+ +
Description of Data Input
+
+The input for PHREEQC is
+arranged by keyword data blocks. Each data block begins with a line that
+contains the keyword (and possibly additional data) followed by additional
+lines containing data related to the keyword. The keywords that define the
+input data for running the program are listed in table 1. Keywords and their associated
+data are read from a database file at the beginning of a run to define the
+elements, exchange reactions, surface complexation reactions, mineral phases,
+gas components, and rate expressions. Any data items read from the database
+file can be redefined by keyword data blocks in the input file. After the
+database file is read, data are read from the input file until the first END keyword is encountered, after
+which the specified calculations are performed. The process of reading data
+from the input file until an END,
+followed by doing the calculations, is repeated until the end of the input file
+is encountered. The set of calculations, defined by keyword data blocks
+terminated by an END, is termed a
+“simulation”. A “run” is a series of one or more simulations that are contained
+in the same input data file and calculated during the same invocation of the
+program PHREEQC.
Each simulation may contain
+one or more of seven types of speciation, batch-reaction, and transport calculations:
+(1) initial solution speciation, (2) determination of the composition of an
+exchange assemblage in equilibrium with a fixed solution composition, (3)
+determination of the composition of a surface assemblage in equilibrium with a
+fixed solution composition, (4) determination of the composition of a
+fixed-volume gas phase in equilibrium with a fixed solution composition, (5)
+calculation of chemical composition as a result of batch reactions, which
+include mixing; kinetically controlled reactions; net addition or removal of
+elements from solution, termed “net stoichiometric reaction”; variation in
+temperature and pressure; equilibration with assemblages of pure phases,
+exchangers, surfaces, and (or) solid solutions; and equilibration with a gas phase
+at a fixed total pressure or fixed volume, (6) advective-reactive transport, or
+(7) advective-dispersive-reactive transport. The combination of capabilities
+allows the modeling of complex geochemical reactions and transport processes
+during one or more simulations.
In addition to speciation,
+batch-reaction, and transport calculations, the code may be used for inverse
+modeling, by which net chemical reactions are deduced that account for
+composition differences between an initial water or a mixture of initial waters
+and a final water.
Conventions for Data
+Input
+
+PHREEQC was designed to
+eliminate some of the input errors due to complicated data formatting in Fortran-type
+input files. Data for the program are free format; spaces or tabs may be used
+to delimit input fields (except SOLUTION_SPREAD,
+which is delimited only with tabs); blank lines are ignored. Keyword data
+blocks within a simulation may be entered in any order. However, data elements
+entered on a single line are order specific. As much as possible, the program
+is case insensitive. However, chemical formulas are case sensitive.
The following conventions are
+used for data input to PHREEQC:
Keywords --Input data blocks are identified with an initial keyword. This
+word must be spelled exactly, although case is not important. Several of the
+keywords have synonyms. For example, PURE_PHASES is a synonym
+for EQUILIBRIUM_PHASES.
Identifiers --Identifiers are options that may be used within a keyword data
+block. Identifiers may have two forms: (1) they may be spelled completely and
+exactly (case insensitive) or (2) they may be preceded by a hyphen and then
+only enough characters to uniquely define the identifier are needed. The form
+with the hyphen is always acceptable and is recommended. Usually, the form
+without the hyphen is acceptable, but in some cases the hyphen is needed to
+indicate the word is an identifier rather than an identically spelled keyword;
+these cases are noted in the definitions of the identifiers in the following
+sections. In this report, the form with the hyphen is used except for
+identifiers of the SOLUTION
+keyword and the identifiers log_k and delta_h
+. The hyphen in the identifier never implies that the negative of a quantity is
+entered.
Chemical
+equations --For aqueous, exchange, and
+surface species, chemical reactions must be association reactions,
+with the defined species occurring in the first position after the equal sign.
