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d7222e4f0b
f627828f Merge commit 'c1c1f286b61ca73ae3204c7fa4831bb2e3066070' c1c1f286 Squashed 'phreeqcpp/' changes from b6a23a2..faf8144 d051e14c Merge remote-tracking branch 'usgs-coupled/master' 7ad5a592 50 apple clang 15 with c++11 or higher reports warnings wwritable strings in pbasiccpp (#57) git-subtree-dir: src git-subtree-split: f627828fb52a2880ff95d7c341dc335b856fd8c5
2162 lines
74 KiB
C++
2162 lines
74 KiB
C++
#ifndef _INC_PHREEQC_H
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#define _INC_PHREEQC_H
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#if defined(WIN32)
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# if defined(PHREEQCI_GUI)
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# ifndef WINVER
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# define WINVER 0x0400
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# endif
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# include <afx.h>
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# endif
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# include <windows.h>
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# if defined(PHREEQCI_GUI)
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# include "../../resource.h"
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# endif
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#endif
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#if defined(WIN32_MEMORY_DEBUG)
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#define _CRTDBG_MAP_ALLOC
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#include <crtdbg.h>
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#endif
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#ifndef boolean
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typedef unsigned char boolean;
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#endif
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/* ----------------------------------------------------------------------
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* INCLUDE FILES
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* ---------------------------------------------------------------------- */
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#include <iostream>
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#include <fstream>
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#include <sstream>
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#include <map>
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#include <string.h>
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#include <stdlib.h>
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#include <ctype.h>
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#include <cmath>
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#include <errno.h>
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#include <cfloat>
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#include "phrqtype.h"
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#include "cvdense.h"
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#include "runner.h"
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#include "dumper.h"
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#include "PHRQ_io.h"
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#include "SelectedOutput.h"
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#include "UserPunch.h"
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#ifdef MULTICHART
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#include "ChartHandler.h"
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#endif
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#include "Keywords.h"
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#include "Pressure.h"
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#include "cxxMix.h"
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#include "Use.h"
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#include "Surface.h"
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#ifdef SWIG_SHARED_OBJ
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#include "thread.h"
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#endif
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class cxxNameDouble;
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class cxxKinetics;
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class cxxKineticsComp;
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class cxxExchange;
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class cxxExchComp;
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class cxxGasPhase;
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class cxxTemperature;
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class cxxPPassemblage;
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class cxxPPassemblageComp;
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class cxxReaction;
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class cxxSolution;
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class cxxISolutionComp;
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class cxxSolutionIsotope;
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class cxxSSassemblage;
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class cxxSS;
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class cxxStorageBin;
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class PBasic;
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#include "global_structures.h"
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class Phreeqc
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{
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public:
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Phreeqc(PHRQ_io* io = NULL);
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Phreeqc(const Phreeqc& src);
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void InternalCopy(const Phreeqc* pSrc);
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Phreeqc& operator=(const Phreeqc& rhs);
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~Phreeqc(void);
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public:
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//
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// Phreeqc class methods
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//
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// advection.cpp -------------------------------
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int advection(void);
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// basicsubs.cpp -------------------------------
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int basic_compile(const char* commands, void** lnbase, void** vbase, void** lpbase);
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int basic_run(char* commands, void* lnbase, void* vbase, void* lpbase);
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void basic_free(void);
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#ifdef IPHREEQC_NO_FORTRAN_MODULE
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double basic_callback(double x1, double x2, const char* str);
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#else
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double basic_callback(double x1, double x2, const char* str);
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#endif
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void register_basic_callback(double (*fcn)(double x1, double x2, const char* str, void* cookie), void* cookie1);
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#ifdef IPHREEQC_NO_FORTRAN_MODULE
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void register_fortran_basic_callback(double (*fcn)(double* x1, double* x2, const char* str, size_t l));
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#else
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void register_fortran_basic_callback(double (*fcn)(double* x1, double* x2, const char* str, int l));
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#endif
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LDBLE activity(const char* species_name);
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LDBLE activity_coefficient(const char* species_name);
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LDBLE log_activity_coefficient(const char* species_name);
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LDBLE aqueous_vm(const char* species_name);
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LDBLE phase_vm(const char* phase_name);
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LDBLE diff_c(const char* species_name);
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LDBLE setdiff_c(const char * species_name, double d, double d_v_d);
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LDBLE flux_mcd(const char* species_name, int option);
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LDBLE sa_declercq(double type, double sa, double d, double m, double m0, double gfw);
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LDBLE calc_SC(void);
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/* VP: Density Start */
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LDBLE calc_dens(void);
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/* VP: Density End */
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LDBLE calc_logk_n(const char* name);
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LDBLE calc_logk_p(const char* name);
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LDBLE calc_logk_s(const char* name);
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LDBLE calc_deltah_s(const char* name);
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LDBLE calc_deltah_p(const char* name);
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LDBLE dh_a0(const char* name);
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LDBLE dh_bdot(const char* name);
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LDBLE calc_surface_charge(const char* surface_name);
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LDBLE calc_t_sc(const char* name);
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LDBLE diff_layer_total(const char* total_name, const char* surface_name);
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LDBLE edl_species(const char* surf_name, LDBLE* count, char*** names, LDBLE** moles, LDBLE* area, LDBLE* thickness);
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int get_edl_species(cxxSurfaceCharge& charge_ref);
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LDBLE equi_phase(const char* phase_name);
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LDBLE equi_phase_delta(const char* phase_name);
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LDBLE equivalent_fraction(const char* name, LDBLE* eq, std::string& elt_name);
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LDBLE find_gas_comp(const char* gas_comp_name);
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LDBLE find_gas_p(void);
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LDBLE find_gas_vm(void);
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LDBLE find_misc1(const char* ss_name);
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LDBLE find_misc2(const char* ss_name);
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LDBLE find_ss_comp(const char* ss_comp_name);
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LDBLE get_calculate_value(const char* name);
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char* iso_unit(const char* total_name);
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LDBLE iso_value(const char* total_name);
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LDBLE kinetics_moles(const char* kinetics_name);
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LDBLE kinetics_moles_delta(const char* kinetics_name);
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LDBLE log_activity(const char* species_name);
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LDBLE log_molality(const char* species_name);
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LDBLE molality(const char* species_name);
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LDBLE pressure(void);
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LDBLE pr_pressure(const char* phase_name);
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LDBLE pr_phi(const char* phase_name);
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LDBLE saturation_ratio(const char* phase_name);
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int saturation_index(const char* phase_name, LDBLE* iap, LDBLE* si);
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int solution_number(void);
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LDBLE solution_sum_secondary(const char* total_name);
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LDBLE sum_match_gases(const char* stemplate, const char* name);
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LDBLE sum_match_species(const char* stemplate, const char* name);
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LDBLE sum_match_ss(const char* stemplate, const char* name);
