pyEQL 1.4.0rc9__cp310-cp310-macosx_10_9_x86_64.whl

pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/global_structures.h

@@ -0,0 +1,1672 @@
+#ifndef _INC_GLOBAL_STRUCTURES_H
+#define _INC_GLOBAL_STRUCTURES_H
+#include "Surface.h"
+#include "GasPhase.h"
+/* ----------------------------------------------------------------------
+ *   #define DEFINITIONS
+ * ---------------------------------------------------------------------- */
+#if !defined(NAN)
+#  if defined(_MSC_VER) && (_MSC_VER <= 1700) // VS2012
+//   https://learn.microsoft.com/en-us/cpp/preprocessor/predefined-macros?view=msvc-170     
+#    include <limits>
+#    define NAN std::numeric_limits<double>::signaling_NaN()
+#  else
+#    define NAN nan("1")
+#  endif
+#endif
+#define MISSING -9999.999            
+#include "NA.h"   /* NA = not available */
+
+#define F_C_MOL 96493.5			/* C/mol or joule/volt-eq */
+#define F_KJ_V_EQ  96.4935		/* kJ/volt-eq */
+#define F_KCAL_V_EQ 23.0623		/* kcal/volt-eq */
+#define R_LITER_ATM 0.0820597	/* L-atm/deg-mol */
+#define R_KCAL_DEG_MOL 0.00198726	/* kcal/deg-mol */
+#define R_KJ_DEG_MOL 0.00831470	/* kJ/deg-mol */
+#define EPSILON 78.5			/* dialectric constant, dimensionless. Is calculated as eps_r(P, T) in calc_dielectrics. Update the code?? */
+#define EPSILON_ZERO 8.854e-12	/* permittivity of free space, C/V-m = C**2/m-J */
+#define JOULES_PER_CALORIE 4.1840
+#define PASCAL_PER_ATM 1.01325E5 /* conversion from atm to Pa */
+#define AVOGADRO 6.02252e23		/* atoms / mole */
+#define pi 3.14159265358979
+#define AH2O_FACTOR 0.017
+
+#define TRUE 1
+#define FALSE 0
+#define OK 1
+#define ERROR 0
+#define STOP 1
+#define CONTINUE 0
+
+#define OPTION_EOF -1
+#define OPTION_KEYWORD -2
+#define OPTION_ERROR -3
+#define OPTION_DEFAULT -4
+#define OPT_1 -5
+
+#define DISP 2
+#define STAG 3
+#define NOMIX 4
+#define MIX_BS 5 // mix boundary solutions in electromigration
+
+#define CONVERGED 2
+#define MASS_BALANCE 3
+
+#define REWRITE 2
+#define INIT -1
+
+/* check_line values, plus EMPTY, EOF, OK */
+#define KEYWORD 3
+
+/* copy_token values */
+#define EMPTY 2
+#define UPPER 4
+#define LOWER 5
+#define DIGIT 6
+#define UNKNOWN 7
+#define OPTION 8
+
+/* species types */
+#define AQ 0
+#define HPLUS 1
+#define H2O 2
+#define EMINUS 3
+#define SOLID 4
+#define EX 5
+#define SURF 6
+#define SURF_PSI 7
+#define SURF_PSI1 8
+#define SURF_PSI2 9
+
+/* unknown types */
+#define MB 10
+#define ALK 11
+#define CB 12
+#define SOLUTION_PHASE_BOUNDARY 13
+#define MU 14
+#define AH2O 15
+#define MH 16
+#define MH2O 17
+#define PP 18
+#define EXCH 19
+#define SURFACE 20
+#define SURFACE_CB 21
+#define SURFACE_CB1 22
+#define SURFACE_CB2 23
+#define GAS_MOLES 24
+#define SS_MOLES 25
+#define PITZER_GAMMA 26
+#define SLACK 28
+/* state */
+#define INITIALIZE	       0
+#define INITIAL_SOLUTION   1
+#define INITIAL_EXCHANGE   2
+#define INITIAL_SURFACE 3
+#define INITIAL_GAS_PHASE  4
+#define REACTION		   5
+#define INVERSE		 6
+#define ADVECTION		 7
+#define TRANSPORT		 8
+#define PHAST		     9
+
+/* constraints in mass balance */
+#define EITHER 0
+#define DISSOLVE 1
+#define PRECIPITATE -1
+
+/* gas phase type */
+#define PRESSURE 1
+#define VOLUME 2
+
+#define MAX_PP_ASSEMBLAGE 10	/* default estimate of the number of phase assemblages */
+#define MAX_ADD_EQUATIONS 20	/* maximum number of equations added together to reduce eqn to
+								   master species */
+#define MAX_ELEMENTS 50			/* default estimate of the number of elements */
+#define MAX_LENGTH 256			/* maximum number of characters component name */
+#define MAX_LINE 4096			/* estimate of maximum line length */
+#define MAX_MASS_BALANCE 10		/* initial guess of number mass balance equations for a solution */
+#define MAX_MASTER 50			/* default estimate of the number of master species */
+#define MAX_ELTS 15				/* default estimate for maximum number of times elements occur in
+								   an equation */
+#define MAX_PHASES 500			/* initial guess of number of phases defined */
+#define MAX_S 500				/* default estimate for maximum number of species in aqueous model */
+#define MAX_SUM_JACOB0 50		/* list used to calculate jacobian */
+#define MAX_SUM_JACOB1 500		/* list used to calculate jacobian */
+#define MAX_SUM_JACOB2 500		/* list used to calculate jacobian */
+#define MAX_SUM_MB 500			/* list used to calculate mass balance sums */
+#define MAX_TRXN 16				/* default estimate for maximum number of components in an eqn */
+#define MAX_UNKNOWNS 15			/* default estimate for maximum number of unknowns in model */
+#define TOL 1e-9				/* tolerance for comparisons of double numbers */
+#define MAX_LM 3.0				/* maximum log molality allowed in intermediate iterations */
+#define MAX_M 1000.0
+#ifdef USE_DECIMAL128
+// #define MIN_LM -80.0			/* minimum log molality allowed before molality set to zero */
+// #define LOG_ZERO_MOLALITY -80	/* molalities <= LOG_ZERO_MOLALITY are considered equal to zero */