+For phases, chemical reactions must be dissolution reactions with the
+formula for the defined phase occurring in the first position on the left-hand
+side of the equation. Additional terms on the left-hand side are allowed. All
+chemical equations must contain an equal sign, “=”. In addition, left- and right-hand
+sides of all chemical equations must balance in numbers of atoms of each
+element and total charge. All equations are checked for these criteria at
+runtime, unless they are specifically excepted. Nested parentheses in chemical
+formulas are acceptable. Spaces and tabs within chemical equations are ignored.
+Waters of hydration and other chemical formulas (that are normally represented
+by a “ · ”, as in the formula for gypsum, CaSO 4 ·2H 2 O)
+are designated with a colon (“:”) in PHREEQC (thus, CaSO 4 :2H
+2 O), but only one colon per formula is permitted.
Element
+names --Two forms of element names
+are available (1) those beginning with an alphabetic character and (2) those
+beginning with a square bracket. For form 1, an element formula, wherever it is
+used, must begin with a capital letter and may be followed by one or more
+lowercase letters or underscores, “_”. Numbers are not permitted, except in
+parentheses for defining the redox state. In general, element names are simply
+the chemical symbols for elements, which have a capital letter and zero or one
+lower case letter. It is sometimes useful to define other entities as elements,
+which allows mole balance and mass-action equations to be applied. Thus,
+“Fulvate” is an acceptable element name, and it would be possible to define
+metal binding constants in terms of metal-Fulvate complexes.
Form 2 of element names is
+less restrictive than form 1. Within the square brackets, any combination of
+alphanumeric characters and the characters plus, minus, equal, colon, decimal
+point, and underscore can be used. The form-2 element name is case dependent,
+but upper and lower case characters can be used in any position. The iso.dat
+database makes extensive use of the square-bracket form for element names by
+using the mass number and chemical symbol for minor-isotope definitions, such
+as [13C], [15N], and [34S].
Charge on a
+chemical species --The charge on a species
+may be defined by the proper number of pluses or minuses following the chemical
+formula or by a single plus or minus followed by an integer designating the
+charge. Either of the following is acceptable, Al+3 or Al+++. However, Al3+
+would be interpreted as a molecule with three aluminum atoms and a charge of
+plus one.
Valence
+states --Redox elements that exist
+in more than one valence state in solution are identified for definition of
+solution composition by the element name followed by a valence in parentheses.
+Thus, sulfur that exists as sulfate is defined as S(6) and total sulfide (H
+2 S, HS - , and others) is identified by S(-2). The valence
+may include a decimal point. The valence number is for identification purposes
+only and does not otherwise affect the calculations.
log K and
+temperature dependence --The
+identifier log_k is used to define the log K at 25 °C
+for a reaction. The temperature dependence for log K may be defined by
+the Van’t Hoff expression or by an analytical expression. The identifier delta_h
+is used to give the standard enthalpy of reaction at 25 °C for a chemical
+reaction, which is used in the Van’t Hoff equation. By default the units of the
+standard enthalpy are kilojoule per mole (kJ/mol). Optionally, for each
+reaction the units may be defined to be kilocalorie per mole (kcal/mol). An
+analytical expression for the temperature dependence of log K for a
+reaction may be defined with the -analytical_expression
+identifier. Up to six numbers may be given, which are the coefficients for the
+equation: 
, where T is in kelvin. A log K is defined either with log_k
+or -analytical_expression (default log_k is
+zero); the enthalpy is optional (default is zero). If present, an analytical
+expression is used in preference to the log_k and enthalpy
+values for calculation of the log K at the specified temperature.
Pressure
+dependence of log K --Pressure dependency of
+reaction constants for species, and the pressure-dependent solubilities of
+minerals and gases, are calculated from the volume change of the reaction. The
+molar volume of solids and parameters for calculating the molal volume of aqueous
+species are defined in Amm.dat, phreeqc.dat, and pitzer.dat.
Comments --The “#” character delimits the beginning of a comment in the input
+file. All characters in the line that follow this character are ignored. If the
+entire line is a comment, the line is not echoed to the output file. If the
+comment follows input data on a line, the entire line, including the comment,
+is echoed to the output file. The “#” is useful for adding comments explaining
+the source of various data or describing the problem setup. In addition, it is
+useful for temporarily removing lines from an input file.
