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iphreeqc/Solution.cxx
Scott R Charlton 1e28de647f changed automatic arrays to dynamic arrays 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@924 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2006-05-16 01:10:25 +00:00

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// Solution.cxx: implementation of the cxxSolution class.
//
//////////////////////////////////////////////////////////////////////
#ifdef _DEBUG
#pragma warning(disable : 4786) // disable truncation warning (Only used by debugger)
#endif
#include "Utils.h" // define first
#include "Solution.h"
#define EXTERNAL extern
#include "global.h"
#include "phqalloc.h"
#include "phrqproto.h"
#include "output.h"
#include <cassert> // assert
#include <algorithm> // std::sort
//////////////////////////////////////////////////////////////////////
// Construction/Destruction
//////////////////////////////////////////////////////////////////////
cxxSolution::cxxSolution()
//
// default constructor for cxxSolution
//
: cxxNumKeyword()
{
tc = 25.0;
ph = 7.0;
pe = 4.0;
mu = 1e-7;
ah2o = 1.0;
total_h = 111.1;
total_o = 55.55;
cb = 0.0;
mass_water = 1.0;
total_alkalinity = 0.0;
totals.type = cxxNameDouble::ND_ELT_MOLES;
master_activity.type = cxxNameDouble::ND_SPECIES_LA;
species_gamma.type = cxxNameDouble::ND_SPECIES_GAMMA;
}
cxxSolution::cxxSolution(double zero)
//
// empty cxxSolution constructor
//
: cxxNumKeyword()
{
assert (zero == 0.0);
tc = 0.0;
ph = 0.0;
pe = 0.0;
mu = 0.0;
ah2o = 0.0;
total_h = 0.0;
total_o = 0.0;
cb = 0.0;
mass_water = 0.0;
total_alkalinity = 0.0;
totals.type = cxxNameDouble::ND_ELT_MOLES;
master_activity.type = cxxNameDouble::ND_SPECIES_LA;
species_gamma.type = cxxNameDouble::ND_SPECIES_GAMMA;
}
cxxSolution::cxxSolution(struct solution *solution_ptr)
//
// constructor for cxxSolution from struct solution
//
:
cxxNumKeyword(),
totals(solution_ptr->totals),
master_activity(solution_ptr->master_activity, solution_ptr->count_master_activity, cxxNameDouble::ND_SPECIES_LA),
species_gamma(solution_ptr->species_gamma, solution_ptr->count_species_gamma, cxxNameDouble::ND_SPECIES_GAMMA),
isotopes(solution_ptr)
{
this->set_description(solution_ptr->description);
n_user = solution_ptr->n_user;
n_user_end = solution_ptr->n_user_end;
tc = solution_ptr->tc;
ph = solution_ptr->ph;
pe = solution_ptr->solution_pe;
mu = solution_ptr->mu;
ah2o = solution_ptr->ah2o;
total_h = solution_ptr->total_h;
total_o = solution_ptr->total_o;
cb = solution_ptr->cb;
mass_water = solution_ptr->mass_water;
total_alkalinity = solution_ptr->total_alkalinity;
// Totals filled in constructor, just save description and moles
// Isotopes
/*
for (i = 0; i < solution_ptr->count_isotopes; i++) {
cxxSolutionIsotope iso(&solution_ptr->isotopes[i]);
isotopes.push_back(iso);
}
*/
// Master_activity in constructor
// Species_gamma in constructor
}
#ifdef SKIP
cxxSolution::cxxSolution(const cxxSolution &old, double intensive, double extensive)
//
// constructor for cxxSolution from struct solution
//
:
cxxNumKeyword(),
totals(old.totals, extensive),
master_activity(old.master_activity, intensive),
species_gamma(old.species_gamma, intensive)
{
this->set_description(old.description);
this->n_user = old.n_user;
this->n_user_end = old.n_user_end;
this->tc = old.tc * intensive;
this->ph = old.ph * intensive;
this->pe = old.pe * intensive;
this->mu = old.mu * intensive;
this->ah2o = old.ah2o * intensive;
this->total_h = old.total_h * extensive;
this->total_o = old.total_o * extensive;
this->cb = old.cb * extensive;
this->mass_water = old.mass_water * extensive;
this->total_alkalinity = old.total_alkalinity * extensive;
/*
cxxNameDouble totals;
std::list<cxxSolutionIsotope> isotopes;
cxxNameDouble master_activity;
cxxNameDouble species_gamma;
*/
for (std::list<cxxSolutionIsotope>::const_iterator it = old.isotopes.begin(); it != old.isotopes.end(); it++) {
this->isotopes.push_back(cxxSolutionIsotope((*it), intensive, extensive));
}
}
#endif
cxxSolution::~cxxSolution()
{
}
struct solution *cxxSolution::cxxSolution2solution()
//
// Builds a solution structure from instance of cxxSolution
//
{
struct solution *solution_ptr = solution_alloc();
solution_ptr->description = this->get_description();
solution_ptr->n_user = this->n_user;
solution_ptr->n_user_end = this->n_user_end;
solution_ptr->new_def = FALSE;
solution_ptr->tc = this->tc;
solution_ptr->ph = this->ph;
solution_ptr->solution_pe = this->pe;
solution_ptr->mu = this->mu;
solution_ptr->ah2o = this->ah2o;
solution_ptr->total_h = this->total_h;
solution_ptr->total_o = this->total_o;
