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iphreeqc/cxxKinetics.cxx
David L Parkhurst 694c07488e Bugs with kinetics in PHAST. 
The formula was not correct when converted to a phreeqcpp class, only the last instance of an element was kept and the rest were lost. Modified NameDouble to accumulate the sum of coefficients for each element when converting from a PHREEQC structure.

The order of the kinetics components was not maintained when converted to a phreeqcpp class. Components were in alphabetical order. This posed a problem with get and put statements because the gets could end up before the puts. Changed from map of components to list of components, which should maintain the order correctly.

Problems with modify solution and redox elements. Laurin pointed out that adding N may leave all the N(x) in place, which increases the total N. Revised read_solution to merge the valence states. If N defined, then all N(x) are removed. If N() defined, then N is removed. Still need to test.


git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3927 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2010-01-14 16:26:14 +00:00

740 lines
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// Kinetics.cxx: implementation of the cxxKinetics 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 "cxxKinetics.h"
#include "cxxMix.h"
#include "phqalloc.h"
#include "phrqproto.h"
//////////////////////////////////////////////////////////////////////
// Construction/Destruction
//////////////////////////////////////////////////////////////////////
cxxKinetics::cxxKinetics()
//
// default constructor for cxxKinetics
//
: cxxNumKeyword()
{
step_divide = 1.0;
rk = 3;
bad_step_max = 500;
use_cvode = false;
cvode_steps = 100;
cvode_order = 5;
totals.type = cxxNameDouble::ND_ELT_MOLES;
}
cxxKinetics::cxxKinetics(struct kinetics *kinetics_ptr)
//
// constructor for cxxKinetics from struct kinetics
//
:
cxxNumKeyword(),
totals(kinetics_ptr->totals)
{
int i;
this->set_description(kinetics_ptr->description);
n_user = kinetics_ptr->n_user;
n_user_end = kinetics_ptr->n_user_end;
step_divide = kinetics_ptr->step_divide;
rk = kinetics_ptr->rk;
bad_step_max = kinetics_ptr->bad_step_max;
use_cvode = (kinetics_ptr->use_cvode == TRUE);
cvode_steps = kinetics_ptr->cvode_steps;
cvode_order = kinetics_ptr->cvode_order;
// kinetics components
for (i = 0; i < kinetics_ptr->count_comps; i++)
{
cxxKineticsComp ec(&(kinetics_ptr->comps[i]));
std::string str(ec.get_rate_name());
//this->kineticsComps[str] = ec;
this->kineticsComps.push_back(ec);
}
// steps
for (i = 0; i < kinetics_ptr->count_steps; i++)
{
this->steps.push_back(kinetics_ptr->steps[i]);
}
}
cxxKinetics::cxxKinetics(const std::map < int, cxxKinetics > &entities,
cxxMix & mix, int n_user):
cxxNumKeyword()
{
this->n_user = this->n_user_end = n_user;
step_divide = 1.0;
rk = 3;
bad_step_max = 500;
use_cvode = false;
cvode_steps = 100;
cvode_order = 5;
totals.type = cxxNameDouble::ND_ELT_MOLES;
//
// Mix
//
std::map < int, double >*mixcomps = mix.comps();
std::map < int, double >::const_iterator it;
for (it = mixcomps->begin(); it != mixcomps->end(); it++)
{
if (entities.find(it->first) != entities.end())
{
const cxxKinetics *entity_ptr =
&(entities.find(it->first)->second);
this->add(*entity_ptr, it->second);
}
}
}
cxxKinetics::~cxxKinetics()
{
}
struct kinetics *
cxxKinetics::cxxKinetics2kinetics(PHREEQC_PTR_ARG)
//
// Builds a kinetics structure from instance of cxxKinetics
//
{
struct kinetics *kinetics_ptr = P_INSTANCE_POINTER kinetics_alloc();
kinetics_ptr->description = P_INSTANCE_POINTER string_duplicate (this->get_description().c_str());
kinetics_ptr->n_user = this->n_user;
kinetics_ptr->n_user_end = this->n_user_end;
kinetics_ptr->step_divide = this->step_divide;