Logical
+line separator --A semicolon (“;”) is
+interpreted as a logical end-of-line character. This allows multiple logical
+lines to be entered on the same physical line. For example, solution data could
+be entered as:
pH 7.0; pe 4.0; temp 25.0+ +
on one line. The semicolon should not be used in character fields,
+such as the title or other comment or description fields.
Logical line continuation --A
+backslash (“\”) at the end of a line may be used to merge two physical lines into
+one logical line. For example, a long chemical equation could be entered as:
Ca0.165Al2.33Si3.67O10(OH)2 + 12 H2O = \
0.165Ca+2 + 2.33 Al(OH)4- + 3.67 H4SiO4 + 2 H+
+ +
on two lines. The program would interpret this sequence as a
+balanced equation entered on a single logical line. For a line to be logically
+continued, the backslash must be the last character in the line except for
+white space.
Repeat count --An
+asterisk (“*”) can be used to indicate a repeat count for the data item that
+follows the asterisk. The format is an integer followed directly by the
+asterisk, which is followed directly by a numeric value. For example “4*1.0” is
+the same as entering four values of 1.0 (“1.0 1.0 1.0 1.0”). Repeat counts can
+be used for specifying data for the identifiers -length and -dispersivity
+in the TRANSPORT data block and
+for specifying reaction steps in the REACTION
+and KINETICS data blocks.
Range of integers --A hyphen
+(“-”) can be used to indicate a range of integers for the keywords with an
+identification number (for example, SOLUTION
+2-5). It is also possible to define a range of cell numbers for the identifiers
+-print_cells and -punch_cells in the ADVECTION and TRANSPORT data blocks and in the
+options for the COPY, DELETE, DUMP, and RUN_CELLS data blocks. A range of
+integers is given in the form m-n
+, where m and n are positive integers, m
+is less than n , and the two numbers are separated by a hyphen without
+intervening spaces.
Special characters --A
+summary of all of the special characters used in PHREEQC formatting is given in
+table 2.
Reducing Chemical
+Equations to a Standard Form
+
+The numerical algorithm of PHREEQC requires that chemical
+equations be written in a particular form. Internally, every equation must be
+written in terms of a minimum set of chemical species; essentially, one species
+for each element or valence state of an element. For the program PHREEQE, these
+species were called “master species” and the reactions for all aqueous
+complexes had to be written using only these species. PHREEQC also needs
+reactions in terms of master species; however, the program contains the logic
+to rewrite the input equations into this form. Thus, it is possible to enter an
+association reaction and log K for an aqueous species in terms of any aqueous
+species in the database (not just master species), and PHREEQC will rewrite the
+equation to the proper internal form.
PHREEQC also will rewrite reactions for phases, exchange
+complexes, and surface complexes. Reactions are required to be dissolution
+reactions for phases and association reactions for aqueous, exchange, or
+surface complexes. Dissolution reactions for phases allow inclusion of names of
+solids and gases in the equations, provided they are appended with the strings
+“(s)” and “(g)”; for example,
CaCO2[18O](s) + H2O(l) = H2[18O](aq) +
+Calcite(s).
The string “(l)” can be appended to the water formula and “(aq)”
+to aqueous species for clarity, but they are not required. The “(s)” and “(g)”
+suffixes cause the program to look in the list of phases to find equations that
+can be used to reduce the original equation to an equation that contains
+exclusively aqueous species. This capability to use solids and gases in
+chemical reactions for phases was implemented primarily to simplify the
+definition of equations for isotopic solid and gas components. The log Ks for
+these isotopic species often depend on the log K for the predominant isotopic
+species (solid or gas) offset by a fractionation factor and (or) a
+symmetry-derived log K. The inclusion of gases and solids in the equations for
+isotopic solids and gases is a straightforward method to define these
+dependencies of the isotopic species equilibrium constant on the equilibrium
+constant for the predominant isotopic species. In the example given here, the
+equilibrium constant for the single oxygen-18 form of calcium carbonate solid
+depends on the equilibrium constant of the pure carbon-12, oxygen-16 form of
+calcite, which is specified by “Calcite(s)” in the example equation and refers
+to the equation and log K defined for the calcite phase.
