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This example calculates the distribution of aqueous species in seawater and the saturation state of seawater relative to a set of minerals. To demonstrate how to expand the model to new elements, uranium is added to the aqueous model defined by phreeqc.dat . [Several of the database files distributed with the program ( wateq4f.dat, llnl.dat, minteq.dat, minteq.v4.dat, and sit.dat) include the element uranium, and use of any one of these databases would make the uranium definitions in this example unnecessary.]
The essential data needed for a speciation calculation are the temperature, pH, and concentrations of elements and (or) element valence states. These data for seawater are given in table 9. The input file for this example calculation is shown in table 10. A comment about the calculations performed in this simulation is included with the TITLE keyword. The SOLUTION data block defines the composition of seawater. Note that valence states are identified by the chemical symbol for the element followed by the valence in parentheses [S(6), N(5), N(-3), and O(0)].
The pe to be used for distributing redox elements and for calculating saturation indices is specified by the redox identifier. In this example, a pe is to be calculated from the O(-2)/O(0) redox couple, which corresponds to the dissolved oxygen/water couple, and this calculated pe will be used for all calculations that require a pe. If redox were not specified, the default would be the input pe. The default redox identifier can be overridden for any redox element, as demonstrated by the manganese input, where the input pe will be used to speciate manganese among its valence states, and the uranium input, where a pe calculated from the nitrate/ammonium couple will be used to speciate uranium among its valence states.
The default units are specified to be ppm in this file ( units identifier). This default can be overridden for any concentration, as demonstrated by the uranium concentration, which is specified to be ppb instead of ppm. Because ppm is a mass unit, not a mole unit, the program must use a gram formula weight to convert each concentration into molal units. The default gram formula weights for each master species are specified in the SOLUTION_MASTER_SPECIES input (the formulas used to calculate gram formula weights for phreeqc.dat are listed in table 3). If the data are reported relative to a gram formula weight different from the default, it is necessary to specify the appropriate gram formula weight in the input file. This can be done with the gfw identifier, where the actual gram formula weight is input--the gram-formula weight by which to convert nitrate is specified to be 62.0 g/mol, or more simply with the as identifier, where the chemical formula for the reported units is input, as shown in the input for alkalinity and ammonium in this example. Note finally that the concentration of O(0), dissolved oxygen, is given an initial estimate of 1 ppm, but that its concentration will be adjusted until a log partial pressure of oxygen gas of -0.7 is achieved. [O2(g) is defined under PHASES input in each database.] When using phase equilibria to specify initial concentrations [like O(0) in this example], only one concentration is adjusted. For example, if gypsum were used to adjust the calcium concentration, the concentration of calcium would vary, but the concentration of sulfate would remain fixed.
Uranium is not included in phreeqc.dat , one of the database files that is distributed with the program. Thus, data to describe the thermodynamics and composition of aqueous uranium species must be included in the input data when using this database. Two keyword data blocks are needed to define the uranium species, SOLUTION_MASTER_SPECIES and SOLUTION_SPECIES. By adding these two data blocks to the input data file, aqueous uranium species will be defined for the duration of the run. To add uranium permanently to the list of elements, these data blocks should be added to the database file. The data for uranium shown here are intended to be illustrative and are not a complete description of uranium speciation.
It is necessary to define a primary master species for uranium with SOLUTION_MASTER_SPECIES input. Because uranium is a redox-active element, it is also necessary to define a secondary master species for each valence state of uranium. The data block SOLUTION_MASTER_SPECIES (table 10) defines U +4 as the primary master species for uranium and also as the secondary master species for the +4 valence state. UO 2 + is the secondary master species for the +5 valence state, and UO 2 +2 is the secondary master species for the +6 valence state. Equations defining these aqueous species plus any other complexes of uranium must be defined through SOLUTION_SPECIES input.
In the data block SOLUTION_SPECIES (table 10), the primary and secondary master species are noted with comments. A primary master species is always defined in the form of an identity reaction (U+4 = U+4). Secondary master species are the only aqueous species that contain electrons in their chemical reaction. Additional hydroxide and carbonate complexes are defined for the +4 and +6 valence states, but none for the +5 state.
Finally, a new phase, uraninite, is defined with PHASES input. This phase will be used in calculating saturation indices in speciation modeling, but could also be used, without redefinition, for batch-reaction, transport, or inverse calculations within the computer run.
The output from the model (table 11) contains several blocks of information delineated by headings. First, the names of the input, output, and database files for the run are listed. Next, all keywords encountered in reading the database file are listed under the heading “Reading data base”. Then, the input data, excluding comments and empty lines, are echoed under the heading “Reading input data for simulation 1”. The simulation is defined by all input data up to and including the END keyword.
Any comment entered within the simulation with the TITLE keyword is printed next. The title is followed by the heading “Beginning of initial solution calculations”, below which are the results of the speciation calculation for seawater. The concentration data, converted to molality, are given under the subheading “Solution composition”. For initial solution calculations, the number of moles in solution is numerically equal to molality because 1 kg of water is assumed. The -water identifier can be used to define a different mass of water for a solution. During batch-reaction calculations, the mass of water may change and the moles in the aqueous phase will not exactly equal the molality of a constituent. Note that the molality of dissolved oxygen that produces a log partial pressure of -0.7 has been calculated and is annotated in the output.
After the subheading “Description of solution”, some of the properties listed in the first block of output are equal to their input values and some are calculated. In this example, pH, pe, and temperature are equal to the input values. The specific conductance, density, activity of water, ionic strength, total carbon (alkalinity was the input datum), total inorganic carbon (“Total CO2”), electrical balance, percent error, total hydrogen, and total oxygen have all been calculated by the model.
Under the subheading “Redox couples” the pe and Eh are printed for each redox couple for which data were available; in this case, ammonium/nitrate and water/dissolved oxygen.
Under the subheading “Distribution of species”, the molalities, activities, activity coefficients, and specific volumes of all species of each element and element valence state are listed. The lists are alphabetical by element name and are descending in terms of molality within each element or element valence state. Beside the name of each element or element valence state, the total molality is given. If -Vm parameters are defined in SOLUTION_SPECIES, specific volumes are calculated relative to the volume of H + (which is zero by convention at all pressures, temperatures and ionic strengths); otherwise, specific volumes are listed as (0).
Finally, under the subheading “Saturation indices”, saturation indices for all minerals that are appropriate for the given analytical data are listed alphabetically by phase name near the end of the output. The saturation index is given in the column headed “SI”, followed by the columns for the log of the ion activity product (“log IAP”) and the log of the solubility constant (“log KT”). The chemical formulas for each of the phases is printed in the right-hand column. Note, for example, that no aluminum-bearing minerals are included because aluminum was not included in the analytical data. Also note that mackinawite (FeS) and other sulfide minerals are not included in the output because no analytical data were specified for S(-2). If a concentration for S [instead of S(6)] or S(-2) had been entered, then a concentration of S(-2) would have been calculated and a saturation index for mackinawite and other sulfide minerals would have been calculated.
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