pyEQL 1.4.0rc9__cp312-cp312-macosx_11_0_arm64.whl

pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/ReadClass.cxx

@@ -0,0 +1,1150 @@
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+#include <iostream>
+#include <fstream>
+#include <sstream>
+
+#include "Utils.h"
+#include "Phreeqc.h"
+#include "Parser.h"
+#include "Solution.h"
+#include "Exchange.h"
+#include "Surface.h"
+#include "PPassemblage.h"
+#include "cxxKinetics.h"
+#include "SSassemblage.h"
+#include "GasPhase.h"
+#include "Reaction.h"
+#include "cxxMix.h"
+#include "Temperature.h"
+#include "dumper.h"
+#include "runner.h"
+#include "cxxMix.h"
+#include "Surface.h"
+#include "phqalloc.h"
+
+#if defined(PHREEQCI_GUI)
+#ifdef _DEBUG
+#define new DEBUG_NEW
+#undef THIS_FILE
+static char THIS_FILE[] = __FILE__;
+#endif
+#endif
+
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+read_dump(void)
+/* ---------------------------------------------------------------------- */
+{
+/*
+ *      Reads DUMP data block
+ *
+ *      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
+ *
+ */
+	int return_value;
+	/*
+	 *  Make parser
+	 */
+	std::istringstream iss_in;
+	return_value = streamify_to_next_keyword(iss_in);
+	CParser parser(iss_in, phrq_io);
+	assert(!reading_database());
+
+	//For testing, need to read line to get started
+	parser.set_echo_file(CParser::EO_NONE);
+	std::vector < std::string > vopts;
+	std::istream::pos_type next_char;
+	parser.get_option(vopts, next_char);
+
+	if (pr.echo_input == FALSE)
+	{
+		parser.set_echo_file(CParser::EO_NONE);
+	}
+	else
+	{
+		parser.set_echo_file(CParser::EO_NOKEYWORDS);
+	}
+
+	dump_info.Read(parser);
+
+	// Need to output the next keyword
+	if (return_value == OPTION_KEYWORD) echo_msg(sformatf( "\t%s\n", line));
+	return (return_value);
+}
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+read_delete(void)
+/* ---------------------------------------------------------------------- */
+{
+/*
+ *      Reads DELETE data block
+ *
+ *      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
+ *
+ */
+	int return_value;
+	/*
+	 *  Make parser
+	 */
+	std::istringstream iss_in;
+	return_value = streamify_to_next_keyword(iss_in);
+	CParser parser(iss_in, phrq_io);
+	//assert(!reading_database());
+
+	//For testing, need to read line to get started
+	parser.set_echo_file(CParser::EO_NONE);
+	std::vector < std::string > vopts;
+	std::istream::pos_type next_char;
+	parser.get_option(vopts, next_char);
+
+	if (pr.echo_input == FALSE)
+	{
+		parser.set_echo_file(CParser::EO_NONE);
+	}
+	else
+	{
+		parser.set_echo_file(CParser::EO_NOKEYWORDS);
+	}
+
+	delete_info.Read(parser);
+
+
+	// Need to output the next keyword
+	if (return_value == OPTION_KEYWORD) echo_msg(sformatf( "\t%s\n", line));
+	return (return_value);
+}
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+read_run_cells(void)
+/* ---------------------------------------------------------------------- */
+{
+/*
+ *      Reads DELETE data block
+ *
+ *      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
+ *
+ */
+	int return_value;
+	/*
+	 *  Make parser
+	 */
+	std::istringstream iss_in;
+	return_value = streamify_to_next_keyword(iss_in);
+	CParser parser(iss_in, phrq_io);
+	assert(!reading_database());
+
+	//For testing, need to read line to get started
+	parser.set_echo_file(CParser::EO_NONE);
+	std::vector < std::string > vopts;
