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("exchange_master_species", 		Keywords::KEY_EXCHANGE_MASTER_SPECIES),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("exchange", 					Keywords::KEY_EXCHANGE),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("surface_species", 				Keywords::KEY_SURFACE_SPECIES),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("surface_master_species", 		Keywords::KEY_SURFACE_MASTER_SPECIES),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("surface", 						Keywords::KEY_SURFACE),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("reaction_temperature", 		Keywords::KEY_REACTION_TEMPERATURE),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("inverse_modeling", 			Keywords::KEY_INVERSE_MODELING),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("gas_phase", 					Keywords::KEY_GAS_PHASE),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("transport", 					Keywords::KEY_TRANSPORT),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("debug", 						Keywords::KEY_KNOBS),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("selected_output", 				Keywords::KEY_SELECTED_OUTPUT),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("select_output", 				Keywords::KEY_SELECTED_OUTPUT),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("knobs", 						Keywords::KEY_KNOBS),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("print", 						Keywords::KEY_PRINT),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("equilibrium_phases", 			Keywords::KEY_EQUILIBRIUM_PHASES),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("equilibria", 					Keywords::KEY_EQUILIBRIUM_PHASES),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("equilibrium", 					Keywords::KEY_EQUILIBRIUM_PHASES),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("pure", 						Keywords::KEY_EQUILIBRIUM_PHASES),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("title", 						Keywords::KEY_TITLE),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("comment", 						Keywords::KEY_TITLE),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("advection", 					Keywords::KEY_ADVECTION),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("kinetics", 					Keywords::KEY_KINETICS),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("incremental_reactions", 		Keywords::KEY_INCREMENTAL_REACTIONS),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("incremental", 					Keywords::KEY_INCREMENTAL_REACTIONS),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("rates", 						Keywords::KEY_RATES),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("solution_s", 					Keywords::KEY_SOLUTION_SPREAD),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("user_print", 					Keywords::KEY_USER_PRINT),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("user_punch", 					Keywords::KEY_USER_PUNCH),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("solid_solutions", 				Keywords::KEY_SOLID_SOLUTIONS),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("solid_solution", 				Keywords::KEY_SOLID_SOLUTIONS),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("solution_spread", 				Keywords::KEY_SOLUTION_SPREAD),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("spread_solution", 				Keywords::KEY_SOLUTION_SPREAD),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("selected_out", 				Keywords::KEY_SELECTED_OUTPUT),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("select_out", 					Keywords::KEY_SELECTED_OUTPUT),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("user_graph", 					Keywords::KEY_USER_GRAPH),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("llnl_aqueous_model_parameters",Keywords::KEY_LLNL_AQUEOUS_MODEL_PARAMETERS),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("llnl_aqueous_model", 			Keywords::KEY_LLNL_AQUEOUS_MODEL_PARAMETERS),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("database",						Keywords::KEY_DATABASE),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("named_analytical_expression", 	Keywords::KEY_NAMED_EXPRESSIONS),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("named_analytical_expressions", Keywords::KEY_NAMED_EXPRESSIONS),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("named_expressions", 			Keywords::KEY_NAMED_EXPRESSIONS),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("named_log_k", 					Keywords::KEY_NAMED_EXPRESSIONS),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("isotopes", 					Keywords::KEY_ISOTOPES),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("calculate_values", 			Keywords::KEY_CALCULATE_VALUES),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("isotope_ratios", 				Keywords::KEY_ISOTOPE_RATIOS),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("isotope_alphas", 				Keywords::KEY_ISOTOPE_ALPHAS),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("copy", 						Keywords::KEY_COPY),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("pitzer", 						Keywords::KEY_PITZER),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("sit", 							Keywords::KEY_SIT),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("equilibrium_phase", 			Keywords::KEY_EQUILIBRIUM_PHASES),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("solution_raw", 				Keywords::KEY_SOLUTION_RAW),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("exchange_raw", 				Keywords::KEY_EXCHANGE_RAW),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("surface_raw", 					Keywords::KEY_SURFACE_RAW),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("equilibrium_phases_raw", 		Keywords::KEY_EQUILIBRIUM_PHASES_RAW),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("kinetics_raw", 				Keywords::KEY_KINETICS_RAW),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("solid_solutions_raw", 			Keywords::KEY_SOLID_SOLUTIONS_RAW),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("gas_phase_raw", 				Keywords::KEY_GAS_PHASE_RAW),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("reaction_raw", 				Keywords::KEY_REACTION_RAW),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("mix_raw", 						Keywords::KEY_MIX_RAW),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("reaction_temperature_raw", 	Keywords::KEY_REACTION_TEMPERATURE_RAW),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("dump", 						Keywords::KEY_DUMP),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("solution_modify", 				Keywords::KEY_SOLUTION_MODIFY),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("equilibrium_phases_modify", 	Keywords::KEY_EQUILIBRIUM_PHASES_MODIFY),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("exchange_modify", 				Keywords::KEY_EXCHANGE_MODIFY),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("surface_modify", 				Keywords::KEY_SURFACE_MODIFY),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("solid_solutions_modify", 		Keywords::KEY_SOLID_SOLUTIONS_MODIFY),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("gas_phase_modify", 			Keywords::KEY_GAS_PHASE_MODIFY),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("kinetics_modify", 				Keywords::KEY_KINETICS_MODIFY),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("delete", 						Keywords::KEY_DELETE),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("run_cells", 					Keywords::KEY_RUN_CELLS),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("reaction_modify", 				Keywords::KEY_REACTION_MODIFY),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("reaction_temperature_modify", 	Keywords::KEY_REACTION_TEMPERATURE_MODIFY),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("solid_solution_modify", 		Keywords::KEY_SOLID_SOLUTIONS_MODIFY),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("reaction_pressure", 			Keywords::KEY_REACTION_PRESSURE),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("reaction_pressures", 			Keywords::KEY_REACTION_PRESSURE),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("reaction_pressure_raw", 		Keywords::KEY_REACTION_PRESSURE_RAW),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("reaction_pressure_modify", 	Keywords::KEY_REACTION_PRESSURE_MODIFY),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("solution_mix", 	            Keywords::KEY_SOLUTION_MIX),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("mix_solution", 	            Keywords::KEY_SOLUTION_MIX),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("exchange_mix", 	            Keywords::KEY_EXCHANGE_MIX),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("mix_exchange", 	            Keywords::KEY_EXCHANGE_MIX),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("gas_phase_mix", 	            Keywords::KEY_GAS_PHASE_MIX),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("mix_gas_phase", 	            Keywords::KEY_GAS_PHASE_MIX),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("kinetics_mix", 	            Keywords::KEY_KINETICS_MIX),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("mix_kinetics", 	            Keywords::KEY_KINETICS_MIX),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("equilibrium_phases_mix", 	    Keywords::KEY_PPASSEMBLAGE_MIX),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("mix_equilibrium_phases", 	    Keywords::KEY_PPASSEMBLAGE_MIX),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("equilibrium_phase_mix", 	    Keywords::KEY_PPASSEMBLAGE_MIX),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("mix_equilibrium_phase", 	    Keywords::KEY_PPASSEMBLAGE_MIX),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("solid_solutions_mix", 	        Keywords::KEY_SSASSEMBLAGE_MIX),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("mix_solid_solutions", 	        Keywords::KEY_SSASSEMBLAGE_MIX),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("solid_solution_mix", 	        Keywords::KEY_SSASSEMBLAGE_MIX),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("mix_solid_solution", 	        Keywords::KEY_SSASSEMBLAGE_MIX),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("surface_mix", 	                Keywords::KEY_SURFACE_MIX),
+std::map<const std::string, Keywords::KEYWORDS>::value_type("mix_surface", 	                Keywords::KEY_SURFACE_MIX)
+};
+const std::map<const std::string, Keywords::KEYWORDS> Keywords::phreeqc_keywords(temp_keywords, temp_keywords + sizeof temp_keywords / sizeof temp_keywords[0]);
+
+const std::map<Keywords::KEYWORDS, std::string>::value_type temp_keyword_names[] = {
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_NONE,							"UNKNOWN"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_END,							"END"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SOLUTION_SPECIES,				"SOLUTION_SPECIES"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SOLUTION_MASTER_SPECIES,		"SOLUTION_MASTER_SPECIES"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SOLUTION,						"SOLUTION"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_PHASES,						"PHASES"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_REACTION,						"REACTION"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_MIX,							"MIX"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_USE,							"USE"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SAVE,							"SAVE"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_EXCHANGE_SPECIES,				"EXCHANGE_SPECIES"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_EXCHANGE_MASTER_SPECIES,		"EXCHANGE_MASTER_SPECIES"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_EXCHANGE,						"EXCHANGE"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SURFACE_SPECIES,				"SURFACE_SPECIES"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SURFACE_MASTER_SPECIES,		"SURFACE_MASTER_SPECIES"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SURFACE,						"SURFACE"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_REACTION_TEMPERATURE,			"REACTION_TEMPERATURE"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_INVERSE_MODELING,				"INVERSE_MODELING"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_GAS_PHASE,					"GAS_PHASE"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_TRANSPORT,					"TRANSPORT"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SELECTED_OUTPUT,				"SELECTED_OUTPUT"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_KNOBS,						"KNOBS"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_PRINT,						"PRINT"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_EQUILIBRIUM_PHASES,			"EQUILIBRIUM_PHASES"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_TITLE,						"TITLE"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_ADVECTION,					"ADVECTION"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_KINETICS,						"KINETICS"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_INCREMENTAL_REACTIONS,		"INCREMENTAL_REACTIONS"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_RATES,						"RATES"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_USER_PRINT,					"USER_PRINT"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_USER_PUNCH,					"USER_PUNCH"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SOLID_SOLUTIONS,				"SOLID_SOLUTIONS"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SOLUTION_SPREAD,				"SOLUTION_SPREAD"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_USER_GRAPH,					"USER_GRAPH"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_LLNL_AQUEOUS_MODEL_PARAMETERS,"LLNL_AQUEOUS_MODEL_PARAMETERS"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_DATABASE,						"DATABASE"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_NAMED_EXPRESSIONS,			"NAMED_EXPRESSIONS"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_ISOTOPES,						"ISOTOPES"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_CALCULATE_VALUES,				"CALCULATE_VALUES"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_ISOTOPE_RATIOS,				"ISOTOPE_RATIOS"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_ISOTOPE_ALPHAS,				"ISOTOPE_ALPHAS"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_COPY,							"COPY"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_PITZER,						"PITZER"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SIT,							"SIT"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SOLUTION_RAW,					"SOLUTION_RAW"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_EXCHANGE_RAW,					"EXCHANGE_RAW"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SURFACE_RAW,					"SURFACE_RAW"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_EQUILIBRIUM_PHASES_RAW,		"EQUILIBRIUM_PHASES_RAW"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_KINETICS_RAW,					"KINETICS_RAW"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SOLID_SOLUTIONS_RAW,			"SOLID_SOLUTIONS_RAW"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_GAS_PHASE_RAW,				"GAS_PHASE_RAW"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_REACTION_RAW,					"REACTION_RAW"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_MIX_RAW,						"MIX_RAW"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_REACTION_TEMPERATURE_RAW,		"REACTION_TEMPERATURE_RAW"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_DUMP,							"DUMP"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SOLUTION_MODIFY,				"SOLUTION_MODIFY"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_EQUILIBRIUM_PHASES_MODIFY,	"EQUILIBRIUM_PHASES_MODIFY"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_EXCHANGE_MODIFY,				"EXCHANGE_MODIFY"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SURFACE_MODIFY,				"SURFACE_MODIFY"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SOLID_SOLUTIONS_MODIFY,		"SOLID_SOLUTIONS_MODIFY"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_GAS_PHASE_MODIFY,				"GAS_PHASE_MODIFY"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_KINETICS_MODIFY,				"KINETICS_MODIFY"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_DELETE,						"DELETE"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_RUN_CELLS,					"RUN_CELLS"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_REACTION_MODIFY,				"REACTION_MODIFY"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_REACTION_TEMPERATURE_MODIFY,	"REACTION_TEMPERATURE_MODIFY"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_REACTION_PRESSURE,			"REACTION_PRESSURE"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_REACTION_PRESSURE_RAW,		"REACTION_PRESSURE_RAW"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_REACTION_PRESSURE_MODIFY,		"REACTION_PRESSURE_MODIFY"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SOLUTION_MIX,		            "SOLUTION_MIX"),	
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_EXCHANGE_MIX,		            "EXCHANGE_MIX"),	
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_GAS_PHASE_MIX,		        "GAS_PHASE_MIX"),	
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_KINETICS_MIX,		            "KINETICS_MIX"),	
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_PPASSEMBLAGE_MIX,		        "EQUILIBRIUM_PHASES_MIX"),
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SSASSEMBLAGE_MIX,		        "SOLID_SOLUTIONS_MIX"),	
+std::map<Keywords::KEYWORDS, const std::string>::value_type(Keywords::KEY_SURFACE_MIX,		            "SURFACE_MIX")	
+};
+const std::map<Keywords::KEYWORDS, const std::string> Keywords::phreeqc_keyword_names(temp_keyword_names, temp_keyword_names + sizeof temp_keyword_names / sizeof temp_keyword_names[0]);

src/phreeqcpp/PhreeqcKeywords/Keywords.h

@@ -0,0 +1,99 @@
+#ifndef _INC_KEYWORDS_H
+#define _INC_KEYWORDS_H
+#include <string>
+#include <map>
+class Keywords
+{
+public:
+		enum KEYWORDS
+	{
+		KEY_NONE,
+		KEY_END,
+		KEY_SOLUTION_SPECIES,
+		KEY_SOLUTION_MASTER_SPECIES,
+		KEY_SOLUTION,
+		KEY_PHASES,
+		KEY_REACTION,
+		KEY_MIX,
+		KEY_USE,
+		KEY_SAVE,
+		KEY_EXCHANGE_SPECIES,
+		KEY_EXCHANGE_MASTER_SPECIES,
+		KEY_EXCHANGE,
+		KEY_SURFACE_SPECIES,
+		KEY_SURFACE_MASTER_SPECIES,
+		KEY_SURFACE,
+		KEY_REACTION_TEMPERATURE,
+		KEY_INVERSE_MODELING,
+		KEY_GAS_PHASE,
+		KEY_TRANSPORT,
+		KEY_SELECTED_OUTPUT,
+		KEY_KNOBS,
+		KEY_PRINT,
+		KEY_EQUILIBRIUM_PHASES,
+		KEY_TITLE,
+		KEY_ADVECTION,
+		KEY_KINETICS,
+		KEY_INCREMENTAL_REACTIONS,
+		KEY_RATES,
+		KEY_USER_PRINT,
+		KEY_USER_PUNCH,
+		KEY_SOLID_SOLUTIONS,
+		KEY_SOLUTION_SPREAD,
+		KEY_USER_GRAPH,
+		KEY_LLNL_AQUEOUS_MODEL_PARAMETERS,
+		KEY_DATABASE,
+		KEY_NAMED_EXPRESSIONS,
+		KEY_ISOTOPES,
+		KEY_CALCULATE_VALUES,
+		KEY_ISOTOPE_RATIOS,
+		KEY_ISOTOPE_ALPHAS,
+		KEY_COPY,
+		KEY_PITZER,
+		KEY_SIT,
+		KEY_SOLUTION_RAW,
+		KEY_EXCHANGE_RAW,
+		KEY_SURFACE_RAW,
+		KEY_EQUILIBRIUM_PHASES_RAW,
+		KEY_KINETICS_RAW,
+		KEY_SOLID_SOLUTIONS_RAW,
+		KEY_GAS_PHASE_RAW,
+		KEY_REACTION_RAW,
+		KEY_MIX_RAW,
+		KEY_REACTION_TEMPERATURE_RAW,
+		KEY_DUMP,
+		KEY_SOLUTION_MODIFY,
+		KEY_EQUILIBRIUM_PHASES_MODIFY,
+		KEY_EXCHANGE_MODIFY,
+		KEY_SURFACE_MODIFY,
+		KEY_SOLID_SOLUTIONS_MODIFY,
+		KEY_GAS_PHASE_MODIFY,
+		KEY_KINETICS_MODIFY,
+		KEY_DELETE,
+		KEY_RUN_CELLS,
+		KEY_REACTION_MODIFY,
+		KEY_REACTION_TEMPERATURE_MODIFY,
+		KEY_REACTION_PRESSURE,
+		KEY_REACTION_PRESSURE_RAW,
+		KEY_REACTION_PRESSURE_MODIFY,
+		KEY_SOLUTION_MIX,
+		KEY_EXCHANGE_MIX,
+		KEY_GAS_PHASE_MIX,
+		KEY_KINETICS_MIX,
+		KEY_PPASSEMBLAGE_MIX,
+		KEY_SSASSEMBLAGE_MIX,
+		KEY_SURFACE_MIX,
+		KEY_COUNT_KEYWORDS // must be last in list
+	};
+
+	Keywords(void);
+	~Keywords(void);
+
+	static KEYWORDS Keyword_search(std::string key);
+	static const std::string & Keyword_name_search(KEYWORDS key);
+
+	static const std::map<const std::string, KEYWORDS> phreeqc_keywords;
+	static const std::map<KEYWORDS, const std::string> phreeqc_keyword_names;
+};
+
+#endif // _INC_KEYWORDS_H

src/phreeqcpp/Pressure.cxx

@@ -0,0 +1,443 @@
+// Pressure.cxx: implementation of the cxxPressure class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <cassert>				// assert
+#include <algorithm>			// std::sort
+
+#include "Utils.h"				// define first
+#include "Parser.h"
+#include "Phreeqc.h"
+#include "Pressure.h"
+#include "phqalloc.h"
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+cxxPressure::cxxPressure(PHRQ_io *io)
+	//
+	// default constructor for cxxPressure 
+	//
+:	cxxNumKeyword(io)
+{
+	count = 0;
+	equalIncrements = false;
+}
+
+cxxPressure::~cxxPressure()
+{
+}
+int
+cxxPressure::read(CParser & parser)
+{
+/*
+ *      Reads pressure data for reaction steps
+ *
+ *      Arguments:
+ *	 none
+ *
+ *      Returns:
+ *	 KEYWORD if keyword encountered, input_error may be incremented if
+ *		    a keyword is encountered in an unexpected position
+ *	 EOF     if eof encountered while reading mass balance concentrations
+ *	 ERROR   if error occurred reading data
+ *
+ */
+	// Number and description set in read_reaction_pressure
+
+	PHRQ_io::LINE_TYPE lt;
+	bool done = false;
+	for (;;)
+	{
+		std::istream::pos_type ptr;
+		std::istream::pos_type next_char = 0;
+		std::string token, str;
+		lt = parser.check_line(str, false, true, true, true);
+
+		if (lt == PHRQ_io::LT_EMPTY || 
+			lt == PHRQ_io::LT_KEYWORD ||
+			lt == PHRQ_io::LT_EOF)
+		{
+			break;
+		}
+		if (lt == PHRQ_io::LT_OPTION)
+		{
+			this->error_msg("Expected numeric value for pressures.", PHRQ_io::OT_CONTINUE);
+			break;
+		}
+
+		if (done)
+		{
+			this->error_msg("Unknown input following equal increment definition.", PHRQ_io::OT_CONTINUE);
+			continue;
+		}
+
+		// LT_OK
+
+		for (;;)
+		{
+			if (done) break;
+			// new token
+			std::string token;
+			CParser::TOKEN_TYPE k =	parser.copy_token(token, next_char);
+
+			// need new line
+			if (k == CParser::TT_EMPTY)
+			{
+				break;
+			}
+
+			// read a pressure
+			if (k == CParser::TT_DIGIT)
+			{
+				std::istringstream iss(token);
+				LDBLE d;
+				if (!(iss >> d))
+				{
+					this->error_msg("Expected numeric value for pressures.",
+									 PHRQ_io::OT_CONTINUE);
+				}
+				else
+				{
+					this->pressures.push_back(d);
+				}
+				continue;
+			}
+
+			// non digit, must be "in"
+			if (k == CParser::TT_UPPER || k == CParser::TT_LOWER)
+			{
+				if (this->pressures.size() != 2)
+				{
+					this->error_msg("To define equal increments, exactly two pressures should be defined.", CONTINUE);
+				}
+				else
+				{
+					int i = parser.copy_token(token, next_char);
+					if (i == EMPTY)
+					{
+						error_msg("To define equal increments, define 'in n steps'.", CONTINUE);
+					}
+					else
+					{
+						std::istringstream iss(token);
+						if ((iss >> i) && i > 0)
+						{
+							this->equalIncrements = true;
+							this->count = i;
+						}
+						else
+						{
+							error_msg("Unknown input for pressure steps.", CONTINUE);
+						}
+					}
+					done = true;
+				}
+				if (k == CParser::TT_UNKNOWN)
+				{
+					error_msg("Unknown input for pressure steps.", CONTINUE);
+				}
+			}
+		} // tokens
+	} // lines
+	return lt;
+}
+
+void
+cxxPressure::dump_raw(std::ostream & s_oss, unsigned int indent, int *n_out) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	s_oss << indent0;
+	int n_user_local = (n_out != NULL) ? *n_out : this->n_user;
+	s_oss << "REACTION_PRESSURE_RAW        " << n_user_local << " " << this->description << "\n";
+
+	s_oss << indent1;
+	s_oss << "-count                     " << this->count << "\n";
+
+	s_oss << indent1;
+	s_oss << "-equal_increments          " << this->equalIncrements << "\n";
+
+	// Temperature element and attributes
+
+	s_oss << indent1;
+	s_oss << "-pressures" << "\n";
+	{
+		int i = 0;
+		s_oss << indent2;
+		for (std::vector < LDBLE >::const_iterator it = this->pressures.begin();
+			 it != this->pressures.end(); it++)
+		{
+			if (i++ == 5)
+			{
+				s_oss << "\n";
+				s_oss << indent2;
+				i = 0;
+			}
+			s_oss << *it << " ";
+		}
+		s_oss << "\n";
+	}
+}
+
+void
+cxxPressure::read_raw(CParser & parser, bool check)
+{
+	// clear steps for modify operation, if pressures are read
+	bool cleared_once = false;
+	LDBLE d;
+	CParser::TOKEN_TYPE k;
+
+	std::istream::pos_type ptr;
+	std::istream::pos_type next_char = 0;
+	std::string token;
+	int opt_save;
+	bool useLastLine(false);
+
+	// Number and description set in read_reaction_pressure_raw
+	this->read_number_description(parser);
+
+	opt_save = CParser::OPT_ERROR;
+	bool equalIncrements_defined(false);
+	bool count_defined(false);
+
+	for (;;)
+	{
+		int opt;
+		if (useLastLine == false)
+		{
+			opt = parser.get_option(vopts, next_char);
+		}
+		else
+		{
+			opt = parser.getOptionFromLastLine(vopts, next_char, true);
+		}
+		if (opt == CParser::OPT_DEFAULT)
+		{
+			opt = opt_save;
+		}
+		switch (opt)
+		{
+		case CParser::OPT_EOF:
+			break;
+		case CParser::OPT_KEYWORD:
+			break;
+		case CParser::OPT_DEFAULT:
+		case CParser::OPT_ERROR:
+			opt = CParser::OPT_EOF;
+			parser.error_msg("Unknown input in REACTION_PRESSURE_RAW keyword.",
+							 PHRQ_io::OT_CONTINUE);
+			parser.error_msg(parser.line().c_str(), PHRQ_io::OT_CONTINUE);
+			useLastLine = false;
+			break;
+
+		case 0:				// pressures
+			if (!cleared_once) 
+			{
+				this->pressures.clear();
+				cleared_once = true;
+			}
+			while ((k =	parser.copy_token(token, next_char)) == CParser::TT_DIGIT)
+			{
+				std::istringstream iss(token);
+				if (!(iss >> d))
+				{
+					parser.incr_input_error();
+					parser.error_msg("Expected numeric value for pressures.",
+									 PHRQ_io::OT_CONTINUE);
+				}
+				else
+				{
+					this->pressures.push_back(d);
+				}
+			}
+			opt_save = 0;
+			useLastLine = false;
+			break;
+
+		case 1:				// equal_increments
+			if (!(parser.get_iss() >> this->equalIncrements))
+			{
+				this->equalIncrements = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected boolean value for equalIncrements.", PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = CParser::OPT_DEFAULT;
+			useLastLine = false;
+			equalIncrements_defined = true;
+			break;
+
+		case 2:				// count
+			if (!(parser.get_iss() >> this->count))
+			{
+				this->count = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected integer value for count.", PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = CParser::OPT_DEFAULT;
+			useLastLine = false;
+			count_defined = true;
+			break;
+		}
+		if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
+			break;
+	}
+	// members that must be defined
+	if (check)
+	{
+		if (equalIncrements_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Equal_increments not defined for REACTION_PRESSURE_RAW input.", 
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (count_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Count_temps not defined for REACTION_PRESSURE_RAW input.",
+				 PHRQ_io::OT_CONTINUE);
+		}
+	}
+}
+#ifdef SKIP
+void
+cxxPressure::dump_xml(std::ostream & s_oss, unsigned int indent) const const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// Temperature element and attributes
+	s_oss << indent0;
+	s_oss << "<temperature " << "\n";
+
+	s_oss << indent1;
+	s_oss << "pitzer_temperature_gammas=\"" << this->
+		pitzer_temperature_gammas << "\"" << "\n";
+
+	// components
+	s_oss << indent1;
+	s_oss << "<component " << "\n";
+	for (std::list < cxxPressureComp >::const_iterator it =
+		 temperatureComps.begin(); it != temperatureComps.end(); ++it)
+	{
+		it->dump_xml(s_oss, indent + 2);
+	}
+
+	return;
+}
+#endif
+/* ---------------------------------------------------------------------- */
+LDBLE cxxPressure::
+Pressure_for_step(int step_number)
+/* ---------------------------------------------------------------------- */
+{
+/*
+ *   Determine pressure of reaction step
+ */
+	LDBLE p_temp;
+	if (this->pressures.size() == 0) 
+	{
+		p_temp = 1;
+	}
+	else if (this->equalIncrements)
+	{
+		if (this->pressures.size() != 2)
+		{
+			error_msg("Number of pressures not equal to 2 for equal increments.", 0);
+		}
+		if (step_number > this->count)
+		{
+			p_temp = this->pressures[1];
+		}
+		else
+		{
+			LDBLE denom;
+			denom = (this->count <= 1) ? 1 : (LDBLE) (this->count - 1);
+			p_temp =  this->pressures[0] + ( this->pressures[1] - this->pressures[0]) *
+				((LDBLE) (step_number - 1)) / (denom);
+		}
+	}
+	else 
+	{
+		if (step_number > (int) this->pressures.size())
+		{
+			p_temp = this->pressures[this->pressures.size() - 1];
+		}
+		else
+		{
+			p_temp = this->pressures[step_number - 1];
+		}
+
+	}
+
+	return (p_temp);
+}
+int cxxPressure::
+Get_count(void) const
+{
+	if (equalIncrements) 
+	{
+		return this->count;
+	}
+	return (int) this->pressures.size();
+}
+void
+cxxPressure::Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles)
+{
+	ints.push_back(this->n_user);
+	{
+		ints.push_back((int) this->pressures.size());
+		for (size_t i = 0; i < this->pressures.size(); i++)
+		{
+			doubles.push_back(pressures[i]);
+		}
+	}
+	ints.push_back(this->count);
+	ints.push_back(this->equalIncrements ? 1 : 0);
+
+}
+
+void
+cxxPressure::Deserialize(Dictionary & dictionary, std::vector < int >&ints, 
+	std::vector < double >&doubles, int &ii, int &dd)
+{
+	this->n_user = ints[ii++];
+	this->n_user_end = this->n_user;
+	this->description = " ";
+
+	{
+		int count = ints[ii++];
+		this->pressures.clear();
+		for (int i = 0; i < count; i++)
+		{
+			this->pressures.push_back(doubles[dd++]);
+		}
+	}
+	this->count = ints[ii++];
+	this->equalIncrements = (ints[ii++] != 0);
+}
+
+const std::vector< std::string >::value_type temp_vopts[] = {
+	std::vector< std::string >::value_type("pressures"),	        //0
+	std::vector< std::string >::value_type("equal_increments"),	    //1
+	std::vector< std::string >::value_type("count") 	            //2
+};									   
+const std::vector< std::string > cxxPressure::vopts(temp_vopts, temp_vopts + sizeof temp_vopts / sizeof temp_vopts[0]);	

src/phreeqcpp/Pressure.h

@@ -0,0 +1,43 @@
+#if !defined(PRESSURE_H_INCLUDED)
+#define PRESSURE_H_INCLUDED
+
+#include <cassert>				// assert
+#include <map>					// std::map
+#include <string>				// std::string
+#include <list>					// std::list
+#include <vector>				// std::vector
+
+#include "NumKeyword.h"
+class Dictionary;
+
+class cxxPressure:public cxxNumKeyword
+{
+
+  public:
+	cxxPressure(PHRQ_io *io=NULL);
+	~cxxPressure();
+
+	//void dump_xml(std::ostream& os, unsigned int indent = 0)const;
+
+	void dump_raw(std::ostream & s_oss, unsigned int indent, int *n_out=NULL) const;
+
+	int read(CParser & parser);
+	void read_raw(CParser & parser, bool check = false);
+	LDBLE Pressure_for_step(int step_number);
+	std::vector<LDBLE> & Get_pressures(void) {return pressures;}
+	const std::vector<LDBLE> & Get_pressures(void)const {return pressures;}
+	int Get_count(void) const;
+	void Set_count(int i) {count = i;}
+	bool Get_equalIncrements(void) const {return equalIncrements;}
+	void Set_equalIncrements(bool tf) {equalIncrements = tf;}
+	void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
+	void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
+	
+protected:
+	std::vector < LDBLE >pressures;
+	int count;
+	bool equalIncrements;
+	const static std::vector < std::string > vopts;
+};
+
+#endif // !defined(PRESSURE_H_INCLUDED)

src/phreeqcpp/Reaction.cxx

@@ -0,0 +1,312 @@
+// Reaction.cxx: implementation of the cxxReaction class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <cassert>				// assert
+#include <algorithm>			// std::sort
+
+#include "Utils.h"				// define first
+#include "Phreeqc.h"
+#include "Reaction.h"
+#include "phqalloc.h"
+
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+cxxReaction::cxxReaction(PHRQ_io *io)
+	//
+	// default constructor for cxxReaction 
+	//
+:	cxxNumKeyword(io)
+{
+	this->Set_units("Mol");
+	countSteps = 0;
+	equalIncrements = false;
+	reactantList.type = cxxNameDouble::ND_NAME_COEF;
+	elementList.type = cxxNameDouble::ND_ELT_MOLES;
+}
+cxxReaction::~cxxReaction()
+{
+}
+
+#ifdef SKIP
+void
+cxxReaction::dump_xml(std::ostream & s_oss, unsigned int indent) const const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// Reaction element and attributes
+	s_oss << indent0;
+	s_oss << "<irrev " << "\n";
+
+	s_oss << indent1;
+	s_oss << "pitzer_irrev_gammas=\"" << this->
+		pitzer_irrev_gammas << "\"" << "\n";
+
+	// components
+	s_oss << indent1;
+	s_oss << "<component " << "\n";
+	for (std::list < cxxReactionComp >::const_iterator it =
+		 irrevComps.begin(); it != irrevComps.end(); ++it)
+	{
+		it->dump_xml(s_oss, indent + 2);
+	}
+
+	return;
+}
+#endif
+
+void
+cxxReaction::dump_raw(std::ostream & s_oss, unsigned int indent, int *n_out) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// Reaction element and attributes
+	s_oss << indent0;
+	int n_user_local = (n_out != NULL) ? *n_out : this->n_user;
+	s_oss << "REACTION_RAW                 " << n_user_local << " " << this->description << "\n";
+
+	s_oss << indent1;
+	s_oss << "-reactant_list" << "\n";
+	this->reactantList.dump_raw(s_oss, indent + 2);
+
+	s_oss << indent1;
+	s_oss << "-steps" << "\n";
+	{
+		int i = 0;
+		s_oss << indent2;
+		for (std::vector < LDBLE >::const_iterator it = this->steps.begin();
+			 it != this->steps.end(); it++)
+		{
+			if (i++ == 5)
+			{
+				s_oss << "\n";
+				s_oss << indent2;
+				i = 0;
+			}
+			s_oss << *it << " ";
+		}
+		s_oss << "\n";
+	}
+
+	s_oss << indent1;
+	s_oss << "-count_steps               " << this->countSteps << "\n";
+
+	s_oss << indent1;
+	s_oss << "-equal_increments          " << this->equalIncrements << "\n";
+
+	s_oss << indent1;
+	s_oss << "-units                     " << this->units << "\n";
+
+	s_oss << indent1 << "# REACTION workspace variables #\n";
+	s_oss << indent1;
+	s_oss << "-element_list" << "\n";
+	this->elementList.dump_raw(s_oss, indent + 2);
+}
+
+void
+cxxReaction::read_raw(CParser & parser, const bool check)
+{
+
+	int j;
+	LDBLE d;
+	CParser::TOKEN_TYPE k;
+
+	// clear steps for modify operation, if steps are read
+	bool cleared_once = false;
+
+	std::istream::pos_type ptr;
+	std::istream::pos_type next_char;
+	std::string token;
+	int opt_save;
+	bool useLastLine(false);
+
+	// Read irrev number and description
+	this->read_number_description(parser);
+
+	opt_save = CParser::OPT_ERROR;
+	bool units_defined(false);
+	bool equalIncrements_defined(false);
+	bool countSteps_defined(false);
+
+	for (;;)
+	{
+		int opt;
+		if (useLastLine == false)
+		{
+			opt = parser.get_option(vopts, next_char);
+		}
+		else
+		{
+			opt = parser.getOptionFromLastLine(vopts, next_char, true);
+		}
+		if (opt == CParser::OPT_DEFAULT)
+		{
+			opt = opt_save;
+		}
+		switch (opt)
+		{
+		case CParser::OPT_EOF:
+			break;
+		case CParser::OPT_KEYWORD:
+			break;
+		case CParser::OPT_DEFAULT:
+		case CParser::OPT_ERROR:
+			opt = CParser::OPT_EOF;
+			parser.error_msg("Unknown input in IRREV_COMP_RAW keyword.",
+							 PHRQ_io::OT_CONTINUE);
+			parser.error_msg(parser.line().c_str(), PHRQ_io::OT_CONTINUE);
+			useLastLine = false;
+			break;
+
+		case 0:				// units
+			j = parser.copy_token(token, next_char);
+			if (j == CParser::TT_EMPTY)
+				break;
+			this->Set_units(token.c_str());
+			opt_save = CParser::OPT_DEFAULT;
+			useLastLine = false;
+			units_defined = true;
+			break;
+
+		case 1:				// reactant_list
+			if (this->reactantList.read_raw(parser, next_char) !=
+				CParser::PARSER_OK)
+			{
+				parser.incr_input_error();
+				parser.error_msg("Expected reactant formula and coefficient.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = 1;
+			useLastLine = false;
+			break;
+
+		case 2:				// element_list
+			if (this->elementList.read_raw(parser, next_char) !=
+				CParser::PARSER_OK)
+			{
+				parser.incr_input_error();
+				parser.error_msg("Expected element formula and coefficient.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = 2;
+			useLastLine = false;
+			break;
+
+		case 3:				// steps
+			if (!cleared_once) 
+			{
+				this->steps.clear();
+				cleared_once = true;
+			}
+			while ((k =
+					parser.copy_token(token, next_char)) == CParser::TT_DIGIT)
+			{
+				std::istringstream iss(token);
+				if (!(iss >> d))
+				{
+					parser.incr_input_error();
+					parser.error_msg("Expected numeric value for steps.",
+									 PHRQ_io::OT_CONTINUE);
+				}
+				else
+				{
+					this->steps.push_back(d);
+				}
+			}
+			opt_save = 3;
+			useLastLine = false;
+			break;
+
+		case 4:				// equal_increments
+			if (!(parser.get_iss() >> this->equalIncrements))
+			{
+				this->equalIncrements = 0;
+				parser.incr_input_error();
+				parser.
+					error_msg("Expected boolean value for equalIncrements.",
+							  PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = CParser::OPT_DEFAULT;
+			useLastLine = false;
+			equalIncrements_defined = true;
+			break;
+
+		case 5:				// countSteps
+			if (!(parser.get_iss() >> this->countSteps))
+			{
+				this->countSteps = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected integer value for countSteps.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = CParser::OPT_DEFAULT;
+			useLastLine = false;
+			countSteps_defined = true;
+			break;
+		}
+		if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
+			break;
+	}
+	if (check)
+	{
+		// members that must be defined
+		if (units_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Units not defined for REACTION_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (equalIncrements_defined == false)
+		{
+			parser.incr_input_error();
+			parser.
+				error_msg("Equal_increments not defined for REACTION_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (countSteps_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Count_steps not defined for REACTION_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+	}
+}
+int cxxReaction::
+Get_reaction_steps(void) const
+{
+	if (equalIncrements) 
+	{
+		return this->countSteps;
+	}
+	return (int) this->steps.size();
+}
+const std::vector< std::string >::value_type temp_vopts[] = {
+	std::vector< std::string >::value_type("units"),	        //0
+	std::vector< std::string >::value_type("reactant_list"),	//1
+	std::vector< std::string >::value_type("element_list"),	    //2
+	std::vector< std::string >::value_type("steps"),	        //3
+	std::vector< std::string >::value_type("equal_increments"),	//4
+	std::vector< std::string >::value_type("count_steps") 	    //5
+};									   
+const std::vector< std::string > cxxReaction::vopts(temp_vopts, temp_vopts + sizeof temp_vopts / sizeof temp_vopts[0]);	

src/phreeqcpp/Reaction.h

@@ -0,0 +1,57 @@
+#if !defined(REACTION_H_INCLUDED)
+#define REACTION_H_INCLUDED
+
+#include <cassert>				// assert
+#include <map>					// std::map
+#include <string>				// std::string
+#include <list>					// std::list
+#include <vector>				// std::vector
+
+#include "NumKeyword.h"
+#include "NameDouble.h"
+
+class cxxReaction:public cxxNumKeyword
+{
+
+  public:
+	cxxReaction(PHRQ_io *io = NULL);
+	 ~cxxReaction();
+
+	//void dump_xml(std::ostream& os, unsigned int indent = 0)const;
+
+	void dump_raw(std::ostream & s_oss, unsigned int indent, int *n_out=NULL) const;
+
+	void read_raw(CParser & parser, bool check=true);
+	const cxxNameDouble &Get_elementList(void) const {return this->elementList;}
+	void Set_elementList(cxxNameDouble nd) {this->elementList = nd;}
+	cxxNameDouble &Get_reactantList(void) {return this->reactantList;}
+	const cxxNameDouble &Get_reactantList(void)const {return this->reactantList;}
+	std::vector < LDBLE > &Get_steps(void) {return this->steps;}
+	const std::vector < LDBLE > &Get_steps(void)const {return this->steps;}
+	void Set_steps(std::vector<LDBLE> &v) {steps = v;}
+	int Get_reaction_steps(void) const;
+	int Get_countSteps(void) const {return this->countSteps;}
+	void Set_countSteps(int i) {countSteps = i;}
+	bool Get_equalIncrements(void) const {return this->equalIncrements;}
+	void Set_equalIncrements(bool tf) {equalIncrements = tf;}
+	const std::string &Get_units(void) const {return this->units;}
+
+	void Set_units(const char * s)
+	{
+		if (s != NULL)
+			this->units = std::string(s);
+		else
+			this->units.clear();
+	}
+
+protected:
+	cxxNameDouble reactantList;
+	cxxNameDouble elementList;
+	std::vector < LDBLE >steps;
+	int countSteps;
+	bool equalIncrements;
+	std::string units;
+	const static std::vector < std::string > vopts;
+};
+
+#endif // !defined(REACTION_H_INCLUDED)

src/phreeqcpp/SS.cxx

@@ -0,0 +1,632 @@
+// SSassemblageSS.cxx: implementation of the cxxSS class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <cassert>				// assert
+#include <algorithm>			// std::sort
+
+#include "Phreeqc.h"
+#include "Utils.h"				// define first
+#include "SS.h"
+#include "Dictionary.h"
+#include "phqalloc.h"
+
+
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+cxxSS::cxxSS(PHRQ_io *io)
+:
+PHRQ_base(io)
+	//
+	// default constructor for cxxSS 
+	//
+{
+
+	total_moles = 0;
+	dn = 0;
+	a0 = 0;
+	a1 = 0;
+	ag0 = 0;
+	ag1 = 0;
+	ss_in = false;
+	miscibility = false;
+	spinodal = false;
+	tk = 298.15;
+	xb1 = 0;
+	xb2 = 0;
+	input_case = SS_PARM_NONE;
+	for (int i = 0; i < 4; i++)
+	{
+		p.push_back(0);
+	}
+}
+cxxSS::~cxxSS()
+{
+}
+
+#ifdef SKIP
+void
+cxxSS::dump_xml(std::ostream & s_oss, unsigned int indent) const const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// S_S element and attributes
+
+	s_oss << indent0 << "name=\"" << this->name << "\"" << "\n";
+	s_oss << indent0 << "add_formula=\"" << this->
+		add_formula << "\"" << "\n";
+	s_oss << indent0 << "si=\"" << this->si << "\"" << "\n";
+	s_oss << indent0 << "moles=\"" << this->moles << "\"" << "\n";
+	s_oss << indent0 << "delta=\"" << this->delta << "\"" << "\n";
+	s_oss << indent0 << "initial_moles=\"" << this->
+		initial_moles << "\"" << "\n";
+	s_oss << indent0 << "dissolve_only=\"" << this->
+		dissolve_only << "\"" << "\n";
+
+}
+#endif
+void
+cxxSS::dump_raw(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+
+	s_oss << indent0 << "# SOLID_SOLUTION_MODIFY candidate identifiers #\n";
+	for (size_t i = 0; i < this->ss_comps.size(); i++)
+	{
+		s_oss << indent0 << "-component               " << this->ss_comps[i].Get_name() << "\n";
+		this->ss_comps[i].dump_raw(s_oss, indent + 1);
+	}
+
+	s_oss << indent0 << "# SOLID_SOLUTION_MODIFY candidate identifiers with new_def=true #\n";
+	s_oss << indent0 << "-tk                      " << this->tk << "\n";
+	s_oss << indent0 << "-input_case              " << this->input_case << "\n";
+	s_oss << indent0 << "-p			              " << 
+		p[0] << "\t"  << 
+		p[1] << "\t"  << 
+		p[2] << "\t"  << 
+		p[3] << "\n";
+
+	s_oss << indent0 << "# solid solution workspace variables #\n";
+	s_oss << indent0 << "-ag0                     " << this->ag0 << "\n";
+	s_oss << indent0 << "-ag1                     " << this->ag1 << "\n";
+	s_oss << indent0 << "-a0                      " << this->a0 << "\n";
+	s_oss << indent0 << "-a1                      " << this->a1 << "\n";
+	s_oss << indent0 << "-xb1                     " << this->xb1 << "\n";
+	s_oss << indent0 << "-xb2                     " << this->xb2 << "\n";
+	s_oss << indent0 << "-miscibility             " << this->miscibility << "\n";
+	s_oss << indent0 << "-spinodal                " << this->spinodal << "\n";
+	s_oss << indent0 << "-ss_in                   " << this->ss_in << "\n";
+	s_oss << indent0 << "-total_moles             " << this->total_moles    << "\n";
+	s_oss << indent0 << "-dn                      " << this->dn             << "\n";
+	s_oss << indent0 << "-totals                  " << "\n";
+	this->totals.dump_raw(s_oss, indent + 1);
+}
+
+void
+cxxSS::read_raw(CParser & parser, bool check)
+{
+	std::string str;
+
+	std::istream::pos_type ptr;
+	std::istream::pos_type next_char;
+	std::string token;
+	int opt_save;
+
+	opt_save = CParser::OPT_ERROR;
+	bool a0_defined(false);
+	bool a1_defined(false);
+	bool ag0_defined(false);
+	bool ag1_defined(false);
+	bool miscibility_defined(false);
+	bool xb1_defined(false);
+	bool xb2_defined(false);
+	bool useLastLine = false;
+
+	for (size_t i = this->Get_p().size(); i < 4; i++)
+	{
+		this->p.push_back(0.0);
+	}
+
+	for (;;)
+	{
+		int opt;
+		if (useLastLine == false)
+		{
+			opt = parser.get_option(vopts, next_char);
+		}
+		else
+		{
+			opt = parser.getOptionFromLastLine(vopts, next_char, false);
+		}
+		if (opt == CParser::OPT_DEFAULT)
+		{
+			opt = opt_save;
+		}
+		useLastLine = false;
+		switch (opt)
+		{
+		case CParser::OPT_EOF:
+			break;
+		case CParser::OPT_KEYWORD:
+			break;
+		case CParser::OPT_DEFAULT:
+		case CParser::OPT_ERROR:
+			opt = CParser::OPT_KEYWORD;
+			// Allow return to Exchange for more processing
+			break;
+
+		case 0:				// name not used
+			parser.warning_msg("-ss_name not used, defined in -solid_solution");
+			opt_save = CParser::OPT_DEFAULT;
+			break;
+
+		case 1:				// total_moles
+			if (!(parser.get_iss() >> this->total_moles))
+			{
+				this->total_moles = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for total_moles.", PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = CParser::OPT_DEFAULT;
+			break;
+
+		case 2:				// a0
+			if (!(parser.get_iss() >> this->a0))
+			{
+				this->a0 = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for a0.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			a0_defined = true;
+			opt_save = CParser::OPT_DEFAULT;
+			break;
+
+		case 3:				// a1
+			if (!(parser.get_iss() >> this->a1))
+			{
+				this->a1 = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for a1.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			a1_defined = true;
+			opt_save = CParser::OPT_DEFAULT;
+			break;
+
+		case 4:				// components
+		case 12:			// component
+			{
+				if (!(parser.get_iss() >> str))
+				{
+					this->name.clear();
+					parser.incr_input_error();
+					parser.error_msg("Expected string value for component name.",
+									 PHRQ_io::OT_CONTINUE);
+				}
+				else
+				{
+					cxxSScomp temp_comp(io);
+					temp_comp.Set_name(str);
+					cxxSScomp * comp_ptr = this->Find(str.c_str());
+					if (comp_ptr)
+					{
+						temp_comp = *comp_ptr;	
+					}
+					temp_comp.read_raw(parser, false);
+					if (comp_ptr)
+					{
+						for (size_t j = 0; j < this->ss_comps.size(); j++)
+						{
+							if (Utilities::strcmp_nocase(this->ss_comps[j].Get_name().c_str(), str.c_str()) == 0)
+							{
+								this->ss_comps[j] = temp_comp;
+							}
+						}
+					}
+					else
+					{
+						this->ss_comps.push_back(temp_comp);
+					}
+					useLastLine = true;
+				}
+			}
+			
+			opt_save = CParser::OPT_DEFAULT;
+			break;
+
+		case 5:				// miscibility
+			if (!(parser.get_iss() >> this->miscibility))
+			{
+				this->miscibility = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected boolean value for miscibility.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			miscibility_defined = true;
+			opt_save = CParser::OPT_DEFAULT;
+			break;
+
+		case 6:				// spinodal
+			if (!(parser.get_iss() >> this->spinodal))
+			{
+				this->spinodal = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected boolean value for spinodal.", PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = CParser::OPT_DEFAULT;
+			break;
+
+		case 7:				// tk
+			if (!(parser.get_iss() >> this->tk))
+			{
+				this->tk = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for tk.", PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = CParser::OPT_DEFAULT;
+			break;
+
+		case 8:				// xb1
+			if (!(parser.get_iss() >> this->xb1))
+			{
+				this->xb1 = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for xb1.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			xb1_defined = true;
+			opt_save = CParser::OPT_DEFAULT;
+			break;
+
+		case 9:				// xb2
+			if (!(parser.get_iss() >> this->xb2))
+			{
+				this->xb2 = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for xb2.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			xb2_defined = true;
+			opt_save = CParser::OPT_DEFAULT;
+			break;
+
+		case 10:				// ag0
+			if (!(parser.get_iss() >> this->ag0))
+			{
+				this->ag0 = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for ag0.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			ag0_defined = true;
+			opt_save = CParser::OPT_DEFAULT;
+			break;
+
+		case 11:				// ag1
+			if (!(parser.get_iss() >> this->ag1))
+			{
+				this->ag1 = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for ag1.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			ag1_defined = true;
+			opt_save = CParser::OPT_DEFAULT;
+			break;
+		case 13:				// input_case
+			{
+				int i;
+				if (!(parser.get_iss() >> i))
+				{
+					this->input_case = cxxSS::SS_PARM_NONE;
+					parser.incr_input_error();
+					parser.error_msg("Expected integer value for parameter type.", PHRQ_io::OT_CONTINUE);
+				}
+				else
+				{
+					this->input_case = (cxxSS::SS_PARAMETER_TYPE) i;
+				}
+			}
+			opt_save = CParser::OPT_DEFAULT;
+			break;
+		case 14:				// p
+			{
+				this->p.clear();
+				this->p.assign(4, 0.0);
+				for (int i = 0; i < 4; i++)
+				{
+					if (!(parser.get_iss() >> this->p[i]))
+					parser.error_msg("Expected 4 parameters.");
+				}
+			}
+			break;
+
+		case 15:				// ss_in
+			{
+				if (!(parser.get_iss() >> this->ss_in))
+				{
+					this->ss_in = false;
+					parser.incr_input_error();
+					parser.error_msg("Expected boolean value for ss_in.",
+						PHRQ_io::OT_CONTINUE);
+				}
+			}
+			break;
+		case 16:				// totals
+			if (this->totals.read_raw(parser, next_char) !=	CParser::PARSER_OK)
+			{
+				parser.incr_input_error();
+				parser.error_msg
+					("Expected element name and molality for cxxSS totals.",
+					 PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = 16;
+			break;
+		case 17:				// dn
+			if (!(parser.get_iss() >> this->dn))
+			{
+				this->dn = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for dn.", PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = CParser::OPT_DEFAULT;
+			break;
+		}
+		if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
+			break;
+	}
+	if (check)
+	{
+		// members that must be defined
+		if (a0_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("A0 not defined for SSassemblageSS input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (a1_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("A1 not defined for SSassemblageSS input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (ag0_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Ag0 not defined for SSassemblageSS input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (ag1_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Ag1 not defined for SSassemblageSS input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (miscibility_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Miscibility not defined for SSassemblageSS input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (xb1_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Xb1 not defined for SSassemblageSS input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (xb2_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Xb2 not defined for SSassemblageSS input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+	}
+}
+
+void
+cxxSS::totalize(Phreeqc * phreeqc_ptr)
+{
+	this->totals.clear();
+	// component structures
+	for (size_t i = 0; i < this->ss_comps.size(); i++)
+	{
+		struct phase *phase_ptr;
+		int l;
+		phase_ptr = phreeqc_ptr-> phase_bsearch(ss_comps[i].Get_name().c_str(), &l, FALSE);
+		if (phase_ptr != NULL)
+		{
+			cxxNameDouble phase_formula(phase_ptr->next_elt);
+			this->totals.add_extensive(phase_formula, ss_comps[i].Get_moles());
+		}
+		else
+		{
+			assert(false);
+		}
+	}
+	return;
+}
+void
+cxxSS::add(const cxxSS & addee_in, LDBLE extensive)
+{
+	if (extensive == 0.0)
+		return;
+	if (addee_in.name.size() == 0)
+		return;
+	cxxSS addee = addee_in;
+	for (size_t j = 0; j < addee.Get_ss_comps().size(); j++)
+	{
+		size_t i; 
+		for (i = 0; i < this->ss_comps.size(); i++)
+		{
+			//look for component in this
+			if (Utilities::strcmp_nocase(this->ss_comps[i].Get_name().c_str(), 
+				addee.Get_ss_comps()[j].Get_name().c_str()) == 0)
+			{
+				LDBLE d = this->ss_comps[i].Get_initial_moles() + 
+					addee.Get_ss_comps()[j].Get_initial_moles() * extensive;
+				this->ss_comps[i].Set_initial_moles(d);
+				d = this->ss_comps[i].Get_moles() + 
+					addee.Get_ss_comps()[j].Get_moles() * extensive;
+				this->ss_comps[i].Set_moles(d);
+				d = this->ss_comps[i].Get_init_moles() + 
+					addee.Get_ss_comps()[j].Get_init_moles() * extensive;
+				this->ss_comps[i].Set_init_moles(d);
+				d = this->ss_comps[i].Get_delta() + 
+					addee.Get_ss_comps()[j].Get_delta() * extensive;
+				this->ss_comps[i].Set_delta(d);
+				break;
+			}
+		}
+		if (i == this->ss_comps.size())
+		{
+			cxxSScomp comp = addee.Get_ss_comps()[j];
+			comp.multiply(extensive);
+			this->Get_ss_comps().push_back(comp);
+		}
+	}
+}
+void
+cxxSS::multiply(LDBLE extensive)
+{
+	size_t i; 
+	for (i = 0; i < this->ss_comps.size(); i++)
+	{
+		LDBLE d = this->ss_comps[i].Get_initial_moles() * extensive;
+		this->ss_comps[i].Set_initial_moles(d);
+		d = this->ss_comps[i].Get_moles() * extensive;
+		this->ss_comps[i].Set_moles(d);
+		d = this->ss_comps[i].Get_init_moles() * extensive;
+		this->ss_comps[i].Set_init_moles(d);
+		d = this->ss_comps[i].Get_delta() * extensive;
+		this->ss_comps[i].Set_delta(d);
+	}
+}
+cxxSScomp *
+cxxSS::Find(const char * comp_name)
+{
+
+	for (size_t i = 0; i < this->ss_comps.size(); i++)
+	{
+		if (ss_comps[i].Get_name() == comp_name)
+			return &(ss_comps[i]);
+	}
+	return NULL;
+}
+void
+cxxSS::Serialize(Dictionary & dictionary, std::vector < int >&ints, 
+	std::vector < double >&doubles)
+{
+	ints.push_back(dictionary.Find(this->name));
+	doubles.push_back(this->ag0);
+	doubles.push_back(this->ag1);
+	{
+		ints.push_back((int) ss_comps.size());
+		for (size_t i = 0; i < ss_comps.size(); i++)
+		{
+			ss_comps[i].Serialize(dictionary, ints, doubles);
+		}
+	}
+	doubles.push_back(this->a0);
+	doubles.push_back(this->a1);
+	ints.push_back(this->miscibility ? 1 : 0);
+	ints.push_back(this->spinodal ? 1 : 0);
+	doubles.push_back(this->tk);
+	doubles.push_back(this->xb1);
+	doubles.push_back(this->xb2);
+	ints.push_back((int) this->input_case);
+	{
+		ints.push_back((int) p.size());
+		for (size_t i = 0; i < p.size(); i++)
+		{
+			doubles.push_back(p[i]);
+		}
+	}
+	doubles.push_back(this->total_moles);
+	doubles.push_back(this->dn);
+	ints.push_back(this->ss_in ? 1 : 0);
+	this->totals.Serialize(dictionary, ints, doubles);
+
+}
+
+void
+cxxSS::Deserialize(Dictionary & dictionary, std::vector < int >&ints, 
+	std::vector < double >&doubles, int &ii, int &dd)
+{
+	this->name = dictionary.GetWords()[ints[ii++]];
+	this->ag0 = doubles[dd++];
+	this->ag1 = doubles[dd++];
+	{
+		int count = ints[ii++];
+		this->ss_comps.clear();
+		for (int i = 0; i < count; i++)
+		{
+			cxxSScomp ssc;
+			ssc.Deserialize(dictionary, ints, doubles, ii, dd);
+			this->ss_comps.push_back(ssc);
+		}
+	}
+	this->a0 = doubles[dd++];
+	this->a1 = doubles[dd++];
+	this->miscibility = (ints[ii++] != 0);
+	this->spinodal = (ints[ii++] != 0);
+	this->tk = doubles[dd++];
+	this->xb1 = doubles[dd++];
+	this->xb2 = doubles[dd++];
+	this->input_case = (SS_PARAMETER_TYPE) ints[ii++];
+	{
+		int count = ints[ii++];
+		this->p.clear();
+		for (int i = 0; i < count; i++)
+		{
+			p.push_back(doubles[dd++]);
+		}
+	}
+	this->total_moles = doubles[dd++];
+	this->dn = doubles[dd++];
+	this->ss_in = (ints[ii++] != 0);
+	this->totals.Deserialize(dictionary, ints, doubles, ii, dd);
+
+}
+
+
+const std::vector< std::string >::value_type temp_vopts[] = {
+	std::vector< std::string >::value_type("ss_name"),	    // 0                                   
+	std::vector< std::string >::value_type("total_moles"),	// 1   
+	std::vector< std::string >::value_type("a0"),           // 2   
+	std::vector< std::string >::value_type("a1"),	        // 3
+	std::vector< std::string >::value_type("components"),	// 4
+	std::vector< std::string >::value_type("miscibility"),	// 5
+	std::vector< std::string >::value_type("spinodal"),	    // 6
+	std::vector< std::string >::value_type("tk"),	        // 7
+	std::vector< std::string >::value_type("xb1"),	        // 8
+	std::vector< std::string >::value_type("xb2"),	        // 9
+	std::vector< std::string >::value_type("ag0"),	        // 10
+	std::vector< std::string >::value_type("ag1"),	        // 11
+	std::vector< std::string >::value_type("component"),	// 12
+	std::vector< std::string >::value_type("input_case"),   //13
+	std::vector< std::string >::value_type("p"),            //14
+	std::vector< std::string >::value_type("ss_in"),        //15
+	std::vector< std::string >::value_type("totals"),       //16
+	std::vector< std::string >::value_type("dn")            //17
+};									   
+const std::vector< std::string > cxxSS::vopts(temp_vopts, temp_vopts + sizeof temp_vopts / sizeof temp_vopts[0]);	