solution_ptr->cb = this->cb;
solution_ptr->mass_water = this->mass_water;
solution_ptr->total_alkalinity = this->total_alkalinity;
solution_ptr->density = 1.0;
solution_ptr->units = moles_per_kilogram_string;
solution_ptr->default_pe = 0;
// pe_data
// totals
solution_ptr->totals = (struct conc *) free_check_null(solution_ptr->totals);
solution_ptr->totals = this->totals.conc();
// master_activity
solution_ptr->master_activity = (struct master_activity *) free_check_null(solution_ptr->master_activity);
solution_ptr->master_activity = this->master_activity.master_activity();
solution_ptr->count_master_activity = this->master_activity.size() + 1;
// species_gamma
solution_ptr->species_gamma = this->species_gamma.master_activity();
solution_ptr->count_species_gamma = this->species_gamma.size();
// isotopes
solution_ptr->isotopes = (struct isotope *) free_check_null(solution_ptr->isotopes);
//solution_ptr->isotopes = cxxSolutionIsotope::list2isotope(this->isotopes);
solution_ptr->isotopes = this->isotopes.cxxSolutionIsotopeList2isotope();
solution_ptr->count_isotopes = this->isotopes.size();
return(solution_ptr);
}
void cxxSolution::dump_xml(std::ostream& s_oss, unsigned int indent)const
{
//const char ERR_MESSAGE[] = "Packing solution message: %s, element not found\n";
unsigned int i;
s_oss.precision(DBL_DIG - 1);
std::string indent0(""), indent1("");
for(i = 0; i < indent; ++i) indent0.append(Utilities::INDENT);
for(i = 0; i < indent + 1; ++i) indent1.append(Utilities::INDENT);
// Solution element and attributes
s_oss << indent0;
s_oss << "<solution " << std::endl;
//s_oss << indent1;
//s_oss << "soln_new_def=\"" << this->new_def << "\"" << std::endl;
s_oss << indent1;
s_oss << "soln_n_user=\"" << this->n_user << "\" " << std::endl;
s_oss << indent1;
s_oss << "soln_description=\"" << this->description << "\"" << std::endl;
s_oss << indent1;
s_oss << "soln_tc=\"" << this->tc << "\"" << std::endl;
s_oss << indent1;
s_oss << "soln_ph=\"" << this->ph << "\"" << std::endl;
s_oss << indent1;
s_oss << "soln_solution_pe=\"" << this->pe << "\"" << std::endl;
s_oss << indent1;
s_oss << "soln_mu=\"" << this->mu << "\"" << std::endl;
s_oss << indent1;
s_oss << "soln_ah2o=\"" << this->ah2o << "\"" << std::endl;
s_oss << indent1;
s_oss << "soln_total_h=\"" << this->total_h << "\"" << std::endl;
s_oss << indent1;
s_oss << "soln_total_o=\"" << this->total_o << "\"" << std::endl;
s_oss << indent1;
s_oss << "soln_cb=\"" << this->cb << "\"" << std::endl;
s_oss << indent1;
s_oss << "soln_mass_water=\"" << this->mass_water << "\"" << std::endl;
s_oss << indent1;
s_oss << "soln_total_alkalinity=\"" << this->total_alkalinity << "\"" << std::endl;
s_oss << indent1;
s_oss << "\">" << std::endl;
// soln_total conc structures
this->totals.dump_xml(s_oss, indent + 1);
/*
{
for (std::map <char *, double, CHARSTAR_LESS>::const_iterator it = totals.begin(); it != totals.end(); ++it) {
s_oss << indent1;
s_oss << "<soln_total";
s_oss << " conc_desc=\"" << it->first << "\"";
s_oss << " conc_moles=\"" << it->second << "\"" ;
s_oss << "\">" << std::endl;
}
}
*/
// master_activity map
this->master_activity.dump_xml(s_oss, indent + 1);
/*
{
for (std::map <char *, double>::const_iterator it = master_activity.begin(); it != master_activity.end(); ++it) {
s_oss << indent1;
s_oss << "<soln_m_a";
s_oss << " m_a_desc=\"" << it->first << "\"" ;
s_oss << " m_a_la=\"" << it->second << "\"" ;
s_oss << "\">" << std::endl;
}
}
*/
// species_gamma map
this->species_gamma.dump_xml(s_oss, indent + 1);
/*
{
for (std::map <char *, double>::const_iterator it = species_gamma.begin(); it != species_gamma.end(); ++it) {
s_oss << indent1;
s_oss << "<soln_s_g";
s_oss << " m_a_desc=\"" << it->first << "\"" ;
s_oss << " m_a_la=\"" << it->second << "\"" ;
s_oss << "\">" << std::endl;
}
}
*/
for (std::list<cxxSolutionIsotope>::const_iterator it = this->isotopes.begin(); it != isotopes.end(); ++it) {
it->dump_xml(s_oss, indent + 1);
}
// End of solution
s_oss << indent0;
s_oss << "</solution>" << std::endl;
return;
}
void cxxSolution::dump_raw(std::ostream& s_oss, unsigned int indent)const
{
//const char ERR_MESSAGE[] = "Packing solution 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);
// Solution element and attributes
s_oss << indent0;
s_oss << "SOLUTION_RAW " << this->n_user << " " << this->description << std::endl;
s_oss << indent1;
s_oss << "-temp " << this->tc << std::endl;
s_oss << indent1;
s_oss << "-pH " << this->ph << std::endl;
s_oss << indent1;
s_oss << "-pe " << this->pe << std::endl;
// new identifier
s_oss << indent1;
s_oss << "-mu " << this->mu << std::endl;
// new identifier