There is one major restriction on the rewriting capabilities for
+aqueous species. PHREEQC calculates mole balances on individual valence states
+or combinations of valence states of an element for initial solution
+calculations. It is necessary for PHREEQC to be able to determine the valence
+state of an element in a species from the chemical equation that defines the
+species. To do this, the program requires that only one aqueous species of an
+element valence state is defined by the electron half-reaction that relates it
+to another valence state. The aqueous species defined by this half-reaction is
+termed a “secondary master species”; there must be a one-to-one correspondence
+between valence states and secondary master species and the coefficient of the
+newly defined species must be one. In addition, there must be one “primary
+master species” for each element, such that reactions for all aqueous species
+for an element can be rewritten in terms of the primary master species. The
+equation for the primary master species is simply an identity reaction. If the
+element is a redox element, the primary master species must also be a secondary
+master species. For example, to be able to calculate mole balances on total
+iron, total ferric iron, or total ferrous iron, a primary master species must
+be defined for Fe (iron) and secondary master species must be defined for
+Fe(+3) (ferric iron) and Fe(+2) (ferrous iron). In the default databases, the
+primary master species for Fe is Fe +2 , the secondary master
+species for Fe(+2) is Fe +2 , and the secondary master species for
+Fe(+3) is Fe +3 . The correspondence between master species and
+elements and element valence states is defined by the SOLUTION_MASTER_SPECIES
+data block, which for iron in phreeqc.dat is as follows:
SOLUTION_MASTER_SPECIES
Fe Fe+2 0.0 Fe 55.847
Fe(+2) Fe+2 0.0 Fe
Fe(+3) Fe+3 -2.0 Fe
+ +
The line with “Fe” (without parentheses) defines the primary
+master species, and the last two lines, which have parentheses following “Fe”,
+define the secondary master species. The chemical equations for the master
+species and all other aqueous species are defined by the SOLUTION_SPECIES
+data block.
Conventions for
+Documentation
+
+The descriptions of keywords and their associated input are now
+described in alphabetical order as listed in table 1. Several formatting
+conventions are used to help the user interpret the input requirements. In this
+report, keywords are always capitalized and bold. Words in bold must be
+included literally when creating input files (although upper and lower case are
+interchangeable and optional spellings may be permitted). “Identifiers” are
+additional keywords that apply only within a given keyword data block; they can
+be considered to be sub-keywords or options. Although identifiers are case
+independent, lowercase bold is used in this report for all identifiers except pH
+, -Donnan , -multi_D , and -interlayer_D
+, for which mixed case is used. “ temperature ” is an
+identifier for SOLUTION input. Each identifier may have two
+forms: (1) the identifier word spelled exactly (“ temperature
+”, in this case), or (2) a hyphen followed by a sufficient number of characters
+to define the identifier uniquely (for example, -t for
+temperature in SOLUTION the data block.). The form with the
+hyphen is recommended. Words in italics are input values that are
+variable and depend on user selection of appropriate values. Items in brackets
+([ ]) are optional input fields. Mutually exclusive input fields are enclosed
+in parentheses and separated by the word “or”. In general, the optional fields
+in a line must be entered in the specified order, but it is sometimes possible
+to omit intervening fields. For clarity, commas sometimes are used to delimit
+input fields in the explanations of data input; however, commas are not allowed
+in the input data file except in Basic programs; in all other cases, only white
+space (spaces and tabs) may be used to delimit fields in input files. Where
+applicable, default values for input fields are stated.
Getting Started
+
+When the program PHREEQC is invoked, two files are used to define
+the thermodynamic model and the types of calculations that will be done, the
+database file and the input file. The database file is read once (to the end of
+the file or until an END keyword is encountered) at the
+beginning of the program. The input file is then read and processed simulation
+by simulation (as defined by END keywords) until the end of
+the file. The formats for the keyword data blocks are the same for either the
+input file or the database file.