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int match_elts_in_species(const char* name, const char* stemplate);
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int extract_bracket(const char** string, char* bracket_string);
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LDBLE surf_total(const char* total_name, const char* surface_name);
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LDBLE surf_total_no_redox(const char* total_name, const char* surface_name);
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static int system_species_compare(const void* ptr1, const void* ptr2);
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static int system_species_compare_name(const void* ptr1, const void* ptr2);
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LDBLE system_total(const char* total_name, LDBLE* count, char*** names,
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char*** types, LDBLE** moles, int i);
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std::string kinetics_formula(std::string kinetics_name, cxxNameDouble& stoichiometry);
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std::string phase_formula(std::string phase_name, cxxNameDouble& stoichiometry);
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std::string species_formula(std::string phase_name, cxxNameDouble& stoichiometry);
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std::string phase_equation(std::string phase_name, std::vector<std::pair<std::string, double> >& stoichiometry);
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std::string species_equation(std::string species_name, std::vector<std::pair<std::string, double> >& stoichiometry);
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LDBLE list_ss(std::string ss_name, cxxNameDouble& composition);
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int system_total_elements(void);
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int system_total_si(void);
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int system_total_aq(void);
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int system_total_ex(void);
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int system_total_surf(void);
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int system_total_gas(void);
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int system_total_equi(void);
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int system_total_kin(void);
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int system_total_ss(void);
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int system_total_elt(const char* total_name);
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int system_total_elt_secondary(const char* total_name);
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LDBLE total(const char* total_name);
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LDBLE total_mole(const char* total_name);
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int system_total_solids(cxxExchange* exchange_ptr,
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cxxPPassemblage* pp_assemblage_ptr,
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cxxGasPhase* gas_phase_ptr,
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cxxSSassemblage* ss_assemblage_ptr,
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cxxSurface* surface_ptr);
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static LDBLE f_rho(LDBLE rho_old, void* cookie);
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static LDBLE f_Vm(LDBLE v1, void* cookie);
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LDBLE calc_solution_volume(void);
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// cl1.cpp -------------------------------
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int cl1(int k, int l, int m, int n,
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int nklmd, int n2d,
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LDBLE* q,
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int* kode, LDBLE toler,
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int* iter, LDBLE* x, LDBLE* res, LDBLE* error,
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LDBLE* cu, int* iu, int* s, int check);
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void cl1_space(int check, int n2d, int klm, int nklmd);
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// cl1mp.cpp -------------------------------
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int cl1mp(int k, int l, int m, int n,
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int nklmd, int n2d,
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LDBLE* q_arg,
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int* kode, LDBLE toler,
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int* iter, LDBLE* x_arg, LDBLE* res_arg, LDBLE* error,
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LDBLE* cu_arg, int* iu, int* s, int check, LDBLE censor_arg);
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// class_main.cpp -------------------------------
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int write_banner(void);
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/* default.cpp */
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public:
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//int close_input_files(void);
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//int close_output_files(void);
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//static int istream_getc(void* cookie);
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int process_file_names(int argc, char* argv[], std::istream** db_cookie,
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std::istream** input_cookie, int log);
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/* PHRQ_io_output.cpp */
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void screen_msg(const char* str);
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void echo_msg(const char* err_str);
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int warning_msg(const char* err_str);
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void set_forward_output_to_log(int value);
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int get_forward_output_to_log(void);
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// dump_ostream
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bool dump_open(const char* file_name);
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void dump_flush(void);
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void dump_close(void);
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void dump_msg(const char* str);
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// log_ostream
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bool log_open(const char* file_name);
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void log_flush(void);
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void log_close(void);
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void log_msg(const char* str);
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// error_ostream
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bool error_open(const char* file_name);
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void error_flush(void);
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void error_close(void);
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void error_msg(const char* str, bool stop = false);
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// output_ostream
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bool output_open(const char* file_name);
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void output_flush(void);
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void output_close(void);
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void output_msg(const char* str);
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// punch_ostream
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bool punch_open(const char* file_name, int n_user);
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void punch_flush(void);
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void punch_close(void);
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void punch_msg(const char* str);
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void fpunchf_heading(const char* name);
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void fpunchf(const char* name, const char* format, double d);
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void fpunchf(const char* name, const char* format, char* d);
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void fpunchf(const char* name, const char* format, int d);
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void fpunchf_user(int user_index, const char* format, double d);
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void fpunchf_user(int user_index, const char* format, char* d);
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int fpunchf_end_row(const char* format);
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// input.cpp -------------------------------
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int reading_database(void);
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void set_reading_database(int reading_database);
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int check_line(const char* string, int allow_empty, int allow_eof,
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int allow_keyword, int print);
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int check_line_impl(const char* string, int allow_empty,
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int allow_eof, int allow_keyword, int print);
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int get_line(void);
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//int get_logical_line(void* cookie, int* l);
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int read_database(void);
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int run_simulations(void);
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// integrate.cpp -------------------------------
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int calc_all_g(void);
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int calc_init_g(void);
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int initial_surface_water(void);
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int sum_diffuse_layer(cxxSurfaceCharge* surface_charge_ptr1);
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int calc_all_donnan(void);
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int calc_init_donnan(void);
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LDBLE calc_psi_avg(cxxSurfaceCharge * charge_ptr, LDBLE surf_chrg_eq, LDBLE nDbl, LDBLE f_free, std::vector<LDBLE> &zcorr);
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LDBLE g_function(LDBLE x_value);
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LDBLE midpnt(LDBLE x1, LDBLE x2, int n);
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void polint(LDBLE* xa, LDBLE* ya, int n, LDBLE xv, LDBLE* yv,
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LDBLE* dy);
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LDBLE qromb_midpnt(cxxSurfaceCharge* charge_ptr, LDBLE x1, LDBLE x2);
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// inverse.cpp -------------------------------
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int inverse_models(void);
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int add_to_file(const char* filename, const char* string);
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int bit_print(unsigned long bits, int l);
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int carbon_derivs(class inverse* inv_ptr);
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int check_isotopes(class inverse* inv_ptr);
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int check_solns(class inverse* inv_ptr);
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bool set_isotope_unknowns(class inverse* inv_ptrs);
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cxxSolutionIsotope* get_isotope(cxxSolution* solution_ptr, const char* elt);
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LDBLE get_inv_total(cxxSolution* solution_ptr, const char* elt);
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int isotope_balance_equation(class inverse* inv_ptr, int row, int n);
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int post_mortem(void);
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bool test_cl1_solution(void);
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unsigned long get_bits(unsigned long bits, int position, int number);
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unsigned long minimal_solve(class inverse* inv_ptr,
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unsigned long minimal_bits);
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void dump_netpath(class inverse* inv_ptr);
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int dump_netpath_pat(class inverse* inv_ptr);