+	std::istream::pos_type next_char;
+	parser.get_option(vopts, next_char);
+
+	if (pr.echo_input == FALSE)
+	{
+		parser.set_echo_file(CParser::EO_NONE);
+	}
+	else
+	{
+		parser.set_echo_file(CParser::EO_NOKEYWORDS);
+	}
+
+	runner r(parser, phrq_io);
+	run_info = r;
+
+
+	// Need to output the next keyword
+	if (return_value == OPTION_KEYWORD) echo_msg(sformatf( "\t%s\n", line));
+	return (return_value);
+}
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+streamify_to_next_keyword(std::istringstream & lines)
+/* ---------------------------------------------------------------------- */
+{
+/*
+ *   Reads to next keyword or eof
+ *
+ *   Returns:
+ *       OPTION_KEYWORD
+ *       OPTION_EOF
+ *       
+ */
+	// Handle echo
+	int save_echo_input = pr.echo_input;
+	pr.echo_input = FALSE;
+
+	std::string accumulate(line);
+	accumulate.append("\n");
+	int j;
+	for (;;)
+	{
+		j = check_line("Streamify", FALSE, TRUE, TRUE, FALSE);
+		if (j == EOF)
+		{						/* end of file */
+			break;
+		}
+		else if (j == KEYWORD)
+		{						/* keyword */
+			break;
+		}
+		else
+		{
+			accumulate.append(line);
+			accumulate.append("\n");
+		}
+	}
+
+	lines.str(accumulate);
+	pr.echo_input = save_echo_input;
+	if (j == EOF) return (OPTION_EOF);
+	if (j == KEYWORD) return (OPTION_KEYWORD);
+
+
+	return (OPTION_ERROR);
+}
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+dump_entities(void)
+/* ---------------------------------------------------------------------- */
+{
+	if (!dump_info.Get_on() || pr.dump == FALSE)
+	{
+		return(OK);
+	}
+	dump_info.Set_on(false);
+	if (!dump_info.Get_bool_any())
+	{
+		return(OK);
+	}
+
+	if (this->phrq_io)
+	{
+		std::ios_base::openmode mode = std::ios_base::out;
+		if (dump_info.Get_append())
+		{
+			mode = std::ios_base::app;
+		}
+		if (this->phrq_io->dump_open(dump_info.Get_file_name().c_str(), mode))
+		{
+			dump_ostream(*this->phrq_io->Get_dump_ostream());
+			this->phrq_io->dump_close();
+		}
+		else
+		{
+			error_string = sformatf( "Unable to open dump file \"%s\"", dump_info.Get_file_name().c_str());
+			error_msg(error_string, STOP);
+		}
+	}
+	return (OK);
+}
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+delete_entities(void)
+/* ---------------------------------------------------------------------- */
+{
+	if (!delete_info.Get_solution().Get_defined() &&
+		!delete_info.Get_pp_assemblage().Get_defined() &&
+		!delete_info.Get_exchange().Get_defined() &&
+		!delete_info.Get_surface().Get_defined() &&
+		!delete_info.Get_ss_assemblage().Get_defined() &&
+		!delete_info.Get_gas_phase().Get_defined() &&
+		!delete_info.Get_kinetics().Get_defined() &&
+		!delete_info.Get_mix().Get_defined() &&
+		!delete_info.Get_reaction().Get_defined() &&
+		!delete_info.Get_temperature().Get_defined() &&
+		!delete_info.Get_pressure().Get_defined())
+	{
+		return(OK);
+	}
+
+	// solutions
+	if (delete_info.Get_solution().Get_defined())
+	{
+		if (delete_info.Get_solution().Get_numbers().size() == 0)
+		{
+			Rxn_solution_map.clear();
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = delete_info.Get_solution().Get_numbers().begin(); it != delete_info.Get_solution().Get_numbers().end(); it++)
+			{
+				Rxn_solution_map.erase(*it);
+			}
+		}
+	}
+
+	// pp_assemblages
+	if (delete_info.Get_pp_assemblage().Get_defined())
+	{
+		if (delete_info.Get_pp_assemblage().Get_numbers().size() == 0)
+		{