src/phreeqcpp/SS.h

@@ -0,0 +1,128 @@
+#if !defined(SSASSEMBLAGESS_H_INCLUDED)
+#define SSASSEMBLAGESS_H_INCLUDED
+
+#include <cassert>				// assert
+#include <vector>
+#include <string>				// std::string
+#include <list>					// std::list
+#include <vector>				// std::vector
+#include "phrqtype.h"
+#include "NameDouble.h"
+#include "SScomp.h"
+
+
+class cxxSS: public PHRQ_base
+{
+
+  public:
+	cxxSS(PHRQ_io *io=NULL);
+	virtual ~cxxSS();
+
+	enum SS_PARAMETER_TYPE
+	{
+		SS_PARM_NONE = -1,
+		SS_PARM_A0_A1 = 0,
+		SS_PARM_GAMMAS = 1,
+		SS_PARM_DIST_COEF = 2,
+		SS_PARM_MISCIBILITY = 3,
+		SS_PARM_SPINODAL = 4,
+		SS_PARM_CRITICAL = 5,
+		SS_PARM_ALYOTROPIC = 6,
+		SS_PARM_DIM_GUGG = 7,
+		SS_PARM_WALDBAUM = 8,
+		SS_PARM_MARGULES = 9
+	};
+
+	void dump_xml(std::ostream & os, unsigned int indent = 0) const;
+
+	void dump_raw(std::ostream & s_oss, unsigned int indent) const;
+
+	void read_raw(CParser & parser, bool check = true);
+
+	const std::string &Get_name() const
+	{
+		return this->name;
+	}
+	void Set_name (const std::string & s) {this->name = s;}
+	void Set_name (const char * s)
+	{
+		if (s != NULL)
+			this->name = std::string(s);
+		else
+			this->name.clear();
+	}
+
+	void totalize(Phreeqc * phreeqc_ptr);
+	const cxxNameDouble & Get_totals() const
+	{
+		return (this->totals);
+	};
+
+	cxxSScomp * Find(const char * comp_name);
+
+	void add(const cxxSS & comp, LDBLE extensive);
+	void multiply(LDBLE extensive);
+
+	LDBLE Get_total_moles(void) const {return total_moles;}
+	void Set_total_moles(LDBLE t) {total_moles = t;}
+
+	LDBLE Get_dn(void) const {return (this->dn);}
+	void Set_dn(LDBLE t) {this->dn = t;}
+
+	LDBLE Get_a0() const {return (this->a0);}
+	void Set_a0(LDBLE t) {a0 = t;}
+	LDBLE Get_a1() const {return (this->a1);}
+	void Set_a1(LDBLE t) {a1 = t;}
+	LDBLE Get_ag0() const {return (this->ag0);}
+	void Set_ag0(LDBLE t) {ag0 = t;}
+	LDBLE Get_ag1() const {return (this->ag1);}
+	void Set_ag1(LDBLE t) {ag1 = t;}
+	bool Get_ss_in() const {return (this->ss_in);}
+	void Set_ss_in(bool t) {ss_in = t;}
+	bool Get_miscibility() const {return (this->miscibility);}
+	void Set_miscibility(bool t) {miscibility = t;}
+	bool Get_spinodal() const {return (this->spinodal);}
+	void Set_spinodal(bool t) {spinodal = t;}
+	LDBLE Get_xb1() const {return (this->xb1);}
+	void Set_xb1(LDBLE t) {xb1 = t;}
+	LDBLE Get_xb2() const {return (this->xb2);}
+	void Set_xb2(LDBLE t) {xb2 = t;}
+	std::vector<cxxSScomp> & Get_ss_comps(void) {return ss_comps;}
+	const std::vector<cxxSScomp> & Get_ss_comps(void)const {return ss_comps;}
+	void Set_ss_comps(const std::vector<cxxSScomp> & comps) {ss_comps = comps;}
+
+	LDBLE Get_tk(void)const {return this->tk;}
+	void Set_tk(LDBLE t) {this->tk = t;}
+	SS_PARAMETER_TYPE Get_input_case(void)const {return this->input_case;}
+	void Set_input_case(SS_PARAMETER_TYPE t) {this->input_case = t;}
+	std::vector<LDBLE> & Get_p(void)             {return this->p;}
+	const std::vector<LDBLE> & Get_p(void)const  {return this->p;}
+	void Set_p(const std::vector<LDBLE> & t) {this->p = t;}
+	void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
+	void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
+
+protected:
+	std::string name;
+	// candidates for SOLID_SOLUTION_MODIFY
+	LDBLE ag0, ag1;
+	std::vector<cxxSScomp> ss_comps;
+
+	// SOLID_SOLUTION keyword data
+	LDBLE a0, a1;
+	bool miscibility;
+	bool spinodal;
+	LDBLE tk, xb1, xb2;
+	SS_PARAMETER_TYPE input_case;
+	std::vector<LDBLE> p;
+
+	// workspace variable
+	LDBLE total_moles;
+	LDBLE dn;
+	bool ss_in;
+	cxxNameDouble totals;
+	const static std::vector < std::string > vopts;
+public:
+
+};
+
+#endif // !defined(SSASSEMBLAGESS_H_INCLUDED)

src/phreeqcpp/SSassemblage.cxx

@@ -0,0 +1,341 @@
+// SSassemblage.cxx: implementation of the cxxSSassemblage class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <float.h>
+#include <cassert>				// assert
+#include <algorithm>			// std::sort
+
+#include "Utils.h"				// define first
+#include "Phreeqc.h"
+#include "SSassemblage.h"
+#include "SS.h"
+#include "cxxMix.h"
+#include "phqalloc.h"
+#include "Dictionary.h"
+
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+cxxSSassemblage::cxxSSassemblage(PHRQ_io * io)
+	//
+	// default constructor for cxxSSassemblage 
+	//
+:	cxxNumKeyword(io)
+{
+	new_def = false;
+}
+
+cxxSSassemblage::cxxSSassemblage(const std::map < int,
+								 cxxSSassemblage > &entities, cxxMix & mix,
+								 int l_n_user, PHRQ_io * io):
+cxxNumKeyword(io)
+{
+	this->n_user = this->n_user_end = l_n_user;
+//
+//   Mix
+//
+	const std::map < int, LDBLE >&mixcomps = mix.Get_mixComps();
+	std::map < int, LDBLE >::const_iterator it;
+	for (it = mixcomps.begin(); it != mixcomps.end(); it++)
+	{
+		if (entities.find(it->first) != entities.end())
+		{
+			const cxxSSassemblage *entity_ptr =
+				&(entities.find(it->first)->second);
+			this->add(*entity_ptr, it->second);
+		}
+	}
+	this->new_def = false;
+}
+
+cxxSSassemblage::~cxxSSassemblage()
+{
+}
+
+#ifdef SKIP
+void
+cxxSSassemblage::dump_xml(std::ostream & s_oss, unsigned int indent) const const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// SSassemblage element and attributes
+	s_oss << indent0;
+	s_oss << "<EQUILIBRIUM_PHASES " << "\n";
+
+	// eltList
+	this->eltList.dump_xml(s_oss, indent + 1);
+
+	// SSs
+	s_oss << indent1;
+	s_oss << "<pure_phases " << "\n";
+	for (std::list < cxxSS >::const_iterator it =
+		 SSs.begin(); it != SSs.end(); ++it)
+	{
+		it->dump_xml(s_oss, indent + 2);
+	}
+}
+#endif
+void
+cxxSSassemblage::dump_raw(std::ostream & s_oss, unsigned int indent, int *n_out) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// SSassemblage element and attributes
+	s_oss << indent0;
+	int n_user_local = (n_out != NULL) ? *n_out : this->n_user;
+	s_oss << "SOLID_SOLUTIONS_RAW          " << n_user_local << " " << this->description << "\n";
+
+	s_oss << indent1 << "# SOLID_SOLUTION_MODIFY candidate identifiers #\n";
+	// SSs
+	for (std::map < std::string, cxxSS >::const_iterator it =
+		 SSs.begin(); it != SSs.end(); ++it)
+	{
+		s_oss << indent1;
+		s_oss << "-solid_solution            " << it->first << "\n";
+		(*it).second.dump_raw(s_oss, indent + 2);
+	}
+
+	s_oss << indent1 << "# SOLID_SOLUTION candidate identifiers with new_def=true #\n";
+	s_oss << indent1;
+	s_oss << "-new_def                   " << (this->new_def ? 1 : 0) << "\n";
+
+	s_oss << indent1 << "# solid solution workspace variables #\n";
+	s_oss << indent1;
+	s_oss << "-SSassemblage_totals       " << "\n";
+	this->totals.dump_raw(s_oss, indent + 2);
+}
+void
+cxxSSassemblage::read_raw(CParser & parser, bool check)
+{
+
+	std::istream::pos_type ptr;
+	std::istream::pos_type next_char;
+	std::string token;
+	int opt_save;
+	bool useLastLine(false);
+	cxxSS *ss_ptr = NULL;
+
+	// Read SSassemblage number and description
+	this->read_number_description(parser);
+	this->Set_new_def(false);
+
+	opt_save = CParser::OPT_ERROR;
+
+	for (;;)
+	{
+		int opt;
+		if (useLastLine == false)
+		{
+			opt = parser.get_option(vopts, next_char);
+		}
+		else
+		{
+			opt = parser.getOptionFromLastLine(vopts, next_char, true);
+		}
+		if (opt == CParser::OPT_DEFAULT)
+		{
+			opt = opt_save;
+		}
+		useLastLine = false;
+		switch (opt)
+		{
+		case CParser::OPT_EOF:
+			break;
+		case CParser::OPT_KEYWORD:
+			break;
+		case CParser::OPT_DEFAULT:
+		case CParser::OPT_ERROR:
+			opt = CParser::OPT_EOF;
+			parser.
+				error_msg("Unknown input in SOLID_SOLUTIONS_RAW or SOLID_SOLUTIONS_MODIFY keyword.",
+						  PHRQ_io::OT_CONTINUE);
+			parser.error_msg(parser.line().c_str(), PHRQ_io::OT_CONTINUE);
+			break;
+
+		case 0:				// solid_solution
+			{
+				std::string str;
+				if (!(parser.get_iss() >> str))
+				{
+						parser.incr_input_error();
+					parser.error_msg("Expected string value for solid solution name.",
+									 PHRQ_io::OT_CONTINUE);
+				}
+				cxxSS temp_ss(this->Get_io());
+				temp_ss.Set_name(str);
+				ss_ptr = this->Find(str);
+				if (ss_ptr)
+				{ 
+					temp_ss = *ss_ptr;
+				}
+				temp_ss.read_raw(parser, false);
+				this->SSs[str] = temp_ss;
+			}
+			useLastLine = true;
+			break;
+		case 1:				// totals
+			if (this->totals.read_raw(parser, next_char) !=
+				CParser::PARSER_OK)
+			{
+				parser.incr_input_error();
+				parser.
+					error_msg
+					("Expected element name and molality for SSassemblage totals.",
+					 PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = 1;
+			break;
+		case 2:				// new_def
+			{
+				int i;
+				if (!(parser.get_iss() >> i))
+				{
+					parser.incr_input_error();
+					parser.error_msg("Expected 0/1 for new_def.", PHRQ_io::OT_CONTINUE);
+				}
+				else
+				{
+					this->new_def = (i == 0) ? false : true;
+				}
+			}
+			break;
+		}
+		if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
+			break;
+	}
+}
+
+void
+cxxSSassemblage::totalize(Phreeqc * phreeqc_ptr)
+{
+	this->totals.clear();
+	// component structures
+	for (std::map < std::string, cxxSS >::iterator it =
+		 SSs.begin(); it != SSs.end(); ++it)
+	{
+		(*it).second.totalize(phreeqc_ptr);
+		this->totals.add_extensive((*it).second.Get_totals(), 1.0);
+	}
+	return;
+}
+void
+cxxSSassemblage::add(const cxxSSassemblage & addee, LDBLE extensive)
+		//
+		// Add to existing ssassemblage to "this" ssassemblage
+		//
+{
+	if (extensive == 0.0)
+		return;
+
+	for (std::map < std::string, cxxSS >::const_iterator itadd =
+		 addee.SSs.begin(); itadd != addee.SSs.end();
+		 ++itadd)
+	{
+		std::map < std::string, cxxSS >::iterator it =
+			this->SSs.find((*itadd).first);
+		if (it != this->SSs.end())
+		{
+			(*it).second.add((*itadd).second, extensive);
+		}
+		else
+		{
+			cxxSS entity = (*itadd).second;
+			entity.multiply(extensive);
+			std::string str(entity.Get_name());
+			this->SSs[str] = entity;
+		}
+	}
+}
+
+std::vector<cxxSS *> cxxSSassemblage::
+Vectorize(void)
+{
+	std::vector<cxxSS *> ss_v;
+	std::map<std::string, cxxSS>::iterator it;
+	for (it = this->SSs.begin(); it != this->SSs.end(); it++)
+	{
+		ss_v.push_back(&(it->second));
+	}
+	return ss_v;
+}
+cxxSS * cxxSSassemblage::
+Find(const std::string &s)
+{
+	std::map<std::string, cxxSS>::iterator it;
+	it = this->SSs.find(s);
+	if (it != this->SSs.end())
+		return &(it->second);
+	return NULL;
+}
+void
+cxxSSassemblage::Serialize(Dictionary & dictionary, std::vector < int >&ints, 
+	std::vector < double >&doubles)
+{
+	/* int n_user; */
+	ints.push_back(this->n_user);
+	{
+		ints.push_back((int) this->SSs.size());
+		std::map < std::string, cxxSS >::iterator it;
+		for (it = this->SSs.begin(); it != this->SSs.end();	it++)
+		{
+			(*it).second.Serialize(dictionary, ints, doubles);
+		}
+	}
+	ints.push_back(this->new_def ? 1 : 0);
+	this->totals.Serialize(dictionary, ints, doubles);
+}
+
+void
+cxxSSassemblage::Deserialize(Dictionary & dictionary, std::vector < int >&ints, 
+	std::vector < double >&doubles, int &ii, int &dd)
+{
+
+	this->n_user = ints[ii++];
+	this->n_user_end = this->n_user;
+	this->description = " ";
+	{
+		int count = ints[ii++];
+		this->SSs.clear();
+		for (int n = 0; n < count; n++)
+		{
+			cxxSS ssc;
+			ssc.Deserialize(dictionary, ints, doubles, ii, dd);
+			std::string str(ssc.Get_name());
+			this->SSs[str] = ssc;
+		}
+	}
+	this->new_def = (ints[ii++] != 0);
+	this->totals.Deserialize(dictionary, ints, doubles, ii, dd);
+
+}
+
+
+
+
+const std::vector< std::string >::value_type temp_vopts[] = {
+	std::vector< std::string >::value_type("solid_solution"),	    // 0
+	std::vector< std::string >::value_type("ssassemblage_totals"),	// 1
+	std::vector< std::string >::value_type("new_def") 	            // 2
+};									   
+const std::vector< std::string > cxxSSassemblage::vopts(temp_vopts, temp_vopts + sizeof temp_vopts / sizeof temp_vopts[0]);	

src/phreeqcpp/SSassemblage.h

@@ -0,0 +1,59 @@
+#if !defined(SSASSEMBLAGE_H_INCLUDED)
+#define SSASSEMBLAGE_H_INCLUDED
+
+
+#include <cassert>				// assert
+#include <map>					// std::map
+#include <string>				// std::string
+#include <list>					// std::list
+#include <vector>				// std::vector
+
+#include "NumKeyword.h"
+#include "NameDouble.h"
+#include "SS.h"
+
+class cxxSS;
+
+//#include "cxxMix.h"
+class cxxMix;
+
+class cxxSSassemblage:public cxxNumKeyword
+{
+
+public:
+	cxxSSassemblage(PHRQ_io * io = NULL);
+	cxxSSassemblage(const std::map < int, cxxSSassemblage > &entity_map,
+		cxxMix & mx, int n_user, PHRQ_io * io = NULL);
+	~cxxSSassemblage();
+
+	//void dump_xml(std::ostream& os, unsigned int indent = 0)const;
+
+	void dump_raw(std::ostream & s_oss, unsigned int indent, int *n_out=NULL) const;
+
+	void read_raw(CParser & parser, bool check = true);
+
+	void totalize(Phreeqc * phreeqc_ptr);
+
+	const cxxNameDouble & Get_totals() const {return this->totals;}
+	std::map < std::string, cxxSS > & Get_SSs(void) {return SSs;}
+	const std::map < std::string, cxxSS > & Get_SSs(void)const {return SSs;}
+	void Set_SSs(std::map < std::string, cxxSS > & ss) {SSs = ss;}
+	bool Get_new_def(void) const {return new_def;}
+	void Set_new_def(bool tf) {new_def = tf;}
+	std::vector<cxxSS *> Vectorize(void);
+	void add(const cxxSSassemblage & addee, LDBLE extensive);
+	cxxSS *Find(const std::string &s);
+	void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
+	void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
+	
+protected:
+	// SOLID_SOLUTION_MODIFY candidate
+	std::map < std::string, cxxSS > SSs;
+	// SOLID_SOLUTION keyword data
+	bool new_def;
+	// internal variables
+	cxxNameDouble totals;
+	const static std::vector < std::string > vopts;
+};
+
+#endif // !defined(SSASSEMBLAGE_H_INCLUDED)

src/phreeqcpp/SScomp.cxx

@@ -0,0 +1,332 @@
+// SScomp.cxx: implementation of the cxxSScomp class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <cassert>				// assert
+#include <algorithm>			// std::sort
+
+#include "Utils.h"				// define first
+#include "Phreeqc.h"
+#include "SScomp.h"
+#include "phqalloc.h"
+#include "Dictionary.h"
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+cxxSScomp::cxxSScomp(PHRQ_io *io)
+:
+PHRQ_base(io)
+	//
+	// default constructor for cxxSScomp 
+	//
+{
+	name = "";
+	initial_moles = 0;
+	moles = 0;
+	init_moles = 0;
+	delta = 0;
+	fraction_x = 0;
+	log10_lambda = 0;
+	log10_fraction_x = 0;
+	dn = 0;
+	dnc = 0; 
+	dnb = 0;
+}
+#ifdef SKIP
+cxxSScomp::cxxSScomp(struct pure_phase * pure_phase_ptr, PHRQ_io *io)
+:
+PHRQ_base(io)
+	//
+	// constructor for cxxSScomp from struct pure_phase
+	//
+{
+	this->Set_name(pure_phase_ptr->name);
+	this->Set_add_formula(pure_phase_ptr->add_formula);
+	si = pure_phase_ptr->si;
+	si_org = pure_phase_ptr->si_org;
+	moles = pure_phase_ptr->moles;
+	delta = pure_phase_ptr->delta;
+	initial_moles = pure_phase_ptr->initial_moles;
+	force_equality = (pure_phase_ptr->force_equality == TRUE);
+	dissolve_only = (pure_phase_ptr->dissolve_only == TRUE);
+	precipitate_only = (pure_phase_ptr->precipitate_only == TRUE);
+}
+#endif
+cxxSScomp::~cxxSScomp()
+{
+}
+
+void
+cxxSScomp::dump_raw(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	s_oss << indent1 << "# SOLID_SOLUTION_MODIFY candidate identifiers #\n";
+	s_oss << indent1 << "-moles               " << this->moles << "\n";
+
+	s_oss << indent1 << "# Solid solution workspace variables #\n";
+	s_oss << indent1 << "-initial_moles       " << this->initial_moles << "\n";
+	s_oss << indent1 << "-init_moles          " << this->init_moles << "\n";
+	s_oss << indent1 << "-delta               " << this->delta << "\n";
+	s_oss << indent1 << "-fraction_x          " << this->fraction_x << "\n";
+	s_oss << indent1 << "-log10_lambda        " << this->log10_lambda << "\n";
+	s_oss << indent1 << "-log10_fraction_x    " << this->log10_fraction_x << "\n";
+	s_oss << indent1 << "-dn                  " << this->dn << "\n";
+	s_oss << indent1 << "-dnc                 " << this->dnc << "\n";
+	s_oss << indent1 << "-dnb                 " << this->dnb << "\n";
+}
+
+void
+cxxSScomp::read_raw(CParser & parser, bool check)
+{
+	std::string str;
+
+	std::istream::pos_type ptr;
+	std::istream::pos_type next_char;
+	std::string token;
+	int opt_save;
+
+	opt_save = CParser::OPT_ERROR;
+	bool initial_moles_defined(false);
+	bool moles_defined(false);
+
+	for (;;)
+	{
+		int opt = parser.get_option(vopts, next_char);
+		if (opt == CParser::OPT_DEFAULT)
+		{
+			opt = opt_save;
+		}
+
+		switch (opt)
+		{
+		case CParser::OPT_EOF:
+			break;
+		case CParser::OPT_KEYWORD:
+			break;
+		case CParser::OPT_DEFAULT:
+		case CParser::OPT_ERROR:
+			opt = CParser::OPT_KEYWORD;
+			// Allow return to Exchange for more processing
+			break;
+
+		case 0:				// name
+			parser.error_msg("-Name ignored. Define with -component.");
+			break;
+
+		case 1:				// initial_moles
+			if (!(parser.get_iss() >> this->initial_moles))
+			{
+				this->initial_moles = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for initial_moles.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			initial_moles_defined = true;
+			break;
+
+		case 2:				// moles
+			if (!(parser.get_iss() >> this->moles))
+			{
+				this->moles = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for moles.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			moles_defined = true;
+			break;
+
+		case 3:				// init_moles
+			if (!(parser.get_iss() >> this->init_moles))
+			{
+				this->init_moles = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for init_moles.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+
+		case 4:				// delta
+			if (!(parser.get_iss() >> this->delta))
+			{
+				this->delta = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for delta.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+
+		case 5:				// fraction_x
+			if (!(parser.get_iss() >> this->fraction_x))
+			{
+				this->fraction_x = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for fraction_x.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+
+
+		case 6:				// log10_lambda
+			if (!(parser.get_iss() >> this->log10_lambda))
+			{
+				this->log10_lambda = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected boolean value for log10_lambda.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+
+		case 7:				// log10_fraction_x
+			if (!(parser.get_iss() >> this->log10_fraction_x))
+			{
+				this->log10_fraction_x = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected boolean value for log10_fraction_x.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+
+		case 8:				// dn
+			if (!(parser.get_iss() >> this->dn))
+			{
+				this->dn = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected boolean value for dn.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+		case 9:				// dnc
+			if (!(parser.get_iss() >> this->dnc))
+			{
+				this->dnc = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for dnc.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+		case 10:				// dnb
+			if (!(parser.get_iss() >> this->dnb))
+			{
+				this->dnb = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for dnb.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+		}
+		if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
+			break;
+	}
+	// members that must be defined
+	if (check)
+	{
+		if (moles_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Moles not defined for PPassemblageComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (initial_moles_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Initial_moles not defined for PPassemblageComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+	}
+}
+
+#ifdef SKIP
+void
+cxxSScomp::totalize(Phreeqc * phreeqc_ptr)
+{
+	this->totals.clear();
+	// component structures
+	if (this->add_formula.size() != 0)
+		return;
+	struct phase *phase_ptr;
+	int l;
+	phase_ptr = phreeqc_ptr-> phase_bsearch(this->name.c_str(), &l, FALSE);
+	if (phase_ptr != NULL)
+	{
+		cxxNameDouble phase_formula(phase_ptr->next_elt);
+		this->totals.add_extensive(phase_formula, this->moles);
+	}
+	else
+	{
+		assert(false);
+	}
+	return;
+}
+#endif
+void
+cxxSScomp::multiply(LDBLE extensive)
+{
+	this->moles *= extensive;
+	this->delta *= extensive;
+	this->initial_moles *= extensive;
+}
+void
+cxxSScomp::Serialize(Dictionary & dictionary, std::vector < int >&ints, 
+	std::vector < double >&doubles)
+{
+
+	ints.push_back(dictionary.Find(this->name));
+	doubles.push_back(this->moles);
+	doubles.push_back(this->initial_moles);
+	doubles.push_back(this->init_moles);
+	doubles.push_back(this->delta);
+	doubles.push_back(this->fraction_x);
+	doubles.push_back(this->log10_lambda);
+	doubles.push_back(this->log10_fraction_x);
+	doubles.push_back(this->dn);
+	doubles.push_back(this->dnc);
+	doubles.push_back(this->dnb);
+
+}
+
+void
+cxxSScomp::Deserialize(Dictionary & dictionary, std::vector < int >&ints, 
+	std::vector < double >&doubles, int &ii, int &dd)
+{
+
+	this->name = dictionary.GetWords()[ints[ii++]];
+	this->moles = doubles[dd++];
+	this->initial_moles = doubles[dd++];
+	this->init_moles = doubles[dd++];
+	this->delta = doubles[dd++];
+	this->fraction_x = doubles[dd++];
+	this->log10_lambda = doubles[dd++];
+	this->log10_fraction_x = doubles[dd++];
+	this->dn = doubles[dd++];
+	this->dnc = doubles[dd++];
+	this->dnb = doubles[dd++];
+
+}
+
+const std::vector< std::string >::value_type temp_vopts[] = {
+	std::vector< std::string >::value_type("name"),	            // 0                 
+	std::vector< std::string >::value_type("initial_moles"),	// 1
+	std::vector< std::string >::value_type("moles"),	        // 2
+	std::vector< std::string >::value_type("init_moles"),	    // 3
+	std::vector< std::string >::value_type("delta"),	        // 4
+	std::vector< std::string >::value_type("fraction_x"),	    // 5     
+	std::vector< std::string >::value_type("log10_lambda"),	    // 6
+	std::vector< std::string >::value_type("log10_fraction_x"),	// 7
+	std::vector< std::string >::value_type("dn"),	            // 8
+	std::vector< std::string >::value_type("dnc"),	            // 9
+	std::vector< std::string >::value_type("dnb") 	            // 10
+};									   
+const std::vector< std::string > cxxSScomp::vopts(temp_vopts, temp_vopts + sizeof temp_vopts / sizeof temp_vopts[0]);	

src/phreeqcpp/SScomp.h

@@ -0,0 +1,66 @@
+#if !defined(SSCOMP_H_INCLUDED)
+#define SSCOMP_H_INCLUDED
+
+#include <cassert>				// assert
+#include <map>					// std::map
+#include <string>				// std::string
+#include <list>					// std::list
+#include <vector>				// std::vector
+
+#include "NameDouble.h"
+
+class cxxSScomp: public PHRQ_base
+{
+
+  public:
+	cxxSScomp(PHRQ_io *io=NULL);
+	virtual ~cxxSScomp();
+
+	void dump_raw(std::ostream & s_oss, unsigned int indent) const;
+	void read_raw(CParser & parser, bool check = true);
+
+	const std::string &Get_name() const	{return this->name;}
+	void Set_name(std::string s) {this->name = s;}
+
+	LDBLE Get_initial_moles() const {return this->initial_moles;}
+	void Set_initial_moles(LDBLE t) {this->initial_moles = t;}
+	LDBLE Get_moles() const {return this->moles;}
+	void Set_moles(LDBLE t) {this->moles = t;}
+	LDBLE Get_init_moles() const {return this->init_moles;}
+	void Set_init_moles(LDBLE t) {this->init_moles = t;}
+	LDBLE Get_delta() const {return this->delta;}
+	void Set_delta(LDBLE t) {this->delta = t;}
+	LDBLE Get_fraction_x() const {return this->fraction_x;}
+	void Set_fraction_x(LDBLE t) {this->fraction_x = t;}
+	LDBLE Get_log10_lambda() const {return this->log10_lambda;}
+	void Set_log10_lambda(LDBLE t) {this->log10_lambda = t;}
+	LDBLE Get_log10_fraction_x() const {return this->log10_fraction_x;}
+	void Set_log10_fraction_x(LDBLE t) {this->log10_fraction_x = t;}
+	LDBLE Get_dn() const {return this->dn;}
+	void Set_dn(LDBLE t) {this->dn = t;}
+	LDBLE Get_dnc() const {return this->dnc;}
+	void Set_dnc(LDBLE t) {this->dnc = t;}
+	LDBLE Get_dnb() const {return this->dnb;}
+	void Set_dnb(LDBLE t) {this->dnb = t;}
+
+	void multiply(LDBLE extensive);
+	void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
+	void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
+	
+protected:
+	std::string name;
+	// SOLID_SOLUTION_MODIFY candidate identifier
+	LDBLE moles;
+
+	// Solid solution workspace variables
+	LDBLE initial_moles;
+	LDBLE init_moles;
+	LDBLE delta;
+	LDBLE fraction_x;
+	LDBLE log10_lambda;
+	LDBLE log10_fraction_x;
+	LDBLE dn, dnc, dnb;
+	const static std::vector < std::string > vopts;
+};
+
+#endif // !defined(SSCOMP_H_INCLUDED)

src/phreeqcpp/SelectedOutput.cpp

@@ -0,0 +1,105 @@
+#include "SelectedOutput.h"
+
+SelectedOutput::SelectedOutput(int n, PHRQ_io *io)
+:	cxxNumKeyword(io)
+{
+	// file_name
+	this->Set_file_name(n);
+
+	// punch_ostream
+	this->punch_ostream = NULL;
+
+	// state vars
+	this->active             = true;
+	this->new_def            = false;
+	this->user_punch_new_def = false;
+	this->have_punch_name    = false;
+
+	// as-is vars
+	//
+	this->user_punch       = true;
+	this->high_precision   = false;
+	this->inverse          = true;
+
+	this->sim              = true;
+	this->state            = true;
+	this->soln             = true;
+	this->dist             = true;
+	this->time             = true;
+
+	this->step             = true;
+	this->ph               = true;
+	this->pe               = true;
+	this->rxn              = false;
+	this->temp             = false;
+
+	this->alk              = false;
+	this->mu               = false;
+	this->water            = false;
+	this->charge_balance   = false;
+	this->percent_error    = false;
+
+	// as-is set flags
+	//
+	this->set_user_punch     = false;
+	this->set_high_precision = false;
+	this->set_inverse        = false;
+
+	this->set_sim            = false;
+	this->set_state          = false;
+	this->set_soln           = false;
+	this->set_dist           = false;
+	this->set_time           = false;
+
+	this->set_step           = false;
+	this->set_ph             = false;
+	this->set_pe             = false;
+	this->set_rxn            = false;
+	this->set_temp           = false;
+
+	this->set_alk            = false;
+	this->set_mu             = false;
+	this->set_water          = false;
+	this->set_charge_balance = false;
+	this->set_percent_error  = false;
+}
+
+SelectedOutput::~SelectedOutput(void)
+{
+	if (this->punch_ostream != NULL)
+	{
+		delete this->punch_ostream;
+	}
+	this->punch_ostream = NULL;
+}
+
+void
+SelectedOutput::Reset(bool value)
+{
+	// as-is vars
+	Set_sim(value);
+	Set_state(value);
+	Set_soln(value);
+	Set_dist(value);
+	Set_time(value);
+
+	Set_step(value);
+	Set_ph(value);
+	Set_pe(value);
+	Set_rxn(value);
+	Set_temp(value);
+
+	Set_alk(value);
+	Set_mu(value);
+	Set_water(value);
+	Set_charge_balance(value);
+	Set_percent_error(value);
+}
+
+void
+SelectedOutput::Set_file_name(int n)
+{
+	std::ostringstream os;
+	os << "selected_output_" << n << ".sel";
+	file_name = os.str();
+}

src/phreeqcpp/SelectedOutput.h

@@ -0,0 +1,204 @@
+#if !defined(SELECTEDOUTPUT_H_INCLUDED)
+#define SELECTEDOUTPUT_H_INCLUDED
+#include <string>				// std::string
+#include <vector>
+#include <map>
+#include "NumKeyword.h"
+
+class SelectedOutput:public cxxNumKeyword
+{
+public:
+	SelectedOutput(int n=1, PHRQ_io *io=NULL);
+	~SelectedOutput(void);
+
+	void Reset(bool tf);
+
+	// vector getters
+	inline std::vector< std::pair< std::string, void * > > & Get_totals(void)           {return this->totals;}
+	inline std::vector< std::pair< std::string, void * > > & Get_molalities(void)       {return this->molalities;}
+	inline std::vector< std::pair< std::string, void * > > & Get_activities(void)       {return this->activities;}
+	inline std::vector< std::pair< std::string, void * > > & Get_pure_phases(void)      {return this->pure_phases;}
+	inline std::vector< std::pair< std::string, void * > > & Get_si(void)               {return this->si;}
+	inline std::vector< std::pair< std::string, void * > > & Get_gases(void)            {return this->gases;}
+	inline std::vector< std::pair< std::string, void * > > & Get_s_s(void)              {return this->s_s;}
+	inline std::vector< std::pair< std::string, void * > > & Get_kinetics(void)         {return this->kinetics;}
+	inline std::vector< std::pair< std::string, void * > > & Get_isotopes(void)         {return this->isotopes;}
+	inline std::vector< std::pair< std::string, void * > > & Get_calculate_values(void) {return this->calculate_values;}
+
+	// const vector getters
+	inline const std::vector< std::pair< std::string, void * > > & Get_totals(void)const           {return this->totals;}
+	inline const std::vector< std::pair< std::string, void * > > & Get_molalities(void)const       {return this->molalities;}
+	inline const std::vector< std::pair< std::string, void * > > & Get_activities(void)const       {return this->activities;}
+	inline const std::vector< std::pair< std::string, void * > > & Get_pure_phases(void)const      {return this->pure_phases;}
+	inline const std::vector< std::pair< std::string, void * > > & Get_si(void)const               {return this->si;}
+	inline const std::vector< std::pair< std::string, void * > > & Get_gases(void)const            {return this->gases;}
+	inline const std::vector< std::pair< std::string, void * > > & Get_s_s(void)const              {return this->s_s;}
+	inline const std::vector< std::pair< std::string, void * > > & Get_kinetics(void)const         {return this->kinetics;}
+	inline const std::vector< std::pair< std::string, void * > > & Get_isotopes(void)const         {return this->isotopes;}
+	inline const std::vector< std::pair< std::string, void * > > & Get_calculate_values(void)const {return this->calculate_values;}
+
+	// file_name getters/setters
+	void Set_file_name(int i);
+	inline void Set_file_name(std::string s)                          {this->file_name = s;}
+	inline std::string & Get_file_name(void)                          {return this->file_name;}
+	inline const std::string & Get_file_name(void)const               {return this->file_name;}
+
+	// punch_ostream getters/setters
+	inline std::ostream* Get_punch_ostream(void)                      {return this->punch_ostream;}
+	inline const std::ostream* Get_punch_ostream(void)const           {return this->punch_ostream;}
+	inline void Set_punch_ostream(std::ostream * os)                  {this->punch_ostream = os;}
+
+	// state var getters
+	inline bool Get_active(void)const                                 {return this->active;}
+	inline bool Get_new_def(void)const                                {return this->new_def;}
+	inline bool Get_user_punch_new_def(void)const                     {return this->user_punch_new_def;}
+	inline bool Get_have_punch_name(void)const                        {return this->have_punch_name;}
+
+	// state var setters
+	inline void Set_active(bool tf)                                   {this->active = tf;}
+	inline void Set_new_def(bool tf)                                  {this->new_def = tf;}
+	inline void Set_user_punch_new_def(bool tf)                       {this->user_punch_new_def = tf;}
+	inline void Set_have_punch_name(bool tf)                          {this->have_punch_name = tf;}
+
+	// as_is getters
+	inline bool Get_user_punch(void)const                             {return this->user_punch;}
+	inline bool Get_high_precision(void)const                         {return this->high_precision;}
+	inline bool Get_inverse(void)const                                {return this->inverse;}
+
+	inline bool Get_sim(void)const                                    {return this->sim;}
+	inline bool Get_state(void)const                                  {return this->state;}
+	inline bool Get_soln(void)const                                   {return this->soln;}
+	inline bool Get_dist(void)const                                   {return this->dist;}
+	inline bool Get_time(void)const                                   {return this->time;}
+
+	inline bool Get_step(void)const                                   {return this->step;}
+	inline bool Get_ph(void)const                                     {return this->ph;}
+	inline bool Get_pe(void)const                                     {return this->pe;}
+	inline bool Get_rxn(void)const                                    {return this->rxn;}
+	inline bool Get_temp(void)const                                   {return this->temp;}
+
+	inline bool Get_alk(void)const                                    {return this->alk;}
+	inline bool Get_mu(void)const                                     {return this->mu;}
+	inline bool Get_water(void)const                                  {return this->water;}
+	inline bool Get_charge_balance(void)const                         {return this->charge_balance;}
+	inline bool Get_percent_error(void)const                          {return this->percent_error;}
+
+	// as-is setters
+	inline void Set_user_punch(bool tf)                               {this->user_punch = tf;              this->set_user_punch = true;}
+	inline void Set_high_precision(bool tf)                           {this->high_precision = tf;          this->set_high_precision = true;}
+	inline void Set_inverse(bool tf)                                  {this->inverse = tf;                 this->set_inverse = true;}
+
+	inline void Set_sim(bool tf)                                      {this->sim = tf;                     this->set_sim = true;}
+	inline void Set_state(bool tf)                                    {this->state = tf;                   this->set_state = true;}
+	inline void Set_soln(bool tf)                                     {this->soln = tf;                    this->set_soln = true;}
+	inline void Set_dist(bool tf)                                     {this->dist = tf;                    this->set_dist = true;}
+	inline void Set_time(bool tf)                                     {this->time = tf;                    this->set_time = true;}
+
+	inline void Set_step(bool tf)                                     {this->step = tf;                    this->set_step = true;}
+	inline void Set_ph(bool tf)                                       {this->ph = tf;                      this->set_ph = true;}
+	inline void Set_pe(bool tf)                                       {this->pe = tf;                      this->set_pe = true;}
+	inline void Set_rxn(bool tf)                                      {this->rxn = tf;                     this->set_rxn = true;}
+	inline void Set_temp(bool tf)                                     {this->temp = tf;                    this->set_temp = true;}
+
+	inline void Set_alk(bool tf)                                      {this->alk = tf;                     this->set_alk = true;}
+	inline void Set_mu(bool tf)                                       {this->mu = tf;                      this->set_mu = true;}
+	inline void Set_water(bool tf)                                    {this->water = tf;                   this->set_water = true;}
+	inline void Set_charge_balance(bool tf)                           {this->charge_balance = tf;          this->set_charge_balance = true;}
+	inline void Set_percent_error(bool tf)                            {this->percent_error = tf;           this->set_percent_error = true;}
+
+	// set flag getters
+	inline bool was_set_user_punch()const                             {return this->set_user_punch;}
+	inline bool was_set_high_precision()const                         {return this->set_high_precision;}
+	inline bool was_set_inverse()const                                {return this->set_inverse;}
+
+	inline bool was_set_sim()const                                    {return this->set_sim;}
+	inline bool was_set_state()const                                  {return this->set_state;}
+	inline bool was_set_soln()const                                   {return this->set_soln;}
+	inline bool was_set_dist()const                                   {return this->set_dist;}
+	inline bool was_set_time()const                                   {return this->set_time;}
+
+	inline bool was_set_step()const                                   {return this->set_step;}
+	inline bool was_set_ph()const                                     {return this->set_ph;}
+	inline bool was_set_pe()const                                     {return this->set_pe;}
+	inline bool was_set_rxn()const                                    {return this->set_rxn;}
+	inline bool was_set_temp()const                                   {return this->set_temp;}
+
+	inline bool was_set_alk()const                                    {return this->set_alk;}
+	inline bool was_set_mu()const                                     {return this->set_mu;}
+	inline bool was_set_water()const                                  {return this->set_water;}
+	inline bool was_set_charge_balance()const                         {return this->set_charge_balance;}
+	inline bool was_set_percent_error()const                          {return this->set_percent_error;}
+	
+protected:
+
+	// vectors
+	std::vector< std::pair< std::string, void * > > totals;
+	std::vector< std::pair< std::string, void * > > molalities;
+	std::vector< std::pair< std::string, void * > > activities;
+	std::vector< std::pair< std::string, void * > > pure_phases;
+	std::vector< std::pair< std::string, void * > > si;
+	std::vector< std::pair< std::string, void * > > gases;
+	std::vector< std::pair< std::string, void * > > s_s;
+	std::vector< std::pair< std::string, void * > > kinetics;
+	std::vector< std::pair< std::string, void * > > isotopes;
+	std::vector< std::pair< std::string, void * > > calculate_values;
+
+	// file_name
+	std::string file_name;
+
+	// punch_ostream
+	std::ostream * punch_ostream;
+
+	// state vars
+	bool active;
+	bool new_def;
+	bool user_punch_new_def;
+	bool have_punch_name;
+
+	// as-is vars
+	bool user_punch;
+	bool high_precision;
+	bool inverse;
+
+	bool sim;
+	bool state;
+	bool soln;
+	bool dist;
+	bool time;
+
+	bool step;
+	bool ph;
+	bool pe;
+	bool rxn;
+	bool temp;
+
+	bool alk;
+	bool mu;
+	bool water;
+	bool charge_balance;
+	bool percent_error;
+
+	// as-is set flags
+	bool set_user_punch;
+	bool set_high_precision;
+	bool set_inverse;
+
+	bool set_sim;
+	bool set_state;
+	bool set_soln;
+	bool set_dist;
+	bool set_time;
+
+	bool set_step;
+	bool set_ph;
+	bool set_pe;
+	bool set_rxn;
+	bool set_temp;
+
+	bool set_alk;
+	bool set_mu;
+	bool set_water;
+	bool set_charge_balance;
+	bool set_percent_error;
+};
+#endif // !defined(SELECTEDOUTPUT_H_INCLUDED)