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int next_set_phases(class inverse* inv_ptr, int first_of_model_size,
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int model_size);
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int phase_isotope_inequalities(class inverse* inv_ptr);
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int print_model(class inverse* inv_ptr);
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int punch_model_heading(class inverse* inv_ptr);
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int punch_model(class inverse* inv_ptr);
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void print_isotope(FILE* netpath_file, cxxSolution* solution_ptr,
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const char* elt, const char* string);
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void print_total(FILE* netpath_file, cxxSolution* solution_ptr,
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const char* elt, const char* string);
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void print_total_multi(FILE* netpath_file, cxxSolution* solution_ptr,
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const char* string, const char* elt0,
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const char* elt1, const char* elt2, const char* elt3,
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const char* elt4);
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void print_total_pat(FILE* netpath_file, const char* elt,
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const char* string);
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int range(class inverse* inv_ptr, unsigned long cur_bits);
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int save_bad(unsigned long bits);
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int save_good(unsigned long bits);
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int save_minimal(unsigned long bits);
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unsigned long set_bit(unsigned long bits, int position, int value);
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int setup_inverse(class inverse* inv_ptr);
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int set_initial_solution(int n_user_old, int n_user_new);
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int set_ph_c(class inverse* inv_ptr,
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int i, cxxSolution* soln_ptr_orig, int n_user_new,
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LDBLE d_alk, LDBLE ph_factor, LDBLE alk_factor);
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int shrink(class inverse* inv_ptr, LDBLE* array_in,
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LDBLE* array_out, int* k, int* l, int* m, int* n,
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unsigned long cur_bits, LDBLE* delta_l, int* col_back_l,
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int* row_back_l);
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int solve_inverse(class inverse* inv_ptr);
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int solve_with_mask(class inverse* inv_ptr, unsigned long cur_bits);
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int subset_bad(unsigned long bits);
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int subset_minimal(unsigned long bits);
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int superset_minimal(unsigned long bits);
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int write_optimize_names(class inverse* inv_ptr);
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// isotopes.cpp -------------------------------
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int add_isotopes(cxxSolution& solution_ptr);
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int calculate_values(void);
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int calculate_isotope_moles(class element* elt_ptr,
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cxxSolution* solution_ptr, LDBLE total_moles);
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LDBLE convert_isotope(class master_isotope* master_isotope_ptr, LDBLE ratio);
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int from_pcil(class master_isotope* master_isotope_ptr);
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int from_permil(class master_isotope* master_isotope_ptr, LDBLE major_total);
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int from_pct(class master_isotope* master_isotope_ptr, LDBLE major_total);
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int from_tu(class master_isotope* master_isotope_ptr);
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class calculate_value* calculate_value_alloc(void);
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int calculate_value_free(class calculate_value* calculate_value_ptr);
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class calculate_value* calculate_value_search(const char* name);
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class calculate_value* calculate_value_store(const char* name,
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int replace_if_found);
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class isotope_alpha* isotope_alpha_alloc(void);
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class isotope_alpha* isotope_alpha_search(const char* name);
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class isotope_alpha* isotope_alpha_store(const char* name,
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int replace_if_found);
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class isotope_ratio* isotope_ratio_alloc(void);
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class isotope_ratio* isotope_ratio_search(const char* name);
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class isotope_ratio* isotope_ratio_store(const char* name,
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int replace_if_found);
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class master_isotope* master_isotope_store(const char* name,
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int replace_if_found);
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class master_isotope* master_isotope_alloc(void);
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class master_isotope* master_isotope_search(const char* name);
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int print_initial_solution_isotopes(void);
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int print_isotope_ratios(void);
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int print_isotope_alphas(void);
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int punch_isotopes(void);
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int punch_calculate_values(void);
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int read_calculate_values(void);
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int read_isotopes(void);
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int read_isotope_ratios(void);
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int read_isotope_alphas(void);
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int calculate_value_init(class calculate_value* calculate_value_ptr);
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int isotope_alpha_init(class isotope_alpha* isotope_alpha_ptr);
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int isotope_ratio_init(class isotope_ratio* isotope_ratio_ptr);
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int master_isotope_init(class master_isotope* master_isotope_ptr);
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// kinetics.cpp -------------------------------
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void cvode_init(void);
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bool cvode_update_reactants(int i, int nsaver, bool save_it);
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int run_reactions(int i, LDBLE kin_time, int use_mix, LDBLE step_fraction);
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int set_and_run(int i, int use_mix, int use_kinetics, int nsaver,
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LDBLE step_fraction);
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int set_and_run_wrapper(int i, int use_mix, int use_kinetics, int nsaver,
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LDBLE step_fraction);
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int set_advection(int i, int use_mix, int use_kinetics, int nsaver);
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int free_cvode(void);
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public:
|
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static void f(integertype N, realtype t, N_Vector y, N_Vector ydot,
|
|
void* f_data);
|
|
static void Jac(integertype N, DenseMat J, RhsFn f, void* f_data, realtype t,
|
|
N_Vector y, N_Vector fy, N_Vector ewt, realtype h,
|
|
realtype uround, void* jac_data, long int* nfePtr,
|
|
N_Vector vtemp1, N_Vector vtemp2, N_Vector vtemp3);
|
|
|
|
int calc_final_kinetic_reaction(cxxKinetics* kinetics_ptr);
|
|
int calc_kinetic_reaction(cxxKinetics* kinetics_ptr,
|
|
LDBLE time_step);
|
|
bool limit_rates(cxxKinetics* kinetics_ptr);
|
|
int rk_kinetics(int i, LDBLE kin_time, int use_mix, int nsaver,
|
|
LDBLE step_fraction);
|
|
int set_reaction(int i, int use_mix, int use_kinetics);
|
|
int set_transport(int i, int use_mix, int use_kinetics, int nsaver);
|
|
int store_get_equi_reactants(int k, int kin_end);
|
|
|
|
// mainsubs.cpp -------------------------------
|
|
std::ifstream* open_input_stream(std::string query, std::string& default_name, std::ios_base::openmode mode, bool batch);
|
|
std::ofstream* open_output_stream(std::string query, std::string& default_name, std::ios_base::openmode mode, bool batch);
|
|
int copy_entities(void);
|
|
void do_mixes(void);
|
|
void initialize(void);
|
|
int initial_exchangers(int print);
|
|
int initial_gas_phases(int print);
|
|
int initial_solutions(int print);
|
|
int step_save_exch(int n_user);
|
|
int step_save_surf(int n_user);
|
|
int initial_surfaces(int print);
|
|
int reactions(void);
|
|
int saver(void);
|
|
int xsolution_save(int k_user);
|
|
int xexchange_save(int n_user);
|
|
int xgas_save(int n_user);
|
|
int xpp_assemblage_save(int n_user);
|
|
int xss_assemblage_save(int n_user);
|
|
int xsurface_save(int n_user);
|
|
int do_initialize(void);
|
|
int do_status(void);
|
|
void save_init(int i);
|
|
int copy_use(int i);
|
|
int set_use(void);
|
|
|
|
// model.cpp -------------------------------
|
|
int check_residuals(void);
|
|
int free_model_allocs(void);
|
|
int ineq(int kode);
|
|
int model(void);
|
|
int jacobian_sums(void);
|
|
int mb_gases(void);
|
|
int mb_ss(void);
|
|
int mb_sums(void);
|
|
int molalities(int allow_overflow);
|
|
int reset(void);
|
|
int residuals(void);
|
|
int set(int initial);
|
|
int sum_species(void);
|
|
int surface_model(void);
|
|
LDBLE ss_root(LDBLE a0, LDBLE a1, LDBLE kc, LDBLE kb, LDBLE xcaq,
|
|
LDBLE xbaq);
|
|
LDBLE ss_halve(LDBLE a0, LDBLE a1, LDBLE x0, LDBLE x1, LDBLE kc,
|
|
LDBLE kb, LDBLE xcaq, LDBLE xbaq);
|
|
LDBLE ss_f(LDBLE xb, LDBLE a0, LDBLE a1, LDBLE kc, LDBLE kb,
|
|
LDBLE xcaq, LDBLE xbaq);
|
|
int numerical_jacobian(void);
|
|
void set_inert_moles(void);
|
|
void unset_inert_moles(void);
|
|
#ifdef SLNQ
|
|
int add_trivial_eqns(int rows, int cols, LDBLE* matrix);
|
|
//int slnq(int n, LDBLE * a, LDBLE * delta, int ncols, int print);
|
|
#endif
|
|
int calc_gas_pressures(void);
|
|
int calc_fixed_volume_gas_pressures(void);
|
|
int calc_ss_fractions(void);
|
|
int gammas(LDBLE mu);
|
|
int gammas_a_f(int i);
|
|
int initial_guesses(void);
|
|
int revise_guesses(void);
|
|
int ss_binary(cxxSS* ss_ptr);
|
|
int ss_ideal(cxxSS* ss_ptr);
|
|
|
|
// parse.cpp -------------------------------
|
|
int check_eqn(int association);
|
|
int get_charge(char* charge, size_t charge_size, LDBLE* z);
|
|
int get_elt(const char** t_ptr, std::string& element, int* i);
|
|
int get_elts_in_species(const char** t_ptr, LDBLE coef);
|
|
int get_num(const char** t_ptr, LDBLE* num);
|
|
int get_secondary_in_species(const char** t_ptr, LDBLE coef);
|
|
int parse_eq(char* eqn, std::vector<class elt_list>& new_elt_list, int association);
|
|
int get_coef(LDBLE* coef, const char** eqnaddr);
|
|
int get_secondary(const char** t_ptr, char* element, int* i);
|
|
int get_species(const char** ptr);
|
|
|
|
// phqalloc.cpp -------------------------------
|
|
public:
|
|
#if !defined(NDEBUG)
|
|
void* PHRQ_malloc(size_t, const char*, int);
|
|
void* PHRQ_calloc(size_t, size_t, const char*, int);
|
|
void* PHRQ_realloc(void*, size_t, const char*, int);
|
|
#else
|
|
void* PHRQ_malloc(size_t);
|
|
void* PHRQ_calloc(size_t, size_t);
|
|
void* PHRQ_realloc(void*, size_t);
|
|
#endif
|
|
void PHRQ_free(void* ptr);
|
|
void PHRQ_free_all(void);
|
|
|
|
public:
|
|
|
|
// pitzer.cpp -------------------------------
|
|
class pitz_param* pitz_param_read(char* string, int n);
|
|
void pitz_param_store(class pitz_param* pzp_ptr);
|
|
void sit_param_store(class pitz_param* pzp_ptr);
|
|
class pitz_param* pitz_param_copy(const class pitz_param* src);
|
|
class theta_param* theta_param_search(LDBLE zj, LDBLE zk);
|
|
void pitzer_make_lists(void);
|
|