kinetics_ptr->rk = this->rk;
kinetics_ptr->bad_step_max = this->bad_step_max;
kinetics_ptr->use_cvode = (int) this->use_cvode;
kinetics_ptr->cvode_steps = this->cvode_steps;
kinetics_ptr->cvode_order = this->cvode_order;
// totals
kinetics_ptr->totals = this->totals.elt_list(P_INSTANCE);
// comps
kinetics_ptr->count_comps = (int) this->kineticsComps.size();
kinetics_ptr->comps =
(struct kinetics_comp *) P_INSTANCE_POINTER free_check_null(kinetics_ptr->comps);
kinetics_ptr->comps =
cxxKineticsComp::cxxKineticsComp2kinetics_comp(P_INSTANCE_COMMA this->kineticsComps);
// steps
kinetics_ptr->count_steps = (int) this->steps.size();
kinetics_ptr->steps = (double *) P_INSTANCE_POINTER free_check_null(kinetics_ptr->steps);
if (this->steps.size() > 0)
{
kinetics_ptr->steps =
(double *)
P_INSTANCE_POINTER PHRQ_malloc((size_t) (this->steps.size() * sizeof(double)));
if (kinetics_ptr->steps == NULL)
P_INSTANCE_POINTER malloc_error();
std::copy(this->steps.begin(), this->steps.end(),
kinetics_ptr->steps);
/*
int i = 0;
for (std::vector<double>::iterator it = this->steps.begin(); it != this->steps.end(); it++) {
kinetics_ptr->steps[i] = *it;
}
*/
}
return (kinetics_ptr);
}
#ifdef SKIP
void
cxxKinetics::dump_xml(std::ostream & s_oss, unsigned int indent) const const
{
//const char ERR_MESSAGE[] = "Packing kinetics 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 element and attributes
s_oss << indent0;
s_oss << "<kinetics " << std::endl;
s_oss << indent1;
s_oss << "pitzer_kinetics_gammas=\"" << this->
pitzer_kinetics_gammas << "\"" << std::endl;
// components
s_oss << indent1;
s_oss << "<component " << std::endl;
for (std::list < cxxKineticsComp >::const_iterator it =
kineticsComps.begin(); it != kineticsComps.end(); ++it)
{
it->dump_xml(s_oss, indent + 2);
}
return;
}
#endif
void
cxxKinetics::dump_raw(std::ostream & s_oss, unsigned int indent) const
{
//const char ERR_MESSAGE[] = "Packing kinetics 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 element and attributes
s_oss << indent0;
s_oss << "KINETICS_RAW " << this->n_user << " " << this->
description << std::endl;
s_oss << indent1;
s_oss << "-step_divide " << this->step_divide << std::endl;
s_oss << indent1;
s_oss << "-rk " << this->rk << std::endl;
s_oss << indent1;
s_oss << "-bad_step_max " << this->bad_step_max << std::endl;
s_oss << indent1;
s_oss << "-use_cvode " << this->use_cvode << std::endl;
s_oss << indent1;
s_oss << "-cvode_steps " << this->cvode_steps << std::endl;
s_oss << indent1;
s_oss << "-cvode_order " << this->cvode_order << std::endl;
// kineticsComps structures
for (std::list < cxxKineticsComp >::const_iterator it =
kineticsComps.begin(); it != kineticsComps.end(); ++it)
{
s_oss << indent1;
s_oss << "-component" << std::endl;
(*it).dump_raw(s_oss, indent + 2);
}
// totals
s_oss << indent1;
s_oss << "-totals " << std::endl;
this->totals.dump_raw(s_oss, indent + 2);
// steps
s_oss << indent1;
s_oss << "-steps " << std::endl;
{
int i = 0;
s_oss << indent2;
for (std::vector < double >::const_iterator it = this->steps.begin();
it != this->steps.end(); it++)
{
if (i++ == 5)
{
s_oss << std::endl;
s_oss << indent2;
i = 0;
}
s_oss << *it << " ";
}
s_oss << std::endl;
}
return;
}
void
cxxKinetics::read_raw(PHREEQC_PTR_ARG_COMMA CParser & parser, bool check)
{
double d;
static std::vector < std::string > vopts;
if (vopts.empty())
{
vopts.reserve(15);
vopts.push_back("step_divide");
vopts.push_back("rk");
vopts.push_back("bad_step_max");
vopts.push_back("use_cvode");
vopts.push_back("component");
vopts.push_back("totals");
vopts.push_back("steps");
vopts.push_back("cvode_steps");
vopts.push_back("cvode_order");
}
std::istream::pos_type ptr;
std::istream::pos_type next_char;
std::string token;
int opt_save;