s_oss << indent1;
s_oss << "-ah2o " << this->ah2o << std::endl;
// new identifier
s_oss << indent1;
s_oss << "-total_h " << this->total_h << std::endl;
// new identifier
s_oss << indent1;
s_oss << "-total_o " << this->total_o << std::endl;
// new identifier
s_oss << indent1;
s_oss << "-cb " << this->cb << std::endl;
// new identifier
s_oss << indent1;
s_oss << "-mass_water " << this->mass_water << std::endl;
// new identifier
s_oss << indent1;
s_oss << "-total_alkalinity " << this->total_alkalinity << std::endl;
// soln_total conc structures
s_oss << indent1;
s_oss << "-totals" << std::endl;
this->totals.dump_raw(s_oss, indent + 2);
/*
for (std::map <char *, double, CHARSTAR_LESS>::const_iterator it = totals.begin(); it != totals.end(); ++it) {
s_oss << indent2;
s_oss << it->first << " " << it->second << std::endl;
}
*/
// master_activity map
s_oss << indent1;
s_oss << "-activities" << std::endl;
this->master_activity.dump_raw(s_oss, indent + 2);
/*
{
for (std::map <char *, double>::const_iterator it = master_activity.begin(); it != master_activity.end(); ++it) {
s_oss << indent2;
s_oss << it->first << " " << it->second << std::endl;
}
}
*/
// species_gamma map
s_oss << indent1;
s_oss << "-gammas" << std::endl;
this->species_gamma.dump_raw(s_oss, indent + 2);
/*
{
{
for (std::map <char *, double>::const_iterator it = species_gamma.begin(); it != species_gamma.end(); ++it) {
s_oss << indent2;
s_oss << it->first << " " << it->second << std::endl;
}
}
}
*/
// Isotopes
s_oss << indent1;
s_oss << "-Isotopes" << std::endl;
{
for (std::list<cxxSolutionIsotope>::const_iterator it = this->isotopes.begin(); it != isotopes.end(); ++it) {
it->dump_raw(s_oss, indent + 2);
}
}
return;
}
void cxxSolution::read_raw(CParser& parser)
{
static std::vector<std::string> vopts;
if (vopts.empty()) {
vopts.reserve(21);
vopts.push_back("totals"); // 0
vopts.push_back("activities"); // 1
vopts.push_back("gammas"); // 2
vopts.push_back("isotopes"); // 3
vopts.push_back("temp"); // 4
vopts.push_back("tc"); // 5
vopts.push_back("temperature"); // 6
vopts.push_back("ph"); // 7
vopts.push_back("pe"); // 8
vopts.push_back("mu"); // 9
vopts.push_back("ionic_strength"); // 10
vopts.push_back("ah2o"); // 11
vopts.push_back("activity_water"); // 12
vopts.push_back("total_h"); // 13
vopts.push_back("total_o"); // 14
vopts.push_back("mass_water"); // 15
vopts.push_back("mass_h2o"); // 16
vopts.push_back("total_alkalinity"); // 17
vopts.push_back("total_alk"); // 18
vopts.push_back("cb"); // 19
vopts.push_back("charge_balance"); // 20
}
std::istream::pos_type ptr;
std::istream::pos_type next_char;
std::string token;
int opt_save;
// Read solution number and description
this->read_number_description(parser);
opt_save = CParser::OPT_ERROR;
bool tc_defined(false);
bool ph_defined(false);
bool pe_defined(false);
bool mu_defined(false);
bool ah2o_defined(false);
bool total_h_defined(false);
bool total_o_defined(false);
bool cb_defined(false);
bool mass_water_defined(false);
bool total_alkalinity_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_EOF;
parser.error_msg("Unknown input in SOLUTION_RAW keyword.", CParser::OT_CONTINUE);
parser.error_msg(parser.line().c_str(), CParser::OT_CONTINUE);
break;
case 0: // totals
if ( this->totals.read_raw(parser, next_char) != CParser::PARSER_OK) {
parser.incr_input_error();
parser.error_msg("Expected element name and moles for totals.", CParser::OT_CONTINUE);
}
opt_save = 0;
break;
case 1: // activities
if ( this->master_activity.read_raw(parser, next_char) != CParser::PARSER_OK) {
parser.incr_input_error();
parser.error_msg("Expected species name and log activity for activities.", CParser::OT_CONTINUE);
}
opt_save = 1;
break;
case 2: // gammas
if ( this->species_gamma.read_raw(parser, next_char) != CParser::PARSER_OK) {
parser.incr_input_error();
parser.error_msg("Expected species name and activity coefficient for gammas.", CParser::OT_CONTINUE);
}
opt_save = 2;
break;
case 3: // isotopes
{
cxxSolutionIsotope iso;
if ( iso.read_raw(parser) != CParser::PARSER_OK) {
parser.incr_input_error();
parser.error_msg("Expected data for isotopes.", CParser::OT_CONTINUE);
} else {
if (iso.get_isotope_name() != NULL) {
this->isotopes.push_back(iso);
}
}
}
opt_save = 3;
break;
case 4: // temp
case 5: // tc
case 6: // temperature
if (!(parser.get_iss() >> this->tc))
{
this->tc = 25.0;
parser.incr_input_error();
parser.error_msg("Expected numeric value for temperature.", CParser::OT_CONTINUE);
}
tc_defined = true;
opt_save = CParser::OPT_DEFAULT;
break;
case 7: // ph
if (!(parser.get_iss() >> this->ph))
{
this->ph = 7.0;
parser.incr_input_error();