int gammas_pz(bool exch_a_f);
|
|
int model_pz(void);
|
|
int pitzer(void);
|
|
int pitzer_clean_up(void);
|
|
int pitzer_init(void);
|
|
int pitzer_tidy(void);
|
|
int read_pitzer(void);
|
|
int set_pz(int initial);
|
|
int calc_pitz_param(class pitz_param* pz_ptr, LDBLE TK, LDBLE TR);
|
|
int check_gammas_pz(void);
|
|
int ISPEC(const char* name);
|
|
LDBLE G(LDBLE Y);
|
|
LDBLE GP(LDBLE Y);
|
|
int ETHETAS(LDBLE ZJ, LDBLE ZK, LDBLE I, LDBLE* etheta,
|
|
LDBLE* ethetap);
|
|
void ETHETA_PARAMS(LDBLE X, LDBLE& JAY, LDBLE& JPRIME);
|
|
int pitzer_initial_guesses(void);
|
|
int pitzer_revise_guesses(void);
|
|
int PTEMP(LDBLE TK);
|
|
int jacobian_pz(void);
|
|
|
|
// prep.cpp -------------------------------
|
|
int add_potential_factor(void);
|
|
int add_cd_music_factors(int n);
|
|
int add_surface_charge_balance(void);
|
|
int add_cd_music_charge_balances(int i);
|
|
int build_gas_phase(void);
|
|
int build_fixed_volume_gas(void);
|
|
int build_jacobian_sums(int k);
|
|
int build_mb_sums(void);
|
|
int build_min_exch(void);
|
|
int build_model(void);
|
|
int build_pure_phases(void);
|
|
int build_ss_assemblage(void);
|
|
int build_solution_phase_boundaries(void);
|
|
int build_species_list(int n);
|
|
int build_min_surface(void);
|
|
LDBLE calc_lk_phase(phase* p_ptr, LDBLE TK, LDBLE pa);
|
|
LDBLE calc_PR(std::vector<class phase*> phase_ptrs, LDBLE P, LDBLE TK, LDBLE V_m);
|
|
LDBLE calc_PR();
|
|
int calc_vm(LDBLE tc, LDBLE pa);
|
|
LDBLE calc_vm0(const char *species_name, LDBLE tc, LDBLE pa, LDBLE mu);
|
|
int clear(void);
|
|
int convert_units(cxxSolution* solution_ptr);
|
|
class unknown* find_surface_charge_unknown(std::string& str_ptr, int plane);
|
|
std::vector<class master*> get_list_master_ptrs(const char* cptr, class master* master_ptr);
|
|
int inout(void);
|
|
int is_special(class species* spec);
|
|
int mb_for_species_aq(int n);
|
|
int mb_for_species_ex(int n);
|
|
int mb_for_species_surf(int n);
|
|
int quick_setup(void);
|
|
int resetup_master(void);
|
|
int save_model(void);
|
|
int setup_exchange(void);
|
|
int setup_gas_phase(void);
|
|
int setup_fixed_volume_gas(void);
|
|
int setup_master_rxn(const std::vector<class master*>& master_ptr_list,
|
|
const std::string& pe_rxn);
|
|
int setup_pure_phases(void);
|
|
int adjust_setup_pure_phases(void);
|
|
int setup_related_surface(void);
|
|
int setup_ss_assemblage(void);
|
|
int setup_solution(void);
|
|
int adjust_setup_solution(void);
|
|
int setup_surface(void);
|
|
int setup_unknowns(void);
|
|
int store_dn(int k, LDBLE* source, int row, LDBLE coef_in,
|
|
LDBLE* gamma_source);
|
|
int store_jacob(LDBLE* source, LDBLE* target, LDBLE coef);
|
|
int store_jacob0(int row, int column, LDBLE coef);
|
|
int store_mb(LDBLE* source, LDBLE* target, LDBLE coef);
|
|
int store_mb_unknowns(class unknown* unknown_ptr, LDBLE* LDBLE_ptr,
|
|
LDBLE coef, LDBLE* gamma_ptr);
|
|
int store_sum_deltas(LDBLE* source, LDBLE* target, LDBLE coef);
|
|
int tidy_redox(void);
|
|
int write_mb_eqn_x(void);
|
|
int write_mb_for_species_list(int n);
|
|
int write_mass_action_eqn_x(int stop);
|
|
|
|
int check_same_model(void);
|
|
int k_temp(LDBLE tc, LDBLE pa);
|
|
LDBLE k_calc(LDBLE* logk, LDBLE tempk, LDBLE presPa);
|
|
int prep(void);
|
|
int reprep(void);
|
|
int rewrite_master_to_secondary(class master* master_ptr1,
|
|
class master* master_ptr2);
|
|
int switch_bases(void);
|
|
int write_phase_sys_total(int n);
|
|
|
|
// print.cpp -------------------------------
|
|
char* sformatf(const char* format, ...);
|
|
int array_print(LDBLE* array_l, int row_count, int column_count,
|
|
int max_column_count);
|
|
int set_pr_in_false(void);
|
|
int print_all(void);
|
|
int print_exchange(void);
|
|
int print_gas_phase(void);
|
|
int print_master_reactions(void);
|
|
int print_species(void);
|
|
int print_surface(void);
|
|
int print_user_print(void);
|
|
int punch_all(void);
|
|
int print_alkalinity(void);
|
|
int print_diffuse_layer(cxxSurfaceCharge* surface_charge_ptr);
|
|
int print_eh(void);
|
|
int print_reaction(void);
|
|
int print_kinetics(void);
|
|
int print_mix(void);
|
|
int print_pp_assemblage(void);
|
|
int print_ss_assemblage(void);
|
|
int print_saturation_indices(void);
|
|
int print_surface_cd_music(void);
|
|
int print_totals(void);
|
|
int print_using(void);
|
|
int punch_gas_phase(void);
|
|
int punch_identifiers(void);
|
|
int punch_kinetics(void);
|
|
int punch_molalities(void);
|
|
int punch_activities(void);
|
|
int punch_pp_assemblage(void);
|
|
int punch_ss_assemblage(void);
|
|
int punch_saturation_indices(void);
|
|
int punch_totals(void);
|
|
int punch_user_punch(void);
|
|
#if defined MULTICHART
|
|
int punch_user_graph(void);
|
|
#endif
|
|
|
|
// read.cpp -------------------------------
|
|
int read_input(void);
|
|
int* read_list_ints_range(const char** ptr, int* count_ints, int positive,
|
|
int* int_list);
|
|
int read_list_ints_range(const char** cptr, bool positive, std::vector<int>& int_list);
|
|
|
|
int read_log_k_only(const char* cptr, LDBLE* log_k);
|
|
int read_t_c_only(const char* cptr, LDBLE* t_c);
|
|
int read_p_c_only(const char* cptr, LDBLE* p_c);
|
|
int read_omega_only(const char* cptr, LDBLE* omega);
|
|
int read_number_description(const char* cptr, int* n_user, int* n_user_end,
|
|
char** description, int allow_negative = FALSE);
|
|
int check_key(const char* str);
|
|
int check_units(std::string& tot_units, bool alkalinity, bool check_compatibility,
|
|
const char* default_units, bool print);
|
|
int find_option(const char* item, int* n, const char** list, int count_list,
|
|
int exact);
|
|
int get_option(const char** opt_list, int count_opt_list, const char** next_char);
|
|
int get_true_false(const char* string, int default_value);
|
|
|
|
int add_psi_master_species(char* token);
|
|
int read_advection(void);
|
|
int read_analytical_expression_only(const char* cptr, LDBLE* log_k);
|
|
/* VP: Density Start */
|
|
int read_millero_abcdef(const char* cptr, LDBLE* abcdef);
|
|
/* VP: Density End */
|
|
int read_viscosity_parms(const char* cptr, LDBLE* Jones_Dole);
|
|
int read_copy(void);
|
|
int read_debug(void);
|
|
int read_delta_h_only(const char* cptr, LDBLE* delta_h,
|
|
DELTA_H_UNIT* units);
|
|
int read_aq_species_vm_parms(const char* cptr, LDBLE* delta_v);
|
|
int read_vm_only(const char* cptr, LDBLE* delta_v,
|
|
DELTA_V_UNIT* units);
|
|
int read_phase_vm(const char* cptr, LDBLE* delta_v,
|
|
DELTA_V_UNIT* units);
|
|
int read_llnl_aqueous_model_parameters(void);
|
|
int read_exchange(void);
|
|
int read_exchange_master_species(void);
|
|
int read_exchange_species(void);
|
|
int read_gas_phase(void);
|
|
int read_incremental_reactions(void);
|
|
int read_inverse(void);
|
|
int read_inv_balances(class inverse* inverse_ptr, const char* next_char);
|
|
int read_inv_isotopes(class inverse* inverse_ptr, const char* cptr);
|
|
int read_inv_phases(class inverse* inverse_ptr, const char* next_char);
|
|
int read_kinetics(void);
|
|
bool read_vector_doubles(const char** ptr, std::vector<double>& v);
|
|
bool read_vector_ints(const char** cptr, std::vector<int>& v, int positive);
|
|
bool read_vector_t_f(const char** ptr, std::vector<bool>& v);
|
|
int read_master_species(void);
|
|
int read_rate_parameters_pk(void);
|
|
int read_rate_parameters_svd(void);
|
|
int read_rate_parameters_hermanska(void);
|
|
int read_mean_gammas(void);
|
|
int read_mix(void);
|
|
int read_entity_mix(std::map<int, cxxMix>& mix_map);
|
|
//int read_solution_mix(void);
|
|
int read_named_logk(void);
|
|
int read_phases(void);
|
|
int read_print(void);
|
|
int read_pp_assemblage(void);
|
|
int read_rates(void);
|
|
int read_reaction(void);
|
|
int read_reaction_reactants(cxxReaction* reaction_ptr);
|
|
int read_reaction_steps(cxxReaction* reaction_ptr);
|
|
int read_solid_solutions(void);
|
|
int read_temperature(void);
|
|
//int read_reaction_temps(struct temperature* temperature_ptr);
|
|
int read_reaction_pressure(void);
|
|
int read_reaction_pressure_raw(void);
|
|
int read_save(void);
|
|
int read_selected_output(void);
|
|
int read_solution(void);
|
|
int read_species(void);
|
|
int read_surface(void);
|
|
int read_surface_master_species(void);
|
|
int read_surface_species(void);
|
|
int read_use(void);
|
|
int read_title(void);
|
|
int read_user_print(void);
|
|
int read_user_punch(void);
|
|
#if defined MULTICHART
|
|
int read_user_graph_handler();
|
|
#endif
|
|
int next_keyword_or_option(const char** opt_list, int count_opt_list);
|
|
int cleanup_after_parser(CParser& parser);
|
|
|
|
// ReadClass.cxx
|
|
int read_dump(void);
|
|
int read_delete(void);
|
|
int read_run_cells(void);
|
|
int streamify_to_next_keyword(std::istringstream& lines);
|
|
int dump_entities(void);
|
|
int delete_entities(void);
|
|
int run_as_cells(void);
|
|
void dump_ostream(std::ostream& os);
|
|
|
|
// readtr.cpp -------------------------------
|
|
int read_transport(void);
|
|
int dump(void);
|
|
//int dump_exchange(int k);
|
|
//int dump_gas_phase(int k);
|
|
//int dump_kinetics(int k);
|
|
//int dump_mix(int k);
|
|
//int dump_pp_assemblage(int k);
|
|
//int dump_reaction(int k);
|
|
//int dump_ss_assemblage(int k);
|
|
//int dump_solution(int k);
|
|
//int dump_surface(int k);
|
|
int dump_cpp(void);
|
|
int read_line_LDBLEs(const char* next_char, LDBLE** d, int* count_d,
|
|
int* count_alloc);
|
|
|
|
// sit.cpp -------------------------------
|
|
int gammas_sit(void);
|
|
int model_sit(void);
|
|
int sit(void);
|
|
int sit_clean_up(void);
|
|
int sit_init(void);
|
|
int sit_tidy(void);
|
|
int read_sit(void);
|
|
int set_sit(int initial);
|
|
int calc_sit_param(class pitz_param* pz_ptr, LDBLE TK, LDBLE TR);
|
|
int check_gammas_sit(void);
|
|
int sit_ISPEC(const char* name);
|
|
/*int DH_AB (LDBLE TK, LDBLE *A, LDBLE *B);*/
|
|
int sit_initial_guesses(void);
|
|
int sit_revise_guesses(void);
|
|
int PTEMP_SIT(LDBLE tk);
|
|
void sit_make_lists(void);
|
|
int jacobian_sit(void);
|
|
|
|
// spread.cpp -------------------------------
|
|
int read_solution_spread(void);
|
|
int copy_token_tab(std::string& token, const char** cptr);
|
|
int get_option_string(const char** opt_list, int count_opt_list,
|
|
const char** next_char);
|
|
int spread_row_free(class spread_row* spread_row_ptr);
|
|
int spread_row_to_solution(class spread_row* heading,
|
|
class spread_row* units,
|
|
class spread_row* data,
|
|
class defaults defaults);
|
|
class spread_row* string_to_spread_row(char* string);
|
|
#ifdef PHREEQCI_GUI
|
|
void add_row(class spread_row* spread_row_ptr);
|
|
void free_spread(void);
|
|
class spread_row* copy_row(class spread_row* spread_row_ptr);
|
|
#endif
|
|
|
|
// step.cpp -------------------------------
|
|
int step(LDBLE step_fraction);
|
|
int xsolution_zero(void);
|
|
int add_exchange(cxxExchange* exchange_ptr);
|
|
int add_gas_phase(cxxGasPhase* gas_phase_ptr);
|
|
int add_kinetics(cxxKinetics* kinetics_ptr);
|
|
int add_mix(cxxMix* mix_ptr);
|
|
int add_pp_assemblage(cxxPPassemblage* pp_assemblage_ptr);
|
|
int add_reaction(cxxReaction* reaction_ptr, int step_number, LDBLE step_fraction);
|
|
int add_ss_assemblage(cxxSSassemblage* ss_assemblage_ptr);
|
|
int add_solution(cxxSolution* solution_ptr, LDBLE extensive,
|
|
LDBLE intensive);
|
|
int add_surface(cxxSurface* surface_ptr);
|
|
int check_pp_assemblage(cxxPPassemblage* pp_assemblage_ptr);
|
|
int gas_phase_check(cxxGasPhase* gas_phase_ptr);
|
|
int pp_assemblage_check(cxxPPassemblage* pp_assemblage_ptr);
|
|
int reaction_calc(cxxReaction* reaction_ptr);
|
|
int solution_check(void);
|
|
int ss_assemblage_check(cxxSSassemblage* ss_assemblage_ptr);
|
|
|
|
// structures.cpp -------------------------------
|
|
int clean_up(void);
|
|
int reinitialize(void);
|
|
|
|
int copier_add(class copier* copier_ptr, int n_user, int start, int end);
|
|
int copier_clear(class copier* copier_ptr);
|
|
//
|
|
CReaction CReaction_internal_copy(CReaction& rxn_ref);
|
|
double rxn_find_coef(CReaction& r_ptr, const char* str);
|
|
//
|
|
static int element_compare(const void* ptr1, const void* ptr2);
|
|
class element* element_store(const char* element);
|
|
//
|
|
int add_elt_list(const cxxNameDouble& nd, LDBLE coef);
|
|
int add_elt_list(const std::vector<class elt_list>& el, double coef);
|
|
int change_hydrogen_in_elt_list(LDBLE charge);
|
|
int elt_list_combine(void);
|
|
static int elt_list_compare(const void* ptr1, const void* ptr2);
|
|
std::vector<class elt_list> elt_list_internal_copy(const std::vector<class elt_list>& el);
|
|
std::vector<class elt_list> elt_list_vsave(void);
|
|
cxxNameDouble elt_list_NameDouble(void);
|
|
//
|
|
enum entity_type get_entity_enum(char* name);
|
|
//
|
|
class inverse* inverse_alloc(void);
|
|
int inverse_delete(int i);
|
|
static int inverse_isotope_compare(const void* ptr1, const void* ptr2);
|
|
class inverse* inverse_search(int n_user, int* n);
|
|
int inverse_sort(void);
|
|
//
|
|
class logk* logk_alloc(void);
|
|
int logk_copy2orig(class logk* logk_ptr);
|
|
class logk* logk_store(const char* name, int replace_if_found);
|
|
class logk* logk_search(const char* name);
|
|
//
|
|
class master* master_alloc(void);
|
|
static int master_compare(const void* ptr1, const void* ptr2);
|
|
int master_delete(const char* cptr);
|
|
class master* master_bsearch(const char* cptr);
|
|
class master* master_bsearch_primary(const char* cptr);
|
|