The database file is used to define static data for the
+thermodynamic model. Although any keyword data block can occur in the database
+file, normally, the file contains the keyword data blocks: EXCHANGE_MASTER_SPECIES
+, EXCHANGE_SPECIES
+, PHASES , RATES , SOLUTION_MASTER_SPECIES
+, SOLUTION_SPECIES , SURFACE_MASTER_SPECIES ,
+and SURFACE_SPECIES . These keyword data blocks define rate
+expressions, master species, and the stoichiometric and thermodynamic
+properties of all of the aqueous phase species, exchange species, surface
+species, and pure phases.
Nine database files are provided with the program: (1)
+phreeqc.dat, a database file derived from PHREEQE (Parkhurst and others, 1980),
+which is consistent with wateq4f.dat, but has a smaller set of elements and
+aqueous species (table 3); (2)
+Amm.dat is the same as phreeqc.dat, except that ammonia redox state has been
+decoupled from the rest of the nitrogen system; that is, ammonia has been
+defined as a separate component; (3) wateq4f.dat, a database file derived from
+WATEQ4F (Ball and Nordstrom, 1991); (4) llnl.dat, a database file derived from
+databases for EQ3/6 and Geochemist’s Workbench that uses thermodynamic data
+compiled by the Lawrence Livermore National Laboratory; (5) minteq.dat, a
+database derived from the databases for the program MINTEQA2 (Allison and
+others, 1990); (6) minteq.v4.dat, a database derived from MINTEQA2 version 4
+(U.S. Environmental Protection Agency, 1998); (7) pitzer.dat, a database for
+the specific-ion-interaction model of Pitzer (Pitzer, 1973) as implemented in
+PHRQPITZ (Plummer and others, 1988); (8) sit.dat, a database implementing the
+Specific ion Interaction Theory (SIT) as described by Grenthe and others
+(1997); and (9) iso.dat, a partial implementation of the individual component
+approach to isotope calculations as described by Thorstenson and Parkhurst
+(2002, 2004). The elements and element valence states, corresponding notation,
+and default formula used to convert mass concentration to mole concentration
+units in the database phreeqc.dat are listed in table 3. Other databases may use
+different sets of elements, different notation for the element names, or
+different default conversion formulas.
The input data file is used (1) to define the types of
+calculations that are to be done, and (2) if necessary, to modify the data read
+from the database file. If new elements and aqueous species, exchange species,
+surface species, or phases need to be included in addition to those defined in
+the database file, or if the stoichiometry, log K , or activity
+coefficient information from the database file needs to be modified for a given
+run, then the keywords mentioned in the previous paragraph can be included in
+the input file. The data read for these keyword data blocks in the input file
+will augment or supersede the data read from the database file. In many cases,
+the thermodynamic model defined in the database will not be modified, and the
+above keywords will not be used in the input data file.
The place to start is with the simplest input file, which contains
+only a SOLUTION data block containing the dissolved
+concentrations of elements. With this input file, PHREEQC will perform a
+speciation calculation and calculate saturation indices for the solution. More
+complex calculations will calculate new solution compositions as a function of
+reactions. Reactions can be understood as occurring in a beaker, where a
+solution (as defined by a SOLUTION data block) is placed in
+the beaker, and then additional reactants are added. The reactants are defined
+with the keywords EQUILIBRIUM_PHASES , EXCHANGE , GAS_PHASE
+, KINETICS , REACTION , SOLID_SOLUTIONS
+, and SURFACE . One or more of these reactants may be
+added to the beaker, and then system equilibrium is calculated, which results
+in mole transfers into and out of solution, and new pH and element
+concentrations. The pressure and temperature of the reaction may be defined
+with REACTION_PRESSURE and REACTION_TEMPERATURE . So, the design of PHREEQC is
+fairly intuitive. You must choose the composition of a starting solution and
+then decide which types of reactants you need to add to the beaker to model
+your system. Transport reactions are simply defined by a series of beakers,
+each containing a set of reactants, and water flows and mixes from one beaker
+to the next and equilibrates with the reactants in each beaker in sequence.