+// #define MIN_TOTAL 1e-60
+// #define MIN_TOTAL_SS MIN_TOTAL/100
+// #define MIN_RELATED_SURFACE MIN_TOTAL*100
+// #define MIN_RELATED_LOG_ACTIVITY -60
+#else
+// #define MIN_LM -30.0			/* minimum log molality allowed before molality set to zero */
+// #define LOG_ZERO_MOLALITY -30	/* molalities <= LOG_ZERO_MOLALITY are considered equal to zero */
+// #define MIN_TOTAL 1e-25
+// #define MIN_TOTAL_SS MIN_TOTAL/100
+// #define MIN_RELATED_SURFACE MIN_TOTAL*100
+// #define MIN_RELATED_LOG_ACTIVITY -30
+#endif
+#define REF_PRES_PASCAL 1.01325E5   /* Reference pressure: 1 atm */
+#define MAX_P_NONLLNL 1500.0
+
+//
+// Typedefs and structure definitions
+//
+typedef enum { kcal, cal, kjoules, joules } DELTA_H_UNIT;
+typedef enum { cm3_per_mol, dm3_per_mol, m3_per_mol } DELTA_V_UNIT;
+enum entity_type
+{ Solution, Reaction, Exchange, Surface, Gas_phase, Pure_phase, Ss_phase,
+	Kinetics, Mix, Temperature, Pressure, UnKnown
+};
+
+typedef enum {
+	logK_T0,
+	delta_h,
+	T_A1,
+	T_A2,
+	T_A3,
+	T_A4,
+	T_A5,
+	T_A6,
+	delta_v,	/* set in calc_delta_v: calculated molar volume-change of the reaction */
+	vm_tc,		/* set in calc_vm: calculated molal volume of the species at tc */
+	vm0,		/* read: molar volume of a phase */
+	vma1, vma2, vma3, vma4, /* read: a1..a4 from supcrt, see calc_vm */
+	wref,       /* from supcrt */
+	b_Av,		/* b in z^2 * A_v * log(1 + b * I^0.5) / (2 * b) */
+	vmi1, vmi2, vmi3, vmi4, /* ionic strength terms: (i1 + i2/(TK - 228) + i3 * (TK - 228) ) * I^i4 */
+	MAX_LOG_K_INDICES	/* Keep this definition at the end of the enum */
+} LOG_K_INDICES;
+
+typedef struct PHRQMemHeader
+{
+	struct PHRQMemHeader *pNext;	/* memory allocated just after this one */
+	struct PHRQMemHeader *pPrev;	/* memory allocated just prior to this one */
+	size_t size;				/* memory request + sizeof(PHRQMemHeader) */
+#if !defined(NDEBUG)
+	char *szFileName;			/* file name */
+	int nLine;					/* line number */
+	int dummy;					/* alignment */
+#endif
+} PHRQMemHeader;
+
+struct Change_Surf
+{
+	const char *comp_name;
+	LDBLE fraction;
+	const char *new_comp_name;
+	LDBLE new_Dw;
+	int cell_no;
+	int next;
+};
+/*----------------------------------------------------------------------
+ *   CReaction
+ *---------------------------------------------------------------------- */
+class rxn_token
+{
+public:
+	~rxn_token() {};
+	rxn_token()
+	{
+		s = NULL;
+		coef = 0.0;
+		name = NULL;
+	}
+	class species* s;
+	LDBLE coef;
+	const char* name;
+};
+class CReaction
+{
+public:
+	CReaction(void);
+	CReaction(size_t ntoken);
+	~CReaction(void) {}
+	double* Get_logk(void) { return this->logk; }
+	void   Set_logk(double* d);
+	double* Get_dz(void) { return this->dz; }
+	void   Set_dz(double* d);
+	size_t size() { return token.size(); }
+	std::vector<class rxn_token>& Get_tokens(void) { return this->token; }
+	void Set_tokens(const std::vector<class rxn_token>& t) { this->token = t; }
+
+public:
+	double logk[MAX_LOG_K_INDICES];
+	double dz[3];
+	std::vector<class rxn_token> token;
+};
+class save
+{
+public:
+	~save() {};
+	save()
+	{
+		solution = 0;
+		n_solution_user = 0;
+		n_solution_user_end = 0;
+		mix = 0;
+		n_mix_user = 0;
+		n_mix_user_end = 0;
+		reaction = 0;
+		n_reaction_user = 0;
+		n_reaction_user_end = 0;
+		pp_assemblage = 0;
+		n_pp_assemblage_user = 0;
+		n_pp_assemblage_user_end = 0;
+		exchange = 0;
+		n_exchange_user = 0;
+		n_exchange_user_end = 0;
+		kinetics = 0;
+		n_kinetics_user = 0;
+		n_kinetics_user_end = 0;
+		surface = 0;
+		n_surface_user = 0;
+		n_surface_user_end = 0;
+		gas_phase = 0;
+		n_gas_phase_user = 0;
+		n_gas_phase_user_end = 0;
+		ss_assemblage = 0;
+		n_ss_assemblage_user = 0;
+		n_ss_assemblage_user_end = 0;
+	}
+	int solution;
+	int n_solution_user;
+	int n_solution_user_end;
+	int mix;
+	int n_mix_user;
+	int n_mix_user_end;
+	int reaction;
+	int n_reaction_user;
+	int n_reaction_user_end;
+	int pp_assemblage;
+	int n_pp_assemblage_user;
+	int n_pp_assemblage_user_end;
+	int exchange;
+	int n_exchange_user;
+	int n_exchange_user_end;
+	int kinetics;
+	int n_kinetics_user;
+	int n_kinetics_user_end;
+	int surface;
+	int n_surface_user;
+	int n_surface_user_end;
+	int gas_phase;
+	int n_gas_phase_user;
+	int n_gas_phase_user_end;
+	int ss_assemblage;
+	int n_ss_assemblage_user;
+	int n_ss_assemblage_user_end;
+};
+
+/*----------------------------------------------------------------------
+ *   Copy
+ *---------------------------------------------------------------------- */
+class copier
+{
+public:
+	~copier() {};
+	copier()
+	{}
+	std::vector<int> n_user;
+	std::vector<int> start;
+	std::vector<int> end;
+};
+/*----------------------------------------------------------------------
+ *   Inverse
+ *---------------------------------------------------------------------- */
+class inv_elts
+{
+public:
+	~inv_elts() {};
+	inv_elts()
+	{
+		name = NULL;
+		master = NULL;
+		row = 0;