class master* master_bsearch_secondary(const char* cptr);
|
|
class master* master_search(const char* cptr, int* n);
|
|
class master* surface_get_psi_master(const char* name, int plane);
|
|
//
|
|
class phase* phase_bsearch(const char* cptr, int* j, int print);
|
|
#ifdef OBSOLETE
|
|
static int phase_compare(const void* ptr1, const void* ptr2);
|
|
#endif
|
|
int phase_delete(int i);
|
|
class phase* phase_store(const char* name);
|
|
//
|
|
class rate* rate_bsearch(const char* cptr, int* j);
|
|
int rate_free(class rate* rate_ptr);
|
|
class rate* rate_copy(const class rate* rate_ptr);
|
|
class rate* rate_search(const char* name, int* n);
|
|
int rate_sort(void);
|
|
//
|
|
static int s_compare(const void* ptr1, const void* ptr2);
|
|
int s_delete(int i);
|
|
class species* s_search(const char* name);
|
|
class species* s_store(const char* name, LDBLE z, int replace_if_found);
|
|
//
|
|
static int isotope_compare(const void* ptr1, const void* ptr2);
|
|
//
|
|
static int species_list_compare_alk(const void* ptr1, const void* ptr2);
|
|
static int species_list_compare_master(const void* ptr1, const void* ptr2);
|
|
int species_list_sort(void);
|
|
//
|
|
struct Change_Surf* change_surf_alloc(int count);
|
|
//
|
|
int system_duplicate(int i, int save_old);
|
|
//
|
|
//
|
|
bool phase_rxn_to_trxn(class phase* phase_ptr, CReaction& rxn_ptr);
|
|
bool trxn_add(CReaction& r_ptr, double coef, bool combine);
|
|
bool trxn_add_phase(CReaction& r_ref, double coef, bool combine);
|
|
int trxn_combine(void);
|
|
static int trxn_compare(const void* ptr1, const void* ptr2);
|
|
bool trxn_copy(CReaction& rxn_ref);
|
|
LDBLE trxn_find_coef(const char* str, int start);
|
|
int trxn_multiply(LDBLE coef);
|
|
int trxn_print(void);
|
|
int trxn_reverse_k(void);
|
|
int trxn_sort(void);
|
|
int trxn_swap(const char* token);
|
|
|
|
class unknown* unknown_alloc(void);
|
|
int unknown_delete(int i);
|
|
int unknown_free(class unknown* unknown_ptr);
|
|
int entity_exists(const char* name, int n_user);
|
|
static int inverse_compare(const void* ptr1, const void* ptr2);
|
|
int inverse_free(class inverse* inverse_ptr);
|
|
int logk_init(class logk* logk_ptr);
|
|
static int master_compare_string(const void* ptr1, const void* ptr2);
|
|
int master_free(class master* master_ptr);
|
|
class phase* phase_alloc(void);
|
|
static int phase_compare_string(const void* ptr1, const void* ptr2);
|
|
int phase_free(class phase* phase_ptr);
|
|
int phase_init(class phase* phase_ptr);
|
|
static int rate_compare(const void* ptr1, const void* ptr2);
|
|
static int rate_compare_string(const void* ptr1, const void* ptr2);
|
|
class species* s_alloc(void);
|
|
int s_free(class species* s_ptr);
|
|
int s_init(class species* s_ptr);
|
|
static int species_list_compare(const void* ptr1, const void* ptr2);
|
|
|
|
void Use2cxxStorageBin(cxxStorageBin& sb);
|
|
void phreeqc2cxxStorageBin(cxxStorageBin& sb);
|
|
void phreeqc2cxxStorageBin(cxxStorageBin& sb, int n);
|
|
void cxxStorageBin2phreeqc(cxxStorageBin& sb, int n);
|
|
void cxxStorageBin2phreeqc(cxxStorageBin& sb);
|
|
|
|
/* tally.cpp */
|
|
void add_all_components_tally(void);
|
|
int build_tally_table(void);
|
|
int calc_dummy_kinetic_reaction_tally(cxxKinetics* kinetics_ptr);
|
|
int diff_tally_table(void);
|
|
int extend_tally_table(void);
|
|
int free_tally_table(void);
|
|
int fill_tally_table(int* n_user, int index_conservative, int n_buffer);
|
|
int get_tally_table_rows_columns(int* rows, int* columns);
|
|
int get_tally_table_column_heading(int column, int* type, char* string);
|
|
int get_tally_table_row_heading(int column, char* string);
|
|
int store_tally_table(LDBLE* array, int row_dim, int col_dim,
|
|
LDBLE fill_factor);
|
|
int zero_tally_table(void);
|
|
int elt_list_to_tally_table(class tally_buffer* buffer_ptr);
|
|
int master_to_tally_table(class tally_buffer* buffer_ptr);
|
|
int get_all_components(void);
|
|
int print_tally_table(void);
|
|
int set_reaction_moles(int n_user, LDBLE moles);
|
|
int set_reaction_temperature(int n_user, LDBLE tc);
|
|
int set_kinetics_time(int n_user, LDBLE step);
|
|
|
|
// tidy.cpp -------------------------------
|
|
int add_other_logk(LDBLE* source_k, std::vector<class name_coef>& add_logk);
|
|
int add_logks(class logk* logk_ptr, int repeats);
|
|
LDBLE halve(LDBLE f(LDBLE x, void*), LDBLE x0, LDBLE x1, LDBLE tol);
|
|
int replace_solids_gases(void);
|
|
int ss_prep(LDBLE t, cxxSS* ss_ptr, int print);
|
|
int select_log_k_expression(LDBLE* source_k, LDBLE* target_k);
|
|
int slnq(int n, LDBLE* a, LDBLE* delta, int ncols, int print);
|
|
public:
|
|
int tidy_punch(void);
|
|
int tidy_model(void);
|
|
int check_species_input(void);
|
|
LDBLE coef_in_master(class master* master_ptr);
|
|
int reset_last_model(void);
|
|
int rewrite_eqn_to_primary(void);
|
|
int rewrite_eqn_to_secondary(void);
|
|
int species_rxn_to_trxn(class species* s_ptr);
|
|
int tidy_logk(void);
|
|
int tidy_exchange(void);
|
|
int tidy_min_exchange(void);
|
|
int update_min_exchange(void);
|
|
int tidy_kin_exchange(void);
|
|
int update_kin_exchange(void);
|
|
int tidy_gas_phase(void);
|
|
int tidy_inverse(void);
|
|
int tidy_isotopes(void);
|
|
int tidy_isotope_ratios(void);
|
|
int tidy_isotope_alphas(void);
|
|
int tidy_kin_surface(void);
|
|
int update_kin_surface(void);
|
|
int tidy_master_isotope(void);
|
|
int tidy_min_surface(void);
|
|
int update_min_surface(void);
|
|
int tidy_phases(void);
|
|
int tidy_pp_assemblage(void);
|
|
int tidy_solutions(void);
|
|
int tidy_ss_assemblage(void);
|
|
int tidy_species(void);
|
|
int tidy_surface(void);
|
|
int scan(LDBLE f(LDBLE x, void*), LDBLE* xx0, LDBLE* xx1);
|
|
static LDBLE f_spinodal(LDBLE x, void*);
|
|
int solve_misc(LDBLE* xxc1, LDBLE* xxc2, LDBLE tol);
|
|
int ss_calc_a0_a1(cxxSS* ss_ptr);
|
|
|
|
// transport.cpp -------------------------------
|
|
int transport(void);
|
|
void print_punch(int i, boolean active);
|
|
int set_initial_moles(int i);
|
|
cxxSurface sum_surface_comp(cxxSurface* source1, LDBLE f1,
|
|
cxxSurface* source2, std::string charge_name, LDBLE f2,
|
|
LDBLE new_Dw);
|
|
int reformat_surf(const char* comp_name, LDBLE fraction, const char* new_comp_name,
|
|
LDBLE new_Dw, int cell);
|
|
LDBLE viscosity(cxxSurface *surf_ptr);
|
|
LDBLE calc_f_visc(const char *name);
|
|
LDBLE calc_vm_Cl(void);
|
|
int multi_D(LDBLE DDt, int mobile_cell, int stagnant);
|
|
LDBLE find_J(int icell, int jcell, LDBLE mixf, LDBLE DDt, int stagnant);
|
|
void calc_b_ij(int icell, int jcell, int k, LDBLE b_i, LDBLE b_j, LDBLE g_i, LDBLE g_j, LDBLE free_i, LDBLE free_j, int stagnant);
|
|
void diffuse_implicit(LDBLE DDt, int stagnant);
|
|
int fill_spec(int cell_no, int ref_cell);
|
|
LDBLE moles_from_redox_states(cxxSolution* sptr, const char* name);
|
|
LDBLE moles_from_donnan_layer(cxxSurface* sptr, const char* name, LDBLE moles_needed);
|
|
LDBLE add_MCD_moles(LDBLE moles, LDBLE min_mol, int i, cxxSolution* sptr, const char* name);
|
|
int fill_m_s(class J_ij* J_ij, int J_ij_count_spec, int i, int stagnant);
|
|
static int sort_species_name(const void* ptr1, const void* ptr2);
|
|
int disp_surf(LDBLE stagkin_time);
|
|
int diff_stag_surf(int mobile_cell);
|
|
int check_surfaces(cxxSurface* surface_ptr1, cxxSurface* surface_ptr2);
|
|
cxxSurface mobile_surface_copy(cxxSurface* surface_old_ptr,
|
|
int n_user_new,
|
|
bool move_old);
|
|
void transport_cleanup(void);
|
|
int init_mix(void);
|
|
int init_heat_mix(int nmix);
|
|
int heat_mix(int heat_nmix);
|
|
int mix_stag(int i, LDBLE stagkin_time, int punch,
|
|
LDBLE step_fraction_kin);
|
|
|
|
// utilities.cpp -------------------------------
|
|
public:
|
|
double calc_alk(CReaction& rxn_ptr);
|
|
double calc_delta_v(CReaction& r_ref, bool phase);
|
|
LDBLE calc_dielectrics(LDBLE tc, LDBLE pa);
|
|
LDBLE calc_rho_0(LDBLE tc, LDBLE pa);
|
|
int compute_gfw(const char* string, LDBLE* gfw);
|
|
static int copy_token(char* token_ptr, const char** ptr, int* length);
|
|
static int copy_token(std::string& token, const char** ptr);
|
|
int dup_print(const char* cptr, int emphasis);
|
|
int equal(LDBLE a, LDBLE b, LDBLE eps);
|
|
void* free_check_null(void* ptr);
|
|
int get_token(const char** eqnaddr, std::string& string, LDBLE* z, int* l);
|
|
int islegit(const char c);
|
|
void malloc_error(void);
|
|
int print_centered(const char* string);
|
|
static int replace(const char* str1, const char* str2, char* str);
|
|
static void replace(std::string &stds, const char* str1, const char* str2);
|
|
static bool replace(const char* str1, const char* str2, std::string& str);
|
|
static int strcmp_nocase(const char* str1, const char* str2);
|
|
static int strcmp_nocase_arg1(const char* str1, const char* str2);
|
|
static void str_tolower(std::string& name);
|
|
void space(void** ptr, int i, int* max, int struct_size);
|
|
void squeeze_white(char* s_l);
|
|
int status(int count, const char* str, bool kinetics = false);
|
|
void str_tolower(char* str);
|
|
void str_toupper(char* str);
|
|
#if !defined(NDEBUG) && defined(WIN32_MEMORY_DEBUG)
|
|
char* _string_duplicate(const char* token, const char* szFileName, int nLine);
|
|
#else
|
|
char* string_duplicate(const char* token);
|
|
#endif
|
|
const char* string_hsave(const char* str);
|
|
void strings_map_clear();
|
|
protected:
|
|
char* string_pad(const char* str, int i);
|
|
static int string_trim(char* str);
|
|
static int string_trim_right(char* str);
|
|
static int string_trim_left(char* str);
|
|
static void string_trim(std::string& str);
|
|
static void string_trim_left(std::string& str);
|
|
static void string_trim_right(std::string& str);
|
|
static LDBLE under(LDBLE xval);
|
|
int get_input_errors(void);
|
|
int isamong(char c, const char* s_l);
|
|
public:
|
|
int main_method(int argc, char* argv[]);
|
|
void set_phast(int);
|
|
int next_user_number(Keywords::KEYWORDS key);
|
|
size_t list_components(std::list<std::string>& list_c);
|
|
size_t list_EquilibriumPhases(std::list<std::string>& list_pp);
|
|
size_t list_GasComponents(std::list<std::string>& list_gc);
|
|
size_t list_KineticReactions(std::list<std::string>& list_kr);
|
|
size_t list_SolidSolutions(std::list<std::string>& list_comps, std::list<std::string>& list_names);
|
|
size_t list_Surfaces(std::list<std::string>& surftype, std::list<std::string>& surf);
|
|
size_t list_Exchangers(std::list<std::string>& ex);
|
|
PHRQ_io* Get_phrq_io(void) { return this->phrq_io; }
|
|
void Set_run_cells_one_step(const bool tf) { this->run_cells_one_step = tf; }
|
|
|
|
|
|
std::map<int, cxxSolution>& Get_Rxn_solution_map() { return this->Rxn_solution_map; }
|
|
std::map<int, cxxExchange>& Get_Rxn_exchange_map() { return this->Rxn_exchange_map; }
|
|
std::map<int, cxxGasPhase>& Get_Rxn_gas_phase_map() { return this->Rxn_gas_phase_map; }
|
|
std::map<int, cxxKinetics>& Get_Rxn_kinetics_map() { return this->Rxn_kinetics_map; }
|
|
std::map<int, cxxPPassemblage>& Get_Rxn_pp_assemblage_map() { return this->Rxn_pp_assemblage_map; }
|
|
std::map<int, cxxSSassemblage>& Get_Rxn_ss_assemblage_map() { return this->Rxn_ss_assemblage_map; }
|
|
std::map<int, cxxSurface>& Get_Rxn_surface_map() { return this->Rxn_surface_map; }
|
|
std::map<int, cxxMix>& Get_Rxn_mix_map() { return this->Rxn_mix_map; }
|
|
std::map<int, cxxReaction>& Get_Rxn_reaction_map() { return this->Rxn_reaction_map; }
|
|
std::map<int, cxxTemperature>& Get_Rxn_temperature_map() { return this->Rxn_temperature_map; }
|
|
std::map<int, cxxPressure>& Get_Rxn_pressure_map() { return this->Rxn_pressure_map; }
|
|
|
|
protected:
|
|
void init(void);
|
|
|
|
//
|
|
//Data members
|
|
//
|
|
protected:
|
|
PHRQ_io* phrq_io;
|
|
PHRQ_io ioInstance;
|
|
int same_model;
|
|
|
|
LDBLE current_tc;
|
|
LDBLE current_pa;
|
|
LDBLE current_mu;
|
|
bool mu_terms_in_logk;
|
|
|
|
/* ----------------------------------------------------------------------
|
|
* STRUCTURES
|
|
* ---------------------------------------------------------------------- */
|
|
|
|
Model last_model;
|
|
//struct punch punch;
|
|
bool high_precision;
|
|
|
|
/* ----------------------------------------------------------------------
|
|
* Temperatures
|
|
* ---------------------------------------------------------------------- */
|
|
|
|
std::map<int, cxxTemperature> Rxn_temperature_map;
|
|
|
|
/* ----------------------------------------------------------------------
|
|
* Pressures
|
|
* ---------------------------------------------------------------------- */
|
|
std::map<int, cxxPressure> Rxn_pressure_map;
|
|
|
|
/* ----------------------------------------------------------------------
|
|
* Surface
|
|
* --------------------------------------------------------------------- */
|
|
|
|
int g_iterations;
|
|
LDBLE G_TOL;
|
|
std::map <int, cxxSurface> Rxn_surface_map;
|
|
std::map <LDBLE, LDBLE> charge_group_map;
|
|
int change_surf_count;
|
|
struct Change_Surf* change_surf;
|
|
|
|
/* ----------------------------------------------------------------------
|
|
* Exchange
|
|
* ---------------------------------------------------------------------- */
|
|
std::map<int, cxxExchange> Rxn_exchange_map;
|
|
|
|
/* ----------------------------------------------------------------------
|
|
* Kinetics
|
|
* ---------------------------------------------------------------------- */
|
|
std::map<int, cxxKinetics> Rxn_kinetics_map;
|
|