+			Rxn_pp_assemblage_map.clear();
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = delete_info.Get_pp_assemblage().Get_numbers().begin(); it != delete_info.Get_pp_assemblage().Get_numbers().end(); it++)
+			{
+				Rxn_pp_assemblage_map.erase(*it);
+			}
+		}
+	}
+	// exchangers
+	if (delete_info.Get_exchange().Get_defined())
+	{
+		if (delete_info.Get_exchange().Get_numbers().size() == 0)
+		{
+			Rxn_exchange_map.clear();
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = delete_info.Get_exchange().Get_numbers().begin(); it != delete_info.Get_exchange().Get_numbers().end(); it++)
+			{
+				Rxn_exchange_map.erase(*it);
+			}
+		}
+	}
+	// surfaces
+	if (delete_info.Get_surface().Get_defined())
+	{
+		if (delete_info.Get_surface().Get_numbers().size() == 0)
+		{
+			Rxn_surface_map.clear();
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = delete_info.Get_surface().Get_numbers().begin(); it != delete_info.Get_surface().Get_numbers().end(); it++)
+			{
+				Rxn_surface_map.erase(*it);
+			}
+		}
+	}
+	// ss_assemblages
+	if (delete_info.Get_ss_assemblage().Get_defined())
+	{
+		if (delete_info.Get_ss_assemblage().Get_numbers().size() == 0)
+		{
+			Rxn_ss_assemblage_map.clear();
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = delete_info.Get_ss_assemblage().Get_numbers().begin(); it != delete_info.Get_ss_assemblage().Get_numbers().end(); it++)
+			{
+				Rxn_ss_assemblage_map.erase(*it);
+			}
+		}
+	}
+	// gas_phases
+	if (delete_info.Get_gas_phase().Get_defined())
+	{
+		if (delete_info.Get_gas_phase().Get_numbers().size() == 0)
+		{
+			Rxn_gas_phase_map.clear();
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = delete_info.Get_gas_phase().Get_numbers().begin(); it != delete_info.Get_gas_phase().Get_numbers().end(); it++)
+			{
+				Rxn_gas_phase_map.erase(*it);
+			}
+		}
+	}
+	// kinetics
+	if (delete_info.Get_kinetics().Get_defined())
+	{
+		if (delete_info.Get_kinetics().Get_numbers().size() == 0)
+		{
+			Rxn_kinetics_map.clear();
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = delete_info.Get_kinetics().Get_numbers().begin(); it != delete_info.Get_kinetics().Get_numbers().end(); it++)
+			{
+				Rxn_kinetics_map.erase(*it);
+			}
+		}
+	}
+	// mixes
+	if (delete_info.Get_mix().Get_defined())
+	{
+		if (delete_info.Get_mix().Get_numbers().size() == 0)
+		{
+			Rxn_mix_map.clear();
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = delete_info.Get_mix().Get_numbers().begin(); it != delete_info.Get_mix().Get_numbers().end(); it++)
+			{
+				Rxn_mix_map.erase(*it);
+			}
+		}
+	}
+	// reactions
+	if (delete_info.Get_reaction().Get_defined())
+	{
+		if (delete_info.Get_reaction().Get_numbers().size() == 0)
+		{
+			Rxn_reaction_map.clear();
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = delete_info.Get_reaction().Get_numbers().begin(); it != delete_info.Get_reaction().Get_numbers().end(); it++)
+			{
+				Rxn_reaction_map.erase(*it);
+			}
+		}
+	}
+	// temperatures
+	if (delete_info.Get_temperature().Get_defined())
+	{
+		if (delete_info.Get_temperature().Get_numbers().size() == 0)
+		{
+			Rxn_temperature_map.clear();
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = delete_info.Get_temperature().Get_numbers().begin(); it != delete_info.Get_temperature().Get_numbers().end(); it++)
+			{
+				Rxn_temperature_map.erase(*it);
+			}
+		}
+	}
+	// pressures
