#ifndef _INC_PHREEQC_H #define _INC_PHREEQC_H #if defined(WIN32) # if defined(PHREEQCI_GUI) # ifndef WINVER # define WINVER 0x0400 # endif # include # endif # include # if defined(PHREEQCI_GUI) # include "../../resource.h" # endif #endif #if defined(WIN32_MEMORY_DEBUG) #define _CRTDBG_MAP_ALLOC #include #endif #ifndef boolean typedef unsigned char boolean; #endif /* ---------------------------------------------------------------------- * INCLUDE FILES * ---------------------------------------------------------------------- */ #include #include #include #include #include #include #include #include #include #include #include "phrqtype.h" #include "cvdense.h" #include "runner.h" #include "dumper.h" #include "PHRQ_io.h" #include "SelectedOutput.h" #include "UserPunch.h" #ifdef MULTICHART #include "ChartHandler.h" #endif #include "Keywords.h" #include "Pressure.h" #include "cxxMix.h" #include "Use.h" #include "Surface.h" #ifdef SWIG_SHARED_OBJ #include "thread.h" #endif class cxxNameDouble; class cxxKinetics; class cxxKineticsComp; class cxxExchange; class cxxExchComp; class cxxGasPhase; class cxxTemperature; class cxxPPassemblage; class cxxPPassemblageComp; class cxxReaction; class cxxSolution; class cxxISolutionComp; class cxxSolutionIsotope; class cxxSSassemblage; class cxxSS; class cxxStorageBin; class PBasic; #include "global_structures.h" class Phreeqc { public: Phreeqc(PHRQ_io* io = NULL); Phreeqc(const Phreeqc& src); void InternalCopy(const Phreeqc* pSrc); Phreeqc& operator=(const Phreeqc& rhs); ~Phreeqc(void); public: // // Phreeqc class methods // // advection.cpp ------------------------------- int advection(void); // basicsubs.cpp ------------------------------- int basic_compile(const char* commands, void** lnbase, void** vbase, void** lpbase); int basic_run(char* commands, void* lnbase, void* vbase, void* lpbase); void basic_free(void); #ifdef IPHREEQC_NO_FORTRAN_MODULE double basic_callback(double x1, double x2, char* str); #else double basic_callback(double x1, double x2, const char* str); #endif void register_basic_callback(double (*fcn)(double x1, double x2, const char* str, void* cookie), void* cookie1); #ifdef IPHREEQC_NO_FORTRAN_MODULE void register_fortran_basic_callback(double (*fcn)(double* x1, double* x2, char* str, size_t l)); #else void register_fortran_basic_callback(double (*fcn)(double* x1, double* x2, const char* str, int l)); #endif LDBLE activity(const char* species_name); LDBLE activity_coefficient(const char* species_name); LDBLE log_activity_coefficient(const char* species_name); LDBLE aqueous_vm(const char* species_name); LDBLE phase_vm(const char* phase_name); LDBLE diff_c(const char* species_name); LDBLE setdiff_c(const char* species_name, double d); LDBLE sa_declercq(double type, double sa, double d, double m, double m0, double gfw); LDBLE calc_SC(void); /* VP: Density Start */ LDBLE calc_dens(void); /* VP: Density End */ LDBLE calc_logk_n(const char* name); LDBLE calc_logk_p(const char* name); LDBLE calc_logk_s(const char* name); LDBLE calc_deltah_s(const char* name); LDBLE calc_deltah_p(const char* name); LDBLE dh_a0(const char* name); LDBLE dh_bdot(const char* name); LDBLE calc_surface_charge(const char* surface_name); LDBLE calc_t_sc(const char* name); LDBLE diff_layer_total(const char* total_name, const char* surface_name); LDBLE edl_species(const char* surf_name, LDBLE* count, char*** names, LDBLE** moles, LDBLE* area, LDBLE* thickness); int get_edl_species(cxxSurfaceCharge& charge_ref); LDBLE equi_phase(const char* phase_name); LDBLE equi_phase_delta(const char* phase_name); LDBLE equivalent_fraction(const char* name, LDBLE* eq, std::string& elt_name); LDBLE find_gas_comp(const char* gas_comp_name); LDBLE find_gas_p(void); LDBLE find_gas_vm(void); LDBLE find_misc1(const char* ss_name); LDBLE find_misc2(const char* ss_name); LDBLE find_ss_comp(const char* ss_comp_name); LDBLE get_calculate_value(const char* name); char* iso_unit(const char* total_name); LDBLE iso_value(const char* total_name); LDBLE kinetics_moles(const char* kinetics_name); LDBLE kinetics_moles_delta(const char* kinetics_name); LDBLE log_activity(const char* species_name); LDBLE log_molality(const char* species_name); LDBLE molality(const char* species_name); LDBLE pressure(void); LDBLE pr_pressure(const