bool use_kinetics_limiter;
|
|
|
|
/*----------------------------------------------------------------------
|
|
* Save
|
|
*---------------------------------------------------------------------- */
|
|
std::map<std::string, double> save_values;
|
|
std::map<std::string, std::string> save_strings;
|
|
class save save;
|
|
|
|
/*----------------------------------------------------------------------
|
|
* Use
|
|
*---------------------------------------------------------------------- */
|
|
cxxUse use;
|
|
|
|
/*----------------------------------------------------------------------
|
|
* Copy
|
|
*---------------------------------------------------------------------- */
|
|
class copier copy_solution;
|
|
class copier copy_pp_assemblage;
|
|
class copier copy_exchange;
|
|
class copier copy_surface;
|
|
class copier copy_ss_assemblage;
|
|
class copier copy_gas_phase;
|
|
class copier copy_kinetics;
|
|
class copier copy_mix;
|
|
class copier copy_reaction;
|
|
class copier copy_temperature;
|
|
class copier copy_pressure;
|
|
|
|
/*----------------------------------------------------------------------
|
|
* Inverse
|
|
*---------------------------------------------------------------------- */
|
|
std::vector<class inverse> inverse;
|
|
int count_inverse;
|
|
/*----------------------------------------------------------------------
|
|
* Rates
|
|
*---------------------------------------------------------------------- */
|
|
std::map<std::string, std::vector<double> > rate_parameters_pk;
|
|
std::map<std::string, std::vector<double> > rate_parameters_svd;
|
|
std::map<std::string, std::vector<double> > rate_parameters_hermanska;
|
|
/*----------------------------------------------------------------------
|
|
* Mean gammas
|
|
*---------------------------------------------------------------------- */
|
|
std::map<std::string, cxxNameDouble> mean_gammas;
|
|
/*----------------------------------------------------------------------
|
|
* Mix
|
|
*---------------------------------------------------------------------- */
|
|
std::map<int, cxxMix> Rxn_mix_map;
|
|
std::map<int, cxxMix> Dispersion_mix_map;
|
|
std::map<int, cxxMix> Rxn_solution_mix_map;
|
|
std::map<int, cxxMix> Rxn_exchange_mix_map;
|
|
std::map<int, cxxMix> Rxn_gas_phase_mix_map;
|
|
std::map<int, cxxMix> Rxn_kinetics_mix_map;
|
|
std::map<int, cxxMix> Rxn_pp_assemblage_mix_map;
|
|
std::map<int, cxxMix> Rxn_ss_assemblage_mix_map;
|
|
std::map<int, cxxMix> Rxn_surface_mix_map;
|
|
/*
|
|
* List new definitions
|
|
*/
|
|
std::set<int> Rxn_new_exchange;
|
|
std::set<int> Rxn_new_gas_phase;
|
|
std::set<int> Rxn_new_kinetics; // not used
|
|
std::set<int> Rxn_new_mix; // not used
|
|
std::set<int> Rxn_new_pp_assemblage;
|
|
std::set<int> Rxn_new_pressure; // not used
|
|
std::set<int> Rxn_new_reaction; // not used
|
|
std::set<int> Rxn_new_solution;
|
|
std::set<int> Rxn_new_ss_assemblage;
|
|
std::set<int> Rxn_new_surface;
|
|
std::set<int> Rxn_new_temperature; // not used
|
|
/*----------------------------------------------------------------------
|
|
* Irreversible reaction
|
|
*---------------------------------------------------------------------- */
|
|
std::map<int, cxxReaction> Rxn_reaction_map;
|
|
|
|
/*----------------------------------------------------------------------
|
|
* Gas phase
|
|
*---------------------------------------------------------------------- */
|
|
std::map<int, cxxGasPhase> Rxn_gas_phase_map;
|
|
|
|
/*----------------------------------------------------------------------
|
|
* Solid solution
|
|
*---------------------------------------------------------------------- */
|
|
std::map<int, cxxSSassemblage> Rxn_ss_assemblage_map;
|
|
|
|
/*----------------------------------------------------------------------
|
|
* Pure-phase assemblage
|
|
*---------------------------------------------------------------------- */
|
|
std::map<int, cxxPPassemblage> Rxn_pp_assemblage_map;
|
|
|
|
/*----------------------------------------------------------------------
|
|
* Species_list
|
|
*---------------------------------------------------------------------- */
|
|
std::vector<class species_list> species_list;
|
|
|
|
/*----------------------------------------------------------------------
|
|
* Jacobian and Mass balance lists
|
|
*---------------------------------------------------------------------- */
|
|
std::vector<class list0> sum_jacob0; /* array of pointers to targets and coefficients for array */
|
|
|
|
std::vector<class list1> sum_mb1; /* array of pointers to sources and targets for mass
|
|
balance summations with coef = 1.0 */
|
|
std::vector<class list1> sum_jacob1; /* array of pointers to sources and targets for array
|
|
equations with coef = 1.0 */
|
|
std::vector<class list2> sum_mb2; /* array of coefficients and pointers to sources and
|
|
targets for mass balance summations with coef != 1.0 */
|
|
std::vector<class list2> sum_jacob2; /* array of coefficients and pointers to sources and
|
|
targets, coef != 1.0 */
|
|
std::vector<class list2> sum_delta; /* array of pointers to sources, targets and coefficients for
|
|
summing deltas for mass balance equations */
|
|
/*----------------------------------------------------------------------
|
|
* Solution
|
|
*---------------------------------------------------------------------- */
|
|
std::map<int, cxxSolution> Rxn_solution_map;
|
|
std::vector<cxxSolution> unnumbered_solutions;
|
|
bool save_species;
|
|
|
|
/*----------------------------------------------------------------------
|
|
* Global solution
|
|
*---------------------------------------------------------------------- */
|
|
std::string title_x;
|
|
std::string last_title_x;
|
|
int new_x;
|
|
std::string description_x;
|
|
LDBLE tc_x;
|
|
LDBLE tk_x;
|
|
LDBLE patm_x;
|
|
LDBLE last_patm_x;
|
|
LDBLE potV_x;
|
|
bool numerical_fixed_volume;
|
|
bool force_numerical_fixed_volume;
|
|
//bool switch_numerical;
|
|
LDBLE ph_x;
|
|
LDBLE solution_pe_x;
|
|
LDBLE mu_x;
|
|
LDBLE ah2o_x;
|
|
LDBLE total_h_x;
|
|
LDBLE total_o_x;
|
|
LDBLE cb_x;
|
|
LDBLE total_ions_x;
|
|
LDBLE mass_water_aq_x;
|
|
LDBLE mass_water_surfaces_x;
|
|
LDBLE mass_water_bulk_x;
|
|
std::string units_x;
|
|
std::map < std::string, CReaction > pe_x;
|
|
std::map<std::string, cxxSolutionIsotope> isotopes_x;
|
|
std::string default_pe_x;
|
|
cxxSurface::DIFFUSE_LAYER_TYPE dl_type_x;
|
|
LDBLE total_carbon;
|
|
LDBLE total_co2;
|
|
LDBLE total_alkalinity;
|
|
LDBLE gfw_water;
|
|
LDBLE step_x;
|
|
LDBLE kin_time_x;
|
|
|
|
/*----------------------------------------------------------------------
|
|
* Transport data
|
|
*---------------------------------------------------------------------- */
|
|
int count_cells;
|
|
int count_shifts;
|
|
int ishift;
|
|
int bcon_first;
|
|
int bcon_last;
|
|
int correct_disp;
|
|
LDBLE tempr;
|
|
LDBLE timest;
|
|
int simul_tr;
|
|
LDBLE diffc;
|
|
LDBLE heat_diffc;
|
|
int cell;
|
|
LDBLE mcd_substeps;
|
|
class stag_data stag_data;
|
|
int print_modulus;
|
|
int punch_modulus;
|
|
int dump_in;
|
|
int dump_modulus;
|
|
int transport_warnings;
|
|
std::vector<class cell_data> cell_data;
|
|
int old_cells, max_cells, all_cells;
|
|
int multi_Dflag; /* signals calc'n of multicomponent diffusion */
|
|
int interlayer_Dflag; /* multicomponent diffusion and diffusion through interlayer porosity */
|
|
int implicit; /* implicit calculation of diffusion */
|
|
LDBLE max_mixf; /* the maximum value of the implicit mixfactor = De * Dt / (Dx^2) */
|
|
LDBLE min_dif_LM; /* the minimal log10(molality) for including a species in multicomponent diffusion */
|
|
LDBLE default_Dw; /* default species diffusion coefficient in water at 25oC, m2/s */
|
|
int correct_Dw; /* if true, Dw is adapted in calc_SC */
|
|
LDBLE multi_Dpor; /* uniform porosity of free porewater in solid medium */
|
|
LDBLE interlayer_Dpor; /* uniform porosity of interlayer space of montmorillonite in solid medium */
|
|
LDBLE multi_Dpor_lim; /* limiting free porewater porosity where transport stops */
|
|
LDBLE interlayer_Dpor_lim; /* limiting interlayer porosity where transport stops */
|
|
LDBLE multi_Dn; /* exponent to calculate pore water diffusion coefficient,
|
|
Dp = Dw * (multi_Dpor)^multi_Dn */
|
|
LDBLE interlayer_tortf; /* tortuosity_factor in interlayer porosity,
|
|
Dpil = Dw / interlayer_tortf */
|
|
|
|
int cell_no, mixrun;
|
|
/*----------------------------------------------------------------------
|
|
* Advection data
|
|
*---------------------------------------------------------------------- */
|
|
int count_ad_cells;
|
|
int count_ad_shifts;
|
|
int print_ad_modulus;
|
|
int punch_ad_modulus;
|
|
std::vector<int> advection_print, advection_punch;
|
|
LDBLE advection_kin_time;
|
|
LDBLE advection_kin_time_defined;
|
|
int advection_warnings;
|
|
|
|
/*----------------------------------------------------------------------
|
|
* Tidy data
|
|
*---------------------------------------------------------------------- */
|
|
int new_model, new_exchange, new_pp_assemblage, new_surface,
|
|
new_reaction, new_temperature, new_mix, new_solution, new_gas_phase,
|
|
new_inverse, new_punch, new_ss_assemblage, new_kinetics, new_copy,
|
|
new_pitzer;
|
|
|
|
/*----------------------------------------------------------------------
|
|
* Elements
|
|
*---------------------------------------------------------------------- */
|
|
std::vector<class element*> elements;
|
|
class element* element_h_one;
|
|
|
|
/*----------------------------------------------------------------------
|
|
* Element List
|
|
*---------------------------------------------------------------------- */
|
|
std::vector<class elt_list> elt_list;
|
|
size_t count_elts; /* number of elements in elt_list = position of next */
|
|
/*----------------------------------------------------------------------
|
|
* Reaction
|
|
*---------------------------------------------------------------------- */
|
|
bool run_cells_one_step;
|
|
/*----------------------------------------------------------------------
|
|
* Species
|
|
*---------------------------------------------------------------------- */
|
|
std::vector<class logk*> logk;
|
|
|
|
std::string moles_per_kilogram_string;
|
|
|
|
std::vector<class species*> s;
|
|
std::vector< std::map < std::string, cxxSpeciesDL > > s_diff_layer;
|
|
std::vector<class species*> s_x;
|
|
|
|
class species* s_h2o;
|
|
class species* s_hplus;
|
|
class species* s_h3oplus;
|
|
class species* s_eminus;
|
|
class species* s_co3;
|
|
class species* s_h2;
|
|
class species* s_o2;
|
|
|
|
/*----------------------------------------------------------------------
|
|
* Phases
|
|
*---------------------------------------------------------------------- */
|
|
std::vector<class phase*> phases;
|
|
|
|
/*----------------------------------------------------------------------
|
|
* Master species
|
|
*---------------------------------------------------------------------- */
|
|
std::vector<class master*> master;
|
|
|
|
/*----------------------------------------------------------------------
|
|
* Unknowns
|
|
*---------------------------------------------------------------------- */
|
|
std::vector<class unknown*> x;
|
|
size_t count_unknowns;
|
|
size_t sit_aqueous_unknowns;
|
|
size_t max_unknowns;
|
|
|
|
class unknown* ah2o_unknown;
|
|
class unknown* alkalinity_unknown;
|
|
class unknown* carbon_unknown;
|
|
class unknown* charge_balance_unknown;
|
|
class unknown* exchange_unknown;
|
|
class unknown* mass_hydrogen_unknown;
|
|
class unknown* mass_oxygen_unknown;
|
|
class unknown* mb_unknown;
|
|
class unknown* mu_unknown;
|
|
class unknown* pe_unknown;
|
|
class unknown* ph_unknown;
|
|
class unknown* pure_phase_unknown;
|
|
class unknown* solution_phase_boundary_unknown;
|
|
class unknown* surface_unknown;
|
|
class unknown* gas_unknown;
|
|
class unknown* ss_unknown;
|
|
std::vector<class unknown*> gas_unknowns;
|
|
|
|
/*----------------------------------------------------------------------
|
|
* Reaction work space
|
|
*---------------------------------------------------------------------- */
|
|
class reaction_temp trxn; /* structure array of working space while reading equations
|
|
species names are in "temp_strings" */
|
|
size_t count_trxn; /* number of reactants in trxn = position of next */
|
|
|
|
std::vector<class unknown_list> mb_unknowns;
|
|
|
|
/* ----------------------------------------------------------------------
|
|
* Print
|
|
* ---------------------------------------------------------------------- */
|
|
class prints pr;
|
|
bool status_on;
|
|
clock_t status_interval;
|
|
clock_t status_timer;
|
|
std::string status_string;
|
|
int count_warnings;
|
|
|
|
/* ----------------------------------------------------------------------
|
|
* RATES
|
|
* ---------------------------------------------------------------------- */
|
|
std::vector<class rate> rates;
|
|
LDBLE rate_m, rate_m0, rate_time, rate_kin_time, rate_sim_time_start,
|
|
rate_sim_time_end, rate_sim_time, rate_moles, initial_total_time;
|
|
std::vector<LDBLE> rate_p;
|
|
int count_rate_p;
|
|
|
|
/* ----------------------------------------------------------------------
|
|
* USER PRINT COMMANDS
|
|
* ---------------------------------------------------------------------- */
|
|
class rate* user_print;
|
|
int n_user_punch_index;
|
|
|
|
int fpunchf_user_s_warning;
