pyEQL 1.4.0rc9__cp310-cp310-macosx_11_0_arm64.whl

pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/IPhreeqc.cpp

@@ -0,0 +1,1889 @@
+#include <memory>                       // auto_ptr
+#include <map>
+#include <string.h>
+#include "IPhreeqc.hpp"                 // IPhreeqc
+#include "Phreeqc.h"                    // Phreeqc
+#include "thread.h"
+#include "Version.h"
+
+#include "Debug.h"                      // ASSERT
+#include "ErrorReporter.hxx"            // CErrorReporter
+#include "CSelectedOutput.hxx"          // CSelectedOutput
+#include "SelectedOutput.h"             // SelectedOutput
+#include "dumper.h"                     // dumper
+
+// statics
+std::map<size_t, IPhreeqc*> IPhreeqc::Instances;
+size_t IPhreeqc::InstancesIndex = 0;
+
+std::string IPhreeqc::Version(VERSION_STRING);
+
+static const char empty[] = "";
+
+
+IPhreeqc::IPhreeqc(void)
+: DatabaseLoaded(false)
+, ClearAccumulated(false)
+, UpdateComponents(true)
+, OutputFileOn(false)
+, LogFileOn(false)
+, ErrorFileOn(false)
+, DumpOn(false)
+, DumpStringOn(false)
+, OutputStringOn(false)
+, LogStringOn(false)
+, ErrorStringOn(true)
+, ErrorReporter(0)
+, WarningStringOn(true)
+, WarningReporter(0)
+, CurrentSelectedOutputUserNumber(1)
+, PhreeqcPtr(0)
+, input_file(0)
+, database_file(0)
+{
+	this->ErrorReporter   = new CErrorReporter<std::ostringstream>;
+	this->WarningReporter = new CErrorReporter<std::ostringstream>;
+	this->PhreeqcPtr      = new Phreeqc(this);
+
+	ASSERT(this->PhreeqcPtr->phast == 0);
+	this->UnLoadDatabase();
+
+	mutex_lock(&map_lock);
+	this->Index = IPhreeqc::InstancesIndex++;
+	std::map<size_t, IPhreeqc*>::value_type instance(this->Index, this);
+	/*std::pair<std::map<size_t, IPhreeqc*>::iterator, bool> pr = */IPhreeqc::Instances.insert(instance);
+	mutex_unlock(&map_lock);
+
+	this->SelectedOutputStringOn[1] = false;
+
+	this->SelectedOutputFileOnMap[1] = false;
+	this->SelectedOutputFileNameMap[1] = this->sel_file_name(1);
+	
+	this->OutputFileName = create_file_name("phreeqc", "out");
+	this->ErrorFileName  = create_file_name("phreeqc", "err");
+	this->LogFileName    = create_file_name("phreeqc", "log");
+
+	this->DumpFileName   = create_file_name("dump", "out");
+	this->PhreeqcPtr->dump_info.Set_file_name(this->DumpFileName);
+}
+
+IPhreeqc::~IPhreeqc(void)
+{
+#if !defined(NDEBUG)
+	this->OutputFileOn = false;
+#endif
+	delete this->PhreeqcPtr;
+	delete this->WarningReporter;
+	delete this->ErrorReporter;
+
+	std::map< int, CSelectedOutput* >::iterator sit = this->SelectedOutputMap.begin();
+	for (; sit != this->SelectedOutputMap.end(); ++sit)
+	{
+		delete (*sit).second;
+	}
+	this->SelectedOutputMap.clear();
+
+	mutex_lock(&map_lock);
+	std::map<size_t, IPhreeqc*>::iterator it = IPhreeqc::Instances.find(this->Index);
+	if (it != IPhreeqc::Instances.end())
+	{
+		IPhreeqc::Instances.erase(it);
+	}
+	mutex_unlock(&map_lock);
+}
+
+VRESULT IPhreeqc::AccumulateLine(const char *line)
+{
+	try
+	{
+		if (this->ClearAccumulated)
+		{
+			this->ClearAccumulatedLines();
+			this->ClearAccumulated = false;
+		}
+
+		this->ErrorReporter->Clear();
+		this->WarningReporter->Clear();
+		this->StringInput.append(line);
+		this->StringInput.append("\n");
+		return VR_OK;
+	}
+	catch (...)
+	{
+		this->AddError("AccumulateLine: An unhandled exception occurred.\n");
+		throw;
+	}
+	return VR_OUTOFMEMORY;
+}
+
+size_t IPhreeqc::AddError(const char* str)
+{
+	return this->ErrorReporter->AddError(str);
+}
+
+size_t IPhreeqc::AddWarning(const char* str)
+{
+	return this->WarningReporter->AddError(str);
+}
+
+void IPhreeqc::ClearAccumulatedLines(void)
+{
+	this->StringInput.erase();
+}
+
+const std::string& IPhreeqc::GetAccumulatedLines(void)
+{
+	return this->StringInput;
+}
+
+const char* IPhreeqc::GetComponent(int n)
+{
+	static const char empty[] = "";
+	this->ListComponents();
+	if (n < 0 || n >= (int)this->Components.size())
+	{
+		return empty;
+	}
+	std::list< std::string >::iterator it = this->Components.begin();
+	for(int i = 0; i < n; ++i)
+	{
+		++it;
+	}
+	return (*it).c_str();
+}
+
+size_t IPhreeqc::GetComponentCount(void)
+{
+	this->ListComponents();
+	return this->Components.size();
+}
+
+int IPhreeqc::GetCurrentSelectedOutputUserNumber(void)const
+{
+	return this->CurrentSelectedOutputUserNumber;
+}
+
+const char* IPhreeqc::GetDumpFileName(void)const
+{
+	return this->DumpFileName.c_str();
+}
+
+bool IPhreeqc::GetDumpFileOn(void)const
+{
+	return this->DumpOn;
+}
+
+const char* IPhreeqc::GetDumpString(void)const
+{
+	static const char err_msg[] = "GetDumpString: DumpStringOn not set.\n";
+	if (!this->DumpStringOn)
+	{
+		return err_msg;
+	}
+	return this->DumpString.c_str();
+}
+
+const char* IPhreeqc::GetDumpStringLine(int n)
+{
+	static const char empty[] = "";
+	if (n < 0 || n >= this->GetDumpStringLineCount())
+	{
+		return empty;
+	}
+	return this->DumpLines[n].c_str();
+}
+
+int IPhreeqc::GetDumpStringLineCount(void)const
+{
+	return (int)this->DumpLines.size();
+}
+
+bool IPhreeqc::GetDumpStringOn(void)const
+{
+	return this->DumpStringOn;
+}
+
+const char* IPhreeqc::GetErrorFileName(void)const
+{
+	return this->ErrorFileName.c_str();
+}
+
+bool IPhreeqc::GetErrorFileOn(void)const
+{
+	return this->ErrorFileOn;
+}
+
+bool IPhreeqc::GetErrorOn(void)const
+{
+	return this->Get_error_on();
+}
+
+const char* IPhreeqc::GetErrorString(void)
+{
+	static const char err_msg[] = "GetErrorString: ErrorStringOn not set.\n";
+	static const char err_msg2[] = "GetErrorString: ErrorOn not set.\n";
+	if (!this->error_on)
+	{
+		return err_msg2;
+	}
+	if (!this->ErrorStringOn)
+	{
+		return err_msg;
+	}
+	this->ErrorString = ((CErrorReporter<std::ostringstream>*)this->ErrorReporter)->GetOS()->str();
+	return this->ErrorString.c_str();
+}
+
+const char* IPhreeqc::GetErrorStringLine(int n)
+{
+	static const char empty[] = "";
+	if (n < 0 || n >= this->GetErrorStringLineCount())
+	{
+		return empty;
+	}
+	return this->ErrorLines[n].c_str();
+}
+
+int IPhreeqc::GetErrorStringLineCount(void)const
+{
+	return (int)this->ErrorLines.size();
+}
+
+bool IPhreeqc::GetErrorStringOn(void)const
+{
+	return this->ErrorStringOn;
+}
+
+int IPhreeqc::GetId(void)const
+{
+	return (int)this->Index;
+}
+
+const char* IPhreeqc::GetLogFileName(void)const
+{
