iphreeqc/KineticsComp.cxx

// 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
#if !defined(PHREEQC_CLASS)
#define EXTERNAL extern
#include "global.h"
#else
#include "Phreeqc.h"
#endif
#include "KineticsComp.h"
#include "Dictionary.h"
#include "phqalloc.h"
#include "phrqproto.h"


//////////////////////////////////////////////////////////////////////
// Construction/Destruction
//////////////////////////////////////////////////////////////////////

cxxKineticsComp::cxxKineticsComp()
	//
	// default constructor for cxxKineticsComp 
	//
{
	tol = 1e-8;
	m = 0.0;
	m0 = 0.0;
	moles = 0.0;
	namecoef.type = cxxNameDouble::ND_NAME_COEF;
}

cxxKineticsComp::cxxKineticsComp(struct kinetics_comp *kinetics_comp_ptr)
		//
		// constructor for cxxKineticsComp from struct kinetics_comp
		//
	:
namecoef(kinetics_comp_ptr->list, kinetics_comp_ptr->count_list)
{
	this->set_rate_name(kinetics_comp_ptr->rate_name);
	tol = kinetics_comp_ptr->tol;
	m = kinetics_comp_ptr->m;
	m0 = kinetics_comp_ptr->m0;
	moles = kinetics_comp_ptr->moles;
	for (int i = 0; i < kinetics_comp_ptr->count_d_params; i++)
	{
		this->d_params.push_back(kinetics_comp_ptr->d_params[i]);
	}
}

cxxKineticsComp::~cxxKineticsComp()
{
}

struct kinetics_comp *
	cxxKineticsComp::cxxKineticsComp2kinetics_comp(PHREEQC_PTR_ARG_COMMA std::list < cxxKineticsComp >
											   &el)
		//
		// Builds kinetics_comp structure from of cxxKineticsComp 
		//
{
	struct kinetics_comp *kinetics_comp_ptr =
		(struct kinetics_comp *)
		P_INSTANCE_POINTER PHRQ_malloc((size_t) (el.size() * sizeof(struct kinetics_comp)));
	if (kinetics_comp_ptr == NULL)
		P_INSTANCE_POINTER malloc_error();

	int i = 0;
	for (std::list < cxxKineticsComp >::iterator it = el.begin();
		 it != el.end(); ++it)
	{
		if ((*it).rate_name.size() == 0)
			kinetics_comp_ptr[i].rate_name = NULL;
		else
			kinetics_comp_ptr[i].rate_name = P_INSTANCE_POINTER string_hsave((*it).rate_name.c_str());
		kinetics_comp_ptr[i].list = (*it).namecoef.name_coef(P_INSTANCE);
		kinetics_comp_ptr[i].count_list = (int) (*it).namecoef.size();
		kinetics_comp_ptr[i].tol = (*it).tol;
		kinetics_comp_ptr[i].m = (*it).m;
		kinetics_comp_ptr[i].initial_moles = 0.;
		kinetics_comp_ptr[i].m0 = (*it).m0;
		kinetics_comp_ptr[i].moles = (*it).moles;
		kinetics_comp_ptr[i].count_c_params = 0;
		kinetics_comp_ptr[i].c_params = NULL;
/*
                kinetics_comp_ptr[i].count_d_params         =  0;
                kinetics_comp_ptr[i].d_params               =  NULL;
*/

		kinetics_comp_ptr[i].count_d_params = (int) (*it).d_params.size();
		kinetics_comp_ptr[i].d_params = NULL;
		if ((*it).d_params.size() > 0)
		{
			kinetics_comp_ptr[i].d_params =	(double *)
				P_INSTANCE_POINTER PHRQ_malloc((size_t) ((*it).d_params.size() * sizeof(double)));
			if (kinetics_comp_ptr[i].d_params == NULL)
				P_INSTANCE_POINTER malloc_error();
			std::copy((*it).d_params.begin(), (*it).d_params.end(),
					  kinetics_comp_ptr[i].d_params);
		}
		i++;
	}
	return (kinetics_comp_ptr);
}