parser.error_msg("Expected numeric value for pH.", CParser::OT_CONTINUE);
}
ph_defined = true;
opt_save = CParser::OPT_DEFAULT;
break;
case 8: // pe
if (!(parser.get_iss() >> this->pe))
{
this->pe = 4.0;
parser.incr_input_error();
parser.error_msg("Expected numeric value for pe.", CParser::OT_CONTINUE);
}
pe_defined = true;
opt_save = CParser::OPT_DEFAULT;
break;
case 9: // mu
case 10: // ionic_strength
if (!(parser.get_iss() >> this->mu))
{
this->mu = 1e-7;
parser.incr_input_error();
parser.error_msg("Expected numeric value for ionic strength.", CParser::OT_CONTINUE);
}
mu_defined = true;
opt_save = CParser::OPT_DEFAULT;
break;
case 11: // ah2o
case 12: // activity_water
if (!(parser.get_iss() >> this->ah2o))
{
this->ah2o = 1.0;
parser.incr_input_error();
parser.error_msg("Expected numeric value for activity of water.", CParser::OT_CONTINUE);
}
ah2o_defined = true;
opt_save = CParser::OPT_DEFAULT;
break;
case 13: // total_h
if (!(parser.get_iss() >> this->total_h))
{
this->total_h = 111.1;
parser.incr_input_error();
parser.error_msg("Expected numeric value for total hydrogen.", CParser::OT_CONTINUE);
}
total_h_defined = true;
opt_save = CParser::OPT_DEFAULT;
break;
case 14: // total_o
if (!(parser.get_iss() >> this->total_o))
{
this->total_o = 55.55;
parser.incr_input_error();
parser.error_msg("Expected numeric value for total oxygen.", CParser::OT_CONTINUE);
}
total_o_defined = true;
opt_save = CParser::OPT_DEFAULT;
break;
case 15: // mass_water
case 16: // mass_h2o
if (!(parser.get_iss() >> this->mass_water))
{
this->mass_water = 1.0;
parser.incr_input_error();
parser.error_msg("Expected numeric value for mass of water.", CParser::OT_CONTINUE);
}
mass_water_defined = true;
opt_save = CParser::OPT_DEFAULT;
break;
case 17: // total_alkalinity
case 18: // total_alk
if (!(parser.get_iss() >> this->total_alkalinity))
{
this->total_alkalinity = 0;
parser.incr_input_error();
parser.error_msg("Expected numeric value for total_alkalinity.", CParser::OT_CONTINUE);
}
total_alkalinity_defined = true;
opt_save = CParser::OPT_DEFAULT;
break;
case 19: // cb
case 20: // charge_balance
if (!(parser.get_iss() >> this->cb))
{
this->cb = 0;
parser.incr_input_error();
parser.error_msg("Expected numeric value for charge balance.", CParser::OT_CONTINUE);
}
cb_defined = true;
opt_save = CParser::OPT_DEFAULT;
break;
}
if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD) break;
}
// all members must be defined
if (tc_defined == false) {
parser.incr_input_error();
parser.error_msg("Temp not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
}
if (ph_defined == false) {
parser.incr_input_error();
parser.error_msg("pH not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
}
if (pe_defined == false) {
parser.incr_input_error();
parser.error_msg("pe not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
}
if (mu_defined == false) {
parser.incr_input_error();
parser.error_msg("Ionic strength not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
}
if (ah2o_defined == false) {
parser.incr_input_error();
parser.error_msg("Activity of water not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
}
if (total_h_defined == false) {
parser.incr_input_error();
parser.error_msg("Total hydrogen not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
}
if (total_o_defined == false) {
parser.incr_input_error();
parser.error_msg("Total oxygen not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
}
if (cb_defined == false) {
parser.incr_input_error();
parser.error_msg("Charge balance not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
}
if (mass_water_defined == false) {
parser.incr_input_error();
parser.error_msg("Temp not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
}
if (total_alkalinity_defined == false) {
parser.incr_input_error();
parser.error_msg("Total alkalinity not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
}
return;
}
void cxxSolution::add(const cxxSolution &old, double intensive, double extensive)
//
// Add existing solution to "this" solution
//
{
this->tc += old.tc * intensive;
this->ph += old.ph * intensive;
this->pe += old.pe * intensive;
this->mu += old.mu * intensive;
this->ah2o += old.ah2o * intensive;
this->total_h += old.total_h * extensive;
this->total_o += old.total_o * extensive;
this->cb += old.cb * extensive;
this->mass_water += old.mass_water * extensive;
this->total_alkalinity += old.total_alkalinity * extensive;
this->totals.add(old.totals, extensive);
this->master_activity.add(old.master_activity, intensive);
this->species_gamma.add(old.species_gamma, intensive);
this->isotopes.add(old.isotopes, intensive, extensive);