+	return this->LogFileName.c_str();
+}
+
+bool IPhreeqc::GetLogFileOn(void)const
+{
+	return this->LogFileOn;
+}
+
+const char* IPhreeqc::GetLogString(void)const
+{
+	static const char err_msg[] = "GetLogString: LogStringOn not set.\n";
+	if (!this->LogStringOn)
+	{
+		return err_msg;
+	}
+	return this->LogString.c_str();
+}
+
+const char* IPhreeqc::GetLogStringLine(int n)const
+{
+	static const char empty[] = "";
+	if (n < 0 || n >= this->GetLogStringLineCount())
+	{
+		return empty;
+	}
+	return this->LogLines[n].c_str();
+}
+
+int IPhreeqc::GetLogStringLineCount(void)const
+{
+	return (int)this->LogLines.size();
+}
+
+bool IPhreeqc::GetLogStringOn(void)const
+{
+	return this->LogStringOn;
+}
+
+int IPhreeqc::GetNthSelectedOutputUserNumber(int n)const
+{
+	int nth = VR_INVALIDARG;
+	std::map< int, SelectedOutput >::const_iterator ci = this->PhreeqcPtr->SelectedOutput_map.begin();
+	for (int i = 0; ci != this->PhreeqcPtr->SelectedOutput_map.end(); ++ci, ++i)
+	{
+		if (i == n)
+		{
+			nth = (*ci).first;
+			break;
+		}
+	}
+	return nth;
+}
+
+const char* IPhreeqc::GetOutputFileName(void)const
+{
+	return this->OutputFileName.c_str();
+}
+
+bool IPhreeqc::GetOutputFileOn(void)const
+{
+	return this->OutputFileOn;
+}
+
+const char* IPhreeqc::GetOutputString(void)const
+{
+	static const char err_msg[] = "GetOutputString: OutputStringOn not set.\n";
+	if (!this->OutputStringOn)
+	{
+		return err_msg;
+	}
+	return this->OutputString.c_str();
+}
+
+const char* IPhreeqc::GetOutputStringLine(int n)const
+{
+	static const char empty[] = "";
+	if (n < 0 || n >= this->GetOutputStringLineCount())
+	{
+		return empty;
+	}
+	return this->OutputLines[n].c_str();
+}
+
+int IPhreeqc::GetOutputStringLineCount(void)const
+{
+	return (int)this->OutputLines.size();
+}
+
+bool IPhreeqc::GetOutputStringOn(void)const
+{
+	return this->OutputStringOn;
+}
+
+int IPhreeqc::GetSelectedOutputColumnCount(void)const
+{
+	std::map< int, CSelectedOutput* >::const_iterator ci = this->SelectedOutputMap.find(this->CurrentSelectedOutputUserNumber);
+	if (ci != this->SelectedOutputMap.end())
+	{
+		return (int)(*ci).second->GetColCount();
+	}
+	return 0;
+}
+
+int IPhreeqc::GetSelectedOutputCount(void)const
+{
+	ASSERT(this->PhreeqcPtr->SelectedOutput_map.size() == this->SelectedOutputMap.size());
+	return (int) this->PhreeqcPtr->SelectedOutput_map.size();
+}
+
+const char* IPhreeqc::GetSelectedOutputFileName(void)const
+{
+	static const char empty[] = "";
+	std::map< int, std::string >::const_iterator ci = this->SelectedOutputFileNameMap.find(this->CurrentSelectedOutputUserNumber);
+	if (ci != this->SelectedOutputFileNameMap.end())
+	{
+		return (*ci).second.c_str();
+	}
+	return empty;
+}
+
+bool IPhreeqc::GetSelectedOutputFileOn(void)const
+{
+	return this->get_sel_out_file_on(this->CurrentSelectedOutputUserNumber);
+}
+
+int IPhreeqc::GetSelectedOutputRowCount(void)const
+{
+	std::map< int, CSelectedOutput* >::const_iterator ci = this->SelectedOutputMap.find(this->CurrentSelectedOutputUserNumber);
+	if (ci != this->SelectedOutputMap.end())
+	{
+		return (int)(*ci).second->GetRowCount();
+	}
+	return 0;
+}
+
+const char* IPhreeqc::GetSelectedOutputString(void)const
+{
+	static const char err_msg[] = "GetSelectedOutputString: SelectedOutputStringOn not set.\n";
+	std::map< int, bool >::const_iterator ci = this->SelectedOutputStringOn.find(this->CurrentSelectedOutputUserNumber);
+	if (ci == this->SelectedOutputStringOn.end())
+	{
+		return err_msg;
+	}
+	std::map< int, std::string >::const_iterator cit = this->SelectedOutputStringMap.find(this->CurrentSelectedOutputUserNumber);
+	if (cit != this->SelectedOutputStringMap.end())
+	{
+		return (*cit).second.c_str();
+	}
+	return empty;
+}
+
+const char* IPhreeqc::GetSelectedOutputStringLine(int n)
+{
+	static const char empty[] = "";
+	if (n < 0 || n >= this->GetSelectedOutputStringLineCount())
+	{
+		return empty;
+	}
+	// don't need to check CurrentSelectedOutputUserNumber since
+	// GetSelectedOutputStringLineCount will catch
+	return this->SelectedOutputLinesMap[this->CurrentSelectedOutputUserNumber][n].c_str();
+}
+
+int IPhreeqc::GetSelectedOutputStringLineCount(void)const
+{
+	std::map< int, std::vector < std::string > >::const_iterator cit = this->SelectedOutputLinesMap.find(this->CurrentSelectedOutputUserNumber);
+	if (cit != this->SelectedOutputLinesMap.end())
+	{
+		return (int) (*cit).second.size();
+	}
+	return 0;
+}
+
+bool IPhreeqc::GetSelectedOutputStringOn(void)const
+{
+	return this->get_sel_out_string_on(this->CurrentSelectedOutputUserNumber);
+}
+
+VRESULT IPhreeqc::GetSelectedOutputValue(int row, int col, VAR* pVAR)
+{
+	VRESULT v;
+	this->ErrorReporter->Clear();
+	if (!pVAR)
+	{
+		this->AddError("GetSelectedOutputValue: VR_INVALIDARG pVAR is NULL.\n");
+		this->update_errors();
+		return VR_INVALIDARG;
+	}
+
+	std::map< int, CSelectedOutput* >::const_iterator ci = this->SelectedOutputMap.find(this->CurrentSelectedOutputUserNumber);
+	if (ci != this->SelectedOutputMap.end())
+	{
+		v = (*ci).second->Get(row, col, pVAR);
+		switch (v)
+		{
+		case VR_OK:
+			break;
+		case VR_INVALIDROW:
+			this->AddError("GetSelectedOutputValue: VR_INVALIDROW Row index out of range.\n");
+			this->update_errors();
+			break;
+		case VR_INVALIDCOL:
+			this->AddError("GetSelectedOutputValue: VR_INVALIDCOL Column index out of range.\n");
+			this->update_errors();
+			break;
+		case VR_OUTOFMEMORY:
+			this->AddError("GetSelectedOutputValue: VR_OUTOFMEMORY Out of memory.\n");
+			this->update_errors();
+			break;
+		case VR_BADVARTYPE:
+			this->AddError("GetSelectedOutputValue: VR_BADVARTYPE pVar must be initialized(VarInit) and/or cleared(VarClear).\n");
+			this->update_errors();
+			break;
+		case VR_INVALIDARG:
+			// not possible
+			break;
+		default:
+			assert(0);
+		}
+	}
+	else
+	{
+		char buffer[120];
+		v = VR_INVALIDARG;
+		::snprintf(buffer, sizeof(buffer), "GetSelectedOutputValue: VR_INVALIDARG Invalid selected-output user number %d.\n", this->CurrentSelectedOutputUserNumber);
+		this->AddError(buffer);
+		this->update_errors();
+	}
+	return v;
+}
+
+VRESULT IPhreeqc::GetSelectedOutputValue2(int row, int col, int *vtype, double* dvalue, char* svalue, unsigned int svalue_length)
+{
+	VRESULT result;
+	VAR v;
+	VarInit(&v);