src/phreeqcpp/Serializer.cxx

@@ -0,0 +1,200 @@
+#include "Serializer.h"
+#include "Phreeqc.h"
+#include "Utils.h"
+#include "Solution.h"
+#include "Exchange.h"
+#include "Temperature.h"
+#include "GasPhase.h"
+#include "cxxKinetics.h"
+#include "PPassemblage.h"
+#include "SSassemblage.h"
+#include "Surface.h"
+Serializer::Serializer(PHRQ_io *io)
+	: PHRQ_base(io)
+{
+}
+Serializer::~Serializer(void)
+{
+}
+bool Serializer::Serialize(Phreeqc &phreeqc_ref, int start, int end, bool include_t, bool include_p, PHRQ_io *io)
+{
+	for (int i = start; i <= end; i++)
+	{
+		cxxSolution *soln_ptr = Utilities::Rxn_find(phreeqc_ref.Get_Rxn_solution_map(), i);
+		if (soln_ptr)
+		{
+			ints.push_back((int) PT_SOLUTION);
+			soln_ptr->Serialize(this->dictionary, this->ints, this->doubles);
+		}
+		// Exchangers
+		{
+			cxxExchange *entity_ptr = Utilities::Rxn_find(phreeqc_ref.Get_Rxn_exchange_map(), i);
+			if (entity_ptr)
+			{
+				ints.push_back((int) PT_EXCHANGE);
+				entity_ptr->Serialize(this->dictionary, this->ints, this->doubles);
+			}
+		}
+		// GasPhases
+		{
+			cxxGasPhase *entity_ptr = Utilities::Rxn_find(phreeqc_ref.Get_Rxn_gas_phase_map(), i);
+			if (entity_ptr)
+			{
+				ints.push_back((int) PT_GASPHASE);
+				entity_ptr->Serialize(this->dictionary, this->ints, this->doubles);
+			}
+		}
+		// Kinetics
+		{
+			cxxKinetics *entity_ptr = Utilities::Rxn_find(phreeqc_ref.Get_Rxn_kinetics_map(), i);
+			if (entity_ptr)
+			{
+				ints.push_back((int) PT_KINETICS);
+				entity_ptr->Serialize(this->dictionary, this->ints, this->doubles);
+			}
+		}
+		// PPassemblages
+		{
+			cxxPPassemblage *entity_ptr = Utilities::Rxn_find(phreeqc_ref.Get_Rxn_pp_assemblage_map(), i);
+			if (entity_ptr)
+			{
+				ints.push_back((int) PT_PPASSEMBLAGE);
+				entity_ptr->Serialize(this->dictionary, this->ints, this->doubles);
+			}
+		}
+		// SSassemblages
+		{
+			cxxSSassemblage *entity_ptr = Utilities::Rxn_find(phreeqc_ref.Get_Rxn_ss_assemblage_map(), i);
+			if (entity_ptr)
+			{
+				ints.push_back((int) PT_SSASSEMBLAGE);
+				entity_ptr->Serialize(this->dictionary, this->ints, this->doubles);
+			}
+		}
+		// Surfaces
+		{
+			cxxSurface *entity_ptr = Utilities::Rxn_find(phreeqc_ref.Get_Rxn_surface_map(), i);
+			if (entity_ptr)
+			{
+				ints.push_back((int) PT_SURFACES);
+				entity_ptr->Serialize(this->dictionary, this->ints, this->doubles);
+			}
+		}
+		// Temperature
+		if (include_t)
+		{		
+			cxxTemperature *entity_ptr = Utilities::Rxn_find(phreeqc_ref.Get_Rxn_temperature_map(), i);
+			if (entity_ptr)
+			{
+				ints.push_back((int) PT_TEMPERATURE);
+				entity_ptr->Serialize(this->dictionary, this->ints, this->doubles);
+			}
+		}
+		// Pressure
+		if (include_p)
+		{		
+			cxxPressure *entity_ptr = Utilities::Rxn_find(phreeqc_ref.Get_Rxn_pressure_map(), i);
+			if (entity_ptr)
+			{
+				ints.push_back((int) PT_PRESSURE);
+				entity_ptr->Serialize(this->dictionary, this->ints, this->doubles);
+			}
+		}			
+	}	
+	return true;
+}
+
+bool 
+Serializer::Deserialize(Phreeqc &phreeqc_ref, Dictionary &dictionary, std::vector<int> &ints, std::vector<double> &doubles)
+{
+	int ii = 0;
+	int dd = 0;
+	while (ii < (int) ints.size())
+	{
+		PACK_TYPE type = (PACK_TYPE) ints[ii++];
+		switch (type)
+		{
+		case PT_SOLUTION:	
+			{
+				cxxSolution soln;
+				soln.Deserialize(dictionary, ints, doubles, ii, dd);
+				int n_user = soln.Get_n_user();
+				//std::cerr << "unpacked solution " << n_user << std::endl;
+				phreeqc_ref.Get_Rxn_solution_map()[n_user] = soln;
+			}
+			break;
+		case PT_EXCHANGE:	
+			{
+				cxxExchange entity;
+				entity.Deserialize(dictionary, ints, doubles, ii, dd);
+				int n_user = entity.Get_n_user();
+				phreeqc_ref.Get_Rxn_exchange_map()[n_user] = entity;
+			}
+			break;
+		case PT_GASPHASE:
+			{
+				cxxGasPhase entity;
+				entity.Deserialize(dictionary, ints, doubles, ii, dd);
+				int n_user = entity.Get_n_user();
+				phreeqc_ref.Get_Rxn_gas_phase_map()[n_user] = entity;
+			}
+			break;
+		case PT_KINETICS:	
+			{
+				cxxKinetics entity;
+				entity.Deserialize(dictionary, ints, doubles, ii, dd);
+				int n_user = entity.Get_n_user();
+				phreeqc_ref.Get_Rxn_kinetics_map()[n_user] = entity;
+			}
+			break;
+		case PT_PPASSEMBLAGE:	
+			{
+				cxxPPassemblage entity;
+				entity.Deserialize(dictionary, ints, doubles, ii, dd);
+				int n_user = entity.Get_n_user();
+				//std::cerr << "unpacked pp assemblage " << n_user << std::endl;
+				phreeqc_ref.Get_Rxn_pp_assemblage_map()[n_user] = entity;
+			}
+			break;
+		case PT_SSASSEMBLAGE:	
+			{
+				cxxSSassemblage entity;
+				entity.Deserialize(dictionary, ints, doubles, ii, dd);
+				int n_user = entity.Get_n_user();
+				phreeqc_ref.Get_Rxn_ss_assemblage_map()[n_user] = entity;
+			}
+			break;
+		case PT_SURFACES:	
+			{
+				cxxSurface entity;
+				entity.Deserialize(dictionary, ints, doubles, ii, dd);
+				int n_user = entity.Get_n_user();
+				phreeqc_ref.Get_Rxn_surface_map()[n_user] = entity;
+			}
+			break;
+		case PT_TEMPERATURE:
+			{
+				cxxTemperature entity;
+				entity.Deserialize(dictionary, ints, doubles, ii, dd);
+				int n_user = entity.Get_n_user();
+				phreeqc_ref.Get_Rxn_temperature_map()[n_user] = entity;
+			}
+			break;
+		case PT_PRESSURE:	
+			{
+				cxxPressure entity;
+				entity.Deserialize(dictionary, ints, doubles, ii, dd);
+				int n_user = entity.Get_n_user();
+				phreeqc_ref.Get_Rxn_pressure_map()[n_user] = entity;
+			}
+			break;
+		default:
+#if !defined(R_SO)
+			std::cerr << "Unknown pack type in deserialize " << type << std::endl;
+			exit(4);
+#endif
+			break;
+		}
+	}
+	return true;
+}

src/phreeqcpp/Serializer.h

@@ -0,0 +1,42 @@
+#if !defined(SERIALIZER_H_INCLUDED)
+#define SERIALIZER_H_INCLUDED
+#include <iostream>
+#include <map>
+#include <vector>
+#include <sstream>
+#include "PHRQ_base.h"
+#include "Dictionary.h"
+class Phreeqc;
+class Serializer : public PHRQ_base
+{
+public:
+	Serializer(PHRQ_io *io = NULL);
+	~Serializer(void);
+
+	enum PACK_TYPE
+	{
+		PT_SOLUTION     = 0,
+		PT_EXCHANGE     = 1,
+		PT_GASPHASE     = 2,
+		PT_KINETICS     = 3,
+		PT_PPASSEMBLAGE = 4,
+		PT_SSASSEMBLAGE = 5,
+		PT_SURFACES     = 6,
+		PT_TEMPERATURE  = 7,
+		PT_PRESSURE     = 8
+	};
+	bool Serialize(Phreeqc &phreeqc_ptr, int start, int end, bool include_t, bool include_p, PHRQ_io *io = NULL);
+	bool Deserialize(Phreeqc &phreeqc_ptr, Dictionary &dictionary, std::vector<int> &ints, std::vector<double> &doubles);
+	Dictionary &GetDictionary(void) {return this->dictionary;}
+	std::vector<int> &GetInts(void) {return this->ints;}
+	std::vector<double> &GetDoubles(void) {return this->doubles;}
+	//std::string &GetWordsString(void) {return this->words_string;}
+
+
+protected:
+	std::vector<int> ints;
+	std::vector<double> doubles;
+	//std::string words_string;
+	Dictionary dictionary;
+};
+#endif // !defined(SERIALIZER_H_INCLUDED)

src/phreeqcpp/Solution.h

@@ -0,0 +1,146 @@
+#if !defined(SOLUTION_H_INCLUDED)
+#define SOLUTION_H_INCLUDED
+
+#include <cassert>				// assert
+#include <map>					// std::map
+#include <string>				// std::string
+#include <vector>				// std::vector
+#include <iostream>
+#include "NumKeyword.h"
+#include "SolutionIsotope.h"
+#include "NameDouble.h"
+#include "PHRQ_base.h"
+#include "PHRQ_io.h"
+#include "ISolution.h"
+class cxxMix;
+
+class cxxSolution:public cxxNumKeyword
+{
+
+  public:
+	cxxSolution(PHRQ_io *io=NULL);
+	cxxSolution(const cxxSolution &old_sol);
+	const cxxSolution & operator = (const cxxSolution &rhs);
+	cxxSolution(std::map < int, cxxSolution > &solution_map,
+				  cxxMix & mx, int n_user, PHRQ_io *io=NULL);
+	virtual ~cxxSolution();
+
+	bool Get_new_def() const  {return this->new_def;}
+	void Set_new_def(bool p)  {this->new_def = p;}
+	LDBLE Get_patm() const    {return this->patm;}
+	void Set_patm(LDBLE p)    {this->patm = p;}
+	LDBLE Get_potV() const    {return this->potV;}
+	void Set_potV(LDBLE p)    {this->potV = p;}
+	LDBLE Get_tc() const      {return this->tc;}
+	void Set_tc(LDBLE l_tc)   {this->tc = l_tc;}
+	LDBLE Get_ph() const      {return this->ph;}
+	void Set_ph(LDBLE pH)     {this->ph = pH;}
+	LDBLE Get_pe() const      {return this->pe;}
+	void Set_pe(LDBLE l_pe)   {this->pe = l_pe;}
+	LDBLE Get_mu() const      {return this->mu;}
+	void Set_mu(LDBLE l_mu)   {this->mu = l_mu;}
+	LDBLE Get_ah2o() const                              {return this->ah2o;}
+	void Set_ah2o(LDBLE l_ah2o)                         {this->ah2o = l_ah2o;}
+	LDBLE Get_total_h() const                           {return this->total_h;}
+	void Set_total_h(LDBLE l_total_h)                   {this->total_h = l_total_h;}
+	LDBLE Get_total_o() const                           {return this->total_o;}
+	void Set_total_o(LDBLE l_total_o)                   {this->total_o = l_total_o;}
+	LDBLE Get_cb() const                                {return this->cb;}
+	void Set_cb(LDBLE l_cb)                             {this->cb = l_cb;}
+	LDBLE Get_density() const                           {return this->density;}
+	void Set_density(LDBLE l_density)                   {this->density = l_density;}
+	LDBLE Get_mass_water() const                        {return this->mass_water;}
+	void Set_mass_water(LDBLE l_mass_water)             {this->mass_water = l_mass_water;}
+	LDBLE Get_total_alkalinity() const                  {return this->total_alkalinity;}
+	void Set_total_alkalinity(LDBLE l_total_alkalinity) {this->total_alkalinity = l_total_alkalinity;}
+	LDBLE Get_soln_vol() const                          {return this->soln_vol;}
+	void Set_soln_vol(LDBLE t)                          {this->soln_vol = t;}
+	cxxNameDouble & Get_totals(void)                    {return this->totals;}
+	const cxxNameDouble & Get_totals(void)const         {return this->totals;}
+	void Set_totals(cxxNameDouble & nd)
+	{
+		this->totals = nd;
+		this->totals.type = cxxNameDouble::ND_ELT_MOLES;
+	}
+	cxxNameDouble & Get_master_activity(void)           {return this->master_activity;}
+	cxxNameDouble & Get_species_gamma(void)             {return this->species_gamma;}
+	std::map<int, double> & Get_species_map(void)       {return this->species_map;}
+	std::map<int, double> & Get_log_gamma_map(void)     {return this->log_gamma_map;}
+	std::map < std::string, cxxSolutionIsotope > & Get_isotopes(void)             {return this->isotopes;}	
+	const std::map < std::string, cxxSolutionIsotope > & Get_isotopes(void)const  {return this->isotopes;}	
+	void Set_isotopes(const std::map < std::string, cxxSolutionIsotope > &iso ) {this->isotopes = iso;}	
+	cxxISolution *Get_initial_data()                    {return this->initial_data;}
+	const cxxISolution *Get_initial_data()const         {return this->initial_data;}
+	void Set_initial_data(const cxxISolution * id)
+	{
+		if (this->initial_data != NULL)
+			delete this->initial_data;
+		this->initial_data = new cxxISolution(*id);
+	}
+	void Create_initial_data()
+	{
+		if (this->initial_data != NULL)
+			delete initial_data;
+		initial_data = new cxxISolution;
+	}
+	void Destroy_initial_data()
+	{
+		if (this->initial_data != NULL)
+			delete initial_data;
+		initial_data = NULL;
+	}
+
+	void clear_totals()					{this->totals.clear();}
+	void clear_master_activity()    	{this->master_activity.clear();}
+
+	void zero();
+	void add(const cxxSolution & addee, LDBLE extensive);
+	void Add_isotopes(const std::map < std::string, cxxSolutionIsotope > &old, LDBLE intensive, LDBLE extensive);
+	void multiply(LDBLE extensive);
+	void Multiply_isotopes(LDBLE extensive);
+	// not checked
+	void dump_xml(std::ostream & os, unsigned int indent = 0) const;
+	void dump_raw(std::ostream & s_oss, unsigned int indent, int *n_out=NULL) const;
+
+	LDBLE Get_master_activity(char *string) const;
+	void Set_master_activity(char *string, LDBLE value);	
+	LDBLE Get_total(const char *string) const;
+	LDBLE Get_total_element(const char *string) const;
+	void Set_total(char *string, LDBLE value);
+	void read_raw(CParser & parser, bool check = true);
+	//void modify_activities(const cxxSolution & original);
+	//void Simplify_totals();
+	void Update(const cxxNameDouble &nd);
+	void Update(LDBLE h_tot, LDBLE o_tot, LDBLE charge, const cxxNameDouble &nd);
+	void Update_activities(const cxxNameDouble &original_tot);
+	void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
+	void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
+
+  protected:
+	bool new_def;
+	LDBLE patm;
+	LDBLE potV;
+	LDBLE tc;
+	LDBLE ph;
+	LDBLE pe;
+	LDBLE mu;
+	LDBLE ah2o;
+	LDBLE total_h;
+	LDBLE total_o;
+	LDBLE cb;
+	LDBLE mass_water;
+	LDBLE density;
+	LDBLE soln_vol;
+	LDBLE total_alkalinity;
+	cxxNameDouble totals;
+	cxxNameDouble master_activity;
+	cxxNameDouble species_gamma;
+	//cxxSolutionIsotopeList isotopes;
+	std::map < std::string, cxxSolutionIsotope > isotopes;
+	cxxISolution *initial_data;
+	const static std::vector < std::string > vopts;
+	std::map<int, double> species_map;
+	std::map<int, double> log_gamma_map;
+};
+
+#endif // !defined(SOLUTION_H_INCLUDED)

src/phreeqcpp/SolutionIsotope.cxx

@@ -0,0 +1,329 @@
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <cassert>
+#include <sstream>				// std::ostrstream
+
+#include "Utils.h"
+#include "Phreeqc.h"
+#include "SolutionIsotope.h"
+#include "phqalloc.h"
+#include "Dictionary.h"
+
+cxxSolutionIsotope::cxxSolutionIsotope(PHRQ_io *io)
+:
+PHRQ_base(io),
+isotope_number(0.0)
+{
+	isotope_number = 0;
+	elt_name.clear();
+	isotope_name.clear();
+	total = 0;
+	ratio = -9999.9;
+	ratio_uncertainty = 1;
+	ratio_uncertainty_defined = false;
+	x_ratio_uncertainty = 0;
+	coef = 0;
+}
+cxxSolutionIsotope::~cxxSolutionIsotope(void)
+{
+}
+
+void
+cxxSolutionIsotope::dump_xml(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+
+	std::string indent0(""), indent1("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+
+	s_oss << indent0;
+	s_oss << "<soln_isotope=\"" << "\n";
+
+	s_oss << indent1;
+	s_oss << "iso_isotope_number=\"" << this->
+		isotope_number << "\"" << "\n";
+
+	s_oss << indent1;
+	s_oss << "iso_elt_name=\"" << this->elt_name << "\"" << "\n";
+
+	s_oss << indent1;
+	s_oss << "iso_isotope_name=\"" << this->isotope_name << "\"" << "\n";
+
+	s_oss << indent1;
+	s_oss << "iso_total=\"" << this->total << "\"" << "\n";
+
+	s_oss << indent1;
+	s_oss << "iso_ratio=\"" << this->ratio << "\"" << "\n";
+
+#ifdef NPP
+	if (!isnan(this->ratio_uncertainty))
+#else
+	if (this->ratio_uncertainty != NAN)
+#endif
+	{
+		s_oss << indent1;
+		s_oss << "iso_ratio_uncertainty=\"" << this->
+			ratio_uncertainty << "\"" << "\n";
+	}
+	s_oss << indent0;
+	s_oss << "\">" << "\n";
+}
+
+void
+cxxSolutionIsotope::dump_raw(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+
+	std::string indent0("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	std::string indent1 = indent0;
+	indent1.append(Utilities::INDENT);
+
+	s_oss << indent0;
+	s_oss << indent0 << "-isotope_number                    " << this->isotope_number << "\n";
+	s_oss << indent0 << "-elt_name                          " << this->elt_name << "\n";
+	s_oss << indent0 << "-total                             " << this->total << "\n";
+	s_oss << indent0 << "-ratio                             " << this->ratio << "\n";
+	s_oss << indent0 << "-ratio_uncertainty_defined         " << this->ratio_uncertainty_defined << "\n";
+	if (this->ratio_uncertainty_defined)
+	{
+		s_oss << indent0 << "-ratio_uncertainty                 " << this->ratio_uncertainty << "\n";
+	}
+	s_oss << indent0 << "-x_ratio_uncertainty               " << this->x_ratio_uncertainty << "\n";
+	s_oss << indent0 << "-coef                              " << this->coef << "\n";
+}
+void cxxSolutionIsotope::read_raw(CParser & parser, bool check )
+{
+
+	std::istream::pos_type ptr;
+	std::istream::pos_type next_char;
+	std::string token;
+	int opt_save;
+
+	opt_save = CParser::OPT_ERROR;
+	bool isotope_number_defined(false);
+	bool elt_name_defined(false);
+	bool total_defined(false);
+	bool ratio_defined(false);
+
+	for (;;)
+	{
+		int opt = parser.get_option(vopts, next_char);
+		if (opt == CParser::OPT_DEFAULT)
+		{
+			opt = opt_save;
+		}
+		
+		opt_save = CParser::OPT_DEFAULT;
+		switch (opt)
+		{
+		case CParser::OPT_EOF:
+			break;
+		case CParser::OPT_KEYWORD:
+			break;
+		case CParser::OPT_DEFAULT:
+		case CParser::OPT_ERROR:
+			opt = CParser::OPT_EOF;
+			parser.error_msg("Unknown input in isotopes of SOLUTION_RAW keyword.",
+							 PHRQ_io::OT_CONTINUE);
+			parser.error_msg(parser.line().c_str(), PHRQ_io::OT_CONTINUE);
+			continue;
+
+		case 0:				// isotope_number                  
+			if (!(parser.get_iss() >> this->isotope_number))
+			{
+				this->isotope_number = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for isotope_number.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			isotope_number_defined = true;
+			break;
+
+		case 1:				// elt_name                
+			if (!(parser.get_iss() >> this->elt_name))
+			{
+				this->elt_name.clear();
+				parser.incr_input_error();
+				parser.error_msg("Expected character value for elt_name.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			elt_name_defined = true;
+			break;
+
+		case 2:				// total
+			if (!(parser.get_iss() >> this->total))
+			{
+				this->total = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for total.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			total_defined = true;
+			break;
+
+		case 3:				// ratio
+			if (!(parser.get_iss() >> this->ratio))
+			{
+				this->ratio = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for ratio.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			total_defined = true;
+			break;
+
+		case 4:				// ratio_uncertainty_defined
+			if (!(parser.get_iss() >> this->ratio_uncertainty_defined))
+			{
+				this->ratio_uncertainty_defined = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected boolean value for ratio_uncertainty_defined.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+
+		case 5:				// ratio_uncertainty
+			if (!(parser.get_iss() >> this->ratio_uncertainty))
+			{
+				this->ratio_uncertainty = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for ratio_uncertainty.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			ratio_uncertainty_defined = true;
+			break;
+
+		case 6:				// x_ratio_uncertainty
+			if (!(parser.get_iss() >> this->x_ratio_uncertainty))
+			{
+				this->x_ratio_uncertainty = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for x_ratio_uncertainty.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+		case 7:				// coef
+			if (!(parser.get_iss() >> this->coef))
+			{
+				this->coef = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for coef.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+		}
+
+		if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
+			break;
+	}
+	if (check)
+	{
+		// all members must be defined
+		if (isotope_number_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("isotope_number not defined for isotopes SOLUTION_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (elt_name_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("elt_name not defined for isotopes SOLUTION_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (total_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("total not defined for isotopes SOLUTION_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (ratio_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("ratio not defined for isotopes SOLUTION_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (ratio_uncertainty_defined == false)
+		{
+			parser.incr_input_error();
+			parser.
+				error_msg("ratio_uncertainty not defined for isotopes SOLUTION_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+	}
+	return;
+}
+bool
+cxxSolutionIsotope::operator<(const cxxSolutionIsotope & isotope) const
+{
+	int i = Utilities::strcmp_nocase(this->elt_name.c_str(), isotope.elt_name.c_str());
+	if (i != 0)
+		return (i < 0);
+	return (this->isotope_number < isotope.isotope_number);
+}
+
+void
+cxxSolutionIsotope::add(const cxxSolutionIsotope & isotope_ptr,
+						LDBLE intensive, LDBLE extensive)
+{
+	if ((this->isotope_number == isotope_ptr.isotope_number) &&
+		(this->elt_name == isotope_ptr.elt_name) &&
+		(this->isotope_name == isotope_ptr.isotope_name))
+	{
+		this->total += isotope_ptr.total * extensive;
+		this->ratio += isotope_ptr.ratio * intensive;
+		this->ratio_uncertainty += isotope_ptr.ratio_uncertainty * intensive;
+		this->ratio_uncertainty_defined = (this->ratio_uncertainty_defined
+										   || isotope_ptr.
+										   ratio_uncertainty_defined);
+	}
+}
+void
+cxxSolutionIsotope::multiply(LDBLE extensive)
+{
+	this->total *= extensive;
+}
+void 
+cxxSolutionIsotope::Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles)
+{
+	doubles.push_back(this->isotope_number);
+	ints.push_back(dictionary.Find(this->elt_name));
+	ints.push_back(dictionary.Find(this->isotope_name));
+	doubles.push_back(this->total);
+	doubles.push_back(this->ratio);
+	doubles.push_back(this->ratio_uncertainty);
+	ints.push_back(this->ratio_uncertainty_defined ? 1 : 0);
+	doubles.push_back(this->x_ratio_uncertainty);
+	doubles.push_back(this->coef);
+}
+void 
+cxxSolutionIsotope::Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd)
+{
+	this->isotope_number = doubles[dd++];
+	this->elt_name = dictionary.GetWords()[ints[ii++]];
+	this->isotope_name = dictionary.GetWords()[ints[ii++]];
+	this->total = doubles[dd++];
+	this->ratio = doubles[dd++];
+	this->ratio_uncertainty = doubles[dd++];
+	this->ratio_uncertainty_defined = (ints[ii++] != 0);
+	this->x_ratio_uncertainty = doubles[dd++];
+	this->coef = doubles[dd++];
+}
+
+const std::vector< std::string >::value_type temp_vopts[] = {
+	std::vector< std::string >::value_type("isotope_number"),	            // 0 
+	std::vector< std::string >::value_type("elt_name"),	                    // 1 
+	std::vector< std::string >::value_type("total"),	                    // 2 
+	std::vector< std::string >::value_type("ratio"),	                    // 3 
+	std::vector< std::string >::value_type("ratio_uncertainty_defined"),	// 4 
+	std::vector< std::string >::value_type("ratio_uncertainty"),	        // 5 
+	std::vector< std::string >::value_type("x_ratio_uncertainty"),	        // 6 
+	std::vector< std::string >::value_type("coef") 	                        // 7 
+};									   
+const std::vector< std::string > cxxSolutionIsotope::vopts(temp_vopts, temp_vopts + sizeof temp_vopts / sizeof temp_vopts[0]);

src/phreeqcpp/SolutionIsotope.h

@@ -0,0 +1,85 @@
+#if !defined(SOLUTIONISOTOPE_H_INCLUDED)
+#define SOLUTIONISOTOPE_H_INCLUDED
+
+#include <ostream>				// std::ostream
+#include <string>				// std::string
+#include <list>					// std::list
+#include "Parser.h"
+class Dictionary;
+
+class cxxSolutionIsotope: public PHRQ_base
+{
+  public:
+	cxxSolutionIsotope(PHRQ_io *io=NULL);
+	cxxSolutionIsotope(struct isotope *isotope_ptr, PHRQ_io *io=NULL);
+	virtual ~cxxSolutionIsotope(void);
+
+	void dump_xml(std::ostream & os, unsigned int indent) const;
+	void dump_raw(std::ostream & os, unsigned int indent) const;
+
+	//CParser::STATUS_TYPE read_raw(CParser & parser, std::istream::pos_type next_char);
+	void read_raw(CParser & parser, bool check);
+
+	LDBLE Get_isotope_number() const
+	{
+		return this->isotope_number;
+	}
+	void Set_isotope_number(LDBLE d)
+	{
+		this->isotope_number = d;
+	}
+	const std::string &Get_elt_name() const	{return this->elt_name;}
+	void Set_elt_name(const char *cstring)
+	{
+		if (cstring != NULL)
+			this->elt_name = std::string(cstring);
+		else
+			this->elt_name.clear();
+	}
+
+	const std::string &Get_isotope_name() const	{return this->isotope_name;}
+	void Set_isotope_name(const char *cstring)
+	{
+		if (cstring != NULL)
+			this->isotope_name = std::string(cstring);
+		else
+			this->isotope_name.clear();
+	}
+
+	LDBLE Get_total() const	{return this->total;}
+	void Set_total(LDBLE d)	{this->total = d;}
+
+	LDBLE Get_ratio() const	            {return this->ratio;}
+	void Set_ratio(LDBLE t)             {this->ratio = t;}
+
+	LDBLE Get_ratio_uncertainty() const	{return this->ratio_uncertainty;}
+	void Set_ratio_uncertainty(LDBLE t) {this->ratio_uncertainty = t;}
+
+	LDBLE Get_x_ratio_uncertainty() const	{return this->x_ratio_uncertainty;}
+	void Set_x_ratio_uncertainty(LDBLE t)   {this->x_ratio_uncertainty = t;}
+
+	bool Get_ratio_uncertainty_defined() const  {return this->ratio_uncertainty_defined;}
+	void Set_ratio_uncertainty_defined(bool tf) {this->ratio_uncertainty_defined = tf;}
+	LDBLE Get_coef() const	{return this->coef;}
+	void Set_coef(LDBLE t)   {this->coef = t;}
+
+	bool operator<(const cxxSolutionIsotope & conc) const;
+	void add(const cxxSolutionIsotope & isotope_ptr, LDBLE intensive,
+			 LDBLE extensive);
+	void multiply(LDBLE extensive);
+	void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
+	void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
+
+  protected:
+	LDBLE isotope_number;
+	std::string elt_name;
+	std::string isotope_name;
+	LDBLE total;
+	LDBLE ratio;
+	LDBLE ratio_uncertainty;
+	bool ratio_uncertainty_defined;
+ 	LDBLE x_ratio_uncertainty;
+ 	LDBLE coef;					/* coefficient of element in phase */
+	const static std::vector < std::string > vopts;
+};
+#endif // SOLUTIONISOTOPE_H_INCLUDED

src/phreeqcpp/StorageBin.h

@@ -0,0 +1,139 @@
+#if !defined(STORAGEBIN_H_INCLUDED)
+#define STORAGEBIN_H_INCLUDED
+#include <cassert>				// assert
+#include <map>					// std::map
+#include <string>				// std::string
+#include <list>					// std::list
+#include <vector>				// std::vector
+
+#include "System.h"
+#include "PHRQ_io.h"
+#include "PHRQ_base.h"
+class cxxSolution;
+class cxxExchange;
+class cxxGasPhase;
+class cxxKinetics;
+class cxxPPassemblage;
+class cxxSSassemblage;
+class cxxSurface;
+class cxxReaction;
+class cxxTemperature;
+class cxxUse;
+
+class cxxStorageBin: public PHRQ_base
+{
+
+  public:
+	cxxStorageBin(PHRQ_io *io=NULL);
+	cxxStorageBin(cxxUse &use_ref, PHRQ_io *io=NULL);
+	virtual ~cxxStorageBin();
+
+	void Copy(int destination, int source);
+	void Remove(int n);
+	void Clear(void);
+
+	cxxSolution *Get_Solution(int n_user);
+	void Set_Solution(int n_user, cxxSolution * entity);
+	void Set_Solution(int n_user, cxxSolution & entity);
+	void Remove_Solution(int n_user);
+
+	cxxExchange *Get_Exchange(int n_user);
+	void Set_Exchange(int n_user, cxxExchange * entity);
+	void Set_Exchange(int n_user, cxxExchange & entity);
+	void Remove_Exchange(int n_user);
+
+	cxxPPassemblage *Get_PPassemblage(int n_user);
+	void Set_PPassemblage(int n_user, cxxPPassemblage * entity);
+	void Set_PPassemblage(int n_user, cxxPPassemblage & entity);
+	void Remove_PPassemblage(int n_user);
+
+	cxxGasPhase *Get_GasPhase(int n_user);
+	void Set_GasPhase(int n_user, cxxGasPhase * entity);
+	void Set_GasPhase(int n_user, cxxGasPhase & entity);
+	void Remove_GasPhase(int n_user);
+
+	cxxSSassemblage *Get_SSassemblage(int n_user);
+	void Set_SSassemblage(int n_user, cxxSSassemblage * entity);
+	void Set_SSassemblage(int n_user, cxxSSassemblage & entity);
+	void Remove_SSassemblage(int n_user);
+
+	cxxKinetics *Get_Kinetics(int n_user);
+	void Set_Kinetics(int n_user, cxxKinetics * entity);
+	void Set_Kinetics(int n_user, cxxKinetics & entity);
+	void Remove_Kinetics(int n_user);
+
+	cxxSurface *Get_Surface(int n_user);
+	void Set_Surface(int n_user, cxxSurface * entity);
+	void Set_Surface(int n_user, cxxSurface & entity);
+	void Remove_Surface(int n_user);
+
+	cxxMix *Get_Mix(int n_user);
+	void Set_Mix(int n_user, cxxMix * entity);
+	void Set_Mix(int n_user, cxxMix & entity);
+	void Remove_Mix(int n_user);
+
+	cxxReaction *Get_Reaction(int n_user);
+	void Set_Reaction(int n_user, cxxReaction * entity);
+	void Set_Reaction(int n_user, cxxReaction & entity);
+	void Remove_Reaction(int n_user);
+
+	cxxTemperature *Get_Temperature(int n_user);
+	void Set_Temperature(int n_user, cxxTemperature * entity);
+	void Set_Temperature(int n_user, cxxTemperature & entity);
+	void Remove_Temperature(int n_user);
+
+	cxxPressure *Get_Pressure(int n_user);
+	void Set_Pressure(int n_user, cxxPressure * entity);
+	void Set_Pressure(int n_user, cxxPressure & entity);
+	void Remove_Pressure(int n_user);
+
+	cxxSystem &Get_System(void);
+	void Set_System(cxxUse *use_ptr);
+	void Set_System(int i);
+
+	void dump_raw(std::ostream & s_oss, unsigned int indent) const;
+
+	void dump_raw(std::ostream & s_oss, int i, unsigned int indent, int *n_out=NULL);
+
+	void read_raw(CParser & parser);
+	int read_raw_keyword(CParser & parser);
+
+	void Add(cxxStorageBin &src, int n);
+
+	//cxxSolution *mix_cxxSolutions(cxxMix &mixmap);
+	cxxExchange *mix_cxxExchange(cxxMix & mixmap);
+
+	std::map < int, cxxSolution > &Get_Solutions();
+	std::map < int, cxxExchange > &Get_Exchangers();
+	std::map < int, cxxGasPhase > &Get_GasPhases();
+	std::map < int, cxxKinetics > &Get_Kinetics();
+	std::map < int, cxxPPassemblage > &Get_PPassemblages();
+	std::map < int, cxxSSassemblage > &Get_SSassemblages();
+	std::map < int, cxxSurface > &Get_Surfaces();
+	std::map < int, cxxMix > &Get_Mixes();
+	std::map < int, cxxReaction > &Get_Reactions();
+	std::map < int, cxxTemperature > &Get_Temperatures();
+	std::map < int, cxxPressure > &Get_Pressures();
+
+	cxxSystem & Get_system(void) {return system;};
+
+  protected:
+	// Tidied classes
+	std::map < int, cxxSolution > Solutions;
+	std::map < int, cxxExchange > Exchangers;
+	std::map < int, cxxGasPhase > GasPhases;
+	std::map < int, cxxKinetics > Kinetics;
+	std::map < int, cxxPPassemblage > PPassemblages;
+	std::map < int, cxxSSassemblage > SSassemblages;
+	std::map < int, cxxSurface > Surfaces;
+
+	// Reaction classes
+	std::map < int, cxxMix > Mixes;
+	std::map < int, cxxReaction > Reactions;
+	std::map < int, cxxTemperature > Temperatures;
+	std::map < int, cxxPressure > Pressures;
+	cxxSystem system;
+
+};
+
+#endif // !defined(STORAGEBIN_H_INCLUDED)

src/phreeqcpp/StorageBinList.cpp

@@ -0,0 +1,350 @@
+#include <algorithm>			// std::replace
+#include "StorageBinList.h"
+#include "Parser.h"
+
+StorageBinListItem::StorageBinListItem(void)
+{
+	this->defined = false;
+}
+
+StorageBinListItem::~StorageBinListItem(void)
+{
+}
+StorageBinListItem::StorageBinListItem(CParser & parser)
+{
+	this->Clear();
+	// Read list of numbers or number ranges 
+	for (;;)
+	{
+		//read lines
+		PHRQ_io::LINE_TYPE l = parser.check_line("read StorageBinListLtem", false, true, true, true);
+		std::istream::pos_type next_char = 0;
+		if (l == PHRQ_io::LT_EOF) break;
+		for (;;)
+		{ 
+			std::string token;
+			CParser::TOKEN_TYPE j = parser.copy_token(token, next_char);
+			if (j == CParser::TT_DIGIT)
+			{
+				this->Augment(token);
+			}
+			else if (j == CParser::TT_EMPTY)
+			{
+				break;
+			}
+		}
+	}
+}
+void StorageBinListItem::Augment(std::string token)
+{
+	this->defined = true;
+	if (token.size() == 0) return;
+
+	// split string accounting for possible negative numbers
+	size_t pos;
+	if ((pos = token.find("--")) != std::string::npos)
+	{
+		token.replace(pos,2," &");
+	}
+	std::replace(token.begin() + 1, token.end(), '-', ' ');
+	std::replace(token.begin() + 1, token.end(), '&', '-');
+
+	// parse string into 1 or 2 numbers
+	std::istringstream iss(token);
+	std::set < int > temp_set;
+	int i;
+	if (iss >> i)
+	{
+		// add first 
+		temp_set.insert(i);
+		if (iss >> i)
+		{
+			// add second if defined
+			temp_set.insert(i);
+		}
+	}
+
+	// add single number or range to StorageBinListItem
+	if (temp_set.size() == 1)
+	{
+		this->numbers.insert(*(temp_set.begin()));
+	}
+	else if (temp_set.size() == 2)
+	{
+		int i1, i2;
+		std::set <int>::iterator it;
+		it = temp_set.begin();
+		i1 = *it;
+		it++;
+		i2 = *it;
+		for (i = i1; i <= i2; i++)
+		{
+			this->numbers.insert(i);
+		}
+	}
+}
+void StorageBinListItem::Augment(int i)
+{
+	// Skip if all are defined
+	if (this->defined == true && this->numbers.size() ==  0) return;
+	this->defined = true;
+	this->numbers.insert(i);
+}
+//
+//Class definitions for StorageBinList
+//
+StorageBinList::StorageBinList(PHRQ_io *io)
+:
+PHRQ_base(io)
+{
+}
+StorageBinList::StorageBinList(CParser & parser, PHRQ_io *io)
+:
+PHRQ_base(io)
+{
+	this->Read(parser);
+}
+StorageBinList::~StorageBinList(void)
+{
+}
+
+std::set<StorageBinListItem *> StorageBinList::GetAllItems(void)
+{
+	// don't include this->cell
+	std::set<StorageBinListItem *> items;
+	items.insert(&this->solution);
+	items.insert(&this->pp_assemblage);
+	items.insert(&this->exchange);
+	items.insert(&this->surface);
+	items.insert(&this->ss_assemblage);
+	items.insert(&this->gas_phase);
+	items.insert(&this->kinetics);
+	items.insert(&this->mix);
+	items.insert(&this->reaction);
+	items.insert(&this->temperature);
+	items.insert(&this->pressure);
+	return items;
+}
+
+void StorageBinList::SetAll(bool tf)
+{
+	std::set<StorageBinListItem *> all = this->GetAllItems();
+	std::set<StorageBinListItem *>::iterator it = all.begin();
+	for (; it != all.end(); ++it)
+	{
+		(*it)->Clear();
+		(*it)->Set_defined(tf);
+	}
+}
+
+bool StorageBinList::Read(CParser & parser)
+{
+	bool return_value(true);
+
+	std::istream::pos_type next_char;
+	std::string token;
+	int opt_save;
+
+	opt_save = CParser::OPT_DEFAULT;
+	// reset cells
+	this->cell.Clear();
+	this->cell.Set_defined(false);
+	for (;;)
+	{
+		int opt;
+		opt = parser.get_option(vopts, next_char);
+		if (opt == CParser::OPT_DEFAULT)
+		{
+			opt = opt_save;
+		}
+		else
+		{
+			opt_save = opt;
+		}
+
+		// Select StorageBinListItem
+		StorageBinListItem *item = NULL;
+		switch (opt)
+		{
+		case 0:
+			item = &(this->Get_solution());
+			break;
+		case 1:
+		case 2:
+			item = &(this->Get_pp_assemblage());
+			break;
+		case 3:
+			item = &(this->Get_exchange());
+			break;
+		case 4:
+			item = &(this->Get_surface());
+			break;
+		case 5:
+		case 6:
+		case 7:
+			item = &(this->Get_ss_assemblage());
+			break;
+		case 8:
+			item = &(this->Get_gas_phase());
+			break;
+		case 9:
+			item = &(this->Get_kinetics());
+			break;
+		case 10:
+			item = &(this->Get_mix());
+			break;
+		case 11:
+			item = &(this->Get_reaction());
+			break;
+		case 12:
+		case 16:
+			item = &(this->Get_temperature());
+			break;
+		case 14:
+		case 15:
+			item = &(this->Get_cell());
+			break;
+		case 17:
+		case 18:
+			item = &(this->Get_pressure());
+			break;
+		default:
+			break;
+		}
+
+		// Read dump entity list of numbers or number ranges for line, store in item
+		if ((opt >= 0 && opt <= 12) || (opt >= 14))
+		{
+			for (;;)
+			{ 
+				CParser::TOKEN_TYPE j = parser.copy_token(token, next_char);
+				if (item)
+				{
+					if (j == CParser::TT_DIGIT)
+					{
+						item->Augment(token);
+					}
+					else if (j == CParser::TT_EMPTY)
+					{
+						item->Augment(token);
+						break;
+					}
+					else
+					{
+						parser.error_msg("Expected single number or range of numbers.",
+							PHRQ_io::OT_CONTINUE);
+						break;
+					}
+				}
+				else
+				{
+						parser.error_msg("Dump entity type not defined.",
+							PHRQ_io::OT_CONTINUE);
+						break;
+				}
+			}
+		}
+
+		// Process other identifiers
+		switch (opt)
+		{
+		case CParser::OPT_EOF:
+			break;
+		case CParser::OPT_KEYWORD:
+			break;
+
+		case 0:
+		case 1:
+		case 2:
+		case 3:
+		case 4:
+		case 5:
+		case 6:
+		case 7:
+		case 8:
+		case 9:
+		case 10:
+		case 11:
+		case 12:
+		case 16:
+		case 17:
+		case 18:
+			break;
+		case 13:			//all
+			this->SetAll(true);
+			break;
+		case 14:
+		case 15:
+			//if (cell_list.Get_numbers().empty())
+			//{
+			//	this->SetAll(true);
+			//}
+			//else
+			//{
+				//this->TransferAll(cell_list);
+			//}
+			break;
+		default:
+		case CParser::OPT_DEFAULT:
+		case CParser::OPT_ERROR:
+			opt = CParser::OPT_EOF;
+			parser.error_msg("Unknown input reading DELETE definition.",
+							 PHRQ_io::OT_CONTINUE);
+			parser.error_msg(parser.line().c_str(), PHRQ_io::OT_CONTINUE);
+			return_value = false;
+			break;
+		}
+		if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
+			break;
+	}
+
+	// Now check to see if cell_list defined 
+	if (this->Get_cell().Get_defined())
+	{
+		if (this->Get_cell().Get_numbers().empty())
+		{
+			this->SetAll(true);
+		}
+		else
+		{
+			this->TransferAll(this->Get_cell());
+		}
+	}
+	return(return_value);
+}
+
+void StorageBinList::TransferAll(StorageBinListItem &source)
+{
+	std::set<StorageBinListItem *> items = this->GetAllItems();
+	std::set < int >::iterator it;
+	for (it = source.Get_numbers().begin(); it != source.Get_numbers().end(); it++)
+	{
+		std::set<StorageBinListItem *>::iterator item = items.begin();
+		for (; item != items.end(); ++item)
+		{
+			(*item)->Augment(*it);
+		}
+	}
+}
+const std::vector< std::string >::value_type temp_vopts[] = {
+	std::vector< std::string >::value_type("solution"),			       // 0 
+	std::vector< std::string >::value_type("pp_assemblage"),		   // 1 
+	std::vector< std::string >::value_type("equilibrium_phases"),	   // 2 
+	std::vector< std::string >::value_type("exchange"),			       // 3 
+	std::vector< std::string >::value_type("surface"),			       // 4 
+	std::vector< std::string >::value_type("ss_assemblage"),		   // 5 
+	std::vector< std::string >::value_type("solid_solution"),		   // 6 
+	std::vector< std::string >::value_type("solid_solutions"),		   // 7 
+	std::vector< std::string >::value_type("gas_phase"),			   // 8 
+	std::vector< std::string >::value_type("kinetics"),			       // 9 
+	std::vector< std::string >::value_type("mix"),				       // 10
+	std::vector< std::string >::value_type("reaction"),			       // 11
+	std::vector< std::string >::value_type("temperature"),			   // 12
+	std::vector< std::string >::value_type("all"),   			       // 13
+	std::vector< std::string >::value_type("cell"),			           // 14
+	std::vector< std::string >::value_type("cells"), 			       // 15
+	std::vector< std::string >::value_type("reaction_temperature"),	   // 16
+	std::vector< std::string >::value_type("pressure"),			       // 17
+	std::vector< std::string >::value_type("reaction_pressure") 	   // 18 
+};									   
+const std::vector< std::string > StorageBinList::vopts(temp_vopts, temp_vopts + sizeof temp_vopts / sizeof temp_vopts[0]);	

src/phreeqcpp/StorageBinList.h

@@ -0,0 +1,81 @@
+#if !defined(STORAGEBINLIST_H_INCLUDED)
+#define STORAGEBINLIST_H_INCLUDED
+#include <set>                  // std::set
+#include <string>               // std::string
+#include <list>                 // std::list
+#include <vector>               // std::vector
+#include "PHRQ_base.h"
+class CParser;
+
+class StorageBinListItem
+{
+public:
+	StorageBinListItem(void);
+	StorageBinListItem(CParser & parser);
+	~StorageBinListItem(void);
+	void Set_defined(bool tf) { this->defined = tf; };
+	bool Get_defined(void)const { return(this->defined); };
+	void Augment(std::string token);
+	void Augment(int i);
+	std::set < int > &Get_numbers(void) { return(this->numbers); };
+	const std::set < int > &Get_numbers(void)const { return(this->numbers); };
+	void Clear(void) { this->numbers.clear(); };
+protected:
+	std::set < int > numbers;
+	bool defined;
+};
+class StorageBinList: public PHRQ_base
+{
+public:
+	StorageBinList(PHRQ_io *io=NULL);
+	StorageBinList(CParser & parser, PHRQ_io *io=NULL);
+	virtual ~StorageBinList(void);
+	bool Read(CParser & parser);
+	void SetAll(bool tf);
+	void TransferAll(StorageBinListItem &source);
+	std::set<StorageBinListItem *> GetAllItems(void);
+
+	StorageBinListItem & Get_solution(void)      { return(this->solution); };
+	StorageBinListItem & Get_pp_assemblage(void) { return(this->pp_assemblage); };
+	StorageBinListItem & Get_exchange(void)      { return(this->exchange); };
+	StorageBinListItem & Get_surface(void)       { return(this->surface); };
+	StorageBinListItem & Get_ss_assemblage(void) { return(this->ss_assemblage); };
+	StorageBinListItem & Get_gas_phase(void)     { return(this->gas_phase); };
+	StorageBinListItem & Get_kinetics(void)      { return(this->kinetics); };
+	StorageBinListItem & Get_mix(void)           { return(this->mix); };
+	StorageBinListItem & Get_reaction(void)      { return(this->reaction); };
+	StorageBinListItem & Get_temperature(void)   { return(this->temperature); };
+	StorageBinListItem & Get_pressure(void)      { return(this->pressure); };
+	StorageBinListItem & Get_cell(void)          { return(this->cell); };
+
+	const StorageBinListItem & Get_solution(void)const      { return(this->solution); };
+	const StorageBinListItem & Get_pp_assemblage(void)const { return(this->pp_assemblage); };
+	const StorageBinListItem & Get_exchange(void)const      { return(this->exchange); };
+	const StorageBinListItem & Get_surface(void)const       { return(this->surface); };
+	const StorageBinListItem & Get_ss_assemblage(void)const { return(this->ss_assemblage); };
+	const StorageBinListItem & Get_gas_phase(void)const     { return(this->gas_phase); };
+	const StorageBinListItem & Get_kinetics(void)const      { return(this->kinetics); };
+	const StorageBinListItem & Get_mix(void)const           { return(this->mix); };
+	const StorageBinListItem & Get_reaction(void)const      { return(this->reaction); };
+	const StorageBinListItem & Get_temperature(void)const   { return(this->temperature); };
+	const StorageBinListItem & Get_pressure(void)const      { return(this->pressure); };
+	const StorageBinListItem & Get_cell(void)const          { return(this->cell); };
+protected:
+	// update GetAllItems() if StorageBinListItem is added/removed
+	StorageBinListItem solution;
+	StorageBinListItem pp_assemblage;
+	StorageBinListItem exchange;
+	StorageBinListItem surface;
+	StorageBinListItem ss_assemblage;
+	StorageBinListItem gas_phase;
+	StorageBinListItem kinetics;
+	StorageBinListItem mix;
+	StorageBinListItem reaction;
+	StorageBinListItem temperature;
+	StorageBinListItem pressure;
+	const static std::vector < std::string > vopts;
+	StorageBinListItem cell; // not included in GetAllItems
+};
+
+
+#endif // !defined(STORAGEBINLIST_H_INCLUDED)