#ifdef SKIP
void
cxxKineticsComp::dump_xml(std::ostream & s_oss, unsigned int indent) const const
{
	//const char    ERR_MESSAGE[] = "Packing kinetics_comp message: %s, element not found\n";
	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 << "\"" << std::endl;
	s_oss << indent0 << "moles=\"" << this->moles << "\"" << std::endl;
	s_oss << indent0 << "la=\"" << this->la << "\"" << std::endl;
	s_oss << indent0 << "charge_balance=\"" << this->
		charge_balance << "\"" << std::endl;
	if (this->phase_name != NULL)
	{
		s_oss << indent0 << "phase_name=\"" << this->
			phase_name << "\"" << std::endl;
	}
	if (this->rate_name != NULL)
	{
		s_oss << indent0 << "rate_name=\"" << this->
			rate_name << "\"" << std::endl;
	}
	s_oss << indent0 << "phase_proportion=\"" << this->
		phase_proportion << "\"" << std::endl;

	// totals
	s_oss << indent0;
	s_oss << "<totals " << std::endl;
	this->totals.dump_xml(s_oss, indent + 1);

	// formula_totals
	s_oss << indent0;
	s_oss << "<formula_totals " << std::endl;
	this->formula_totals.dump_xml(s_oss, indent + 1);
}
#endif
void
cxxKineticsComp::dump_raw(std::ostream & s_oss, unsigned int indent) const
{
	//const char    ERR_MESSAGE[] = "Packing kinetics_comp message: %s, element not found\n";
	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 << "-rate_name             " << this->
		rate_name << std::endl;
	s_oss << indent1 << "-tol                   " << this->tol << std::endl;
	s_oss << indent1 << "-m                     " << this->m << std::endl;
	s_oss << indent1 << "-m0                    " << this->m0 << std::endl;
	s_oss << indent1 << "-moles                 " << this->moles << std::endl;

	// namecoef
	s_oss << indent1;
	s_oss << "-namecoef" << std::endl;
	this->namecoef.dump_raw(s_oss, indent + 2);

	// d_params
	s_oss << indent1;
	s_oss << "-d_params" << std::endl;
	{
		int i = 0;
		s_oss << indent2;
		for (std::vector < double >::const_iterator it = d_params.begin();
			 it != d_params.end(); it++)
		{
			if (i++ == 5)
			{
				s_oss << std::endl;
				s_oss << indent2;
				i = 0;
			}
			s_oss << *it << " ";
		}
		s_oss << std::endl;
	}
}

void
cxxKineticsComp::read_raw(PHREEQC_PTR_ARG_COMMA CParser & parser, bool check)
{
	std::string str;
	double d;

	static std::vector < std::string > vopts;
	if (vopts.empty())
	{
		vopts.reserve(10);
		vopts.push_back("rate_name");	// 0
		vopts.push_back("tol");	// 1
		vopts.push_back("m");	// 2
		vopts.push_back("m0");	// 3
		vopts.push_back("moles");	// 4
		vopts.push_back("namecoef");	// 5
		vopts.push_back("d_params");	// 6
	}

	std::istream::pos_type ptr;
	std::istream::pos_type next_char;
	std::string token;
	int opt_save;

	std::vector < double > temp_d_params;
	opt_save = CParser::OPT_ERROR;
	bool rate_name_defined(false);
	bool tol_defined(false);
	bool m_defined(false);
	bool m0_defined(false);
	bool moles_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
			//parser.error_msg("Unknown input in KINETICS_COMP read.", CParser::OT_CONTINUE);
			//parser.error_msg(parser.line().c_str(), CParser::OT_CONTINUE);
			break;

		case 0:				// rate_name
			if (!(parser.get_iss() >> str))
			{
				this->rate_name.clear();
				parser.incr_input_error();
				parser.error_msg("Expected string value for rate_name.",
								 CParser::OT_CONTINUE);
			}
			else
			{
				this->rate_name = str;
			}
			rate_name_defined = true;
			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.",
								 CParser::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.",
								 CParser::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.",
								 CParser::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.",
								 CParser::OT_CONTINUE);
			}
			moles_defined = true;
			break;