+	char buffer[100];
+
+	result = this->GetSelectedOutputValue(row, col, &v);
+
+	switch (v.type)
+	{
+	case TT_EMPTY:
+		*vtype = v.type;
+		break;
+	case TT_ERROR:
+		*vtype = v.type;
+		break;
+	case TT_LONG:
+		*vtype = TT_DOUBLE;
+		*dvalue = (double)v.lVal;
+		::snprintf(buffer, sizeof(buffer), "%ld", v.lVal);
+		::strncpy(svalue, buffer, svalue_length);
+		break;
+	case TT_DOUBLE:
+		*vtype = v.type;
+		*dvalue = v.dVal;
+		::snprintf(buffer, sizeof(buffer), "%23.15e", v.dVal);
+		::strncpy(svalue, buffer, svalue_length);
+		break;
+	case TT_STRING:
+		*vtype = v.type;
+		::strncpy(svalue, v.sVal, svalue_length);
+		break;
+	default:
+		assert(0);
+	}
+	::VarClear(&v);
+	return result;
+}
+
+const char* IPhreeqc::GetVersionString(void)
+{
+	return IPhreeqc::Version.c_str();
+}
+
+const char* IPhreeqc::GetWarningString(void)
+{
+	this->WarningString = ((CErrorReporter<std::ostringstream>*)this->WarningReporter)->GetOS()->str();
+	return this->WarningString.c_str();
+}
+
+const char* IPhreeqc::GetWarningStringLine(int n)
+{
+	static const char empty[] = "";
+	if (n < 0 || n >= this->GetWarningStringLineCount())
+	{
+		return empty;
+	}
+	return this->WarningLines[n].c_str();
+}
+
+int IPhreeqc::GetWarningStringLineCount(void)const
+{
+	return (int)this->WarningLines.size();
+}
+
+std::list< std::string > IPhreeqc::ListComponents(void)
+{
+	if (this->UpdateComponents)
+	{
+		this->Components.clear();
+		this->PhreeqcPtr->list_components(this->Components);
+		this->PhreeqcPtr->list_EquilibriumPhases(this->EquilibriumPhasesList);
+		this->PhreeqcPtr->list_GasComponents(this->GasComponentsList);
+		this->PhreeqcPtr->list_KineticReactions(this->KineticReactionsList);
+		this->PhreeqcPtr->list_SolidSolutions(this->SolidSolutionComponentsList,this->SolidSolutionNamesList);
+		this->PhreeqcPtr->list_Surfaces(this->SurfaceTypeList, this->SurfaceNamesList);
+		this->PhreeqcPtr->list_Exchangers(this->ExchangeNamesList);
+		this->UpdateComponents = false;
+	}
+	return this->Components;
+}
+
+int IPhreeqc::load_db(const char* filename)
+{
+	try
+	{
+		// cleanup
+		//
+		this->UnLoadDatabase();
+
+		// open file
+		//
+		std::ifstream ifs;
+		ifs.open(filename);
+
+		if (!ifs.is_open())
+		{
+			std::ostringstream oss;
+			oss << "LoadDatabase: Unable to open:" << "\"" << filename << "\".";
+			this->PhreeqcPtr->error_msg(oss.str().c_str(), STOP); // throws
+		}
+
+		// read input
+		//
+		ASSERT(this->PhreeqcPtr->phrq_io->get_istream() == NULL);
+		this->PhreeqcPtr->phrq_io->push_istream(&ifs, false);
+		this->PhreeqcPtr->read_database();
+	}
+	catch (const IPhreeqcStop&)
+	{
+		this->close_input_files();
+	}
+	catch (...)
+	{
+		const char *errmsg = "LoadDatabase: An unhandled exception occurred.\n";
+		try
+		{
+			this->PhreeqcPtr->error_msg(errmsg, STOP); // throws IPhreeqcStop
+		}
+		catch (const IPhreeqcStop&)
+		{
+			// do nothing
+		}
+		throw;
+	}
+	this->PhreeqcPtr->phrq_io->clear_istream();
+	this->DatabaseLoaded = (this->PhreeqcPtr->get_input_errors() == 0);
+	return this->PhreeqcPtr->get_input_errors();
+}
+
+int IPhreeqc::LoadDatabase(const char* filename)
+{
+	// save I/O state
+	bool bSaveErrorFileOn  = this->ErrorFileOn;
+	bool bSaveOutputOn     = this->OutputFileOn;
+	bool bSaveLogFileOn    = this->LogFileOn;
+	this->ErrorFileOn      = false;
+	this->OutputFileOn     = false;
+	this->LogFileOn        = false;
+
+	int n = this->load_db(filename);
+	if (n == 0)
+	{
+		n = this->test_db();
+	}
+
+	// restore I/O state
+	this->ErrorFileOn  = bSaveErrorFileOn;
+	this->OutputFileOn = bSaveOutputOn;
+	this->LogFileOn    = bSaveLogFileOn;
+
+	return n;
+}
+
+int IPhreeqc::load_db_str(const char* input)
+{
+	try
+	{
+		// cleanup
+		//
+		this->UnLoadDatabase();
+
+		std::string s(input);
+		std::istringstream iss(s);
+
+		// read input
+		//
+		ASSERT(this->PhreeqcPtr->phrq_io->get_istream() == NULL);
+		this->PhreeqcPtr->phrq_io->push_istream(&iss, false);
+		this->PhreeqcPtr->read_database();
+	}
+	catch (const IPhreeqcStop&)
+	{
+		this->close_input_files();
+	}
+	catch(...)
+	{
+		const char *errmsg = "LoadDatabaseString: An unhandled exception occurred.\n";
+		try
+		{
+			this->PhreeqcPtr->error_msg(errmsg, STOP); // throws PhreeqcStop
+		}
+		catch (const IPhreeqcStop&)
+		{
+			// do nothing
+		}
+		throw;
+	}
+
+	this->PhreeqcPtr->phrq_io->clear_istream();
+	this->DatabaseLoaded = (this->PhreeqcPtr->get_input_errors() == 0);
+	return this->PhreeqcPtr->get_input_errors();
+}
+
+int IPhreeqc::LoadDatabaseString(const char* input)
+{
+	// save I/O state
+	bool bSaveErrorFileOn  = this->ErrorFileOn;
+	bool bSaveOutputOn     = this->OutputFileOn;
+	bool bSaveLogFileOn    = this->LogFileOn;
+	this->ErrorFileOn      = false;
+	this->OutputFileOn     = false;
+	this->LogFileOn        = false;
+
+	int n = this->load_db_str(input);
+	if (n == 0)
+	{
+		n = this->test_db();
+	}
+
+	// restore I/O state
+	this->ErrorFileOn  = bSaveErrorFileOn;
+	this->OutputFileOn = bSaveOutputOn;
+	this->LogFileOn    = bSaveLogFileOn;
+
+	return n;
+}
+
+void IPhreeqc::OutputAccumulatedLines(void)
+{
+#if !defined(R_SO)
+	std::cout << this->StringInput.c_str() << std::endl;
+#endif
+}
+
+void IPhreeqc::OutputErrorString(void)
+{
+#if !defined(R_SO)
+	std::cout << this->GetErrorString() << std::endl;
+#endif
+}
+
+void IPhreeqc::OutputWarningString(void)
+{
+#if !defined(R_SO)
+	std::cout << this->GetWarningString() << std::endl;
+#endif
+}
+
+int IPhreeqc::RunAccumulated(void)
+{
+	static const char *sz_routine = "RunAccumulated";
+	try
+	{
+		// DON'T clear accumulated (just set
+		// flag to on next AccumulateLine)
+
+		// these may throw
+		this->open_output_files(sz_routine);
+		this->check_database(sz_routine);
+
+		this->PhreeqcPtr->input_error = 0;
+		this->io_error_count = 0;
+
+		// create input stream
+		std::istringstream iss(this->GetAccumulatedLines());
+
+		// this may throw
+		this->do_run(sz_routine, &iss, NULL, NULL, NULL);
+	}
+	catch (const IPhreeqcStop&)
+	{
+		// do nothing
+	}
+	catch(std::exception &e)
+	{
+		std::string errmsg("RunAccumulated: ");
+		errmsg += e.what();
+		try
+		{
+			this->PhreeqcPtr->error_msg(errmsg.c_str(), STOP); // throws PhreeqcStop
+		}
+		catch (const IPhreeqcStop&)
+		{
+			// do nothing
+		}
+		throw;
+	}
+	catch(...)