src/phreeqcpp/Surface.cxx

@@ -0,0 +1,852 @@
+// Surface.cxx: implementation of the cxxSurface class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <cassert>				// assert
+#include <algorithm>			// std::sort
+#include "Utils.h"				// define first
+#include "Phreeqc.h"
+#include "Surface.h"
+#include "cxxMix.h"
+#include "phqalloc.h"
+
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+cxxSurface::cxxSurface(PHRQ_io *io)
+	//
+	// default constructor for cxxSurface 
+	//
+:	cxxNumKeyword(io)
+{
+	new_def = false;
+	type = DDL;
+	dl_type = NO_DL;
+	sites_units = SITES_ABSOLUTE;
+	only_counter_ions = false;
+	thickness = 1e-8;
+	debye_lengths = 0.0;
+	DDL_viscosity = 1.0;
+	DDL_limit = 0.8;
+	transport = false;
+	solution_equilibria = false;
+	n_solution = -999;
+}
+cxxSurface::cxxSurface(std::map < int, cxxSurface > &entities,
+					   cxxMix & mix, int l_n_user, PHRQ_io *io):
+cxxNumKeyword(io)
+{
+	this->n_user = this->n_user_end = l_n_user;
+	this->new_def = false;
+	type = DDL;
+	dl_type = NO_DL;
+	sites_units = SITES_ABSOLUTE;
+	only_counter_ions = false;
+	thickness = 1e-8;
+	debye_lengths = 0.0;
+	DDL_viscosity = 1.0;
+	DDL_limit = 0.8;
+	transport = false;
+	solution_equilibria = false;
+	n_solution = -999;
+//
+//   Mix surfaces
+//
+	const std::map < int, LDBLE >&mixcomps = mix.Get_mixComps();
+	std::map < int, LDBLE >::const_iterator it;
+	for (it = mixcomps.begin(); it != mixcomps.end(); it++)
+	{
+		if (entities.find(it->first) != entities.end())
+		{
+			this->add(entities.find(it->first)->second, it->second);
+		}
+	}
+}
+
+cxxSurface::~cxxSurface()
+{
+}
+
+bool
+cxxSurface::Get_related_phases() const
+{
+	for (size_t i = 0; i != this->surface_comps.size(); i++)
+	{
+		if (this->surface_comps[i].Get_phase_name().size() == 0)
+			continue;
+		return (true);
+	}
+	return (false);
+}
+
+bool
+cxxSurface::Get_related_rate() const
+{
+	for (size_t i = 0; i != this->surface_comps.size(); i++)
+	{
+		if (this->surface_comps[i].Get_rate_name().size() == 0)
+			continue;
+		return (true);
+	}
+	return (false);
+}
+#ifdef SKIP
+void
+cxxSurface::dump_xml(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// Surface element and attributes
+	s_oss << indent0;
+	s_oss << "<surface " << "\n";
+
+	s_oss << indent1;
+	s_oss << "surface_type=\"" << this->type << "\"" << "\n";
+
+	s_oss << indent1;
+	s_oss << "dl_type=\"" << this->dl_type << "\"" << "\n";
+
+	s_oss << indent1;
+	s_oss << "sites_units=\"" << this->sites_units << "\"" << "\n";
+
+	s_oss << indent1;
+	s_oss << "only_counter_ions=\"" << this->
+		only_counter_ions << "\"" << "\n";
+
+	s_oss << indent1;
+	s_oss << "thickness=\"" << this->thickness << "\"" << "\n";
+
+	s_oss << indent1;
+	s_oss << "debye_lengths=\"" << this->debye_lengths << "\"" << "\n";
+
+	s_oss << indent1;
+	s_oss << "DDL_viscosity=\"" << this->DDL_viscosity << "\"" << "\n";
+
+	s_oss << indent1;
+	s_oss << "DDL_limit=\"" << this->DDL_limit << "\"" << "\n";
+
+	s_oss << indent1;
+	s_oss << "transport=\"" << this->transport << "\"" << "\n";
+
+	// surface component structures
+	s_oss << indent1;
+	s_oss << "<component " << "\n";
+	{
+		for (std::map < std::string, cxxSurfaceComp >::const_iterator it =
+			 this->surfaceComps.begin(); it != this->surfaceComps.end(); ++it)
+		{
+			(*it).second.dump_xml(s_oss, indent + 2);
+		}
+	}
+	// surface charge structures
+	s_oss << indent1;
+	s_oss << "<charge_component " << "\n";
+	for (std::map < std::string, cxxSurfaceCharge >::const_iterator it =
+		 surface_charges.begin(); it != surface_charges.end(); ++it)
+	{
+		(*it).second.dump_xml(s_oss, indent + 2);
+	}
+
+	return;
+}
+#endif
+void
+cxxSurface::dump_raw(std::ostream & s_oss, unsigned int indent, int *n_out) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// Surface element and attributes
+	s_oss << indent0;
+	int n_user_local = (n_out != NULL) ? *n_out : this->n_user;
+	s_oss << "SURFACE_RAW                  " << n_user_local << " " << this->description << "\n";
+	s_oss << indent1 << "# SURFACE_MODIFY candidate identifiers #\n";
+	s_oss << indent1;
+	s_oss << "-type                      " << this->type << "\n";
+	s_oss << indent1;
+	s_oss << "-dl_type                   " << this->dl_type << "\n";
+	s_oss << indent1;
+	s_oss << "-only_counter_ions         " << this->only_counter_ions << "\n";
+	s_oss << indent1;
+	s_oss << "-thickness                 " << this->thickness << "\n";
+	s_oss << indent1;
+	s_oss << "-debye_lengths             " << this->debye_lengths << "\n";
+	s_oss << indent1;
+	s_oss << "-DDL_viscosity             " << this->DDL_viscosity << "\n";
+	s_oss << indent1;
+	s_oss << "-DDL_limit                 " << this->DDL_limit << "\n";
+	// surfaceComps 
+	for (size_t i = 0; i != this->surface_comps.size(); i++)
+	{
+		const cxxSurfaceComp * comp_ptr = &(this->surface_comps[i]);
+		s_oss << indent1;
+		s_oss << "-component                 " << comp_ptr->Get_formula() << "\n";
+		comp_ptr->dump_raw(s_oss, indent + 2);
+	}
+	// surface charge 
+	for (size_t i = 0; i != this->surface_charges.size(); i++)
+	{
+		const cxxSurfaceCharge * charge_ptr = &(this->surface_charges[i]);
+		s_oss << indent1;
+		s_oss << "-charge_component          " << charge_ptr->Get_name() << "\n";
+		charge_ptr->dump_raw(s_oss, indent + 2);
+	}
+
+	s_oss << indent1 << "# SURFACE_MODIFY candidates with new_def=true #\n";
+	s_oss << indent1;
+	s_oss << "-new_def                   " << this->new_def << "\n";
+	s_oss << indent1;
+	s_oss << "-sites_units               " << this->sites_units << "\n";
+	s_oss << indent1;
+	s_oss << "-solution_equilibria       " << this->solution_equilibria << "\n";
+	s_oss << indent1;
+	s_oss << "-n_solution                " << this->n_solution << "\n";
+
+	s_oss << indent1 << "# Surface workspace variables #\n";
+	s_oss << indent1;
+	s_oss << "-transport                 " << this->transport << "\n";
+	s_oss << indent1;
+	s_oss << "-totals                    " << "\n";
+	this->totals.dump_raw(s_oss, indent + 2);
+
+	return;
+}
+
+void
+cxxSurface::read_raw(CParser & parser, bool check)
+{
+	int i = 0;
+	std::istream::pos_type ptr;
+	std::istream::pos_type next_char;
+	std::string token;
+	bool useLastLine(false);
+
+	// Read surface number and description
+	this->read_number_description(parser);
+	this->Set_new_def(false);
+
+	bool only_counter_ions_defined(false);
+	bool thickness_defined(false);
+	bool type_defined(false);
+	bool dl_type_defined(false);
+	bool sites_units_defined(false);
+	bool debye_lengths_defined(false);
+	bool DDL_viscosity_defined(false);
+	bool DDL_limit_defined(false);
+	bool transport_defined(false);
+
+	for (;;)
+	{
+		int opt;
+		if (useLastLine == false)
+		{
+			opt = parser.get_option(vopts, next_char);
+		}
+		else
+		{
+			opt = parser.getOptionFromLastLine(vopts, next_char, true);
+		}
+		useLastLine = false;
+		switch (opt)
+		{
+		case CParser::OPT_EOF:
+			break;
+		case CParser::OPT_KEYWORD:
+			break;
+		case CParser::OPT_DEFAULT:
+		case CParser::OPT_ERROR:
+			opt = CParser::OPT_EOF;
+			parser.error_msg("Unknown input in SURFACE keyword.",
+							 PHRQ_io::OT_CONTINUE);
+			parser.error_msg(parser.line().c_str(), PHRQ_io::OT_CONTINUE);
+			break;
+
+		case 0:				// diffuse_layer
+			parser.incr_input_error();
+			parser.error_msg("Diffuse layer is obsolete, use -type.",
+							 PHRQ_io::OT_CONTINUE);
+			break;
+
+		case 1:				// edl
+			parser.incr_input_error();
+			parser.error_msg("-edl is obsolete, use -type.",
+							 PHRQ_io::OT_CONTINUE);
+			break;
+
+		case 2:				// only_counter_ions
+			if (!(parser.get_iss() >> this->only_counter_ions))
+			{
+				this->only_counter_ions = false;
+				parser.incr_input_error();
+				parser.
+					error_msg("Expected boolean value for only_counter_ions.",
+							  PHRQ_io::OT_CONTINUE);
+			}
+			only_counter_ions_defined = true;
+			break;
+
+		case 3:				// donnan
+			parser.incr_input_error();
+			parser.error_msg("-Donnan is obsolete, use -dl_type.",
+							 PHRQ_io::OT_CONTINUE);
+			break;
+
+		case 4:				// thickness
+			if (!(parser.get_iss() >> this->thickness))
+			{
+				this->thickness = 0.0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for thickness.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			thickness_defined = true;
+			break;
+		case 5:				// component
+			{
+				std::string str;
+				if (!(parser.get_iss() >> str))
+				{
+					parser.incr_input_error();
+					parser.error_msg("Expected string value for component name.",
+									 PHRQ_io::OT_CONTINUE);
+				}
+				else
+				{
+					cxxSurfaceComp temp_comp(this->io);
+					temp_comp.Set_formula(str.c_str());
+					cxxSurfaceComp *comp_ptr = this->Find_comp(str);
+					if (comp_ptr)
+					{
+						temp_comp = *comp_ptr;
+					}
+					temp_comp.read_raw(parser, check);
+					if (comp_ptr)
+					{
+						for (size_t j = 0; j < this->surface_comps.size(); j++)
+						{
+							if (Utilities::strcmp_nocase(this->surface_comps[j].Get_formula().c_str(), str.c_str()) == 0)
+							{
+								this->surface_comps[j] = temp_comp;
+							}
+						}
+					}
+					else
+					{
+						this->surface_comps.push_back(temp_comp);
+					}
+					useLastLine = true;
+				}
+			}
+			break;
+		case 6:				// charge_component
+			{
+				std::string str;
+				if (!(parser.get_iss() >> str))
+				{
+					parser.incr_input_error();
+					parser.error_msg("Expected string value for charge name.",
+									 PHRQ_io::OT_CONTINUE);
+				}
+				else
+				{
+					cxxSurfaceCharge temp_charge(this->io);
+					temp_charge.Set_name(str.c_str());
+					cxxSurfaceCharge *charge_ptr = this->Find_charge(str);
+					if (charge_ptr)
+					{
+						temp_charge = *charge_ptr;
+					}
+					temp_charge.read_raw(parser, check);
+					if (charge_ptr)
+					{
+						for (size_t j = 0; j < this->surface_charges.size(); j++)
+						{
+							if (Utilities::strcmp_nocase(this->surface_charges[j].Get_name().c_str(), str.c_str()) == 0)
+							{
+								this->surface_charges[j] = temp_charge;
+							}
+						}
+					}
+					else
+					{
+						this->surface_charges.push_back(temp_charge);
+					}
+					useLastLine = true;
+				}
+			}	
+			useLastLine = true;
+			break;
+		case 7:				// type
+			i = 0;
+			if (!(parser.get_iss() >> i))
+			{
+				this->type = NO_EDL;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for type.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			this->type = (SURFACE_TYPE) i;
+			type_defined = true;
+			break;
+		case 8:				// dl_type
+			i = 0;
+			if (!(parser.get_iss() >> i))
+			{
+				this->dl_type = NO_DL;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for dl_type.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			this->dl_type = (DIFFUSE_LAYER_TYPE) i;
+			dl_type_defined = true;
+			break;
+		case 9:				// sites_units
+			i = 0;
+			if (!(parser.get_iss() >> i))
+			{
+				this->sites_units = SITES_ABSOLUTE;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for sites_units.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			this->sites_units = (SITES_UNITS) i;
+			sites_units_defined = true;
+			break;
+
+		case 10:				// debye_lengths
+			if (!(parser.get_iss() >> this->debye_lengths))
+			{
+				this->debye_lengths = 0.0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for debye_lengths.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			debye_lengths_defined = true;
+			break;
+
+		case 11:				// DDL_viscosity
+			if (!(parser.get_iss() >> this->DDL_viscosity))
+			{
+				this->DDL_viscosity = 0.0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for DDL_viscosity.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			DDL_viscosity_defined = true;
+			break;
+
+		case 12:				// DDL_limit
+			if (!(parser.get_iss() >> this->DDL_limit))
+			{
+				this->DDL_limit = 0.0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for DDL_limit.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			DDL_limit_defined = true;
+			break;
+
+		case 13:				// transport
+			if (!(parser.get_iss() >> this->transport))
+			{
+				this->transport = false;
+				parser.incr_input_error();
+				parser.error_msg("Expected boolean value for transport.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			transport_defined = true;
+			break;
+
+		case 14:				// new_def
+			if (!(parser.get_iss() >> this->new_def))
+			{
+				this->new_def = false;
+				parser.incr_input_error();
+				parser.error_msg("Expected boolean value for new_def.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+
+		case 15:				// new_def
+			if (!(parser.get_iss() >> this->solution_equilibria))
+			{
+				this->solution_equilibria = false;
+				parser.incr_input_error();
+				parser.error_msg("Expected boolean value for solution_equilibria.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+
+		case 16:				// n_solution
+			if (!(parser.get_iss() >> this->n_solution))
+			{
+				this->n_solution = -999;
+				parser.incr_input_error();
+				parser.error_msg("Expected integer value for n_solution.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+		case 17:				// totals
+			if (this->totals.read_raw(parser, next_char) !=	CParser::PARSER_OK)
+			{
+				parser.incr_input_error();
+				parser.
+					error_msg
+					("Expected element name and molality for Surface totals.",
+					 PHRQ_io::OT_CONTINUE);
+			}
+			break;
+		}
+		if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
+			break;
+	}
+	if (check)
+	{
+		// members that must be defined
+		if (only_counter_ions_defined == false)
+		{
+			parser.incr_input_error();
+			parser.
+				error_msg("Only_counter_ions not defined for SURFACE_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (thickness_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Thickness not defined for SURFACE_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (type_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Surface type not defined for SURFACE_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (dl_type_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Dl_type not defined for SURFACE_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (sites_units_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Sites_units not defined for SURFACE_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (debye_lengths_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Debye_lengths not defined for SURFACE_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (DDL_viscosity_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("DDL_viscosity not defined for SURFACE_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (DDL_limit_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("DDL_limit not defined for SURFACE_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (transport_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Transport not defined for SURFACE_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+	}
+	this->Sort_comps();
+}
+
+void
+cxxSurface::totalize()
+{
+	this->totals.clear();
+	// component structures
+	for (size_t i = 0; i != this->surface_comps.size(); i++)
+	{
+		cxxSurfaceComp * comp_ptr = &(this->surface_comps[i]);
+		this->totals.add_extensive(comp_ptr->Get_totals(), 1.0);
+		this->totals.add("Charge", comp_ptr->Get_charge_balance());
+	}
+	return;
+}
+void
+cxxSurface::add(const cxxSurface & addee_in, LDBLE extensive)
+		//
+		// Add surface to "this" surface
+		//
+{
+	cxxSurface addee = addee_in;
+	if (extensive == 0.0)
+		return;
+	if (this->surface_comps.size() == 0)
+	{
+		this->only_counter_ions = addee.only_counter_ions;
+		this->dl_type = addee.dl_type;
+		this->type = addee.type;
+		this->sites_units = addee.sites_units;
+		this->thickness = addee.thickness;
+		this->debye_lengths = addee.debye_lengths;
+		this->DDL_viscosity = addee.DDL_viscosity;
+		this->DDL_limit = addee.DDL_limit;
+		this->solution_equilibria = addee.solution_equilibria;
+		this->n_solution = addee.n_solution;
+		this->transport = addee.transport;
+	}
+
+	for (size_t i_add = 0; i_add < addee.Get_surface_comps().size(); i_add++)
+	{
+		const cxxSurfaceComp & comp_add_ptr = addee.Get_surface_comps()[i_add];
+		size_t i_this;
+		for (i_this = 0; i_this < this->surface_comps.size(); i_this++)
+		{
+			cxxSurfaceComp & comp_this_ptr = this->surface_comps[i_this];
+			if(comp_add_ptr.Get_formula() == comp_this_ptr.Get_formula())
+			{
+				comp_this_ptr.add(addee.surface_comps[i_add], extensive);
+				break;
+			}
+		}
+		if (i_this == this->surface_comps.size())
+		{
+			
+			cxxSurfaceComp entity = comp_add_ptr;
+			entity.multiply(extensive);
+			this->surface_comps.push_back(entity);
+		}
+	}
+	for (size_t i_add = 0; i_add < addee.Get_surface_charges().size(); i_add++)
+	{
+		const cxxSurfaceCharge & charge_add_ptr = addee.Get_surface_charges()[i_add];
+
+		size_t i_this;
+		for (i_this = 0; i_this < this->surface_charges.size(); i_this++)
+		{
+			cxxSurfaceCharge & charge_this_ptr = this->Get_surface_charges()[i_this];
+			if(charge_add_ptr.Get_name() == charge_this_ptr.Get_name())
+			{
+				charge_this_ptr.add(addee.surface_charges[i_add], extensive);
+				break;
+			}
+		}
+		if (i_this == this->surface_charges.size())
+		{
+			
+			cxxSurfaceCharge entity = charge_add_ptr;
+			entity.multiply(extensive);
+			this->surface_charges.push_back(entity);
+		}
+	}
+}
+
+void
+cxxSurface::multiply(LDBLE extensive)
+		//
+		// Add surface to "this" surface
+		//
+{
+
+	for (size_t i = 0; i < this->surface_comps.size(); i++)
+	{
+		cxxSurfaceComp *comp_ptr = &(this->surface_comps[i]);
+		comp_ptr->multiply(extensive);
+	}
+	for (size_t i = 0; i < this->surface_charges.size(); i++)
+	{
+		cxxSurfaceCharge *charge_ptr = &(this->surface_charges[i]);
+		charge_ptr->multiply(extensive);
+	}
+}
+cxxSurfaceComp * cxxSurface::
+Find_comp(std::string str)
+{
+		for (size_t i = 0; i < this->surface_comps.size(); i++)
+		{
+			if (Utilities::strcmp_nocase(str.c_str(), this->surface_comps[i].Get_formula().c_str()) == 0)
+				return &(this->surface_comps[i]);
+		}
+		return NULL;
+}
+
+cxxSurfaceCharge * cxxSurface::
+Find_charge(std::string str)
+{
+	for (size_t i = 0; i < this->surface_charges.size(); i++)
+	{
+		if (Utilities::strcmp_nocase(str.c_str(), this->surface_charges[i].Get_name().c_str()) == 0)
+			return &(this->surface_charges[i]);
+	}
+	return NULL;
+}
+const cxxSurfaceCharge * cxxSurface::
+Find_charge(std::string str)const
+{
+	for (size_t i = 0; i < this->surface_charges.size(); i++)
+	{
+		if (Utilities::strcmp_nocase(str.c_str(), this->surface_charges[i].Get_name().c_str()) == 0)
+			return &(this->surface_charges[i]);
+	}
+	return NULL;
+}
+void cxxSurface::
+Sort_comps(void)
+{
+	// sort comps
+	{
+		std::map<std::string, cxxSurfaceComp> comp_map;
+		for (size_t i = 0; i < this->surface_comps.size(); i++)
+		{
+			comp_map[this->surface_comps[i].Get_formula()] = this->surface_comps[i];
+		}
+		this->surface_comps.clear();
+		std::map<std::string, cxxSurfaceComp>::iterator it;
+		for (it = comp_map.begin(); it != comp_map.end(); it++)
+		{
+			this->surface_comps.push_back(it->second);
+		}
+	}
+
+	// sort charge too
+	{
+		std::map<std::string, cxxSurfaceCharge> charge_map;
+		for (size_t i = 0; i < this->surface_charges.size(); i++)
+		{
+			charge_map[this->surface_charges[i].Get_name()] = this->surface_charges[i];
+		}
+		this->surface_charges.clear();
+		std::map<std::string, cxxSurfaceCharge>::iterator it;
+		for (it = charge_map.begin(); it != charge_map.end(); it++)
+		{
+			this->surface_charges.push_back(it->second);
+		}
+	}
+}
+/* ---------------------------------------------------------------------- */
+void
+cxxSurface::Serialize(Dictionary & dictionary, std::vector < int >&ints, 
+	std::vector < double >&doubles)
+/* ---------------------------------------------------------------------- */
+{
+
+	ints.push_back(this->n_user);
+	ints.push_back((int) this->surface_comps.size());
+	{
+		for (size_t i = 0; i < this->surface_comps.size(); i++)
+		{
+			surface_comps[i].Serialize(dictionary, ints, doubles);
+		}	
+	}
+	ints.push_back((int) this->surface_charges.size());
+	{
+		for (size_t i = 0; i < 	this->surface_charges.size(); i++)
+		{
+			surface_charges[i].Serialize(dictionary, ints, doubles);
+		}
+	}
+	ints.push_back(this->new_def ? 1 : 0);
+	ints.push_back((int) this->type);
+	ints.push_back((int) this->dl_type);
+	ints.push_back((int) this->sites_units);
+	ints.push_back(this->only_counter_ions ? 1 : 0);
+	doubles.push_back(this->thickness);
+	doubles.push_back(this->debye_lengths);
+	doubles.push_back(this->DDL_viscosity);
+	doubles.push_back(this->DDL_limit);
+	ints.push_back(this->transport ? 1 : 0);
+	this->totals.Serialize(dictionary, ints, doubles);
+	ints.push_back(this->solution_equilibria ? 1 : 0);
+	ints.push_back((int) this->n_solution);
+
+}
+
+/* ---------------------------------------------------------------------- */
+void
+cxxSurface::Deserialize(Dictionary & dictionary, std::vector < int >&ints, 
+	std::vector < double >&doubles, int &ii, int &dd)
+/* ---------------------------------------------------------------------- */
+{
+	this->n_user = ints[ii++];
+	this->n_user_end = this->n_user;
+	this->description = " ";
+	{
+		int count = ints[ii++];
+		this->surface_comps.clear();
+		for (int n = 0; n < count; n++)
+		{
+			cxxSurfaceComp sc;
+			sc.Deserialize(dictionary, ints, doubles, ii, dd);
+			this->surface_comps.push_back(sc);
+		}
+	}
+	{
+		int count = ints[ii++];
+		this->surface_charges.clear();
+		for (int n = 0; n < count; n++)
+		{
+			cxxSurfaceCharge sc;
+			sc.Deserialize(dictionary, ints, doubles, ii, dd);
+			this->surface_charges.push_back(sc);
+		}
+	}
+	this->new_def = (ints[ii++] != 0);
+	this->type = (SURFACE_TYPE) ints[ii++];
+	this->dl_type = (DIFFUSE_LAYER_TYPE) ints[ii++];
+	this->sites_units = (SITES_UNITS) ints[ii++];
+	this->only_counter_ions = (ints[ii++] != 0);
+	this->thickness = doubles[dd++];
+	this->debye_lengths = doubles[dd++];
+	this->DDL_viscosity = doubles[dd++];
+	this->DDL_limit = doubles[dd++];
+	this->transport = (ints[ii++] != 0);
+	this->totals.Deserialize(dictionary, ints, doubles, ii, dd);
+	this->solution_equilibria = (ints[ii++] != 0);
+	this->n_solution = ints[ii++];
+
+}
+
+
+const std::vector< std::string >::value_type temp_vopts[] = {
+	std::vector< std::string >::value_type("diffuse_layer"),	    // 0 
+	std::vector< std::string >::value_type("edl"),	                // 1 
+	std::vector< std::string >::value_type("only_counter_ions"),	// 2 
+	std::vector< std::string >::value_type("donnan"),	            // 3 
+	std::vector< std::string >::value_type("thickness"),	        // 4 
+	std::vector< std::string >::value_type("component"),	        // 5
+	std::vector< std::string >::value_type("charge_component"),	    // 6 
+	std::vector< std::string >::value_type("type "),	            // 7
+	std::vector< std::string >::value_type("dl_type"),	            // 8 
+	std::vector< std::string >::value_type("sites_units"),	        // 9 
+	std::vector< std::string >::value_type("debye_lengths"),	    // 10
+	std::vector< std::string >::value_type("ddl_viscosity"),	    // 11
+	std::vector< std::string >::value_type("ddl_limit"),	        // 12
+	std::vector< std::string >::value_type("transport"),	        // 13
+	std::vector< std::string >::value_type("new_def"),	            // 14
+	std::vector< std::string >::value_type("solution_equilibria"),	// 15
+	std::vector< std::string >::value_type("n_solution"),	        // 16
+	std::vector< std::string >::value_type("totals") 	            // 17
+};									   
+const std::vector< std::string > cxxSurface::vopts(temp_vopts, temp_vopts + sizeof temp_vopts / sizeof temp_vopts[0]);	

src/phreeqcpp/Surface.h

@@ -0,0 +1,98 @@
+#if !defined(SURFACE_H_INCLUDED)
+#define SURFACE_H_INCLUDED
+
+#include <cassert>				// assert
+#include <map>					// std::map
+#include <string>				// std::string
+#include <list>					// std::list
+#include <vector>				// std::vector
+
+#include "NumKeyword.h"
+#include "SurfaceComp.h"
+#include "SurfaceCharge.h"
+class cxxMix;
+
+class cxxSurface:public cxxNumKeyword
+{
+
+public:
+	enum SURFACE_TYPE
+	{ UNKNOWN_DL, NO_EDL, DDL, CD_MUSIC, CCM };
+	enum DIFFUSE_LAYER_TYPE
+	{ NO_DL, BORKOVEK_DL, DONNAN_DL };
+	enum SITES_UNITS
+	{ SITES_ABSOLUTE, SITES_DENSITY };
+
+	cxxSurface(PHRQ_io *io=NULL);
+	cxxSurface(std::map < int, cxxSurface > &entity_map, cxxMix & mx,
+				 int n_user, PHRQ_io *io=NULL);
+	~cxxSurface();
+
+	//void dump_xml(std::ostream & os, unsigned int indent = 0) const;
+	void dump_raw(std::ostream & s_oss, unsigned int indent, int *n_out=NULL) const;
+	void read_raw(CParser & parser, bool check = true);
+	bool Get_related_phases(void) const;
+	bool Get_related_rate(void) const;
+	void totalize();
+	cxxSurfaceComp *Find_comp(std::string str);
+	cxxSurfaceCharge *Find_charge(const std::string str);
+	const cxxSurfaceCharge *Find_charge(const std::string str)const;
+	void Sort_comps();
+
+	void add(const cxxSurface & addee, LDBLE extensive);
+	void multiply(LDBLE extensive);
+
+	std::vector < cxxSurfaceComp > & Get_surface_comps() {return this->surface_comps;}
+	const std::vector < cxxSurfaceComp > & Get_surface_comps()const {return this->surface_comps;}
+	void Set_surface_comps(std::vector < cxxSurfaceComp > &sc) {this->surface_comps = sc;}
+	std::vector < cxxSurfaceCharge > & Get_surface_charges() {return this->surface_charges;}
+	void Set_surface_charges(std::vector < cxxSurfaceCharge > &sc) {this->surface_charges = sc;}
+	bool Get_new_def(void) {return new_def;}
+	void Set_new_def(bool tf) {new_def = tf;}
+	SURFACE_TYPE Get_type(void) const {return this->type;}
+	void Set_type(SURFACE_TYPE t) {this->type = t;}
+	DIFFUSE_LAYER_TYPE Get_dl_type(void) const {return dl_type;}
+	void Set_dl_type(DIFFUSE_LAYER_TYPE t) {dl_type = t;}
+	SITES_UNITS Get_sites_units(void) const {return sites_units;}
+	void Set_sites_units(SITES_UNITS u) {sites_units = u;}
+	bool Get_only_counter_ions(void) const {return only_counter_ions;}
+	void Set_only_counter_ions(bool tf) {only_counter_ions = tf;}
+	LDBLE Get_thickness(void) const {return thickness;}
+	void Set_thickness(LDBLE t) {thickness = t;}
+	LDBLE Get_debye_lengths(void) const {return debye_lengths;}
+	void Set_debye_lengths(LDBLE t) {debye_lengths = t;}
+	LDBLE Get_DDL_viscosity(void) const {return DDL_viscosity;}
+	void Set_DDL_viscosity(LDBLE t) {DDL_viscosity = t;}
+	LDBLE Get_DDL_limit(void) const {return DDL_limit;}
+	void Set_DDL_limit(LDBLE t) {DDL_limit = t;}
+	bool Get_transport(void) const {return transport;}
+	void Set_transport(bool tf) {transport = tf;}
+	cxxNameDouble & Get_totals() {return this->totals;}
+	void Get_totals(cxxNameDouble &nd) {this->totals = nd;}
+	bool Get_solution_equilibria(void)const {return solution_equilibria;}
+	void Set_solution_equilibria(bool tf) {solution_equilibria = tf;}
+	int Get_n_solution(void)const {return n_solution;}
+	void Set_n_solution(int i) {n_solution = i;}
+	void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
+	void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
+	
+protected:
+	std::vector < cxxSurfaceComp > surface_comps;
+	std::vector < cxxSurfaceCharge > surface_charges;
+	bool new_def;
+	SURFACE_TYPE type;
+	DIFFUSE_LAYER_TYPE dl_type;
+	SITES_UNITS sites_units;
+	bool only_counter_ions;
+	LDBLE thickness;
+	LDBLE debye_lengths;
+	LDBLE DDL_viscosity;
+	LDBLE DDL_limit;
+	bool transport;
+	cxxNameDouble totals;
+	bool solution_equilibria;
+	int n_solution;
+	const static std::vector < std::string > vopts;
+};
+
+#endif // !defined(SURFACE_H_INCLUDED)

src/phreeqcpp/SurfaceCharge.cxx

@@ -0,0 +1,579 @@
+// SurfaceCharge.cxx: implementation of the cxxSurfaceCharge class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <cassert>				// assert
+#include <algorithm>			// std::sort
+
+#include "Utils.h"				// define first
+#include "Phreeqc.h"
+#include "SurfaceCharge.h"
+#include "phqalloc.h"
+#include "Dictionary.h"
+
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+cxxSurfaceCharge::cxxSurfaceCharge(PHRQ_io *io)
+:
+PHRQ_base(io)
+//
+// default constructor for cxxSurfaceCharge 
+//
+{
+	specific_area = 0.0;
+	grams = 0.0;
+	charge_balance = 0.0;
+	mass_water = 0.0;
+	la_psi = 0.0;
+	capacitance[0] = 1.0;
+	capacitance[1] = 5.0;
+	sigma0 = sigma1 = sigma2 = sigmaddl = 0;
+	diffuse_layer_totals.type = cxxNameDouble::ND_ELT_MOLES;
+}
+cxxSurfaceCharge::~cxxSurfaceCharge()
+{
+}
+
+void
+cxxSurfaceCharge::dump_xml(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// Surf_Charge element and attributes
+	s_oss << indent0 << "name=\"" << this->name << "\"" << "\n";
+	s_oss << indent0 << "specific_area=\"" << this->
+		specific_area << "\"" << "\n";
+	s_oss << indent0 << "grams=\"" << this->grams << "\"" << "\n";
+	s_oss << indent0 << "charge_balance=\"" << this->
+		charge_balance << "\"" << "\n";
+	s_oss << indent0 << "mass_water=\"" << this->
+		mass_water << "\"" << "\n";
+	s_oss << indent0 << "la_psi=\"" << this->la_psi << "\"" << "\n";
+	s_oss << indent0 << "capacitance=\"" << this->
+		capacitance[0] << " " << this->capacitance[0] << "\"" << "\n";
+
+	// totals
+	s_oss << indent0;
+	s_oss << "<diffuse_layer_totals " << "\n";
+	this->diffuse_layer_totals.dump_xml(s_oss, indent + 1);
+
+}
+
+void
+cxxSurfaceCharge::dump_raw(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// Surf_Charge element and attributes
+	s_oss << indent0 << "# SURFACE_MODIFY candidate identifiers #\n";
+	s_oss << indent0 << "-specific_area           " << this->specific_area << "\n";
+	s_oss << indent0 << "-grams                   " << this->grams << "\n";
+	s_oss << indent0 << "-charge_balance          " << this->charge_balance << "\n";
+	s_oss << indent0 << "-mass_water              " << this->mass_water << "\n";
+	s_oss << indent0 << "-la_psi                  " << this->la_psi << "\n";
+	s_oss << indent0 << "-capacitance0            " << this->capacitance[0] << "\n";
+	s_oss << indent0 << "-capacitance1            " << this->capacitance[1] << "\n";
+	// totals
+	s_oss << indent0;
+	s_oss << "-diffuse_layer_totals" << "\n";
+	this->diffuse_layer_totals.dump_raw(s_oss, indent + 1);
+
+	// DL species
+	//s_oss << indent0;
+	//s_oss << "-diffuse_layer_species" << "\n";
+	if (dl_species_map.size() > 0)
+	{
+		s_oss << indent0;
+		s_oss << "-diffuse_layer_species" << "\n";
+		std::map<int, double>::const_iterator it = this->dl_species_map.begin();
+		for ( ; it != dl_species_map.end(); it++)
+		{
+			s_oss << indent1;
+			s_oss << it->first << " " << it->second << "\n";
+		}
+	}
+	s_oss << indent0 << "# Surface workspace variables #\n";
+	s_oss << indent0 << "-sigma0                  " << this->sigma0 << "\n";
+	s_oss << indent0 << "-sigma1                  " << this->sigma1 << "\n";
+	s_oss << indent0 << "-sigma2                  " << this->sigma2 << "\n";
+	s_oss << indent0 << "-sigmaddl                " << this->sigmaddl << "\n";
+	std::map<LDBLE, cxxSurfDL>::const_iterator git;
+	for (git = this->g_map.begin(); git != g_map.end(); git++)
+	{
+		s_oss << indent0 << "-g_map                   " << git->first << "\t";
+		s_oss << git->second.Get_g() << "\t";
+		s_oss << git->second.Get_dg() << "\t";
+		s_oss << git->second.Get_psi_to_z() << "\n";
+	}
+}
+
+void
+cxxSurfaceCharge::read_raw(CParser & parser, bool check)
+{
+	std::string str;
+
+
+	std::istream::pos_type ptr;
+	std::istream::pos_type next_char;
+	std::string token;
+	int opt_save;
+
+	opt_save = CParser::OPT_ERROR;
+	bool specific_area_defined(false);
+	bool grams_defined(false);
+	bool charge_balance_defined(false);
+	bool mass_water_defined(false);
+	bool la_psi_defined(false);
+	bool capacitance0_defined(false);
+	bool capacitance1_defined(false);
+	bool g_map_first(true);
+
+	for (;;)
+	{
+		int opt = parser.get_option(vopts, next_char);
+		if (opt == CParser::OPT_DEFAULT)
+		{
+			opt = opt_save;
+		}
+
+		switch (opt)
+		{
+		case CParser::OPT_EOF:
+			break;
+		case CParser::OPT_KEYWORD:
+			break;
+		case CParser::OPT_DEFAULT:
+		case CParser::OPT_ERROR:
+			opt = CParser::OPT_KEYWORD;
+			// Allow return to Surface for more processing
+			break;
+
+		case 0:				// name
+			warning_msg("-name ignored. Defined with -charge_component.");
+			break;
+
+		case 1:				// specific_area
+			if (!(parser.get_iss() >> this->specific_area))
+			{
+				this->specific_area = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for specific_area.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			specific_area_defined = true;
+			break;
+
+		case 2:				// grams
+			if (!(parser.get_iss() >> this->grams))
+			{
+				this->grams = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for grams.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			grams_defined = true;
+			break;
+
+
+		case 3:				// charge_balance
+			if (!(parser.get_iss() >> this->charge_balance))
+			{
+				this->charge_balance = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for charge_balance.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			charge_balance_defined = true;
+			break;
+
+		case 4:				// mass_water
+			if (!(parser.get_iss() >> this->mass_water))
+			{
+				this->mass_water = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for mass_water.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			mass_water_defined = true;
+			break;
+
+
+		case 5:				// la_psi
+			if (!(parser.get_iss() >> this->la_psi))
+			{
+				this->la_psi = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for la_psi.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			la_psi_defined = true;
+			break;
+
+
+		case 6:				// diffuse_layer_totals
+			if (this->diffuse_layer_totals.read_raw(parser, next_char) !=
+				CParser::PARSER_OK)
+			{
+				parser.incr_input_error();
+				parser.
+					error_msg
+					("Expected element name and molality for SurfaceCharge diffuse_layer_totals.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = 6;
+			break;
+
+		case 7:				// la_psi1
+			parser.warning_msg("-la_psi1 identifier not used");
+			break;
+
+		case 8:				// la_psi2
+			parser.warning_msg("-la_psi2 identifier not used");
+			break;
+
+		case 9:				// capacitance0
+			if (!(parser.get_iss() >> this->capacitance[0]))
+			{
+				this->capacitance[0] = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for capacitance0.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			capacitance0_defined = true;
+			break;
+
+		case 10:				// capacitance1
+			if (!(parser.get_iss() >> this->capacitance[1]))
+			{
+				this->capacitance[1] = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for capacitance1.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			capacitance1_defined = true;
+			break;
+		case 11:				// sigma0
+			if (!(parser.get_iss() >> this->sigma0))
+			{
+				this->sigma0 = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for sigma0.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			break;
+		case 12:				// sigma1
+			if (!(parser.get_iss() >> this->sigma1))
+			{
+				this->sigma1 = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for sigma1.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			break;
+		case 13:				// sigma2
+			if (!(parser.get_iss() >> this->sigma2))
+			{
+				this->sigma2 = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for sigma2.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			break;
+		case 14:				// sigmaddl
+			if (!(parser.get_iss() >> this->sigmaddl))
+			{
+				this->sigmaddl = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for sigmaddl.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			break;
+		case 15:				// g_map
+			{
+				if (g_map_first)
+				{
+					this->g_map.clear();
+					g_map_first = false;
+				}
+				LDBLE z, dummy;
+				if (!(parser.get_iss() >> z))
+					break;
+				cxxSurfDL temp_surf_dl;
+				this->g_map[z] = temp_surf_dl;
+				std::map<LDBLE, cxxSurfDL>::iterator git = g_map.find(z);
+				if (!(parser.get_iss() >> dummy))
+					break;
+				else
+					git->second.Set_g(dummy);
+				if (!(parser.get_iss() >> dummy))
+					break;
+				else
+					git->second.Set_dg(dummy);
+				if (!(parser.get_iss() >> dummy))
+					break;
+				else
+					git->second.Set_psi_to_z(dummy);
+			}
+			break;
+		case 16:				// dl_species_map
+			int s_num;
+			if (parser.peek_token() != CParser::TT_EMPTY)
+			{
+				if (!(parser.get_iss() >> s_num))
+				{
+					parser.incr_input_error();
+					parser.error_msg("Expected integer for species number.",
+						PHRQ_io::OT_CONTINUE);
+				}
+				else
+				{
+					double d; 
+					if (!(parser.get_iss() >> d))
+					{
+						parser.incr_input_error();
+						parser.error_msg("Expected double for species concentration.",
+							PHRQ_io::OT_CONTINUE);
+					}
+					this->dl_species_map[s_num] = d;
+				}
+			}
+			opt_save = 16;
+
+
+
+			break;
+		}
+		if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
+			break;
+	}
+	if (check)
+	{
+		// members that must be defined
+		if (specific_area_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Specific_area not defined for SurfaceCharge input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (grams_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Grams not defined for SurfaceCharge input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (charge_balance_defined == false)
+		{
+			parser.incr_input_error();
+			parser.
+				error_msg("Charge_balance not defined for SurfaceCharge input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (mass_water_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Mass_water not defined for SurfaceCharge input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (la_psi_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("La_psi not defined for SurfaceCharge input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (capacitance0_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Capacitance0 not defined for SurfaceCharge input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (capacitance1_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Capacitance1 not defined for SurfaceCharge input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+	}
+}
+
+void
+cxxSurfaceCharge::add(const cxxSurfaceCharge & addee, LDBLE extensive)
+{
+	if (extensive == 0.0)
+		return;
+
+	if (this->name.size() == 0 && addee.name.size() == 0)
+	{
+		return;
+	}
+	assert(this->name == addee.name);
+
+	LDBLE ext1, ext2, f1, f2;
+	ext1 = this->specific_area * this->grams;
+	ext2 = addee.specific_area * addee.grams * extensive;
+	if (ext1 + ext2 != 0)
+	{
+		f1 = ext1 / (ext1 + ext2);
+		f2 = ext2 / (ext1 + ext2);
+	}
+	else
+	{
+		f1 = 0.5;
+		f2 = 0.5;
+	}
+	this->specific_area = f1 * this->specific_area + f2 * addee.specific_area;
+	this->grams += addee.grams * extensive;
+	this->charge_balance += addee.charge_balance * extensive;
+	this->mass_water += addee.mass_water * extensive;
+	this->la_psi = this->la_psi * f1 + addee.la_psi * f2;
+	this->capacitance[0] =
+		this->capacitance[0] * f1 + this->capacitance[0] * f2;
+	this->capacitance[1] =
+		this->capacitance[1] * f1 + this->capacitance[1] * f2;
+	this->diffuse_layer_totals.add_extensive(addee.diffuse_layer_totals, extensive);
+}
+
+void
+cxxSurfaceCharge::multiply(LDBLE extensive)
+{
+	this->grams *= extensive;
+	this->charge_balance *= extensive;
+	this->mass_water *= extensive;
+	this->diffuse_layer_totals.multiply(extensive);
+}
+void
+cxxSurfaceCharge::Serialize(Dictionary & dictionary, std::vector < int >&ints, 
+	std::vector < double >&doubles)
+{
+
+	ints.push_back(dictionary.Find(this->name));
+	doubles.push_back(this->specific_area);
+	doubles.push_back(this->grams);
+	doubles.push_back(this->charge_balance);
+	doubles.push_back(this->mass_water);
+	doubles.push_back(this->la_psi);
+	doubles.push_back(this->capacitance[0]);
+	doubles.push_back(this->capacitance[1]);
+	this->diffuse_layer_totals.Serialize(dictionary, ints, doubles);
+	doubles.push_back(this->sigma0);
+	doubles.push_back(this->sigma1);
+	doubles.push_back(this->sigma2);
+	doubles.push_back(this->sigmaddl);
+	ints.push_back((int) this->g_map.size());
+	{
+		std::map<LDBLE, cxxSurfDL>::iterator it;
+		for (it = this->g_map.begin(); it != this->g_map.end(); it++) 
+		{
+			doubles.push_back(it->first);
+			it->second.Serialize(dictionary, ints, doubles);
+		}
+	}
+	ints.push_back((int) this->dl_species_map.size());
+	{
+		std::map<int, double>::iterator it;
+		for (it = this->dl_species_map.begin(); it != this->dl_species_map.end(); it++) 
+		{
+			ints.push_back(it->first);
+			doubles.push_back(it->second);
+		}
+	}
+}
+
+void
+cxxSurfaceCharge::Deserialize(Dictionary & dictionary, std::vector < int >&ints, 
+	std::vector < double >&doubles, int &ii, int &dd)
+{
+	this->name = dictionary.GetWords()[ints[ii++]];
+	this->specific_area = doubles[dd++];
+	this->grams = doubles[dd++];
+	this->charge_balance = doubles[dd++];
+	this->mass_water = doubles[dd++];
+	this->la_psi = doubles[dd++];
+	this->capacitance[0] = doubles[dd++];
+	this->capacitance[1] = doubles[dd++];
+	this->diffuse_layer_totals.Deserialize(dictionary, ints, doubles, ii, dd);
+	this->sigma0 = doubles[dd++];
+	this->sigma1 = doubles[dd++];
+	this->sigma2 = doubles[dd++];
+	this->sigmaddl = doubles[dd++];
+	{
+		this->g_map.clear();
+		int count = ints[ii++];
+		for (int i = 0; i < count; i++)
+		{
+			double d = doubles[dd++];
+			cxxSurfDL sdl;
+			sdl.Deserialize(dictionary, ints, doubles, ii, dd);
+			this->g_map[d] = sdl;
+		}
+	}
+	{
+		this->dl_species_map.clear();
+		int count = ints[ii++];
+		for (int i = 0; i < count; i++)
+		{
+			int j = ints[ii++];
+			double d = doubles[dd++];
+			dl_species_map[j] = d;
+		}
+	}
+
+
+}
+void
+cxxSurfDL::Serialize(Dictionary & dictionary, std::vector < int >&ints, 
+	std::vector < double >&doubles)
+{
+	doubles.push_back(this->g);
+	doubles.push_back(this->dg);
+	doubles.push_back(this->psi_to_z);
+}
+
+void
+cxxSurfDL::Deserialize(Dictionary & dictionary, std::vector < int >&ints, 
+	std::vector < double >&doubles, int &ii, int &dd)
+{
+	this->g = doubles[dd++];
+	this->dg = doubles[dd++];
+	this->psi_to_z = doubles[dd++];
+}
+const std::vector< std::string >::value_type temp_vopts[] = {
+	std::vector< std::string >::value_type("name"),	                // 0 
+	std::vector< std::string >::value_type("specific_area"),	    // 1 
+	std::vector< std::string >::value_type("grams"),	            // 2 
+	std::vector< std::string >::value_type("charge_balance"),	    // 3 
+	std::vector< std::string >::value_type("mass_water"),	        // 4 
+	std::vector< std::string >::value_type("la_psi"),	            // 5 
+	std::vector< std::string >::value_type("diffuse_layer_totals"),	// 6 
+	std::vector< std::string >::value_type("la_psi1"),	            // 7 
+	std::vector< std::string >::value_type("la_psi2"),	            // 8 
+	std::vector< std::string >::value_type("capacitance0"),	        // 9 
+	std::vector< std::string >::value_type("capacitance1"),	        // 10 
+	std::vector< std::string >::value_type("sigma0"),	            // 11 
+	std::vector< std::string >::value_type("sigma1"),	            // 12 
+	std::vector< std::string >::value_type("sigma2"),	            // 13 
+	std::vector< std::string >::value_type("sigmaddl"),	            // 14
+	std::vector< std::string >::value_type("g_map"),	            // 15
+	std::vector< std::string >::value_type("diffuse_layer_species") // 16
+};									   
+const std::vector< std::string > cxxSurfaceCharge::vopts(temp_vopts, temp_vopts + sizeof temp_vopts / sizeof temp_vopts[0]);	

