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Can read a solution result from Orchestra.cxx
Now will write routines to put results into unknown structures so that results can be printed. git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2166 1feff8c3-07ed-0310-ac33-dd36852eb9cd
This commit is contained in:
David L Parkhurst
parent
1848045bd9
commit
ea61d055f0
150
ISolution.cxx
150
ISolution.cxx
@ -30,6 +30,7 @@ units("mMol/kgw")
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{
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density = 1.0;
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default_pe = -1;
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pes = NULL;
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}
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cxxISolution::cxxISolution(struct solution *solution_ptr)
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@ -419,7 +420,7 @@ void cxxISolution::dump_xml(std::ostream& os, unsigned int indent)const
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}
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#endif
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void cxxISolution::ORCH_write_chemistry(std::ostringstream &chemistry_dat)
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void cxxISolution::ORCH_write_chemistry(std::ostream &chemistry_dat)
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{
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this->ORCH_write_chemistry_water(chemistry_dat);
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this->ORCH_write_chemistry_primary(chemistry_dat);
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@ -430,7 +431,7 @@ void cxxISolution::ORCH_write_chemistry(std::ostringstream &chemistry_dat)
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}
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void cxxISolution::ORCH_write_chemistry_water(std::ostringstream &chemistry_dat)
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void cxxISolution::ORCH_write_chemistry_water(std::ostream &chemistry_dat)
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{
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//
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// Write water entities
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@ -488,7 +489,7 @@ void cxxISolution::ORCH_write_chemistry_water(std::ostringstream &chemistry_dat)
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chemistry_dat << std::endl;
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}
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void cxxISolution::ORCH_write_chemistry_primary(std::ostringstream &chemistry_dat)
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void cxxISolution::ORCH_write_chemistry_primary(std::ostream &chemistry_dat)
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{
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chemistry_dat << std::endl << "//********* The primary species" << std::endl;
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//
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@ -535,7 +536,7 @@ void cxxISolution::ORCH_write_chemistry_primary(std::ostringstream &chemistry_da
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chemistry_dat << std::endl;
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}
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void cxxISolution::ORCH_write_chemistry_total_O_H(std::ostringstream &chemistry_dat)
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void cxxISolution::ORCH_write_chemistry_total_O_H(std::ostream &chemistry_dat)
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{
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chemistry_dat << std::endl << "//********* Define total hydrogen and oxygen" << std::endl;
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// Define total hydrogen, total oxygen, and difference
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@ -587,7 +588,7 @@ void cxxISolution::ORCH_write_chemistry_total_O_H(std::ostringstream &chemistry_
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chemistry_dat << std::endl;
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}
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void cxxISolution::ORCH_write_chemistry_alkalinity(std::ostringstream &chemistry_dat)
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void cxxISolution::ORCH_write_chemistry_alkalinity(std::ostream &chemistry_dat)
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{
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chemistry_dat << std::endl << "//********* Alkalinity definitions" << std::endl;
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//
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@ -655,7 +656,7 @@ void cxxISolution::ORCH_write_chemistry_alkalinity(std::ostringstream &chemistry
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}
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}
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}
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void cxxISolution::ORCH_write_chemistry_species(std::ostringstream &chemistry_dat)
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void cxxISolution::ORCH_write_chemistry_species(std::ostream &chemistry_dat)
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{
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chemistry_dat << std::endl << "//********* Aqueous species" << std::endl;
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//
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@ -690,7 +691,7 @@ void cxxISolution::ORCH_write_chemistry_species(std::ostringstream &chemistry_da
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}
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chemistry_dat << std::endl;
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}
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void cxxISolution::ORCH_write_chemistry_minerals(std::ostringstream &chemistry_dat)
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void cxxISolution::ORCH_write_chemistry_minerals(std::ostream &chemistry_dat)
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{
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chemistry_dat << std::endl << "//********* Adjustments to mineral equilibrium" << std::endl;
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//
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@ -731,7 +732,7 @@ void cxxISolution::ORCH_write_chemistry_minerals(std::ostringstream &chemistry_d
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}
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}
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}
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void cxxISolution::ORCH_write_input(std::ostringstream &input_dat)
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void cxxISolution::ORCH_write_input(std::ostream &input_dat)
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{
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@ -749,6 +750,8 @@ void cxxISolution::ORCH_write_input(std::ostringstream &input_dat)
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//s_oss << "SOLUTION_RAW " << this->n_user << " " << this->description << std::endl;
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//s_oss << "-temp " << this->tc << std::endl;