bool useLastLine(false);
std::vector < double > temp_steps;
// Read kinetics number and description
this->read_number_description(parser);
opt_save = CParser::OPT_ERROR;
bool step_divide_defined(false);
bool rk_defined(false);
bool bad_step_max_defined(false);
bool use_cvode_defined(false);
bool cvode_steps_defined(false);
bool cvode_order_defined(false);
bool steps_defined(false);
for (;;)
{
int opt;
if (useLastLine == false)
{
opt = parser.get_option(vopts, next_char);
}
else
{
opt = parser.getOptionFromLastLine(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_EOF;
parser.error_msg("Unknown input in KINETICS_COMP_RAW keyword.",
CParser::OT_CONTINUE);
parser.error_msg(parser.line().c_str(), CParser::OT_CONTINUE);
useLastLine = false;
break;
case 0: // step_divide
if (!(parser.get_iss() >> this->step_divide))
{
this->step_divide = 1.0;
parser.incr_input_error();
parser.error_msg("Expected numeric value for step_divide.",
CParser::OT_CONTINUE);
}
step_divide_defined = true;
useLastLine = false;
break;
case 1: // rk
if (!(parser.get_iss() >> this->rk))
{
this->rk = 3;
parser.incr_input_error();
parser.error_msg("Expected integer value for rk.",
CParser::OT_CONTINUE);
}
rk_defined = true;
useLastLine = false;
break;
case 2: // bad_step_max
if (!(parser.get_iss() >> this->bad_step_max))
{
this->bad_step_max = 500;
parser.incr_input_error();
parser.error_msg("Expected integer value for bad_step_max.",
CParser::OT_CONTINUE);
}
bad_step_max_defined = true;
useLastLine = false;
break;
case 3: // use_cvode
if (!(parser.get_iss() >> this->use_cvode))
{
this->use_cvode = false;
parser.incr_input_error();
parser.error_msg("Expected boolean value for use_cvode.",
CParser::OT_CONTINUE);
}
use_cvode_defined = true;
useLastLine = false;
break;
case 4: // component
{
cxxKineticsComp ec;
// preliminary read
#ifdef SKIP
std::istream::pos_type pos = parser.tellg();
CParser::ECHO_OPTION eo = parser.get_echo_file();
parser.set_echo_file(CParser::EO_NONE);
CParser::ECHO_OPTION eo_s = parser.get_echo_stream();
parser.set_echo_stream(CParser::EO_NONE);
ec.read_raw(parser, false);
parser.set_echo_file(eo);
parser.set_echo_stream(eo_s);
parser.seekg(pos).clear();
parser.seekg(pos);
if (this->kineticsComps.find(ec.get_rate_name()) != this->kineticsComps.end())
{
cxxKineticsComp & comp = this->kineticsComps.find(ec.get_rate_name())->second;
comp.read_raw(parser, false);
}
else
{
cxxKineticsComp ec1;
ec1.read_raw(parser, false);
std::string str(ec1.get_rate_name());
this->kineticsComps[str] = ec1;
}
#endif
parser.set_accumulate(true);
ec.read_raw(P_INSTANCE_COMMA parser, false);
parser.set_accumulate(false);
std::istringstream is(parser.get_accumulated());
CParser reread(P_INSTANCE_COMMA is);
reread.set_echo_file(CParser::EO_NONE);
reread.set_echo_stream(CParser::EO_NONE);
std::list < cxxKineticsComp >::iterator kit;
bool found = false;
for (kit = this->kineticsComps.begin(); kit != this->kineticsComps.end(); kit++)
{
if (kit->get_rate_name() == ec.get_rate_name())
{
found = true;
break;
}
}
if (found)
{
kit->read_raw(P_INSTANCE_COMMA reread, false);
}
else
{
cxxKineticsComp ec1;
ec1.read_raw(P_INSTANCE_COMMA reread, false);
std::string str(ec1.get_rate_name());
this->kineticsComps.push_back(ec1);
}
/*
if (this->kineticsComps.find(ec.get_rate_name()) != this->kineticsComps.end())
{
cxxKineticsComp & comp = this->kineticsComps.find(ec.get_rate_name())->second;
comp.read_raw(P_INSTANCE_COMMA reread, false);
}
else
{
cxxKineticsComp ec1;
ec1.read_raw(P_INSTANCE_COMMA reread, false);
std::string str(ec1.get_rate_name());
this->kineticsComps[str] = ec1;
}
*/
}
useLastLine = true;
break;
case 5: // totals
if (this->totals.read_raw(P_INSTANCE_COMMA parser, next_char) !=
CParser::PARSER_OK)
{
parser.incr_input_error();
parser.
