************************************************************
************************************************************
*        Features not documented in WRIR 99-4259.          *
************************************************************
************************************************************

------------------------------------------------------------
Version 2.14.3: November 17, 2007
------------------------------------------------------------
        --------
        svn 2312
        --------
	Added new option to PITZER datablock, use_etheta t/f.
	If true, the nonsymmetric mixing terms--cation/cation and
	anion/anion of different charge--are included; if false
	these terms are excluded from all equations. Default is true.

	PITZER
		-use_etheta true

        --------
        svn 2270
        --------
        Added additional parameters Pitzer activity formulation for
	neutral species, MU and ETA. MU applies to nnn, nnn', nn'n'',
	nna, nn'a, nnc, nn'c interactions, where n, n', and n'' are
	neutral species, a is an anion and c is a cation. ETA applies
	to ncc' and naa' interactions. Also modified LAMDA for the
	special case of nn interactions (coefficients in osmotic and
	ln equations are different than other interaction types).
	Source of equations is Clegg and Whitfield, 1991, Activity
	coefficients in natural waters, Chapter 6, in Pitzer, K.S.
	(Ed.) Activity Coefficients in Electrolyte Solutions, 2nd
	Ed. CRC Press, Boca Raton. Removal of the 6 coefficient in
	last two terms of eq 35 and 36 (p. 2404) per Cleg and
	Whitfield, 1995, Geochimica et Cosmochemica Acta, v. 59,
	no. 12, pp 2403-2421.  Order of species in definitions should
	not matter.

        PITZER
	-MU
		CO2	CO2	CO2	?     # nnn
		CO2     CO2     NH3     ?     # nnn'
		CO2     B(OH)3  NH3     ?     # nn'n''
		CO2     CO2     Ca+2    ?     # nnc
		CO2     CO2     Cl-     ?     # nna
		CO2     NH3     Ca+2    ?     # nn'c
		CO2     NH3     Cl-     ?     # nn'a
        -ETA
		CO2     Ca+2    Mg+2    ?     # ncc'
		CO2     Cl-     SO4-2   ?     # naa'

        As with all other Pitzer parameters, a five-term expression 
	for temperature dependence is available:
            P = A0 + A1*(1/TK - 1/TR) + A2log(TK/TR) + A3*(TK-TR) +
                A4*(TK*TK - TR*TR),
        where TK is Kelvin and TR is 298.15. A0 through A4 are
	defined in order. Any undefined values are assumed to 
	be zero.

	-MU
		CO2	CO2	CO2	? ? ? ? ? # nnn

------------------------------------------------------------
Version 2.14.2: September 17, 2007
------------------------------------------------------------

	Fixed logic of memory checking for PhreeqcI. This serious
	bug makes versions 2.14.0 and 2.14.1 unusable.

------------------------------------------------------------
Version 2.14.1: September 5, 2007
------------------------------------------------------------

        No new features.

------------------------------------------------------------
Version 2.14.0: August 30, 2007
------------------------------------------------------------

        No new features.

------------------------------------------------------------
Version 2.13.3: February 15, 2007
------------------------------------------------------------

        No new features.

------------------------------------------------------------
Version 2.13.2: February 1, 2007
------------------------------------------------------------

        No new features.

------------------------------------------------------------
Version 2.13.1: January 16, 2007
------------------------------------------------------------

        No new features.

------------------------------------------------------------
Version 2.13.0: November 3, 2006
------------------------------------------------------------

        --------
        svn 1368
        --------
(1)     Added multicomponent diffusion (MCD) to transport
        capabilities. MCD allows different tracer diffusion
        coefficients for species, but calculates charge balanced
        transport. In the example, MCD is specified to be true,
        default tracer diffusion coefficient for species (Dw) is 1e-9,
        porosity is set to 0.3, porosity limit is set to 0.05, and an
        exponent of porosity (n) is set to 1.0. Effective diffusion
        coefficient is defined by the equation: De = Dw * porosity^n.
        Diffusion stops when the porosity falls below the porosity
        limit.

        TRANSPORT
                -multi_d true 1e-9 0.3 0.05 1.0

        Added tracer diffusion coefficient to SOLUTION_SPECIES
        definitions, -dw identifier.

        SOLUTION_SPECIES
        H+ = H+
                log_k   0.0
                -gamma  9.0     0.0
                -dw     9.31e-9

(2)     Added phreeqd.dat database with diffusion coefficients (-dw)
        defined for aqueous species in database directory.

(3)     Added BASIC functions to obtain and modify the porosity
        in a cell. The functions can be used in BASIC programs
        defined with keyword RATES, USER_PRINT, USER_PUNCH and
        USER_GRAPH.

          get_por(cell_no)              # returns the porosity in cell
                                        # 'cell_no'

          change_por(0.21, cell_no)     # porosity of cell 'cell_no'
                                        # becomes 0.21

(4)     Mobile surface and Donnan option in SURFACE. Mobile surfaces
        are meant for modeling transport of colloids. Only surfaces with
        a diffuse double layer can be transported (the ensemble must be
        electrically neutral). Surfaces related to equilibrium-phases
        and kinetics cannot be transported.

        Example 1: Use donnan assumption to calculate the explicit
        composition of the diffuse layer of surfaces. Thickness of the
        diffuse layer is defined to be 1e-7 meters. (Default thickness
        is 1e-8 meters.) Hfo (both sites Hfo_w and Hfo_s) is a surface
        that is transported with advection and dispersion. The diffusion
        coefficient of 1e-13 m^2/s is used with option -multi_d true in
        TRANSPORT. Sfo is an immobile surface (Dw = 0).

        SURFACE
                -donnan 1e-7
                Hfo_w 97.5e-5 600 88e-3 Dw 1e-13
                Hfo_s 2.5e-5
                Sfo_w 97.5e-5 600 88e-3 Dw 0
                Sfo_s 2.5e-5

        Example 2: Define Donnan calculation information. Thickness
        of the diffuse layer is 1e-8 meters, and relative viscosity is
        0.5. Relative viscosity only applies to multicomponent diffusion
        of solutes in the diffuse layer. (Default viscosity is 1.0.)

        SURFACE
                -donnan 1e-8 viscosity 0.5

        Example 3: Define Donnan calculation information. Thickness
        of the diffuse layer is 1.5 Debye lengths, maximum fraction of
        water that can be in the diffuse layer is 0.9. (Default
        thickness in Debye lengths is 1, default limit is 0.8.)

        SURFACE
                -donnan debye_lengths 1.5 limit_ddl 0.9

        When option '-only_counter_ions' is used in conjunction with
        with '-donnan', all the co-ions (with the same sign of charge as
        the surface) will be excluded from the DDL, and will be given a
        concentration of (near) zero in the DDL.

(5)     Added special BASIC function to change the diffusion
        coefficient of (part of) a SURFACE, and hence to change the
        status from mobile to immobile or immobile to mobile.

        Example 1: take a fraction 0.2 of 'Hfo', rename it to
        'Sorbedhfo', with a diffusion coefficient of 0, in cell 'cell_no'

        USER_PRINT
                10 print 'Changing surface in cell ', cell_no
                20  change_surf("Hfo", 0.2, "Sorbedhfo", 0, cell_no)

        Example 2: change the diffusion coefficient of 'Hfo' to  1e-12
        m2/s in cell 'cell_no'

                10 change_surf("Hfo", 1, "Hfo", 1e-12, cell_no)

        This function can be used in BASIC programs defined with keywords
        RATES, USER_PRINT, USER_PUNCH and USER_GRAPH. For correct
        operation of 'change_surf', the surface components must have
        been defined with the same surface species (the association
        constants may differ) and the same diffuse layer thickness or
        Debye length. The surfaces will be adapted at the end of a
        calculation step. The result of change_surf does not show up in
        print or punch results of that step, but the reformatting is
        effective in the next timestep calculations.

        --------
        svn 1337
        --------
        Added -add_logk to NAMED_EXPRESSIONS keyword.

        NAMED_EXPRESSIONS
        Log_alpha_14C_CO3-2/CO2(aq)
        -add_logk       Log_alpha_14C_CO3-2/CO2(g)      1
        -add_logk       Log_alpha_14C_CO2(aq)/CO2(g)   -1

        --------
        svn 1281
        --------
        Added new option to PITZER data block to allow definition of
        alpha1 and alpha2 for specific electrolytes. Entries are 
        following -ALPHAS are Ion1, Ion2, alpha1, alpha2. Both
        alpha1 and alpha2 should be defined. Default is 0.0 for
        undefined values following Ion1 and Ion2.

        Example:

        PITZER
        -ALPHAS
        #
        # Defaults for ion valences in salts
        #
        #   1-N (only B1): alpha1 = 2 
        #   2-2:           alpha1 = 1.4  alpha2 = 12.0
        #   3-2, 4-2:      alpha1 = 2    alpha2 = 50
        #
        #Ion1     Ion2      Alpha1   Alpha2
        Fe+2      Cl-       2        1
        Fe+2      SO4-2     1.559    5.268

        --------
        svn 1279
        --------
        Added new Basic function OSMOTIC that returns the
        osmotic coefficient if the Pitzer model (PITZER keyword data
        block) is used or 0.0 if the ion-association model is used.