+		//uncertainties.clear();
+	}
+	const char* name;
+	class master* master;
+	size_t row;
+	std::vector<double> uncertainties;
+};
+class isotope
+{
+public:
+	~isotope() {};
+	isotope()
+	{
+		isotope_number = 0;
+		elt_name = NULL;
+		isotope_name = NULL;
+		total = 0;
+		ratio = 0;
+		ratio_uncertainty = 0;
+		x_ratio_uncertainty = 0;
+		master = NULL;
+		primary = NULL;
+		coef = 0;					/* coefficient of element in phase */
+	}
+	LDBLE isotope_number;
+	const char* elt_name;
+	const char* isotope_name;
+	LDBLE total;
+	LDBLE ratio;
+	LDBLE ratio_uncertainty;
+	LDBLE x_ratio_uncertainty;
+	class master* master;
+	class master* primary;
+	LDBLE coef;
+};
+class inv_isotope
+{
+public:
+	~inv_isotope() {};
+	inv_isotope()
+	{
+		isotope_name = NULL;
+		isotope_number = 0;
+		elt_name = NULL;
+		//uncertainties.clear();
+	}
+	const char* isotope_name;
+	LDBLE isotope_number;
+	const char* elt_name;
+	std::vector<double> uncertainties;
+};
+class inv_phases
+{
+public:
+	~inv_phases() {};
+	inv_phases()
+	{
+		name = NULL;
+		phase = NULL;
+		column = 0;
+		constraint = EITHER;
+		force = FALSE;
+		//isotopes.clear();
+	}
+	const char* name;
+	class phase* phase;
+	int column;
+	int constraint;
+	int force;
+	std::vector<class isotope> isotopes;
+};
+class inverse
+{
+public:
+	~inverse() {};
+	inverse()
+	{
+		n_user = -1;
+		description = NULL;
+		new_def = FALSE;
+		minimal = FALSE;
+		range = FALSE;
+		mp = FALSE;
+		mp_censor = 1e-20;
+		range_max = 1000.0;
+		tolerance = 1e-10;
+		mp_tolerance = 1e-12;
+		//uncertainties.clear();
+		//ph_uncertainties.clear();
+		water_uncertainty = 0.0;
+		mineral_water = TRUE;
+		carbon = TRUE;
+		//dalk_dph.clear();
+		//dalk_dc.clear();
+		count_solns = 0;
+		//solns.clear();
+		//force_solns.clear();
+		//elts.clear();
+		//phases.clear();
+		count_redox_rxns = 0;
+		//isotopes.clear();
+		//i_u.clear();
+		//isotope_unknowns.clear();
+		netpath = NULL;
+		pat = NULL;
+	}
+	int n_user;
+	char* description;
+	int new_def;
+	int minimal;
+	int range;
+	int mp;
+	LDBLE mp_censor;
+	LDBLE range_max;
+	LDBLE tolerance;
+	LDBLE mp_tolerance;
+	std::vector<double> uncertainties;
+	std::vector<double> ph_uncertainties;
+	LDBLE water_uncertainty;
+	int mineral_water;
+	int carbon;
+	std::vector<double> dalk_dph;
+	std::vector<double> dalk_dc;
+	size_t count_solns;
+	std::vector<int> solns;
+	std::vector<bool> force_solns;
+	std::vector<class inv_elts> elts;
+	std::vector<class inv_phases> phases;
+	size_t count_redox_rxns;
+	std::vector<class inv_isotope> isotopes;
+	std::vector<class inv_isotope> i_u;
+	std::vector<class isotope> isotope_unknowns;
+	const char* netpath;
+	const char* pat;
+};
+/*----------------------------------------------------------------------
+ *   Jacobian and Mass balance lists
+ *---------------------------------------------------------------------- */
+class Model
+{
+public:
+	Model()
+	{
+		force_prep = true;
+		gas_phase_type = cxxGasPhase::GP_UNKNOWN;
+		numerical_fixed_volume = false;
+		dl_type = cxxSurface::NO_DL;
+		surface_type = cxxSurface::UNKNOWN_DL;
+	};
+	~Model()
+	{
+	};
+	bool force_prep;
+	bool numerical_fixed_volume;
+	cxxGasPhase::GP_TYPE gas_phase_type;
+	std::vector<class phase*> gas_phase;
+	std::vector<const char*> ss_assemblage;
+	std::vector<class phase*> pp_assemblage;
+	std::vector<double> si;
+	std::vector<const char*> add_formula;
+	cxxSurface::DIFFUSE_LAYER_TYPE dl_type;
+	cxxSurface::SURFACE_TYPE surface_type;
+	std::vector<const char*> surface_comp;
+	std::vector<const char*> surface_charge;
+};
+class name_coef
+{
+public:
+	~name_coef() {};
+	name_coef()
+	{
+		name = NULL;
+		coef = 0;
+	}
+	const char* name;
+	LDBLE coef;
+};
+/*----------------------------------------------------------------------
+ *   Species_list
+ *---------------------------------------------------------------------- */
+class species_list
+{
+public:
+	~species_list() {};
+	species_list()
+	{
+		master_s = NULL;
+		s = NULL;
+		coef = 0;
+	}
+	class species* master_s;
+	class species* s;
+	LDBLE coef;
+};
+/*----------------------------------------------------------------------
+ *   Jacobian and Mass balance lists
+ *---------------------------------------------------------------------- */
+class list0
+{
+public:
+	~list0() {};
+	list0()
+	{
+		target = NULL;
+		coef = 0;
+	}
+	LDBLE* target;
+	LDBLE coef;
+};
+class list1
+{
+public:
+	~list1() {};
+	list1()
+	{
+		source = NULL;
+		target = NULL;
+	}
+	LDBLE* source;
+	LDBLE* target;
+};
+class list2
+{
+public:
+	~list2() {};
+	list2()
+	{
+		source = NULL;
+		target = NULL;
+		coef = 0;
+	}
+	LDBLE* source;
+	LDBLE* target;
+	LDBLE coef;
+};
+class iso
+{
+public:
+	~iso() {};
+	iso()
+	{
+		name = NULL;
+		value = 0;
+		uncertainty = 0.05;
+	}
+	const char* name;
+	LDBLE value;
+	LDBLE uncertainty;
+};
+/*----------------------------------------------------------------------