+	{
+		const char *errmsg = "RunAccumulated: An unhandled exception occurred.\n";
+		try
+		{
+			this->PhreeqcPtr->error_msg(errmsg, STOP); // throws PhreeqcStop
+		}
+		catch (const IPhreeqcStop&)
+		{
+			// do nothing
+		}
+		throw;
+	}
+
+	this->ClearAccumulated = true;
+	this->close_output_files();
+	this->update_errors();
+	this->PhreeqcPtr->phrq_io->clear_istream();
+
+	return this->PhreeqcPtr->get_input_errors();
+}
+
+int IPhreeqc::RunFile(const char* filename)
+{
+	static const char *sz_routine = "RunFile";
+	try
+	{
+		// clear accumulated
+		//
+		this->ClearAccumulatedLines();
+		this->ClearAccumulated = false;
+
+		// these may throw
+		this->open_output_files(sz_routine);
+		this->check_database(sz_routine);
+
+		this->PhreeqcPtr->input_error = 0;
+		this->io_error_count = 0;
+
+		// open file
+		//
+		std::ifstream ifs;
+		ifs.open(filename);
+		if (!ifs.is_open())
+		{
+			std::ostringstream oss;
+			oss << "RunFile: Unable to open:" << "\"" << filename << "\".";
+			this->PhreeqcPtr->error_msg(oss.str().c_str(), STOP); // throws
+		}
+
+		// this may throw
+		this->do_run(sz_routine, &ifs, NULL, NULL, NULL);
+	}
+	catch (const IPhreeqcStop&)
+	{
+		this->close_input_files();
+	}
+	catch(std::exception &e)
+	{
+		std::string errmsg("RunFile: ");
+		errmsg += e.what();
+		try
+		{
+			this->PhreeqcPtr->error_msg(errmsg.c_str(), STOP); // throws PhreeqcStop
+		}
+		catch (const IPhreeqcStop&)
+		{
+			// do nothing
+		}
+		throw;
+	}
+	catch(...)
+	{
+		const char *errmsg = "RunFile: An unhandled exception occurred.\n";
+		try
+		{
+			this->PhreeqcPtr->error_msg(errmsg, STOP); // throws PhreeqcStop
+		}
+		catch (const IPhreeqcStop&)
+		{
+			// do nothing
+		}
+		throw;
+	}
+
+	this->close_output_files();
+	this->update_errors();
+	this->PhreeqcPtr->phrq_io->clear_istream();
+
+	return this->PhreeqcPtr->get_input_errors();
+}
+
+int IPhreeqc::RunString(const char* input)
+{
+	static const char *sz_routine = "RunString";
+	try
+	{
+		// clear accumulated
+		//
+		this->ClearAccumulatedLines();
+		this->ClearAccumulated = false;
+
+		// these may throw
+		this->open_output_files(sz_routine);
+		this->check_database(sz_routine);
+
+		this->PhreeqcPtr->input_error = 0;
+		this->io_error_count = 0;
+
+		// create input stream
+		std::string s(input);
+		std::istringstream iss(s);
+
+		// this may throw
+		this->do_run(sz_routine, &iss, NULL, NULL, NULL);
+	}
+	catch (const IPhreeqcStop&)
+	{
+		this->close_input_files();
+	}
+	catch(std::exception &e)
+	{
+		std::string errmsg("RunString: ");
+		errmsg += e.what();
+		try
+		{
+			this->PhreeqcPtr->error_msg(errmsg.c_str(), STOP); // throws PhreeqcStop
+		}
+		catch (const IPhreeqcStop&)
+		{
+			// do nothing
+		}
+		throw;
+	}
+	catch(...)
+	{
+		const char *errmsg = "RunString: An unhandled exception occurred.\n";
+		try
+		{
+			this->PhreeqcPtr->error_msg(errmsg, STOP); // throws PhreeqcStop
+		}
+		catch (const IPhreeqcStop&)
+		{
+			// do nothing
+		}
+		throw;
+	}
+
+	this->close_output_files();
+	this->update_errors();
+	this->PhreeqcPtr->phrq_io->clear_istream();
+
+	return this->PhreeqcPtr->get_input_errors();
+}
+
+void IPhreeqc::SetBasicCallback(double (*fcn)(double x1, double x2, const char *str, void *cookie), void *cookie1)
+{
+	this->PhreeqcPtr->register_basic_callback(fcn, cookie1);
+}
+#ifdef IPHREEQC_NO_FORTRAN_MODULE
+void IPhreeqc::SetBasicFortranCallback(double (*fcn)(double *x1, double *x2, const char *str, size_t l))
+{
+	this->PhreeqcPtr->register_fortran_basic_callback(fcn);
+}
+#else
+void IPhreeqc::SetBasicFortranCallback(double (*fcn)(double *x1, double *x2, const char *str, int l))
+{
+	this->PhreeqcPtr->register_fortran_basic_callback(fcn);
+}
+#endif
+VRESULT IPhreeqc::SetCurrentSelectedOutputUserNumber(int n)
+{
+	if (0 <= n)
+	{
+		this->CurrentSelectedOutputUserNumber = n;
+		return VR_OK;
+	}
+	return VR_INVALIDARG;
+}
+
+void IPhreeqc::SetDumpFileName(const char *filename)
+{
+	if (filename && ::strlen(filename))
+	{
+		this->DumpFileName = filename;
+		this->PhreeqcPtr->dump_info.Set_file_name(this->DumpFileName);
+	}
+}
+
+void IPhreeqc::SetDumpFileOn(bool bValue)
+{
+	this->DumpOn = bValue;
+}
+
+void IPhreeqc::SetDumpStringOn(bool bValue)
+{
+	this->DumpStringOn = bValue;
+}
+
+void IPhreeqc::SetErrorFileName(const char *filename)
+{
+	if (filename && ::strlen(filename))
+	{
+		this->ErrorFileName = filename;
+	}
+}
+
+void IPhreeqc::SetErrorFileOn(bool bValue)
+{
+	this->ErrorFileOn = bValue;
+}
+
+void IPhreeqc::SetErrorOn(bool bValue)
+{
+	this->Set_error_on(bValue);
+}
+
+void IPhreeqc::SetErrorStringOn(bool bValue)
+{
+	this->ErrorStringOn = bValue;
+}
+
+void IPhreeqc::SetLogFileName(const char *filename)
+{
+	if (filename && ::strlen(filename))
+	{
+		this->LogFileName = filename;
+	}
+}
+
+void IPhreeqc::SetLogFileOn(bool bValue)
+{
+	this->LogFileOn = bValue;
+}
+
+void IPhreeqc::SetLogStringOn(bool bValue)
+{
+	this->LogStringOn = bValue;
+}
+
+void IPhreeqc::SetOutputFileName(const char *filename)
+{
+	if (filename && ::strlen(filename))
+	{
+		this->OutputFileName = filename;
+	}
+}
+
+void IPhreeqc::SetOutputStringOn(bool bValue)
+{
+	this->OutputStringOn = bValue;
+}
+
+void IPhreeqc::SetOutputFileOn(bool bValue)
+{
+	this->OutputFileOn = bValue;
+}
+
+void IPhreeqc::SetSelectedOutputFileName(const char *filename)
+{
+	if (filename && ::strlen(filename))
+	{
+		// Can't use this->PhreeqcPtr->SelectedOutput_map since it's necessary
+		// to override the default filename "selected_output_%d.%d.sel" 
+		this->SelectedOutputFileNameMap[this->CurrentSelectedOutputUserNumber] = std::string(filename);
+	}
+}
+
+void IPhreeqc::SetSelectedOutputFileOn(bool bValue)
+{
+	if (0 <= this->CurrentSelectedOutputUserNumber)
+	{
+		this->SelectedOutputFileOnMap[this->CurrentSelectedOutputUserNumber] = bValue;
+	}
+}
+
+void IPhreeqc::SetSelectedOutputStringOn(bool bValue)
+{
+	this->SelectedOutputStringOn[this->CurrentSelectedOutputUserNumber] = bValue;
+}
+
+int IPhreeqc::test_db(void)
+{
+	std::ostringstream oss;
+	int sn = this->PhreeqcPtr->next_user_number(Keywords::KEY_SOLUTION);
+	//oss << "SOLUTION " << sn <<"; DELETE; -solution " << sn;
+	oss << "SOLUTION " << sn << ";";
+	if (this->PhreeqcPtr->llnl_temp.size() > 0)
+	{
+		oss << "-temp " << this->PhreeqcPtr->llnl_temp[0] << ";";
+	}
+	oss << "DELETE; -solution " << sn;