        Example:

        USER_PRINT
        10 PRINT "Osmotic coefficient: ", OSMOTIC

        --------
        svn 1245 
        --------
        Enabled redox in Pitzer model with option in
        PITZER keyword. Typically, the option will be included
        in the pitzer database file. 

        Example:

        PITZER
        -redox  TRUE

        The default database for the Pitzer model does not contain 
        any redox definitions and the default value for the option 
        is FALSE. At a minimum, species O2 and H2 must be defined 
        in the database or input file to allow redox calculations.
        
        --------
        svn 1207 
        --------
        Added option to force an equilibrium phase to be 
        included in the equality constraints. Normally, the SIs of 
        equilibrium phases are optimized to be negative and the
        sum of SIs is minimized. If -force_equality is used, then
        the phase must reach its target SI or the calculation fails
        with an error.

        Example: 

        EQUILIBRIUM_PHASES
        Fix_pH  -7  NaOH
             -force_equality
        Calcite  0
        Dolomite 0
        CO2      -3.5

        One example of using the new option would be to ensure that 
        a target pH is attained, as in the example above. 

        --------
        svn 1179 
        --------
        New option (-sites_units density) allows alternative
        units (sites/nm^2) for definition of number of sites for a
        surface. This approach requires better consistency among the
        parameters as both the number of sites and the surface area
        are based on the mass. It makes more sense than the default,
        which requires the number of sites (first numeric item in a
        line) to be defined in units of moles, independently of the
        number of grams of sorbent.

        Example:

        SURFACE 1
        -sites_units     DENSITY
        SurfOH  2.6    600.    1.0
        SurfaOH 2.6    30.     2.0

        Explanation: 

        In this example, Surf has a site density of 2.6 sites per
        nanometer squared, a specific area of 600 meters squared per
        gram, and a mass of 1 gram. Surfa has a site density of 2.6
        sites per nanometer squared, a specific area of 30 meters
        squared per gram, and mass of 2 grams.

        --------
        svn 1096 
        --------

        Allows solids and gases in the equations for PHASES. This
        capability simplifies the definitions for gas and solid
        isotopic components. Solids must be identified with "(s)" and
        gases with "(g)". The first entity on the left- hand-side of
        the equation must be the stoichiometric formula of the solid
        or gas component being defined, optionally with (g) or (s). In
        turn gases and solids included in the equation must be defined
        with reactions that ultimately allow the defined species
        (C[18O]2(g) in this case) in terms of aqueous species.

        Example:

        PHASES
        C[18O]2(g)
                C[18O]2(g) + CO2(g) = 2CO[18O](g) 
                log_k          0.602059991327962396        # log10(4)

        --------
        svn 1092 
        --------
        CD_MUSIC sorption model has been implemented.
        Still missing logic for surfaces related to equilibrium-
        phases and kinetics. Has explicit calculation of diffuse
        layer composition with Donnan assumption. Old diffuse-layer
        calculation will not be implemented.
        
        Example:

        SURFACE
        Goe_uniOH .000552 96.387 1
             -capacitance    1.1   5
        Goe_triO  .000432
        -cd_music
        -donnan

        Explanation:

        1.1 5 are capacitances for the cd-music model for 0-1 and 1-2
            planes, respectively. 
        -cd_music specifies that the surface is a cd-music surface.
        -donnan optionally calculates the diffuse layer composition
                with the Donnan model.

        Example:

        SURFACE_SPECIES
        Goe_uniOH-0.5 + H+ + AsO4-3 = Goe_uniOAsO3-2.5 + H2O
             log_k     20.1                 # eq 7   K1, Kin1
             -cd_music  -1 -6 0 0.25 5

        Explanation:

        -cd_music gives the charge contribution of the surface species
        to the three planes. Plane 0 is -1 + 0.25*5; Plane 1 is -6 +
        (1-0.25)*5; Plane 2 (or d) is 0.

        --------
        svn 675:
        --------
        Added PRINT option to print the species that contribute
        to alkalinity. Alkalinity distribution is printed in
        the output file following the distribution of species.
        Default at program startup is false.

        Example:

        PRINT
                -alkalinity true

------------------------------------------------------------
Version 2.12:
------------------------------------------------------------

*       Made aqueous activity coefficients the default activity
        coefficients for exchange species when using the 
        Pitzer formulation. New option in EXCHANGE is
        -pitzer_exchange_gammas T/F, default is true; 
        defining "false" sets exchange activity coefficients
        to 1.0. Option has no effect for ion-association
        model (non-Pitzer).

*       Added multiplier format to REACTION steps and KINETICS steps, 
        which simplifies definition of multiple equal reaction increments.

            This definition:

                   INCREMENTAL_REACTIONS true
                   REACTION
                        H2O 1
                        -36 3*-4 2*-.25 -0.19 4*-0.1 3*-0.05 moles

            is equivalent to this definition:

                   INCREMENTAL_REACTIONS true
                   REACTION
                        H2O 1
                        -36 -4 -4 -4 -.25 -.25 -0.19 -0.1 -0.1 -0.1
                        -0.1  -0.05 -0.05 -0.05  moles

        

*       Added Pitzer activity formulation. Use pitzer.dat database
        to invoke the Pitzer model. Should have same capabilities
        as ion-association model except explicit diffuse layer 
        calculation is not implemented with the Pitzer model.
        New keyword is PITZER with following options:

        PITZER
        -MacInnes   T/F   # uses MacInnes assumption or unscaled for
                          # individual activities and activity coefficients
        -B0
          Na+       Cl-       0.0765     -777.03     -4.4706        0.008946   -3.3158E-6
        -B1                                              
          Na+       Cl-       0.2664        0           0           6.1608E-5   1.0715E-6
        -B2
          Mg+2      SO4-2    -37.23         0           0          -0.253
        -C0
          Na+       Cl-       0.00127     33.317      0.09421    -4.655E-5
        -THETA
          K+        Na+      -0.012
        -LAMDA
          Na+       CO2       0.1
        -ZETA
          H+        Cl-       B(OH)3    -0.0102
        -PSI
          Na+       K+        Cl-       -0.0018

        A five-term expression for temperature dependence is available
        for all Pitzer parameter values: 
            P = A0 + A1*(1/TK - 1/TR) + A2log(TK/TR) + A3*(TK-TR) +
                A4*(TK*TK - TR*TR),
        where TK is Kelvin and TR is 298.15.

*       Cl1mp is a new multiple precision version of routine cl1,
        a simplex-based optimization routine. Cl1mp was develeped
        by using the Gnu Multiple Precision package (gmp).
        Calculations are carried out to about 30 significant
        digits. Cl1mp may help in some situations where roundoff 
        errors are a problem, but it is still possible that roundoff 
        errors will cause cl1mp to fail to find a solution to an 
        optimization problem. The mp version has the following 
        options in INVERSE_MODELING:

                -multiple_precision T/F--causes the mp version 
                        to be used in inverse modeling calculations.
                -mp_tolerance 1e-12--tolerance for mp version of
                        cl1. As in cl1, numbers less than the
                        tolerance are considered to be zero. 
                        1e-12 is the default.
                -censor_mp 1e-20--as calculations occur in the
                        linear equation array, elements less
                        than this value are set to zero. Default
                        is 1e-20. A value of 0.0 causes no
                        censoring to occur.

------------------------------------------------------------
Version 2.11:
------------------------------------------------------------

*       A new database, minteq.v4.dat, has been translated from
        version 4.02 of MINTEQA2 and is included in all
        distributions. The database minteq.dat from earlier
        version of MINTEQA2 has been slightly revised and is 
        also included.

------------------------------------------------------------
Version 2.10:
------------------------------------------------------------

        No new features.

------------------------------------------------------------
Version 2.9:
------------------------------------------------------------
*       Added new keyword COPY that allows a data entity 
                to be copied from one index to a new index 
                or to a range of indicies. Format is 

        COPY keyword index index_start[-index_end]

        where keyword may be    SOLUTION
                                EQUILIBRIUM_PHASES
                                EXCHANGE
                                GAS_PHASE
                                KINETICS
                                MIX
                                REACTION
                                REACTION_TEMPERATURE
                                SOLID_SOLUTION
                                SURFACE

*       Added new Basic functions
        b$ = PAD(a$, 20)   pads a$ to a total of 20 characters
                with spaces and stores result in b$. PAD returns
                a copy of a$ if a$ is more than 20 characters.
        i = INSTR(a$, b$)  sets i to the character position of
                string b$ in a$, 0 in not found.
        b$ = LTRIM(a$)     trims white space from beginning of 
                string a$ and stores result in b$.
        b$ = RTRIM(a$)     trims white space from end of string 
                a$ and stores result in b$.
        b$ = TRIM(a$)     trims white space from beginning and
                end of string a$ and stores result in b$.