		case 5:				// namecoef
			if (this->namecoef.read_raw(P_INSTANCE_COMMA parser, next_char) !=
				CParser::PARSER_OK)
			{
				parser.incr_input_error();
				parser.
					error_msg
					("Expected element name and molality for namecoef.",
					 CParser::OT_CONTINUE);
			}
			opt_save = 5;
			break;

		case 6:				// d_params
			while (parser.copy_token(token, next_char) == CParser::TT_DIGIT)
			{
				sscanf(token.c_str(), "%lf", &d);
				temp_d_params.push_back(d);
				d_params_defined = true;
			}
			opt_save = 6;
		}
		if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
			break;
	}

	if (d_params_defined)
	{
		this->d_params = temp_d_params;
	}
	// members that must be defined
	if (rate_name_defined == false)
	{
		parser.incr_input_error();
		parser.error_msg("Rate_name not defined for KineticsComp input.",
						 CParser::OT_CONTINUE);
	}
	if (tol_defined == false)
	{
		parser.incr_input_error();
		parser.error_msg("Tol not defined for KineticsComp input.",
						 CParser::OT_CONTINUE);
	}
	if (m_defined == false)
	{
		parser.incr_input_error();
		parser.error_msg("M not defined for KineticsComp input.",
						 CParser::OT_CONTINUE);
	}
	if (m0_defined == false)
	{
		parser.incr_input_error();
		parser.error_msg("M0 not defined for KineticsComp input.",
						 CParser::OT_CONTINUE);
	}
	if (moles_defined == false)
	{
		parser.incr_input_error();
		parser.error_msg("Moles not defined for KineticsComp input.",
						 CParser::OT_CONTINUE);
	}
}

#ifdef USE_MPI
void
cxxKineticsComp::mpi_pack(std::vector < int >&ints,
						  std::vector < double >&doubles)
{
	extern cxxDictionary dictionary;
	ints.push_back(dictionary.string2int(this->rate_name));
	this->namecoef.mpi_pack(ints, doubles);
	doubles.push_back(this->tol);
	doubles.push_back(this->m);
	doubles.push_back(this->m0);
	doubles.push_back(this->moles);
	ints.push_back((int) this->d_params.size());
	for (std::vector < double >::iterator it = this->d_params.begin();
		 it != this->d_params.end(); it++)
	{
		doubles.push_back(*it);
	}
}
void
cxxKineticsComp::mpi_unpack(int *ints, int *ii, double *doubles, int *dd)
{
	extern cxxDictionary dictionary;
	int i = *ii;
	int d = *dd;
	this->rate_name = dictionary.int2stdstring(ints[i++]);
	this->namecoef.mpi_unpack(ints, &i, doubles, &d);
	this->tol = doubles[d++];
	this->m = doubles[d++];
	this->m0 = doubles[d++];
	this->moles = doubles[d++];
	int n = ints[i++];
	this->d_params.clear();
	for (int j = 0; j < n; j++)
	{
		this->d_params.push_back(doubles[d++]);
	}
	*ii = i;
	*dd = d;
}
#endif
void
cxxKineticsComp::add(const cxxKineticsComp & addee, double 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;
	}
	//char * rate_name;
	assert(this->rate_name == addee.rate_name);
	//cxxNameDouble namecoef;
	//double tol;
	//double m;
	this->m += addee.m * extensive;
	//double m0;
	this->m0 += addee.m0 * extensive;
	//double moles;  
	this->moles += addee.moles * extensive;
	//std::vector<double> d_params;
}

void
cxxKineticsComp::multiply(double extensive)
{
	//char * rate_name;
	//cxxNameDouble namecoef;
	//double tol;
	//double m;
	this->m *= extensive;
	//double m0;
	this->m0 *= extensive;
	//double moles;  
	this->moles *= extensive;
	//std::vector<double> d_params;
}