|
|
char fpunchf_user_buffer[80];
|
|
|
|
#if defined MULTICHART
|
|
ChartHandler chart_handler;
|
|
public:
|
|
ChartHandler& Get_chart_handler(void)
|
|
{
|
|
return chart_handler;
|
|
}
|
|
const ChartHandler& Get_chart_handler(void)const
|
|
{
|
|
return chart_handler;
|
|
}
|
|
protected:
|
|
#endif
|
|
|
|
/* ----------------------------------------------------------------------
|
|
* GLOBAL DECLARATIONS
|
|
* ---------------------------------------------------------------------- */
|
|
const char* error_string;
|
|
int simulation;
|
|
int state;
|
|
int reaction_step;
|
|
int transport_step;
|
|
int transport_start;
|
|
int advection_step;
|
|
int stop_program;
|
|
int incremental_reactions;
|
|
|
|
double MIN_LM;
|
|
double LOG_ZERO_MOLALITY;
|
|
double MIN_TOTAL;
|
|
double MIN_TOTAL_SS;
|
|
double MIN_RELATED_SURFACE;
|
|
double MIN_RELATED_LOG_ACTIVITY;
|
|
|
|
int count_strings;
|
|
int max_strings;
|
|
|
|
std::vector<double> my_array, delta, residual;
|
|
|
|
int input_error;
|
|
|
|
Keywords::KEYWORDS next_keyword;
|
|
int parse_error;
|
|
int paren_count;
|
|
int iterations;
|
|
int gamma_iterations;
|
|
size_t density_iterations;
|
|
LDBLE kgw_kgs;
|
|
int run_reactions_iterations;
|
|
int overall_iterations;
|
|
|
|
int max_line;
|
|
char* line;
|
|
char* line_save;
|
|
|
|
LDBLE LOG_10;
|
|
|
|
int debug_model;
|
|
int debug_prep;
|
|
int debug_mass_action;
|
|
int debug_mass_balance;
|
|
int debug_set;
|
|
int debug_diffuse_layer;
|
|
int debug_inverse;
|
|
|
|
LDBLE inv_tol_default;
|
|
int itmax;
|
|
int max_tries;
|
|
LDBLE ineq_tol;
|
|
LDBLE convergence_tolerance;
|
|
LDBLE step_size;
|
|
LDBLE pe_step_size;
|
|
LDBLE step_size_now;
|
|
LDBLE pe_step_size_now;
|
|
LDBLE pp_scale;
|
|
LDBLE pp_column_scale;
|
|
int diagonal_scale; /* 0 not used, 1 used */
|
|
int mass_water_switch;
|
|
int delay_mass_water;
|
|
int equi_delay;
|
|
bool dampen_ah2o;
|
|
LDBLE censor;
|
|
int aqueous_only;
|
|
int negative_concentrations;
|
|
int calculating_deriv;
|
|
int numerical_deriv;
|
|
|
|
int count_total_steps;
|
|
int phast;
|
|
bool output_newline;
|
|
inline void Set_output_newline(bool tf) { this->output_newline = tf; }
|
|
inline bool Get_output_newline() { return this->output_newline; }
|
|
double a_llnl, b_llnl, bdot_llnl;
|
|
std::vector<double> llnl_temp, llnl_adh, llnl_bdh, llnl_bdot, llnl_co2_coefs;
|
|
|
|
//char *selected_output_file_name;
|
|
std::map<int, SelectedOutput> SelectedOutput_map;
|
|
SelectedOutput* current_selected_output;
|
|
|
|
std::map <int, UserPunch> UserPunch_map;
|
|
UserPunch* current_user_punch;
|
|
|
|
char* dump_file_name;
|
|
int remove_unstable_phases;
|
|
std::string screen_string;
|
|
#ifdef PHREEQCI_GUI
|
|
class spread_sheet g_spread_sheet;
|
|
#endif
|
|
int spread_length;
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
/*
|
|
* Map definitions
|
|
*/
|
|
|
|
std::map<std::string, std::string*> strings_map;
|
|
std::map<std::string, class element*> elements_map;
|
|
std::map<std::string, class species*> species_map;
|
|
std::map<std::string, class phase*> phases_map;
|
|
std::map<std::string, class logk*> logk_map;
|
|
std::map<std::string, class master_isotope*> master_isotope_map;
|
|
|
|
#if defined(PHREEQCI_GUI)
|
|
#include "../../phreeqci_gui.h"
|
|
#endif /* defined(PHREEQCI_GUI) */
|
|
/* ----------------------------------------------------------------------
|
|
* ISOTOPES
|
|
* ---------------------------------------------------------------------- */
|
|
std::vector<class master_isotope*> master_isotope;
|
|
int initial_solution_isotopes;
|
|
std::vector<class calculate_value*> calculate_value;
|
|
std::map<std::string, class calculate_value*> calculate_value_map;
|
|
public:
|
|
std::map<std::string, class calculate_value*>& GetCalculateValueMap()
|
|
{
|
|
return this->calculate_value_map;
|
|
}
|
|
protected:
|
|
std::vector<class isotope_ratio*> isotope_ratio;
|
|
std::map<std::string, class isotope_ratio*> isotope_ratio_map;
|
|
std::vector<class isotope_alpha*> isotope_alpha;
|
|
std::map<std::string, class isotope_alpha*> isotope_alpha_map;
|
|
int phreeqc_mpi_myself;
|
|
int first_read_input;
|
|
std::string user_database;
|
|
|
|
//int have_punch_name;
|
|
/* VP: Density Start */
|
|
int print_density;
|
|
/* VP: Density End */
|
|
|
|
int print_viscosity;
|
|
LDBLE viscos, viscos_0, viscos_0_25; // viscosity of the solution, of pure water, of pure water at 25 C
|
|
LDBLE density_x;
|
|
LDBLE solution_volume_x;
|
|
LDBLE solution_mass_x;
|
|
LDBLE cell_pore_volume;
|
|
LDBLE cell_porosity;
|
|
LDBLE cell_volume;
|
|
LDBLE cell_saturation;
|
|
std::vector<class system_species> sys;
|
|
LDBLE sys_tot;
|
|
|
|
LDBLE V_solutes, rho_0, rho_0_sat, kappa_0, p_sat/*, ah2o_x0*/;
|
|
LDBLE SC; // specific conductance mS/cm
|
|
LDBLE eps_r; // relative dielectric permittivity
|
|
LDBLE DH_A, DH_B, DH_Av; // Debye-Hueckel A, B and Av
|
|
LDBLE QBrn; // Born function d(ln(eps_r))/dP / eps_r * 41.84004, for supcrt calc'n of molal volume
|
|
LDBLE ZBrn; // Born function (-1/eps_r + 1) * 41.84004, for supcrt calc'n of molal volume
|
|
LDBLE dgdP; // dg / dP, pressure derivative of g-function, for supcrt calc'n of molal volume
|
|
|
|
int need_temp_msg;
|
|
LDBLE solution_mass, solution_volume;
|
|
|
|
/* phqalloc.cpp ------------------------------- */
|
|
PHRQMemHeader* s_pTail;
|
|
|
|
/* Basic */
|
|
PBasic* basic_interpreter;
|
|
|
|
double (*basic_callback_ptr) (double x1, double x2, const char* str, void* cookie);
|
|
void* basic_callback_cookie;
|
|
#ifdef IPHREEQC_NO_FORTRAN_MODULE
|
|
double (*basic_fortran_callback_ptr) (double* x1, double* x2, const char* str, size_t l);
|
|
#else
|
|
double (*basic_fortran_callback_ptr) (double* x1, double* x2, const char* str, int l);
|
|
#endif
|
|
#if defined(SWIG) || defined(SWIG_IPHREEQC)
|
|
class BasicCallback* basicCallback;
|
|
void SetCallback(BasicCallback* cb) { basicCallback = cb; }
|
|
#endif
|
|
|
|
/* cl1.cpp ------------------------------- */
|
|
std::vector<double> x_arg, res_arg, scratch;
|
|
/* gases.cpp ------------------------------- */
|
|
LDBLE a_aa_sum, b2, b_sum, R_TK;
|
|
|
|
/* input.cpp ------------------------------- */
|
|
int check_line_return;
|
|
int reading_db;
|
|
|
|
/* integrate.cpp ------------------------------- */
|
|
LDBLE midpoint_sv;
|
|
LDBLE z_global, xd_global, alpha_global;
|
|
|
|
/* inverse.cpp ------------------------------- */
|
|
size_t max_row_count, max_column_count;
|
|
int carbon;
|
|
std::vector<const char*> col_name, row_name;
|
|
size_t count_rows, count_optimize;
|
|
size_t col_phases, col_redox, col_epsilon, col_ph, col_water,
|
|
col_isotopes, col_phase_isotopes;
|
|
size_t row_mb, row_fract, row_charge, row_carbon, row_isotopes,
|
|
row_epsilon, row_isotope_epsilon, row_water;
|
|
std::vector<double> inv_zero, array1, inv_res, inv_delta1, delta2,
|
|
delta3, inv_cu, delta_save;
|
|
std::vector<double> min_delta, max_delta;
|
|
std::vector<int> inv_iu, inv_is;
|
|
size_t klmd, nklmd, n2d;
|
|
int kode, iter;
|
|
LDBLE toler, error, max_pct, scaled_error;
|
|
class master* master_alk;
|
|
std::vector<int> row_back, col_back;
|
|
std::vector<unsigned long> good, bad, minimal;
|
|
size_t max_good, max_bad, max_minimal;
|
|
int count_good, count_bad, count_minimal, count_calls;
|
|
unsigned long soln_bits, phase_bits, current_bits, temp_bits;
|
|
FILE* netpath_file;
|
|
int count_inverse_models, count_pat_solutions;
|
|
int min_position[32], max_position[32], now[32];
|
|
std::vector <std::string> inverse_heading_names;
|
|
|
|
/* kinetics.cpp ------------------------------- */
|
|
public:
|
|
int count_pp, count_pg, count_ss;
|
|
void* cvode_kinetics_ptr;
|
|
int cvode_test;
|
|
int cvode_error;
|
|
int cvode_n_user;
|
|
int cvode_n_reactions;
|
|
realtype cvode_step_fraction;
|
|
realtype cvode_rate_sim_time;
|
|
realtype cvode_rate_sim_time_start;
|
|
realtype cvode_last_good_time;
|
|
realtype cvode_prev_good_time;
|
|
N_Vector cvode_last_good_y;
|
|
N_Vector cvode_prev_good_y;
|
|
M_Env kinetics_machEnv;
|
|
N_Vector kinetics_y, kinetics_abstol;
|
|
void* kinetics_cvode_mem;
|
|
cxxSSassemblage* cvode_ss_assemblage_save;
|
|
cxxPPassemblage* cvode_pp_assemblage_save;
|
|
protected:
|
|
std::vector<double> m_temp, m_original, rk_moles, x0_moles;
|
|
int set_and_run_attempt;
|
|
|
|
/* model.cpp ------------------------------- */
|
|
int gas_in;
|
|
LDBLE min_value;
|
|
std::vector<double> normal, ineq_array, res, cu, zero, delta1;
|
|
std::vector<int> iu, is, back_eq;
|
|
|
|
/* phrq_io_output.cpp ------------------------------- */
|
|
int forward_output_to_log;
|
|
|
|
/* phreeqc_files.cpp ------------------------------- */
|
|
std::string default_data_base;
|
|
/* Pitzer */
|
|
int pitzer_model, sit_model, pitzer_pe;
|
|
int full_pitzer, always_full_pitzer, ICON, IC;
|
|
LDBLE COSMOT;
|
|
LDBLE AW;
|
|
LDBLE VP, DW0;
|
|
std::vector<class pitz_param*> pitz_params;
|
|
std::map< std::string, size_t > pitz_param_map;
|
|
std::vector<class theta_param*> theta_params;
|
|
int use_etheta;
|
|
LDBLE OTEMP, OPRESS;
|
|
LDBLE A0;
|
|
class pitz_param* aphi/* = NULL*/;
|
|
std::vector<class species*> spec;
|
|
class species** cations, ** anions, ** neutrals; // pointers to spec
|
|
int count_cations, count_anions, count_neutrals;
|
|
int MAXCATIONS, FIRSTANION, MAXNEUTRAL;
|
|
class pitz_param* mcb0, * mcb1, * mcc0;
|
|
std::vector<int> IPRSNT;
|
|
std::vector<double> M, LGAMMA;
|
|
LDBLE BK[23], DK[23];
|
|
|
|
LDBLE dummy;
|
|
|
|
/* print.cpp ------------------------------- */
|
|
|
|
/* read.cpp */
|
|
const char* prev_next_char;
|
|
#if defined PHREEQ98
|
|
int shifts_as_points;
|
|
#endif
|
|
|
|
/* read_class.cxx */
|
|
dumper dump_info;
|
|
StorageBinList delete_info;
|
|
runner run_info;
|
|
char* sformatf_buffer;
|
|
size_t sformatf_buffer_size;
|
|
|
|
/* readtr.cpp */
|
|
std::string dump_file_name_cpp;
|
|
|
|
/* sit.cpp ------------------------------- */
|
|
std::vector<class pitz_param*> sit_params;
|
|
std::map< std::string, size_t > sit_param_map;
|
|
LDBLE sit_A0;
|
|
int sit_count_cations, sit_count_anions, sit_count_neutrals;
|
|
int sit_MAXCATIONS, sit_FIRSTANION, sit_MAXNEUTRAL;
|
|
std::vector<int> sit_IPRSNT;
|
|
std::vector<double> sit_M, sit_LGAMMA;
|
|
std::vector<int> s_list, cation_list, neutral_list, anion_list, ion_list, param_list;
|
|
|
|
/* tidy.cpp ------------------------------- */
|
|
LDBLE a0, a1, kc, kb;
|
|
|
|
/* tally.cpp ------------------------------- */
|
|
class tally_buffer* t_buffer;
|
|
size_t tally_count_component;
|
|
//class tally* tally_table;
|
|
std::vector<class tally> tally_table;
|
|
size_t count_tally_table_columns;
|
|
size_t count_tally_table_rows;
|
|
|
|
/* transport.cpp ------------------------------- */
|
|
class sol_D* sol_D;
|
|
class sol_D* sol_D_dbg;
|
|
class J_ij* J_ij, * J_ij_il;
|
|
int J_ij_count_spec;
|
|
|
|
class M_S* m_s;
|
|
int count_m_s;
|
|
LDBLE tot1_h, tot1_o, tot2_h, tot2_o;
|
|
LDBLE diffc_max, diffc_tr, J_ij_sum;
|
|
int transp_surf;
|
|
LDBLE* heat_mix_array;
|
|
LDBLE* temp1, * temp2;
|
|
int nmix, heat_nmix;
|
|
LDBLE heat_mix_f_imm, heat_mix_f_m;
|
|
int warn_MCD_X, warn_fixed_Surf;
|
|
LDBLE current_x, current_A, fix_current; // current: coulomb / s, Ampere, fixed current (Ampere)
|
|
|
|
/* utilities.cpp ------------------------------- */
|
|
int spinner;
|
|
std::map<std::string, double> gfw_map;
|
|
std::map<const char*, int> rates_map;
|
|
|
|
/* new after release of Version 3 */
|
|
std::map<std::string, std::vector < std::string> > sum_species_map;
|
|
std::map<std::string, std::vector < std::string> > sum_species_map_db;
|
|
|
|
friend class PBasic;
|
|
friend class ChartObject;
|
|
friend class IPhreeqc;
|
|
friend class TestIPhreeqc;
|
|
friend class TestSelectedOutput;
|
|
friend class IPhreeqcMMS;
|
|
friend class IPhreeqcPhast;
|
|
friend class PhreeqcRM;
|
|
|
|
std::vector<int> keycount; // used to mark keywords that have been read
|
|
|
|
public:
|
|
static const class const_iso iso_defaults[];
|
|
static const int count_iso_defaults;
|
|
};
|
|
#endif /* _INC_PHREEQC_H */
|
|
|
|
#ifndef _INC_ISFINITE_H
|
|
#define _INC_ISFINITE_H
|
|
/*********************************
|
|
isfinite handling
|
|
(Note: Should NOT be guarded)
|
|
**********************************/
|
|
|
|
#if defined (PHREEQ98) || defined (_MSC_VER)
|
|
# define HAVE_FINITE
|
|
# define finite _finite
|
|
#else /*defined (PHREEQ98) || defined (_MSC_VER)*/
|
|
# if defined(DJGPP)
|
|
# define HAVE_FINITE
|
|
# endif
|
|
#endif /*defined (PHREEQ98) || defined (_MSC_VER)*/
|
|
|
|
#if defined(HAVE_ISFINITE)
|
|
# if __GNUC__ && (__cplusplus >= 201103L)
|
|
# define PHR_ISFINITE(x) std::isfinite(x)
|
|
# else
|
|
# define PHR_ISFINITE(x) std::isfinite(x) /* changed when <math.h> was changed to <cmath> */
|
|
# endif
|
|
#elif defined(HAVE_FINITE)
|
|
# define PHR_ISFINITE(x) finite(x)
|
|
#elif defined(HAVE_ISNAN)
|
|
# define PHR_ISFINITE(x) ( ((x) == 0.0) || ((!std::isnan(x)) && ((x) != (2.0 * (x)))) )
|
|
#else
|
|
# define PHR_ISFINITE(x) ( ((x) == 0.0) || (((x) == (x)) && ((x) != (2.0 * (x)))) )
|
|
#endif
|
|
#endif // _INC_ISFINITE_H
|
|
|
|
#ifndef _INC_UTILITIES_NAMESPACE_H
|
|
#define _INC_UTILITIES_NAMESPACE_H
|
|
namespace Utilities
|
|
{
|
|
LDBLE get_nan(void);
|
|
|
|
// operations on maps of entities (Solution, Exchange, ...)