*       Added new Basic function SYS that calculates the to
        total amount of an element in all phases (solution,
        equilibrium_phases, surfaces, exchangers, solid solutions, 
        and gas phase). KINETIC reactions are not included.
        The function has two forms: (1) one element name as an
        argument (variable names are user specified)

        10 t = SYS("As")

        the function will return the total arsenic in the system.
        (2) 5 argumens

        10 t = SYS("As", count_species, names$, types$, moles)

        will return the total arsenic in the system to tot; count_species--
        the number of species that contain arsenic, including
        solution, equilibrium_phases, surfaces, exchangers, solid solutions, 
        and gas phase species; names$--a character array that has the
        name of each species; type$--a character array that specifies the
        type of phase for the species, aq, equi, surf, ex, s_s, gas, diff. 
        Diff refers to the amount of the element in the diffuse layer of 
        a surface when the explicit diffuse layer calculation is used; 
        moles--an array containing the number of moles of the element in 
        the species. The sum of moles(i) is equal to tot.

        SYS has several special arguments for the form 
        SYS("arg", count, names$, types$, values)
                arg     is one of the options listed below.
                count   is a single numeric value and is the number of elements
                                in the following arrays.
                name$   is an array of string values.
                type$   is an array of string values.
                values  is an array of numeric values.

        Values of arg:

        elt_name        returns total number of moles of element in system.
                        count is the number of species for the element in
                                the system, including aqueous, exchange, surface,
                                equilibrium_phase, solid solution component, and
                                gas phase "species".
                        Arrays are filled for each "species"; values are moles.
        "elements"      returns total number of moles of dissolved elements other
                                than H and O.
                        count is number of elements, valence states, 
                                exchangers, and surfaces.
                        Arrays are filled for each element and valence state,
                                type is "dis"; exchanger, type is "ex",
                                and surface, type is "surf". Values are moles.
        "phases"        returns maximum saturation index of all phases.
                        count is number of phases in system.
                        Arrays are filled for each phase; values are
                                saturation indexes.
        "aq"            returns sum of moles of all aqueous species.
                        count is number of aqueous species in system.
                        Arrays are filled with each aqueous species;
                                values are moles.
        "ex"            returns sum of moles of all exchange species.
                        count is number of exchange species in system.
                        Arrays are filled with each exchange species;
                                values are moles.
        "surf"          returns sum of moles of all surface species.
                        count is number of surface species in system.
                        Arrays are filled with each surface species;
                                values are moles.
        "s_s"           returns sum of moles of all solid solution components.
                        count is number of solid solution components in system.
                        Arrays are filled with each solid solution component;
                                values are moles.
        "gas"           returns sum of moles of all gas components.
                        count is number of gas components in system.
                        Arrays are filled with each gas component;
                                values are moles.

*       Added new Basic function, DESCRIPTION, that has the value
        defined for the description field of the SOLUTION keyword line. 

*       Added alternative ordinary differential equation solver
        called CVODE, a set of C routines from the Lawrence 
        Livermore National Labs. CVODE is part of the SUNDIALS
        package. CVODE is used in place of the Runge Kutta method
        when "-cvode true" is used within a KINETICS data block.

        KINETICS
                -cvode true

------------------------------------------------------------
Version 2.8:
------------------------------------------------------------

        No new features.

------------------------------------------------------------
Version 2.7:
------------------------------------------------------------
Changed format of selected output file:
        Removed quotations surrounding strings in headings.
        Removed quotations surrounding strings in state variable.
        All fields are 12 or 20 places depending on 
                -high_precision.
        Headings are not truncated even if longer than 
                specified precision.
        For isotopes, missing value is -9999.9
        Selected output is updated each simulation.
                If a species or phase is defined
                subsequent to the simulation where SELECTED_OUTPUT
                was defined it will appear in the selected output
                file in the simulation in which it is defined and
                in subsequent simulations.

Added strings for each file, which can be extracted from the
        executable file with the "ident" command.

Fixed null pointer for isotope_ratios if Basic routine 
        was undefined.

Fixed problem in C++ if structure name is same as member name.
        logk member of logk structure was renamed to log_k.

Added identifier -add_constant to PHASES, EXCHANGE_SPECIES,
        SOLUTION_SPECIES, and SURFACE_SPECIES. 

        -add_constant  -0.301  

        log K is augmented by the specified constant. 

Theory and implementation of isotopes in PHREEQC is documented in:

Thorstenson, D.C., and Parkhurst, D.L., 2002, Calculation of
individual isotope equilibrium constants for implementation in
geochemical models: U.S. Geological Survey Water-Resources
Investigations Report 02-4172, 129 p.

Added KEYWORDS:

ISOTOPES
        Element
        -isotope  isotope_name units standard_ratio
        -total_is_major  T/F (OPTION IS DISABLED!!)

CALCULATE_VALUES
        Name
        -start
        Basic statements, must have SAVE
        -end

ISOTOPE_RATIOS (for printing)
        Name=Calculate_values_name      Isotope_name

ISOTOPE_ALPHAS (for printing)
        Name=Calculate_values_name      Named_logk=named_expression_name

Basic functions:
        calc_value("calc_value_name")           evaluates a definition of CALCULATE_VALUES
        lk_named("name")                        log10(K) of definition in NAMED_EXPRESSIONS
        lk_phase("name")                        log10(K) of definition in PHASES
        lk_species("name")                      log10(K) of definition in (SOLUTION, EXCHANGE, SURFACE)_SPECIES
        sum_gas("template","element")           Sum of element in gases with specified template, moles.
						Example:
                                                template="{C,[13C],[14C]}{O,[18O]}2" includes all CO2 gases
        sum_species("template","element")       Sum of element in aqueous, exchange, and surface species with
                                                specified template (moles)
        sum_s_s("s_s_name","element")           Sum of element in a specified solid solution (moles)

PRINT keyword:
        -initial_isotopes  T/F
        -isotope_ratios    T/F
        -isotope_alphas    T/F
        -censor_species    1e-8   # omit species from Distribution of Species if less than 
                                  # relative minimum of an element or element redox state
                                  # total concentration

SELECTED_OUTPUT keyword:
        -calculate_values  name1 name2 ...
        -isotopes minor_isotope1 minor_isotope2 ....

Added functions LK_SPECIES, LK_NAMED, LK_PHASE for Basic
        interpreter. LK_SPECIES("CaHCO3+") returns the
        log k for the association reaction for the ion pair
        CaHCO3+ at the current temperature. The log K is 
        for the reaction as defined in the database or 
        input file. Similarly, 
        LK_NAMED("Log_alpha_18O_CO2(aq)/CO2(g)") returns the 
        value for the log K at the current temperature using
        expressions defined in NAMED_LOG_K data block; 
        LK_PHASE("Calcite") returns the value of log K 
        for calcite at the current temperature for the 
        dissociation reaction defined in the database or 
        input file. Values are "log10" values.
Example for Basic program:
        10 PRINT "Log10 KCalcite: ", LK_PHASE("Calcite")
        20 PRINT "Log10 KCaHCO3+: ", LK_SPECIES("CaHCO3+")
        30 PRINT " 1000ln(alpha): ", LK_NAMED("Log_alpha_18O_CO2(aq)/CO2(g)")*LOG(10)*1000

NAMED_EXPRESSION--New keyword data block.

        This data block was implemented to facilitate isotopic
        calculations.  It allows analytical expressions that
        are functions of temperature to be defined. The purpose
        is to separate the fractionation factors from the log
        K, so that the fractionation factor or its temperature
        dependence can be easily modified. The named expression
        can be added to a log K for a species or phase by the
        -add_logk identifier in SOLUTION_SPECIES
        EXCHANGE_SPECIES, SURFACE_SPECIES, or PHASES data
        block. Log K, Delta H, and analytical expressions for a 
        log K can be defined with identifiers -log_k, -delta_h,
        and -analytical_expression as described in SOLUTION_SPECIES
        in WRIR 99-4259. Fractionation factors are often defined
        as 1000*ln(alpha). The identifier -ln_alpha1000 can be used
        to enter data in this form. The analytical expression is the
        same as defined in SOLUTION_SPECIES, but the result of the 
        expression is converted to log10(alpha) by dividing by 
        1000*ln(10) before it is summed into log K values.

NAMED_EXPRESSIONS
        Log_K_calcite           #       CaCO3 + 2H3O+ = Ca+2 + 3H2O + CO2
                log_k           8.201   
                delta_h         -8.035  kcal
                -analytic       292.29  0.015455        -24146.841      -94.16451       2248628.9 

        Log_alpha_18O_CO2(aq)/Calcite
                -ln_alpha1000   3.8498  0.0     10.611e3        0.0     -1.8034e6

        Log_alpha_13C_CO2(aq)/Calcite           
                -ln_alpha1000   2.72    0.0     0.0     0.0     -1.1877e6

------------------------------------------------------------
Added identifier -add_logk to SOLUTION_SPECIES
        EXCHANGE_SPECIES, SURFACE_SPECIES, and PHASES data
        block.