+ *   Transport data
+ *---------------------------------------------------------------------- */
+class stag_data
+{
+public:
+	~stag_data() {};
+	stag_data()
+	{
+		count_stag = 0;
+		exch_f = 0;
+		th_m = 0;
+		th_im = 0;
+	}
+	int count_stag;
+	LDBLE exch_f;
+	LDBLE th_m;
+	LDBLE th_im;
+};
+class cell_data
+{
+public:
+	~cell_data() {};
+	cell_data()
+	{
+		length = 1;
+		mid_cell_x = 1.;
+		disp = 1.0;
+		temp = 25.;
+		// free (uncharged) porewater porosities
+		por = 0.1;
+		// interlayer water porosities
+		por_il = 0.01;
+		// potential (V)
+		potV = 0;
+		punch = FALSE;
+		print = FALSE;
+		same_model = FALSE;
+	}
+	LDBLE length;
+	LDBLE mid_cell_x;
+	LDBLE disp;
+	LDBLE temp;
+	LDBLE por;
+	LDBLE por_il;
+	LDBLE potV;
+	int punch;
+	int print;
+	int same_model;
+};
+/*----------------------------------------------------------------------
+ *   Keywords
+ *---------------------------------------------------------------------- */
+//class key
+//{
+//public:
+//	~key() {};
+//	key()
+//	{
+//		name = NULL;
+//		keycount = 0;
+//	}
+//	char* name;
+//	int keycount = 0;
+// };
+//class const_key
+//{
+//public:
+//	~const_key() {};
+//	const_key()
+//	{
+//		name = NULL;
+//		keycount = 0;
+//	}
+//	const char* name;
+//	int keycount;
+//};
+/*----------------------------------------------------------------------
+ *   Elements
+ *---------------------------------------------------------------------- */
+class element
+{
+public:
+	~element() {};
+	element()
+	{
+		// element name
+		name = NULL;
+		/*    int in; */
+		master = NULL;
+		primary = NULL;
+		gfw = 0;
+	}
+	const char* name;
+	class master* master;
+	class master* primary;
+	LDBLE gfw;
+};
+/*----------------------------------------------------------------------
+ *   Element List
+ *---------------------------------------------------------------------- */
+class elt_list
+{
+public:
+	~elt_list() {};
+	elt_list()
+	{	/* list of name and number of elements in an equation */
+		elt = NULL;	/* pointer to element structure */
+		coef = 0.0;			/* number of element e's in eqn */
+	}
+	class element* elt;
+	LDBLE coef;
+};
+/*----------------------------------------------------------------------
+ *   Species
+ *---------------------------------------------------------------------- */
+class species
+{
+public:
+	~species() {};
+	species()
+	{	/* all data pertinent to an aqueous species */
+		name = NULL;          // name of species 
+		mole_balance = NULL;  // formula for mole balance 
+		in = FALSE;           // set internally if species in model
+		number = 0;
+		// points to master species list, NULL if not primary master
+		primary = NULL;
+		// points to master species list, NULL if not secondary master
+		secondary = NULL;
+		gfw = 0;              // gram formula wt of species
+		z = 0;                // charge of species
+		dw = 0;		// tracer diffusion coefficient in water at 25oC, m2/s
+		dw_t = 0;	// correct Dw for temperature: Dw(TK) = Dw(298.15) * exp(dw_t / TK - dw_t / 298.15)
+		// parms for calc'ng SC = SC0 * exp(-dw_a * z * mu^0.5 / (1 + DH_B * dw_a2 * mu^0.5) / (1 + mu^dw_a3))
+		// with DHO: ka = DH_B * dw_a * (1 + DD(V_apparent)^dw_a2 * sqrt_mu, dw_a3 is a switch, see calc_SC in PBasic
+		dw_a = 0;
+		dw_a2 = 0;
+		dw_a3 = 0;
+		dw_a_visc = 0;   // exponent in viscosity correction of SC
+		dw_a_v_dif = 0;  // exponent in viscosity correction of D, the diffusion coefficient of the species
+		dw_t_SC = 0;     // contribution to SC, for calc'ng transport number with BASIC
+		dw_t_visc = 0;   // contribution to viscosity
+		dw_corr = 0;	 // dw corrected for mu and TK
+		erm_ddl = 0;     // enrichment factor in DDL
+		equiv = 0;       // equivalents in exchange species
+		alk = 0;	     // alkalinity of species, used for cec in exchange
+		carbon = 0;      // stoichiometric coefficient of carbon in species
+		co2 = 0;         // stoichiometric coefficient of C(4) in species
+		h = 0;           // stoichiometric coefficient of H in species
+		// stoichiometric coefficient of O in species
+		o = 0;
+		// WATEQ Debye Huckel a and b-dot; active_fraction coef for exchange species
+		dha = 0, dhb = 0, a_f = 0;
+		lk = 0;           // log10 k at working temperature
+		// log kt0, delh, 6 coefficients analytical expression + volume terms
+		for (size_t i = 0; i < MAX_LOG_K_INDICES; i++) logk[i] = 0;
+		// 7 coefficients analytical expression for B, D, anion terms and pressure in Jones_Dole viscosity eqn
+		for (size_t i = 0; i < 10; i++) Jones_Dole[i] = 0;
+		// regression coefficients to calculate temperature dependent phi_0and b_v of Millero density model
+		for (size_t i = 0; i < 7; i++) millero[i] = 0;
+		original_units = kjoules;  // enum with original delta H units
+		//add_logk.clear();
+		lg = 0;            // log10 activity coefficient, gamma
+		lg_pitzer = 0;     // log10 activity coefficient, from pitzer calculation
+		lm = 0;            // log10 molality