src/phreeqcpp/SurfaceCharge.h

@@ -0,0 +1,131 @@
+#if !defined(SURFACECHARGE_H_INCLUDED)
+#define SURFACECHARGE_H_INCLUDED
+
+#include <cassert>				// assert
+#include <map>					// std::map
+#include <string>				// std::string
+#include <list>					// std::list
+#include <vector>				// std::vector
+
+#include "NameDouble.h"
+#include "PHRQ_base.h"
+class cxxSpeciesDL
+{
+public:
+	cxxSpeciesDL()
+	{
+		g_moles = dg_g_moles = dx_moles = dh2o_moles = drelated_moles = 0;
+	}
+	LDBLE Get_g_moles(void) const {return g_moles;}
+	void Set_g_moles(LDBLE t) {g_moles = t;}
+	LDBLE Get_dg_g_moles(void) const {return dg_g_moles;}
+	void Set_dg_g_moles(LDBLE t) {dg_g_moles = t;}
+	LDBLE Get_dx_moles(void) const {return dx_moles;}
+	void Set_dx_moles(LDBLE t) {dx_moles = t;}
+	LDBLE Get_dh2o_moles(void) const {return dh2o_moles;}
+	void Set_dh2o_moles(LDBLE t) {dh2o_moles = t;}
+	LDBLE Get_drelated_moles(void) const {return drelated_moles;}
+	void Set_drelated_moles(LDBLE t) {drelated_moles = t;}
+
+	LDBLE *Get_g_moles_address(void) {return &g_moles;}
+	LDBLE *Get_dg_g_moles_address(void) {return &dg_g_moles;}
+	LDBLE *Get_dx_moles_address(void) {return &dx_moles;}
+	LDBLE *Get_dh2o_moles_address(void) {return &dh2o_moles;}
+	LDBLE *Get_drelated_moles_address(void) {return &drelated_moles;}
+	
+protected:
+	LDBLE g_moles;
+	LDBLE dg_g_moles;			/* g_moles*dgterm */
+	LDBLE dx_moles;
+	LDBLE dh2o_moles;			/* moles*g*Ws/Waq */
+	LDBLE drelated_moles;		/* for related phase */
+};
+class cxxSurfDL
+{
+public:
+	cxxSurfDL()
+	{
+		g = dg = psi_to_z = 0;
+	}
+	LDBLE Get_g(void) const {return g;}
+	void Set_g(LDBLE t) {g = t;}
+	LDBLE Get_dg(void) const {return dg;}
+	void Set_dg(LDBLE t) {dg = t;}
+	LDBLE Get_psi_to_z(void) const {return psi_to_z;}
+	void Set_psi_to_z(LDBLE t) {psi_to_z = t;}
+	void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
+	void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
+	
+protected:
+	LDBLE g;
+	LDBLE dg;
+	LDBLE psi_to_z;
+};
+class cxxSurfaceCharge: public PHRQ_base
+{
+
+public:
+
+	cxxSurfaceCharge(PHRQ_io *io=NULL);
+	cxxSurfaceCharge(struct surface_charge *, PHRQ_io *io=NULL);
+	virtual ~cxxSurfaceCharge();
+
+	struct master *Get_psi_master();
+	void dump_xml(std::ostream & os, unsigned int indent = 0) const;
+	void dump_raw(std::ostream & s_oss, unsigned int indent) const;
+	void read_raw(CParser & parser, bool check = true);
+	void add(const cxxSurfaceCharge & comp, LDBLE extensive);
+	void multiply(LDBLE extensive);
+
+	const std::string &Get_name() const	{return this->name;}
+	void Set_name(const char * f) {this->name = f ? f : "";}
+	LDBLE Get_specific_area() const {return this->specific_area;}
+	void Set_specific_area(LDBLE d) {this->specific_area = d;}
+	LDBLE Get_grams() const {return this->grams;}
+	void Set_grams(LDBLE d) {this->grams = d;}
+	LDBLE Get_charge_balance() const {return this->charge_balance;}
+	void Set_charge_balance(LDBLE d) {this->charge_balance = d;}
+	LDBLE Get_mass_water() const {return this->mass_water;}
+	void Set_mass_water(LDBLE d) {this->mass_water = d;}
+	LDBLE Get_la_psi() const {return this->la_psi;}
+	void Set_la_psi(LDBLE d) {this->la_psi = d;}
+	LDBLE Get_capacitance0() const {return this->capacitance[0];}
+	void Set_capacitance0(LDBLE d) {this->capacitance[0] = d;}
+	LDBLE Get_capacitance1() const {return this->capacitance[1];}
+	void Set_capacitance1(LDBLE d) {this->capacitance[1] = d;}
+	LDBLE Get_sigma0() const {return this->sigma0;}
+	void Set_sigma0(LDBLE d) {this->sigma0 = d;}
+	LDBLE Get_sigma1() const {return this->sigma1;}
+	void Set_sigma1(LDBLE d) {this->sigma1 = d;}
+	LDBLE Get_sigma2() const {return this->sigma2;}
+	void Set_sigma2(LDBLE d) {this->sigma2 = d;}
+	LDBLE Get_sigmaddl() const {return this->sigmaddl;}
+	void Set_sigmaddl(LDBLE d) {this->sigmaddl = d;}
+	cxxNameDouble & Get_diffuse_layer_totals(void) { return this->diffuse_layer_totals; }
+	const cxxNameDouble & Get_diffuse_layer_totals(void)const { return this->diffuse_layer_totals; }
+	void Set_diffuse_layer_totals(cxxNameDouble & nd) {this->diffuse_layer_totals = nd;}
+	std::map<LDBLE, cxxSurfDL> &Get_g_map(void) {return g_map;}
+	void Set_g_map(std::map<LDBLE, cxxSurfDL> & t) {g_map = t;}
+	std::map<LDBLE, LDBLE> &Get_z_gMCD_map(void) { return z_gMCD_map; } // z, exp(-zF Psi / RT) * fraction of dl water
+	std::map<int, double> & Get_dl_species_map(void)       {return this->dl_species_map;}
+	void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
+	void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
+
+protected:
+	std::string name;
+	LDBLE specific_area;
+	LDBLE grams;
+	LDBLE charge_balance;
+	LDBLE mass_water;
+	LDBLE la_psi;
+	LDBLE capacitance[2];
+	cxxNameDouble diffuse_layer_totals;
+	// workspace variables
+	LDBLE sigma0, sigma1, sigma2, sigmaddl;
+	std::map<LDBLE, cxxSurfDL> g_map;
+	std::map<LDBLE, LDBLE> z_gMCD_map;
+	const static std::vector < std::string > vopts;
+	std::map<int, double> dl_species_map;
+};
+
+#endif // !defined(SURFACECHARGE_H_INCLUDED)

src/phreeqcpp/SurfaceComp.cxx

@@ -0,0 +1,499 @@
+// SurfaceComp.cxx: implementation of the cxxSurfaceComp class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <cassert>				// assert
+#include <algorithm>			// std::sort
+
+#include "Utils.h"				// define first
+#include "Phreeqc.h"
+#include "SurfaceComp.h"
+#include "phqalloc.h"
+#include "Dictionary.h"
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+cxxSurfaceComp::cxxSurfaceComp(PHRQ_io *io)
+:
+PHRQ_base(io)
+//
+// default constructor for cxxSurfaceComp 
+//
+{
+	formula_z = 0.0;
+	moles = 0.0;
+	totals.type = cxxNameDouble::ND_ELT_MOLES;
+	la = 0.0;
+	charge_balance = 0;
+	phase_proportion = 0.0;
+	Dw = 0.0;
+}
+cxxSurfaceComp::~cxxSurfaceComp()
+{
+}
+
+void
+cxxSurfaceComp::dump_xml(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// Surf_Comp element and attributes
+
+	//s_oss << indent0 << "formula=\"" << this->formula << "\"" << "\n";
+	s_oss << indent0 << "formula_z=\"" << this->formula_z << "\"" << "\n";
+	s_oss << indent0 << "moles=\"" << this->moles << "\"" << "\n";
+	s_oss << indent0 << "la=\"" << this->la << "\"" << "\n";
+	s_oss << indent0 << "charge_balance=\"" << this->charge_balance << "\"" << "\n";
+	s_oss << indent0 << "phase_proportion=\"" << this->phase_proportion << "\"" << "\n";
+	s_oss << indent0 << "Dw=\"" << this->Dw << "\"" << "\n";
+	s_oss << indent0 << "charge_name=\"" << this->charge_name << "\"" << "\n";
+	if (this->phase_name.size() != 0)
+	{
+		s_oss << indent0 << "phase_name=\"" << this->phase_name << "\"" << "\n";
+	}
+	if (this->rate_name.size() != 0)
+	{
+		s_oss << indent0 << "rate_name=\"" << this->rate_name << "\"" << "\n";
+	}
+
+	// totals
+	s_oss << indent0;
+	s_oss << "<totals " << "\n";
+	this->totals.dump_xml(s_oss, indent + 1);
+}
+
+void
+cxxSurfaceComp::dump_raw(std::ostream & s_oss, unsigned int indent) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	s_oss << indent0 << "# SURFACE_MODIFY candidate identifiers #\n";
+	s_oss << indent0 << "-formula_z               " << this->formula_z << "\n";
+	s_oss << indent0 << "-moles                   " << this->moles << "\n";
+	s_oss << indent0 << "-la                      " << this->la << "\n";
+	s_oss << indent0 << "-charge_balance          " << this->charge_balance << "\n";
+	if (this->phase_name.size() != 0)
+	{
+		s_oss << indent0 << "-phase_name              " << this->phase_name << "\n";
+	}
+	if (this->rate_name.size() != 0)
+	{
+		s_oss << indent0 << "-rate_name               " << this->rate_name << "\n";
+	}
+	s_oss << indent0 << "-phase_proportion        " << this->phase_proportion << "\n";
+	s_oss << indent0 << "-Dw                      " << this->Dw << "\n";
+	s_oss << indent0 << "-charge_name             " << this->charge_name << "\n";
+	s_oss << indent0 << "-master_element          " << this->master_element << "\n";
+	// totals
+	s_oss << indent0;
+	s_oss << "-totals" << "\n";
+	this->totals.dump_raw(s_oss, indent + 1);
+}
+
+void
+cxxSurfaceComp::read_raw(CParser & parser, bool check)
+{
+	std::string str;
+
+
+	std::istream::pos_type ptr;
+	std::istream::pos_type next_char;
+	std::string token;
+	int opt_save;
+
+	opt_save = CParser::OPT_ERROR;
+
+	bool master_element_defined(false);
+	bool charge_name_defined(false);
+	bool moles_defined(false);
+	bool la_defined(false);
+	bool charge_balance_defined(false);
+	bool formula_z_defined(false);
+	bool Dw_defined(false);
+	bool totals_defined(false);
+
+	for (;;)
+	{
+		int opt = parser.get_option(vopts, next_char);
+		if (opt == CParser::OPT_DEFAULT)
+		{
+			opt = opt_save;
+		}
+
+		switch (opt)
+		{
+		case CParser::OPT_EOF:
+			break;
+		case CParser::OPT_KEYWORD:
+			break;
+		case CParser::OPT_DEFAULT:
+		case CParser::OPT_ERROR:
+			opt = CParser::OPT_KEYWORD;
+			// Allow return to Surface for more processing
+			break;
+
+		case 0:				// formula
+			output_msg("-formula is obsolete in surface comp raw");
+			break;
+
+		case 1:				// moles
+			if (!(parser.get_iss() >> this->moles))
+			{
+				this->moles = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for moles.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			moles_defined = true;
+			break;
+
+		case 2:				// la
+			if (!(parser.get_iss() >> this->la))
+			{
+				this->la = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for la.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			la_defined = true;
+			break;
+		case 3:				// charge_number not used
+			parser.warning_msg("-charge_number identifier is obsolete.");
+			break;
+
+		case 4:				// charge_balance
+			if (!(parser.get_iss() >> this->charge_balance))
+			{
+				this->charge_balance = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for charge_balance.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			charge_balance_defined = true;
+			break;
+
+		case 5:				// phase_name
+			if (!(parser.get_iss() >> str))
+			{
+				this->phase_name.clear();
+				parser.incr_input_error();
+				parser.error_msg("Expected string value for phase_name.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			else
+			{
+				this->phase_name = str;
+			}
+			break;
+
+		case 6:				// rate_name
+			if (!(parser.get_iss() >> str))
+			{
+				this->rate_name.clear();
+				parser.incr_input_error();
+				parser.error_msg("Expected string value for rate_name.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			else
+			{
+				this->rate_name = str;
+			}
+			break;
+
+		case 7:				// phase_proportion
+			if (!(parser.get_iss() >> this->phase_proportion))
+			{
+				this->phase_proportion = 0;
+				parser.incr_input_error();
+				parser.
+					error_msg("Expected numeric value for phase_proportion.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			break;
+
+		case 8:				// totals
+			if (this->totals.read_raw(parser, next_char) !=
+				CParser::PARSER_OK)
+			{
+				parser.incr_input_error();
+				parser.
+					error_msg
+					("Expected element name and molality for SurfaceComp totals.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			totals_defined = true;
+			opt_save = 8;
+			break;
+
+		case 9:				// formula_z
+			if (!(parser.get_iss() >> this->formula_z))
+			{
+				this->formula_z = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for formula_z.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			formula_z_defined = true;
+			break;
+
+		case 10:				// formula_totals
+			parser.warning_msg("-formula_totals is an obsolete identifier.");
+			break;
+
+		case 11:				// Dw
+			if (!(parser.get_iss() >> this->Dw))
+			{
+				this->Dw = 0.0;
+				parser.incr_input_error();
+				parser.error_msg("Expected numeric value for Dw.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			Dw_defined = true;
+			break;
+		case 12:				// charge_name
+			if (!(parser.get_iss() >> str))
+			{
+				this->charge_name.clear();
+				parser.incr_input_error();
+				parser.error_msg("Expected string value for charge_name.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			else
+			{
+				this->charge_name = str;
+			}
+			charge_name_defined = true;
+			break;
+		case 13:				// master_element
+			if (!(parser.get_iss() >> str))
+			{
+				this->master_element.clear();
+				parser.incr_input_error();
+				parser.error_msg("Expected string value for master_element.",
+					PHRQ_io::OT_CONTINUE);
+			}
+			else
+			{
+				this->master_element = str;
+			}
+			master_element_defined = true;
+			break;
+		}
+		if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
+			break;
+	}
+	if (check)
+	{
+		// members that must be defined
+		if (charge_name_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Charge_name not defined for SurfaceComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (formula_z_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Formula_z not defined for ExchComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (moles_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Moles not defined for SurfaceComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (la_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("La not defined for SurfaceComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+
+		if (charge_balance_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Charge_balance not defined for SurfaceComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (Dw_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Dw not defined for SurfaceComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (master_element_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Master_element name not defined for SurfaceComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (totals_defined == false)
+		{
+			parser.incr_input_error();
+			parser.error_msg("Totals not defined for SurfaceComp input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+	}
+}
+
+void
+cxxSurfaceComp::add(const cxxSurfaceComp & addee, LDBLE extensive)
+{
+	if (extensive == 0.0)
+		return;
+	if (addee.formula.size() == 0)
+		return;
+
+	if (this->formula.size() == 0 && addee.formula.size() == 0)
+	{
+		return;
+	}
+	assert(this->formula == addee.formula);
+	assert(this->formula_z == addee.formula_z);
+	if (this->formula.size() == 0 && addee.formula.size() != 0)
+	{
+		this->formula = addee.formula;
+	}
+
+	// this and addee must have same formula
+	// otherwise generate a new exchcomp with multiply
+	LDBLE ext1, ext2, f1, f2;
+	ext1 = this->moles;
+	ext2 = addee.moles * extensive;
+	if (ext1 + ext2 != 0)
+	{
+		f1 = ext1 / (ext1 + ext2);
+		f2 = ext2 / (ext1 + ext2);
+	}
+	else
+	{
+		f1 = 0.5;
+		f2 = 0.5;
+	}
+	this->moles += addee.moles * extensive;
+	this->totals.add_extensive(addee.totals, extensive);
+	this->la = f1 * this->la + f2 * addee.la;
+	this->charge_balance += addee.charge_balance * extensive;
+	if (this->phase_name != addee.phase_name)
+	{
+		std::ostringstream oss;
+		oss <<
+			"Cannot mix two Surface components with same formula and different related phases, "
+			<< this->formula;
+		error_msg(oss.str().c_str(), CONTINUE);
+		return;
+	}
+	else if (this->phase_name.size() != 0)
+	{
+		this->phase_proportion =
+			this->phase_proportion * f1 + addee.phase_proportion * f2;
+	}
+
+	if (this->rate_name != addee.rate_name)
+	{
+		std::ostringstream oss;
+		oss <<
+			"Cannot mix two exchange components with same formula and different related kinetics, "
+			<< this->formula;
+		error_msg(oss.str().c_str(), CONTINUE);
+		return;
+	}
+	else if (this->rate_name.size() != 0)
+	{
+		//LDBLE phase_proportion;
+		this->phase_proportion =
+			this->phase_proportion * f1 + addee.phase_proportion * f2;
+	}
+	if ((this->rate_name.size() != 0 && addee.phase_name.size() != 0) ||
+		(this->phase_name.size() != 0 && addee.rate_name.size() != 0))
+	{
+		std::ostringstream oss;
+		oss <<
+			"Cannot mix exchange components related to phase with exchange components related to kinetics, "
+			<< this->formula;
+		error_msg(oss.str().c_str(), CONTINUE);
+		return;
+	}
+
+}
+void
+cxxSurfaceComp::multiply(LDBLE extensive)
+{
+	this->moles *= extensive;
+
+	this->totals.multiply(extensive);
+
+	this->charge_balance *= extensive;
+}
+void
+cxxSurfaceComp::Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles)
+{
+	ints.push_back(dictionary.Find(this->formula));
+	doubles.push_back(this->formula_z);
+	doubles.push_back(this->moles);
+	this->totals.Serialize(dictionary, ints, doubles);
+	doubles.push_back(this->la);
+	ints.push_back(dictionary.Find(this->charge_name));
+	doubles.push_back(this->charge_balance);
+	ints.push_back(dictionary.Find(this->phase_name));
+	doubles.push_back(this->phase_proportion);
+	ints.push_back(dictionary.Find(this->rate_name));
+	doubles.push_back(this->Dw);
+	ints.push_back(dictionary.Find(this->master_element));
+}
+
+void
+cxxSurfaceComp::Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd)
+{
+	this->formula = dictionary.GetWords()[ints[ii++]];
+	this->formula_z = doubles[dd++];
+	this->moles = doubles[dd++];
+	this->totals.Deserialize(dictionary, ints, doubles, ii, dd);
+	this->la = doubles[dd++];
+	this->charge_name = dictionary.GetWords()[ints[ii++]];
+	this->charge_balance = doubles[dd++];
+	this->phase_name = dictionary.GetWords()[ints[ii++]];
+	this->phase_proportion = doubles[dd++];
+	this->rate_name = dictionary.GetWords()[ints[ii++]];
+	this->Dw = doubles[dd++];
+	this->master_element = dictionary.GetWords()[ints[ii++]];
+}
+
+const std::vector< std::string >::value_type temp_vopts[] = {
+	std::vector< std::string >::value_type("formula"),	        // 0 
+	std::vector< std::string >::value_type("moles"),	        // 1
+	std::vector< std::string >::value_type("la"),	            // 2 
+	std::vector< std::string >::value_type("charge_number"),	// 3 
+	std::vector< std::string >::value_type("charge_balance"),	// 4
+	std::vector< std::string >::value_type("phase_name"),	    // 5 
+	std::vector< std::string >::value_type("rate_name"),	    // 6 
+	std::vector< std::string >::value_type("phase_proportion"),	// 7 
+	std::vector< std::string >::value_type("totals"),	        // 8
+	std::vector< std::string >::value_type("formula_z"),	    // 9
+	std::vector< std::string >::value_type("formula_totals"),	// 10
+	std::vector< std::string >::value_type("dw"),	            // 11
+	std::vector< std::string >::value_type("charge_name"),	    // 12
+	std::vector< std::string >::value_type("master_element") 	// 13
+};									   
+const std::vector< std::string > cxxSurfaceComp::vopts(temp_vopts, temp_vopts + sizeof temp_vopts / sizeof temp_vopts[0]);	

src/phreeqcpp/SurfaceComp.h

@@ -0,0 +1,70 @@
+#if !defined(SURFACECOMP_H_INCLUDED)
+#define SURFACECOMP_H_INCLUDED
+
+#include <cassert>				// assert
+#include <map>					// std::map
+#include <string>				// std::string
+#include <list>					// std::list
+#include <vector>				// std::vector
+#include "NameDouble.h"
+
+class cxxSurfaceComp: public PHRQ_base
+{
+
+public:
+
+	cxxSurfaceComp(PHRQ_io *io=NULL);
+	virtual ~cxxSurfaceComp();
+
+	void dump_xml(std::ostream & os, unsigned int indent = 0) const;
+	void dump_raw(std::ostream & s_oss, unsigned int indent) const;
+	void read_raw(CParser & parser, bool check = true);
+	void add(const cxxSurfaceComp & comp, LDBLE extensive);
+	void multiply(LDBLE extensive);
+
+	const std::string &Get_formula() const {return this->formula;}
+	void Set_formula(const char * f) {this->formula = f ? f : "";}
+	LDBLE Get_formula_z(void) const {return formula_z;};
+	void Set_formula_z(LDBLE t) {this->formula_z = t;}
+	LDBLE Get_moles(void) const {return moles;}
+	void Set_moles(LDBLE t) {this->moles = t;}
+	cxxNameDouble & Get_totals() {return (this->totals);}
+	void Set_totals(cxxNameDouble & nd) {this->totals = nd;}
+	LDBLE Get_la(void) const {return la;};
+	void Set_la(LDBLE t) {this->la = t;}
+	LDBLE Get_charge_balance() const {return this->charge_balance;}
+	void Set_charge_balance(LDBLE d) {this->charge_balance = d;}
+	const std::string &Get_charge_name() const {return this->charge_name;}
+	void Set_charge_name(const char * f) {this->charge_name = f ? f : "";}
+	const std::string &Get_phase_name() const {return this->phase_name;}
+	void Set_phase_name(const char * f) {this->phase_name = f ? f : "";}
+	LDBLE Get_phase_proportion(void) const {return phase_proportion;}
+	void Set_phase_proportion(LDBLE d) {this->phase_proportion = d;}
+	const std::string &Get_rate_name() const {return this->rate_name;}
+	void Set_rate_name(const char * f) {this->rate_name = f ? f : "";}
+	LDBLE Get_Dw(void) const {return Dw;}
+	void Set_Dw(LDBLE d) {this->Dw = d;}
+	const std::string &Get_master_element() const {return this->master_element;}
+	void Set_master_element(const char * f) {this->master_element = f ? f : "";}
+	void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
+	void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
+	
+protected:
+	std::string formula;
+	LDBLE formula_z;
+	LDBLE moles;
+	cxxNameDouble totals;
+	LDBLE la;
+	std::string charge_name;
+	LDBLE charge_balance;
+	std::string phase_name;
+	LDBLE phase_proportion;
+	std::string rate_name;
+	LDBLE Dw;
+	std::string master_element;
+	const static std::vector < std::string > vopts;
+public:
+
+};
+
+#endif // !defined(SURFACECOMP_H_INCLUDED)

src/phreeqcpp/System.cxx

@@ -0,0 +1,95 @@
+#include <algorithm>			// std::replace 
+
+#include "Phreeqc.h"
+#include "System.h"
+#include "SSassemblage.h"
+#include "Solution.h"
+#include "Exchange.h"
+#include "GasPhase.h"
+#include "cxxKinetics.h"
+#include "PPassemblage.h"
+#include "SS.h"
+#include "SSassemblage.h"
+#include "Surface.h"
+#include "cxxMix.h"
+#include "Reaction.h"
+#include "Temperature.h"
+
+cxxSystem::cxxSystem(PHRQ_io *io)
+:
+PHRQ_base(io)
+{
+	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;
+	this->pressure = 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;
+	this->pressure = NULL;
+} 
+void
+cxxSystem::totalize(Phreeqc * phreeqc_ptr) 
+{
+	//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(phreeqc_ptr);
+		this->totals.add_extensive(this->ppassemblage->Get_assemblage_totals(), 1.0);
+	}
+	if (this->gasphase != NULL)
+	{
+		this->gasphase->totalize(phreeqc_ptr);
+		this->totals.add_extensive(this->gasphase->Get_totals(), 1.0);
+	}
+	if (this->ssassemblage != NULL)
+	{
+		this->ssassemblage->totalize(phreeqc_ptr);
+		this->totals.add_extensive(this->ssassemblage->Get_totals(), 1.0);
+	}
+	if (this->surface != NULL)
+	{
+		this->surface->totalize();
+		this->totals.add_extensive(this->surface->Get_totals(), 1.0);
+	}
+	return;
+}

src/phreeqcpp/System.h

@@ -0,0 +1,89 @@
+#if !defined(SYSTEM_H_INCLUDED)
+#define SYSTEM_H_INCLUDED
+#include "NameDouble.h"
+#include "PHRQ_base.h"
+class cxxSolution;
+class cxxExchange;
+class cxxGasPhase;
+class cxxKinetics;
+class cxxPPassemblage;
+class cxxSSassemblage;
+class cxxSurface;
+class cxxReaction;
+class cxxTemperature;
+class cxxPressure;
+class cxxMix;
+
+class cxxSystem: public PHRQ_base 
+{
+public:
+	cxxSystem(PHRQ_io *io=NULL);
+	virtual ~cxxSystem(void);
+	void Initialize(void);
+	void Set_Solution(cxxSolution * entity)
+	{
+		this->solution = entity;
+	} 
+	void Set_Exchange(cxxExchange * entity)
+	{
+		this->exchange = entity;
+	} 
+	void Set_PPassemblage(cxxPPassemblage * entity)
+	{
+		this->ppassemblage = entity;
+	} 
+	void Set_GasPhase(cxxGasPhase * entity)
+	{
+		this->gasphase = entity;
+	} 
+	void Set_SSassemblage(cxxSSassemblage * entity)
+	{
+		this->ssassemblage = entity;
+	} 
+	void Set_Kinetics(cxxKinetics * entity)
+	{
+		this->kinetics = entity;
+	} 
+	void Set_Surface(cxxSurface * entity)
+	{
+		this->surface = entity;
+	} 
+	void Set_Mix(cxxMix * entity)
+	{
+		this->mix = entity;
+	} 
+	void Set_Reaction(cxxReaction * entity)
+	{
+		this->reaction = entity;
+	} 
+	void Set_Temperature(cxxTemperature * entity)
+	{
+		this->temperature = entity;
+	} 
+	void Set_Pressure(cxxPressure * entity)
+	{
+		this->pressure = entity;
+	} 
+	void totalize(Phreeqc * phreeqc_ptr);
+	cxxNameDouble &Get_Totals(void)
+	{
+		return this->totals;
+	}
+	
+protected:
+	cxxSolution * solution;
+	cxxExchange * exchange;
+	cxxPPassemblage * ppassemblage;
+	cxxGasPhase * gasphase;
+	cxxSSassemblage * ssassemblage;
+	cxxKinetics * kinetics;
+	cxxSurface * surface;
+	cxxMix * mix;
+	cxxReaction * reaction;
+	cxxTemperature * temperature;
+	cxxPressure * pressure;
+	cxxNameDouble totals;
+};
+
+
+#endif // !defined(SYSTEM_H_INCLUDED)

src/phreeqcpp/Temperature.cxx

@@ -0,0 +1,452 @@
+// Temperature.cxx: implementation of the cxxTemperature class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <cassert>				// assert
+#include <algorithm>			// std::sort
+
+#include "Utils.h"				// define first
+#include "Parser.h"
+#include "Phreeqc.h"
+#include "Temperature.h"
+#include "phqalloc.h"
+
+
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+
+cxxTemperature::cxxTemperature(PHRQ_io *io)
+	//
+	// default constructor for cxxTemperature 
+	//
+:	cxxNumKeyword(io)
+{
+	countTemps = 0;
+	equalIncrements = false;
+}
+cxxTemperature::~cxxTemperature()
+{
+}
+
+#ifdef SKIP
+void
+cxxTemperature::dump_xml(std::ostream & s_oss, unsigned int indent) const const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	// Temperature element and attributes
+	s_oss << indent0;
+	s_oss << "<temperature " << "\n";
+
+	s_oss << indent1;
+	s_oss << "pitzer_temperature_gammas=\"" << this->
+		pitzer_temperature_gammas << "\"" << "\n";
+
+	// components
+	s_oss << indent1;
+	s_oss << "<component " << "\n";
+	for (std::list < cxxTemperatureComp >::const_iterator it =
+		 temperatureComps.begin(); it != temperatureComps.end(); ++it)
+	{
+		it->dump_xml(s_oss, indent + 2);
+	}
+
+	return;
+}
+#endif
+
+int
+cxxTemperature::read(CParser & parser)
+{
+/*
+ *      Reads temperature data for reaction steps
+ *
+ *      Arguments:
+ *	 none
+ *
+ *      Returns:
+ *	 KEYWORD if keyword encountered, input_error may be incremented if
+ *		    a keyword is encountered in an unexpected position
+ *	 EOF     if eof encountered while reading mass balance concentrations
+ *	 ERROR   if error occurred reading data
+ *
+ */
+	// Number and description set in read_reaction_temperature
+
+	PHRQ_io::LINE_TYPE lt;
+	bool done = false;
+	for (;;)
+	{
+		std::istream::pos_type ptr;
+		std::istream::pos_type next_char = 0;
+		std::string token, str;
+		lt = parser.check_line(str, false, true, true, true);
+
+		if (lt == PHRQ_io::LT_EMPTY || 
+			lt == PHRQ_io::LT_KEYWORD ||
+			lt == PHRQ_io::LT_EOF)
+		{
+			break;
+		}
+		if (lt == PHRQ_io::LT_OPTION)
+		{
+			this->error_msg("Expected numeric value for temperatures.", PHRQ_io::OT_CONTINUE);
+			break;
+		}
+
+		if (done)
+		{
+			this->error_msg("Unknown input following equal increment definition.", PHRQ_io::OT_CONTINUE);
+			continue;
+		}
+
+		// LT_OK
+
+		for (;;)
+		{
+			if (done) break;
+			// new token
+			std::string token;
+			CParser::TOKEN_TYPE k =	parser.copy_token(token, next_char);
+
+			// need new line
+			if (k == CParser::TT_EMPTY)
+			{
+				break;
+			}
+
+			// read a pressure
+			if (k == CParser::TT_DIGIT)
+			{
+				std::istringstream iss(token);
+				LDBLE d;
+				if (!(iss >> d))
+				{
+					this->error_msg("Expected numeric value for temperatures.",
+									 PHRQ_io::OT_CONTINUE);
+				}
+				else
+				{
+					this->temps.push_back(d);
+				}
+				continue;
+			}
+
+			// non digit, must be "in"
+			if (k == CParser::TT_UPPER || k == CParser::TT_LOWER)
+			{
+				if (this->temps.size() != 2)
+				{
+					this->error_msg("To define equal increments, exactly two temperatures should be defined.", CONTINUE);
+				}
+				else
+				{
+					int i = parser.copy_token(token, next_char);
+					if (i == EMPTY)
+					{
+						error_msg("To define equal increments, define 'in n steps'.", CONTINUE);
+					}
+					else
+					{
+						std::istringstream iss(token);
+						if ((iss >> i) && i > 0)
+						{
+							this->equalIncrements = true;
+							this->countTemps = i;
+						}
+						else
+						{
+							error_msg("Unknown input for temperature steps.", CONTINUE);
+						}
+					}
+					done = true;
+				}
+				if (k == CParser::TT_UNKNOWN)
+				{
+					error_msg("Unknown input for temperature steps.", CONTINUE);
+				}
+			}
+		} // tokens
+	} // lines
+	return lt;
+}
+
+void
+cxxTemperature::dump_raw(std::ostream & s_oss, unsigned int indent, int *n_out) const
+{
+	unsigned int i;
+	s_oss.precision(DBL_DIG - 1);
+	std::string indent0(""), indent1(""), indent2("");
+	for (i = 0; i < indent; ++i)
+		indent0.append(Utilities::INDENT);
+	for (i = 0; i < indent + 1; ++i)
+		indent1.append(Utilities::INDENT);
+	for (i = 0; i < indent + 2; ++i)
+		indent2.append(Utilities::INDENT);
+
+	s_oss << indent0;
+	int n_user_local = (n_out != NULL) ? *n_out : this->n_user;
+	s_oss << "REACTION_TEMPERATURE_RAW     " << n_user_local << " " << this->description << "\n";
+
+	s_oss << indent1;
+	s_oss << "-count_temps               " << this->Get_countTemps() << "\n";
+
+	s_oss << indent1;
+	s_oss << "-equal_increments          " << this->equalIncrements << "\n";
+
+	// Temperature element and attributes
+
+	s_oss << indent1;
+	s_oss << "-temps                     " << "\n";
+	{
+		int i = 0;
+		s_oss << indent2;
+		for (std::vector < LDBLE >::const_iterator it = this->temps.begin();
+			 it != this->temps.end(); it++)
+		{
+			if (i++ == 5)
+			{
+				s_oss << "\n";
+				s_oss << indent2;
+				i = 0;
+			}
+			s_oss << *it << " ";
+		}
+		s_oss << "\n";
+	}
+}
+
+void
+cxxTemperature::read_raw(CParser & parser, bool check)
+{
+	LDBLE d;
+	CParser::TOKEN_TYPE k;
+	// clear steps for modify operation, if pressures are read
+	bool cleared_once = false;
+
+	std::istream::pos_type ptr;
+	std::istream::pos_type next_char;
+	std::string token;
+	int opt_save;
+	bool useLastLine(false);
+
+	// Read temperature number and description
+	this->read_number_description(parser);
+
+	opt_save = CParser::OPT_ERROR;
+	bool equalIncrements_defined(false);
+	bool countTemps_defined(false);
+
+	for (;;)
+	{
+		int opt;
+		if (useLastLine == false)
+		{
+			opt = parser.get_option(vopts, next_char);
+		}
+		else
+		{
+			opt = parser.getOptionFromLastLine(vopts, next_char, true);
+		}
+		if (opt == CParser::OPT_DEFAULT)
+		{
+			opt = opt_save;
+		}
+		switch (opt)
+		{
+		case CParser::OPT_EOF:
+			break;
+		case CParser::OPT_KEYWORD:
+			break;
+		case CParser::OPT_DEFAULT:
+		case CParser::OPT_ERROR:
+			opt = CParser::OPT_EOF;
+			parser.error_msg("Unknown input in TEMPERATURE_COMP_RAW keyword.",
+							 PHRQ_io::OT_CONTINUE);
+			parser.error_msg(parser.line().c_str(), PHRQ_io::OT_CONTINUE);
+			useLastLine = false;
+			break;
+
+		case 0:				// temps
+			if (!cleared_once) 
+			{
+				this->temps.clear();
+				cleared_once = true;
+			}
+			while ((k =
+					parser.copy_token(token, next_char)) == CParser::TT_DIGIT)
+			{
+				std::istringstream iss(token);
+				if (!(iss >> d))
+				{
+					parser.incr_input_error();
+					parser.error_msg("Expected numeric value for temps.",
+									 PHRQ_io::OT_CONTINUE);
+				}
+				else
+				{
+					this->temps.push_back(d);
+				}
+			}
+			opt_save = 0;
+			useLastLine = false;
+			break;
+
+		case 1:				// equal_increments
+			if (!(parser.get_iss() >> this->equalIncrements))
+			{
+				this->equalIncrements = 0;
+				parser.incr_input_error();
+				parser.
+					error_msg("Expected boolean value for equalIncrements.",
+							  PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = CParser::OPT_DEFAULT;
+			useLastLine = false;
+			equalIncrements_defined = true;
+			break;
+
+		case 2:				// countTemps
+			if (!(parser.get_iss() >> this->countTemps))
+			{
+				this->countTemps = 0;
+				parser.incr_input_error();
+				parser.error_msg("Expected integer value for countTemps.",
+								 PHRQ_io::OT_CONTINUE);
+			}
+			opt_save = CParser::OPT_DEFAULT;
+			useLastLine = false;
+			countTemps_defined = true;
+			break;
+		}
+		if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
+			break;
+	}
+	// members that must be defined
+	if (check)
+	{
+		if (equalIncrements_defined == false)
+		{
+			parser.incr_input_error();
+			parser.
+				error_msg
+				("Equal_increments not defined for REACTION_TEMPERATURE_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+		if (countTemps_defined == false)
+		{
+			parser.incr_input_error();
+			parser.
+				error_msg
+				("Count_temps not defined for REACTION_TEMPERATURE_RAW input.",
+				PHRQ_io::OT_CONTINUE);
+		}
+	}
+}
+/* ---------------------------------------------------------------------- */
+LDBLE cxxTemperature::
+Temperature_for_step(int step_number)
+/* ---------------------------------------------------------------------- */
+{
+/*
+ *   Determine pressure of reaction step
+ */
+	LDBLE t_temp;
+	if (this->temps.size() == 0) 
+	{
+		t_temp = 1;
+	}
+	else if (this->equalIncrements)
+	{
+		if (this->temps.size() != 2)
+		{
+			error_msg("Number of temperatures not equal to 2 for equal increments.", 0);
+		}
+		if (step_number > this->countTemps)
+		{
+			t_temp = this->temps[1];
+		}
+		else
+		{
+			LDBLE denom;
+			denom = (this->countTemps <= 1) ? 1 : (LDBLE) (this->countTemps - 1);
+			t_temp =  this->temps[0] + ( this->temps[1] - this->temps[0]) *
+				((LDBLE) (step_number - 1)) / (denom);
+		}
+	}
+	else 
+	{
+		if (step_number > (int) this->temps.size())
+		{
+			t_temp = this->temps[this->temps.size() - 1];
+		}
+		else
+		{
+			t_temp = this->temps[step_number - 1];
+		}
+
+	}
+
+	return (t_temp);
+}
+int cxxTemperature::
+Get_countTemps(void) const
+{
+	if (equalIncrements) 
+	{
+		return this->countTemps;
+	}
+	return (int) this->temps.size();
+}
+void
+cxxTemperature::Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles)
+{
+	ints.push_back(this->n_user);
+	{
+		ints.push_back((int) this->temps.size());
+		for (size_t i = 0; i < this->temps.size(); i++)
+		{
+			doubles.push_back(temps[i]);
+		}
+	}
+	ints.push_back(this->countTemps);
+	ints.push_back(this->equalIncrements ? 1 : 0);
+}
+
+void
+cxxTemperature::Deserialize(Dictionary & dictionary, std::vector < int >&ints, 
+	std::vector < double >&doubles, int &ii, int &dd)
+{
+	this->n_user = ints[ii++];
+	this->n_user_end = this->n_user;
+	this->description = " ";
+
+	{
+		int count = ints[ii++];
+		this->temps.clear();
+		for (int i = 0; i < count; i++)
+		{
+			this->temps.push_back(doubles[dd++]);
+		}
+	}
+	this->countTemps = ints[ii++];
+	this->equalIncrements = (ints[ii++] != 0);
+}
+const std::vector< std::string >::value_type temp_vopts[] = {
+	std::vector< std::string >::value_type("temps"),	        //0
+	std::vector< std::string >::value_type("equal_increments"),	//1
+	std::vector< std::string >::value_type("count_temps") 	    //2
+};									   
+const std::vector< std::string > cxxTemperature::vopts(temp_vopts, temp_vopts + sizeof temp_vopts / sizeof temp_vopts[0]);	

src/phreeqcpp/Temperature.h

@@ -0,0 +1,42 @@
+#if !defined(TEMPERATURE_H_INCLUDED)
+#define TEMPERATURE_H_INCLUDED
+
+#include <cassert>				// assert
+#include <map>					// std::map
+#include <string>				// std::string
+#include <list>					// std::list
+#include <vector>				// std::vector
+
+#include "NumKeyword.h"
+
+class cxxTemperature:public cxxNumKeyword
+{
+
+  public:
+	cxxTemperature(PHRQ_io *io=NULL);
+	~cxxTemperature();
+
+	//void dump_xml(std::ostream& os, unsigned int indent = 0)const;
+
+	void dump_raw(std::ostream & s_oss, unsigned int indent, int *n_out=NULL) const;
+
+	void read_raw(CParser & parser, bool check = false);
+	int read(CParser & parser);
+	LDBLE Temperature_for_step(int step_number);
+	std::vector<LDBLE> & Get_temps(void) {return temps;}
+	const std::vector<LDBLE> & Get_temps(void)const {return temps;}
+	int Get_countTemps(void) const;
+	void Set_countTemps(int i) {countTemps = i;}
+	bool Get_equalIncrements(void) const {return equalIncrements;}
+	void Set_equalIncrements(bool tf) {equalIncrements = tf;}
+	void Serialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles);
+	void Deserialize(Dictionary & dictionary, std::vector < int >&ints, std::vector < double >&doubles, int &ii, int &dd);
+	
+protected:
+	std::vector < LDBLE >temps;
+	int countTemps;
+	bool equalIncrements;
+	const static std::vector < std::string > vopts;
+};
+
+#endif // !defined(TEMPERATURE_H_INCLUDED)

src/phreeqcpp/Use.cpp

@@ -0,0 +1,70 @@
+#include <stdio.h>
+#include "Use.h"
+
+cxxUse::cxxUse()
+{
+	this->init();
+
+}
+
+
+cxxUse::~cxxUse(void)
+{
+}
+void cxxUse::
+init(void)
+{
+	solution_in = false;
+	n_solution_user = -999;
+	solution_ptr = NULL;
+
+	pp_assemblage_in = false;
+	n_pp_assemblage_user = -999;
+	pp_assemblage_ptr = NULL;
+
+	mix_in = false;
+	n_mix_user = -999;
+	mix_ptr = NULL;
+	n_mix_user_orig = -999;
+
+	reaction_in = false;
+	n_reaction_user = -999;
+	reaction_ptr = NULL;
+
+	exchange_in = false;
+	n_exchange_user = -999;
+	exchange_ptr = NULL;
+
+	kinetics_in = false;
+	n_kinetics_user = -999;
+	kinetics_ptr = NULL;
+
+	surface_in = false;
+	n_surface_user = -999;
+	surface_ptr = NULL;
+
+	pressure_in = false;
+	n_pressure_user = -999;
+	pressure_ptr = NULL;
+
+	temperature_in = false;
+	n_temperature_user = -999;
+	temperature_ptr = NULL;
+
+	inverse_in = false;
+	n_inverse_user = -999;
+	inverse_ptr = NULL;
+
+	gas_phase_in = false;
+	n_gas_phase_user = -999;
+	gas_phase_ptr = NULL;
+
+	ss_assemblage_in = false;
+	n_ss_assemblage_user = -999;
+	ss_assemblage_ptr = NULL;
+
+	trans_in = false;
+	advect_in = false;
+}
+
+

src/phreeqcpp/Use.h

@@ -0,0 +1,159 @@
+#if !defined(USE_H_INCLUDED)
+#define USE_H_INCLUDED
+class cxxPPassemblage;
+class cxxMix;
+class cxxReaction;
+class cxxExchange;
+class cxxGasPhase;
+class cxxPressure;
+class cxxTemperature;
+class cxxSSassemblage;
+class cxxKinetics;
+class cxxSurface;
+class cxxSolution;
+
+class cxxUse
+{
+public:
+	cxxUse();
+	virtual ~cxxUse(void);
+	void init(void);
+
+	bool Get_solution_in(void) const      {return this->solution_in;}
+	bool Get_pp_assemblage_in(void) const {return this->pp_assemblage_in;}
+	bool Get_mix_in(void) const           {return this->mix_in;}
+	bool Get_reaction_in(void) const      {return this->reaction_in;}
+	bool Get_exchange_in(void) const      {return this->exchange_in;}
+	bool Get_kinetics_in(void) const      {return this->kinetics_in;}
+	bool Get_surface_in(void) const       {return this->surface_in;}
+	bool Get_pressure_in(void) const      {return this->pressure_in;}
+	bool Get_temperature_in(void) const   {return this->temperature_in;}
+	bool Get_gas_phase_in(void) const     {return this->gas_phase_in;}
+	bool Get_inverse_in(void) const       {return this->inverse_in;}
+	bool Get_ss_assemblage_in(void) const {return this->ss_assemblage_in;}
+	bool Get_advect_in(void) const        {return this->advect_in;}
+	bool Get_trans_in(void) const         {return this->trans_in;}
+
+	void Set_solution_in(bool tf)         {solution_in = tf;}
+	void Set_pp_assemblage_in(bool tf)    {pp_assemblage_in = tf;}
+	void Set_mix_in(bool tf)              {mix_in = tf;}
+	void Set_reaction_in(bool tf)         {reaction_in = tf;}
+	void Set_exchange_in(bool tf)         {exchange_in = tf;}
+	void Set_kinetics_in(bool tf)         {kinetics_in = tf;}
+	void Set_surface_in(bool tf)          {surface_in = tf;}
+	void Set_pressure_in(bool tf)         {pressure_in = tf;}
+	void Set_temperature_in(bool tf)      {temperature_in = tf;}
+	void Set_gas_phase_in(bool tf)        {gas_phase_in = tf;}
+	void Set_inverse_in(bool tf)          {inverse_in = tf;}
+	void Set_ss_assemblage_in(bool tf)    {ss_assemblage_in = tf;}
+	void Set_advect_in(bool tf)           {advect_in = tf;}
+	void Set_trans_in(bool tf)            {trans_in = tf;}
+
+	int Get_n_solution_user(void) const       {return n_solution_user;}
+	int Get_n_pp_assemblage_user(void) const  {return n_pp_assemblage_user;}
+	int Get_n_mix_user(void) const            {return n_mix_user;}
+	int Get_n_mix_user_orig(void) const       {return n_mix_user_orig;}
+	int Get_n_reaction_user(void) const       {return n_reaction_user;}
+	int Get_n_exchange_user(void) const       {return n_exchange_user;}
+	int Get_n_kinetics_user(void) const       {return n_kinetics_user;}
+	int Get_n_surface_user(void) const        {return n_surface_user;}
+	int Get_n_pressure_user(void) const       {return n_pressure_user;}
+	int Get_n_temperature_user(void) const    {return n_temperature_user;}
+	int Get_n_gas_phase_user(void) const      {return n_gas_phase_user;}
+	int Get_n_inverse_user(void) const        {return n_inverse_user;}
+	int Get_n_ss_assemblage_user(void) const  {return n_ss_assemblage_user;}
+
+	void Set_n_solution_user(int i)       {n_solution_user = i;}
+	void Set_n_pp_assemblage_user(int i)  {n_pp_assemblage_user = i;}
+	void Set_n_mix_user(int i)            {n_mix_user = i;}
+	void Set_n_mix_user_orig(int i)       {n_mix_user_orig = i;}
+	void Set_n_reaction_user(int i)       {n_reaction_user = i;}
+	void Set_n_exchange_user(int i)       {n_exchange_user = i;}
+	void Set_n_kinetics_user(int i)       {n_kinetics_user = i;}
+	void Set_n_surface_user(int i)        {n_surface_user = i;}
+	void Set_n_pressure_user(int i)       {n_pressure_user = i;}
+	void Set_n_temperature_user(int i)    {n_temperature_user = i;}
+	void Set_n_gas_phase_user(int i)      {n_gas_phase_user = i;}
+	void Set_n_inverse_user(int i)        {n_inverse_user = i;}
+	void Set_n_ss_assemblage_user(int i)  {n_ss_assemblage_user = i;}
+
+	cxxSolution * Get_solution_ptr(void) const               {return this->solution_ptr;}
+	cxxPPassemblage * Get_pp_assemblage_ptr(void) const      {return this->pp_assemblage_ptr;}
+	cxxMix * Get_mix_ptr(void) const                         {return this->mix_ptr;}
+	cxxReaction * Get_reaction_ptr(void) const               {return this->reaction_ptr;}
+	cxxExchange * Get_exchange_ptr(void) const               {return this->exchange_ptr;}
+	cxxKinetics * Get_kinetics_ptr(void) const               {return this->kinetics_ptr;}
+	cxxSurface * Get_surface_ptr(void) const                 {return this->surface_ptr;}
+	cxxPressure * Get_pressure_ptr(void) const               {return this->pressure_ptr;}
+	cxxTemperature * Get_temperature_ptr(void) const         {return this->temperature_ptr;}
+	cxxGasPhase * Get_gas_phase_ptr(void) const              {return this->gas_phase_ptr;}
+	struct inverse * Get_inverse_ptr(void) const             {return this->inverse_ptr;}
+	cxxSSassemblage * Get_ss_assemblage_ptr(void)            {return this->ss_assemblage_ptr;}
+
+	void Set_solution_ptr(cxxSolution * p)                   {this->solution_ptr = p;}
+	void Set_pp_assemblage_ptr(cxxPPassemblage * p)          {this->pp_assemblage_ptr = p;}
+	void Set_mix_ptr(cxxMix * p)                             {this->mix_ptr = p;}
+	void Set_reaction_ptr(cxxReaction * p)                   {this->reaction_ptr = p;}
+	void Set_exchange_ptr(cxxExchange * p)                   {this->exchange_ptr = p;}
+	void Set_kinetics_ptr(cxxKinetics * p)                   {this->kinetics_ptr = p;}
+	void Set_surface_ptr(cxxSurface * p)                     {this->surface_ptr = p;}
+	void Set_pressure_ptr(cxxPressure * p)                   {this->pressure_ptr = p;}
+	void Set_temperature_ptr(cxxTemperature * p)             {this->temperature_ptr = p;}
+	void Set_gas_phase_ptr(cxxGasPhase * p)                  {this->gas_phase_ptr = p;}
+	void Set_inverse_ptr(struct inverse * p)                 {this->inverse_ptr = p;}
+	void Set_ss_assemblage_ptr(cxxSSassemblage * p)     {this->ss_assemblage_ptr = p;}
+
+protected:
+	bool solution_in;
+	int n_solution_user;
+	cxxSolution *solution_ptr;
+
+	bool pp_assemblage_in;
+	int n_pp_assemblage_user;
+	cxxPPassemblage *pp_assemblage_ptr;
+
+	bool mix_in;
+	int n_mix_user;
+	cxxMix * mix_ptr;
+	int n_mix_user_orig;
+
+	bool reaction_in;
+	int n_reaction_user;
+	cxxReaction * reaction_ptr;
+
+	bool exchange_in;
+	int n_exchange_user;
+	cxxExchange * exchange_ptr;
+
+	bool kinetics_in;
+	int n_kinetics_user;
+	cxxKinetics *kinetics_ptr;
+
+	bool surface_in;
+	int n_surface_user;
+	cxxSurface *surface_ptr;
+
+	bool pressure_in;
+	int n_pressure_user;
+	cxxPressure *pressure_ptr;
+
+	bool temperature_in;
+	int n_temperature_user;
+	cxxTemperature *temperature_ptr;
+
+	bool inverse_in;
+	int n_inverse_user;
+	struct inverse *inverse_ptr;
+
+	bool gas_phase_in;
+	int n_gas_phase_user;
+	cxxGasPhase * gas_phase_ptr;
+
+	bool ss_assemblage_in;
+	int n_ss_assemblage_user;
+	cxxSSassemblage *ss_assemblage_ptr;
+
+	bool trans_in;
+	bool advect_in;
+};
+#endif // !defined(USE_H_INCLUDED)