        Allows a named expression to be added to the definition
        of the log K for a species or phase. In the following
        example, the log K for the phase Ca[14C][18O]3 is summed from
        four parts, one defined with the log_k identifier and the
        other three parts from expressions defined in NAMED_EXPRESSIONS.
        The named expression is multiplied by the coefficient at the
        end of the line before it is summed into the log K. A missing
        coefficient is 1.0 by default.

PHASES
        Ca[13C][18O]3
        Ca[13C][18O]3 + 3CO2 + 2H3O+ = Ca+2 + 3H2O + 3CO[18O] + [13C]O2
        log_k           0.903089986991                          # 3*log10(2)
        -add_logk       Log_K_calcite                           1.0
        -add_logk       Log_alpha_13C_CO2(aq)/Calcite           1.0
        -add_logk       Log_alpha_18O_CO2(aq)/Calcite           3.0

SOLUTION keyword:
        At present, can only define isotopes in the units defined in ISOTOPES.

------------------------------------------------------------
Version 2.6:
------------------------------------------------------------

        No new features.

------------------------------------------------------------
Version 2.5:
------------------------------------------------------------
Added the capability to use square brackets to define an
        "element" name. The brackets act like quotation marks
        in that any character string can be used within the 
        brackets as an element name. For example, [Fe3], [13C],
        and [N5] are now legal "element" names. All element 
        names without brackets must begin with a capital letter, 
        followed by zero or more lower case letters and underscores.

Added identifier -activity_water for a species in SOLUTION_SPECIES
        data block. This identifier has been added for future updates
        that will allow isotopic calculations. It is intended to be
        used only for isotopic variations of H2O, like D2O or 
        H2[O18]. It forces the activity coefficient for the 
        species to be activity(water)/55.5. This effectively sets 
        the activity of the species to the mole fraction in 
        solution.

Added identifier -bad_step_max to KINETICS data block.
        An integer following -bad_step_max gives the maximum number 
        of times a rate integration may fail before execution of the
        program is terminated. Default is 500.

------------------------------------------------------------
Version 2.4:
------------------------------------------------------------

------------------------------------------------------------
Added identifier -warnings to PRINT keyword. 

        An integer following -warnings gives the maximum number 
        of warnings to print into the output file. A negative 
        number allows all warnings to be printed.

        Example:        -warnings 20

------------------------------------------------------------
Changed the results of the function CELL_NO in Basic programs.

        Function cell_no in Basic now prints a number equivalent 
        to -solution in SELECTED_OUTPUT data block. It gives the 
        solution number for initial solution calculations and the 
        solution being used in batch reaction calculations. 
        Result is the same as previous versions for ADVECTION or 
        TRANSPORT calculations.

------------------------------------------------------------
Version 2.3:
------------------------------------------------------------
DATABASE--New keyword data block

        It must be the first keyword in the input file. 
        The character string following the keyword is 
        the pathname for the database file to be used
        in the calculation. The file that is specified
        takes precedence over any default database
        name, including environmental variable
        PHREEQC_DATABASE and command line arguments.

LLNL_AQUEOUS_MODEL_PARAMETERS--New keyword data block

        Added new keyword to make aqueous model similar to
        EQ3/6 and Geochemists Workbench when using
        llnl.dat as the database file. Values
        of Debye-Huckel a and b and bdot (ionic strength
        coefficient) are read at fixed temperatures.
        Linear interpolation occurs between temperatures.

        New options for SOLUTION_SPECIES are
                -llnl_gamma  a   , where a is the ion-size parameter.
                -co2_llnl_gamma  , indicates the temperature dependent
                        function for the bdot term given in 
                        -co2_coefs of LLNL_AQUEOUS_MODEL_PARAMETERS
                        will be used. Applies to uncharged
                        species only.

LLNL_AQUEOUS_MODEL_PARAMETERS
-temperatures
         0.0100   25.0000   60.0000  100.0000
       150.0000  200.0000  250.0000  300.0000
#debye huckel a (adh)
-dh_a
         0.4939    0.5114    0.5465    0.5995
         0.6855    0.7994    0.9593    1.2180
#debye huckel b (bdh)
-dh_b
         0.3253    0.3288    0.3346    0.3421
         0.3525    0.3639    0.3766    0.3925
-bdot
         0.0394    0.0410    0.0438    0.0460
         0.0470    0.0470    0.0340    0.0000
#cco2   (coefficients for the Drummond (1981) polynomial)
-co2_coefs
        -1.0312              0.0012806
          255.9                 0.4445
      -0.001606

------------------------------------------------------------
Added function SURF to Basic.

        SURF("element", "surface") gives the amount of element 
        sorbed on "surface". "surface" should be the surface 
        name, not the surface-site name (that is, no underscore).

------------------------------------------------------------
Allow decimals in definition of secondary master species.

        Some redox states do not average to integers,
        for convenience in identifying them, decimal numbers
        may be used within the parentheses that define the 
        redox state, example S(0.3) could be used in the
        MASTER_SPECIES data block for the valence state of
        aqueous species S6-2.

------------------------------------------------------------
Eliminate echo of input file in PRINT data block. 

        -echo_input T/F turns echoing on and off. 
        Default is true, initial value is true.
        
------------------------------------------------------------
Added option for an equilibrium-phase to dissolve only. 
        "dis" is added at the end of a line defining an equilibrium-
                phase. No data fields may be omitted. Should not
                be used when adding an alternative reaction.
        Example:
                EQUILIBRIUM_PHASES
                Dolomite 0.0  0.001 dis

------------------------------------------------------------
Version 2.2:
------------------------------------------------------------
Added function EDL to Basic.
        EDL("element", "surface") gives the amount of 
        element in the diffuse layer for "surface", not
        including sorbed species. "surface" should be 
        the surface name, not the surface-site name 
        (that is, no underscore).

        Special values for "element" include:
                "charge" - gives surface charge, equivalents.
                "sigma"  - surface charge density, C/m**2.
                "psi"    - potential at the surface, Volts.
                "water"  - mass of water in the diffuse layer, kg.

------------------------------------------------------------
End of Features not documented in WRIR 99-4259.
------------------------------------------------------------

************************************************************
************************************************************
*               Revisions and bug fixes                    *
************************************************************
************************************************************
------------------------------------------------------------
Version 2.14.3: November 17, 2007
------------------------------------------------------------

        --------
        svn 2386
        --------
	Fixed bug in routine find_Jstag. Incorrect index (cell_no)
	caused segmentation violation in rare instances.

        --------
        svn 2312
        --------
	Added new option to PITZER datablock, use_etheta t/f.

        --------
	svn 2279
        --------
        Error lost 200 moles of mineral. Should only be a problem
	in some cases where moles of mineral is greater than 200.

        --------
	svn 2270
        --------
        Added additional parameters Pitzer activity formulation for
	neutral species, MU and ETA. 

        --------
	svn 2269
        --------
	Fixed buffer overrun in SOLUTION_SPREAD when pasting.

        --------
	svn 2268
        --------
	Fixed error in prep.c where realloc was called instead
	of PHRQ_realloc, which eliminated a memory leak.

------------------------------------------------------------
Version 2.14.2: September 17, 2007
------------------------------------------------------------
	
        --------
	svn 2267
        --------
	Fixed logic of memory checking for PhreeqcI. This serious
	bug makes versions 2.14.0 and 2.14.1 unusable.

------------------------------------------------------------
Version 2.14.1: September 5, 2007
------------------------------------------------------------
        --------
	svn 2219
        --------
	Updated transport.c to adjust transport in diffuse 
	layer to be charge balanced for MCD calculation.

------------------------------------------------------------
Version 2.14.0: August 30, 2007
------------------------------------------------------------
        -------------
	svn 2203-2204
        -------------
	Revised logic for using phqalloc memory checker. Compiler
	option USE_PHRQ_ALLOC now turns on memory checker. If
	USE_PHRQ_ALLOC is defined and NDEBUG is not defined, file name
	and line number are also used in memory checking. Model.c
	now uses same compile options as all other files.

        --------
	svn 2199
        --------
	Initialized variables that caused problems when rerunning
	simulations in PfW and PhreeqcI.

        --------
	svn 2138
        --------
	Fixed bugs in MCD calculation related to saving solutions
	after initialization.

        --------
	svn 2055
        --------
	Profiled and optimized of code. Automatic string in Basic
	factor saves many mallocs. Reordered to minimize call to
	strcmp_nocase in basicsubs.c and xsolution_save. Minimized
	mallocs for solver.

        --------
	svn 2051
        --------
	Fixed bugs in MCD calculation.

        --------
	svn 2040
        --------
	Fixed warnings for type-punned with new gcc. 

	Reverted to 2.12 for infilling solutions for transport. 
	Only solutions are used, not additional reactants for solution
	0 and n+1.

	Added digits to printout of REACTION stoichiometry.

        --------
	svn 1852
        --------
	Fixed error in CDMUSIC surface related to a phase.
	Stoichiometry of H was calculated incorrectly.