+	if (delete_info.Get_pressure().Get_defined())
+	{
+		if (delete_info.Get_pressure().Get_numbers().size() == 0)
+		{
+			Rxn_pressure_map.clear();
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = delete_info.Get_pressure().Get_numbers().begin(); it != delete_info.Get_pressure().Get_numbers().end(); it++)
+			{
+				Rxn_pressure_map.erase(*it);
+			}
+		}
+	}
+	// Turn off delete until next read
+	delete_info.SetAll(false);
+	return (OK);
+}
+#ifdef USE_OPTIMIZED_BUT_NOT_MUCH
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+run_as_cells(void)
+/* ---------------------------------------------------------------------- */
+{
+	class save save_data;
+	LDBLE kin_time;
+	int count_steps, use_mix;
+	char token[2 * MAX_LENGTH];
+
+	state = REACTION;
+	if (run_info.Get_cells().Get_numbers().size() == 0 ||
+		!(run_info.Get_cells().Get_defined())) return(OK);
+
+	// running cells
+	run_info.Set_run_cells(true);
+
+	dup_print("Beginning of run as cells.", TRUE);
+	LDBLE initial_total_time_save;
+	if (run_info.Get_start_time() != NA)
+	{
+		initial_total_time_save = run_info.Get_start_time();
+	}
+	else
+	{
+		initial_total_time_save = initial_total_time;
+	}
+
+	std::set < int >::iterator it = run_info.Get_cells().Get_numbers().begin();
+
+	for ( ; it != run_info.Get_cells().Get_numbers().end(); it++)
+	{
+		int i = *it;
+		if (i < 0) continue;
+		initial_total_time = initial_total_time_save;
+		cxxKinetics *kinetics_ptr = NULL;
+/*
+ *   Run reaction step
+ */
+		/*
+		*   Find maximum number of steps
+		*/
+		dup_print("Beginning of batch-reaction calculations.", TRUE);
+		count_steps = 1;
+		if (cxxReaction *rxn_ptr = Utilities::Rxn_find(Rxn_reaction_map, i))
+		{
+			int count = rxn_ptr->Get_reaction_steps();
+			if (count > count_steps)
+				count_steps = count;
+		}
+		if (cxxKinetics *rxn_ptr = Utilities::Rxn_find(Rxn_kinetics_map, i))
+		{
+			kinetics_ptr = rxn_ptr;
+			if (rxn_ptr->Get_reaction_steps() > count_steps)
+				count_steps = rxn_ptr->Get_reaction_steps();
+		}
+		if (cxxTemperature *rxn_ptr = Utilities::Rxn_find(Rxn_temperature_map, i))
+		{
+			int count = rxn_ptr->Get_countTemps();
+			if (count > count_steps)
+			{
+				count_steps = count;
+			}
+		}
+		if (cxxPressure *rxn_ptr = Utilities::Rxn_find(Rxn_pressure_map, i))
+		{
+			int count = rxn_ptr->Get_count();
+			if (count > count_steps)
+			{
+				count_steps = count;
+			}
+		}
+		count_total_steps = count_steps;
+		if (count_steps > 1)
+		{
+			state = ADVECTION;
+			set_advection(i, TRUE, TRUE, i);
+			/*
+			*  save data for saving solutions
+			*/
+			memcpy(&save_data, &save, sizeof(class save));
+			/* 
+			*Copy everything to -2
+			*/
+			copy_use(-2);
+			rate_sim_time_start = 0;
+			rate_sim_time = 0;
+			for (reaction_step = 1; reaction_step <= count_steps; reaction_step++)
+			{
+				snprintf(token, sizeof(token), "Reaction step %d.", reaction_step);
+				if (reaction_step > 1 && incremental_reactions == FALSE)
+				{
+					copy_use(-2);
+				}
+				set_initial_moles(-2);
+				dup_print(token, FALSE);
+				/*
+				*  Determine time step for kinetics
+				*/
+				kin_time = 0.0;
+				if (use.Get_kinetics_in() == TRUE)
+				{
+					// runner kin_time
+					// equivalent to kin_time in count_steps
+					if (run_info.Get_time_step() != NA)
+					{
+						if (incremental_reactions == FALSE)
+						{
+							/* not incremental reactions */