src/phreeqcpp/UserPunch.cpp

@@ -0,0 +1,23 @@
+#include "UserPunch.h"
+#include "Phreeqc.h"
+UserPunch::UserPunch(int n, PHRQ_io *io)
+:	cxxNumKeyword(io)
+{
+	this->PhreeqcPtr    = NULL;
+	this->rate          = NULL;
+}
+
+
+UserPunch::~UserPunch(void)
+{
+	if (this->rate != NULL)
+	{
+		if (this->PhreeqcPtr != NULL)
+		{
+			this->PhreeqcPtr->rate_free(this->rate);
+			this->PhreeqcPtr->free_check_null(this->rate);
+		}
+	}
+	this->PhreeqcPtr = NULL;
+	this->rate = NULL;
+}

src/phreeqcpp/UserPunch.h

@@ -0,0 +1,39 @@
+#if !defined(USERPUNCH_H_INCLUDED)
+#define USERPUNCH_H_INCLUDED
+#include <vector>
+#include <string>				// std::string
+#include "NumKeyword.h"
+class Phreeqc;
+class UserPunch:public cxxNumKeyword
+{
+public:
+	UserPunch(int n=1, PHRQ_io *io=NULL);
+	~UserPunch(void);
+
+	// headings
+	//
+	std::vector <std::string> &Get_headings() {return this->headings;}
+	const std::vector <std::string> &Get_headings()const {return this->headings;}
+
+	void Set_headings(std::vector <std::string> & h) {this->headings = h;}
+
+	// phreeqc pointer
+	//
+	Phreeqc * Get_PhreeqcPtr() {return this->PhreeqcPtr;}
+	const Phreeqc * Get_PhreeqcPtr()const {return this->PhreeqcPtr;}
+
+	void Set_PhreeqcPtr(Phreeqc * p) {this->PhreeqcPtr = p;}
+
+	// rate
+	//
+	struct rate * Get_rate() {return this->rate;}
+	const struct rate * Get_rate()const {return this->rate;}
+
+	void Set_rate(struct rate * r) {this->rate = r;}
+
+protected:
+	std::vector <std::string> headings;
+	struct rate *             rate;
+	Phreeqc *                 PhreeqcPtr;
+};
+#endif // !defined(USERPUNCH_H_INCLUDED)

src/phreeqcpp/advection.cpp

@@ -0,0 +1,132 @@
+#include "Utils.h"
+#include "Phreeqc.h"
+#include "phqalloc.h"
+#include "cxxKinetics.h"
+#include "Solution.h"
+
+
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+advection(void)
+/* ---------------------------------------------------------------------- */
+{
+	int i;
+	LDBLE kin_time;
+/*
+ *   Calculate advection
+ */
+	state = ADVECTION;
+/*	mass_water_switch = TRUE; */
+/*
+ *   Check existence of all solutions
+ */
+	for (i = 0; i <= count_ad_cells; i++)
+	{
+		if (Utilities::Rxn_find(Rxn_solution_map, i) == NULL)
+		//if (solution_bsearch(i, &n, TRUE) == NULL)
+		{
+			input_error++;
+			error_string = sformatf(
+					"Solution %d is needed for advection, but is not defined.",
+					i);
+			error_msg(error_string, CONTINUE);
+		}
+	}
+/*
+ *   Check kinetics logic
+ */
+	kin_time = advection_kin_time;
+	if (kin_time <= 0.0)
+	{
+		for (i = 1; i <= count_ad_cells; i++)
+		{
+			if (Utilities::Rxn_find(Rxn_kinetics_map, i) != NULL)
+			{
+				input_error++;
+				error_string = sformatf(
+						"KINETIC reaction(s) defined, but time_step is not defined in ADVECTION keyword.");
+				error_msg(error_string, CONTINUE);
+				break;
+			}
+		}
+	}
+/*
+ *   Quit on error
+ */
+	if (get_input_errors() > 0)
+	{
+		error_msg("Program terminating due to input errors.", STOP);
+	}
+/*
+ *   Equilibrate solutions with phases, exchangers, surfaces
+ */
+	last_model.force_prep = TRUE;
+	rate_sim_time_start = 0;
+	for (advection_step = 1; advection_step <= count_ad_shifts;
+		 advection_step++)
+	{
+		log_msg(sformatf(
+				   "\nBeginning of advection time step %d, cumulative pore volumes %f.\n",
+				   advection_step,
+				   (double) (((LDBLE) advection_step) /
+							 ((LDBLE) count_ad_cells))));
+		if (pr.use == TRUE && pr.all == TRUE)
+		{
+			output_msg(sformatf(
+					   "Beginning of advection time step %d, cumulative pore volumes %f.\n",
+					   advection_step,
+					   (double) (((LDBLE) advection_step) /
+								 ((LDBLE) count_ad_cells))));
+		}
+/*
+ *  Advect
+ */
+		for (i = count_ad_cells; i > 0; i--)
+		{
+			//solution_duplicate(i - 1, i);
+			Utilities::Rxn_copy(Rxn_solution_map, i -1, i);
+		}
+/*
+ *  Equilibrate and (or) mix
+ */
+		for (i = 1; i <= count_ad_cells; i++)
+		{
+			set_initial_moles(i);
+			cell_no = i;
+			set_advection(i, TRUE, TRUE, i);
+			run_reactions(i, kin_time, TRUE, 1.0);
+			if (advection_kin_time_defined == TRUE)
+			{
+				rate_sim_time = rate_sim_time_start + kin_time;
+			}
+			log_msg(sformatf( "\nCell %d.\n\n", i));
+			if (pr.use == TRUE && pr.all == TRUE &&
+				advection_step % print_ad_modulus == 0 &&
+				advection_print[i - 1] == TRUE)
+			{
+				output_msg(sformatf( "\nCell %d.\n\n", i));
+			}
+			if (advection_step % punch_ad_modulus == 0 &&
+				advection_punch[i - 1] == TRUE)
+			{
+				punch_all();
+			}
+			if (advection_step % print_ad_modulus == 0 &&
+				advection_print[i - 1] == TRUE)
+			{
+				print_all();
+			}
+			if (i > 1)
+				Utilities::Rxn_copy(Rxn_solution_map, -2, i - 1);
+				//solution_duplicate(-2, i - 1);
+			saver();
+		}
+		Utilities::Rxn_copy(Rxn_solution_map, -2, count_ad_cells);
+		//solution_duplicate(-2, count_ad_cells);
+		rate_sim_time_start += kin_time;
+	}
+	initial_total_time += rate_sim_time_start;
+	/* free_model_allocs(); */
+	mass_water_switch = FALSE;
+	return (OK);
+}

src/phreeqcpp/cl1.cpp

@@ -0,0 +1,896 @@
+#include <stdio.h>
+#include <string.h>
+#include <math.h>
+#include <stdlib.h>
+#include "Phreeqc.h"
+#include "phqalloc.h"
+
+/* debug
+#define DEBUG_CL1
+#define CHECK_ERRORS
+ */
+
+int Phreeqc::
+cl1(int k, int l, int m, int n,
+	int l_nklmd, int l_n2d,
+	LDBLE * q,
+	int *l_kode, LDBLE l_toler,
+	int *l_iter, LDBLE * l_x, LDBLE * l_res, LDBLE * l_error,
+	LDBLE * l_cu, int *l_iu, int *l_s, int check)
+{
+	/* System generated locals */
+	union double_or_int
+	{
+		int ival;
+		LDBLE dval;
+	} *q2;
+
+	/* Local variables */
+	int nklm;
+	LDBLE xmin, xmax;
+	int iout = 0;
+	// static i runs faster on windows
+	register int i, j;
+	register LDBLE l_z;
+	int maxit, n1, n2;
+	LDBLE pivot;
+	int ia, ii, kk, nk, js;
+	int in = 0;
+	LDBLE sn;
+	int iphase, kforce;
+	LDBLE zu, zv;
+	LDBLE tpivot;
+	int klm, jmn, nkl, jpn;
+	LDBLE cuv;
+	long double sum;
+	int klm1;
+	int q_dim, cu_dim;
+	int kode_arg;
+	LDBLE check_toler;
+#ifdef CHECK_ERRORS
+	char **col_name, **row_name;
+	int *row_back, *col_back;
+#endif
+/* THIS SUBROUTINE USES A MODIFICATION OF THE SIMPLEX */
+/* METHOD OF LINEAR PROGRAMMING TO CALCULATE AN L1 SOLUTION */
+/* TO A K BY N SYSTEM OF LINEAR EQUATIONS */
+/*             AX=B */
+/* SUBJECT TO L LINEAR EQUALITY CONSTRAINTS */
+/*             CX=D */
+/* AND M LINEAR INEQUALITY CONSTRAINTS */
+/*             EX.LE.F. */
+/* DESCRIPTION OF PARAMETERS */
+/* K      NUMBER OF ROWS OF THE MATRIX A (K.GE.1). */
+/* L      NUMBER OF ROWS OF THE MATRIX C (L.GE.0). */
+/* M      NUMBER OF ROWS OF THE MATRIX E (M.GE.0). */
+/* N      NUMBER OF COLUMNS OF THE MATRICES A,C,E (N.GE.1). */
+/* KLMD   SET TO AT LEAST K+L+M FOR ADJUSTABLE DIMENSIONS. */
+/* KLM2D  SET TO AT LEAST K+L+M+2 FOR ADJUSTABLE DIMENSIONS. */
+/* NKLMD  SET TO AT LEAST N+K+L+M FOR ADJUSTABLE DIMENSIONS. */
+/* N2D    SET TO AT LEAST N+2 FOR ADJUSTABLE DIMENSIONS */
+/* Q      TWO DIMENSIONAL REAL ARRAY WITH KLM2D ROWS AND */
+/*        AT LEAST N2D COLUMNS. */
+/*        ON ENTRY THE MATRICES A,C AND E, AND THE VECTORS */
+/*        B,D AND F MUST BE STORED IN THE FIRST K+L+M ROWS */
+/*        AND N+1 COLUMNS OF Q AS FOLLOWS */
+/*             A B */
+/*         Q = C D */
+/*             E F */
+/*        THESE VALUES ARE DESTROYED BY THE SUBROUTINE. */
+/* KODE   A CODE USED ON ENTRY TO, AND EXIT */
+/*        FROM, THE SUBROUTINE. */
+/*        ON ENTRY, THIS SHOULD NORMALLY BE SET TO 0. */
+/*        HOWEVER, IF CERTAIN NONNEGATIVITY CONSTRAINTS */
+/*        ARE TO BE INCLUDED IMPLICITLY, RATHER THAN */
+/*        EXPLICITLY IN THE CONSTRAINTS EX.LE.F, THEN KODE */
+/*        SHOULD BE SET TO 1, AND THE NONNEGATIVITY */
+/*        CONSTRAINTS INCLUDED IN THE ARRAYS X AND */
+/*        RES (SEE BELOW). */
+/*        ON EXIT, KODE HAS ONE OF THE */
+/*        FOLLOWING VALUES */
+/*             0- OPTIMAL SOLUTION FOUND, */
+/*             1- NO FEASIBLE SOLUTION TO THE */
+/*                CONSTRAINTS, */
+/*             2- CALCULATIONS TERMINATED */
+/*                PREMATURELY DUE TO ROUNDING ERRORS, */
+/*             3- MAXIMUM NUMBER OF ITERATIONS REACHED. */
+/* TOLER  A SMALL POSITIVE TOLERANCE. EMPIRICAL */
+/*        EVIDENCE SUGGESTS TOLER = 10**(-D*2/3), */
+/*        WHERE D REPRESENTS THE NUMBER OF DECIMAL */
+/*        DIGITS OF ACCURACY AVAILABLE. ESSENTIALLY, */
+/*        THE SUBROUTINE CANNOT DISTINGUISH BETWEEN ZERO */
+/*        AND ANY QUANTITY WHOSE MAGNITUDE DOES NOT EXCEED */
+/*        TOLER. IN PARTICULAR, IT WILL NOT PIVOT ON ANY */
+/*        NUMBER WHOSE MAGNITUDE DOES NOT EXCEED TOLER. */
+/* ITER   ON ENTRY ITER MUST CONTAIN AN UPPER BOUND ON */
+/*        THE MAXIMUM NUMBER OF ITERATIONS ALLOWED. */
+/*        A SUGGESTED VALUE IS 10*(K+L+M). ON EXIT ITER */
+/*        GIVES THE NUMBER OF SIMPLEX ITERATIONS. */
+/* X      ONE DIMENSIONAL REAL ARRAY OF SIZE AT LEAST N2D. */
+/*        ON EXIT THIS ARRAY CONTAINS A */
+/*        SOLUTION TO THE L1 PROBLEM. IF KODE=1 */
+/*        ON ENTRY, THIS ARRAY IS ALSO USED TO INCLUDE */
+/*        SIMPLE NONNEGATIVITY CONSTRAINTS ON THE */
+/*        VARIABLES. THE VALUES -1, 0, OR 1 */
+/*        FOR X(J) INDICATE THAT THE J-TH VARIABLE */
+/*        IS RESTRICTED TO BE .LE.0, UNRESTRICTED, */
+/*        OR .GE.0 RESPECTIVELY. */
+/* RES    ONE DIMENSIONAL REAL ARRAY OF SIZE AT LEAST KLMD. */
+/*        ON EXIT THIS CONTAINS THE RESIDUALS B-AX */
+/*        IN THE FIRST K COMPONENTS, D-CX IN THE */
+/*        NEXT L COMPONENTS (THESE WILL BE =0),AND */
+/*        F-EX IN THE NEXT M COMPONENTS. IF KODE=1 ON */
+/*        ENTRY, THIS ARRAY IS ALSO USED TO INCLUDE SIMPLE */
+/*        NONNEGATIVITY CONSTRAINTS ON THE RESIDUALS */
+/*        B-AX. THE VALUES -1, 0, OR 1 FOR RES(I) */
+/*        INDICATE THAT THE I-TH RESIDUAL (1.LE.I.LE.K) IS */
+/*        RESTRICTED TO BE .LE.0, UNRESTRICTED, OR .GE.0 */
+/*        RESPECTIVELY. */
+/* ERROR  ON EXIT, THIS GIVES THE MINIMUM SUM OF */
+/*        ABSOLUTE VALUES OF THE RESIDUALS. */
+/* CU     A TWO DIMENSIONAL REAL ARRAY WITH TWO ROWS AND */
+/*        AT LEAST NKLMD COLUMNS USED FOR WORKSPACE. */
+/* IU     A TWO DIMENSIONAL INTEGER ARRAY WITH TWO ROWS AND */
+/*        AT LEAST NKLMD COLUMNS USED FOR WORKSPACE. */
+/* S      INTEGER ARRAY OF SIZE AT LEAST KLMD, USED FOR */
+/*        WORKSPACE. */
+/*      DOUBLE PRECISION DBLE */
+/*      REAL */
+
+/* INITIALIZATION. */
+
+	zv = 0;
+	kode_arg = *l_kode;
+	cl1_space(check, l_n2d, k + l + m, l_nklmd);
+
+/* Parameter adjustments */
+	q_dim = l_n2d;
+	q2 = (union double_or_int *) q;
+	cu_dim = l_nklmd;
+
+/* Function Body */
+	maxit = *l_iter;
+	n1 = n + 1;
+	n2 = n + 2;
+	nk = n + k;
+	nkl = nk + l;
+	klm = k + l + m;
+	klm1 = klm + 1;
+	nklm = n + klm;
+	kforce = 1;
+	*l_iter = 0;
+	js = 0;
+	ia = -1;
+
+/* SET UP LABELS IN Q. */
+	for (j = 0; j < n; ++j)
+	{
+		q2[klm1 * q_dim + j].ival = j + 1;
+	}
+/* L10: */
+	for (i = 0; i < klm; ++i)
+	{
+		q2[i * q_dim + n1].ival = n + i + 1;
+		if (q2[i * q_dim + n].dval < 0.)
+		{
+			for (j = 0; j < n1; ++j)
+			{
+				q2[i * q_dim + j].dval = -q2[i * q_dim + j].dval;
+			}
+			q2[i * q_dim + n1].ival = -q2[i * q_dim + n1].ival;
+/* L20: */
+		}
+	}
+/* L30: */
+/* SET UP PHASE 1 COSTS. */
+	iphase = 2;
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "Set up phase 1 costs\n"));
+#endif
+/* Zero first row of cu and iu */
+	memcpy((void *) &(l_cu[0]), (void *) &(scratch[0]),
+		   (size_t) nklm * sizeof(LDBLE));
+	for (j = 0; j < nklm; ++j)
+	{
+		l_iu[j] = 0;
+	}
+/* L40: */
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "L40\n"));
+#endif
+	if (l != 0)
+	{
+		for (j = nk; j < nkl; ++j)
+		{
+			l_cu[j] = 1.;
+			l_iu[j] = 1;
+		}
+/* L50: */
+		iphase = 1;
+	}
+
+/* Copy first row of cu and iu to second row */
+	memcpy((void *) &(l_cu[cu_dim]), (void *) &(l_cu[0]),
+		   (size_t) nklm * sizeof(LDBLE));
+	memcpy((void *) &(l_iu[cu_dim]), (void *) &(l_iu[0]),
+		   (size_t) nklm * sizeof(int));
+
+/* L60: */
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "L60\n"));
+#endif
+	if (m != 0)
+	{
+		for (j = nkl; j < nklm; ++j)
+		{
+			l_cu[cu_dim + j] = 1.;
+			l_iu[cu_dim + j] = 1;
+			jmn = j - n;
+			if (q2[jmn * q_dim + n1].ival < 0)
+			{
+				iphase = 1;
+			}
+		}
+/* L70: */
+	}
+/* L80: */
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "L80\n"));
+#endif
+	if (*l_kode != 0)
+	{
+		for (j = 0; j < n; ++j)
+		{
+			if (l_x[j] < 0.)
+			{
+/* L90: */
+				l_cu[j] = 1.;
+				l_iu[j] = 1;
+			}
+			else if (l_x[j] > 0.)
+			{
+				l_cu[cu_dim + j] = 1.;
+				l_iu[cu_dim + j] = 1;
+			}
+		}
+/* L110: */
+#ifdef DEBUG_CL1
+		output_msg(sformatf( "L110\n"));
+#endif
+		for (j = 0; j < k; ++j)
+		{
+			jpn = j + n;
+			if (l_res[j] < 0.)
+			{
+/* L120: */
+				l_cu[jpn] = 1.;
+				l_iu[jpn] = 1;
+				if (q2[j * q_dim + n1].ival > 0)
+				{
+					iphase = 1;
+				}
+			}
+			else if (l_res[j] > 0.)
+			{
+/* L130: */
+				l_cu[cu_dim + jpn] = 1.;
+				l_iu[cu_dim + jpn] = 1;
+				if (q2[j * q_dim + n1].ival < 0)
+				{
+					iphase = 1;
+				}
+			}
+		}
+/* L140: */
+	}
+/* L150: */
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "L150\n"));
+#endif
+	if (iphase == 2)
+	{
+		goto L500;
+	}
+/* COMPUTE THE MARGINAL COSTS. */
+  L160:
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "L160\n"));
+#endif
+	for (j = js; j < n1; ++j)
+	{
+	sum = 0.;
+		for (i = 0; i < klm; ++i)
+		{
+			ii = q2[i * q_dim + n1].ival;
+			if (ii < 0)
+			{
+				l_z = l_cu[cu_dim - ii - 1];
+			}
+			else
+			{
+				l_z = l_cu[ii - 1];
+			}
+			sum += (long double) q2[i * q_dim + j].dval * (long double) l_z;
+		}
+		q2[klm * q_dim + j].dval = (double)sum;
+	}
+	for (j = js; j < n; ++j)
+	{
+		ii = q2[klm1 * q_dim + j].ival;
+		if (ii < 0)
+		{
+			l_z = l_cu[cu_dim - ii - 1];
+		}
+		else
+		{
+			l_z = l_cu[ii - 1];
+		}
+		q2[klm * q_dim + j].dval -= l_z;
+	}
+/* DETERMINE THE VECTOR TO ENTER THE BASIS. */
+  L240:
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "L240, xmax %e\n", xmax));
+#endif
+	xmax = 0.;
+	if (js >= n)
+	{
+		goto L490;				/* test for optimality */
+	}
+	for (j = js; j < n; ++j)
+	{
+		zu = q2[klm * q_dim + j].dval;
+		ii = q2[klm1 * q_dim + j].ival;
+		if (ii > 0)
+		{
+			zv = -zu - l_cu[ii - 1] - l_cu[cu_dim + ii - 1];
+		}
+		else
+		{
+			ii = -ii;
+			zv = zu;
+			zu = -zu - l_cu[ii - 1] - l_cu[cu_dim + ii - 1];
+		}
+/* L260 */
+		if (kforce == 1 && ii > n)
+		{
+			continue;
+		}
+		if (l_iu[ii - 1] != 1 && zu > xmax)
+		{
+			xmax = zu;
+			in = j;
+		}
+/* L270 */
+		if (l_iu[cu_dim + ii - 1] != 1 && zv > xmax)
+		{
+			xmax = zv;
+			in = j;
+		}
+	}
+/* L280 */
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "L280 xmax %e, toler %e\n", xmax, l_toler));
+#endif
+	if (xmax <= l_toler)
+	{
+#ifdef DEBUG_CL1
+		output_msg(sformatf( "xmax before optimality test %e\n", xmax));
+#endif
+		goto L490;				/* test for optimality */
+	}
+	if (q2[klm * q_dim + in].dval != xmax)
+	{
+		for (i = 0; i < klm1; ++i)
+		{
+			q2[i * q_dim + in].dval = -q2[i * q_dim + in].dval;
+		}
+		q2[klm1 * q_dim + in].ival = -q2[klm1 * q_dim + in].ival;
+/* L290: */
+		q2[klm * q_dim + in].dval = xmax;
+	}
+/* DETERMINE THE VECTOR TO LEAVE THE BASIS. */
+	if (iphase != 1 && ia != -1)
+	{
+		xmax = 0.;
+/* find maximum absolute value in column "in" */
+		for (i = 0; i <= ia; ++i)
+		{
+			l_z = fabs(q2[i * q_dim + in].dval);
+			if (l_z > xmax)
+			{
+				xmax = l_z;
+				iout = i;
+			}
+		}
+/* L310: */
+#ifdef DEBUG_CL1
+		output_msg(sformatf( "L310, xmax %e\n", xmax));
+#endif
+/* switch row ia with row iout, use memcpy */
+		if (xmax > l_toler)
+		{
+			if (ia != iout)
+			{
+				memcpy((void *) &(scratch[0]), (void *) &(q2[ia * q_dim]),
+					   (size_t) n2 * sizeof(LDBLE));
+				memcpy((void *) &(q2[ia * q_dim]), (void *) &(q2[iout * q_dim]),
+					   (size_t) n2 * sizeof(LDBLE));
+				memcpy((void *) &(q2[iout * q_dim]), (void *) &(scratch[0]),
+					   (size_t) n2 * sizeof(LDBLE));
+			}
+/* L320: */
+/* set pivot to row ia, column in */
+			iout = ia;
+			--ia;
+			pivot = q2[iout * q_dim + in].dval;
+			goto L420;			/* Gauss Jordan */
+		}
+	}
+/* L330: */
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "L330, xmax %e\n", xmax));
+#endif
+	kk = -1;
+/* divide column n1 by positive value in column "in" greater than toler */
+	for (i = 0; i < klm; ++i)
+	{
+		l_z = q2[i * q_dim + in].dval;
+		if (l_z > l_toler)
+		{
+			++kk;
+			l_res[kk] = q2[i * q_dim + n].dval / l_z;
+			l_s[kk] = i;
+		}
+	}
+/* L340: */
+#ifdef DEBUG_CL1
+	if (kk < 0)
+	{
+		output_msg(sformatf( "kode = 2 in loop 340.\n"));
+	}
+#endif
+  L350:
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "L350, xmax %e\n", xmax));
+#endif
+	if (kk < 0)
+	{
+/* no positive value found in L340 or bypass intermediate verticies */
+		*l_kode = 2;
+		goto L590;
+	}
+/* L360: */
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "L360, xmax %e\n", xmax));
+#endif
+/* find minimum residual */
+	xmin = l_res[0];
+	iout = l_s[0];
+	j = 0;
+	if (kk != 0)
+	{
+		for (i = 1; i <= kk; ++i)
+		{
+			if (l_res[i] < xmin)
+			{
+				j = i;
+				xmin = l_res[i];
+				iout = l_s[i];
+			}
+		}
+/* L370: */
+/* put kk in position j */
+		l_res[j] = l_res[kk];
+		l_s[j] = l_s[kk];
+	}
+/* L380: */
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "L380 iout %d, xmin %e, xmax %e\n", iout,
+			   xmin, xmax));
+#endif
+	--kk;
+	pivot = q2[iout * q_dim + in].dval;
+	ii = q2[iout * q_dim + n1].ival;
+	if (iphase != 1)
+	{
+		if (ii < 0)
+		{
+/* L390: */
+			if (l_iu[-ii - 1] == 1)
+			{
+				goto L420;
+			}
+		}
+		else
+		{
+			if (l_iu[cu_dim + ii - 1] == 1)
+			{
+				goto L420;
+			}
+		}
+	}
+/* L400: */
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "L400\n"));
+#endif
+	ii = abs(ii);
+	cuv = l_cu[ii - 1] + l_cu[cu_dim + ii - 1];
+	if (q2[klm * q_dim + in].dval - pivot * cuv > l_toler)
+	{
+
+/* BYPASS INTERMEDIATE VERTICES. */
+		for (j = js; j < n1; ++j)
+		{
+			l_z = q2[iout * q_dim + j].dval;
+			q2[klm * q_dim + j].dval -= l_z * cuv;
+			q2[iout * q_dim + j].dval = -l_z;
+		}
+/* L410: */
+		q2[iout * q_dim + n1].ival = -q2[iout * q_dim + n1].ival;
+		goto L350;
+	}
+/* GAUSS-JORDAN ELIMINATION. */
+  L420:
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "Gauss Jordon %d\n", *l_iter));
+#endif
+	if (*l_iter >= maxit)
+	{
+		*l_kode = 3;
+		goto L590;
+	}
+/* L430: */
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "L430\n"));
+#endif
+	++(*l_iter);
+	for (j = js; j < n1; ++j)
+	{
+		if (j != in)
+		{
+			q2[iout * q_dim + j].dval /= pivot;
+		}
+	}
+/* L440: */
+	for (j = js; j < n1; ++j)
+	{
+		if (j != in)
+		{
+			l_z = -q2[iout * q_dim + j].dval;
+			for (i = 0; i < klm1; ++i)
+			{
+				if (i != iout)
+				{
+					q2[i * q_dim + j].dval += l_z * q2[i * q_dim + in].dval;
+				}
+			}
+/* L450: */
+		}
+	}
+/* L460: */
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "L460\n"));
+#endif
+	tpivot = -pivot;
+	for (i = 0; i < klm1; ++i)
+	{
+		if (i != iout)
+		{
+			q2[i * q_dim + in].dval /= tpivot;
+		}
+	}
+/* L470: */
+	q2[iout * q_dim + in].dval = 1. / pivot;
+	ii = q2[iout * q_dim + n1].ival;
+	q2[iout * q_dim + n1].ival = q2[klm1 * q_dim + in].ival;
+	q2[klm1 * q_dim + in].ival = ii;
+	ii = abs(ii);
+	if (l_iu[ii - 1] == 0 || l_iu[cu_dim + ii - 1] == 0)
+	{
+		goto L240;
+	}
+/* switch column */
+	for (i = 0; i < klm1; ++i)
+	{
+		l_z = q2[i * q_dim + in].dval;
+		q2[i * q_dim + in].dval = q2[i * q_dim + js].dval;
+		q2[i * q_dim + js].dval = l_z;
+	}
+	i = q2[klm1 * q_dim + in].ival;
+	q2[klm1 * q_dim + in].ival = q2[klm1 * q_dim + js].ival;
+	q2[klm1 * q_dim + js].ival = i;
+/* L480: */
+	++js;
+	goto L240;
+/* TEST FOR OPTIMALITY. */
+  L490:
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "L490\n"));
+#endif
+	if (kforce == 0)
+	{
+		if (iphase == 1)
+		{
+			if (q2[klm * q_dim + n].dval <= l_toler)
+			{
+				goto L500;
+			}
+#ifdef DEBUG_CL1
+			output_msg(sformatf( "q2[klm1-1, n1-1] > *toler. %e\n",
+					   q2[(klm1 - 1) * q_dim + n1 - 1].dval));
+#endif
+			*l_kode = 1;
+			goto L590;
+		}
+		*l_kode = 0;
+		goto L590;
+	}
+	if (iphase != 1 || q2[klm * q_dim + n].dval > l_toler)
+	{
+		kforce = 0;
+		goto L240;
+	}
+/* SET UP PHASE 2 COSTS. */
+  L500:
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "Set up phase 2 costs %d\n", *l_iter));
+#endif
+	iphase = 2;
+	for (j = 0; j < nklm; ++j)
+	{
+		l_cu[j] = 0.;
+	}
+/* L510: */
+	for (j = n; j < nk; ++j)
+	{
+		l_cu[j] = 1.;
+	}
+	memcpy((void *) &(l_cu[cu_dim]), (void *) &(l_cu[0]),
+		   (size_t) nklm * sizeof(LDBLE));
+/* L520: */
+	for (i = 0; i < klm; ++i)
+	{
+		ii = q2[i * q_dim + n1].ival;
+		if (ii <= 0)
+		{
+			if (l_iu[cu_dim - ii - 1] == 0)
+			{
+				continue;
+			}
+			l_cu[cu_dim - ii - 1] = 0.;
+		}
+		else
+		{
+/* L530: */
+			if (l_iu[ii - 1] == 0)
+			{
+				continue;
+			}
+			l_cu[ii - 1] = 0.;
+		}
+/* L540: */
+		++ia;
+/* switch row */
+		if (ia != i)
+		{
+			memcpy((void *) &(scratch[0]), (void *) &(q2[ia * q_dim]),
+				   (size_t) n2 * sizeof(LDBLE));
+			memcpy((void *) &(q2[ia * q_dim]), (void *) &(q2[i * q_dim]),
+				   (size_t) n2 * sizeof(LDBLE));
+			memcpy((void *) &(q2[i * q_dim]), (void *) &(scratch[0]),
+				   (size_t) n2 * sizeof(LDBLE));
+		}
+/* L550: */
+	}
+/* L560: */
+	goto L160;
+
+
+/* PREPARE OUTPUT. */
+  L590:
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "L590\n"));
+#endif
+	sum = 0.;
+	for (j = 0; j < n; ++j)
+	{
+		l_x[j] = 0.;
+	}
+/* L600: */
+	for (i = 0; i < klm; ++i)
+	{
+		l_res[i] = 0.;
+	}
+/* L610: */
+	for (i = 0; i < klm; ++i)
+	{
+		ii = q2[i * q_dim + n1].ival;
+		sn = 1.;
+		if (ii < 0)
+		{
+			ii = -ii;
+			sn = -1.;
+		}
+		if (ii <= n)
+		{
+/* L620: */
+			l_x[ii - 1] = sn * q2[i * q_dim + n].dval;
+		}
+		else
+		{
+/* L630: */
+			l_res[ii - n - 1] = sn * q2[i * q_dim + n].dval;
+			if (ii >= n1 && ii <= nk)
+			{
+/*     *    DBLE(Q(I,N1)) */
+			  sum += (long double) q2[i * q_dim + n].dval;
+			}
+		}
+	}
+/* L640: */
+#ifdef DEBUG_CL1
+	output_msg(sformatf( "L640\n"));
+#endif
+	*l_error = (double)sum;
+	/*
+	 *  Check calculation
+	 */
+	if ((check == 1) && (*l_kode == 0))
+	{
+		check_toler = 10. * l_toler;
+		/*
+		 *  Check optimization constraints
+		 */
+		if (kode_arg == 1)
+		{
+			for (i = 0; i < k; ++i)
+			{
+				if (res_arg[i] < 0.0)
+				{
+					if (l_res[i] > check_toler)
+					{
+#ifdef CHECK_ERRORS
+						output_msg(sformatf(
+								   "\tCL1: optimization constraint not satisfied row %d, res %s, constraint %f.\n",
+								   row_name[row_back[i]], l_res[i], res_arg[i]));
+#endif
+						*l_kode = 1;
+					}
+				}
+				else if (res_arg[i] > 0.0)
+				{
+					if (l_res[i] < -check_toler)
+					{
+#ifdef CHECK_ERRORS
+						output_msg(sformatf(
+								   "\tCL1: optimization constraint not satisfied row %s, res %e, constraint %f.\n",
+								   row_name[row_back[i]], l_res[i], res_arg[i]));
+#endif
+						*l_kode = 1;
+					}
+				}
+			}
+		}
+		/*
+		 *  Check equalities
+		 */
+		for (i = k; i < k + l; ++i)
+		{
+			if (fabs(l_res[i]) > check_toler)
+			{
+#ifdef CHECK_ERRORS
+				output_msg(sformatf(
+						   "\tCL1: equality constraint not satisfied row %s, res %e, tolerance %e.\n",
+						   row_name[row_back[i]], l_res[i], check_toler));
+#endif
+				*l_kode = 1;
+			}
+		}
+		/*
+		 *  Check inequalities
+		 */
+		for (i = k + l; i < k + l + m; ++i)
+		{
+			if (l_res[i] < -check_toler)
+			{
+#ifdef CHECK_ERRORS
+				output_msg(sformatf(
+						   "\tCL1: inequality constraint not satisfied row %s, res %e, tolerance %e.\n",
+						   row_name[row_back[i]], l_res[i], check_toler));
+#endif
+				*l_kode = 1;
+			}
+		}
+		/*
+		 *   Check dissolution/precipitation constraints
+		 */
+		if (kode_arg == 1)
+		{
+			for (i = 0; i < n; ++i)
+			{
+				if (x_arg[i] < 0.0)
+				{
+					if (l_x[i] > check_toler)
+					{
+#ifdef CHECK_ERRORS
+						output_msg(sformatf(
+								   "\tCL1: dis/pre constraint not satisfied column %s, x %e, constraint %f.\n",
+								   col_name[col_back[i]], l_x[i], x_arg[i]));
+#endif
+						*l_kode = 1;
+					}
+				}
+				else if (x_arg[i] > 0.0)
+				{
+					if (l_x[i] < -check_toler)
+					{
+#ifdef CHECK_ERRORS
+						output_msg(sformatf(
+								   "\tCL1: dis/pre constraint not satisfied column %s, x %e, constraint %f.\n",
+								   col_name[col_back[i]], l_x[i], x_arg[i]));
+#endif
+						*l_kode = 1;
+					}
+				}
+			}
+		}
+		if (*l_kode == 1)
+		{
+			output_msg(sformatf(
+					   "\n\tCL1: Roundoff errors in optimization.\n\t     Try using -multiple_precision in INVERSE_MODELING\n"));
+		}
+	}
+	return 0;
+}
+
+void Phreeqc::
+cl1_space(int check, int l_n2d, int klm, int l_nklmd)
+{
+	if (check == 1)
+	{
+		if (x_arg == NULL)
+		{
+			x_arg = (LDBLE *) PHRQ_malloc((size_t) (l_n2d * sizeof(LDBLE)));
+		}
+		else if (l_n2d > x_arg_max)
+		{
+			x_arg =
+				(LDBLE *) PHRQ_realloc(x_arg, (size_t) (l_n2d * sizeof(LDBLE)));
+			x_arg_max = l_n2d;
+		}
+		if (x_arg == NULL)
+			malloc_error();
+		zero_double(x_arg, l_n2d);
+
+		if (res_arg == NULL)
+		{
+			res_arg = (LDBLE *) PHRQ_malloc((size_t) ((klm) * sizeof(LDBLE)));
+		}
+		else if (klm > res_arg_max)
+		{
+			res_arg =
+				(LDBLE *) PHRQ_realloc(res_arg,
+									   (size_t) ((klm) * sizeof(LDBLE)));
+			res_arg_max = klm;
+		}
+		if (res_arg == NULL)
+			malloc_error();
+		zero_double(res_arg, klm);
+	}
+
+/* Make scratch space */
+	if (scratch == NULL)
+	{
+		scratch = (LDBLE *) PHRQ_malloc((size_t) l_nklmd * sizeof(LDBLE));
+	}
+	else if (l_nklmd > scratch_max)
+	{
+		scratch =
+			(LDBLE *) PHRQ_realloc(scratch, (size_t) l_nklmd * sizeof(LDBLE));
+		scratch_max = l_nklmd;
+	}
+	if (scratch == NULL)
+		malloc_error();
+	zero_double(scratch, l_nklmd);
+}