+		la = 0;		       // log10 activity
+		dg = 0;		       // gamma term for jacobian
+		dg_total_g = 0;
+		moles = 0;		   // moles in solution; moles/mass_water = molality
+		type = 0;          // flag indicating presence in model and types of equations
+		gflag = 0;		   // flag for preferred activity coef eqn
+		exch_gflag = 0;    // flag for preferred activity coef eqn
+		// vector of elements
+		//next_elt.clear();
+		//next_secondary.clear();
+		//next_sys_total.clear();
+		// switch to check equation for charge and element balance
+		check_equation = TRUE;
+		//CReaction rxn;   // data base reaction
+		//CReaction rxn_s; // reaction converted to secondary and primary master species
+		//CReaction rxn_x; // reaction to be used in model
+		// (1 + sum(g)) * moles
+		tot_g_moles = 0;
+		// sum(moles*g*Ws/Waq)
+		tot_dh2o_moles = 0;
+		for (size_t i = 0; i < 5; i++) cd_music[i] = 0;
+		for (size_t i = 0; i < 3; i++) dz[i] = 0;
+		original_deltav_units = cm3_per_mol;
+	}
+	const char* name;
+	const char* mole_balance; 
+	int in;
+	int number;
+	class master* primary;
+	class master* secondary;
+	LDBLE gfw;
+	LDBLE z;
+	LDBLE dw;
+	LDBLE dw_t;
+	LDBLE dw_a;
+	LDBLE dw_a2;
+	LDBLE dw_a3;
+	LDBLE dw_a_visc;
+	LDBLE dw_a_v_dif;
+	LDBLE dw_t_SC;
+	LDBLE dw_t_visc;
+	LDBLE dw_corr;
+	LDBLE erm_ddl;
+	LDBLE equiv;
+	LDBLE alk;
+	LDBLE carbon;
+	LDBLE co2;
+	LDBLE h;
+	LDBLE o;	
+	LDBLE dha, dhb, a_f;
+	LDBLE lk;
+	LDBLE logk[MAX_LOG_K_INDICES];
+	LDBLE Jones_Dole[10];
+	LDBLE millero[7];
+	DELTA_H_UNIT original_units;
+	std::vector<class name_coef> add_logk;
+	LDBLE lg;
+	LDBLE lg_pitzer;
+	LDBLE lm;
+	LDBLE la;
+	LDBLE dg;
+	LDBLE dg_total_g;
+	LDBLE moles;
+	int type;
+	int gflag;
+	int exch_gflag;
+	std::vector<class elt_list> next_elt;
+	std::vector<class elt_list> next_secondary;
+	std::vector<class elt_list> next_sys_total;
+	int check_equation;
+	CReaction rxn;
+	CReaction rxn_s;
+	CReaction rxn_x;
+	LDBLE tot_g_moles;
+	LDBLE tot_dh2o_moles;
+	LDBLE cd_music[5];
+	LDBLE dz[3];
+	DELTA_V_UNIT original_deltav_units;
+};
+class logk
+{
+public:
+	~logk() {};
+	logk()
+	{	/* Named log K's */
+		name = NULL;		 // name of species 
+		lk = 0.0;	         // log10 k at working temperature                   
+		// log kt0, delh, 6 coefficients analalytical expression 
+		for (size_t i = 0; i < MAX_LOG_K_INDICES; i++) log_k[i] = 0;
+		// enum with original delta H units 
+		original_units = kjoules;	   
+		done = FALSE;
+		//add_logk.clear();
+		// log kt0, delh, 5 coefficients analalytical expression 
+		for (size_t i = 0; i < MAX_LOG_K_INDICES; i++) log_k_original[i] = 0;
+		original_deltav_units = cm3_per_mol;
+	}
+	const char* name;
+	LDBLE lk;
+	LDBLE log_k[MAX_LOG_K_INDICES];
+	DELTA_H_UNIT original_units;
+	int done;
+	std::vector<class name_coef> add_logk;
+	LDBLE log_k_original[MAX_LOG_K_INDICES];
+	DELTA_V_UNIT original_deltav_units;
+};
+/*----------------------------------------------------------------------
+ *   Phases
+ *---------------------------------------------------------------------- */
+class phase
+{
+public:
+	~phase() {};
+	phase()
+	{	/* all data pertinent to a pure solid phase */
+		name = NULL;                //name of species 
+		formula = NULL;				// chemical formula 
+		in = FALSE;					// species used in model if TRUE 
+		lk = 0;					    // log10 k at working temperature 
+		// log kt0, delh, 6 coefficients analalytical expression
+		for (size_t i = 0; i < MAX_LOG_K_INDICES; i++) logk[i] = 0;
+		// enum with original delta H units 
+		original_units = kjoules;	
+		original_deltav_units = cm3_per_mol;
+		//add_logk.clear();
+		moles_x = 0;
+		delta_max = 0;
+		p_soln_x = 0;
+		fraction_x = 0;
+		log10_lambda = 0;
+		log10_fraction_x = 0;
+		dn = 0, dnb = 0, dnc = 0;
+		gn = 0, gntot = 0;
+		gn_n = 0, gntot_n = 0;
+		// gas: critical TK, critical P(atm), Pitzer acentric coeff 
+		t_c = 0, p_c = 0, omega = 0;  
+		// Peng-Robinson parm's
+		pr_a = 0, pr_b = 0, pr_alpha = 0;	
+		// Temperature (K), Pressure (atm)
+		pr_tk = 0, pr_p = 0;
+		// fugacity coefficient (-) 
+		pr_phi = 0;		
+		// for calculating multicomponent phi 
+		pr_aa_sum2 = 0;
+		// delta_v[0] = [1] + [2]*T + [3]/T + [4]*log10(T) + [5]/T^2 + [6]*T^2 + [7]*P
+		for (size_t i = 0; i < 9; i++) delta_v[i] = 0;
+		// si adapter: log10(phi) - delta_v[0] * (P - 1) /RT
+		pr_si_f = 0;	
+		// Peng-Robinson in the calc's, or not
+		pr_in = false;
+		// flag indicating presence in model and types of equations
+		type = SOLID;	
+		// list of elements in phase 
+		//next_elt.clear();	    
+		//next_sys_total.clear();
+		// switch to check equation for charge and element balance
+		check_equation = TRUE;
+		// data base reaction
+		//CReaction rxn;
+		// reaction converted to secondary and primary master species
+		//CReaction rxn_s;
+		// reaction to be used in model
+		//CReaction rxn_x;
+		// equation contains solids or gases                    