        --------
	svn 1837
        --------
	Initialize flag for MCD calculation. PhreeqcI would
	do MCD calculation after TRANSPORT was redefined not
	to do MCD calculation.

------------------------------------------------------------
Version 2.13.2: February 1, 2007
------------------------------------------------------------
        --------
        svn 1700
        --------
        Fixed bug with redox elements in multi_diffusion
	stagnant zones.

        --------
        svn 1683
        --------
        Worked on convergence problems when optimizer fails to
	find a solution. Censored values greater than 1e8.

        --------
        svn 1637
        --------
        Fixed bug with dissolve only in ADVECTION calculations.

        --------
        svn 1629
        --------
        Fixed bug with redox elements in multi_diffusions. Added
        Phreeqc For Windows changes from 2.13.1.

------------------------------------------------------------
Version 2.13.1: January 16, 2007
------------------------------------------------------------
        --------
        svn 1600
        --------
        Fixed logic error that required rebuilding aqueous model
        when not necessary. Now runs faster (sometimes 3X) than
        version 2.13.0.

        --------
        svn 1590
        --------
        Removed porosity from one statement to eliminate oscillations
        in multicomponent diffusion calculation.

        --------
        svn 1558
        --------
        Dissolve-only option did not work correctly for stagnant cells
        in TRANSPORT calculations. The moles of equilibrium phases,
        kinetics, gas_phase, and solid solutions were not initialized
        at the beginning of each transport step. Thus, the printed values
        for delta moles for the step in the output and punch file were 
        incorrect for stagnant-zone cells. "Dissolve only" was
        always tested relative to the number of moles initially in the
        cells, not the amount remaining at a given time step.

        --------
        svn 1485
        --------
        Pitzer version with gas_phase did not work. Added
        gas_phase and cd_music to numerical derivative routine.

        svn 1368: (1) Added multicomponent diffusion in transport and
        SOLUTION_SPECIES. (2) Added BASIC functions to obtain and
        modify the porosity in a cell. (3) Aded mobile surface and Donnan
        option in SURFACE.  (4) Added special BASIC function to change
        the diffusion coefficient of a SURFACE, and hence to
        change the status from mobile to immobile or immobile to
        mobile.

        svn 1337: Added -add_logk to NAMED_EXPRESSIONS keyword.

        svn 1306: Revised printing of distribution of species,
        pure phase assemblages, and solid solutions to use 
        longer fields for names. More revisions to logic
        for using gases and solids in equations for phases.
        Revised logic for solid solutions with small (1e-25) amounts
        of component.

        svn 1282: Fixed bug when gas phase had no gas components.
        Looked the same as not having a gas phase at all.

        svn 1245: Enabled redox in Pitzer model with option in
        PITZER keyword. Typically, the option will be included
        in the pitzer database file. 

PITZER
    -redox  TRUE

        The default database for the Pitzer model does not contain 
        any redox definitions and the default value for the option 
        is FALSE. At a minimum, species O2 and H2 must be defined 
        in the database or input file to allow redox calculations.

        svn 1179: New option (-sites_units density) allows alternative
        units (sites/nm^2) for definition of number of sites for a
        surface. This approach requires better consistency among the
        parameters as both the number of sites and the surface area
        are based on the mass. It makes more sense than the default,
        which requires the number of sites (first numeric item in a
        line) to be defined in units of moles, independently of the
        number of grams of sorbent.

SURFACE 1
        -sites     DENSITY
        SurfOH  2.6    600.    1.0
        SurfaOH 2.6    30.     2.0

        In this example, Surf has a site density of 2.6 sites per
        nanometer squared, a specific area of 600 meters squared per
        gram, and a mass of 1 gram. Surfa has a site density of 2.6
        sites per nanometer squared, a specific area of 30 meters
        squared per gram, and mass of 2 grams.

        svn 1128: Fixed bug with value of time printed to selected
        output file when using cvode. Value printed was an
        intermediate integration time step, not time at end 
        of integration.
        
        svn 1096: Allows solids and gases in the equations for
        PHASES. This capability simplifies the definitions for
        gas and solid isotopic components. Solids must be identified
        with "(s)" and gases with "(g)". The first entity on the left-
        hand-side of the equation must be the stoichiometric formula
        of the solid of gas component being defined, optionally with
        (g) or (s). In turn gases and solids included in the equation
        must be defined with reactions that ultimately allow the
        defined species (C[18O]2(g) in this case) in terms of aqueous
        species.

C[18O]2(g)
        C[18O]2(g) + CO2(g) = 2CO[18O](g) 
        log_k           0.602059991327962396                   # log10(4)

        svn 1092: CD_MUSIC sorption model has been implemented.
        Still missing logic for surfaces related to equilibrium-
        phases and kinetics. Has explicit calculation of diffuse
        layer composition with Donnan assumption. Old diffuse-layer
        calculation will not be implemented.
        
        Example:

SURFACE
        Goe_uniOH .000552 96.387 1
                  -capacitance    1.1   5
        Goe_triO  .000432
        -cd_music
        -donnan

        1.1 5 are capacitances for the cd-music model for 0-1 and 1-2
            planes, respectively. 
        -cd_music specifies that the surface is a cd-music surface.
        -donnan optionally calculates the diffuse layer composition
                with the Donnan model.

SURFACE_SPECIES
        Goe_uniOH-0.5 + H+ + AsO4-3 = Goe_uniOAsO3-2.5 + H2O
             log_k     20.1                 # eq 7   K1, Kin1
             -cd_music  -1 -6 0 0.25 5

        -cd_music gives the charge contribution of the surface
                  species to the three planes. Plane 0 is
                  -1 + 0.25*5; Plane 1 is -6 + (1-0.25)*5; 
                  Plane 2 (or d) is 0.

        svn 1030: Fixed bug in tranport. Mixing was not printed
        when using -cvode in kinetics.

        svn 984: Fixed bug in transport when cell without a
        surface followed a cell with a diffuse-layer surface.
        Fixed bug in TOTAL function; code ran of the end of
        the list of master species; changed logic to recognize
        the end of the list.

        svn 874: Fixed bug in check_same_model. Thought surface
        calculation was the same even though -edl switch was
        different, which gave irratic results and possible 
        crash. Now checks more carefully to make sure calculation
        for surfaces is really the same and reinitializes if
        not.

        svn 847: Fixed bug with DESCRIPTION function. Did not
        give correct solution description for reactions.

        svn 826: Update tally.c to avoid conflicts in C++
        version of phast.

        svn 801: Wrote around underflow in fabs in subroutine 
        reset. 

        svn 794: Errors in minteq.v4.dat database. Several redox
        reactions had delta H listed as kcal instead of kJ. kcal
        is correct only for the following species H2, NO2-, and
        NH4+.

        svn 675:
        Added PRINT option to print the species that contribute
        to alkalinity. Alkalinity distribution is printed in
        the output file following the distribution of species.
        Default at program startup is false.

        PRINT
                -alkalinity true
        
        svn 655:
        IAP and log K printed in Phase assemblage data 
        block were calculated from reactions rewritten to
        new master species. Now the original data base 
        reaction is used to calculate IAP and log K.
        Also fixed check that ensured all elements of 
        phase in are in solution before SI is calculated.

        svn 631:
        Fixed bug with alternate formula for equilibrium phase,
        nothing happened if all other equations were satisfied
        at beginning of reaction calculation.

        svn 603:
        Link gmp library statically.

        svn 601:
        Fixed statement on multiprecision.

        svn 581:
        Fixed bug in PhreeqcI that did not reinitialize
        Chebyschev parameters leading to incorrect results
        with Pitzer activity coefficients. Results were
        correct on first run, but erroneous on subsequent 
        runs.

        Added statement to identify multiprecision or
        standard solver for inverse modeling. 

        svn 578:

        Distribution changes. Fixed names in README file.
        Modified Makefile to use specified version. Split
        Linux and source distribution procedure.

------------------------------------------------------------
Version 2.12 Date: Wed September 28, 2005
------------------------------------------------------------

        Executables and output files for Sun operating systems
        are no longer provided.

        Limited log activities of master species to be greater
        than the smallest machine precision exponential number.
        Avoids a matherr exception and allows trial of additional
        parameter sets to attempt to solve the system of 
        equations.

        Made aqueous activity coefficients the default activity
        coefficients for exchange species when using the 
        Pitzer formulation. New option in EXCHANGE is
        -pitzer_exchange_gammas T/F, default is true; 
        defining "false" sets exchange activity coefficients
        to 1.0. Option has no effect for ion-association
        model (non-Pitzer).

        Edited phreeqc.dat to add -gamma expression for 
        CdX2 and PbX2. 

        Replaced O2(g) log K in phreeqc.dat and wateq4f.dat
        with data from llnl.dat, which appears to be better.

        Added multiplier format to REACTION increments, which
        simplifies definition of multiple equal reaction increments.

                   REACTION
                        H2O 1
                        -36 3*-4 2*-.25 -0.19 4*-0.1 3*-0.05 moles

        Added Pitzer activity formulation. Use pizer.dat database
        to invoke the Pitzer model. Should have same capabilities
        as ion-association model except explicit diffuse layer 
        calculation is not implemented with the Pitzer model.