|
|
template < typename T >
|
|
void Rxn_dump_raw(const T& b, std::ostream& s_oss, unsigned int indent)
|
|
{
|
|
typename T::const_iterator it;
|
|
for (it = b.begin(); it != b.end(); ++it)
|
|
{
|
|
// Adding logic to dump only non-negative entities
|
|
//if (it->second.Get_n_user() >= 0)
|
|
if (it->first >= 0 && it->second.Get_n_user() >= 0)
|
|
{
|
|
it->second.dump_raw(s_oss, indent);
|
|
}
|
|
}
|
|
return;
|
|
}
|
|
|
|
template < typename T >
|
|
void Rxn_dump_raw_range(const T& b, std::ostream& s_oss, int start, int end, unsigned int indent)
|
|
{
|
|
typename T::const_iterator it;
|
|
for (int i = start; i <= end; i++)
|
|
{
|
|
if (i < 0) continue;
|
|
it = b.find(i);
|
|
if (it != b.end())
|
|
{
|
|
it->second.dump_raw(s_oss, indent);
|
|
}
|
|
}
|
|
return;
|
|
}
|
|
|
|
template < typename T >
|
|
T* Rxn_find(std::map < int, T >& b, int i)
|
|
{
|
|
if (b.find(i) != b.end())
|
|
{
|
|
return (&(b.find(i)->second));
|
|
}
|
|
else
|
|
{
|
|
return (NULL);
|
|
}
|
|
}
|
|
|
|
template < typename T >
|
|
int Rxn_next_user_number(std::map < int, T >& b)
|
|
{
|
|
int ret = 0;
|
|
if (b.size() != 0)
|
|
{
|
|
ret = b.rbegin()->first + 1;
|
|
}
|
|
return ret;
|
|
}
|
|
|
|
template < typename T >
|
|
T* Rxn_copy(std::map < int, T >& b, int i, int j)
|
|
{
|
|
typename std::map < int, T >::iterator it;
|
|
it = b.find(i);
|
|
if (it != b.end())
|
|
{
|
|
b[j] = it->second;
|
|
it = b.find(j);
|
|
it->second.Set_n_user(j);
|
|
it->second.Set_n_user_end(j);
|
|
return &(it->second);
|
|
}
|
|
else
|
|
{
|
|
return (NULL);
|
|
}
|
|
}
|
|
|
|
template < typename T >
|
|
void Rxn_copies(std::map < int, T >& b, int n_user, int n_user_end)
|
|
{
|
|
if (n_user_end <= n_user) return;
|
|
typename std::map < int, T >::iterator it;
|
|
it = b.find(n_user);
|
|
if (it != b.end())
|
|
{
|
|
for (int j = n_user + 1; j <= n_user_end; j++)
|
|
{
|
|
b[j] = it->second;
|
|
it = b.find(j);
|
|
it->second.Set_n_user(j);
|
|
it->second.Set_n_user_end(j);
|
|
}
|
|
}
|
|
}
|
|
template < typename T >
|
|
int Rxn_read_raw(std::map < int, T >& m, std::set < int >& s, Phreeqc* phreeqc_cookie)
|
|
{
|
|
typename std::map < int, T >::iterator it;
|
|
assert(!phreeqc_cookie->reading_database());
|
|
|
|
T entity(phreeqc_cookie->Get_phrq_io());
|
|
|
|
CParser parser(phreeqc_cookie->Get_phrq_io());
|
|
entity.read_raw(parser);
|
|
|
|
// Store
|
|
if (entity.Get_base_error_count() == 0)
|
|
{
|
|
m[entity.Get_n_user()] = entity;
|
|
}
|
|
|
|
// Make copies if necessary
|
|
Utilities::Rxn_copies(m, entity.Get_n_user(), entity.Get_n_user_end());
|
|
for (int i = entity.Get_n_user(); i <= entity.Get_n_user_end(); i++)
|
|
{
|
|
s.insert(i);
|
|
}
|
|
return phreeqc_cookie->cleanup_after_parser(parser);
|
|
}
|
|
|
|
template < typename T >
|
|
int Rxn_read_modify(std::map < int, T >& m, std::set < int >& s, Phreeqc* phreeqc_cookie)
|
|
{
|
|
typename std::map < int, T >::iterator it;
|
|
|
|
CParser parser(phreeqc_cookie->Get_phrq_io());
|
|
|
|
std::string key_name;
|
|
std::string::iterator b = parser.line().begin();
|
|
std::string::iterator e = parser.line().end();
|
|
CParser::copy_token(key_name, b, e);
|
|
|
|
cxxNumKeyword nk;
|
|
nk.read_number_description(parser);
|
|
T* entity_ptr = Utilities::Rxn_find(m, nk.Get_n_user());
|
|
if (!entity_ptr)
|
|
{
|
|
std::ostringstream errstr;
|
|
errstr << "Could not find " << key_name << " " << nk.Get_n_user() << ", ignoring modify data.\n";
|
|
phreeqc_cookie->warning_msg(errstr.str().c_str());
|
|
//phreeqc_cookie->error_msg(errstr.str().c_str(), PHRQ_io::OT_STOP);
|
|
|
|
// Don't throw, read data into dummy entity, then ignore
|
|
T entity;
|
|
entity_ptr = &entity;
|
|
entity_ptr->read_raw(parser, false);
|
|
return phreeqc_cookie->cleanup_after_parser(parser);
|
|
}
|
|
|
|
entity_ptr->read_raw(parser, false);
|
|
entity_ptr->Set_n_user(nk.Get_n_user());
|
|
entity_ptr->Set_n_user_end(nk.Get_n_user_end());
|
|
entity_ptr->Set_description(nk.Get_description());
|
|
s.insert(entity_ptr->Get_n_user());
|
|
|
|
return phreeqc_cookie->cleanup_after_parser(parser);
|
|
}
|
|
|
|
template < typename T >
|
|
int SB_read_modify(std::map < int, T >& m, CParser& parser)
|
|
{
|
|
typename std::map < int, T >::iterator it;
|
|
|
|
std::string key_name;
|
|
std::string::iterator b = parser.line().begin();
|
|
std::string::iterator e = parser.line().end();
|
|
CParser::copy_token(key_name, b, e);
|
|
|
|
cxxNumKeyword nk;
|
|
nk.read_number_description(parser);
|
|
T* entity_ptr = Utilities::Rxn_find(m, nk.Get_n_user());
|
|
if (!entity_ptr)
|
|
{
|
|
std::ostringstream errstr;
|
|
errstr << "Could not find " << key_name << " " << nk.Get_n_user() << ", ignoring modify data.\n";
|
|
//io->warning_msg(errstr.str().c_str());
|
|
|
|
// Don't throw, read data into dummy entity, then ignore
|
|
T entity;
|
|
entity_ptr = &entity;
|
|
entity_ptr->read_raw(parser, false);
|
|
return FALSE;
|
|
}
|
|
|
|
entity_ptr->read_raw(parser, false);
|
|
entity_ptr->Set_n_user(nk.Get_n_user());
|
|
entity_ptr->Set_n_user_end(nk.Get_n_user_end());
|
|
entity_ptr->Set_description(nk.Get_description());
|
|
|
|
return TRUE;
|
|
}
|
|
|
|
template < typename T >
|
|
void Rxn_mix(std::map <int, cxxMix>& mix_map, std::map < int, T >& entity_map, Phreeqc* phreeqc_cookie)
|
|
{
|
|
std::map<int, cxxMix>::iterator mix_it;
|
|
for (mix_it = mix_map.begin(); mix_it != mix_map.end(); mix_it++)
|
|
{
|
|
T entity(entity_map, mix_it->second, mix_it->second.Get_n_user(), phreeqc_cookie->Get_phrq_io());
|
|
entity_map[mix_it->second.Get_n_user()] = entity;
|
|
Utilities::Rxn_copies(entity_map, mix_it->second.Get_n_user(), mix_it->second.Get_n_user_end());
|
|
}
|
|
mix_map.clear();
|
|
}
|
|
|
|
} // namespace Utilities
|
|
|
|
|
|
#if defined(PHREEQCI_GUI)
|
|
void PhreeqcIWait(Phreeqc* phreeqc);
|
|
#endif
|
|
|
|
#if !defined(NDEBUG) && defined(WIN32_MEMORY_DEBUG)
|
|
#define string_duplicate(s) _string_duplicate(s, __FILE__, __LINE__)
|
|
#endif
|
|
#if defined(_DEBUG)
|
|
char* _string_duplicate(const char* token, const char* szFileName, int nLine);
|
|
#endif
|
|
|
|
#endif //_INC_UTILITIES_NAMESPACE_H
|
|
|
|
#ifndef _INC_MISSING_SNPRINTF_H
|
|
#define _INC_MISSING_SNPRINTF_H
|
|
|
|
// Section _INC_MISSING_SNPRINTF_H is based on
|
|
// https://stackoverflow.com/questions/2915672/snprintf-and-visual-studio-2010
|
|
|
|
#if defined(_MSC_VER) && (_MSC_VER < 1900)
|
|
#if (_MSC_VER <= 1700) // VS2012
|
|
namespace std {
|
|
__inline bool isnan(double num) {
|
|
return _isnan(num) != 0;
|
|
}
|
|
}
|
|
#endif
|
|
#include <stdarg.h>
|
|
|
|
#define snprintf c99_snprintf
|
|
#define vsnprintf c99_vsnprintf
|
|
|
|
#pragma warning( push )
|
|
// warning C4793: 'vararg' : causes native code generation
|
|
#pragma warning( disable : 4793 )
|
|
|
|
__inline int c99_vsnprintf(char *outBuf, size_t size, const char *format, va_list ap)
|
|
{
|
|
int count = -1;
|
|
|
|
if (size != 0)
|
|
count = _vsnprintf_s(outBuf, size, _TRUNCATE, format, ap);
|
|
if (count == -1)
|
|
count = _vscprintf(format, ap);
|
|
|
|
return count;
|
|
}
|
|
|
|
__inline int c99_snprintf(char *outBuf, size_t size, const char *format, ...)
|
|
{
|
|
int count;
|
|
va_list ap;
|
|
|
|
va_start(ap, format);
|
|
count = c99_vsnprintf(outBuf, size, format, ap);
|
|
va_end(ap);
|
|
|
|
return count;
|
|
}
|
|
#pragma warning( pop )
|
|
#endif // defined(_MSC_VER) && (_MSC_VER < 1900)
|
|
|
|
#endif //_INC_MISSING_SNPRINTF_H
|