+		replaced = FALSE;                       
+		in_system = FALSE;
+	}
+	const char* name;
+	const char* formula;
+	int in;
+	LDBLE lk;
+	LDBLE logk[MAX_LOG_K_INDICES];
+	DELTA_H_UNIT original_units;
+	DELTA_V_UNIT original_deltav_units;
+	std::vector<class name_coef> add_logk;
+	LDBLE moles_x;
+	LDBLE delta_max;
+	LDBLE p_soln_x;
+	LDBLE fraction_x;
+	LDBLE log10_lambda;
+	LDBLE log10_fraction_x;
+	LDBLE dn, dnb, dnc;
+	LDBLE gn, gntot;
+	LDBLE gn_n, gntot_n;
+	LDBLE t_c, p_c, omega; 
+	LDBLE pr_a, pr_b, pr_alpha;
+	LDBLE pr_tk, pr_p;
+	LDBLE pr_phi;
+	LDBLE pr_aa_sum2;
+	LDBLE delta_v[9];
+	LDBLE pr_si_f;
+	bool pr_in;
+	int type;	
+	std::vector<class elt_list> next_elt;
+	std::vector<class elt_list> next_sys_total;
+	int check_equation;
+	CReaction rxn;
+	CReaction rxn_s;
+	CReaction rxn_x;
+	int replaced;
+	int in_system;
+};
+/*----------------------------------------------------------------------
+ *   Master species
+ *---------------------------------------------------------------------- */
+class master
+{
+public:
+	~master() {};
+	master()
+	{	
+		// TRUE if in model, FALSE if out, REWRITE if other mb eq
+		in = 0;
+		// sequence number in list of masters
+		number = 0;
+		// saved to determine if model has changed
+		last_model = FALSE;
+		// AQ or EX
+		type = 0;
+		// TRUE if master species is primary
+		primary = FALSE;
+		// coefficient of element in master species
+		coef = 0;
+		// total concentration for element or valence state
+		total = 0;
+		isotope_ratio = 0;
+		isotope_ratio_uncertainty = 0;
+		isotope = 0;
+		total_primary = 0;
+		// element structure
+		elt = NULL;
+		// alkalinity of species
+		alk = 0;
+		// default gfw for species
+		gfw = 1;
+		// formula from which to calculate gfw
+		gfw_formula = NULL;
+		// pointer to unknown structure
+		unknown = NULL;
+		// pointer to species structure
+		s = NULL;
+		// reaction writes master species in terms of primary  master species
+		//CReaction rxn_primary;
+		// reaction writes master species in terms of secondary master species
+		//CReaction rxn_secondary;
+		pe_rxn = NULL;
+		minor_isotope = FALSE;
+	}
+	int in;
+	size_t number;
+	int last_model;
+	int type;
+	int primary;
+	LDBLE coef;
+	LDBLE total;
+	LDBLE isotope_ratio;
+	LDBLE isotope_ratio_uncertainty;
+	int isotope;
+	LDBLE total_primary;
+	class element* elt;
+	LDBLE alk;
+	LDBLE gfw;
+	const char* gfw_formula;
+	class unknown* unknown;
+	class species* s;
+	CReaction rxn_primary;
+	CReaction rxn_secondary;
+	const char* pe_rxn;
+	int minor_isotope;
+};
+/*----------------------------------------------------------------------
+ *   Unknowns
+ *---------------------------------------------------------------------- */
+class unknown
+{
+public:
+	~unknown() {};
+	unknown()
+	{
+		type = 0;
+		moles = 0;
+		ln_moles = 0;
+		f = 0;
+		sum = 0;
+		delta = 0;
+		la = 0;
+		number = 0;
+		description = NULL;
+		//master.clear();
+		phase = NULL;
+		si = 0;
+		n_gas_phase_user = 0;
+		s = NULL;
+		exch_comp = NULL;
+		pp_assemblage_comp_name = NULL;
+		pp_assemblage_comp_ptr = NULL;
+		ss_name = NULL;
+		ss_ptr = NULL;
+		ss_comp_name = NULL;
+		ss_comp_ptr = NULL;
+		ss_comp_number = 0;
+		ss_in = FALSE;
+		surface_comp = NULL;
+		surface_charge = NULL;
+		related_moles = 0;
+		potential_unknown = NULL;
+		potential_unknown1 = NULL;
+		potential_unknown2 = NULL;
+		// list for CD_MUSIC of comps that contribute to 0 plane mass-balance term
+		//comp_unknowns.clear();
+		phase_unknown = NULL;
+		mass_water = 1;
+		dissolve_only = FALSE;
+		inert_moles = 0;
+		V_m = 0;
+		pressure = 1;
+		mb_number = 0;
+		iteration = 0;
+	}
+	int type;
+	LDBLE moles;
+	LDBLE ln_moles;
+	LDBLE f;
+	LDBLE sum;
+	LDBLE delta;
+	LDBLE la;
+	size_t number;
+	const char* description;
+	std::vector<class master*> master;
+	class phase* phase;
+	LDBLE si;
+	int n_gas_phase_user;
+	class species* s;
+	const char* exch_comp;
+	const char* pp_assemblage_comp_name;
+	void* pp_assemblage_comp_ptr;
+	const char* ss_name;
+	void* ss_ptr;
+	const char* ss_comp_name;
+	void* ss_comp_ptr;
+	int ss_comp_number;
+	int ss_in;
+	const char* surface_comp;
+	const char* surface_charge;
+	LDBLE related_moles;
+	class unknown* potential_unknown;
+	class unknown* potential_unknown1;
+	class unknown* potential_unknown2;
+	std::vector<class unknown*> comp_unknowns;
+	class unknown* phase_unknown;
+	LDBLE mass_water;
+	int dissolve_only;
+	LDBLE inert_moles;
+	LDBLE V_m;
+	LDBLE pressure;
+	int mb_number;
+	int iteration;
+};
+/*----------------------------------------------------------------------
+ *   Reaction work space
+ *---------------------------------------------------------------------- */
+class rxn_token_temp
+{
+public:
+	~rxn_token_temp() {};
+	rxn_token_temp()
+	{	// data for equations, aq. species or minerals
+		name = NULL;		// pointer to a species name (formula)
+		z = 0;		// charge on species 
+		s = NULL;