        Fixed bug in surface sites related to mineral and exchange
        sites related to mineral. Did not have complete logic to 
        handle redox valence states in formula for species.

        Modified to remove non standard usage of va_list.

        Removed exchange master species from SYS("ex",..)
        list of species. This species is fictive and should
        not be included in the list.

        Changed -redox in SOLUTION so that if one of the
        redox states of a couple is not defined, then 
        redox defaults to pe.

        Fixed buffer overrun in PhreeqcI with SOLUTION_SPREAD, 
        caused segmenatation fault with lines greater than 
        500 characters.

        Added bigger string for some error messages to avoid 
        access violation in cvode.

        Changed output_msg to warning_msg for combinations
        of convergence parameters so that message would
        be controlled by -warnings identifier.

        Carriage returns are now stripped from Basic program 
        statements. Switching files from Windows to Unix sometimes
        leaves extra carriage returns at the ends of lines, which
        caused a syntax error for some Basic commands.

        Two bugs were fixed in inverse modeling. (1) Potential 
        models are now checked for all equality and inequality
        constraints. Previously some constraints were not checked.
        (2) One loop of cl1 did not include the last row when 
        checking for the pivot element. Also printing of headers
        was slightly modified for inverse modeling.

        A new multiple precision version of cl1 was develeped by 
        using the Gnu Multiple Precision package (gmp). Calculations 
        are carried out to about 30 significant digits. The mp 
        version may help in some situations where roundoff errors are
        a problem, but it is still possible that roundoff errors will 
        cause cl1mp to fail to find a solution to the optimization
        problem. The mp version has the following options in 
        INVERSE_MODELING:
                -multiple_precision T/F--causes the mp version 
                        to be used in inverse modeling calculations.
                -mp_tolerance 1e-12--tolerance for mp version of
                        cl1. As in cl1, numbers less than the
                        tolerance are considered to be zero. 
                        1e-12 is the default.
                -censor_mp 1e-20--as calculations occur in the
                        linear equation array, elements less
                        than this value are set to zero. Default
                        is 1e-20. A value of 0.0 causes no
                        censoring to occur.

------------------------------------------------------------
Version 2.11 Date: Mon February 7, 2005
------------------------------------------------------------

        Fixed error in selected output file with mixing reaction. 
        MIX number was written to two columns, should be one.

        Fixed memory leak with PAD function.

        New database minteq.v4.dat has been translated from version
        4.02 of MINTEQA2. An older version of the MINTEQA2 database is
        retained in file minteq.dat.

        Switched version control to subversion. Simplified,
        reorganized makefiles. 

        Fixed bug with PRINT; -warnings n. Use of this option 
        generally eliminated all warning messages instead of
        all messages after the nth. Default number of warning 
        messages printed in now 100 per simulation.

        Fixed memory leaks in cvode that caused phreeqci to crash.
        Now uses PHRQ_malloc in case of other memory leaks. Also
        fixed potential memory error with PAD Basic function.

        Saturation index phases that included water had wrong
        value if distribution of species, exchange, or surface 
        not written also.

        Fixed error message in cvode, if max iterations exceeded
        the error caused a segmentation fault.

        Made printing of parameter combination message a warning
        message so that it could be turned off.

------------------------------------------------------------
Version 2.10 Date: Tue November 2, 2004
------------------------------------------------------------

        Rearranged i/o for PHREEQC and reorganized driver
        subroutine. The object of these changes is to make 
        the program more functional as a module for other 
        programs (PHAST) and eventually to produce a callable 
        C and Fortran module.

        Fixed a problem with surface related to a phase, when
        phase was not part of system (for example, Fe(OH)3a when
        there is no iron in system.

        Added convergence parameter set that requires mineral
        transfers to produce positive concentrations in the 
        event that negative concentrations have been produced in
        the prior Newton-Raphson iteration. (Fluorite example).

        Fixed bug with kinetics formulas; did not account for
        stoichiometric coefficient correctly when using
        phase names. Generalized to allow multiple phase
        names in the -formula definition.

------------------------------------------------------------
Version 2.9 Date: Wed September 15, 2004
------------------------------------------------------------

        In inverse modeling, program terminates if sum of initial
        solutions and phases is > 32.

        Fixed bug with isotopes. Log activity estimate after initial
        solution calculation was inf under some conditions. An initial
        surface calculation failed when using D.

        Changed saturation index print out to use reaction and log K
        defined in PHASES definition. Previously, reaction could be 
        rewritten to predominant redox species.

        Fixed incorrect print of elapsed time for kinetics in advection.

        Added phrqproto.h prototype file and phrqtype.h for
        switching compilation to long double.

        Fixed incorrect printout of kinetics delta moles with
        advection.

        Added convergence parameter set that skips mineral
        equations for first 5 iterations. 

        Added entity_exists for module.

        Tried to fix bug with mix index incorrect (-2) for
        mixing with kinetics.

        Added new keyword COPY that allows a data entity 
                to be copied from one index to a new index 
                or to a range of indicies. Format is 

                COPY keyword index index_start[-index_end]
        
                where keyword is one of the following:
                                SOLUTION
                                EQUILIBRIUM_PHASES
                                EXCHANGE
                                GAS_PHASE
                                KINETICS
                                MIX
                                REACTION
                                REACTION_TEMPERATURE
                                SOLID_SOLUTION
                                SURFACE

        Numerical method had a bug with ionic strength, if
                mass of water was not approximately 1. Routine
                revise_guesses did not divide by the mass of 
                water. Also changed check in routine molalities
                to check by molality, not moles.

        Fixed a null pointer when surface was related to a
                mineral and mineral was not in database.

        Added new Basic functions
        i = INSTR(a$, b$)  sets i to the character position of
                string b$ in a$, 0 in not found.
        b$ = LTRIM(a$)     trims white space from beginning of 
                string a$ and stores result in b$.
        b$ = RTRIM(a$)     trims white space from end of string 
                a$ and stores result in b$.
        b$ = LTRIM(a$)     trims white space from beginning and
                end of string a$ and stores result in b$.

        Added new Basic function SYS that calculates the to
        total amount of an element in all phases (solution,
        equilibrium_phases, surfaces, exchangers, solid solutions, 
        and gas phase). KINETIC reactions are not included.
        The function has two forms: (1) one element name as an
        argument (variable names are user specified)

        10 t = SYS("As")

        the function will return the total arsenic in the system.
        (2) 5 argumens

        10 t = SYS("As", count_species, names$, types$, moles)

        will return the total arsenic in the system to tot; count_species--
        the number of species that contain arsenic, including
        solution, equilibrium_phases, surfaces, exchangers, solid solutions, 
        and gas phase species; names$--a character array that has the
        name of each species; type$--a character array that specifies the
        type of phase for the species, aq, equi, surf, ex, s_s, gas, diff. 
        Diff refers to the amount of the element in the diffuse layer of 
        a surface when the explicit diffuse layer calculation is used; 
        moles--an array containing the number of moles of the element in 
        the species. The sum of moles(i) is equal to tot.

        SYS has several special arguments for the form 
        SYS("arg", count, names$, types$, values)
                arg     is one of the options listed below.
                count   is a single numeric value and is the number of elements
                                in the following arrays.
                name$   is an array of string values.
                type$   is an array of string values.
                values  is an array of numeric values.

        Values of arg:

        elt_name        returns total number of moles of element in system.
                        count is the number of species for the element in
                                the system, including aqueous, exchange, surface,
                                equilibrium_phase, solid solution component, and
                                gas phase "species".
                        Arrays are filled for each "species"; values are moles.
        "elements"      returns total number of moles of all elements, 
                                valence states, exchangers, and surfaces.
                        count is number of elements, valence states, 
                                exchangers, and surfaces.
                        Arrays are filled for each element, valence state,
                                exchanger, and surface; values are moles.
        "phases"        returns maximum saturation index of all phases.
                        count is number of phases in system.
                        Arrays are filled for each phase; values are
                                saturation indexes.
        "aq"            returns sum of moles of all aqueous species.
                        count is number of aqueous species in system.
                        Arrays are filled with each aqueous species;
                                values are moles.
        "ex"            returns sum of moles of all exchange species.
                        count is number of exchange species in system.
                        Arrays are filled with each exchange species;
                                values are moles.
        "surf"          returns sum of moles of all surface species.
                        count is number of surface species in system.
                        Arrays are filled with each surface species;
                                values are moles.
        "surf"          returns sum of moles of all solid solution components.
                        count is number of solid solution components in system.
                        Arrays are filled with each solid solution component;
                                values are moles.
        "gas"           returns sum of moles of all gas components.
                        count is number of gas components in system.
                        Arrays are filled with each gas component;
                                values are moles.

        Added new Basic function, DESCRIPTION, that has the value
        defined for the description field of the SOLUTION keyword line. 