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headings << "tempc\t";
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data << this->tc << "\t";
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//s_oss << "-pH " << this->ph << std::endl;
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headings << "pH\t";
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@ -847,18 +850,39 @@ void cxxISolution::ORCH_write_input(std::ostringstream &input_dat)
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return;
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}
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void cxxISolution::ORCH_write_output(std::ostringstream &outstream)
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void cxxISolution::ORCH_write_output(std::ostream &outstream)
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{
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outstream << "Var:";
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outstream << "\tnr_iter";
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//
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// Write total concentrations in solution
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// Serialize solution
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//
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outstream << "\tstart_solution";
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//tc
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outstream << "\ttempc";
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//pH
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outstream << "\tpH";
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//pe
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outstream << "\tpe";
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//mu
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outstream << "\tI";
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//ah2o
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outstream << "\tH2O.act";
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//total_h;
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outstream << "\ttotal_hydrogen";
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//total_o;
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outstream << "\ttotal_oxygen";
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//cb
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outstream << "\tchargebalance";
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//mass_water;
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outstream << "\tH2O.diss";
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outstream << "\te-.diss";
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//total_alkalinity;
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outstream << "\tAlkalinity";
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//orchestra master variables
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outstream << "\tH+.diss";
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std::map<char *, cxxISolutionComp, CHARSTAR_LESS>::iterator iter = this->comps.begin();
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for(; iter != this->comps.end(); ++iter)
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outstream << "\te-.diss";
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//totals
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for(std::map<char *, cxxISolutionComp, CHARSTAR_LESS>::iterator iter = this->comps.begin(); iter != this->comps.end(); ++iter)
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{
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std::string name(iter->second.get_description());
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if (name == "H(1)" || name == "E" || name == "Alkalinity") continue;
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@ -871,8 +895,21 @@ void cxxISolution::ORCH_write_output(std::ostringstream &outstream)
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assert(s_ptr != NULL);
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outstream << "\t" << s_ptr->name << ".diss";
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}
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outstream << "\tchargebalance";
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outstream<< "\tI";
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outstream << "\tend_totals";
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for(std::map<char *, cxxISolutionComp, CHARSTAR_LESS>::iterator iter = this->comps.begin(); iter != this->comps.end(); ++iter)
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{
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std::string name(iter->second.get_description());
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if (name == "H(1)" || name == "E" || name == "Alkalinity") continue;
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struct element *elt;
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char *element_name = string_hsave(name.c_str());
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elt = element_store(element_name);
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assert(elt != NULL);
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struct species *s_ptr;
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s_ptr = elt->master->s;
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assert(s_ptr != NULL);
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outstream << "\t" << s_ptr->name << ".act";
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}
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outstream << "\tend_master_activities";
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//
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// Write all species activities and concentrations
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//
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@ -883,6 +920,89 @@ void cxxISolution::ORCH_write_output(std::ostringstream &outstream)
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std::replace(name.begin(), name.end(), ')', ']');
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outstream << "\t" << name.c_str() << ".act" << "\t" << name.c_str() << ".con";
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}
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outstream << "\tend_species";
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outstream << std::endl;
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return;
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}
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/* ---------------------------------------------------------------------- */
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int
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initial_solutions (int print)
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/* ---------------------------------------------------------------------- */
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{
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/*
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* Go through list of solutions, make initial solution calculations
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* for any marked "new".