src/phreeqcpp/class_main.cpp

@@ -0,0 +1,949 @@
+#include "Phreeqc.h"
+
+#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 <sys/signal.h>
+//#include <fenv.h>
+/* ----------------------------------------------------------------------
+ *   MAIN
+ * ---------------------------------------------------------------------- */
+int
+main(int argc, char *argv[])
+/*
+ *   Main program for PHREEQC
+ */
+{
+
+  // check for floating point exceptions on Linux
+  // feenableexcept(FE_DIVBYZERO|FE_INVALID|FE_OVERFLOW|FE_UNDERFLOW);
+#if defined(WIN32_MEMORY_DEBUG)
+	int tmpDbgFlag;
+
+	/*
+	 * Set the debug-heap flag to keep freed blocks in the
+	 * heap's linked list - This will allow us to catch any
+	 * inadvertent use of freed memory
+	 */
+#ifdef SKIP
+	// Send messages (leaks) to stderr
+    _CrtSetReportMode( _CRT_ERROR, _CRTDBG_MODE_FILE );
+    _CrtSetReportFile( _CRT_ERROR, _CRTDBG_FILE_STDERR );
+    _CrtSetReportMode( _CRT_WARN, _CRTDBG_MODE_FILE );
+    _CrtSetReportFile( _CRT_WARN, _CRTDBG_FILE_STDERR );
+    _CrtSetReportMode( _CRT_ASSERT, _CRTDBG_MODE_FILE );
+    _CrtSetReportFile( _CRT_ASSERT, _CRTDBG_FILE_STDERR );
+#endif
+	tmpDbgFlag = _CrtSetDbgFlag(_CRTDBG_REPORT_FLAG);
+	//tmpDbgFlag |= _CRTDBG_DELAY_FREE_MEM_DF;
+	tmpDbgFlag |= _CRTDBG_LEAK_CHECK_DF;
+	///tmpDbgFlag |= _CRTDBG_CHECK_ALWAYS_DF;
+	_CrtSetDbgFlag(tmpDbgFlag);
+	//_crtBreakAlloc = 31195;
+#endif
+#ifdef SKIP
+//Set the x86 floating-point control word according to what
+//exceptions you want to trap.
+_clearfp(); //Always call _clearfp before setting the control
+            //word
+//Because the second parameter in the following call is 0, it
+//only returns the floating-point control word
+unsigned int cw = _controlfp(0, 0); //Get the default control
+                                    //word
+//Set the exception masks off for exceptions that you want to
+//trap.  When a mask bit is set, the corresponding floating-point
+//exception is //blocked from being generating.
+cw &=~(EM_OVERFLOW|EM_UNDERFLOW|EM_ZERODIVIDE|
+       EM_DENORMAL|EM_INVALID);
+//For any bit in the second parameter (mask) that is 1, the
+//corresponding bit in the first parameter is used to update
+//the control word.
+unsigned int cwOriginal = _controlfp(cw, MCW_EM); //Set it.
+                            //MCW_EM is defined in float.h.
+                            //Restore the original value when done:
+                            //_controlfp(cwOriginal, MCW_EM);
+#endif
+	Phreeqc phreeqc_instance;
+	return phreeqc_instance.main_method(argc, argv);
+}
+//#define TEST_COPY
+#ifdef TEST_COPY
+int Phreeqc::
+main_method(int argc, char *argv[])
+/*
+ *   Main program for PHREEQC
+ */
+{
+
+	int errors;
+	std::istream *db_cookie = NULL;
+	std::istream *input_cookie = NULL;
+#if defined(WIN32_MEMORY_DEBUG)
+	int tmpDbgFlag;
+
+	/*
+	 * Set the debug-heap flag to keep freed blocks in the
+	 * heap's linked list - This will allow us to catch any
+	 * inadvertent use of freed memory
+	 */
+	tmpDbgFlag = _CrtSetDbgFlag(_CRTDBG_REPORT_FLAG);
+	//tmpDbgFlag |= _CRTDBG_DELAY_FREE_MEM_DF;
+	tmpDbgFlag |= _CRTDBG_LEAK_CHECK_DF;
+	///tmpDbgFlag |= _CRTDBG_CHECK_ALWAYS_DF;
+	_CrtSetDbgFlag(tmpDbgFlag);
+	//_crtBreakAlloc = 9482;
+#endif
+
+	phast = FALSE;
+/*
+ *   Open input/output files
+ */
+	errors = process_file_names(argc, argv, &db_cookie, &input_cookie, TRUE);
+	if (errors != 0)
+	{
+		return errors;
+	}
+#ifdef DOS
+	write_banner();
+#endif
+
+/*
+ *   Initialize arrays
+ */
+	errors = do_initialize();
+	if (errors != 0)
+	{
+		return errors;
+	}
+/*
+ *   Load database into memory
+ */
+	this->phrq_io->push_istream(db_cookie);
+	errors = read_database();
+	this->phrq_io->clear_istream();
+
+	if (errors != 0)
+	{
+		return errors;
+	}
+	Phreeqc MyCopy;
+	MyCopy = *this;
+	this->clean_up();
+	this->init();
+	this->initialize();
+/*
+ *   Read input data for simulation
+ */
+
+	MyCopy.phrq_io->push_istream(input_cookie);
+	errors = MyCopy.run_simulations();
+
+	//Phreeqc mycopy(*this);
+	MyCopy.phrq_io->clear_istream();
+
+	if (errors != 0)
+	{
+		return errors;
+	}
+/*
+ *   Display successful status
+ */
+	pr.headings = TRUE;
+	errors = do_status();
+	if (errors != 0)
+	{
+		return errors;
+	}
+	return 0;
+}
+#else
+int Phreeqc::
+main_method(int argc, char *argv[])
+/*
+ *   Main program for PHREEQC
+ */
+{
+
+	int errors;
+	std::istream *db_cookie = NULL;
+	std::istream *input_cookie = NULL;
+#if defined(WIN32_MEMORY_DEBUG)
+	int tmpDbgFlag;
+
+	/*
+	 * Set the debug-heap flag to keep freed blocks in the
+	 * heap's linked list - This will allow us to catch any
+	 * inadvertent use of freed memory
+	 */
+	tmpDbgFlag = _CrtSetDbgFlag(_CRTDBG_REPORT_FLAG);
+	//tmpDbgFlag |= _CRTDBG_DELAY_FREE_MEM_DF;
+	tmpDbgFlag |= _CRTDBG_LEAK_CHECK_DF;
+	///tmpDbgFlag |= _CRTDBG_CHECK_ALWAYS_DF;
+	_CrtSetDbgFlag(tmpDbgFlag);
+	//_crtBreakAlloc = 9482;
+#endif
+	try
+	{
+		phast = FALSE;
+		/*
+		*   Open input/output files
+		*/
+		errors = process_file_names(argc, argv, &db_cookie, &input_cookie, TRUE);
+		if (errors != 0)
+		{
+			return errors;
+		}
+#ifdef DOS
+		write_banner();
+#endif
+
+		/*
+		*   Initialize arrays
+		*/
+		errors = do_initialize();
+		if (errors != 0)
+		{
+			return errors;
+		}
+		/*
+		*   Load database into memory
+		*/
+		this->phrq_io->push_istream(db_cookie);
+		errors = read_database();
+		this->phrq_io->clear_istream();
+
+		if (errors != 0)
+		{
+			return errors;
+		}
+
+		/*
+		*   Read input data for simulation
+		*/
+
+		this->phrq_io->push_istream(input_cookie);
+		errors = run_simulations();
+
+		//Phreeqc mycopy(*this);
+		this->phrq_io->clear_istream();
+
+		if (errors != 0)
+		{
+			return errors;
+		}
+		/*
+		*   Display successful status
+		*/
+		pr.headings = TRUE;
+		errors = do_status();
+		if (errors != 0)
+		{
+			return errors;
+		}
+	}
+	catch (...)
+	{
+		int e = get_input_errors();
+		std::cerr << "Unhandled exception in PHREEQC." << std::endl;
+		if (e > 0)
+		{
+			return e;
+		}
+		else
+		{
+			return 1;
+		}
+	}
+	return 0;
+}
+#endif //TEST_COPY
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+write_banner(void)
+/* ---------------------------------------------------------------------- */
+{
+	char buffer[80];
+	int len, indent;
+	screen_msg(
+			   "              ÛßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßÛ\n");
+	screen_msg(
+			   "              º                                            º\n");
+
+	/* version */
+#ifdef NPP
+	//len = sprintf(buffer, "* PHREEQC-%s *", "3.4.2 AmpŠre");
+	len = sprintf(buffer, "* PHREEQC-%s *", "3.4.2");
+#else
+	len = sprintf(buffer, "* PHREEQC-%s *", "@VERSION@");
+#endif
+	indent = (44 - len) / 2;
+	screen_msg(sformatf("%14cº%*c%s%*cº\n", ' ', indent, ' ', buffer,
+			   44 - indent - len, ' '));
+
+	screen_msg(
+			   "              º                                            º\n");
+	screen_msg(
+			   "              º      A hydrogeochemical transport model    º\n");
+	screen_msg(
+			   "              º                                            º\n");
+	screen_msg(
+			   "              º                    by                      º\n");
+	screen_msg(
+			   "              º       D.L. Parkhurst and C.A.J. Appelo     º\n");
+	screen_msg(
+			   "              º                                            º\n");
+
+
+	/* date */
+#ifdef NPP
+	len = sprintf(buffer, "%s", "February 27, 2018");
+#else
+	len = sprintf(buffer, "%s", "@VER_DATE@");
+#endif
+	indent = (44 - len) / 2;
+	screen_msg(sformatf("%14cº%*c%s%*cº\n", ' ', indent, ' ', buffer,
+			   44 - indent - len, ' '));
+
+	screen_msg(
+			   "              ÛÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÛ\n\n");
+
+	return 0;
+}
+#ifdef ERROR_OSTREAM
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+process_file_names(int argc, char *argv[], std::istream **db_cookie,
+				   std::istream **input_cookie, int log)
+/* ---------------------------------------------------------------------- */
+{
+	int l;
+	char token[2 * MAX_LENGTH], default_name[2 * MAX_LENGTH];
+	char query[2 * MAX_LENGTH];
+	char in_file[2 * MAX_LENGTH], out_file[2 * MAX_LENGTH], db_file[2 * MAX_LENGTH];
+	char *env_ptr;
+	char *ptr;
+/*
+ *   Prepare error handling
+ */
+	try {
+		if (phrq_io == NULL)
+		{
+			std::cerr << "No PHRQ_io output handler defined in process_file_names" << "\n";
+		}
+/*
+ *   Prep for get_line
+ */
+		max_line = MAX_LINE;
+		space((void **) ((void *) &line), INIT, &max_line, sizeof(char));
+		space((void **) ((void *) &line_save), INIT, &max_line, sizeof(char));
+/*
+ *   Open error ostream
+ */
+		if (argc > 4)
+		{
+			if (!phrq_io->error_open(argv[4]))
+			{
+				error_string = sformatf( "Error opening file, %s.", argv[4]);
+				warning_msg(error_string);
+			}
+		}
+		else
+		{
+			phrq_io->error_open(NULL);
+		}
+/*
+ *   Open user-input file
+ */
+		strcpy(query, "Name of input file?");
+		std::ifstream * local_input_stream = NULL;
+		if (argc <= 1)
+		{
+			default_name[0] = '\0';
+			local_input_stream = open_input_stream(query, default_name, std::ios_base::in, false);
+		}
+		else
+		{
+			strcpy(default_name, argv[1]);
+			local_input_stream = open_input_stream(query, default_name, std::ios_base::in, true);
+		}
+		screen_msg(sformatf("Input file: %s\n\n", default_name));
+		strcpy(in_file, default_name);
+/*
+ *   Open file for output
+ */
+		strcpy(query, "Name of output file?");
+		ptr = default_name;
+		copy_token(token, &ptr, &l);
+		strcpy(token, default_name);
+		strcat(token, ".out");
+		std::ofstream * local_output_stream = NULL;
+		if (argc <= 1)
+		{
+			local_output_stream = open_output_stream(query, token, std::ios_base::out, false);
+		}
+		else if (argc == 2)
+		{
+			local_output_stream = open_output_stream(query, token, std::ios_base::out, true);
+		}
+		else if (argc >= 3)
+		{
+			strcpy(token, argv[2]);
+			local_output_stream = open_output_stream(query, token, std::ios_base::out, true);
+		}
+		screen_msg(sformatf("Output file: %s\n\n", token));
+		strcpy(out_file, token);
+		phrq_io->Set_output_ostream(local_output_stream);
+/*
+ *   Open log file
+ */
+		if (log == TRUE)
+		{
+			if (!phrq_io->log_open("phreeqc.log"))
+			{
+				error_msg("Cannot open log file, phreeqc.log.", STOP);
+			}
+		}
+/*
+ *  Read input file for DATABASE keyword
+ */
+		if (local_input_stream->is_open())
+		{
+			phrq_io->push_istream(local_input_stream);
+			if (get_line() == KEYWORD)
+			{
+				ptr = line;
+				copy_token(token, &ptr, &l);
+				if (strcmp_nocase(token, "database") == 0)
+				{
+					user_database = (char *) free_check_null(user_database);
+#ifdef PHREEQ98
+					user_database = string_duplicate(prefix_database_dir(ptr));
+#else
+					user_database = string_duplicate(ptr);
+#endif
+					if (string_trim(user_database) == EMPTY)
+					{
+						warning_msg("DATABASE file name is missing; default database will be used.");
+						user_database = (char *) free_check_null(user_database);
+					}
+				}
+			}
+			phrq_io->pop_istream();
+		}
+		else
+		{
+			delete local_input_stream;
+			error_string = sformatf( "Error opening file, %s.", in_file);
+			error_msg(error_string, STOP);
+		}
+
+/*
+ *   Open data base
+ */
+		strcpy(query, "Name of database file?");
+		env_ptr = getenv("PHREEQC_DATABASE");
+		if (user_database != NULL)
+		{
+			strcpy(token, user_database);
+		}
+		else if (env_ptr != NULL)
+		{
+			strcpy(token, env_ptr);
+		}
+		else
+		{
+			strcpy(token, default_data_base);
+		}
+
+		std::ifstream * local_database_file = NULL;
+		if (argc <= 1)
+		{
+			local_database_file = open_input_stream(query, token, std::ios_base::in, false);
+		}
+		else if (argc < 4)
+		{
+			local_database_file = open_input_stream(query, token, std::ios_base::in, true);
+		}
+		else if (argc >= 4)
+		{
+			if (user_database == NULL)
+			{
+				strcpy(token, argv[3]);
+			}
+			else
+			{
+#ifndef PHREEQCI_GUI
+				warning_msg	("Database file from DATABASE keyword is used; command line argument ignored.");
+#endif
+			}
+			local_database_file = open_input_stream(query, token, std::ios_base::in, true);
+		}
+		local_database_file->close();
+		delete local_database_file;
+		
+		user_database = (char *) free_check_null(user_database);
+		user_database = string_duplicate(token);
+		screen_msg(sformatf("Database file: %s\n\n", token));
+		strcpy(db_file, token);
+#ifdef NPP
+		//output_msg(sformatf("Using PHREEQC: version 3.4.2 Ampère, compiled February 27, 2018\n"));
+#endif
+		output_msg(sformatf("   Input file: %s\n", in_file));
+		output_msg(sformatf("  Output file: %s\n", out_file));
+#ifdef NPP
+		output_msg(sformatf("Using PHREEQC: version 3.4.2, compiled February 27, 2018\n"));
+#endif
+		output_msg(sformatf("Database file: %s\n\n", token));
+#ifdef NPP
+		output_flush();
+#endif
+		/*
+		*   local cleanup
+		*/
+		user_database = (char *) free_check_null(user_database);
+		line = (char *) free_check_null(line);
+		line_save = (char *) free_check_null(line_save);
+
+		*db_cookie = new std::ifstream(db_file, std::ios_base::in);
+		*input_cookie = new std::ifstream(in_file, std::ios_base::in);
+	}
+	catch (const PhreeqcStop&)
+	{
+		return get_input_errors();
+	}
+	return 0;
+}
+#else
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+process_file_names(int argc, char *argv[], std::istream **db_cookie,
+				   std::istream **input_cookie, int log)
+/* ---------------------------------------------------------------------- */
+{
+	int l;
+	char token[2 * MAX_LENGTH], default_name[2 * MAX_LENGTH];
+	char query[2 * MAX_LENGTH];
+	char in_file[2 * MAX_LENGTH], out_file[2 * MAX_LENGTH], db_file[2 * MAX_LENGTH];
+	char *env_ptr;
+	char *ptr;
+/*
+ *   Prepare error handling
+ */
+	try {
+		if (phrq_io == NULL)
+		{
+			std::cerr << "No PHRQ_io output handler defined in process_file_names" << "\n";
+		}
+/*
+ *   Prep for get_line
+ */
+		max_line = MAX_LINE;
+		space((void **) ((void *) &line), INIT, &max_line, sizeof(char));
+		space((void **) ((void *) &line_save), INIT, &max_line, sizeof(char));
+/*
+ *   Open error ostream
+ */
+		if (argc > 4)
+		{
+			if (!phrq_io->error_open(argv[4]))
+			{
+				error_string = sformatf( "Error opening file, %s.", argv[4]);
+				warning_msg(error_string);
+			}
+		}
+		else
+		{
+			phrq_io->error_open(NULL);
+		}
+/*
+ *   Open user-input file
+ */
+		strcpy(query, "Name of input file?");
+		std::ifstream * local_input_stream = NULL;
+		if (argc <= 1)
+		{
+			default_name[0] = '\0';
+			local_input_stream = open_input_stream(query, default_name, std::ios_base::in, false);
+		}
+		else
+		{
+			strcpy(default_name, argv[1]);
+			local_input_stream = open_input_stream(query, default_name, std::ios_base::in, true);
+		}
+		screen_msg(sformatf("Input file: %s\n\n", default_name));
+		strcpy(in_file, default_name);
+/*
+ *   Open file for output
+ */
+		strcpy(query, "Name of output file?");
+		ptr = default_name;
+		copy_token(token, &ptr, &l);
+		strcat(token, ".out");
+		std::ofstream * local_output_stream;
+		if (argc <= 1)
+		{
+			local_output_stream = open_output_stream(query, token, std::ios_base::out, false);
+		}
+		else if (argc == 2)
+		{
+			local_output_stream = open_output_stream(query, token, std::ios_base::out, true);
+		}
+		else if (argc >= 3)
+		{
+			strcpy(token, argv[2]);
+			local_output_stream = open_output_stream(query, token, std::ios_base::out, true);
+		}
+		screen_msg(sformatf("Output file: %s\n\n", token));
+		strcpy(out_file, token);
+		phrq_io->Set_output_ostream(local_output_stream);
+/*
+ *   Open log file
+ */
+		if (log == TRUE)
+		{
+			if (!phrq_io->log_open("phreeqc.log"))
+			{
+				error_msg("Cannot open log file, phreeqc.log.", STOP);
+			}
+		}
+/*
+ *  Read input file for DATABASE keyword
+ */
+		if (local_input_stream->is_open())
+		{
+			phrq_io->push_istream(local_input_stream);
+			if (get_line() == KEYWORD)
+			{
+				ptr = line;
+				copy_token(token, &ptr, &l);
+				if (strcmp_nocase(token, "database") == 0)
+				{
+					user_database = (char *) free_check_null(user_database);
+#ifdef PHREEQ98
+					user_database = string_duplicate(prefix_database_dir(ptr));
+#else
+					user_database = string_duplicate(ptr);
+#endif
+					if (string_trim(user_database) == EMPTY)
+					{
+						warning_msg("DATABASE file name is missing; default database will be used.");
+						user_database = (char *) free_check_null(user_database);
+					}
+				}
+			}
+			phrq_io->pop_istream();
+		}
+		else
+		{
+			delete local_input_stream;
+			error_string = sformatf( "Error opening file, %s.", in_file);
+			error_msg(error_string, STOP);
+		}
+
+/*
+ *   Open data base
+ */
+		strcpy(query, "Name of database file?");
+		env_ptr = getenv("PHREEQC_DATABASE");
+		if (user_database != NULL)
+		{
+			strcpy(token, user_database);
+		}
+		else if (env_ptr != NULL)
+		{
+			strcpy(token, env_ptr);
+		}
+		else
+		{
+			strcpy(token, default_data_base);
+		}
+
+		std::ifstream * local_database_file;
+		if (argc <= 1)
+		{
+			local_database_file = open_input_stream(query, token, std::ios_base::in, false);
+		}
+		else if (argc < 4)
+		{
+			local_database_file = open_input_stream(query, token, std::ios_base::in, true);
+		}
+		else if (argc >= 4)
+		{
+			if (user_database == NULL)
+			{
+				strcpy(token, argv[3]);
+			}
+			else
+			{
+#ifndef PHREEQCI_GUI
+				warning_msg	("Database file from DATABASE keyword is used; command line argument ignored.");
+#endif
+			}
+			local_database_file = open_input_stream(query, token, std::ios_base::in, true);
+		}
+		local_database_file->close();
+		delete local_database_file;
+		screen_msg(sformatf("Database file: %s\n\n", token));
+		strcpy(db_file, token);
+
+		output_msg(sformatf("   Input file: %s\n", in_file));
+		output_msg(sformatf("  Output file: %s\n", out_file));
+		output_msg(sformatf("Database file: %s\n\n", token));
+		/*
+		*   local cleanup
+		*/
+		user_database = (char *) free_check_null(user_database);
+		user_database = string_duplicate(token);
+		line = (char *) free_check_null(line);
+		line_save = (char *) free_check_null(line_save);
+
+		*db_cookie = new std::ifstream(db_file, std::ios_base::in);
+		*input_cookie = new std::ifstream(in_file, std::ios_base::in);
+	}
+	catch (const PhreeqcStop& e)
+	{
+		return get_input_errors();
+	}
+	return 0;
+}
+#endif
+/* ---------------------------------------------------------------------- */
+std::ifstream * Phreeqc::
+open_input_stream(char *query, char *default_name, std::ios_base::openmode mode, bool batch)
+/* ---------------------------------------------------------------------- */
+{
+	char name[MAX_LENGTH];
+	std::ifstream *new_stream;
+	int l;
+#ifdef ERROR_OSTREAM
+	std::ostream * error_ostream_save = phrq_io->Get_error_ostream();
+#else
+	FILE * error_file_save = phrq_io->Get_error_file();
+#endif
+
+	for (;;)
+	{
+/*
+ *   Get file name
+ */
+		strcpy(name, default_name);
+		if (!batch )
+		{
+#ifdef ERROR_OSTREAM
+			phrq_io->Set_error_ostream(&std::cerr);
+#else
+			phrq_io->Set_error_file(stderr);
+#endif
+			screen_msg(sformatf("%s\n", query));
+			if (default_name[0] != '\0')
+			{
+				screen_msg(sformatf("Default: %s\n", default_name));
+			}
+			char *s_ptr = fgets(name, MAX_LENGTH, stdin);
+			if (s_ptr == NULL)
+			{
+			    std::cerr << "Failed defining name." << std::endl;
+			}
+
+			l = (int) strlen(name);
+			name[l - 1] = '\0';
+			if (name[0] == '\0')
+			{
+				strcpy(name, default_name);
+			}
+		}
+/*
+ *   Open existing file to read
+ */
+		new_stream = new std::ifstream(name, mode);
+		if (new_stream == NULL || !new_stream->is_open())
+		{
+#ifdef ERROR_OSTREAM
+			phrq_io->Set_error_ostream(&std::cerr);
+#else
+			phrq_io->Set_error_file(stderr);
+#endif
+			error_string = sformatf( "\nERROR: Cannot open file, %s.\n", name);
+			screen_msg(error_string);
+#ifdef NPP
+			error_msg(sformatf( "\nERROR: Cannot open file, %s.\n       Please check, and give the correct, full path + name.\n", name), STOP);
+			break;
+#endif
+			error_flush();
+			batch = FALSE;
+			continue;
+		}
+		break;
+	}
+	strncpy(default_name, name, MAX_LENGTH);
+	if (!batch )
+	{
+		//phrq_io->Set_error_ostream(error_file_save);
+#ifdef ERROR_OSTREAM
+		phrq_io->Set_error_ostream(error_ostream_save);
+#else
+		phrq_io->Set_error_file(error_file_save);
+#endif
+	}
+	return (new_stream);
+}
+/* ---------------------------------------------------------------------- */
+std::ofstream * Phreeqc::
+open_output_stream(char *query, char *default_name, std::ios_base::openmode mode, bool batch)
+/* ---------------------------------------------------------------------- */
+{
+	char name[MAX_LENGTH];
+	std::ofstream *new_stream;
+	int l;
+#ifdef ERROR_OSTREAM
+	std::ostream * error_ostream_save = phrq_io->Get_error_ostream();
+#else
+	FILE * error_file_save = phrq_io->Get_error_file();
+#endif
+
+	for (;;)
+	{
+/*
+ *   Get file name
+ */
+		strcpy(name, default_name);
+		if (!batch )
+		{
+#ifdef ERROR_OSTREAM
+			phrq_io->Set_error_ostream(&std::cerr);
+#else
+			phrq_io->Set_error_file(stderr);
+#endif
+
+			screen_msg(sformatf("%s\n", query));
+			if (default_name[0] != '\0')
+			{
+				screen_msg(sformatf("Default: %s\n", default_name));
+			}
+			char *s_ptr = fgets(name, MAX_LENGTH, stdin);
+			if (s_ptr == NULL)
+			{
+			    std::cerr << "Failed defining name." << std::endl;
+			}
+
+			l = (int) strlen(name);
+			name[l - 1] = '\0';
+			if (name[0] == '\0')
+			{
+				strcpy(name, default_name);
+			}
+		}
+/*
+ *   Open existing file to read
+ */
+		new_stream = new std::ofstream(name, mode);
+		if (new_stream == NULL || !new_stream->is_open())
+		{
+#ifdef ERROR_OSTREAM
+			phrq_io->Set_error_ostream(&std::cerr);
+#else
+			phrq_io->Set_error_file(stderr);
+#endif
+			error_string = sformatf( "\nERROR: Cannot open file, %s.\n", name);
+			screen_msg(error_string);
+			error_flush();
+			batch = FALSE;
+			continue;
+		}
+		break;
+	}
+	strncpy(default_name, name, MAX_LENGTH);
+	if (!batch )
+	{
+#ifdef ERROR_OSTREAM
+		phrq_io->Set_error_ostream(error_ostream_save);
+#else
+		phrq_io->Set_error_file(error_file_save);
+#endif
+	}
+	return (new_stream);
+}
+#ifdef SKIP
+/* ---------------------------------------------------------------------- */
+std::ofstream * Phreeqc::
+open_output_file(char *query, char *default_name, std::ios_base::openmode mode, bool batch)
+/* ---------------------------------------------------------------------- */
+{
+	char name[MAX_LENGTH];
+	std::ofstream *new_stream;
+	int l;
+#ifdef ERROR_OSTREAM
+		std::ostream * error_ostream_save = phrq_io->Get_error_ostream();
+#else
+		FILE * error_file_save = phrq_io->Get_error_file();
+#endif
+
+
+	for (;;)
+	{
+/*
+ *   Get file name
+ */
+		strcpy(name, default_name);
+		if (!batch )
+		{
+#ifdef ERROR_OSTREAM
+			phrq_io->Set_error_ostream(&std::cerr);
+#else
+			phrq_io->Set_error_file(stderr);
+#endif
+			screen_msg(sformatf("%s\n", query));
+			if (default_name[0] != '\0')
+			{
+				screen_msg(sformatf("Default: %s\n", default_name));
+			}
+			char *s_ptr = fgets(name, MAX_LENGTH, stdin);
+			if (s_ptr == NULL)
+			{
+			    std::cerr << "Failed defining name." << std::endl;
+			}
+
+			l = (int) strlen(name);
+			name[l - 1] = '\0';
+			if (name[0] == '\0')
+			{
+				strcpy(name, default_name);
+			}
+		}
+/*
+ *   Open existing file to read
+ */
+		new_stream = new std::ofstream(name, mode);
+		if (new_stream == NULL || !new_stream->is_open())
+		{
+#ifdef ERROR_OSTREAM
+			phrq_io->Set_error_ostream(&std::cerr);
+#else
+			phrq_io->Set_error_file(stderr);
+#endif
+			error_string = sformatf( "\nERROR: Cannot open file, %s.\n", name);
+			screen_msg(error_string);
+			error_flush();
+			batch = FALSE;
+			continue;
+		}
+		break;
+	}
+	strncpy(default_name, name, MAX_LENGTH);
+	if (!batch )
+	{
+#ifdef ERROR_OSTREAM
+		phrq_io->Set_error_ostream(error_ostream_save);
+#else
+		phrq_io->Set_error_file(error_file_save);
+#endif
+	}
+	return (new_stream);
+}
+#endif

src/phreeqcpp/common/PHRQ_base.cxx

@@ -0,0 +1,108 @@
+#include "PHRQ_base.h"
+#include <iostream>
+#include "PHRQ_io.h"
+PHRQ_base::
+PHRQ_base(void)
+{
+	this->io = NULL;
+	base_error_count = 0;
+}
+
+PHRQ_base::
+PHRQ_base(PHRQ_io * p_io)
+{
+	this->io = p_io;
+	base_error_count = 0;
+}
+
+PHRQ_base::
+~PHRQ_base()
+{
+}
+
+void PHRQ_base::
+error_msg(const std::string & stdstr, int stop)
+{
+	this->base_error_count++;
+	std::ostringstream msg;
+	msg << "ERROR: " << stdstr << "\n";
+	if (this->io)
+	{
+		this->io->output_msg(msg.str().c_str());
+		this->io->log_msg(msg.str().c_str());
+		this->io->error_msg("\n");
+		this->io->error_msg(msg.str().c_str(), stop!=0);
+	}
+	else
+	{
+#if !defined(R_SO)
+		std::cerr << msg.str().c_str();
+		std::cout << msg.str().c_str();
+#endif
+	}
+	if (stop != 0)
+	{
+		throw PhreeqcStop();
+	}
+}
+
+void PHRQ_base::
+warning_msg(const std::string & stdstr)
+{
+	if (this->io)
+	{
+		this->io->warning_msg(stdstr.c_str());
+	}
+	else
+	{
+#if !defined(R_SO)
+		std::cerr << stdstr << "\n";
+		std::cout << stdstr << "\n";
+#endif
+	}
+}
+
+void PHRQ_base::
+output_msg(const std::string & stdstr)
+{
+	if (this->io)
+	{
+		this->io->output_msg(stdstr.c_str());
+	}
+	else
+	{
+#if !defined(R_SO)
+		std::cout << stdstr << "\n";
+#endif
+	}
+}
+
+void PHRQ_base::
+screen_msg(const std::string & stdstr)
+{
+	if (this->io)
+	{
+		this->io->screen_msg(stdstr.c_str());
+	}
+	else
+	{
+#if !defined(R_SO)
+		std::cerr << stdstr << "\n";
+#endif
+	}
+}
+
+void PHRQ_base::
+echo_msg(const std::string & stdstr)
+{
+	if (this->io)
+	{
+		this->io->echo_msg(stdstr.c_str());
+	}
+	else
+	{
+#if !defined(R_SO)
+		std::cout << stdstr << "\n";
+#endif
+	}
+}

src/phreeqcpp/common/PHRQ_base.h

@@ -0,0 +1,52 @@
+#ifndef _PHRQBASE_H
+#define _PHRQBASE_H
+
+#include <sstream>
+
+#if defined(_WINDLL)
+#define IPQ_DLL_EXPORT __declspec(dllexport)
+#else
+#define IPQ_DLL_EXPORT
+#endif
+
+class PHRQ_io;
+class IPQ_DLL_EXPORT PHRQ_base
+{
+public:
+	// constructors
+	PHRQ_base(void);
+	PHRQ_base(PHRQ_io *);
+	virtual ~ PHRQ_base();
+
+
+	// methods
+	void output_msg(const std::string &);
+	void error_msg(const std::string &, int stop=0);
+	void warning_msg(const std::string &);
+	void screen_msg(const std::string &);
+	void echo_msg(const std::string &);
+
+
+	void Set_io(PHRQ_io * p_io)
+	{
+		this->io = p_io;
+	}
+	PHRQ_io * Get_io(void)
+	{
+		return this->io;
+	}
+	void Set_base_error_count(int i)
+	{
+		this->base_error_count = i;
+	}
+	int Get_base_error_count(void)
+	{
+		return this->base_error_count;
+	}
+	// data
+protected:
+	PHRQ_io * io;
+	int base_error_count;
+};
+
+#endif /* _PHRQBASE_H */

src/phreeqcpp/common/PHRQ_io.cpp

@@ -0,0 +1,904 @@
+#include <assert.h>
+#include "PHRQ_io.h"
+#include "Parser.h"
+
+#include <algorithm>
+#include <cctype>
+#include <fstream>
+#include <iostream>
+#include <sstream>
+#include <set>
+
+#include <string.h>
+#include <stdio.h>
+#include <stdarg.h>
+
+PHRQ_io::
+PHRQ_io(void)
+{
+	output_ostream = NULL;
+	log_ostream = NULL;
+	punch_ostream = NULL;
+#ifdef ERROR_OSTREAM
+	error_ostream = NULL;
+#else
+	error_file = NULL;
+#endif
+	dump_ostream = NULL;
+	io_error_count = 0;
+
+	output_on = true;
+	log_on = false;
+	punch_on = true;
+	error_on = true;
+	dump_on = true;
+	echo_on = true; //**appt
+	screen_on = true;
+	echo_destination = ECHO_OUTPUT;
+
+	m_next_keyword = Keywords::KEY_NONE;
+	accumulate = false;
+	m_line_type = PHRQ_io::LT_EMPTY;
+}
+
+PHRQ_io::
+~PHRQ_io()
+{
+}
+// ---------------------------------------------------------------------- */
+// output ostream methods
+// ---------------------------------------------------------------------- */
+
+bool PHRQ_io::
+ofstream_open(std::ostream **os, const char *file_name, std::ios_base::openmode mode)
+{
+	std::ofstream *ofs = new std::ofstream(file_name, mode);
+	if (ofs && ofs->is_open())
+	{
+		*os = ofs;
+		return true;
+	}
+	delete ofs;
+	return false;
+}
+
+/* ---------------------------------------------------------------------- */
+bool PHRQ_io::
+output_open(const char *file_name, std::ios_base::openmode mode)
+/* ---------------------------------------------------------------------- */
+{
+	return ofstream_open(&output_ostream, file_name, mode);
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+output_flush(void)
+/* ---------------------------------------------------------------------- */
+{
+	if (output_ostream)
+	{
+		output_ostream->flush();
+	}
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+output_close(void)
+/* ---------------------------------------------------------------------- */
+{
+	safe_close(&output_ostream);
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+output_msg(const char * str)
+/* ---------------------------------------------------------------------- */
+{
+	if (output_ostream != NULL && output_on)
+	{
+		(*output_ostream) << str;
+	}
+	//output_flush();
+}
+// ---------------------------------------------------------------------- */
+// log ostream methods
+// ---------------------------------------------------------------------- */
+bool PHRQ_io::
+log_open(const char *file_name, std::ios_base::openmode mode)
+/* ---------------------------------------------------------------------- */
+{
+	return ofstream_open(&log_ostream, file_name, mode);
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+log_flush(void)
+/* ---------------------------------------------------------------------- */
+{
+	if (log_ostream)
+	{
+		log_ostream->flush();
+	}
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+log_close(void)
+/* ---------------------------------------------------------------------- */
+{
+	safe_close(&log_ostream);
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+log_msg(const char * str)
+/* ---------------------------------------------------------------------- */
+{
+	if (log_ostream != NULL && log_on)
+	{
+		(*log_ostream) << str;
+	}
+}
+// ---------------------------------------------------------------------- */
+// punch ostream methods
+// ---------------------------------------------------------------------- */
+bool PHRQ_io::
+punch_open(const char *file_name, std::ios_base::openmode mode, int n_user)
+/* ---------------------------------------------------------------------- */
+{
+	return ofstream_open(&punch_ostream, file_name, mode);
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+punch_flush(void)
+/* ---------------------------------------------------------------------- */
+{
+	if (punch_ostream)
+	{
+		punch_ostream->flush();
+	}
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+punch_close(void)
+/* ---------------------------------------------------------------------- */
+{
+	safe_close(&punch_ostream);
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+punch_msg(const char * str)
+/* ---------------------------------------------------------------------- */
+{
+	if (punch_ostream != NULL && punch_on)
+	{
+		(*punch_ostream) << str;
+	}
+}
+// ---------------------------------------------------------------------- */
+// error file methods
+// ---------------------------------------------------------------------- */
+#ifdef ERROR_OSTREAM
+/* ---------------------------------------------------------------------- */
+bool PHRQ_io::
+error_open(const char *file_name, std::ios_base::openmode mode)
+/* ---------------------------------------------------------------------- */
+{
+	if (file_name != NULL)
+	{
+		if (!ofstream_open(&error_ostream, file_name, mode))
+		{
+#if !defined(R_SO)
+			error_ostream = &std::cerr;
+#endif
+			return false;
+		}
+	}
+	else
+	{
+#if !defined(R_SO)
+		error_ostream = &std::cerr;
+#endif
+	}
+	return true;
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+error_flush(void)
+/* ---------------------------------------------------------------------- */
+{
+	if (error_ostream)
+	{
+		error_ostream->flush();
+	}
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+error_close(void)
+/* ---------------------------------------------------------------------- */
+{
+	safe_close(&error_ostream);
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+error_msg(const char *err_str, bool stop)
+/* ---------------------------------------------------------------------- */
+{
+
+	io_error_count++;
+	if (error_ostream != NULL && error_on)
+	{
+		//(*error_ostream) << err_str;
+		screen_msg(err_str);
+		error_flush();
+	}
+	if (stop)
+	{
+		if (error_ostream != NULL && error_on)
+		{
+			//(*error_ostream) << "Stopping.\n";
+			screen_msg("Stopping.\n");
+			error_ostream->flush();
+		}
+		output_msg("Stopping.\n");
+		log_msg("Stopping.\n");
+
+		throw PhreeqcStop();
+	}
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+warning_msg(const char *err_str)
+/* ---------------------------------------------------------------------- */
+{
+	if (error_ostream != NULL && error_on)
+	{
+		//(*error_ostream) << err_str << "\n";
+		std::string err_stdstr(err_str);
+		err_stdstr.append("\n");
+		screen_msg(err_stdstr.c_str());
+		error_ostream->flush();
+	}
+	std::ostringstream warn_str;
+	warn_str << err_str << "\n";
+	log_msg(warn_str.str().c_str());
+	log_flush();
+	output_msg(warn_str.str().c_str());
+	output_flush();
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+screen_msg(const char * str)
+/* ---------------------------------------------------------------------- */
+{
+	if (error_ostream != NULL && screen_on)
+	{
+		(*error_ostream) << str;
+	}
+}
+#else
+/* ---------------------------------------------------------------------- */
+bool PHRQ_io::
+error_open(const char *file_name, const char * mode)
+/* ---------------------------------------------------------------------- */
+{
+	if (file_name != NULL)
+	{
+		if ((error_file = fopen(file_name, mode)) == NULL)
+		{
+			error_file = stderr;
+			return false;
+		}
+	}
+	else
+	{
+		error_file = stderr;
+	}
+	return true;
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+error_flush(void)
+/* ---------------------------------------------------------------------- */
+{
+	if (error_file)
+	{
+		fflush(error_file);
+	}
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+error_close(void)
+/* ---------------------------------------------------------------------- */
+{
+	safe_close(&error_file);
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+error_msg(const char *err_str, bool stop)
+/* ---------------------------------------------------------------------- */
+{
+
+	io_error_count++;
+	if (error_file != NULL && error_on)
+	{
+		//(*error_file) << err_str;
+		screen_msg(err_str);
+		error_flush();
+	}
+	if (stop)
+	{
+		if (error_file != NULL && error_on)
+		{
+			//(*error_file) << "Stopping.\n";
+			screen_msg("Stopping.\n");
+			fflush(error_file);
+		}
+		output_msg("Stopping.\n");
+		log_msg("Stopping.\n");
+	}
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+warning_msg(const char *err_str)
+/* ---------------------------------------------------------------------- */
+{
+	if (error_file != NULL && error_on)
+	{
+		//(*error_file) << err_str << "\n";
+		std::string err_stdstr(err_str);
+		err_stdstr.append("\n");
+		screen_msg(err_stdstr.c_str());
+		error_flush();
+	}
+	std::ostringstream warn_str;
+	warn_str << err_str << "\n";
+	log_msg(warn_str.str().c_str());
+	log_flush();
+	output_msg(warn_str.str().c_str());
+	output_flush();
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+screen_msg(const char * str)
+/* ---------------------------------------------------------------------- */
+{
+	std::string stdstr(str);
+	if (error_file != NULL && screen_on)
+	{
+		fprintf(error_file, "%s", str);
+	}
+}
+#endif
+// ---------------------------------------------------------------------- */
+// dump ostream methods
+// ---------------------------------------------------------------------- */
+/* ---------------------------------------------------------------------- */
+bool PHRQ_io::
+dump_open(const char *file_name, std::ios_base::openmode mode)
+/* ---------------------------------------------------------------------- */
+{
+	return ofstream_open(&dump_ostream, file_name, mode);
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+dump_flush(void)
+/* ---------------------------------------------------------------------- */
+{
+	if (dump_ostream)
+	{
+		dump_ostream->flush();
+	}
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+dump_close(void)
+/* ---------------------------------------------------------------------- */
+{
+	safe_close(&dump_ostream);
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+dump_msg(const char * str)
+/* ---------------------------------------------------------------------- */
+{
+	if (dump_ostream != NULL && dump_on)
+	{
+		(*dump_ostream) << str;
+	}
+}
+int PHRQ_io::
+getc(void)
+{
+	if (std::istream* is = get_istream())
+	{
+		int n = is->get();
+		if (n == 13 && is->peek() == 10)
+		{
+			n = is->get();
+		}
+		return n;
+	}
+	return EOF;
+}
+
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+fpunchf(const char *name, const char *format, double d)
+/* ---------------------------------------------------------------------- */
+{
+	if (punch_ostream != NULL && punch_on)
+	{
+		fpunchf_helper(punch_ostream, format, d);
+	}
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+fpunchf(const char *name, const char *format, char * s)
+/* ---------------------------------------------------------------------- */
+{
+	if (punch_ostream != NULL && punch_on)
+	{
+		fpunchf_helper(punch_ostream, format, s);
+	}
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+fpunchf(const char *name, const char *format, int d)
+/* ---------------------------------------------------------------------- */
+{
+	if (punch_ostream != NULL && punch_on)
+	{
+		fpunchf_helper(punch_ostream, format, d);
+	}
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+fpunchf_helper(std::ostream *os, const char *format, ...)
+/* ---------------------------------------------------------------------- */
+{
+	if (os)
+	{
+		const size_t STACK_MAX = 2048;
+		char stack_buffer[STACK_MAX];
+
+		va_list args;
+		va_start(args, format);
+		int j = ::vsnprintf(stack_buffer, STACK_MAX, format, args);
+		bool success = (j >= 0 && j < (int) STACK_MAX);
+		va_end(args);
+
+		if (success)
+		{
+			(*os) << stack_buffer;
+		}
+		else
+		{
+			size_t alloc_buffer_size = STACK_MAX * 2;
+			char *alloc_buffer = new char[alloc_buffer_size];
+			do
+			{
+				va_list args;
+				va_start(args, format);
+				j = ::vsnprintf(alloc_buffer, alloc_buffer_size, format, args);
+				success = (j >= 0 && j < (int) alloc_buffer_size);
+				va_end(args);
+				if (!success)
+				{
+					delete[] alloc_buffer;
+					alloc_buffer_size *= 2;
+					alloc_buffer = new char[alloc_buffer_size];
+				}
+			}
+			while (!success);
+
+			(*os) << alloc_buffer;
+			delete[] alloc_buffer;
+		}
+	}
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+fpunchf_helper(std::string *str, const char *format, ...)
+/* ---------------------------------------------------------------------- */
+{
+	if (str)
+	{
+		const size_t STACK_MAX = 2048;
+		char stack_buffer[STACK_MAX];
+
+		va_list args;
+		va_start(args, format);
+		int j = ::vsnprintf(stack_buffer, STACK_MAX, format, args);
+		bool success = (j >= 0 && j < (int) STACK_MAX);
+		va_end(args);
+
+		if (success)
+		{
+			(*str) += stack_buffer;
+		}
+		else
+		{
+			size_t alloc_buffer_size = STACK_MAX * 2;
+			char *alloc_buffer = new char[alloc_buffer_size];
+			do
+			{
+				va_list args;
+				va_start(args, format);
+				j = ::vsnprintf(alloc_buffer, alloc_buffer_size, format, args);
+				success = (j >= 0 && j < (int) alloc_buffer_size);
+				va_end(args);
+				if (!success)
+				{
+					delete[] alloc_buffer;
+					alloc_buffer_size *= 2;
+					alloc_buffer = new char[alloc_buffer_size];
+				}
+			}
+			while (!success);
+
+			(*str) += alloc_buffer;
+			delete[] alloc_buffer;
+		}
+	}
+}
+
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::fpunchf_end_row(const char *format)
+/* ---------------------------------------------------------------------- */
+{
+	//NOOP for Phreeqc
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+close_ostreams(void)
+/* ---------------------------------------------------------------------- */
+{
+	std::set<std::ostream *> streams;
+
+	streams.insert(output_ostream);
+	streams.insert(log_ostream);
+//	streams.insert(punch_ostream);   // Should be deleted in ~SelectedOutput
+#ifdef ERROR_OSTREAM
+	streams.insert(error_ostream);
+#else
+	safe_close(&error_file);
+#endif
+	streams.insert(dump_ostream);
+
+	std::set<std::ostream *>::iterator it = streams.begin();
+	for (; it != streams.end(); it++)
+	{
+		std::ostream * x = *it;
+		safe_close(&x);
+	}
+
+	output_ostream = NULL;
+	log_ostream = NULL;
+	punch_ostream = NULL;
+#ifdef ERROR_OSTREAM
+	error_ostream = NULL;
+#else
+	error_file = NULL;
+#endif
+	dump_ostream = NULL;
+}
+//safe_close is static method
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+safe_close(std::ostream **stream_ptr)
+/* ---------------------------------------------------------------------- */
+{
+	if (
+#if !defined(R_SO)
+		*stream_ptr != &std::cerr &&
+		*stream_ptr != &std::cout &&
+		*stream_ptr != &std::clog &&
+#endif
+		*stream_ptr != NULL)
+	{
+		delete *stream_ptr;
+		*stream_ptr = NULL;
+	}
+}
+void PHRQ_io::
+safe_close(FILE **file_ptr)
+/* ---------------------------------------------------------------------- */
+{
+	if (
+#if !defined(R_SO)
+		*file_ptr != stderr &&
+		*file_ptr != stdout &&
+		*file_ptr != stdin &&
+#endif
+		*file_ptr != NULL)
+	{
+		fclose(*file_ptr);
+		*file_ptr = NULL;
+	}
+}
+/* ---------------------------------------------------------------------- */
+void PHRQ_io::
+echo_msg(const char * str)
+/* ---------------------------------------------------------------------- */
+{
+	if (echo_on)
+	{
+		switch (this->echo_destination)
+		{
+		case ECHO_LOG:
+			log_msg(str);
+			break;
+		case ECHO_OUTPUT:
+			output_msg(str);
+			break;
+		}
+	}
+}
+
+std::istream * PHRQ_io::
+get_istream()
+{
+	if (istream_list.size() > 0)
+	{
+		return istream_list.front();
+	}
+	else
+	{
+		return NULL;
+	}
+}
+void PHRQ_io::
+push_istream(std::istream * cookie, bool auto_delete)
+{
+	istream_list.push_front(cookie);
+	delete_istream_list.push_front(auto_delete);
+}
+void PHRQ_io::
+clear_istream(void)
+{
+	while (istream_list.size() > 0)
+	{
+		pop_istream();
+	}
+}
+void PHRQ_io::
+pop_istream()
+{
+	if (istream_list.size() > 0)
+	{
+		if (delete_istream_list.front())
+		{
+			delete istream_list.front();
+		}
+		istream_list.pop_front();
+		delete_istream_list.pop_front();
+	}
+}
+/* ---------------------------------------------------------------------- */
+PHRQ_io::LINE_TYPE PHRQ_io::
+get_line(void)
+/* ---------------------------------------------------------------------- */
+{
+/*
+ *   Read a line from input file put in "line".
+ *   Copy of input line is stored in "line_save".
+ *   Characters after # are discarded in line but retained in "line_save"
+ *
+ *   Arguments:
+ *      fp is file name
+ *   Returns:
+ *      EMPTY,
+ *      EOF,
+ *      KEYWORD,
+ *      OK,
+ *      OPTION
+ */
+	std::string stdtoken;
+	bool continue_loop = true;;
+
+	PHRQ_io::LINE_TYPE return_value;
+	// loop for include files
+	for (;;)
+	{
+		if (this->get_istream() == NULL)
+		{
+			break;
+		}
+		return_value = LT_EMPTY;
+		while (return_value == LT_EMPTY)
+		{
+			/*
+			*   Eliminate all characters after # sign as a comment
+			*/
+			/*
+			*   Get line, check for eof
+			*/
+			continue_loop = false;
+
+			if (get_logical_line() == LT_EOF)
+			{
+				//pop next file
+				this->pop_istream();
+				continue_loop = true;
+				break;
+			}
+			/*
+			*   Get long lines
+			*/
+			bool empty = true;
+			m_line = m_line_save.substr(0, m_line_save.find_first_of('#'));
+			for (unsigned int i = 0; i < m_line.size(); ++i)
+			{
+				if (!::isspace(m_line[i]))
+				{
+					empty = false;
+					break;
+				}
+			}
+
+			if (this->accumulate)
+			{
+				this->accumulated.append(m_line_save);
+				this->accumulated.append("\n");
+			}
+			//
+			// New line character encountered
+			//
+			return_value = (empty ? LT_EMPTY : LT_OK);
+
+		}
+		if (continue_loop) continue;
+		//
+		// Determine return_value
+		//
+		if (return_value == LT_OK)
+		{
+			if (check_key(m_line.begin(), m_line.end()))
+			{
+				return_value = LT_KEYWORD;
+			}
+			else
+			{
+				std::string::iterator beg = m_line.begin();
+				std::string::iterator end = m_line.end();
+				std::string token;
+				CParser::copy_token(token, beg, end);
+
+				if (token.size() > 1 && token[0] == '-' &&::isalpha(token[1]))
+				{
+					return_value = LT_OPTION;
+				}
+			}
+		}
+
+		// add new include file to stack
+		std::string::iterator beg = m_line.begin();
+		std::string::iterator end = m_line.end();
+		CParser::copy_token(stdtoken, beg, end);
+		std::transform(stdtoken.begin(), stdtoken.end(), stdtoken.begin(), ::tolower);
+		if ((strstr(stdtoken.c_str(),"include$") == stdtoken.c_str()) ||
+			(strstr(stdtoken.c_str(),"include_file") == stdtoken.c_str()))
+		{
+			std::string file_name;
+			file_name.assign(beg, end);
+			file_name = trim(file_name);
+
+			if (file_name.size() > 0)
+			{
+				std::ifstream *next_stream = new std::ifstream(file_name.c_str(), std::ios_base::in);
+				if (!next_stream->is_open())
+				{
+					std::ostringstream errstr;
+					errstr << "\n***********  Could not open include file " << file_name
+						   <<".\n             Please, write the full path to this file. ***********\n\n";
+					delete next_stream;
+#if defined(PHREEQCI_GUI)
+					warning_msg(errstr.str().c_str());
+					continue;
+#else
+					output_msg(errstr.str().c_str());
+					error_msg(errstr.str().c_str(), OT_STOP);
+#endif
+				}
+				else
+				{
+					this->push_istream(next_stream);
+					std::ostringstream errstr;
+					errstr << "\n\tReading data from " << file_name <<" ...\n";
+					output_msg(errstr.str().c_str()); // **appt
+				}
+				continue;
+			}
+		}
+		return return_value;
+	}
+	m_next_keyword = Keywords::KEY_END;
+	return LT_EOF;
+}
+
+/**
+        Reads input stream until end of line, ";", or eof
+        stores characters in line_save
+
+        returns:
+                EOF on empty line on end of file or
+                OK otherwise
+*/
+PHRQ_io::LINE_TYPE PHRQ_io::
+get_logical_line(void)
+{
+	int j;
+	unsigned int pos;
+	char c;
+
+	m_line_save.erase(m_line_save.begin(), m_line_save.end());	// m_line_save.clear();
+	while ((j = getc()) != EOF)
+	{
+		c = (char) j;
+		if (c == '#')
+		{
+			// ignore all chars after # until newline
+			do
+			{
+				c = (char) j;
+				if (c == '\n')
+				{
+					break;
+				}
+				m_line_save += c;
+			}
+			while ((j = getc()) != EOF);
+		}
+		if (c == ';')
+			break;
+		if (c == '\n')
+		{
+			break;
+		}
+		if (c == '\\')
+		{
+			pos = (int) m_line_save.size();
+			m_line_save += c;
+			while ((j = getc()) != EOF)
+			{
+				c = (char) j;
+				if (c == '\\')
+				{
+					pos = (int) m_line_save.size();
+					m_line_save += c;
+					continue;
+				}
+				if (c == '\n')
+				{
+					// remove '\\'
+					m_line_save = m_line_save.substr(0,pos);
+					break;
+				}
+				m_line_save += c;
+				if (!::isspace(j))
+					break;
+			}
+		}
+		else
+		{
+			m_line_save += c;
+		}
+	}
+	if (j == std::char_traits < char >::eof() && m_line_save.size() == 0)
+	{
+		return (LT_EOF);
+	}
+	return (LT_OK);
+}
+
+bool PHRQ_io::
+check_key(std::string::iterator begin, std::string::iterator end)
+{
+	std::string lowercase;
+	CParser::copy_token(lowercase, begin, end);
+	std::transform(lowercase.begin(), lowercase.end(), lowercase.begin(),
+				   tolower);
+
+	m_next_keyword = Keywords::Keyword_search(lowercase);
+	if (m_next_keyword == Keywords::KEY_NONE)
+	{
+		return false;
+	}
+	return true;
+}
+

src/phreeqcpp/common/PHRQ_io.h

@@ -0,0 +1,211 @@
+#ifndef _PHRQIO_H
+#define _PHRQIO_H
+
+#if defined(_WINDLL)
+#define IPQ_DLL_EXPORT __declspec(dllexport)
+#else
+#define IPQ_DLL_EXPORT
+#endif
+
+#include <iostream>
+#include <exception>
+#include <list>
+#include "Keywords.h"
+#include <time.h>
+
+#define ERROR_OSTREAM
+
+class PhreeqcStop : public std::exception
+{
+};
+
+class IPQ_DLL_EXPORT PHRQ_io
+{
+public:
+	enum LINE_TYPE
+	{
+		LT_EOF = -1,
+		LT_OK = 1,
+		LT_EMPTY = 2,
+		LT_KEYWORD = 3,
+		LT_OPTION = 8
+	};
+
+	enum ONERROR_TYPE
+	{
+		OT_CONTINUE = 0,
+		OT_STOP = 1
+	};
+	// constructor/destructor
+	PHRQ_io(void);
+	virtual ~ PHRQ_io();
+
+	// methods
+	static void safe_close(std::ostream **stream_ptr);
+	static void safe_close(FILE **file_ptr);
+	void close_ostreams(void);
+	void Set_io_error_count(int i)				{this->io_error_count = i;};
+	int Get_io_error_count(void)				{return this->io_error_count;};
+
+
+	// istreams
+	std::istream *get_istream();
+	void pop_istream();
+	void push_istream(std::istream * cookie, bool auto_delete = true);
+	void clear_istream(void);
+
+	// helper
+	bool ofstream_open(std::ostream **os, const char *file_name, std::ios_base::openmode mode = std::ios_base::out);
+
+	// output_ostream
+	virtual bool output_open(const char *file_name, std::ios_base::openmode mode = std::ios_base::out);
+	void output_flush(void);
+	void output_close(void);
+	virtual void output_msg(const char * str);
+	void Set_output_ostream(std::ostream * out)		{this->output_ostream = out;};
+	std::ostream *Get_output_ostream(void)			{return this->output_ostream;};
+	void Set_output_on(bool tf)						{this->output_on = tf;};
+	bool Get_output_on(void)						{return this->output_on;};
+
+	// log_ostream
+	virtual bool log_open(const char *file_name, std::ios_base::openmode mode = std::ios_base::out);
+	void log_flush(void);
+	void log_close(void);
+	virtual void log_msg(const char * str);
+	void Set_log_ostream(std::ostream * out)		{this->log_ostream = out;}
+	std::ostream *Get_log_ostream(void)				{return this->log_ostream;}
+	void Set_log_on(bool tf)						{this->log_on = tf;}
+	bool Get_log_on(void)							{return this->log_on;}
+
+	// punch_ostream
+	virtual bool punch_open(const char *file_name, std::ios_base::openmode mode = std::ios_base::out, int n_user = 1);
+	void punch_flush(void);
+	void punch_close(void);
+	virtual void punch_msg(const char * str);
+	void Set_punch_ostream(std::ostream * out)		{this->punch_ostream = out;}
+	std::ostream *Get_punch_ostream(void)			{return this->punch_ostream;}
+	void Set_punch_on(bool tf)						{this->punch_on = tf;}
+	bool Get_punch_on(void)							{return this->punch_on;}
+	
+	// error_ostream
+#ifdef ERROR_OSTREAM
+	virtual bool error_open(const char *file_name, std::ios_base::openmode mode = std::ios_base::out);
+	void error_flush(void);
+	void error_close(void);
+	virtual void error_msg(const char * str, bool stop=false);
+	void Set_error_ostream(std::ostream * out)		{this->error_ostream = out;}
+	std::ostream *Get_error_ostream(void)			{return this->error_ostream;}
+	void Set_error_on(bool tf)						{this->error_on = tf;}
+	bool Get_error_on(void)							{return this->error_on;}
+	virtual void warning_msg(const char *err_str);
+#else
+	virtual bool error_open(const char *file_name, const char * mode = "w");
+	void error_flush(void);
+	void error_close(void);
+	virtual void error_msg(const char * str, bool stop=false);
+	void Set_error_file(FILE * out)				{this->error_file = out;}
+	FILE *Get_error_file(void)					{return this->error_file;}
+	void Set_error_on(bool tf)						{this->error_on = tf;}
+	bool Get_error_on(void)							{return this->error_on;}
+	virtual void warning_msg(const char *err_str);
+#endif
+
+	// dump_ostream
+	virtual bool dump_open(const char *file_name, std::ios_base::openmode mode = std::ios_base::out);
+	void dump_flush(void);
+	void dump_close(void);
+	virtual void dump_msg(const char * str);
+	void Set_dump_ostream(std::ostream * out)		{this->dump_ostream = out;};
+	std::ostream *Get_dump_ostream(void)			{return this->dump_ostream;};
+	void Set_dump_on(bool tf)						{this->dump_on = tf;};
+	bool Get_dump_on(void)							{return this->dump_on;};
+
+	// fpunchf
+	virtual void fpunchf(const char *name, const char *format, double d);
+	virtual void fpunchf(const char *name, const char *format, char * d);
+	virtual void fpunchf(const char *name, const char *format, int d);
+	virtual void fpunchf_end_row(const char *format);
+	static void fpunchf_helper(std::ostream *os, const char *format, ...);
+	static void fpunchf_helper(std::string *str, const char *format, ...);
+
+	virtual void screen_msg(const char * str);
+	void Set_screen_on(bool tf)						{this->screen_on = tf;};
+	bool Get_screen_on(void)						{return this->screen_on;};
+
+	// input methods
+	virtual int getc(void);
+	virtual LINE_TYPE get_line(void);
+	virtual LINE_TYPE get_logical_line(void);
+	bool check_key(std::string::iterator begin, std::string::iterator end);
+	std::string & Get_m_line()       {return m_line;}
+	std::string & Get_m_line_save()  {return m_line_save;}
+	std::string & Get_accumulated()	 {return accumulated;}
+	LINE_TYPE Get_m_line_type()      {return m_line_type;};
+	void Set_accumulate(bool tf) 
+	{ 
+		if (tf)
+		{
+			accumulated.clear();
+		}
+		this->accumulate = tf; 
+	}
+	Keywords::KEYWORDS Get_m_next_keyword() const {return m_next_keyword;}
+
+	// echo 
+	enum ECHO_OPTION
+	{
+		ECHO_LOG,
+		ECHO_OUTPUT
+	};
+	virtual void echo_msg(const char * str);
+	void Set_echo_on(bool tf)					{this->echo_on = tf;};
+	bool Get_echo_on(void)						{return this->echo_on;};
+	void Set_echo_destination(ECHO_OPTION eo)   {this->echo_destination = eo;};
+	ECHO_OPTION Get_echo_destination(void)      {return this->echo_destination;};
+
+	// data
+protected:
+	std::ostream *output_ostream;	
+	std::ostream *log_ostream;		
+	std::ostream *punch_ostream;	
+#ifdef ERROR_OSTREAM
+	std::ostream *error_ostream;
+#else
+	FILE * error_file;
+#endif
+	std::ostream *dump_ostream;
+	int io_error_count;
+
+	bool output_on;
+	bool log_on;
+	bool punch_on;
+	bool error_on;
+	bool dump_on;
+	bool echo_on;
+	bool screen_on;
+	ECHO_OPTION echo_destination;
+
+#if defined(_MSC_VER)
+/* disable warning C4251: 'identifier' : class 'type' needs to have dll-interface to be used by clients of class 'type2' */
+#pragma warning(disable:4251)
+#endif
+
+	std::list <std::istream *> istream_list;
+	std::list <bool> delete_istream_list;
+
+	std::string m_line;
+	std::string m_line_save;
+	std::string accumulated;
+
+#if defined(_MSC_VER)
+/* reset warning C4251 */
+#pragma warning(default:4251)
+#endif
+
+	// input data members
+	Keywords::KEYWORDS m_next_keyword;
+	bool accumulate;
+	LINE_TYPE m_line_type;
+};
+
+#endif /* _PHRQIO_H */