        Added alternative ordinary differential equation solver
        called CVODE, a set of C routines from the Lawrence 
        Livermore National Labs. CVODE is part of the SUNDIALS
        package. CVODE is used in place of the Runge Kutta method
        when "-cvode true" is used within a KINETICS data block.

        KINETICS
                -cvode true

        Fixed error in SOLUTION_SPREAD, defining -redox
        did not set the default redox for the solutions
        that were defined; pe was always used as default.

        Modified code to allocate space differently for
        pp_assemblage, exchange, surface, gas_phase, 
        kinetics, and s_s_assemblage. Enough space is allocated
        at beginning of distribute_initial_conditions.
        May speed up phast initialization and make better
        use of available memory.

        Changed gfw of water to 18 if isotopes of water are 
        included. Solvent is [1H]2[16O].

        Fixed a bug in surface integration where order of ions
        in the list of g's was incorrect.

        Pyrite rate was not 0 if supersaturated in phreeqc.dat
        and wateq4f.dat

        Segmentation error if a surface species was not 
        defined with an equation that contained another surface
        species. In this case, the surface master species
        had been redefined to be an aqueous species (SOLUTION_SPECIES).

------------------------------------------------------------
Version 2.8 Date: Tue April 15, 2003
------------------------------------------------------------

        Updated arsenic data in wateq4f.dat to be consistent with
        Archer and Nordstrom (2002).

        Revised Basic interpreter to allow lines of any length
        and character strings of any length.

        Renumbering basic statement that included the function
        SURF in PhreeqcI caused SURF to be omitted and generated
        a syntax error. SURF and other functions had not been
        implemented in PhreeqcI.

        Fixed a bug in the Basic Interpreter. If elements of
        a dimensioned variable (character or number) were used on 
        both sides of an equation, the result was erroneously 
        stored in the last element of the variable used on the 
        right-hand side instead of the element specified on the 
        left-hand side.

        Using comma in some fields caused an infinite loop.

        Fixed bug with SOLUTION_SPREAD, Phreeqc was not
        calculating solution numbers for solution_spread 
        solutions without solution numbers.

        Fixed bug with stagnant zone calculations. If solutions
        not defined for stagnant cells, PhreeqcI crashed.

        Added new state for calculations, PHAST. Previously
        phast used the state TRANSPORT, which caused some
        erroneous results with temperature when TRANSPORT was
        used in the PHREEQC part of the calculation.

        Trying to define dump file in TRANSPORT caused a file 
        opening error. Fixed logic so now can open a file
        and the name can include blanks.

------------------------------------------------------------
Version 2.7 Date: Fri February 14, 2003
------------------------------------------------------------

        Initialized gfw in elements structure.

        Fixed bug where "time" would be wrong for initial
                solution calculation. Needed to initialize
                rate variables for PhreeqcI.

        Added print of simulation number to error file for
                phreeqci

        Limited printing of cell numbers to output file in advection
                calculations. Cell numbers only printed if results
                for cell are going to be printed.

        PhreeqcI captured status messages for kinetics, which
                made a very large error file in some cases and
                a long wait to view the output file in PhreeqcI.
                Now PhreeqcI does not capture these intermediate
                status messages.

        Removed old code related to redirecting error file

        Corrected error in transport where wrong time step was used
        for integration.

        Changes to speed up transport algorithm.

        Allow file names with spaces in selected_output file name and
                dump_file name.

        Modifications to work with RC1 phast log file.

        Allow any characters in square brackets for element name.
                - and + and perhaps others caused problems before.

        Fixed log molality of water in species printout, was
                equal to log activity of water. Also fixed
                basic function for LM.

        Changed solid solution prints to print 0 if solid solution
                is not present.

        Fixed bug if no rate name was defined before options
                in RATES.

        Fixed warning on Mac compilation in fpunchf.

        Fixed bug if isotopes were used but H and O isotopes 
                were not defined.

        Fixed bug where special initial solution calculations
                were done at later calculation stages.
                Needed to set initial_solution_isotopes = FALSE;

        Fixed problem in C++ if structure name is same as member name.
                logk member of logk structure was renamed to log_k.

        Added identifier -add_constant to PHASES, EXCHANGE_SPECIES,
                SOLUTION_SPECIES, and SURFACE_SPECIES. 

                -add_constant  -0.301  

                log K is augmented by the specified constant. 

        Added punch_isotopes and punch_calculate_values to allow
                printing isotope ratios and any CALCULATE_VALUES result.

        Added KEYWORDS:

        ISOTOPES
        Element
        -isotope  isotope_name units standard_ratio
        -total_is_major  T/F (OPTION IS DISABLED!!)

        CALCULATE_VALUES
        Name
        -start
        Basic statements, must have SAVE
        -end

        ISOTOPE_RATIOS (for printing)
        Name=Calculate_values_name      Isotope_name

        ISOTOPE_ALPHAS (for printing)
        Name=Calculate_values_name      Named_logk=named_expression_name

        Basic functions:
        calc_value("calc_value_name")           evaluates a definition of CALCULATE_VALUES
        lk_named("name")                        log10(K) of definition in NAMED_EXPRESSIONS
        lk_phase("name")                        log10(K) of definition in PHASES
        lk_species("name")                      log10(K) of definition in (SOLUTION, EXCHANGE, SURFACE)_SPECIES
        sum_gas("template","element")           Sum of element in gases with specified template
                                                template="{C,[13C],[14C]}{O,[18O]}2" includes all CO2 gases
        sum_species("template","element")       Sum of element in aqueous, exchange, and surface species with
                                                specified template
        sum_s_s("s_s_name","element")           Sum of element in a specified solid solution

        PRINT keyword:
        -initial_isotopes T/F
        -isotope_ratios   T/F
        -isotope_alphas   T/F
        -censor_species   1e-8    # Omits print of species if less than relative criterion

        SELECTED_OUTPUT keyword:
        -calculate_values  name1 name2 ...
        -isotopes minor_isotope1 minor_isotope2 ....

        Added functions LK_SPECIES, LK_NAMED, LK_PHASE for Basic
                interpreter. LK_SPECIES("CaHCO3+") returns the
                log k for the association reaction for the ion pair
                CaHCO3+ at the current temperature. The log K is 
                for the reaction as defined in the database or 
                input file. Similarly, 
                LK_NAMED("Log_alpha_18O_CO2(aq)/CO2(g)") returns the 
                value for the log K at the current temperature using
                expressions defined in NAMED_LOG_K data block; 
                LK_PHASE("Calcite") returns the value of log K 
                for calcite at the current temperature for the 
                dissociation reaction defined in the database or 
                input file. Values are "log10" values.
                Example for Basic program:

                10 PRINT "Log10 KCalcite: ", LK_PHASE("Calcite")
                20 PRINT "Log10 KCaHCO3+: ", LK_SPECIES("CaHCO3+")
                30 PRINT " 1000ln(alpha): ", LK_NAMED("Log_alpha_18O_CO2(aq)/CO2(g)")*LOG(10)*1000

        Added NAMED_EXPRESSIONS data block. This data block was
                implemented to facilitate isotopic calculations.
                It allows analytical expressions that are functions
                of temperature to be defined. The purpose is to 
                separate the fractionation factors from the log K, 
                so that the fractionation factor or its temperature 
                dependence can be easily modified. The named 
                expression can be added to a log K for a species
                or phase by the -add_logk identifier in SOLUTION_SPECIES
                EXCHANGE_SPECIES, SURFACE_SPECIES, or PHASES data
                block.

------------------------------------------------------------
Version 2.6 Date: Mon April 22, 2002
------------------------------------------------------------

        PhreeqcI  released.

        All selected_output is routed through a single routine.

        Allow "_" inside square brackets, [A_bcd].

        Fixed bug match_elts_in_species, check for "e-" was wrong.

        Modified minteq.dat to put CuS4S5-3, Cu(S4)2-3 in
                in Cu(1) mole balance equations instead of
                Cu(2). Before the change, the program would 
                not converge if Cu(2) were defined in an 
                initial solution.
                
        Made revisions hopefully to improve SOLID_SOLUTIONS
                convergence with small numbers of moles of
                solids.

        Made changes related to dump file and PhreeqcI.

        Iterations now sums iterations in all kinetics calculations

        Fixed bug with LA("H2O"), which was returning natural log
                of activity of water.
        

------------------------------------------------------------
Version 2.5  Date: Mon October 1, 2001
------------------------------------------------------------

        In llnl.dat, fixed sign errors in RRE (rare earth elements) 
                for some redox reactions and removed some redundant 
                species, generally ReeO2- was retained and Ree(OH)4- 
                was removed.

        Added the capability to use square brackets to define an
                "element" name. The brackets act like quotation marks
                in that any character string can be used within the 
                brackets as an element name. This was introduced to
                simplify expansion of the model to isotopic species.
                [13C], [14C], and [18O] are legal element names.

        Added identifier -activity_water for a species in 
                SOLUTION_SPECIES data block. This identifier has been 
                added for future updates that will allow isotopic 
                calculations. It is intended to be used only for 
                isotopic variations of H2O, like D2O or H2[O18]. It
                forces the activity coefficient for the species to be
                activity(water)/55.5. This effectively sets the activity 
                of the species to the mole fraction in solution.