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*/
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int i, converge, converge1;
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int n, last, n_user, print1;
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char token[2 * MAX_LENGTH];
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state = INITIAL_SOLUTION;
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set_use ();
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for (n = 0; n < count_solution; n++)
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{
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initial_solution_isotopes = FALSE;
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if (solution[n] != NULL && solution[n]->new_def == TRUE)
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{
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if (print1 == TRUE && print == TRUE)
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{
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dup_print ("Beginning of initial solution calculations.", TRUE);
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print1 = FALSE;
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}
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if (print == TRUE)
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{
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sprintf (token, "Initial solution %d.\t%.350s", solution[n]->n_user,
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solution[n]->description);
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dup_print (token, FALSE);
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}
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use.solution_ptr = solution[n];
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prep ();
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k_temp (solution[n]->tc);
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set (TRUE);
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converge = model ();
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if (converge == ERROR && diagonal_scale == FALSE)
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{
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diagonal_scale = TRUE;
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set (TRUE);
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converge = model ();
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diagonal_scale = FALSE;
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}
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converge1 = check_residuals ();
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sum_species ();
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add_isotopes (solution[n]);
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punch_all ();
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print_all ();
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/* free_model_allocs(); */
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if (converge == ERROR || converge1 == ERROR)
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{
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error_msg ("Model failed to converge for initial solution.", STOP);
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}
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n_user = solution[n]->n_user;
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last = solution[n]->n_user_end;
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/* copy isotope data */
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if (solution[n]->count_isotopes > 0)
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{
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count_isotopes_x = solution[n]->count_isotopes;
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isotopes_x =
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(struct isotope *) PHRQ_realloc (isotopes_x,
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(size_t) count_isotopes_x *
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sizeof (struct isotope));
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if (isotopes_x == NULL)
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malloc_error ();
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memcpy (isotopes_x, solution[n]->isotopes,
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(size_t) count_isotopes_x * sizeof (struct isotope));
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}
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else
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{
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count_isotopes_x = 0;
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}
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xsolution_save (n_user);
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for (i = n_user + 1; i <= last; i++)
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{
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solution_duplicate (n_user, i);
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}
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}
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}
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initial_solution_isotopes = FALSE;
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return (OK);
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}
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18
ISolution.h
18
ISolution.h
@ -41,9 +41,9 @@ public:
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//void dump_xml(std::ostream& os, unsigned int indent = 0)const;
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void ConvertUnits();
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void ORCH_write_chemistry(std::ostringstream &chemistry_dat);
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void ORCH_write_input(std::ostringstream &input_dat);
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void ORCH_write_output(std::ostringstream &input_dat);
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void ORCH_write_chemistry(std::ostream &chemistry_dat);
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void ORCH_write_input(std::ostream &input_dat);
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void ORCH_write_output(std::ostream &input_dat);
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void print();
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protected:
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friend class cxxISolutionComp; // for this->pe access
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@ -57,12 +57,12 @@ public:
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//static std::map<int, cxxISolution>& map;
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private:
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void ORCH_write_chemistry_water(std::ostringstream &chemistry_dat);
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void ORCH_write_chemistry_primary(std::ostringstream &chemistry_dat);
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void ORCH_write_chemistry_total_O_H(std::ostringstream &chemistry_dat);
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void ORCH_write_chemistry_alkalinity(std::ostringstream &chemistry_dat);
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void ORCH_write_chemistry_species(std::ostringstream &chemistry_dat);
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void ORCH_write_chemistry_minerals(std::ostringstream &chemistry_dat);
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void ORCH_write_chemistry_water(std::ostream &chemistry_dat);
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void ORCH_write_chemistry_primary(std::ostream &chemistry_dat);
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void ORCH_write_chemistry_total_O_H(std::ostream &chemistry_dat);
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void ORCH_write_chemistry_alkalinity(std::ostream &chemistry_dat);
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void ORCH_write_chemistry_species(std::ostream &chemistry_dat);
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void ORCH_write_chemistry_minerals(std::ostream &chemistry_dat);
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};
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#endif // !defined(ISOLUTION_H_INCLUDED)
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84
Solution.cxx
84
Solution.cxx
@ -343,8 +343,8 @@ void cxxSolution::dump_xml(std::ostream& s_oss, unsigned int indent)const
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s_oss << indent1;
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s_oss << "soln_total_o=\"" << this->total_o << "\"" << std::endl;
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s_oss << indent1;
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s_oss << indent1;
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s_oss << "soln_cb=\"" << this->cb << "\"" << std::endl;
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s_oss << indent1;