+							kin_time = reaction_step * run_info.Get_time_step() / ((LDBLE) count_steps);
+						}
+						else
+						{
+							/* incremental reactions */
+							kin_time = run_info.Get_time_step() / ((LDBLE) count_steps);
+						}
+					}
+					// runner kin_time not defined
+					else
+					{
+						cxxKinetics *kinetics_ptr = Utilities::Rxn_find(Rxn_kinetics_map, -2);
+						kin_time = kinetics_ptr->Current_step((incremental_reactions==TRUE), reaction_step);
+					}
+				}
+				if (incremental_reactions == FALSE ||
+					(incremental_reactions == TRUE && reaction_step == 1))
+				{
+					use_mix = TRUE;
+				}
+				else
+				{
+					use_mix = FALSE;
+				}
+				/*
+				*   Run reaction step
+				*/
+				run_reactions(-2, kin_time, use_mix, 1.0);
+				if (incremental_reactions == TRUE)
+				{
+					rate_sim_time_start += kin_time;
+					rate_sim_time = rate_sim_time_start;
+				}
+				else
+				{
+					rate_sim_time = kin_time;
+				}
+				punch_all();
+				print_all();
+				/* saves back into -2 */
+				if (reaction_step < count_steps)
+				{
+					saver();
+				}
+			}
+			/*
+			*   save end of reaction
+			*/
+			memcpy(&save, &save_data, sizeof(class save));
+			if (use.Get_kinetics_in() == TRUE)
+			{
+				Utilities::Rxn_copy(Rxn_kinetics_map, -2, use.Get_n_kinetics_user());
+			}
+			saver();
+		}
+		else
+			// only 1 step, no worries about incremental reactions
+		{
+			state = TRANSPORT;
+
+			rate_sim_time_start = 0;
+			rate_sim_time = 0;
+			reaction_step = 1;
+
+			snprintf(token, sizeof(token), "Reaction step %d.", reaction_step);
+
+			dup_print(token, FALSE);
+			/*
+			*  Determine time step for kinetics
+			*/
+			kin_time = 0.0;
+			if (kinetics_ptr)
+			{
+				// runner kin_time
+				// equivalent to kin_time in count_steps
+				if (run_info.Get_time_step() != NA)
+				{
+					kin_time = run_info.Get_time_step();
+				}
+				// runner kin_time not defined
+				else
+				{
+					kin_time = kinetics_ptr->Get_steps()[0];
+				}
+			}
+			/*
+			*   Run reaction step
+			*/
+			use_mix = TRUE;
+			run_reactions(i, kin_time, use_mix, 1.0);
+			rate_sim_time = kin_time;
+			saver();
+		}
+	}
+	initial_total_time += rate_sim_time;
+	run_info.Get_cells().Set_defined(false);
+	// not running cells
+	run_info.Set_run_cells(false);
+	return (OK);
+}
+#else
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+run_as_cells(void)
+/* ---------------------------------------------------------------------- */
+{
+	class save save_data;
+	LDBLE kin_time;
+	int count_steps, use_mix;
+	char token[2 * MAX_LENGTH];
+
+	state = REACTION;
+	if (run_info.Get_cells().Get_numbers().size() == 0 ||
+		!(run_info.Get_cells().Get_defined())) return(OK);
+
+	// running cells
+	run_info.Set_run_cells(true);
+
+	dup_print("Beginning of run as cells.", TRUE);
+	LDBLE initial_total_time_save;
+	if (run_info.Get_start_time() != NA)
+	{
+		initial_total_time_save = run_info.Get_start_time();
+	}
+	else
+	{
+		initial_total_time_save = initial_total_time;
+	}
+
+	std::set < int >::iterator it = run_info.Get_cells().Get_numbers().begin();
+
+	for ( ; it != run_info.Get_cells().Get_numbers().end(); it++)
+	{
+		int i = *it;
+		if (i < 0) continue;
+		if (Utilities::Rxn_find(Rxn_solution_map, i) == NULL
+			&& Utilities::Rxn_find(Rxn_mix_map, i) == NULL)
+			continue;
+		initial_total_time = initial_total_time_save;
+		set_advection(i, TRUE, TRUE, i);
+/*