#ifdef SKIP
//
// isotopes
// go through old list, update or add to current list
//
for (std::list <cxxSolutionIsotope>::const_iterator itold = old.isotopes.begin(); itold != old.isotopes.end(); ++itold) {
bool found = false;
for (std::list <cxxSolutionIsotope>::iterator it = this->isotopes.begin(); it != this->isotopes.end(); ++it) {
if ((it->isotope_number == itold->isotope_number) &&
(it->elt_name == itold->elt_name) &&
(it->isotope_name == itold->isotope_name)) {
it->total += itold->total * extensive;
it->ratio += itold->ratio * intensive;
it->ratio_uncertainty += itold->ratio_uncertainty * intensive;
it->ratio_uncertainty_defined = (it->ratio_uncertainty_defined || itold->ratio_uncertainty_defined);
found = true;
break;
}
}
if (!found) {
this->isotopes.push_back(*itold);
}
}
#endif
/*
cxxNameDouble totals;
std::list<cxxSolutionIsotope> isotopes;
cxxNameDouble master_activity;
cxxNameDouble species_gamma;
*/
}
double cxxSolution::get_total(char *string)const
{
cxxNameDouble::const_iterator it = this->totals.find(string);
if (it == this->totals.end()) {
return(0.0);
} else {
return(it->second);
}
}
void cxxSolution::set_total(char *string, double d)
{
this->totals[string] = d;
}
double cxxSolution::get_master_activity(char *string)const
{
cxxNameDouble::const_iterator it = this->master_activity.find(string);
if (it == this->master_activity.end()) {
return(0.0);
} else {
return(it->second);
}
}
#ifdef USE_MPI
#include <mpi.h>
/* ---------------------------------------------------------------------- */
void cxxSolution::mpi_pack(std::vector<int>& ints, std::vector<double>& doubles)
/* ---------------------------------------------------------------------- */
{
/*
* Make list of list of ints and doubles from solution structure
* This list is not the complete structure, but only enough
* for batch-reaction, advection, and transport calculations
*/
ints.push_back(this->n_user);
doubles.push_back(this->tc);
doubles.push_back(this->ph);
doubles.push_back(this->pe);
doubles.push_back(this->mu);
doubles.push_back(this->ah2o);
doubles.push_back(this->total_h);
doubles.push_back(this->total_o);
doubles.push_back(this->cb);
doubles.push_back(this->mass_water);
doubles.push_back(this->total_alkalinity);
/*
* struct conc *totals;
*/
this->totals.mpi_pack(ints, doubles);
/*
* struct master_activity *master_activity;
*/
this->master_activity.mpi_pack(ints, doubles);
/*
* struct master_activity *species_gamma
*/
this->species_gamma.mpi_pack(ints, doubles);
/*
position = 0;
int i = ints.size();
int int_array[i];
int d = doubles.size();
double double_array[d];
for (int j = 0; j < i; j++) {
int_array[j] = ints[j];
}
for (int j = 0; j < d; j++) {
double_array[j] = ints[j];
}
MPI_Send(&max_size, 1, MPI_INT, task_number, 0, MPI_COMM_WORLD);
MPI_Pack(&i, 1, MPI_INT, buffer, max_size, &position, MPI_COMM_WORLD);
MPI_Pack(&int_array, i, MPI_INT, buffer, max_size, &position, MPI_COMM_WORLD);
MPI_Pack(&d, 1, MPI_INT, buffer, max_size, &position, MPI_COMM_WORLD);
MPI_Pack(&double_array, d, MPI_DOUBLE, buffer, max_size, &position, MPI_COMM_WORLD);
MPI_Send(buffer, position, MPI_PACKED, task_number, 0, MPI_COMM_WORLD);
buffer = (void *) free_check_null(buffer);
*/
}
/* ---------------------------------------------------------------------- */
void cxxSolution::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 = " ";
this->tc = doubles[d++];
this->ph = doubles[d++];
this->pe = doubles[d++];
this->mu = doubles[d++];
this->ah2o = doubles[d++];
this->total_h = doubles[d++];
this->total_o = doubles[d++];
this->cb = doubles[d++];
this->mass_water = doubles[d++];
this->total_alkalinity = doubles[d++];
/*
* struct conc *totals;
*/
this->totals.mpi_unpack(ints, &i, doubles, &d);
/*
* struct master_activity *master_activity;
*/
this->master_activity.mpi_unpack(ints, &i, doubles, &d);
/*
* struct master_activity *species_gamma;
*/
this->species_gamma.mpi_unpack(ints, &i, doubles, &d);
*ii = i;
*dd = d;
}
/* ---------------------------------------------------------------------- */
void cxxSolution::mpi_send(int task_number)
/* ---------------------------------------------------------------------- */
{
//int count_totals, count_totals_position, count_activity, count_activity_position;
int max_size, member_size, position;
//int ints[MESSAGE_MAX_NUMBERS];
//double doubles[MESSAGE_MAX_NUMBERS];
void *buffer;
std::vector<int> ints;
std::vector<double> doubles;
/*
* Make list of list of ints and doubles from solution structure
* This list is not the complete structure, but only enough
* for batch-reaction, advection, and transport calculations
*/