error_msg
("Expected element name and molality for KineticsComp totals.",
CParser::OT_CONTINUE);
}
opt_save = 5;
useLastLine = false;
break;
case 6: // steps
while (parser.copy_token(token, next_char) == CParser::TT_DIGIT)
{
//sscanf(token.c_str(), "%lf", &d);
//this->steps.push_back(d);
std::istringstream iss(token);
if (!(iss >> d))
{
parser.incr_input_error();
parser.error_msg("Expected numeric value for steps.",
CParser::OT_CONTINUE);
}
else
{
temp_steps.push_back(d);
steps_defined = true;
}
}
opt_save = 6;
useLastLine = false;
break;
case 7: // cvode_steps
if (!(parser.get_iss() >> this->cvode_steps))
{
this->cvode_steps = 100;
parser.incr_input_error();
parser.error_msg("Expected integer value for cvode_steps.",
CParser::OT_CONTINUE);
}
cvode_steps_defined = true;
useLastLine = false;
break;
case 8: // cvode_order
if (!(parser.get_iss() >> this->cvode_order))
{
this->cvode_order = 5;
parser.incr_input_error();
parser.error_msg("Expected integer value for cvode_order.",
CParser::OT_CONTINUE);
}
cvode_order_defined = true;
useLastLine = false;
break;
}
if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD)
break;
}
if (steps_defined)
{
this->steps = temp_steps;
}
if (check)
{
// members that must be defined
if (step_divide_defined == false)
{
parser.incr_input_error();
parser.error_msg("Step_divide not defined for KINETICS_RAW input.",
CParser::OT_CONTINUE);
}
if (rk_defined == false)
{
parser.incr_input_error();
parser.error_msg("Rk not defined for KINETICS_RAW input.",
CParser::OT_CONTINUE);
}
if (bad_step_max_defined == false)
{
parser.incr_input_error();
parser.error_msg("Bad_step_max not defined for KINETICS_RAW input.",
CParser::OT_CONTINUE);
}
if (use_cvode_defined == false)
{
parser.incr_input_error();
parser.error_msg("Use_cvode not defined for KINETICS_RAW input.",
CParser::OT_CONTINUE);
}
if (cvode_steps_defined == false)
{
parser.incr_input_error();
parser.error_msg("Cvode_steps not defined for KINETICS_RAW input.",
CParser::OT_CONTINUE);
}
if (cvode_order_defined == false)
{
parser.incr_input_error();
parser.error_msg("Cvode_order not defined for KINETICS_RAW input.",
CParser::OT_CONTINUE);
}
}
}
#ifdef USE_MPI
void
cxxKinetics::mpi_pack(std::vector < int >&ints,
std::vector < double >&doubles)
{
ints.push_back(this->n_user);
ints.push_back((int) this->kineticsComps.size());
std::list < cxxKineticsComp >::iterator it;
for (it = this->kineticsComps.begin(); it != this->kineticsComps.end(); it++)
{
(*it).mpi_pack(ints, doubles);
}
/*
for (std::map < std::string, cxxKineticsComp >::iterator it =
this->kineticsComps.begin(); it != this->kineticsComps.end(); it++)
{
(*it).second.mpi_pack(ints, doubles);
}
*/
ints.push_back((int) this->steps.size());
for (std::vector < double >::iterator it = this->steps.begin();
it != this->steps.end(); it++)
{
doubles.push_back(*it);
}
doubles.push_back(this->step_divide);
ints.push_back(this->rk);
ints.push_back(this->bad_step_max);
ints.push_back(this->use_cvode);
ints.push_back(this->cvode_steps);
ints.push_back(this->cvode_order);
}
void