+ *   Run reaction step
+ */
+		/*
+		*   Find maximum number of steps
+		*/
+		dup_print("Beginning of batch-reaction calculations.", TRUE);
+		count_steps = 1;
+		if (!this->run_cells_one_step)
+		{
+			if (use.Get_reaction_in() == TRUE && use.Get_reaction_ptr() != NULL)
+			{
+				int count = use.Get_reaction_ptr()->Get_reaction_steps();
+				if (count > count_steps)
+					count_steps = count;
+			}
+			if (use.Get_kinetics_in() == TRUE && use.Get_kinetics_ptr() != NULL)
+			{
+				if (use.Get_kinetics_ptr()->Get_reaction_steps() > count_steps)
+					count_steps = use.Get_kinetics_ptr()->Get_reaction_steps();
+			}
+			if (use.Get_temperature_in() == TRUE && use.Get_temperature_ptr() != NULL)
+			{
+				int count = use.Get_temperature_ptr()->Get_countTemps();
+				if (count > count_steps)
+				{
+					count_steps = count;
+				}
+			}
+			if (use.Get_pressure_in() == TRUE && use.Get_pressure_ptr() != NULL)
+			{
+				int count = use.Get_pressure_ptr()->Get_count();
+				if (count > count_steps)
+				{
+					count_steps = count;
+				}
+			}
+		}
+		count_total_steps = count_steps;
+		/*
+		*  save data for saving solutions
+		*/
+		// memcpy(&save_data, &save, sizeof(class save));
+		save_data = save;
+		/* 
+		*Copy everything to -2
+		*/
+		copy_use(-2);
+		rate_sim_time_start = 0;
+		rate_sim_time = 0;
+		for (reaction_step = 1; reaction_step <= count_steps; reaction_step++)
+		{
+			snprintf(token, sizeof(token), "Reaction step %d.", reaction_step);
+			if (reaction_step > 1 && incremental_reactions == FALSE)
+			{
+				copy_use(-2);
+			}
+			set_initial_moles(-2);
+			dup_print(token, FALSE);
+			/*
+			*  Determine time step for kinetics
+			*/
+			kin_time = 0.0;
+			if (use.Get_kinetics_in() == TRUE)
+			{
+				// runner kin_time
+				// equivalent to kin_time in count_steps
+				if (run_info.Get_time_step() != NA)
+				{
+					if (incremental_reactions == FALSE)
+					{
+						/* not incremental reactions */
+						kin_time = reaction_step * run_info.Get_time_step() / ((LDBLE) count_steps);
+					}
+					else
+					{
+						/* incremental reactions */
+						kin_time = run_info.Get_time_step() / ((LDBLE) count_steps);
+					}
+				}
+				// runner kin_time not defined
+				else
+				{
+					cxxKinetics *kinetics_ptr = Utilities::Rxn_find(Rxn_kinetics_map, -2);
+					kin_time = kinetics_ptr->Current_step((incremental_reactions==TRUE), reaction_step);
+				}
+			}
+			if (incremental_reactions == FALSE ||
+				(incremental_reactions == TRUE && reaction_step == 1))
+			{
+				use_mix = TRUE;
+			}
+			else
+			{
+				use_mix = FALSE;
+			}
+			/*
+			*   Run reaction step
+			*/
+			run_reactions(-2, kin_time, use_mix, 1.0);
+			if (incremental_reactions == TRUE)
+			{
+				rate_sim_time_start += kin_time;
+				rate_sim_time = rate_sim_time_start;
+			}
+			else
+			{
+				rate_sim_time = kin_time;
+			}
+			if (state != ADVECTION)
+			{
+				punch_all();
+				print_all();
+			}
+			/* saves back into -2 */
+			if (reaction_step < count_steps)
+			{
+				saver();
+			}
+		}
+		/*
+		*   save end of reaction
+		*/
+		// memcpy(&save, &save_data, sizeof(class save));
+		save = save_data;
+		if (use.Get_kinetics_in() == TRUE)
+		{
+			Utilities::Rxn_copy(Rxn_kinetics_map, -2, use.Get_n_kinetics_user());
+		}
+		saver();
+	}
+	initial_total_time += rate_sim_time;
+	run_info.Get_cells().Set_defined(false);
+	// not running cells