ints.push_back(this->n_user);
/* int n_user_end; */
/* char *description; */
doubles.push_back(this->tc);
doubles.push_back(this->ph);
doubles.push_back(this->pe);
doubles.push_back(this->mu);
doubles.push_back(this->ah2o);
doubles.push_back(this->total_h);
doubles.push_back(this->total_o);
doubles.push_back(this->cb);
doubles.push_back(this->mass_water);
doubles.push_back(this->total_alkalinity);
/*
* struct conc *totals;
*/
this->totals.mpi_pack(ints, doubles);
/*
* struct master_activity *master_activity;
*/
this->master_activity.mpi_pack(ints, doubles);
/*
* struct master_activity *species_gamma
*/
this->species_gamma.mpi_pack(ints, doubles);
/* int count_isotopes; */
/* struct isotope *isotopes; */
if (input_error > 0) {
std::string errstr("Stopping due to errors\n");
error_msg(errstr.c_str(), STOP);
}
/*
* Malloc space for a buffer
*/
max_size = 0;
//MPI_Pack_size(MESSAGE_MAX_NUMBERS, MPI_INT, MPI_COMM_WORLD, &member_size);
MPI_Pack_size(ints.size(), MPI_INT, MPI_COMM_WORLD, &member_size);
max_size += member_size;
//MPI_Pack_size(MESSAGE_MAX_NUMBERS, MPI_DOUBLE, MPI_COMM_WORLD, &member_size);
MPI_Pack_size(doubles.size(), MPI_DOUBLE, MPI_COMM_WORLD, &member_size);
max_size += member_size + 10;
buffer = PHRQ_malloc(max_size);
if (buffer == NULL) malloc_error();
/*
* Send message to processor
*/
position = 0;
int i = ints.size();
int *int_array = new int[i];
int d = doubles.size();
double *double_array = new double[d];
for (int j = 0; j < i; j++) {
int_array[j] = ints[j];
}
for (int j = 0; j < d; j++) {
double_array[j] = doubles[j];
}
MPI_Send(&max_size, 1, MPI_INT, task_number, 0, MPI_COMM_WORLD);
MPI_Pack(&i, 1, MPI_INT, buffer, max_size, &position, MPI_COMM_WORLD);
MPI_Pack(&int_array, i, MPI_INT, buffer, max_size, &position, MPI_COMM_WORLD);
MPI_Pack(&d, 1, MPI_INT, buffer, max_size, &position, MPI_COMM_WORLD);
MPI_Pack(&double_array, d, MPI_DOUBLE, buffer, max_size, &position, MPI_COMM_WORLD);
MPI_Send(buffer, position, MPI_PACKED, task_number, 0, MPI_COMM_WORLD);
buffer = (void *) free_check_null(buffer);
delete[] int_array;
delete[] double_array;
}
/* ---------------------------------------------------------------------- */
void cxxSolution::mpi_recv(int task_number)
/* ---------------------------------------------------------------------- */
{
MPI_Status mpi_status;
/*
* Malloc space for a buffer
*/
int max_size;
// buffer size
MPI_Recv(&max_size, 1, MPI_INT, task_number, 0, MPI_COMM_WORLD, &mpi_status);
void *buffer = PHRQ_malloc(max_size);
if (buffer == NULL) malloc_error();
/*
* Recieve solution
*/
MPI_Recv(buffer, max_size, MPI_PACKED, task_number, 0, MPI_COMM_WORLD, &mpi_status);
int position = 0;
int msg_size;
MPI_Get_count(&mpi_status, MPI_PACKED, &msg_size);
/* Unpack ints */
int count_ints;
MPI_Unpack(buffer, msg_size, &position, &count_ints, 1, MPI_INT, MPI_COMM_WORLD);
int *ints = new int[count_ints];
MPI_Unpack(buffer, msg_size, &position, ints, count_ints, MPI_INT, MPI_COMM_WORLD);
/* Unpack doubles */
int count_doubles;
MPI_Unpack(buffer, msg_size, &position, &count_doubles, 1, MPI_INT, MPI_COMM_WORLD);
double *doubles = new double[count_doubles];
MPI_Unpack(buffer, msg_size, &position, doubles, count_doubles, MPI_DOUBLE, MPI_COMM_WORLD);
buffer = free_check_null(buffer);
/*
* Make list of list of ints and doubles from solution structure
* This list is not the complete structure, but only enough
* for batch-reaction, advection, and transport calculations
*/
int i = 0;
int d = 0;
/* int new_def; */
/* solution_ptr->new_def = FALSE; */
/* int n_user; */
this->n_user = ints[i++];
/* int n_user_end; */
this->n_user_end = this->n_user;
/*debugging*/
//this->description = (char *) free_check_null(this->description);
//this->description = string_duplicate(" ");
this->description = " ";
this->tc = doubles[d++];
this->ph = doubles[d++];
this->pe = doubles[d++];
this->mu = doubles[d++];
this->ah2o = doubles[d++];
this->total_h = doubles[d++];
this->total_o = doubles[d++];
this->cb = doubles[d++];
this->mass_water = doubles[d++];
this->total_alkalinity = 0;
/*
* struct conc *totals;
*/
this->totals.mpi_unpack(ints, &i, doubles, &d);
/*
* struct master_activity *master_activity;
*/
this->master_activity.mpi_unpack(ints, &i, doubles, &d);
/*
* struct master_activity *species_gamma;
*/
this->species_gamma.mpi_unpack(ints, &i, doubles, &d);
delete[] ints;
delete[] doubles;
}
#endif
void cxxSolution::set_master_activity(char *string, double d)
{
this->master_activity[string] = d;
}
#ifdef SKIP
#include "../hst.h"
/* ---------------------------------------------------------------------- */
void cxxSolution::xsolution_save(int n)