cxxKinetics::mpi_unpack(int *ints, int *ii, double *doubles, int *dd)
{
int i = *ii;
int d = *dd;
this->n_user = ints[i++];
this->n_user_end = this->n_user;
this->description = " ";
int n = ints[i++];
this->kineticsComps.clear();
for (int j = 0; j < n; j++)
{
cxxKineticsComp kc;
kc.mpi_unpack(ints, &i, doubles, &d);
//std::string str(kc.get_rate_name());
//this->kineticsComps[str] = kc;
this->kineticsComps.push_back(kc);
}
n = ints[i++];
this->steps.clear();
for (int j = 0; j < n; j++)
{
this->steps.push_back(doubles[d++]);
}
this->step_divide = doubles[d++];
this->rk = ints[i++];
this->bad_step_max = ints[i++];
this->use_cvode = (ints[i++] == TRUE);
this->cvode_steps = ints[i++];
this->cvode_order = ints[i++];
*ii = i;
*dd = d;
}
#endif
#ifdef SKIP
void
cxxKinetics::add(const cxxKinetics & addee, double extensive)
//
// Add to existing ppassemblage to "this" ppassemblage
//
{
if (extensive == 0.0)
return;
//std::list<cxxKineticsComp> kineticsComps;
for (std::list < cxxKineticsComp >::const_iterator itadd =
addee.kineticsComps.begin(); itadd != addee.kineticsComps.end();
++itadd)
{
bool found = false;
for (std::list < cxxKineticsComp >::iterator it =
this->kineticsComps.begin(); it != this->kineticsComps.end();
++it)
{
if (it->get_rate_name() == itadd->get_rate_name())
{
it->add((*itadd), extensive);
found = true;
break;
}
}
if (!found)
{
cxxKineticsComp entity = *itadd;
entity.multiply(extensive);
this->kineticsComps.push_back(entity);
}
}
//std::vector<double> steps;
this->steps = addee.steps;
//cxxNameDouble totals;
//double step_divide;
this->step_divide = addee.step_divide;
//int rk;
this->rk = addee.rk;
//int bad_step_max;
this->bad_step_max = addee.bad_step_max;
//bool use_cvode;
this->use_cvode = addee.use_cvode;
this->cvode_steps = addee.cvode_steps;
this->cvode_order = addee.cvode_order;
}
#endif
void
cxxKinetics::add(const cxxKinetics & addee, double extensive)
//
// Add to existing ppassemblage to "this" ppassemblage
//
{
if (extensive == 0.0)
return;
//std::map < std::string, cxxKineticsComp> kineticsComps;
for (std::list < cxxKineticsComp >::const_iterator itadd =
addee.kineticsComps.begin(); itadd != addee.kineticsComps.end();
++itadd)
{
bool found(false);
std::list < cxxKineticsComp >::iterator it;
for (it = this->kineticsComps.begin(); it != this->kineticsComps.end(); it++)
{
if ((*it).get_rate_name() == (*itadd).get_rate_name())
{
found = true;
break;
}
}
//std::map < std::string, cxxKineticsComp >::iterator it = this->kineticsComps.find((*itadd).first);
if (found)
{
(*it).add((*itadd), extensive);
}
else
{
cxxKineticsComp entity = (*itadd);
entity.multiply(extensive);
this->kineticsComps.push_back(entity);
}
}
//std::vector<double> steps;
this->steps = addee.steps;
//cxxNameDouble totals;
//double step_divide;
this->step_divide = addee.step_divide;
//int rk;
this->rk = addee.rk;
//int bad_step_max;
this->bad_step_max = addee.bad_step_max;
//bool use_cvode;
this->use_cvode = addee.use_cvode;
this->cvode_steps = addee.cvode_steps;
this->cvode_order = addee.cvode_order;
}
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