+	this->PhreeqcPtr->set_reading_database(TRUE);
+	int n = this->RunString(oss.str().c_str());
+	this->PhreeqcPtr->set_reading_database(FALSE);
+	return n;
+}
+
+void IPhreeqc::UnLoadDatabase(void)
+{
+	// init IPhreeqc
+	//
+	this->DatabaseLoaded   = false;
+	this->UpdateComponents = true;
+	this->Components.clear();
+
+	// clear accumulated
+	//
+	this->ClearAccumulatedLines();
+	this->ClearAccumulated = false;
+
+	// clear error state
+	//
+	ASSERT(this->ErrorReporter);
+	this->ErrorReporter->Clear();
+	this->ErrorString.clear();
+
+	// clear warning state
+	//
+	ASSERT(this->WarningReporter);
+	this->WarningReporter->Clear();
+	this->WarningString.clear();
+
+	// clear selectedoutput
+	//
+	this->CurrentSelectedOutputUserNumber = 1;
+	this->SelectedOutputFileOnMap.clear();
+	this->SelectedOutputFileOnMap[1] = false;
+	this->SelectedOutputStringOn.clear();
+	this->SelectedOutputStringOn[1] = false;
+
+	std::map< int, CSelectedOutput* >::iterator itt = this->SelectedOutputMap.begin();
+	for (; itt != this->SelectedOutputMap.end(); ++itt)
+	{
+		delete (*itt).second;
+	}
+	this->SelectedOutputMap.clear();
+	this->SelectedOutputStringMap.clear();
+	this->SelectedOutputLinesMap.clear();
+
+
+	// clear dump string
+	//
+	this->DumpString.clear();
+	this->DumpLines.clear();
+
+	// initialize phreeqc
+	//
+	this->PhreeqcPtr->clean_up();
+	this->PhreeqcPtr->init();
+	this->PhreeqcPtr->do_initialize();
+	this->PhreeqcPtr->input_error = 0;
+	this->io_error_count = 0;
+}
+
+int IPhreeqc::EndRow(void)
+{
+	if (this->PhreeqcPtr->current_selected_output)
+	{
+		std::map< int, CSelectedOutput* >::iterator it =
+			this->SelectedOutputMap.find(this->PhreeqcPtr->current_selected_output->Get_n_user());
+
+		if (it != this->SelectedOutputMap.end())
+		{
+			// ensure all user_punch headings are included
+			ASSERT(this->PhreeqcPtr->n_user_punch_index >= 0);
+			if (this->PhreeqcPtr->current_user_punch)
+			{
+				for (size_t i = this->PhreeqcPtr->n_user_punch_index; i < this->PhreeqcPtr->current_user_punch->Get_headings().size(); ++i)
+				{
+					(*it).second->PushBackEmpty(this->PhreeqcPtr->current_user_punch->Get_headings()[i].c_str());
+				}
+			}
+			return (*it).second->EndRow();
+		}
+	}
+	return 0;
+}
+
+void IPhreeqc::check_database(const char* sz_routine)
+{
+ 	this->ErrorReporter->Clear();
+	this->WarningReporter->Clear();
+	std::map< int, CSelectedOutput* >::iterator it = this->SelectedOutputMap.begin();
+	for (; it != this->SelectedOutputMap.end(); ++it)
+	{
+		delete (*it).second;
+	}
+	this->SelectedOutputMap.clear();
+	this->SelectedOutputStringMap.clear();
+	this->SelectedOutputLinesMap.clear();
+
+	// release
+	this->LogString.clear();
+	this->LogLines.clear();
+	this->OutputString.clear();
+	this->OutputLines.clear();
+
+
+	if (!this->DatabaseLoaded)
+	{
+		std::ostringstream oss;
+		oss << sz_routine << ": No database is loaded";
+		this->PhreeqcPtr->input_error = 1;
+		this->PhreeqcPtr->error_msg(oss.str().c_str(), STOP); // throws
+	}
+}
+
+void IPhreeqc::do_run(const char* sz_routine, std::istream* pis, PFN_PRERUN_CALLBACK pfn_pre, PFN_POSTRUN_CALLBACK pfn_post, void *cookie)
+{
+	char token[MAX_LENGTH];
+
+/*
+ *   Maybe should be in read_input
+ */
+	this->PhreeqcPtr->first_read_input = TRUE;
+
+/*
+ *   call pre-run callback
+ */
+	if (pfn_pre)
+	{
+		pfn_pre(cookie);
+	}
+
+/*
+ *   set read callback
+ */
+#if (__GNUC__ && (__cplusplus >= 201103L)) || (_MSC_VER >= 1600)
+	std::unique_ptr<std::istringstream> auto_iss=NULL;
+#else
+	std::auto_ptr<std::istringstream> auto_iss(0);
+#endif
+	if (!pis)
+	{
+		auto_iss.reset(new std::istringstream(this->GetAccumulatedLines()));
+		this->PhreeqcPtr->phrq_io->push_istream(auto_iss.get(), false);
+	}
+	else
+	{
+		ASSERT(this->PhreeqcPtr->phrq_io->get_istream() == NULL);
+		this->PhreeqcPtr->phrq_io->push_istream(pis, false);
+	}
+
+
+/*
+ *   Read input data for simulation
+ */
+	for (this->PhreeqcPtr->simulation = 1; ; this->PhreeqcPtr->simulation++)
+	{
+
+#ifdef PHREEQ98
+   		AddSeries = !connect_simulations;
+#endif
+		::snprintf(token, sizeof(token), "Reading input data for simulation %d.", this->PhreeqcPtr->simulation);
+
+		// bool save_punch_in = this->PhreeqcPtr->SelectedOutput_map.size() > 0;
+
+		this->PhreeqcPtr->dup_print(token, TRUE);
+		if (this->PhreeqcPtr->read_input() == EOF)
+			break;
+		
+		if (this->PhreeqcPtr->simulation == 1)
+		{
+			// force headings for selected output (on every call to do_run)
+			// might want to split tidy_punch to avoid duplicate searches like master_bsearch
+			std::map< int, SelectedOutput >::iterator pit = this->PhreeqcPtr->SelectedOutput_map.begin();
+			for (; pit != this->PhreeqcPtr->SelectedOutput_map.end(); ++pit)
+			{
+				(*pit).second.Set_new_def(true);
+				this->PhreeqcPtr->keycount[Keywords::KEY_SELECTED_OUTPUT] = 1;
+			}
+		}
+
+		// bool bWarning = false;
+		std::map< int, SelectedOutput >::iterator mit = this->PhreeqcPtr->SelectedOutput_map.begin();
+		for (; mit != this->PhreeqcPtr->SelectedOutput_map.end(); ++mit)
+		{
+			if (this->SelectedOutputMap.find(mit->first) == this->SelectedOutputMap.end())
+			{
+				// int -> CSelectedOutput*
+				std::map< int, CSelectedOutput* >::value_type item((*mit).first, new CSelectedOutput());
+				this->SelectedOutputMap.insert(item);
+
+				// int -> std::string
+				this->SelectedOutputStringMap.insert(
+					std::map< int, std::string >::value_type((*mit).first, std::string()));
+			}
+			else
+			{
+				ASSERT(this->SelectedOutputMap.find((*mit).first) != this->SelectedOutputMap.end());
+				ASSERT(this->SelectedOutputStringMap.find((*mit).first) != this->SelectedOutputStringMap.end());
+			}
+		}
+		ASSERT(this->PhreeqcPtr->SelectedOutput_map.size() == this->SelectedOutputMap.size());
+		ASSERT(this->PhreeqcPtr->SelectedOutput_map.size() == this->SelectedOutputStringMap.size());
+		if (!this->PhreeqcPtr->title_x.empty())
+		{
+			::snprintf(token, sizeof(token), "TITLE");
+			this->PhreeqcPtr->dup_print(token, TRUE);
+			if (this->PhreeqcPtr->pr.headings == TRUE)
+			{
+				this->PhreeqcPtr->output_msg(this->PhreeqcPtr->title_x.c_str());
+				this->PhreeqcPtr->output_msg("\n\n");
+			}
+		}
+
+#ifdef SWIG_SHARED_OBJ
+		if (this->PhreeqcPtr->SelectedOutput_map.size() > 0)
+		{
+			//
+			// (punch.in == TRUE) when any "RUN" has contained
+			// a SELECTED_OUTPUT block since the last LoadDatabase call.