+	run_info.Set_run_cells(false);
+	return (OK);
+}
+#endif
+/* ---------------------------------------------------------------------- */
+void Phreeqc::
+dump_ostream(std::ostream& os)
+/* ---------------------------------------------------------------------- */
+{
+	// solutions
+	if (dump_info.Get_bool_solution())
+	{
+		if (dump_info.Get_solution().size() == 0)
+		{
+			Utilities::Rxn_dump_raw(Rxn_solution_map, os, 0);
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = dump_info.Get_solution().begin(); it != dump_info.Get_solution().end(); it++)
+			{
+				cxxSolution *p = Utilities::Rxn_find(Rxn_solution_map, *it);
+				if (p != NULL && p->Get_n_user() >= 0)
+				{
+					p->dump_raw(os, 0);
+				}
+			}
+		}
+	}
+
+	// pp_assemblages
+	if (dump_info.Get_bool_pp_assemblage())
+	{
+		if (dump_info.Get_pp_assemblage().size() == 0)
+		{
+			Utilities::Rxn_dump_raw(Rxn_pp_assemblage_map, os, 0);
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = dump_info.Get_pp_assemblage().begin(); it != dump_info.Get_pp_assemblage().end(); it++)
+			{
+				cxxPPassemblage *p = Utilities::Rxn_find(Rxn_pp_assemblage_map, *it);
+
+				if (p != NULL && p->Get_n_user() >= 0)
+				{
+					p->dump_raw(os, 0);
+				}
+			}
+		}
+	}
+	// exchanges
+	if (dump_info.Get_bool_exchange())
+	{
+		if (dump_info.Get_exchange().size() == 0)
+		{
+			Utilities::Rxn_dump_raw(Rxn_exchange_map, os, 0);
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = dump_info.Get_exchange().begin(); it != dump_info.Get_exchange().end(); it++)
+			{
+				cxxExchange *p = Utilities::Rxn_find(Rxn_exchange_map, *it);
+
+				if (p != NULL && p->Get_n_user() >= 0)
+				{
+					p->dump_raw(os, 0);
+				}
+			}
+		}
+	}
+
+	// surfaces
+	if (dump_info.Get_bool_surface())
+	{
+		if (dump_info.Get_surface().size() == 0)
+		{
+			Utilities::Rxn_dump_raw(Rxn_surface_map, os, 0);
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = dump_info.Get_surface().begin(); it != dump_info.Get_surface().end(); it++)
+			{
+				cxxSurface *p = Utilities::Rxn_find(Rxn_surface_map, *it);
+
+				if (p != NULL && p->Get_n_user() >= 0)
+				{
+					p->dump_raw(os, 0);
+				}
+			}
+		}
+	}
+	// ss_assemblages
+	if (dump_info.Get_bool_ss_assemblage())
+	{
+		if (dump_info.Get_ss_assemblage().size() == 0)
+		{
+			Utilities::Rxn_dump_raw(Rxn_ss_assemblage_map, os, 0);
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = dump_info.Get_ss_assemblage().begin(); it != dump_info.Get_ss_assemblage().end(); it++)
+			{
+				cxxSSassemblage *p = Utilities::Rxn_find(Rxn_ss_assemblage_map, *it);
+
+				if (p != NULL && p->Get_n_user() >= 0)
+				{
+					p->dump_raw(os, 0);
+				}
+			}
+		}
+	}
+	// gas_phases
+	if (dump_info.Get_bool_gas_phase())
+	{
+		if (dump_info.Get_gas_phase().size() == 0)
+		{
+			Utilities::Rxn_dump_raw(Rxn_gas_phase_map, os, 0);
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = dump_info.Get_gas_phase().begin(); it != dump_info.Get_gas_phase().end(); it++)
+			{
+				cxxGasPhase *p = Utilities::Rxn_find(Rxn_gas_phase_map, *it);
+
+				if (p != NULL && p->Get_n_user() >= 0)
+				{
+					p->dump_raw(os, 0);
+				}
+			}
+		}
+	}
+
+	// kinetics
+	if (dump_info.Get_bool_kinetics())
+	{
+		if (dump_info.Get_kinetics().size() == 0)
+		{
+			Utilities::Rxn_dump_raw(Rxn_kinetics_map, os, 0);
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = dump_info.Get_kinetics().begin(); it != dump_info.Get_kinetics().end(); it++)