/* ---------------------------------------------------------------------- */
{
/*
* Save solution composition into Solution class
*
* input: n is pointer number in solution
*/
this->set_description(" ");
this->n_user = n;
this->n_user_end = n;
this->tc = tc_x;
this->ph = ph_x;
this->pe = solution_pe_x;
this->mu = mu_x;
this->ah2o = ah2o_x;
this->total_h = total_h_x;
this->total_o = total_o_x;
this->cb = cb_x;
this->mass_water = mass_water_aq_x;
this->total_alkalinity = total_alkalinity;
/*
* Copy totals data
*/
for (int j = 2; j < count_total; j++) {
this->totals.insert(buffer[j].master->elt->name, buffer[j].master->total_primary);
}
for (int j = 0; j < count_activity_list; j++) {
this->master_activity.insert(activity_list[j].master->elt->name, activity_list[j].master->s->la);
}
if (pitzer_model == TRUE) {
for (int j= 0; j < count_s; j++) {
if (s[j]->lg != 0.0) {
this->species_gamma.insert(s[j]->name, s[j]->lg);
}
}
}
}
#endif
#include "ISolution.h"
#include "Exchange.h"
#include "Surface.h"
#include "PPassemblage.h"
#include "cxxKinetics.h"
#include "SSassemblage.h"
#include "GasPhase.h"
#include "Reaction.h"
#include "Temperature.h"
#include "StorageBin.h"
#include "NumKeyword.h"
#include <iostream> // std::cout std::cerr
//#include <strstream>
#include <sstream>
#include <fstream>
void test_classes(void)
{
/*
int i;
std::map<int, cxxSolution> Solutions;
cxxSolution soln(solution[0]);
Solutions[solution[0]->n_user] = soln;
bool b = Utilities::exists(Solutions, 1);
*/
/*
cxxEntityMap x;
cxxSolution soln(solution[0]);
cxxNumKeyword nk;
x[solution[0]->n_user] = soln;
*/
#ifdef SKIP
for (i=0; i < count_solution; i++) {
if (solution[i]->new_def == TRUE) {
cxxISolution sol(solution[i]);
solution[i] = (struct solution *) solution_free(solution[i]);
solution[i] = sol.cxxISolution2solution();
struct solution *soln_ptr;
soln_ptr = solution[i];
soln_ptr = solution[i];
} else {
std::ostringstream oss;
cxxSolution sol(solution[i]);
solution[i] = (struct solution *) solution_free(solution[i]);
sol.dump_raw(oss, 0);
//std::fstream myfile("t");
//CParser cparser(myfile, std::cout, std::cerr);
cxxSolution sol1;
std::string keyInput = oss.str();
std::istringstream iss(keyInput);
CParser cparser(iss, oss, std::cerr);
//For testing, need to read line to get started
std::vector<std::string> vopts;
std::istream::pos_type next_char;
cparser.get_option(vopts, next_char);
sol1.read_raw(cparser);
solution[i] = sol1.cxxSolution2solution();
}
}
for (i=0; i < count_exchange; i++) {
if (exchange[i].new_def != TRUE) {
std::ostringstream oss;
cxxExchange ex(&(exchange[i]));
ex.dump_raw(oss, 0);
std::cerr << oss.str();
cxxExchange ex1;
std::string keyInput = oss.str();
std::istringstream iss(keyInput);
CParser cparser(iss, oss, std::cerr);
//For testing, need to read line to get started
std::vector<std::string> vopts;
std::istream::pos_type next_char;
cparser.get_option(vopts, next_char);
ex1.read_raw(cparser);
struct exchange *exchange_ptr = ex1.cxxExchange2exchange();
exchange_free(&exchange[i]);
exchange_copy(exchange_ptr, &exchange[i], exchange_ptr->n_user);
exchange_free(exchange_ptr);
free_check_null(exchange_ptr);
}
}
for (i=0; i < count_surface; i++) {
if (surface[i].new_def != TRUE) {
std::ostringstream oss;
cxxSurface ex(&(surface[i]));
ex.dump_raw(oss, 0);
std::cerr << oss.str();
cxxSurface ex1;
std::string keyInput = oss.str();
std::istringstream iss(keyInput);
CParser cparser(iss, oss, std::cerr);
//For testing, need to read line to get started
std::vector<std::string> vopts;
std::istream::pos_type next_char;
cparser.get_option(vopts, next_char);
ex1.read_raw(cparser);
struct surface *surface_ptr = ex1.cxxSurface2surface();
surface_free(&surface[i]);
surface_copy(surface_ptr, &surface[i], surface_ptr->n_user);
surface_free(surface_ptr);
free_check_null(surface_ptr);
}
}
for (i=0; i < count_pp_assemblage; i++) {
if (pp_assemblage[i].new_def != TRUE) {
std::ostringstream oss;
cxxPPassemblage ex(&(pp_assemblage[i]));
ex.dump_raw(oss, 0);
std::cerr << oss.str();
cxxPPassemblage ex1;
std::string keyInput = oss.str();
std::istringstream iss(keyInput);
CParser cparser(iss, oss, std::cerr);
//For testing, need to read line to get started
std::vector<std::string> vopts;
std::istream::pos_type next_char;
cparser.get_option(vopts, next_char);
ex1.read_raw(cparser);
struct pp_assemblage *pp_assemblage_ptr = ex1.cxxPPassemblage2pp_assemblage();
pp_assemblage_free(&pp_assemblage[i]);
pp_assemblage_copy(pp_assemblage_ptr, &pp_assemblage[i], pp_assemblage_ptr->n_user);
pp_assemblage_free(pp_assemblage_ptr);
free_check_null(pp_assemblage_ptr);
}
}