Units
+
+The concentrations of elements in solution and the mass of water
+in the solution are defined through the SOLUTION or SOLUTION_SPREAD data block.
+Internally, all concentrations are converted to molality and the number of
+moles of each element in solution (including hydrogen and oxygen) is calculated
+from the molalities and the mass of water. Thus, internally, a solution is
+simply a list of elements and the number of moles of each element.
PHREEQC allows each reactant to be defined independently. In
+particular, reactants ( EQUILIBRIUM_PHASES , EXCHANGE ,
+GAS_PHASE , KINETICS , REACTION ,
+SOLID_SOLUTIONS, and SURFACE
+) are defined in terms of moles, without reference to a volume or mass
+of water. Systems are defined by combining a solution with a set of reactants
+that react either reversibly ( EQUILIBRIUM_PHASES , EXCHANGE
+, GAS_PHASE , SOLID_SOLUTIONS,
+and SURFACE ) or irreversibly ( KINETICS or REACTION
+). Essentially, all of the moles of elements in the solution and the
+reversible reactants are combined, the moles of irreversible reactants are
+added (or removed), and a new system equilibrium is calculated. Only after
+system equilibrium is calculated is the mass of water in the system known, and
+only then the molalities of all entities can be calculated.
For transport calculations, each cell is a system that is defined
+by the solution and all the reactants contained in keywords that bear the same
+number as the cell number. The system for the cell initially is defined by the
+moles of elements that are present in the solution and the moles of each
+reactant. The compositions of all these entities evolve as the transport
+calculations proceed.
Keywords
+
+The following sections describe the data input requirements for
+the program. Each type of data is input through a specific keyword data block.
+Most keywords are listed in alphabetical order within this section of the
+report; however, a set of keywords most pertinent to model developers is
+described in See Appendix A. Keyword
+Data Blocks for Programmers. Each keyword data block may have a number of
+identifiers, many of which are optional. Identifiers may be entered in any
+order; the line numbers given in examples for the keyword data blocks are for
+identification purposes only. Default values for identifiers are used if the
+identifier is omitted.
ADVECTION
+
+CALCULATE_VALUES
+
+COPY
+
+DATABASE
+
+DELETE
+
+DUMP
+
+END
+
+EQUILIBRIUM_PHASES
+
+
+EXCHANGE
+
+EXCHANGE_MASTER_SPECIES
+
+
+EXCHANGE_SPECIES
+
+
+GAS_PHASE
+
+INCLUDE$
+
+INCREMENTAL_REACTIONS
+
+
+INVERSE_MODELING
+
+
+ISOTOPES
+
+ISOTOPE_ALPHAS
+
+ISOTOPE_RATIOS
+
+KINETICS
+
+KNOBS
+
+LLNL_AQUEOUS_MODEL_PARAMETERS
+
+
+MEAN_GAMMAS
+
+MIX
+
+MIX_EQUILIBRIUM_PHASES
+
+MIX_EXCHANGE
+
+MIX_GAS_PHASE
+
+MIX_KINETICS
+
+MIX_SOLID_SOLUTION
+
+MIX_SOLUTION
+
+MIX_SURFACE
+
+NAMED_EXPRESSIONS
+
+
+PHASES
+
+PITZER
+
+PRINT
+
+RATE_PARAMETERS_HERMANSKA
+
+RATE_PARAMETERS_PK
+
+RATE_PARAMETERS_SVD
+
+RATES
+
+REACTION
+
+REACTION_PRESSURE
+
+
+REACTION_TEMPERATURE
+
+
+RUN_CELLS
+
+SAVE
+
+SELECTED_OUTPUT
+
+SIT
+
+SOLID_SOLUTIONS
+
+SOLUTION
+
+SOLUTION_MASTER_SPECIES
+
+
+SOLUTION_SPECIES
+
+
+SOLUTION_SPREAD
+
+SURFACE
+
+SURFACE_MASTER_SPECIES
+
+
+SURFACE_SPECIES
+
+TITLE
+
+TRANSPORT
+
+USE
+
+USER_GRAPH
+
+USER_PRINT
+
+USER_PUNCH
+
++ +