+		unknown = NULL;
+		coef = 0;			// coefficient of species name 
+	}
+	const char* name;
+	LDBLE z;
+	class species* s;
+	class unknown* unknown;
+	LDBLE coef;
+};
+class reaction_temp
+{
+public:
+	~reaction_temp() {};
+	reaction_temp()
+	{
+		for (size_t i = 0; i < MAX_LOG_K_INDICES; i++) logk[i] = 0;
+		for (size_t i = 0; i < 3; i++) dz[i] = 0;
+		//token.clear();
+	}
+	LDBLE logk[MAX_LOG_K_INDICES];
+	LDBLE dz[3];
+	std::vector<class rxn_token_temp> token;
+};
+class unknown_list
+{
+public:
+	~unknown_list() {};
+	unknown_list()
+	{
+		unknown = NULL;
+		source = NULL;
+		gamma_source = NULL;
+		coef = 0;
+	}
+	class unknown* unknown;
+	LDBLE* source;
+	LDBLE* gamma_source;
+	LDBLE coef;
+};
+/* ----------------------------------------------------------------------
+ *   Print
+ * ---------------------------------------------------------------------- */
+class prints
+{
+public:
+	~prints() {};
+	prints()
+	{
+		all = 0;
+		initial_solutions = 0;
+		initial_exchangers = 0;
+		reactions = 0;
+		gas_phase = 0;
+		ss_assemblage = 0;
+		pp_assemblage = 0;
+		surface = 0;
+		exchange = 0;
+		kinetics = 0;
+		totals = 0;
+		eh = 0;
+		species = 0;
+		saturation_indices = 0;
+		irrev = 0;
+		mix = 0;
+		reaction = 0;
+		use = 0;
+		logfile = 0;
+		punch = 0;
+		status = 0;
+		inverse = 0;
+		dump = 0;
+		user_print = 0;
+		headings = 0;
+		user_graph = 0;
+		echo_input = 0;
+		warnings = 0;
+		initial_isotopes = 0;
+		isotope_ratios = 0;
+		isotope_alphas = 0;
+		hdf = 0;
+		alkalinity = 0;
+	}
+	int all;
+	int initial_solutions;
+	int initial_exchangers;
+	int reactions;
+	int gas_phase;
+	int ss_assemblage;
+	int pp_assemblage;
+	int surface;
+	int exchange;
+	int kinetics;
+	int totals;
+	int eh;
+	int species;
+	int saturation_indices;
+	int irrev;
+	int mix;
+	int reaction;
+	int use;
+	int logfile;
+	int punch;
+	int status;
+	int inverse;
+	int dump;
+	int user_print;
+	int headings;
+	int user_graph;
+	int echo_input;
+	int warnings;
+	int initial_isotopes;
+	int isotope_ratios;
+	int isotope_alphas;
+	int hdf;
+	int alkalinity;
+};
+/* ----------------------------------------------------------------------
+ *   RATES
+ * ---------------------------------------------------------------------- */
+class rate
+{
+public:
+	~rate() {};
+	rate()
+	{
+		name = NULL;
+		//std::string commands;
+		new_def = 0;
+		linebase = NULL;
+		varbase = NULL;
+		loopbase = NULL;
+	}
+	const char* name;
+	std::string commands;
+	int new_def;
+	void* linebase;
+	void* varbase;
+	void* loopbase;
+};
+/* ----------------------------------------------------------------------
+ *   GLOBAL DECLARATIONS
+ * ---------------------------------------------------------------------- */
+class spread_row
+{
+public:
+	~spread_row() {};
+	spread_row()
+	{
+		count = 0;
+		empty = 0, string = 0, number = 0;
+		//char_vector.clear();
+		//d_vector.clear();
+		//type_vector.clear();
+	}
+	size_t count;
+	size_t empty, string, number;
+	std::vector<std::string> str_vector;
+	std::vector<int> type_vector;
+};
+class defaults
+{
+public:
+	~defaults() {};
+	defaults()
+	{
+		temp = 25;
+		density = 1;
+		calc_density = false;
+		units = NULL;
+		redox = NULL;
+		ph = 7;
+		pe = 4;
+		water = 1;
+		//iso.clear();
+		pressure = 1;	/* pressure in atm */
+	}
+	LDBLE temp;
+	LDBLE density;
+	bool calc_density;
+	const char* units;
+	const char* redox;
+	LDBLE ph;
+	LDBLE pe;
+	LDBLE water;
+	std::vector<class iso> iso;
+	LDBLE pressure;
+};
+class spread_sheet
+{
+public:
+	~spread_sheet() {};
+	spread_sheet()
+	{
+		heading = NULL;
+		units = NULL;
+		//class defaults defaults;
+	}
+	class spread_row* heading;
+	class spread_row* units;
+	std::vector<class spread_row*> rows;
+	class defaults defaults;
+};
+/* ----------------------------------------------------------------------
+ *   ISOTOPES
+ * ---------------------------------------------------------------------- */
+class master_isotope
+{
+public:
+	~master_isotope() {};
+	master_isotope()
+	{
+		name = NULL;
+		master = NULL;
+		elt = NULL;
+		units = NULL;
+		standard = 0;
+		ratio = 0;
+		moles = 0;
+		total_is_major = 0;
+		minor_isotope = 0;
+	}
+	const char* name;
+	class master* master;
+	class element* elt;
+	const char* units;
+	LDBLE standard;
+	LDBLE ratio;
+	LDBLE moles;
+	int total_is_major;
+	int minor_isotope;
+};
+class calculate_value
+{
+public:
+	~calculate_value() {};
+	calculate_value()
+	{
+		name = NULL;
+		value = 0;
+		//commands.clear();
+		new_def = 0;
+		calculated = 0;
+		linebase = NULL;
+		varbase = NULL;
+		loopbase = NULL;
+	}
+	const char* name;
+	LDBLE value;
+	std::string commands;
+	int new_def;
+	int calculated;
+	void* linebase;
+	void* varbase;
+	void* loopbase;
+};
+class isotope_ratio
+{
+public:
+	isotope_ratio()
+	{
+		name = NULL;
+		isotope_name = NULL;
+		ratio = 0;
+		converted_ratio = 0;
+	}
+	~isotope_ratio() {};
+
+	const char* name;