+			//
+			// Since LoadDatabase initializes punch.in to FALSE
+			// (via UnLoadDatabase...do_initialize)
+			// and punch.in is set to TRUE in read_selected_output
+			//
+			// This causes the SELECTED_OUTPUT to contain the same headings
+			// until another SELECTED_OUTPUT is defined which sets the variable
+			// punch.new_def to TRUE
+			//
+			// WHAT IF A USER_PUNCH IS DEFINED?? IS punch.new_def SET TO
+			// TRUE ???
+			//
+			//
+			std::map< int, SelectedOutput >::iterator ai = this->PhreeqcPtr->SelectedOutput_map.begin();
+			for (; ai != this->PhreeqcPtr->SelectedOutput_map.end(); ++ai)
+			{
+				if (!this->SelectedOutputFileOnMap[(*ai).first])
+				{
+					ASSERT((*ai).second.Get_punch_ostream() == 0);
+				}
+			}
+
+			if (this->PhreeqcPtr->pr.punch == FALSE)
+			{
+				// No selected_output for this simulation
+				// this happens when
+				//    PRINT;  -selected_output false
+				// is given as input
+				// Note: this also disables the CSelectedOutput object
+				ASSERT(TRUE);
+			}
+			else
+			{
+				std::map< int, SelectedOutput >::iterator it = this->PhreeqcPtr->SelectedOutput_map.begin();
+				for (; it != this->PhreeqcPtr->SelectedOutput_map.end(); ++it)
+				{
+					if (this->SelectedOutputFileOnMap[(*it).first] && !(*it).second.Get_punch_ostream())
+					{
+						//
+						// LoadDatabase
+						// do_run -- containing SELECTED_OUTPUT ****TODO**** check -file option
+						// another do_run without SELECTED_OUTPUT
+						//
+						ASSERT(!this->SelectedOutputFileNameMap[(*it).first].empty());
+						std::string filename = this->SelectedOutputFileNameMap[(*it).first];
+						if (!punch_open(filename.c_str(), std::ios_base::out, (*it).first))
+						{
+							std::ostringstream oss;
+							oss << sz_routine << ": Unable to open:" << "\"" << filename << "\".\n";
+							this->PhreeqcPtr->warning_msg(oss.str().c_str());
+						}
+						else
+						{
+							ASSERT(this->Get_punch_ostream() != NULL);
+							ASSERT((*it).second.Get_punch_ostream() == NULL);
+
+							int n_user = (*it).first;
+							this->PhreeqcPtr->SelectedOutput_map[n_user].Set_punch_ostream(this->Get_punch_ostream());
+							this->Set_punch_ostream(NULL);
+							
+							// output selected_output headings
+							(*it).second.Set_new_def(TRUE);
+							this->PhreeqcPtr->tidy_punch();
+						}
+					}
+				}
+			}
+		}
+		else
+		{
+			ASSERT(TRUE);
+		}
+		
+
+		std::map< int, SelectedOutput >::iterator it = this->PhreeqcPtr->SelectedOutput_map.begin();
+		for (; it != this->PhreeqcPtr->SelectedOutput_map.end(); ++it)
+		{
+			if (this->SelectedOutputFileOnMap[(*it).first])
+			{
+				ASSERT((*it).second.Get_punch_ostream());
+			}
+			else
+			{
+				ASSERT(!(*it).second.Get_punch_ostream());
+			}
+		}
+
+		// Consider this addition
+		{
+			this->PhreeqcPtr->pr.all = (this->OutputFileOn || this->OutputStringOn) ? TRUE : FALSE;
+			//this->PhreeqcPtr->pr.punch = (this->SelectedOutputFileOn || this->SelectedOutputStringOn) ? TRUE : FALSE;
+		}
+		/* the converse is not necessarily true */
+
+		this->PhreeqcPtr->n_user_punch_index = -1;
+#endif // SWIG_SHARED_OBJ
+		{
+			this->PhreeqcPtr->pr.all = (this->OutputFileOn || this->OutputStringOn) ? TRUE : FALSE;
+		}
+
+		this->PhreeqcPtr->tidy_model();
+#ifdef PHREEQ98
+                if (!phreeq98_debug)
+				{
+#endif
+
+/*
+ *   Calculate distribution of species for initial solutions
+ */
+		if (this->PhreeqcPtr->new_solution)
+			this->PhreeqcPtr->initial_solutions(TRUE);
+/*
+ *   Calculate distribution for exchangers
+ */
+		if (this->PhreeqcPtr->new_exchange)
+			this->PhreeqcPtr->initial_exchangers(TRUE);
+/*
+ *   Calculate distribution for surfaces
+ */
+		if (this->PhreeqcPtr->new_surface)
+			this->PhreeqcPtr->initial_surfaces(TRUE);
+/*
+ *   Calculate initial gas composition
+ */
+		if (this->PhreeqcPtr->new_gas_phase)
+			this->PhreeqcPtr->initial_gas_phases(TRUE);
+/*
+ *   Calculate reactions
+ */
+		this->PhreeqcPtr->reactions();
+/*
+ *   Calculate inverse models
+ */
+		this->PhreeqcPtr->inverse_models();
+/*
+ *   Calculate advection
+ */
+		if (this->PhreeqcPtr->use.Get_advect_in())
+		{
+			this->PhreeqcPtr->dup_print("Beginning of advection calculations.", TRUE);
+			this->PhreeqcPtr->advection();
+		}
+/*
+ *   Calculate transport
+ */
+		if (this->PhreeqcPtr->use.Get_trans_in())
+		{
+			this->PhreeqcPtr->dup_print("Beginning of transport calculations.", TRUE);
+			this->PhreeqcPtr->transport();
+		}
+/*
+ *   run
+ */
+		this->PhreeqcPtr->run_as_cells();
+/*
+ *   Calculate mixes
+ */
+		this->PhreeqcPtr->do_mixes();
+/*
+ *   Copy
+ */
+		if (this->PhreeqcPtr->new_copy) this->PhreeqcPtr->copy_entities();
+/*
+ *   dump
+ */
+		dumper dump_info_save(this->PhreeqcPtr->dump_info);
+		if (this->DumpOn)
+		{
+			this->PhreeqcPtr->dump_entities();
+			this->DumpFileName = this->PhreeqcPtr->dump_info.Get_file_name();
+		}
+		if (this->DumpStringOn)
+		{
+			this->PhreeqcPtr->dump_info = dump_info_save;
+			if (this->PhreeqcPtr->dump_info.Get_bool_any())
+			{
+				std::ostringstream oss;
+				this->PhreeqcPtr->dump_ostream(oss);
+				if (this->PhreeqcPtr->dump_info.Get_append())
+				{
+					this->DumpString += oss.str();
+				}
+				else
+				{
+					this->DumpString = oss.str();
+				}
+
+				/* Fill dump lines */
+				this->DumpLines.clear();
+				std::istringstream iss(this->DumpString);
+				std::string line;
+				while (std::getline(iss, line))
+				{
+					this->DumpLines.push_back(line);
+				}
+			}
+		}
+/*
+ *   delete
+ */
+		this->PhreeqcPtr->delete_entities();
+
+/*