char* phase_name); LDBLE pr_phi(const char* phase_name); LDBLE saturation_ratio(const char* phase_name); int saturation_index(const char* phase_name, LDBLE* iap, LDBLE* si); int solution_number(void); LDBLE solution_sum_secondary(const char* total_name); LDBLE sum_match_gases(const char* stemplate, const char* name); LDBLE sum_match_species(const char* stemplate, const char* name); LDBLE sum_match_ss(const char* stemplate, const char* name); int match_elts_in_species(const char* name, const char* stemplate); int extract_bracket(const char** string, char* bracket_string); LDBLE surf_total(const char* total_name, const char* surface_name); LDBLE surf_total_no_redox(const char* total_name, const char* surface_name); static int system_species_compare(const void* ptr1, const void* ptr2); static int system_species_compare_name(const void* ptr1, const void* ptr2); LDBLE system_total(const char* total_name, LDBLE* count, char*** names, char*** types, LDBLE** moles, int i); std::string kinetics_formula(std::string kinetics_name, cxxNameDouble& stoichiometry); std::string phase_formula(std::string phase_name, cxxNameDouble& stoichiometry); std::string species_formula(std::string phase_name, cxxNameDouble& stoichiometry); LDBLE list_ss(std::string ss_name, cxxNameDouble& composition); int system_total_elements(void); int system_total_si(void); int system_total_aq(void); int system_total_ex(void); int system_total_surf(void); int system_total_gas(void); int system_total_equi(void); int system_total_kin(void); int system_total_ss(void); int system_total_elt(const char* total_name); int system_total_elt_secondary(const char* total_name); LDBLE total(const char* total_name); LDBLE total_mole(const char* total_name); int system_total_solids(cxxExchange* exchange_ptr, cxxPPassemblage* pp_assemblage_ptr, cxxGasPhase* gas_phase_ptr, cxxSSassemblage* ss_assemblage_ptr, cxxSurface* surface_ptr); static LDBLE f_rho(LDBLE rho_old, void* cookie); static LDBLE f_Vm(LDBLE v1, void* cookie); LDBLE calc_solution_volume(void); // cl1.cpp ------------------------------- int cl1(int k, int l, int m, int n, int nklmd, int n2d, LDBLE* q, int* kode, LDBLE toler, int* iter, LDBLE* x, LDBLE* res, LDBLE* error, LDBLE* cu, int* iu, int* s, int check); void cl1_space(int check, int n2d, int klm, int nklmd); // cl1mp.cpp ------------------------------- int cl1mp(int k, int l, int m, int n, int nklmd, int n2d, LDBLE* q_arg, int* kode, LDBLE toler, int* iter, LDBLE* x_arg, LDBLE* res_arg, LDBLE* error, LDBLE* cu_arg, int* iu, int* s, int check, LDBLE censor_arg); // class_main.cpp ------------------------------- int write_banner(void); /* default.cpp */ public: //int close_input_files(void); //int close_output_files(void); //static int istream_getc(void* cookie); int process_file_names(int argc, char* argv[], std::istream** db_cookie, std::istream** input_cookie, int log); /* PHRQ_io_output.cpp */ void screen_msg(const char* str); void echo_msg(const char* err_str); int warning_msg(const char* err_str); void set_forward_output_to_log(int value); int get_forward_output_to_log(void); // dump_ostream bool dump_open(const char* file_name); void dump_flush(void); void dump_close(void); void dump_msg(const char* str); // log_ostream bool log_open(const char* file_name); void log_flush(void); void log_close(void); void log_msg(const char* str); // error_ostream bool error_open(const char* file_name); void error_flush(void); void error_close(void); void error_msg(const char* str, bool stop = false); // output_ostream bool output_open(const char* file_name); void output_flush(void); void output_close(void); void output_msg(const char* str); // punch_ostream bool punch_open(const char* file_name, int n_user); void punch_flush(void); void punch_close(void); void punch_msg(const char* str); void fpunchf_heading(const char* name); void fpunchf(const char* name, const char* format, double d); void fpunchf(const char* name, const char* format, char* d); void fpunchf(const char* name, const char* format, int d); void fpunchf_user(int user_index, const char* format, double d); void fpunchf_user(int user_index, const char* format, char* d); int fpunchf_end_row(const char* format); // input.cpp ------------------------------- int reading_database(void); void set_reading_database(int