+			{
+				cxxKinetics *p = Utilities::Rxn_find(Rxn_kinetics_map, *it);
+
+				if (p != NULL && p->Get_n_user() >= 0)
+				{
+					p->dump_raw(os, 0);
+				}
+			}
+		}
+	}
+	// mix
+	if (dump_info.Get_bool_mix())
+	{
+		if (dump_info.Get_mix().size() == 0)
+		{
+			Utilities::Rxn_dump_raw(Rxn_mix_map, os, 0);
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = dump_info.Get_mix().begin(); it != dump_info.Get_mix().end(); it++)
+			{
+				cxxMix *p = Utilities::Rxn_find(Rxn_mix_map, *it);
+
+				if (p != NULL && p->Get_n_user() >= 0)
+				{
+					p->dump_raw(os, 0);
+				}
+			}
+		}
+	}
+
+	// reaction
+	if (dump_info.Get_bool_reaction())
+	{
+		if (dump_info.Get_reaction().size() == 0)
+		{
+			Utilities::Rxn_dump_raw(Rxn_reaction_map, os, 0);
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = dump_info.Get_reaction().begin(); it != dump_info.Get_reaction().end(); it++)
+			{
+				cxxReaction *p = Utilities::Rxn_find(Rxn_reaction_map, *it);
+
+				if (p != NULL && p->Get_n_user() >= 0)
+				{
+					p->dump_raw(os, 0);
+				}
+			}
+		}
+	}
+
+	// temperature
+	if (dump_info.Get_bool_temperature())
+	{
+		if (dump_info.Get_temperature().size() == 0)
+		{
+			Utilities::Rxn_dump_raw(Rxn_temperature_map, os, 0);
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = dump_info.Get_temperature().begin(); it != dump_info.Get_temperature().end(); it++)
+			{
+				cxxTemperature *p = Utilities::Rxn_find(Rxn_temperature_map, *it);
+
+				if (p != NULL && p->Get_n_user() >= 0)
+				{
+					p->dump_raw(os, 0);
+				}
+			}
+		}
+	}
+	// pressure
+	if (dump_info.Get_bool_pressure())
+	{
+		if (dump_info.Get_pressure().size() == 0)
+		{
+			Utilities::Rxn_dump_raw(Rxn_pressure_map, os, 0);
+		}
+		else
+		{
+			std::set < int >::iterator it;
+			for (it = dump_info.Get_pressure().begin(); it != dump_info.Get_pressure().end(); it++)
+			{
+				cxxPressure *p = Utilities::Rxn_find(Rxn_pressure_map, *it);
+
+				if (p != NULL && p->Get_n_user() >= 0)
+				{
+					p->dump_raw(os, 0);
+				}
+			}
+		}
+	}
+	// Turn off any reaction calculation
+	os << "USE mix none" << "\n";
+	os << "USE reaction none" << "\n";
+	os << "USE reaction_temperature none" << "\n";
+	os << "USE reaction_pressure none" << "\n";
+
+	// Turn off dump until next read
+	dump_info.SetAll(false);
+}
+#if defined MULTICHART
+/* ---------------------------------------------------------------------- */
+int Phreeqc::
+read_user_graph_handler(void)
+/* ---------------------------------------------------------------------- */
+{
+/*
+ *      Reads USER_GRAPH_DATA_BLOCK data block
+ *
+ *      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
+ *
+ */
+	int return_value;
+
+	/*
+	 *  Make parser
+	 */
+	std::istringstream iss_in;
+	return_value = streamify_to_next_keyword(iss_in);
+	CParser parser(iss_in, phrq_io);
+
+	//For testing, need to read line to get started
+	std::vector < std::string > vopts;
+	std::istream::pos_type next_char;
+
+	if (pr.echo_input == FALSE)
+	{
+		parser.set_echo_file(CParser::EO_NONE);
+	}
+	else
+	{
+		parser.set_echo_file(CParser::EO_NOKEYWORDS);
+	}
+
+	assert(!reading_database());
+
+	bool success = chart_handler.Read(this, parser);
+
+	// Need to output the next keyword
+	if (return_value == OPTION_KEYWORD) echo_msg(sformatf( "\t%s\n", line));
+	return (return_value);
+}
+#endif