+ *   End of simulation
+ */
+		this->PhreeqcPtr->dup_print( "End of simulation.", TRUE);
+#ifdef PHREEQ98
+                } /* if (!phreeq98_debug) */
+#endif
+	}
+
+/*
+ *   Display successful status
+ */
+	this->PhreeqcPtr->do_status();
+
+/*
+ *   call post-run callback
+ */
+	if (pfn_post)
+	{
+		pfn_post(cookie);
+	}
+
+	this->UpdateComponents = true;
+	this->update_errors();
+
+	// update lines
+	//
+
+	if (this->LogStringOn)
+	{
+		// output lines
+		std::istringstream iss(this->LogString);
+		std::string line;
+		while (std::getline(iss, line))
+		{
+			this->LogLines.push_back(line);
+		}
+	}
+
+	if (this->OutputStringOn)
+	{
+		// output lines
+		std::istringstream iss(this->OutputString);
+		std::string line;
+		while (std::getline(iss, line))
+		{
+			this->OutputLines.push_back(line);
+		}
+	}
+
+	for (int i = 0; i < this->GetSelectedOutputCount(); ++i)
+	{
+		int n = this->GetNthSelectedOutputUserNumber(i);
+		if (this->get_sel_out_string_on(n))
+		{
+			std::map< int, std::string >::iterator mit = this->SelectedOutputStringMap.find(n);
+			ASSERT(mit != this->SelectedOutputStringMap.end());
+			if (mit != this->SelectedOutputStringMap.end())
+			{
+				// output lines
+				std::istringstream iss((*mit).second);
+				std::string line;
+				while (std::getline(iss, line))
+				{
+					this->SelectedOutputLinesMap[(*mit).first].push_back(line);
+				}
+			}
+		}
+	}
+}
+
+void IPhreeqc::update_errors(void)
+{
+	this->ErrorLines.clear();
+	this->ErrorString = ((CErrorReporter<std::ostringstream>*)this->ErrorReporter)->GetOS()->str();
+	if (this->ErrorString.size())
+	{
+		std::istringstream iss(this->ErrorString);
+		std::string line;
+		while (std::getline(iss, line))
+		{
+			this->ErrorLines.push_back(line);
+		}
+	}
+
+	this->WarningLines.clear();
+	this->WarningString = ((CErrorReporter<std::ostringstream>*)this->WarningReporter)->GetOS()->str();
+	if (this->WarningString.size())
+	{
+		std::istringstream iss(this->WarningString);
+		std::string line;
+		while (std::getline(iss, line))
+		{
+			this->WarningLines.push_back(line);
+		}
+	}
+}
+
+void IPhreeqc::log_msg(const char * str)
+{
+	if (this->LogStringOn && this->log_on)
+	{
+		this->LogString += str;
+	}
+	ASSERT(!(this->LogFileOn != (this->log_ostream != 0)));
+	this->PHRQ_io::log_msg(str);
+}
+
+void IPhreeqc::error_msg(const char *str, bool stop)
+{
+	ASSERT(this->error_ostream == &std::cerr || (!(this->ErrorFileOn != (this->error_ostream != 0))));
+
+	if (this->error_ostream != NULL && this->error_on)
+	{
+		(*this->error_ostream) << str;
+	}
+	bool save_error_on = this->error_on;
+	this->error_on = false;
+	this->PHRQ_io::error_msg(str);
+	this->error_on = save_error_on;
+
+	if (this->ErrorStringOn && this->error_on)
+	{
+		this->AddError(str);
+	}
+	if (stop)
+	{
+		if (this->error_ostream && this->error_on)
+		{
+			(*this->error_ostream) << "Stopping.\n";
+			this->error_ostream->flush();
+		}
+		throw IPhreeqcStop();
+	}
+}
+
+void IPhreeqc::warning_msg(const char *str)
+{
+	ASSERT(this->error_ostream == &std::cerr || (!(this->ErrorFileOn != (this->error_ostream != 0))));
+
+	if (this->error_ostream != NULL && this->error_on)
+	{
+		(*this->error_ostream) << str << "\n";
+	}
+	bool save_error_on = this->error_on;
+	this->error_on = false;
+	this->PHRQ_io::warning_msg(str);
+	this->error_on = save_error_on;
+
+	std::ostringstream oss;
+	oss << str << std::endl;
+	if (this->WarningStringOn)
+	{
+		this->AddWarning(oss.str().c_str());
+	}
+}
+
+void IPhreeqc::output_msg(const char * str)
+{
+	if (this->OutputStringOn && this->output_on)
+	{
+		this->OutputString += str;
+	}
+	ASSERT(!(this->OutputFileOn != (this->output_ostream != 0)));
+	this->PHRQ_io::output_msg(str);
+}
+
+void IPhreeqc::screen_msg(const char *err_str)
+{
+	// no-op
+}
+
+void IPhreeqc::punch_msg(const char *str)
+{
+	if (this->get_sel_out_string_on(this->PhreeqcPtr->current_selected_output->Get_n_user()) && this->punch_on)
+	{
+		ASSERT(this->PhreeqcPtr->current_selected_output);
+		if (this->PhreeqcPtr->current_selected_output)
+		{
+			this->SelectedOutputStringMap[this->PhreeqcPtr->current_selected_output->Get_n_user()] += str;
+		}
+	}
+	ASSERT(!(this->SelectedOutputFileOnMap[this->PhreeqcPtr->current_selected_output->Get_n_user()] != (this->PhreeqcPtr->current_selected_output->Get_punch_ostream() != 0)));
+	this->PHRQ_io::punch_msg(str);
+}
+
+void IPhreeqc::open_output_files(const char* sz_routine)
+{
+	if (this->OutputFileOn)
+	{
+		if (this->output_ostream != NULL)
+		{
+			safe_close(&this->output_ostream);
+		}
+		if (!this->output_ostream)
+		{
+			if ( (this->output_ostream = new std::ofstream(this->OutputFileName.c_str())) == NULL)
+			{
+				std::ostringstream oss;
+				oss << sz_routine << ": Unable to open:" << "\"" << this->OutputFileName << "\".\n";
+				this->warning_msg(oss.str().c_str());
+			}
+		}
+	}
+	if (this->ErrorFileOn)
+	{
+		if (this->error_ostream != NULL)
+		{
+			safe_close(&this->error_ostream);
+		}
+		if (!this->error_ostream)
+		{
+			if ( (this->error_ostream = new std::ofstream(this->ErrorFileName.c_str())) == NULL)
+			{
+				std::ostringstream oss;
+				oss << sz_routine << ": Unable to open:" << "\"" << this->ErrorFileName << "\".\n";
+				this->warning_msg(oss.str().c_str());
+			}
+		}
+	}
+	if (this->LogFileOn)
+	{
+		if (this->log_ostream != NULL)
+		{
+			safe_close(&this->log_ostream);
+		}
+		if (!this->log_ostream)
+		{
+			if ( (this->log_ostream = new std::ofstream(this->LogFileName.c_str())) == NULL)
+			{
+				std::ostringstream oss;