reading_database); int check_line(const char* string, int allow_empty, int allow_eof, int allow_keyword, int print); int check_line_impl(const char* string, int allow_empty, int allow_eof, int allow_keyword, int print); int get_line(void); //int get_logical_line(void* cookie, int* l); int read_database(void); int run_simulations(void); // integrate.cpp ------------------------------- int calc_all_g(void); int calc_init_g(void); int initial_surface_water(void); int sum_diffuse_layer(cxxSurfaceCharge* surface_charge_ptr1); int calc_all_donnan(void); int calc_init_donnan(void); LDBLE g_function(LDBLE x_value); LDBLE midpnt(LDBLE x1, LDBLE x2, int n); void polint(LDBLE* xa, LDBLE* ya, int n, LDBLE xv, LDBLE* yv, LDBLE* dy); LDBLE qromb_midpnt(cxxSurfaceCharge* charge_ptr, LDBLE x1, LDBLE x2); LDBLE calc_psi_avg(cxxSurfaceCharge* charge_ptr, LDBLE surf_chrg_eq); // inverse.cpp ------------------------------- int inverse_models(void); int add_to_file(const char* filename, const char* string); int bit_print(unsigned long bits, int l); int carbon_derivs(class inverse* inv_ptr); int check_isotopes(class inverse* inv_ptr); int check_solns(class inverse* inv_ptr); bool set_isotope_unknowns(class inverse* inv_ptrs); cxxSolutionIsotope* get_isotope(cxxSolution* solution_ptr, const char* elt); LDBLE get_inv_total(cxxSolution* solution_ptr, const char* elt); int isotope_balance_equation(class inverse* inv_ptr, int row, int n); int post_mortem(void); bool test_cl1_solution(void); unsigned long get_bits(unsigned long bits, int position, int number); unsigned long minimal_solve(class inverse* inv_ptr, unsigned long minimal_bits); void dump_netpath(class inverse* inv_ptr); int dump_netpath_pat(class inverse* inv_ptr); int next_set_phases(class inverse* inv_ptr, int first_of_model_size, int model_size); int phase_isotope_inequalities(class inverse* inv_ptr); int print_model(class inverse* inv_ptr); int punch_model_heading(class inverse* inv_ptr); int punch_model(class inverse* inv_ptr); void print_isotope(FILE* netpath_file, cxxSolution* solution_ptr, const char* elt, const char* string); void print_total(FILE* netpath_file, cxxSolution* solution_ptr, const char* elt, const char* string); void print_total_multi(FILE* netpath_file, cxxSolution* solution_ptr, const char* string, const char* elt0, const char* elt1, const char* elt2, const char* elt3, const char* elt4); void print_total_pat(FILE* netpath_file, const char* elt, const char* string); int range(class inverse* inv_ptr, unsigned long cur_bits); int save_bad(unsigned long bits); int save_good(unsigned long bits); int save_minimal(unsigned long bits); unsigned long set_bit(unsigned long bits, int position, int value); int setup_inverse(class inverse* inv_ptr); int set_initial_solution(int n_user_old, int n_user_new); int set_ph_c(class inverse* inv_ptr, int i, cxxSolution* soln_ptr_orig, int n_user_new, LDBLE d_alk, LDBLE ph_factor, LDBLE alk_factor); int shrink(class inverse* inv_ptr, LDBLE* array_in, LDBLE* array_out, int* k, int* l, int* m, int* n, unsigned long cur_bits, LDBLE* delta_l, int* col_back_l, int* row_back_l); int solve_inverse(class inverse* inv_ptr); int solve_with_mask(class inverse* inv_ptr, unsigned long cur_bits); int subset_bad(unsigned long bits); int subset_minimal(unsigned long bits); int superset_minimal(unsigned long bits); int write_optimize_names(class inverse* inv_ptr); // isotopes.cpp ------------------------------- int add_isotopes(cxxSolution& solution_ptr); int calculate_values(void); int calculate_isotope_moles(class element* elt_ptr, cxxSolution* solution_ptr, LDBLE total_moles); LDBLE convert_isotope(class master_isotope* master_isotope_ptr, LDBLE ratio); int from_pcil(class master_isotope* master_isotope_ptr); int from_permil(class master_isotope* master_isotope_ptr, LDBLE major_total); int from_pct(class master_isotope* master_isotope_ptr, LDBLE major_total); int from_tu(class master_isotope* master_isotope_ptr); class calculate_value* calculate_value_alloc(void); int calculate_value_free(class calculate_value* calculate_value_ptr); class calculate_value* calculate_value_search(const char* name); class calculate_value* calculate_value_store(const char* name, int replace_if_found); class isotope_alpha* isotope_alpha_alloc(void); class