        Fixed bug in checking solid solutions for presence or
                absence of elements in the system. Programming
                error caused segmentation fault if an error
                was detected under certain conditions.

        Changed return value of MOL to be molality of water
                if argument is "H2O". Also changed return value
                of LA to be activity of water if argument is 
                "H2O".

        Diffuse layer calculation was incorrect if aqueous phase did not
                have 1 kilogram of water. Eq. 74 of manual has molality,
                but code used moles. The code was corrected by adding
                the mass of water to the formulation.

        Stagnant zones with first-order exchange approximation (1 stagnant 
                cell, exchange factor, and porosities defined) did not work 
                correctly if mobile and immobile cells did not have equal 
                volumes of water. The mixing factors were revised to account
                for the masses of water in the stagnant and mobile zones.

        A fatal error was erroneously detected if the database file
                had a DATABASE data block. DATABASE data block is
                now ignored while reading the database file.

        Added identifier -bad_step_max to KINETICS data block.
                An integer following -bad_step_max gives the maximum number 
                of times a rate integration may fail before execution of the
                program is terminated. Default is 500.

------------------------------------------------------------
Version 2.4.2: Date: Fri June 15, 2001
------------------------------------------------------------

        Fixed spreadsheet bug. Program was not ignoring columns
                that could not be identified as either element 
                names or allowed data (ph, pe, number, description, 
                etc). Also, the program failed if a spreadsheet solution
                number was negative.

------------------------------------------------------------
Version 2.4.1: Date: Mon June 4, 2001
------------------------------------------------------------

        Fixed spreadsheet bugs with isotopes.

------------------------------------------------------------
Version 2.4: Date: Fri June 1, 2001
------------------------------------------------------------

        Added structure for spreadsheet for use by PhreeqcI.

        Isotope value initialized incorrectly if only an -uncertainty was 
                defined in SOLUTION_SPREAD.

        Fixed segmentation violation when primary and secondary master
                species were defined improperly.

        Corrected enthalpies of reaction in llnl.dat. Previous release had
                erroneously had enthalpies of formation in -delta_H
                parameter; the values should be enthalpies of reaction.
                Enthalpies of reaction were calculated from the
                enthalpies of formation and these values are now included
                in the -delta_H parameter. This change will have very
                little impact on calculations because the analytical
                expression has precedence over -delta_H in calculating
                temperature dependence of log K, and nearly all species
                and minerals have an analytical expression or lack both
                an analytical expression and an enthalpy of reaction.

        Corrected bugs in punch of solid solution components that caused
                both selected output and output file errors:  moles
                were incorrect in selected output, and total moles and
                mole fraction were incorrect in output file.

        Added surface complexation constants for Fe+2; two complexes for 
                weak sites and one complex for strong sites.  phreeqc.dat
                and wateq4f.dat modified.

        Comment for units of parameters for calcite rate equation was
                wrong. Rate equation now uses cm^2/L for area parameter. 
                Previously the correct units would have been 1/decimeter. 
                phreeqc.dat and wateq4f.dat modified.

        Fixed a bug when rates were equal within tolerance, but negative
                concentrations occurred because of small initial
                concentrations.

        Added -warnings to PRINT keyword for specification of maximum
                number of warnings to print. Negative number allows
                all warnings to be printed.

        Function CELL_NO in Basic now prints a number equivalent to
                -solution in SELECTED_OUTPUT data block. This does not
                change printing for ADVECTION or TRANSPORT calculations.

        Kinetics time is halved for advective part of reaction in 
                transport; time incorrectly accounted for before.

        -punch_ identifiers printed -1 instead of the correct solution 
                number for batch-reaction calculations.

        -high_precision is no longer reset to false with every 
                SELECTED_OUTPUT data block.

        SELECTED_OUTPUT file name stored for use by PhreeqcI.

        Alkalinity for NH3 corrected to 1.0 in llnl.dat.

        Fixed bug with USER_PRINT of kinetics. Did not find correct
                kinetics information in some cases. 

        Fixed bug in default values for SOLUTION_SPREAD. Cannot use phase 
                name and SI for pH or pe, and bug did not allow PHREEQC
                to run. Now PHREEQC runs, but warns that this is not
                allowed.

------------------------------------------------------------
Version 2.3: Date: Tue January 2, 2001
------------------------------------------------------------

        Added new keyword DATABASE. It must be the first keyword in
                the input file. The character string following the
                keyword is the pathname for the database file to
                be used in the calculation. The file that is 
                specified takes precedence over any default
                database name, including environmental variable
                PHREEQC_DATABASE and command line arguments.

        Fixed bug in SOLUTION_SPREAD. If first heading in
                the spread-sheet input was an identifier--pH,
                pe, units, etc--then the headings were interpreted
                as an identifier and bad things happened.

        Added new keyword to make aqueous model similar to
                LLNL and Geochemists Workbench when using
                llnl.dat as the database file. Values
                of Debye-Huckel a and b and bdot (ionic strength
                coefficient) are read at fixed temperatures.
                Linear interpolation occurs between temperatures.

        New options for SOLUTION_SPECIES are
                -llnl_gamma  a   , where a is the ion-size parameter.
                -co2_llnl_gamma  , indicates the temperature dependent
                                function for the bdot term given in 
                                -co2_coefs of LLNL_AQUEOUS_MODEL_PARAMETERS
                                will be used. Applies to uncharged
                                species only.

LLNL_AQUEOUS_MODEL_PARAMETERS
-temperatures
         0.0100   25.0000   60.0000  100.0000
       150.0000  200.0000  250.0000  300.0000
#debye huckel a (adh)
-dh_a
         0.4939    0.5114    0.5465    0.5995
         0.6855    0.7994    0.9593    1.2180
#debye huckel b (bdh)
-dh_b
         0.3253    0.3288    0.3346    0.3421
         0.3525    0.3639    0.3766    0.3925
-bdot
         0.0394    0.0410    0.0438    0.0460
         0.0470    0.0470    0.0340    0.0000
#cco2   (coefficients for the Drummond (1981) polynomial)
-co2_coefs
        -1.0312              0.0012806
          255.9                 0.4445
      -0.001606
        

        Fixed bug in basic interpreter. A number like "..524" would
                cause an infinite loop.

        Added function SURF to Basic.
                SURF("element", "surface") gives the amount of 
                        element sorbed on "surface". "surface" 
                        should be the surface name, not the 
                        surface-site name (that is, no underscore).

        Fixed option to "runge_kutta" from "runge-kutta" to match
                documentation for KINETICS.

        Fixed UO2+2 and Mn+2 reaction stoichiometry for Hfo surface complexation
                in wateq4f.dat.

        Added option for an equilibrium-phase to dissolve only. 
                "dis" is added at the end of a line defining an equilibrium-
                        phase. No data fields may be omitted. Should not
                        be used when adding an alternative reaction.
                Example:
                EQUILIBRIUM_PHASES
                        Dolomite 0.0  0.001 dis
        R-K integration failed when only the final rate generated
                negative concentrations.
        Allow decimals in definition of secondary master species, for
                example S(0.3).
        Fixed bug if description was more than about 85 characters;
                now allows about 400 characters.
        Fixed bug for surface/exchange sites related to phases. Was
                checking internal copies of surfaces/exchange with negative
                numbers.
        Fixed bug in quick prep that did not set the correct pointer
                for gas phases.
        Fixed segmentation fault that occurred if all elements for
                phase-boundary mineral were not in the solution.
                Only applied to a phase used to define concentration
                in an initial solution calculation.
        Added option to eliminate echo of input file in PRINT
                data block. -echo_input T/F turns echoing on
                and off. Default is on.
        

------------------------------------------------------------
Release 2.2: Date: Wed March 1, 2000
------------------------------------------------------------

        Fixed bug in MIX if no solutions are defined.
        Changed printout for surface.
                Only gives net surface charge for diffuse layer 
                        calculation.
                Prints correct value for the surface charge and
                        surface charge density for diffuse-layer 
                        calculation.    

        Added function EDL to Basic.
                EDL("element", "surface") gives the amount of 
                        element in the diffuse layer for "surface".
                        not including sorbed species. "surface" should 
                        be the surface name, not the surface-site name 
                        (that is, no underscore).

                Special values for "element" include:
                        "charge" - gives surface charge, equivalents.
                        "sigma"  - surface charge density, C/m**2.
                        "psi"    - potential at the surface, Volts.
                        "water"  - mass of water in the diffuse layer, kg.
        Changed distribution to be more consistent with other USGS 
                water-resources applications.

------------------------------------------------------------
Release 2.1: Date: Wed January 19, 2000
------------------------------------------------------------

        Added additional #ifdef's for PhreeqcI.
        Fixed problem with formats for USER_PUNCH and
                others with Microsoft C++ 3 digit 
                exponents.

Initial Release 2.0: Date: Wed December 15, 1999

Version: C_54 = Version 2.0