for (i=0; i < count_kinetics; i++) {
std::ostringstream oss;
cxxKinetics ex(&(kinetics[i]));
ex.dump_raw(oss, 0);
std::cerr << oss.str();
cxxKinetics ex1;
std::string keyInput = oss.str();
std::istringstream iss(keyInput);
CParser cparser(iss, oss, std::cerr);
//For testing, need to read line to get started
std::vector<std::string> vopts;
std::istream::pos_type next_char;
cparser.get_option(vopts, next_char);
ex1.read_raw(cparser);
struct kinetics *kinetics_ptr = ex1.cxxKinetics2kinetics();
kinetics_free(&kinetics[i]);
kinetics_copy(kinetics_ptr, &kinetics[i], kinetics_ptr->n_user);
kinetics_free(kinetics_ptr);
free_check_null(kinetics_ptr);
}
for (i=0; i < count_s_s_assemblage; i++) {
if (s_s_assemblage[i].new_def != TRUE) {
std::ostringstream oss;
cxxSSassemblage ex(&(s_s_assemblage[i]));
ex.dump_raw(oss, 0);
std::cerr << oss.str();
cxxSSassemblage ex1;
std::string keyInput = oss.str();
std::istringstream iss(keyInput);
CParser cparser(iss, oss, std::cerr);
//For testing, need to read line to get started
std::vector<std::string> vopts;
std::istream::pos_type next_char;
cparser.get_option(vopts, next_char);
ex1.read_raw(cparser);
struct s_s_assemblage *s_s_assemblage_ptr = ex1.cxxSSassemblage2s_s_assemblage();
s_s_assemblage_free(&s_s_assemblage[i]);
s_s_assemblage_copy(s_s_assemblage_ptr, &s_s_assemblage[i], s_s_assemblage_ptr->n_user);
s_s_assemblage_free(s_s_assemblage_ptr);
free_check_null(s_s_assemblage_ptr);
}
}
for (i=0; i < count_gas_phase; i++) {
if (gas_phase[i].new_def != TRUE) {
std::ostringstream oss;
cxxGasPhase ex(&(gas_phase[i]));
ex.dump_raw(oss, 0);
std::cerr << oss.str();
cxxGasPhase ex1;
std::string keyInput = oss.str();
std::istringstream iss(keyInput);
CParser cparser(iss, oss, std::cerr);
//For testing, need to read line to get started
std::vector<std::string> vopts;
std::istream::pos_type next_char;
cparser.get_option(vopts, next_char);
ex1.read_raw(cparser);
struct gas_phase *gas_phase_ptr = ex1.cxxGasPhase2gas_phase();
gas_phase_free(&gas_phase[i]);
gas_phase_copy(gas_phase_ptr, &gas_phase[i], gas_phase_ptr->n_user);
gas_phase_free(gas_phase_ptr);
free_check_null(gas_phase_ptr);
}
}
for (i=0; i < count_irrev; i++) {
std::ostringstream oss;
cxxReaction ex(&(irrev[i]));
ex.dump_raw(oss, 0);
std::cerr << oss.str();
cxxReaction ex1;
std::string keyInput = oss.str();
std::istringstream iss(keyInput);
CParser cparser(iss, oss, std::cerr);
//For testing, need to read line to get started
std::vector<std::string> vopts;
std::istream::pos_type next_char;
cparser.get_option(vopts, next_char);
ex1.read_raw(cparser);
struct irrev *irrev_ptr = ex1.cxxReaction2irrev();
irrev_free(&irrev[i]);
irrev_copy(irrev_ptr, &irrev[i], irrev_ptr->n_user);
irrev_free(irrev_ptr);
free_check_null(irrev_ptr);
}
for (i=0; i < count_mix; i++) {
std::ostringstream oss;
cxxMix ex(&(mix[i]));
ex.dump_raw(oss, 0);
std::cerr << oss.str();
cxxMix ex1;
std::string keyInput = oss.str();
std::istringstream iss(keyInput);
CParser cparser(iss, oss, std::cerr);
//For testing, need to read line to get started
std::vector<std::string> vopts;
std::istream::pos_type next_char;
cparser.get_option(vopts, next_char);
ex1.read_raw(cparser);
struct mix *mix_ptr = ex1.cxxMix2mix();
mix_free(&mix[i]);
mix_copy(mix_ptr, &mix[i], mix_ptr->n_user);
mix_free(mix_ptr);
free_check_null(mix_ptr);
}
for (i=0; i < count_temperature; i++) {
std::ostringstream oss;
cxxTemperature ex(&(temperature[i]));
ex.dump_raw(oss, 0);
std::cerr << oss.str();
cxxTemperature ex1;
std::string keyInput = oss.str();
std::istringstream iss(keyInput);
CParser cparser(iss, oss, std::cerr);
//For testing, need to read line to get started
std::vector<std::string> vopts;
std::istream::pos_type next_char;
cparser.get_option(vopts, next_char);
ex1.read_raw(cparser);
struct temperature *temperature_ptr = ex1.cxxTemperature2temperature();
temperature_free(&temperature[i]);
temperature_copy(temperature_ptr, &temperature[i], temperature_ptr->n_user);
temperature_free(temperature_ptr);
free_check_null(temperature_ptr);
}
#endif
{
// get all c storage
cxxStorageBin cstorage;
cstorage.import_phreeqc();
//std::ostringstream oss;
//cstorage.dump_raw(oss, 0);
//write it out
std::fstream myfile;
myfile.open("tfile", std::ios_base::out);
cstorage.dump_raw(myfile, 0);
myfile.close();
}
{
// empty storage bin
cxxStorageBin cstorage;
// fstream
std::fstream myfile;
myfile.open("tfile", std::ios_base::in);
// ostream
std::ostringstream oss;
// parser
CParser cparser(myfile, oss, std::cerr);
cstorage.read_raw(cparser);
//std::cerr << oss.str();
// read it back
}
}
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