isotope_alpha* isotope_alpha_search(const char* name); class isotope_alpha* isotope_alpha_store(const char* name, int replace_if_found); class isotope_ratio* isotope_ratio_alloc(void); class isotope_ratio* isotope_ratio_search(const char* name); class isotope_ratio* isotope_ratio_store(const char* name, int replace_if_found); class master_isotope* master_isotope_store(const char* name, int replace_if_found); class master_isotope* master_isotope_alloc(void); class master_isotope* master_isotope_search(const char* name); int print_initial_solution_isotopes(void); int print_isotope_ratios(void); int print_isotope_alphas(void); int punch_isotopes(void); int punch_calculate_values(void); int read_calculate_values(void); int read_isotopes(void); int read_isotope_ratios(void); int read_isotope_alphas(void); int calculate_value_init(class calculate_value* calculate_value_ptr); int isotope_alpha_init(class isotope_alpha* isotope_alpha_ptr); int isotope_ratio_init(class isotope_ratio* isotope_ratio_ptr); int master_isotope_init(class master_isotope* master_isotope_ptr); // kinetics.cpp ------------------------------- void cvode_init(void); bool cvode_update_reactants(int i, int nsaver, bool save_it); int run_reactions(int i, LDBLE kin_time, int use_mix, LDBLE step_fraction); int set_and_run(int i, int use_mix, int use_kinetics, int nsaver, LDBLE step_fraction); int set_and_run_wrapper(int i, int use_mix, int use_kinetics, int nsaver, LDBLE step_fraction); int set_advection(int i, int use_mix, int use_kinetics, int nsaver); int free_cvode(void); public: 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, 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& 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 phase_ptrs, LDBLE P, LDBLE TK, LDBLE V_m); LDBLE calc_PR(); int calc_vm(LDBLE tc, LDBLE pa); int clear(void); int convert_units(cxxSolution* solution_ptr); class unknown* find_surface_charge_unknown(std::string& str_ptr, int plane); std::vector 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& 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_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& v); bool read_vector_ints(const char** cptr, std::vector& v, int positive); bool read_vector_t_f(const char** ptr, std::vector& v); int read_master_species(void); int read_mix(void); int read_entity_mix(std::map& 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& 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 elt_list_internal_copy(const std::vector& el); std::vector 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); static int phase_compare(const void* ptr1, const void* ptr2); 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& 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(void); 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 parse_couple(char* token); 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& list_c); size_t list_EquilibriumPhases(std::list& list_pp); size_t list_GasComponents(std::list& list_gc); size_t list_KineticReactions(std::list& list_kr); size_t list_SolidSolutions(std::list& list_comps, std::list& list_names); size_t list_Surfaces(std::list& surftype, std::list& surf); size_t list_Exchangers(std::list& 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& Get_Rxn_solution_map() { return this->Rxn_solution_map; } std::map& Get_Rxn_exchange_map() { return this->Rxn_exchange_map; } std::map& Get_Rxn_gas_phase_map() { return this->Rxn_gas_phase_map; } std::map& Get_Rxn_kinetics_map() { return this->Rxn_kinetics_map; } std::map& Get_Rxn_pp_assemblage_map() { return this->Rxn_pp_assemblage_map; } std::map& Get_Rxn_ss_assemblage_map() { return this->Rxn_ss_assemblage_map; } std::map& Get_Rxn_surface_map() { return this->Rxn_surface_map; } std::map& Get_Rxn_mix_map() { return this->Rxn_mix_map; } std::map& Get_Rxn_reaction_map() { return this->Rxn_reaction_map; } std::map& Get_Rxn_temperature_map() { return this->Rxn_temperature_map; } std::map& 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 Rxn_temperature_map; /* ---------------------------------------------------------------------- * Pressures * ---------------------------------------------------------------------- */ std::map Rxn_pressure_map; /* ---------------------------------------------------------------------- * Surface * --------------------------------------------------------------------- */ int g_iterations; LDBLE G_TOL; std::map Rxn_surface_map; std::map charge_group_map; int change_surf_count; struct Change_Surf* change_surf; /* ---------------------------------------------------------------------- * Exchange * ---------------------------------------------------------------------- */ std::map Rxn_exchange_map; /* ---------------------------------------------------------------------- * Kinetics * ---------------------------------------------------------------------- */ std::map Rxn_kinetics_map; bool use_kinetics_limiter; /*---------------------------------------------------------------------- * Save *---------------------------------------------------------------------- */ std::map save_values; 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 inverse; int count_inverse; /*---------------------------------------------------------------------- * Mix *---------------------------------------------------------------------- */ std::map Rxn_mix_map; std::map Dispersion_mix_map; std::map Rxn_solution_mix_map; std::map Rxn_exchange_mix_map; std::map Rxn_gas_phase_mix_map; std::map Rxn_kinetics_mix_map; std::map Rxn_pp_assemblage_mix_map; std::map Rxn_ss_assemblage_mix_map; std::map Rxn_surface_mix_map; /* * List new definitions */ std::set Rxn_new_exchange; std::set Rxn_new_gas_phase; std::set Rxn_new_kinetics; // not used std::set Rxn_new_mix; // not used std::set Rxn_new_pp_assemblage; std::set Rxn_new_pressure; // not used std::set Rxn_new_reaction; // not used std::set Rxn_new_solution; std::set Rxn_new_ss_assemblage; std::set Rxn_new_surface; std::set Rxn_new_temperature; // not used /*---------------------------------------------------------------------- * Irreversible reaction *---------------------------------------------------------------------- */ std::map Rxn_reaction_map; /*---------------------------------------------------------------------- * Gas phase *---------------------------------------------------------------------- */ std::map Rxn_gas_phase_map; /*---------------------------------------------------------------------- * Solid solution *---------------------------------------------------------------------- */ std::map Rxn_ss_assemblage_map; /*---------------------------------------------------------------------- * Pure-phase assemblage *---------------------------------------------------------------------- */ std::map Rxn_pp_assemblage_map; /*---------------------------------------------------------------------- * Species_list *---------------------------------------------------------------------- */ std::vector species_list; /*---------------------------------------------------------------------- * Jacobian and Mass balance lists *---------------------------------------------------------------------- */ std::vector sum_jacob0; /* array of pointers to targets and coefficients for array */ std::vector sum_mb1; /* array of pointers to sources and targets for mass balance summations with coef = 1.0 */ std::vector sum_jacob1; /* array of pointers to sources and targets for array equations with coef = 1.0 */ std::vector sum_mb2; /* array of coefficients and pointers to sources and targets for mass balance summations with coef != 1.0 */ std::vector sum_jacob2; /* array of coefficients and pointers to sources and targets, coef != 1.0 */ std::vector sum_delta; /* array of pointers to sources, targets and coefficients for summing deltas for mass balance equations */ /*---------------------------------------------------------------------- * Solution *---------------------------------------------------------------------- */ std::map Rxn_solution_map; std::vector 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 density_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 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 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 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 elements; class element* element_h_one; /*---------------------------------------------------------------------- * Element List *---------------------------------------------------------------------- */ std::vector elt_list; size_t count_elts; /* number of elements in elt_list = position