src/phreeqcpp/common/Parser.h

@@ -0,0 +1,296 @@
+#if !defined(PARSER_H_INCLUDED)
+#define PARSER_H_INCLUDED
+#if defined(WIN32)
+#include <windows.h>
+#endif
+#include <string>				// std::string
+#include <map>					// std::map
+#include <vector>				// std::vector
+#include <sstream>				// std::istringstream std::ostringstream
+#include <ostream>				// std::ostream
+#include <istream>				// std::istream
+#include <cctype>               // std::isspace
+#include <algorithm>            // std::find_if
+#include <functional>           // std::ptr_fun std::not1
+
+#include "PHRQ_base.h"
+#include "Keywords.h"
+#include "PHRQ_io.h"
+
+#ifdef _DEBUG
+#define isspace(a) isspace((a) < -1 ? (a) + 256 : (a)) 
+#define isupper(a) isupper((a) < -1 ? (a) + 256 : (a))
+#define islower(a) islower((a) < -1 ? (a) + 256 : (a)) 
+#define isdigit(a) isdigit((a) < -1 ? (a) + 256 : (a)) 
+#define isalpha(a) isalpha((a) < -1 ? (a) + 256 : (a))
+#endif
+
+class CParser: public PHRQ_base
+{
+  public:
+	CParser(PHRQ_io *io=NULL);
+	CParser(std::istream & input, PHRQ_io *io=NULL);
+	//CParser(std::istream & input, std::ostream & output, PHRQ_io *io=NULL);
+	//CParser(std::istream & input, std::ostream & output,
+	//		std::ostream & error, PHRQ_io *io=NULL);
+
+	virtual ~ CParser();
+	enum TOKEN_TYPE
+	{
+		TT_EMPTY = 2,
+		TT_UPPER = 4,
+		TT_LOWER = 5,
+		TT_DIGIT = 6,
+		TT_UNKNOWN = 7
+	};
+
+	enum FIND_TYPE
+	{
+		FT_OK = 0,
+		FT_ERROR = 1
+	};
+
+	enum OPT_TYPE
+	{
+		OPT_DEFAULT = -4,
+		OPT_ERROR = -3,
+		OPT_KEYWORD = -2,
+		OPT_EOF = -1
+	};
+	enum ECHO_OPTION
+	{
+		EO_NONE = 0,
+		EO_ALL = 1,
+		EO_KEYWORDS = 2,
+		EO_NOKEYWORDS = 3
+	};
+
+	enum STATUS_TYPE
+	{
+		PARSER_ERROR = 0,
+		PARSER_OK = 1
+	};
+
+
+		/**
+                Function gets a new line and checks for empty, eof, and keywords.
+
+                Arguments:
+                        string        Input, character string used in printing error message
+                        allow_empty   Input, True or false, if a blank line is accepable
+                                      if false, another line is read
+                        allow_eof     Input, True or false, if EOF is acceptable
+                        allow_keyword Input, True or false, if a keyword is acceptable
+
+                Returns:
+                        LT_EMPTY         if empty line read and allow_empty == true
+                        LT_KEYWORD       if line begins with keyword
+                        LT_EOF           if eof and allow_eof == true
+                        LT_OK            otherwise
+                        LT_OPTION        if line begins with -[alpha]
+
+           Terminates       if EOF and allow_eof == false.
+        */
+	PHRQ_io::LINE_TYPE check_line(const std::string & str, bool allow_empty,
+						 bool allow_eof, bool allow_keyword, bool print);
+
+		/**
+                Read a line from input file put in "line".
+                Copy of input line is stored in "line_save".
+                Characters after # are discarded in line but retained in "line_save"
+
+                Arguments:
+                        None
+                Returns:
+                        LT_EMPTY,
+                        LT_EOF,
+                        LT_KEYWORD,
+                        LT_OK,
+                        LT_OPTION
+        */
+	PHRQ_io::LINE_TYPE get_line();
+	PHRQ_io::LINE_TYPE get_line_phrq_io();
+
+	// bool check_key(const std::string::iterator ptr);
+	bool check_key(std::string::iterator begin, std::string::iterator end);
+
+	STATUS_TYPE check_units(std::string & tot_units, bool alkalinity,
+							bool check_compatibility,
+							const std::string & default_units, bool print);
+
+
+	//KEY_TYPE next_keyword() const
+	Keywords::KEYWORDS next_keyword() const
+	{
+		return m_next_keyword;
+	}
+	int get_option(const std::vector < std::string > &opt_list,
+				   std::string::iterator & next_char);
+	int get_option(const std::vector < std::string > &opt_list,
+				   std::istream::pos_type & next_pos);
+	int getOptionFromLastLine(const std::vector < std::string > &opt_list,
+							  std::string::iterator & next_char, bool flag_error);
+	int getOptionFromLastLine(const std::vector < std::string > &opt_list,
+							  std::istream::pos_type & next_pos, bool flag_error);
+
+
+	std::string & line()
+	{
+		return m_line;
+	}
+	std::string & line_save()
+	{
+		return m_line_save;
+	}
+	std::string & get_accumulated()
+	{
+		return accumulated;
+	}
+	void set_accumulate(bool tf) 
+	{ 
+		if (tf)
+		{
+			accumulated.clear();
+		}
+		this->accumulate = tf; 
+	}
+	std::istringstream & get_iss()
+	{
+		return m_line_iss;
+	}
+	int incr_input_error();
+	int get_input_error()
+	{
+		return m_input_error;
+	}
+
+		/**
+                Copies from begin to token until first space is encountered.
+
+                Arguments:
+                        token    output, the token
+                        begin    input, begin iterator
+                        end      input, end iterator
+
+                Returns:
+                        TT_EMPTY
+                        TT_UPPER
+                        TT_LOWER
+                        TT_DIGIT
+                        TT_UNKNOWN
+        */
+	static CParser::TOKEN_TYPE copy_token(std::string & token,
+								 std::string::iterator & begin,
+								 std::string::iterator & end);
+	static CParser::TOKEN_TYPE copy_title(std::string & token,
+										std::string::iterator & begin,
+										std::string::iterator & end);
+	static CParser::TOKEN_TYPE token_type(const std::string & token);
+	static CParser::TOKEN_TYPE copy_token(std::string & token, std::istream & is);
+	CParser::TOKEN_TYPE copy_token(std::string & token, std::istream::pos_type & pos);
+	bool get_true_false(std::istream::pos_type & pos, bool def);
+	CParser::TOKEN_TYPE get_rest_of_line(std::string &token);
+	static CParser::TOKEN_TYPE parse_delimited(std::string & source, std::string & result, const std::string& t);
+	CParser::TOKEN_TYPE peek_token();
+	PHRQ_io::LINE_TYPE get_m_line_type(void) const {return this->m_line_type;}
+
+		/**
+                Function reads an element name out of the equation string.
+                An element name is composed of a capital letter followed by any number
+                of lower case characters.
+
+                Arguments:
+                        begin    input, points to position in the equation to begin
+                                        output, points to next character of equation after
+                                        element name.
+                        end      input, points to last position in the equation
+                        element  input pointer to place to return element character string
+        */
+	STATUS_TYPE get_elt(std::string::iterator & begin,
+						const std::string::iterator end,
+						std::string & element);
+
+
+		/**
+                Compares a string value to match beginning letters of a list of options
+
+                Arguments:
+                        item    entry: pointer to string to compare
+                        n       exit:  item in list that was matched
+                        list    entry: pointer to list of character values, assumed to
+                                be lower case
+                        count_list entry: number of character values in list
+
+                Returns:
+                        OK      item matched
+                        ERROR   item not matched
+                        n       -1      item not matched
+                                i       position of match in list
+        */
+	static FIND_TYPE find_option(const std::string & item, int *n,
+								 const std::vector < std::string > &list,
+								 bool exact);
+
+	void set_echo_file(ECHO_OPTION opt)
+	{
+		echo_file = opt;
+	}
+	ECHO_OPTION get_echo_file()
+	{
+		return this->echo_file;
+	};
+
+	void set_echo_stream(ECHO_OPTION opt)
+	{
+		echo_stream = opt;
+	}
+	ECHO_OPTION get_echo_stream()
+	{
+		return this->echo_stream;
+	};
+
+	STATUS_TYPE parse_couple(std::string & token);
+
+	template <class T>
+	STATUS_TYPE addPair(std::map < std::string, T >&totals,
+						std::istream::pos_type & pos);
+
+  protected:
+	PHRQ_io::LINE_TYPE get_logical_line();
+
+  protected:
+	std::istream & m_input_stream;
+	//std::ostream & m_output_stream;
+	//std::ostream & m_error_stream;
+	int m_input_error;
+	//KEY_TYPE m_next_keyword;
+	Keywords::KEYWORDS m_next_keyword;
+	std::string m_line;
+	std::string m_line_save;
+	std::istringstream m_line_iss;
+	PHRQ_io::LINE_TYPE m_line_type;
+	ECHO_OPTION echo_stream;
+	ECHO_OPTION echo_file;
+	std::string accumulated;
+	bool accumulate;
+	bool phrq_io_only;
+
+};
+
+// Global functions
+static inline std::string &trim_left(std::string &s)
+{ 
+	s.erase(s.begin(), std::find_if(s.begin(), s.end(), std::not1(std::ptr_fun<int, int>(std::isspace)))); 
+	return s; 
+} 
+static inline std::string &trim_right(std::string &s)
+{ 
+	s.erase(std::find_if(s.rbegin(), s.rend(), std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end()); 
+	return s; 
+} 
+static inline std::string &trim(std::string &s)
+{ 
+	return trim_left(trim_right(s)); 
+} 
+
+#endif // PARSER_H_INCLUDED

src/phreeqcpp/common/Utils.cxx

@@ -0,0 +1,186 @@
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <stdlib.h>				// ::tolower
+#include <ctype.h>				// ::tolower
+#include <algorithm>			// std::transform
+#include <iostream>				// std::cout std::cerr
+#include <string.h>
+
+#include "Utils.h"
+#include "Parser.h"
+#include "float.h"
+#include "math.h"
+
+////////////////////////////////////////////////////////////////////////////
+int
+Utilities::strcmp_nocase_arg1(const char *str1, const char *str2)
+////////////////////////////////////////////////////////////////////////////
+{
+	//
+	// Compare two strings disregarding case
+	//
+	int c1, c2;
+	while ((c1 =::tolower(*str1++)) == (c2 = *str2++))
+	{
+		if (c1 == '\0')
+			return (0);
+	}
+	if (c1 < c2)
+		return (-1);
+	return (1);
+}
+
+////////////////////////////////////////////////////////////////////////////
+int
+Utilities::strcmp_nocase(const char *str1, const char *str2)
+////////////////////////////////////////////////////////////////////////////
+{
+	//
+	// Compare two strings disregarding case
+	//
+	int c1, c2;
+	while ((c1 =::tolower(*str1++)) == (c2 =::tolower(*str2++)))
+	{
+		if (c1 == '\0')
+			return (0);
+	}
+	if (c1 < c2)
+		return (-1);
+	return (1);
+}
+
+////////////////////////////////////////////////////////////////////////////
+void
+Utilities::str_tolower(std::string & str)
+////////////////////////////////////////////////////////////////////////////
+{
+	std::transform(str.begin(), str.end(), str.begin(), tolower);
+}
+
+////////////////////////////////////////////////////////////////////////////
+void
+Utilities::str_toupper(std::string & str)
+////////////////////////////////////////////////////////////////////////////
+{
+	std::transform(str.begin(), str.end(), str.begin(), toupper);
+}
+////////////////////////////////////////////////////////////////////////////
+std::string 
+Utilities::pad_right(const std::string & str, size_t l)
+////////////////////////////////////////////////////////////////////////////
+{
+	std::string new_str(str);
+	size_t length = new_str.size();
+	if (length < l)
+	{
+		new_str = new_str.insert(length, l - length, ' ');
+	}
+	return new_str;
+}
+
+
+////////////////////////////////////////////////////////////////////////////
+bool
+Utilities::replace(const char *str1, const char *str2, std::string & str)
+////////////////////////////////////////////////////////////////////////////
+{
+	std::string::size_type n = str.find(str1, 0);
+	if (n == std::string::npos)
+		return false;
+
+	str.replace(n, ::strlen(str1), str2);
+	return true;
+}
+
+////////////////////////////////////////////////////////////////////////////
+void
+Utilities::squeeze_white(std::string & s_l)
+////////////////////////////////////////////////////////////////////////////
+{
+	std::string str;
+	std::string::iterator beg = s_l.begin();
+	std::string::iterator end = s_l.end();
+	//CParser::copy_token(str, beg, end);
+	std::string::iterator pos;
+	for (pos = beg; pos != end; pos++)
+	{
+		int c = *pos;
+		if (!::isspace(c))
+		{
+			str += c;
+		}
+	}
+	s_l = str;
+}
+////////////////////////////////////////////////////////////////////////////
+double 
+Utilities::convert_time(double t, std::string in, std::string out)
+////////////////////////////////////////////////////////////////////////////
+{
+	Utilities::str_tolower(in);
+
+	// convert t to seconds
+	if (in.substr(0,1) == "m")
+	{
+		t = t * 60.;
+	}
+	if (in.substr(0,1) == "h")
+	{
+		t = t * 3600.;
+	}
+	if (in.substr(0,1) == "d")
+	{
+		t = t * 3600. * 24.;
+	}
+	if (in.substr(0,1) == "y")
+	{
+		t = t * 3600. * 24. * 365.25;
+	}
+	// convert to ouput units
+	if (out.substr(0,1) == "m")
+	{
+		t = t / 60.;
+	}
+	if (out.substr(0,1) == "h")
+	{
+		t = t / 3600.;
+	}
+	if (out.substr(0,1) == "d")
+	{
+		t = t / ( 3600. * 24.);
+	}
+	if (out.substr(0,1) == "y")
+	{
+		t = t / (3600. * 24. * 365.25);
+	}
+	return t;
+
+}
+LDBLE 
+Utilities::safe_exp(LDBLE t)
+////////////////////////////////////////////////////////////////////////////
+{
+	LDBLE f = 1.442695*t; // convert to exp for 2.0
+
+	if (f > DBL_MAX_EXP - 50.0)
+	{
+		return pow(2, DBL_MAX_EXP - 50.0);
+	}
+	else if (f < DBL_MIN_EXP + 50.0)
+	{
+		return pow(2, DBL_MIN_EXP + 50.0);
+	}
+	return exp(t);
+}
+//+NAN LDBLE: 7ff8000000000000
+//-NAN LDBLE: fff8000000000000
+/*
+LDBLE Utilities::get_nan(void)
+{
+	unsigned long long raw = 0x7ff0000000000000;
+	LDBLE d = *( LDBLE* )&raw;
+	return(d);
+
+}
+*/

src/phreeqcpp/common/Utils.h

@@ -0,0 +1,28 @@
+#if !defined(UTILITIES_H_INCLUDED)
+#define UTILITIES_H_INCLUDED
+
+#include <string>
+#include <sstream>				// std::istringstream std::ostringstream
+#include <ostream>				// std::ostream
+#include <istream>				// std::istream
+#include <map>					// std::map
+#include "phrqtype.h"
+namespace Utilities
+{
+
+	const char INDENT[] = "  ";
+
+	int strcmp_nocase(const char *str1, const char *str2);
+
+	int strcmp_nocase_arg1(const char *str1, const char *str2);
+
+	void str_tolower(std::string & str);
+	void str_toupper(std::string & str);
+	std::string pad_right(const std::string & str, size_t l);
+	bool replace(const char *str1, const char *str2, std::string & str);
+
+	void squeeze_white(std::string & s_l);
+	double convert_time(double t, std::string in, std::string out);
+	LDBLE safe_exp(LDBLE t);
+}
+#endif // UTILITIES_H_INCLUDED

src/phreeqcpp/common/phrqtype.h

@@ -0,0 +1,18 @@
+#ifndef _INC_PHRQTYPE_H
+#define _INC_PHRQTYPE_H
+/*
+ *   The following implements long double
+ *   Many machines long double = double so there is no advantage
+ *   Check float.h include file for number of digits (LDBL_DIG)
+ *   Need to define here and in cl1.c
+ */
+
+/*#define USE_LONG_DOUBLE*/
+#ifdef USE_LONG_DOUBLE
+#define LDBLE long double
+#define SCANFORMAT "%Lf"
+#else
+#define LDBLE double
+#define SCANFORMAT "%lf"
+#endif
+#endif /* _INC_PHRQTYPE_H */

src/phreeqcpp/cvdense.cpp

@@ -0,0 +1,557 @@
+/**************************************************************************
+ *                                                                        *
+ * File          : cvdense.c                                              *
+ * Programmers   : Scott D. Cohen, Alan C. Hindmarsh, and                 *
+ *                 Radu Serban @ LLNL                                     *
+ * Version of    : 26 June 2002                                           *
+ *------------------------------------------------------------------------*
+ * Copyright (c) 2002, The Regents of the University of California        *
+ * Produced at the Lawrence Livermore National Laboratory                 *
+ * All rights reserved                                                    *
+ * For details, see LICENSE below                                         *
+ *------------------------------------------------------------------------*
+ * This is the implementation file for the CVODE dense linear             *
+ * solver, CVDENSE.                                                       *
+ *                                                                        *
+ *------------------------------------------------------------------------*
+ * LICENSE                                                                *
+ *------------------------------------------------------------------------*
+ * Copyright (c) 2002, The Regents of the University of California.       *
+ * Produced at the Lawrence Livermore National Laboratory.                *
+ * Written by S.D. Cohen, A.C. Hindmarsh, R. Serban,                      *
+ *            D. Shumaker, and A.G. Taylor.                               *
+ * UCRL-CODE-155951    (CVODE)                                            *
+ * UCRL-CODE-155950    (CVODES)                                           *
+ * UCRL-CODE-155952    (IDA)                                              *
+ * UCRL-CODE-237203    (IDAS)                                             *
+ * UCRL-CODE-155953    (KINSOL)                                           *
+ * All rights reserved.                                                   *
+ *                                                                        *
+ * This file is part of SUNDIALS.                                         *
+ *                                                                        *
+ * Redistribution and use in source and binary forms, with or without     *
+ * modification, are permitted provided that the following conditions     *
+ * are met:                                                               *
+ *                                                                        *
+ * 1. Redistributions of source code must retain the above copyright      *
+ * notice, this list of conditions and the disclaimer below.              *
+ *                                                                        *
+ * 2. Redistributions in binary form must reproduce the above copyright   *
+ * notice, this list of conditions and the disclaimer (as noted below)    *
+ * in the documentation and/or other materials provided with the          *
+ * distribution.                                                          *
+ *                                                                        *
+ * 3. Neither the name of the UC/LLNL nor the names of its contributors   *
+ * may be used to endorse or promote products derived from this software  *
+ * without specific prior written permission.                             *
+ *                                                                        *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS    *
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT      *
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS      *
+ * FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE         *
+ * REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE U.S. DEPARTMENT OF ENERGY *
+ * OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,        *
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT       *
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,  *
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY  *
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT    *
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE  *
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.   *
+ **************************************************************************/
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "cvdense.h"
+#include "cvode.h"
+#include "dense.h"
+#include "sundialstypes.h"
+#include "nvector.h"
+#include "sundialsmath.h"
+
+
+#include "Phreeqc.h"
+#if !defined(WIN32_MEMORY_DEBUG)
+#define malloc PHRQ_malloc
+#endif
+#define MACHENV machEnv->phreeqc_ptr->
+#define CVMEM cv_mem->cv_machenv->phreeqc_ptr->
+#define MACHENV_MALLOC MACHENV
+#define CVMEM_MALLOC CVMEM
+
+#include "phqalloc.h"
+/* WARNING don`t include any headers below here */
+
+/* Error Messages */
+
+#define CVDENSE  "CVDense/CVReInitDense-- "
+
+#define MSG_CVMEM_NULL  CVDENSE "CVode Memory is NULL.\n\n"
+
+#define MSG_MEM_FAIL    CVDENSE "A memory request failed.\n\n"
+
+#define MSG_WRONG_NVEC  CVDENSE "Incompatible NVECTOR implementation.\n\n"
+
+/* Other Constants */
+
+#define MIN_INC_MULT RCONST(1000.0)
+#define ZERO         RCONST(0.0)
+#define ONE          RCONST(1.0)
+#define TWO          RCONST(2.0)
+
+
+/******************************************************************
+ *                                                                *
+ * Types : CVDenseMemRec, CVDenseMem                              *
+ *----------------------------------------------------------------*
+ * The type CVDenseMem is pointer to a CVDenseMemRec. This        *
+ * structure contains CVDense solver-specific data.               *
+ *                                                                *
+ ******************************************************************/
+
+typedef struct
+{
+
+	CVDenseJacFn d_jac;			/* jac = Jacobian routine to be called    */
+
+	DenseMat d_M;				/* M = I - gamma J, gamma = h / l1        */
+
+	integertype *d_pivots;		/* pivots = pivot array for PM = LU       */
+
+	DenseMat d_savedJ;			/* savedJ = old Jacobian                  */
+
+	long int d_nstlj;			/* nstlj = nst at last Jacobian eval.     */
+
+	long int d_nje;				/* nje = no. of calls to jac              */
+
+	void *d_J_data;				/* J_data is passed to jac                */
+
+} CVDenseMemRec, *CVDenseMem;
+
+
+/* CVDENSE linit, lsetup, lsolve, lfree, and DQJac routines */
+
+static int CVDenseInit(CVodeMem cv_mem);
+
+static int CVDenseSetup(CVodeMem cv_mem, int convfail, N_Vector ypred,
+						N_Vector fpred, booleantype * jcurPtr,
+						N_Vector vtemp1, N_Vector vtemp2, N_Vector vtemp3);
+
+static int CVDenseSolve(CVodeMem cv_mem, N_Vector b, N_Vector ycur,
+						N_Vector fcur);
+
+static void CVDenseFree(CVodeMem cv_mem);
+
+static void CVDenseDQJac(integertype N, DenseMat J, RhsFn f, void *f_data,
+						 realtype t, N_Vector y, N_Vector fy, N_Vector ewt,
+						 realtype h, realtype uround, void *jac_data,
+						 long int *nfePtr, N_Vector vtemp1,
+						 N_Vector vtemp2, N_Vector vtemp3);
+
+
+/*************** CVDenseDQJac ****************************************
+
+ This routine generates a dense difference quotient approximation to
+ the Jacobian of f(t,y). It assumes that a dense matrix of type
+ DenseMat is stored column-wise, and that elements within each column
+ are contiguous. The address of the jth column of J is obtained via
+ the macro DENSE_COL and an N_Vector with the jth column as the
+ component array is created using N_VMake and N_VSetData. Finally, the
+ actual computation of the jth column of the Jacobian is done with a
+ call to N_VLinearSum.
+
+**********************************************************************/
+
+static void
+CVDenseDQJac(integertype N, DenseMat J, RhsFn f, void *f_data,
+			 realtype tn, N_Vector y, N_Vector fy, N_Vector ewt,
+			 realtype h, realtype uround, void *jac_data,
+			 long int *nfePtr, N_Vector vtemp1,
+			 N_Vector vtemp2, N_Vector vtemp3)
+{
+	realtype fnorm, minInc, inc, inc_inv, yjsaved, srur;
+	realtype *y_data, *ewt_data;
+	N_Vector ftemp, jthCol;
+	M_Env machEnv;
+	integertype j;
+
+	machEnv = y->menv;			/* Get machine environment */
+
+	ftemp = vtemp1;				/* Rename work vector for use as f vector value */
+
+	/* Obtain pointers to the data for ewt, y */
+	ewt_data = N_VGetData(ewt);
+	y_data = N_VGetData(y);
+
+	/* Set minimum increment based on uround and norm of f */
+	srur = RSqrt(uround);
+	fnorm = N_VWrmsNorm(fy, ewt);
+	minInc = (fnorm != ZERO) ?
+		(MIN_INC_MULT * ABS(h) * uround * N * fnorm) : ONE;
+
+	jthCol = N_VMake(N, y_data, machEnv);	/* j loop overwrites this data address */
+
+	/* This is the only for loop for 0..N-1 in CVODE */
+	for (j = 0; j < N; j++)
+	{
+
+		/* Generate the jth col of J(tn,y) */
+
+		N_VSetData(DENSE_COL(J, j), jthCol);
+		yjsaved = y_data[j];
+		inc = MAX(srur * ABS(yjsaved), minInc / ewt_data[j]);
+		y_data[j] += inc;
+		f(N, tn, y, ftemp, f_data);
+		inc_inv = ONE / inc;
+		N_VLinearSum(inc_inv, ftemp, -inc_inv, fy, jthCol);
+		y_data[j] = yjsaved;
+	}
+
+	N_VDispose(jthCol);
+
+	/* Increment counter nfe = *nfePtr */
+	*nfePtr += N;
+}
+
+
+/* Readability Replacements */
+
+#define N         (cv_mem->cv_N)
+#define lmm       (cv_mem->cv_lmm)
+#define f         (cv_mem->cv_f)
+#define f_data    (cv_mem->cv_f_data)
+#define uround    (cv_mem->cv_uround)
+#define nst       (cv_mem->cv_nst)
+#define tn        (cv_mem->cv_tn)
+#define h         (cv_mem->cv_h)
+#define gamma     (cv_mem->cv_gamma)
+#define gammap    (cv_mem->cv_gammap)
+#define gamrat    (cv_mem->cv_gamrat)
+#define ewt       (cv_mem->cv_ewt)
+#define nfe       (cv_mem->cv_nfe)
+#define errfp     (cv_mem->cv_errfp)
+#define iopt      (cv_mem->cv_iopt)
+#define linit     (cv_mem->cv_linit)
+#define lsetup    (cv_mem->cv_lsetup)
+#define lsolve    (cv_mem->cv_lsolve)
+#define lfree     (cv_mem->cv_lfree)
+#define lmem      (cv_mem->cv_lmem)
+#define setupNonNull (cv_mem->cv_setupNonNull)
+#define machenv   (cv_mem->cv_machenv)
+
+#define jac       (cvdense_mem->d_jac)
+#define M         (cvdense_mem->d_M)
+#define pivots    (cvdense_mem->d_pivots)
+#define savedJ    (cvdense_mem->d_savedJ)
+#define nstlj     (cvdense_mem->d_nstlj)
+#define nje       (cvdense_mem->d_nje)
+#define J_data    (cvdense_mem->d_J_data)
+
+
+/*************** CVDense *********************************************
+
+ This routine initializes the memory record and sets various function
+ fields specific to the dense linear solver module.  CVDense first
+ calls the existing lfree routine if this is not NULL.  Then it sets
+ the cv_linit, cv_lsetup, cv_lsolve, cv_lfree fields in (*cvode_mem)
+ to be CVDenseInit, CVDenseSetup, CVDenseSolve, and CVDenseFree,
+ respectively.  It allocates memory for a structure of type
+ CVDenseMemRec and sets the cv_lmem field in (*cvode_mem) to the
+ address of this structure.  It sets setupNonNull in (*cvode_mem) to
+ TRUE, the d_J_data field in CVDenseMemRec to be the input
+ parameter jac_data, and the d_jac field to be:
+   (1) the input parameter djac if djac != NULL or
+   (2) CVDenseDQJac if djac == NULL.
+ Finally, it allocates memory for M, savedJ, and pivots.
+ The return value is SUCCESS = 0, or LMEM_FAIL = -1.
+
+ NOTE: The dense linear solver assumes a serial implementation
+       of the NVECTOR package. Therefore, CVDense will first
+       test for compatible a compatible N_Vector internal
+       representation by checking (1) the machine environment
+       ID tag and (2) that the functions N_VMake, N_VDispose,
+       N_VGetData, and N_VSetData are implemented.
+
+**********************************************************************/
+
+int
+CVDense(void *cvode_mem, CVDenseJacFn djac, void *jac_data)
+{
+	CVodeMem cv_mem;
+	CVDenseMem cvdense_mem;
+
+	/* Return immediately if cvode_mem is NULL */
+	cv_mem = (CVodeMem) cvode_mem;
+	if (cv_mem == NULL)
+	{							/* CVode reports this error */
+		return (LMEM_FAIL);
+	}
+
+	/* Test if the NVECTOR package is compatible with the DENSE solver */
+	if ((strcmp(machenv->tag, "serial")) ||
+		machenv->ops->nvmake == NULL ||
+		machenv->ops->nvdispose == NULL ||
+		machenv->ops->nvgetdata == NULL || machenv->ops->nvsetdata == NULL)
+	{
+		CVMEM warning_msg( MSG_WRONG_NVEC);
+		return (LMEM_FAIL);
+	}
+
+	if (lfree != NULL)
+		lfree(cv_mem);
+
+	/* Set four main function fields in cv_mem */
+	linit = CVDenseInit;
+	lsetup = CVDenseSetup;
+	lsolve = CVDenseSolve;
+	lfree = CVDenseFree;
+
+	/* Get memory for CVDenseMemRec */
+#if defined(WIN32_MEMORY_DEBUG)
+	lmem = cvdense_mem = (CVDenseMem) malloc(sizeof(CVDenseMemRec));
+#else
+	lmem = cvdense_mem = (CVDenseMem) CVMEM_MALLOC malloc(sizeof(CVDenseMemRec));
+#endif
+	if (cvdense_mem == NULL)
+	{
+		CVMEM warning_msg( MSG_MEM_FAIL);
+		return (LMEM_FAIL);
+	}
+
+	/* Set Jacobian routine field, J_data, and setupNonNull */
+	if (djac == NULL)
+	{
+		jac = CVDenseDQJac;
+	}
+	else
+	{
+		jac = djac;
+	}
+	J_data = jac_data;
+	setupNonNull = TRUE;
+
+	/* Allocate memory for M, savedJ, and pivot array */
+
+	M = DenseAllocMat(N);
+	if (M == NULL)
+	{
+		CVMEM warning_msg( MSG_MEM_FAIL);
+		return (LMEM_FAIL);
+	}
+	savedJ = DenseAllocMat(N);
+	if (savedJ == NULL)
+	{
+		CVMEM warning_msg( MSG_MEM_FAIL);
+		DenseFreeMat(M);
+		return (LMEM_FAIL);
+	}
+	pivots = DenseAllocPiv(N);
+	if (pivots == NULL)
+	{
+		CVMEM warning_msg( MSG_MEM_FAIL);
+		DenseFreeMat(M);
+		DenseFreeMat(savedJ);
+		return (LMEM_FAIL);
+	}
+
+	return (SUCCESS);
+}
+
+/*************** CVReInitDense****************************************
+
+ This routine resets the link between the main CVODE module and the
+ dense linear solver module CVDENSE.  No memory freeing or allocation
+ operations are done, as the existing linear solver memory is assumed
+ sufficient.  All other initializations are the same as in CVDense.
+ The return value is SUCCESS = 0, or LMEM_FAIL = -1.
+
+**********************************************************************/
+
+int
+CVReInitDense(void *cvode_mem, CVDenseJacFn djac, void *jac_data)
+{
+	CVodeMem cv_mem;
+	CVDenseMem cvdense_mem;
+
+	/* Return immediately if cvode_mem is NULL */
+	cv_mem = (CVodeMem) cvode_mem;
+	if (cv_mem == NULL)
+	{							/* CVode reports this error */
+		//CVMEM warning_msg( MSG_CVMEM_NULL);
+#if !defined(R_SO)
+		std::cerr << MSG_CVMEM_NULL << std::endl;
+#endif
+		return (LMEM_FAIL);
+	}
+
+	/* Test if the NVECTOR package is compatible with the DENSE solver */
+	if ((strcmp(machenv->tag, "serial")) ||
+		machenv->ops->nvmake == NULL ||
+		machenv->ops->nvdispose == NULL ||
+		machenv->ops->nvgetdata == NULL || machenv->ops->nvsetdata == NULL)
+	{
+		CVMEM warning_msg( MSG_WRONG_NVEC);
+		return (LMEM_FAIL);
+	}
+
+	cvdense_mem = (CVDenseMem) lmem;	/* Use existing linear solver memory pointer */
+
+	/* Set four main function fields in cv_mem */
+	linit = CVDenseInit;
+	lsetup = CVDenseSetup;
+	lsolve = CVDenseSolve;
+	lfree = CVDenseFree;
+
+	/* Set Jacobian routine field, J_data, and setupNonNull */
+	if (djac == NULL)
+	{
+		jac = CVDenseDQJac;
+	}
+	else
+	{
+		jac = djac;
+	}
+	J_data = jac_data;
+	setupNonNull = TRUE;
+
+	return (SUCCESS);
+}
+
+/*************** CVDenseInit *****************************************
+
+ This routine does remaining initializations specific to the dense
+ linear solver.
+
+**********************************************************************/
+
+static int
+CVDenseInit(CVodeMem cv_mem)
+{
+	CVDenseMem cvdense_mem;
+	cvdense_mem = (CVDenseMem) lmem;
+
+	/* Initialize nje and nstlj, and set workspace lengths */
+
+	nje = 0;
+	if (iopt != NULL)
+	{
+		iopt[DENSE_NJE] = nje;
+		iopt[DENSE_LRW] = 2 * N * N;
+		iopt[DENSE_LIW] = N;
+	}
+	nstlj = 0;
+
+	return (LINIT_OK);
+}
+
+/*************** CVDenseSetup ****************************************
+
+ This routine does the setup operations for the dense linear solver.
+ It makes a decision whether or not to call the Jacobian evaluation
+ routine based on various state variables, and if not it uses the
+ saved copy.  In any case, it constructs the Newton matrix
+ M = I - gamma*J, updates counters, and calls the dense LU
+ factorization routine.
+
+**********************************************************************/
+
+static int
+CVDenseSetup(CVodeMem cv_mem, int convfail, N_Vector ypred,
+			 N_Vector fpred, booleantype * jcurPtr,
+			 N_Vector vtemp1, N_Vector vtemp2, N_Vector vtemp3)
+{
+	booleantype jbad, jok;
+	realtype dgamma;
+	integertype ier;
+	CVDenseMem cvdense_mem;
+
+	cvdense_mem = (CVDenseMem) lmem;
+
+	/* Use nst, gamma/gammap, and convfail to set J eval. flag jok */
+
+	dgamma = ABS((gamma / gammap) - ONE);
+	jbad = (nst == 0) || (nst > nstlj + CVD_MSBJ) ||
+		((convfail == FAIL_BAD_J) && (dgamma < CVD_DGMAX)) ||
+		(convfail == FAIL_OTHER);
+	jok = !jbad;
+
+	if (jok)
+	{
+		/* If jok = TRUE, use saved copy of J */
+		*jcurPtr = FALSE;
+		DenseCopy(savedJ, M);
+	}
+	else
+	{
+		/* If jok = FALSE, call jac routine for new J value */
+		nje++;
+		if (iopt != NULL)
+			iopt[DENSE_NJE] = nje;
+		nstlj = nst;
+		*jcurPtr = TRUE;
+		DenseZero(M);
+		jac(N, M, f, f_data, tn, ypred, fpred, ewt, h,
+			uround, J_data, &nfe, vtemp1, vtemp2, vtemp3);
+		DenseCopy(M, savedJ);
+	}
+
+	/* Scale and add I to get M = I - gamma*J */
+	DenseScale(-gamma, M);
+	DenseAddI(M);
+
+	/* Do LU factorization of M */
+	ier = DenseFactor(M, pivots);
+
+	/* Return 0 if the LU was complete; otherwise return 1 */
+	if (ier > 0)
+		return (1);
+	return (0);
+}
+
+/*************** CVDenseSolve ****************************************
+
+ This routine handles the solve operation for the dense linear solver
+ by calling the dense backsolve routine.  The returned value is 0.
+
+**********************************************************************/
+
+static int
+CVDenseSolve(CVodeMem cv_mem, N_Vector b, N_Vector ycur, N_Vector fcur)
+{
+	CVDenseMem cvdense_mem;
+	realtype *bd;
+
+	cvdense_mem = (CVDenseMem) lmem;
+
+	bd = N_VGetData(b);
+	DenseBacksolve(M, pivots, bd);
+	N_VSetData(bd, b);
+
+	/* If BDF, scale the correction to account for change in gamma */
+	if ((lmm == BDF) && (gamrat != ONE))
+	{
+		N_VScale(TWO / (ONE + gamrat), b, b);
+	}
+
+	return (0);
+}
+
+/*************** CVDenseFree *****************************************
+
+ This routine frees memory specific to the dense linear solver.
+
+**********************************************************************/
+
+static void
+CVDenseFree(CVodeMem cv_mem)
+{
+	CVDenseMem cvdense_mem;
+
+	cvdense_mem = (CVDenseMem) lmem;
+
+	DenseFreeMat(M);
+	DenseFreeMat(savedJ);
+	DenseFreePiv(pivots);
+	CVMEM_MALLOC PHRQ_free(cvdense_mem);
+}

src/phreeqcpp/cvdense.h

@@ -0,0 +1,267 @@
+#ifndef _INC_CVDENSE_H
+#define _INC_CVDENSE_H
+/**************************************************************************
+ *                                                                        *
+ * File          : cvdense.h                                              *
+ * Programmers   : Scott D. Cohen, Alan C. Hindmarsh, and                 *
+ *                 Radu Serban @ LLNL                                     *
+ * Version of    : 26 June 2002                                           *
+ *------------------------------------------------------------------------*
+ * Copyright (c) 2002, The Regents of the University of California        *
+ * Produced at the Lawrence Livermore National Laboratory                 *
+ * All rights reserved                                                    *
+ * For details, see LICENSE below                                         *
+ *------------------------------------------------------------------------*
+ * This is the header file for the CVODE dense linear solver,             *
+ * CVDENSE.                                                               *
+ *                                                                        *
+ * Note: The type integertype must be large enough to store the           *
+ * value of the linear system size N.                                     *
+ *                                                                        *
+ *------------------------------------------------------------------------*
+ * LICENSE                                                                *
+ *------------------------------------------------------------------------*
+ * Copyright (c) 2002, The Regents of the University of California.       *
+ * Produced at the Lawrence Livermore National Laboratory.                *
+ * Written by S.D. Cohen, A.C. Hindmarsh, R. Serban,                      *
+ *            D. Shumaker, and A.G. Taylor.                               *
+ * UCRL-CODE-155951    (CVODE)                                            *
+ * UCRL-CODE-155950    (CVODES)                                           *
+ * UCRL-CODE-155952    (IDA)                                              *
+ * UCRL-CODE-237203    (IDAS)                                             *
+ * UCRL-CODE-155953    (KINSOL)                                           *
+ * All rights reserved.                                                   *
+ *                                                                        *
+ * This file is part of SUNDIALS.                                         *
+ *                                                                        *
+ * Redistribution and use in source and binary forms, with or without     *
+ * modification, are permitted provided that the following conditions     *
+ * are met:                                                               *
+ *                                                                        *
+ * 1. Redistributions of source code must retain the above copyright      *
+ * notice, this list of conditions and the disclaimer below.              *
+ *                                                                        *
+ * 2. Redistributions in binary form must reproduce the above copyright   *
+ * notice, this list of conditions and the disclaimer (as noted below)    *
+ * in the documentation and/or other materials provided with the          *
+ * distribution.                                                          *
+ *                                                                        *
+ * 3. Neither the name of the UC/LLNL nor the names of its contributors   *
+ * may be used to endorse or promote products derived from this software  *
+ * without specific prior written permission.                             *
+ *                                                                        *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS    *
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT      *
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS      *
+ * FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE         *
+ * REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE U.S. DEPARTMENT OF ENERGY *
+ * OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,        *
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT       *
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,  *
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY  *
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT    *
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE  *
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.   *
+ **************************************************************************/
+
+#ifndef _cvdense_h
+#define _cvdense_h
+
+
+#include <stdio.h>
+#include "cvode.h"
+#include "sundialstypes.h"
+#include "dense.h"
+#include "nvector.h"
+
+
+/******************************************************************
+ *                                                                *
+ * CVDENSE solver statistics indices                              *
+ *----------------------------------------------------------------*
+ * The following enumeration gives a symbolic name to each        *
+ * CVDENSE statistic. The symbolic names are used as indices into *
+ * the iopt and ropt arrays passed to CVodeMalloc.                *
+ * The CVDENSE statistics are:                                    *
+ *                                                                *
+ * iopt[DENSE_NJE] : number of Jacobian evaluations, i.e. of      *
+ *                   calls made to the dense Jacobian routine     *
+ *                   (default or user-supplied).                  *
+ *                                                                *
+ * iopt[DENSE_LRW] : size (in realtype words) of real workspace   *
+ *                   matrices and vectors used by this solver.    *
+ *                                                                *
+ * iopt[DENSE_LIW] : size (in integertype words) of integer       *
+ *                   workspace vectors used by this solver.       *
+ *                                                                *
+ ******************************************************************/
+
+	enum
+	{ DENSE_NJE = CVODE_IOPT_SIZE, DENSE_LRW, DENSE_LIW };
+
+
+/******************************************************************
+ *                                                                *
+ * CVDENSE solver constants                                       *
+ *----------------------------------------------------------------*
+ * CVD_MSBJ  : maximum number of steps between dense Jacobian     *
+ *             evaluations                                        *
+ *                                                                *
+ * CVD_DGMAX : maximum change in gamma between dense Jacobian     *
+ *             evaluations                                        *
+ *                                                                *
+ ******************************************************************/
+
+#define CVD_MSBJ  50
+
+#define CVD_DGMAX RCONST(0.2)
+
+
+/******************************************************************
+ *                                                                *
+ * Type : CVDenseJacFn                                            *
+ *----------------------------------------------------------------*
+ * A dense Jacobian approximation function Jac must have the      *
+ * prototype given below. Its parameters are:                     *
+ *                                                                *
+ * N is the length of all vector arguments.                       *
+ *                                                                *
+ * J is the dense matrix (of type DenseMat) that will be loaded   *
+ * by a CVDenseJacFn with an approximation to the Jacobian matrix *
+ * J = (df_i/dy_j) at the point (t,y).                            *
+ * J is preset to zero, so only the nonzero elements need to be   *
+ * loaded. Two efficient ways to load J are:                      *
+ *                                                                *
+ * (1) (with macros - no explicit data structure references)      *
+ *     for (j=0; j < N; j++) {                                    *
+ *       col_j = DENSE_COL(J,j);                                  *
+ *       for (i=0; i < N; i++) {                                  *
+ *         generate J_ij = the (i,j)th Jacobian element           *
+ *         col_j[i] = J_ij;                                       *
+ *       }                                                        *
+ *     }                                                          *
+ *                                                                *
+ * (2) (without macros - explicit data structure references)      *
+ *     for (j=0; j < N; j++) {                                    *
+ *       col_j = (J->data)[j];                                    *
+ *       for (i=0; i < N; i++) {                                  *
+ *         generate J_ij = the (i,j)th Jacobian element           *
+ *         col_j[i] = J_ij;                                       *
+ *       }                                                        *
+ *     }                                                          *
+ *                                                                *
+ * The DENSE_ELEM(A,i,j) macro is appropriate for use in small    *
+ * problems in which efficiency of access is NOT a major concern. *
+ *                                                                *
+ * f is the right hand side function for the ODE problem.         *
+ *                                                                *
+ * f_data is a pointer to user data to be passed to f, the same   *
+ *        as the F_data parameter passed to CVodeMalloc.          *
+ *                                                                *
+ * t is the current value of the independent variable.            *
+ *                                                                *
+ * y is the current value of the dependent variable vector,       *
+ *      namely the predicted value of y(t).                       *
+ *                                                                *
+ * fy is the vector f(t,y).                                       *
+ *                                                                *
+ * ewt is the error weight vector.                                *
+ *                                                                *
+ * h is a tentative step size in t.                               *
+ *                                                                *
+ * uround is the machine unit roundoff.                           *
+ *                                                                *
+ * jac_data is a pointer to user data - the same as the jac_data  *
+ *          parameter passed to CVDense.                          *
+ *                                                                *
+ * nfePtr is a pointer to the memory location containing the      *
+ * CVODE problem data nfe = number of calls to f. The Jacobian    *
+ * routine should update this counter by adding on the number     *
+ * of f calls made in order to approximate the Jacobian, if any.  *
+ * For example, if the routine calls f a total of N times, then   *
+ * the update is *nfePtr += N.                                    *
+ *                                                                *
+ * vtemp1, vtemp2, and vtemp3 are pointers to memory allocated    *
+ * for vectors of length N which can be used by a CVDenseJacFn    *
+ * as temporary storage or work space.                            *
+ *                                                                *
+ ******************************************************************/
+
+	typedef void (*CVDenseJacFn) (integertype N, DenseMat J, RhsFn f,
+								  void *f_data, realtype t, N_Vector y,
+								  N_Vector fy, N_Vector ewt, realtype h,
+								  realtype uround, void *jac_data,
+								  long int *nfePtr, N_Vector vtemp1,
+								  N_Vector vtemp2, N_Vector vtemp3);
+
+
+/******************************************************************
+ *                                                                *
+ * Function : CVDense                                             *
+ *----------------------------------------------------------------*
+ * A call to the CVDense function links the main CVODE integrator *
+ * with the CVDENSE linear solver.                                *
+ *                                                                *
+ * cvode_mem is the pointer to CVODE memory returned by           *
+ *              CVodeMalloc.                                      *
+ *                                                                *
+ * djac is the dense Jacobian approximation routine to be used.   *
+ *         A user-supplied djac routine must be of type           *
+ *         CVDenseJacFn. Pass NULL for djac to use the default    *
+ *         difference quotient routine CVDenseDQJac supplied      *
+ *         with this solver.                                      *
+ *                                                                *
+ * jac_data is a pointer to user data which is passed to the      *
+ *         djac routine every time it is called.                  *
+ *                                                                *
+ * The return values of CVDense are:                              *
+ *    SUCCESS   = 0  if successful                                *
+ *    LMEM_FAIL = -1 if there was a memory allocation failure     *
+ *                                                                *
+ * NOTE: The dense linear solver assumes a serial implementation  *
+ *       of the NVECTOR package. Therefore, CVDense will first    *
+ *       test for a compatible N_Vector internal representation   *
+ *       by checking (1) the machine environment ID tag and       *
+ *       (2) that the functions N_VMake, N_VDispose, N_VGetData,  *
+ *       and N_VSetData are implemented.                          *
+ *                                                                *
+ ******************************************************************/
+
+	int CVDense(void *cvode_mem, CVDenseJacFn djac, void *jac_data);
+
+
+/******************************************************************
+ *                                                                *
+ * Function : CVReInitDense                                       *
+ *----------------------------------------------------------------*
+ * A call to the CVReInitDense function resets the link between   *
+ * the main CVODE integrator and the CVDENSE linear solver.       *
+ * After solving one problem using CVDENSE, call CVReInit and then*
+ * CVReInitDense to solve another problem of the same size, if    *
+ * there is a change in the CVDense parameters djac or jac_data.  *
+ * If there is no change in parameters, it is not necessary to    *
+ * call either CVReInitDense or CVDense for the new problem.      *
+ *                                                                *
+ * All arguments to CVReInitDense have the same names and meanings*
+ * as those of CVDense.  The cvode_mem argument must be identical *
+ * to its value in the previous CVDense call.                     *
+ *                                                                *
+ * The return values of CVReInitDense are:                        *
+ *   SUCCESS   = 0      if successful, or                         *
+ *   LMEM_FAIL = -1     if the cvode_mem argument is NULL         *
+ *                                                                *
+ * NOTE: CVReInitDense performs the same compatibility tests as   *
+ *       CVDense.                                                 *
+ *                                                                *
+ ******************************************************************/
+
+	int CVReInitDense(void *cvode_mem, CVDenseJacFn djac, void *jac_data);
+
+
+#endif
+/*
+#ifdef __cplusplus
+}
+#endif
+*/
+#endif /* _INC_CVDENSE_H */