+				oss << sz_routine << ": Unable to open:" << "\"" << this->LogFileName << "\".\n";
+				this->warning_msg(oss.str().c_str());
+			}
+		}
+	}
+}
+
+int IPhreeqc::close_input_files(void)
+{
+	int i = 0;
+	if (this->database_file)
+	{
+		i |= fclose(this->database_file);
+	}
+	if (this->input_file)
+	{
+		i |= fclose(this->input_file);
+	}
+	this->input_file = this->database_file = NULL;
+	return (i);
+}
+
+int IPhreeqc::close_output_files(void)
+{
+	int ret = 0;
+
+	safe_close(&this->output_ostream);
+	safe_close(&this->log_ostream);
+	safe_close(&this->dump_ostream);
+	safe_close(&this->error_ostream);
+
+	std::map< int, SelectedOutput >::iterator it = this->PhreeqcPtr->SelectedOutput_map.begin();
+	for (; it != this->PhreeqcPtr->SelectedOutput_map.end(); ++it)
+	{
+		std::ostream *ptr = (*it).second.Get_punch_ostream();
+		safe_close(&ptr);
+		(*it).second.Set_punch_ostream(NULL);
+	}
+
+	this->punch_ostream = 0;
+
+	return ret;
+}
+
+void IPhreeqc::fpunchf(const char *name, const char *format, double d)
+{
+	try
+	{
+		this->PHRQ_io::fpunchf(name, format, d);
+		if (this->get_sel_out_string_on(this->PhreeqcPtr->current_selected_output->Get_n_user()) && this->punch_on)
+		{
+			ASSERT(this->SelectedOutputStringMap.find(this->PhreeqcPtr->current_selected_output->Get_n_user()) != this->SelectedOutputStringMap.end());
+			PHRQ_io::fpunchf_helper(&(this->SelectedOutputStringMap[this->PhreeqcPtr->current_selected_output->Get_n_user()]), format, d);
+		}
+		ASSERT(this->SelectedOutputMap.find(this->PhreeqcPtr->current_selected_output->Get_n_user()) != this->SelectedOutputMap.end());
+		this->SelectedOutputMap[this->PhreeqcPtr->current_selected_output->Get_n_user()]->PushBackDouble(name, d);
+	}
+	catch (const std::bad_alloc&)
+	{
+		this->PhreeqcPtr->malloc_error();
+	}
+}
+
+void IPhreeqc::fpunchf(const char *name, const char *format, char *s)
+{
+	try
+	{
+		this->PHRQ_io::fpunchf(name, format, s);
+		if (this->get_sel_out_string_on(this->PhreeqcPtr->current_selected_output->Get_n_user()) && this->punch_on)
+		{
+			ASSERT(this->SelectedOutputStringMap.find(this->PhreeqcPtr->current_selected_output->Get_n_user()) != this->SelectedOutputStringMap.end());
+			PHRQ_io::fpunchf_helper(&(this->SelectedOutputStringMap[this->PhreeqcPtr->current_selected_output->Get_n_user()]), format, s);
+		}
+		ASSERT(this->SelectedOutputMap.find(this->PhreeqcPtr->current_selected_output->Get_n_user()) != this->SelectedOutputMap.end());
+		this->SelectedOutputMap[this->PhreeqcPtr->current_selected_output->Get_n_user()]->PushBackString(name, s);
+	}
+	catch (const std::bad_alloc&)
+	{
+		this->PhreeqcPtr->malloc_error();
+	}
+}
+
+void IPhreeqc::fpunchf(const char *name, const char *format, int i)
+{
+	try
+	{
+		this->PHRQ_io::fpunchf(name, format, i);
+		if (this->get_sel_out_string_on(this->PhreeqcPtr->current_selected_output->Get_n_user()) && this->punch_on)
+		{
+			ASSERT(this->SelectedOutputStringMap.find(this->PhreeqcPtr->current_selected_output->Get_n_user()) != this->SelectedOutputStringMap.end());
+			PHRQ_io::fpunchf_helper(&(this->SelectedOutputStringMap[this->PhreeqcPtr->current_selected_output->Get_n_user()]), format, i);
+		}
+		ASSERT(this->SelectedOutputMap.find(this->PhreeqcPtr->current_selected_output->Get_n_user()) != this->SelectedOutputMap.end());
+		this->SelectedOutputMap[this->PhreeqcPtr->current_selected_output->Get_n_user()]->PushBackLong(name, (long)i);
+	}
+	catch (const std::bad_alloc&)
+	{
+		this->PhreeqcPtr->malloc_error();
+	}
+}
+
+void IPhreeqc::fpunchf_end_row(const char *format)
+{
+	this->EndRow();
+}
+
+bool IPhreeqc::get_sel_out_file_on(int n)const
+{
+	// if not found in list SelectedOutputFileOn is false
+	std::map< int, bool >::const_iterator ci = this->SelectedOutputFileOnMap.find(n);
+	if (ci != this->SelectedOutputFileOnMap.end())
+	{
+		return (*ci).second;
+	}
+	return false;
+}
+
+bool IPhreeqc::get_sel_out_string_on(int n)const
+{
+	// if not found in list SelectedOutputStringOn is false
+	std::map< int, bool >::const_iterator ci = this->SelectedOutputStringOn.find(this->CurrentSelectedOutputUserNumber);
+	if (ci != this->SelectedOutputStringOn.end())
+	{
+		return (*ci).second;
+	}
+	return false;
+}
+
+bool IPhreeqc::punch_open(const char *file_name, std::ios_base::openmode mode, int n_user)
+{
+	if (this->PhreeqcPtr->SelectedOutput_map[n_user].Get_have_punch_name() &&
+		!this->PhreeqcPtr->SelectedOutput_map[n_user].Get_file_name().empty())
+	{
+		this->SelectedOutputFileNameMap[n_user] = this->PhreeqcPtr->SelectedOutput_map[n_user].Get_file_name();
+	}
+	else if (this->SelectedOutputFileNameMap[n_user].empty())
+	{
+		this->SelectedOutputFileNameMap[n_user] = this->sel_file_name(n_user);
+	}
+	if (this->get_sel_out_file_on(n_user))
+	{
+		ASSERT(!this->SelectedOutputFileNameMap[n_user].empty());
+		this->PhreeqcPtr->SelectedOutput_map[n_user].Set_file_name(this->SelectedOutputFileNameMap[n_user]);
+		return this->ofstream_open(&punch_ostream, this->SelectedOutputFileNameMap[n_user].c_str(), mode);
+	}
+	return true;
+}
+
+bool IPhreeqc::output_open(const char *file_name, std::ios_base::openmode mode)
+{
+	if (this->OutputFileOn)
+	{
+		return this->PHRQ_io::output_open(file_name, mode);
+	}
+	return true;
+}
+
+std::string IPhreeqc::sel_file_name(int n_user)
+{
+	std::ostringstream oss;
+	oss << "selected_" << n_user << "." << this->Index << ".out";
+	return oss.str();
+}
+
+std::string IPhreeqc::create_file_name(const char *prefix, const char *suffix)
+{
+	std::ostringstream oss;
+	oss << prefix << "." << this->Index << "." << suffix;
+	return oss.str();
+}