of next */ /*---------------------------------------------------------------------- * Reaction *---------------------------------------------------------------------- */ bool run_cells_one_step; /*---------------------------------------------------------------------- * Species *---------------------------------------------------------------------- */ std::vector logk; std::string moles_per_kilogram_string; std::vector s; std::vector< std::map < std::string, cxxSpeciesDL > > s_diff_layer; std::vector 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 phases; /*---------------------------------------------------------------------- * Master species *---------------------------------------------------------------------- */ std::vector master; /*---------------------------------------------------------------------- * Unknowns *---------------------------------------------------------------------- */ std::vector 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 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 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 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 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 my_array, delta, residual; int input_error; Keywords::KEYWORDS next_keyword; int parse_error; int paren_count; int iterations; int gamma_iterations; 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 llnl_temp, llnl_adh, llnl_bdh, llnl_bdot, llnl_co2_coefs; //char *selected_output_file_name; std::map SelectedOutput_map; SelectedOutput* current_selected_output; std::map 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 strings_map; std::map elements_map; std::map species_map; std::map phases_map; std::map logk_map; std::map master_isotope_map; #if defined(PHREEQCI_GUI) #include "../../phreeqci_gui.h" #endif /* defined(PHREEQCI_GUI) */ /* ---------------------------------------------------------------------- * ISOTOPES * ---------------------------------------------------------------------- */ std::vector master_isotope; int initial_solution_isotopes; std::vector calculate_value; std::map calculate_value_map; std::vector isotope_ratio; std::map isotope_ratio_map; std::vector isotope_alpha; std::map 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 cell_pore_volume; LDBLE cell_porosity; LDBLE cell_volume; LDBLE cell_saturation; std::vector 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, 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 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 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 inv_zero, array1, inv_res, inv_delta1, delta2, delta3, inv_cu, delta_save; std::vector min_delta, max_delta; std::vector 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 row_back, col_back; std::vector 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 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 m_temp, m_original, rk_moles, x0_moles; int set_and_run_attempt; /* model.cpp ------------------------------- */ int gas_in; LDBLE min_value; std::vector normal, ineq_array, res, cu, zero, delta1; std::vector 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 pitz_params; std::map< std::string, size_t > pitz_param_map; std::vector theta_params; int use_etheta; LDBLE OTEMP, OPRESS; LDBLE A0; class pitz_param* aphi/* = NULL*/; std::vector 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 IPRSNT; std::vector 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 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 sit_IPRSNT; std::vector sit_M, sit_LGAMMA; std::vector 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 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 gfw_map; std::map rates_map; /* new after release of Version 3 */ std::map > sum_species_map; std::map > 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 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) isfinite(x) # endif #elif defined(HAVE_FINITE) # define PHR_ISFINITE(x) finite(x) #elif defined(HAVE_ISNAN) # define PHR_ISFINITE(x) ( ((x) == 0.0) || ((!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) { 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 & mix_map, std::map < int, T >& entity_map, Phreeqc* phreeqc_cookie) { std::map::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