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@ -446,7 +446,7 @@ void cxxSolution::dump_raw(std::ostream& s_oss, unsigned int indent)const
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s_oss << indent1;
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s_oss << "-total_o " << this->total_o << std::endl;
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// new identifier
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// new identifier
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s_oss << indent1;
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s_oss << "-cb " << this->cb << std::endl;
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@ -819,7 +819,8 @@ void cxxSolution::read_raw(CParser& parser)
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break;
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}
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if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD) break;
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if (opt == CParser::OPT_EOF || opt == CParser::OPT_KEYWORD) break;
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}
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// all members must be defined
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if (tc_defined == false) {
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@ -862,7 +863,7 @@ void cxxSolution::read_raw(CParser& parser)
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parser.incr_input_error();
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parser.error_msg("Total alkalinity not defined for SOLUTION_RAW input.", CParser::OT_CONTINUE);
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}
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return;
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return;
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}
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void cxxSolution::zero()
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@ -963,6 +964,79 @@ double cxxSolution::get_master_activity(char *string)const
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return(it->second);
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}
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}
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void cxxSolution::read_orchestra(std::vector <std::pair <std::string, double> > output_vector, std::vector < std::pair < std::string, double > >::iterator &it)
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{
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this->tc = it->second; it++;
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this->ph = it->second; it++;
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this->pe = it->second; it++;
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this->mu = it->second; it++;
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this->ah2o = it->second; it++;
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this->total_h = it->second; it++;
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this->total_o = it->second; it++;
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this->cb = it->second; it++;
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this->mass_water = it->second * gfw_water; it++;
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this->total_alkalinity = it->second; it++;
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it++; //orch total H+
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it++; //orch total e-
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//cxxNameDouble totals;
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char token[MAX_LENGTH];
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while (it->first.compare("end_totals") != 0)
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{
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strcpy(token, it->first.c_str());
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replace(".diss","",token);
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struct species *s_ptr = s_search(token);
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if (s_ptr == NULL) error_msg("Species not found in orchestra read", STOP);
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if (s_ptr->secondary != NULL)
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{
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this->totals[s_ptr->secondary->elt->name] = it->second;
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} else if (s_ptr->primary != NULL)
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{
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this->totals[s_ptr->primary->elt->name] = it->second;
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} else
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{
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error_msg("Species not secondary or primary master species in orchestra read", STOP);
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}
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it++;
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}
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//cxxNameDouble master_activity;
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it++;
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while (it->first.compare("end_master_activities") != 0)
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{
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strcpy(token, it->first.c_str());
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replace(".act","",token);
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struct species *s_ptr = s_search(token);
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if (s_ptr == NULL) error_msg("Species not found in orchestra read", STOP);
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if (s_ptr->secondary != NULL)
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{
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this->master_activity[s_ptr->secondary->elt->name] = log10(it->second);
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} else if (s_ptr->primary != NULL)
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{
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this->master_activity[s_ptr->primary->elt->name] = log10(it->second);
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} else
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{
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error_msg("Species not secondary or primary master species in orchestra read", STOP);
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}
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it++;
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}
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//cxxNameDouble species_gamma;
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//cxxSolutionIsotopeList isotopes;
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//
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// Also process aqueous species data
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//
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it++;
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while (it->first.compare("end_species") != 0)
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{
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strcpy(token, it->first.c_str());
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replace(".act","",token);
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while (replace("[","(", token));
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while (replace("]",")", token));
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struct species *s_ptr = s_search(token);
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if (s_ptr == NULL) error_msg("Species not found in orchestra read", STOP);
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s_ptr->la = log10(it->second); it++;
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s_ptr->lm = log10(it->second); it++;
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s_ptr->lg = s_ptr->la - s_ptr->lm;
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}
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}
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#ifdef USE_MPI
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#include <mpi.h>
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/* ---------------------------------------------------------------------- */
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@ -84,6 +84,7 @@ public:
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void read_raw(CParser& parser);
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void multiply(double extensive);
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void read_orchestra(std::vector <std::pair <std::string, double>> output_vector, std::vector < std::pair < std::string, double > >::iterator &it);
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#ifdef USE_MPI
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