+	const char* isotope_name;
+	LDBLE ratio;
+	LDBLE converted_ratio;
+};
+class isotope_alpha
+{
+public:
+	isotope_alpha()
+	{
+		name = NULL;
+		named_logk = NULL;
+		value = 0;
+	}
+	~isotope_alpha() {};
+	const char* name;
+	const char* named_logk;
+	LDBLE value;
+};
+class system_species
+{
+public:
+	~system_species() {};
+	system_species()
+	{
+		name = NULL;
+		type = NULL;
+		moles = 0;
+	}
+	char* name;
+	char* type;
+	LDBLE moles;
+};
+/* tally.c ------------------------------- */
+class tally_buffer
+{
+public:
+	~tally_buffer() {};
+	tally_buffer()
+	{
+		name = NULL;
+		master = NULL;
+		moles = 0;
+		gfw = 0;
+	}
+	const char* name;
+	class master* master;
+	LDBLE moles;
+	LDBLE gfw;
+};
+class tally
+{
+public:
+	~tally() {};
+	tally()
+	{
+		name = NULL;
+		type = UnKnown;
+		add_formula = NULL;
+		moles = 0;
+		//formula.clear();
+		/*
+		 * first total is initial
+		 * second total is final
+		 * third total is difference (final - initial)
+		 */
+		for(size_t i = 0; i < 3; i++) total[i]= NULL;
+	}
+	const char* name;
+	enum entity_type type;
+	const char* add_formula;
+	LDBLE moles;
+	std::vector<class elt_list> formula;
+	/*
+	 * first total is initial
+	 * second total is final
+	 * third total is difference (final - initial)
+	 */
+	class tally_buffer* total[3];
+};
+/* transport.c ------------------------------- */
+class spec
+{
+public:
+	~spec() {};
+	spec()
+	{
+		// name of species
+		name = NULL;
+		// name of aqueous species in EX species
+		aq_name = NULL;
+		// type: AQ or EX
+		type = 0;
+		// activity
+		a = 0;
+		// log(concentration)
+		lm = 0;
+		// log(gamma)
+		lg = 0;
+		// concentration for AQ, equivalent fraction for EX
+		c = 0;
+		// charge number
+		z = 0;
+		// free water diffusion coefficient, m2/s
+		Dw = 0;
+		// temperature and viscosity corrected free water diffusion coefficient, m2/s
+		Dwt = 0;
+		// temperature factor for Dw
+		dw_t = 0;
+		// viscosity factor for Dw
+		dw_a_v_dif = 0;
+		// enrichment factor in ddl
+		erm_ddl = 0;
+	}
+	const char* name;
+	const char* aq_name;
+	int type;
+	LDBLE a;
+	LDBLE lm;
+	LDBLE lg;
+	LDBLE c;
+	LDBLE z;
+	LDBLE Dw;
+	LDBLE Dwt;
+	LDBLE dw_t;
+	LDBLE dw_a_v_dif;
+	LDBLE erm_ddl;
+};
+
+class sol_D
+{
+public:
+	~sol_D() {};
+	sol_D()
+	{
+		// number of aqueous + exchange species
+		count_spec = 0;
+		// number of exchange species
+		count_exch_spec = 0;
+		// total moles of X-, max X- in transport step in sol_D[1], tk
+		exch_total = 0, x_max = 0, tk_x = 0;
+		// viscos_0 at I = 0
+		viscos_0 = 0;
+		// viscosity of solution
+		viscos = 0;
+		spec = NULL;
+		spec_size = 0;
+	}
+	int count_spec;
+	int count_exch_spec;
+	LDBLE exch_total, x_max, tk_x;
+	LDBLE viscos_0, viscos;
+	class spec* spec;
+	int spec_size;
+};
+class J_ij
+{
+public:
+	~J_ij() {};
+	J_ij()
+	{
+		name = NULL;
+		// species change in cells i and j
+		tot1 = 0;
+		tot2 = 0;
+		tot_stag = 0;
+		charge = 0;
+	}
+	const char* name;
+	LDBLE tot1, tot2, tot_stag, charge;
+};
+class J_ij_save
+{
+public:
+	~J_ij_save() {};
+	J_ij_save()
+	{
+		// species change in cells i and j
+		flux_t = 0;
+		flux_c = 0;
+	}
+	double flux_t, flux_c;
+};
+class M_S
+{
+public:
+	~M_S() {};
+	M_S()
+	{
+		name = NULL;
+		// master species transport in cells i and j 
+		tot1 = 0;
+		tot2 = 0;
+		tot_stag = 0;
+		charge = 0;
+	}
+	const char* name;
+	LDBLE tot1, tot2, tot_stag, charge;
+};
+// Pitzer definitions
+typedef enum
+{ TYPE_B0, TYPE_B1, TYPE_B2, TYPE_C0, TYPE_THETA, TYPE_LAMBDA, TYPE_ZETA,
+  TYPE_PSI, TYPE_ETHETA, TYPE_ALPHAS, TYPE_MU, TYPE_ETA, TYPE_Other,
+  TYPE_SIT_EPSILON, TYPE_SIT_EPSILON_MU, TYPE_APHI
+} pitz_param_type;
+class pitz_param
+{
+public:
+	~pitz_param() {};
+	pitz_param()
+	{
+		for(size_t i = 0; i < 3; i++) species[i] = NULL;
+		for (size_t i = 0; i < 3; i++) ispec[i] = -1;
+		type = TYPE_Other;
+		p = 0;
+		U.b0 = 0;
+		for (size_t i = 0; i < 6; i++) a[i] = 0;
+		alpha = 0;
+		os_coef = 0;
+		for (size_t i = 0; i < 3; i++) ln_coef[i] = 0;
+		thetas = NULL;
+	}
+	const char* species[3];
+	int ispec[3];
+	pitz_param_type type;
+	LDBLE p;
+	union
+	{
+		LDBLE b0;
+		LDBLE b1;
+		LDBLE b2;
+		LDBLE c0;
+		LDBLE theta;
+		LDBLE lambda;
+		LDBLE zeta;
+		LDBLE psi;
+		LDBLE alphas;
+		LDBLE mu;
+		LDBLE eta;
+		LDBLE eps;
+		LDBLE eps1;
+		LDBLE aphi;
+	} U;
+	LDBLE a[6];
+	LDBLE alpha;
+	LDBLE os_coef;
+	LDBLE ln_coef[3];
+	class theta_param* thetas;
+};
+class theta_param
+{
+public:
+	~theta_param() {};
+	theta_param()
+	{
+		zj = 0;
+		zk = 0;
+		etheta = 0;
+		ethetap = 0;
+	}
+	LDBLE zj;
+	LDBLE zk;
+	LDBLE etheta;
+	LDBLE ethetap;
+};
+class const_iso
+{
+public:
+	~const_iso() {};
+	const_iso()
+	{
+		name = NULL;
+		value = 0;
+		uncertainty = 0;
+	}
+	const_iso(const char *n, LDBLE v, LDBLE u)
+	{
+		name = n;
+		value = v;
+		uncertainty = u;
+	}
+	const char* name;
+	LDBLE value;
+	LDBLE uncertainty;
+};
+
+#endif /* _INC_GLOBAL_STRUCTURES_H  */