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Input file for PHREEQC is marked as <name>.phrq and in it every line gives a specific command or parameter, typically a keyword followed by a value. If a keyword is not given for a parameter needed for the calculation, a default value is assumed (e.g. default temperature is 25 centigrade, default pH is 7, default pe is +4).
Example 1, input file for dissolution of calcite in pure water at 25 °C until water is saturated:
calcite 0 0.2
First line starts the case, after this would come the specifications for solution used (in this case pure water all parameters use default values). Second line is a command specifying that a solid phase is dissolved in the solution. Third line names the solid phase followed by saturation index in the end (in this case SI=0, solution is saturated), and amount of solid phase in moles available (0.2 mol, in excess for one litre of solution). Fourth line ends the case and input file is ready to be calculated by pressing "calculate" button.
Example 2, input file for dissolution of calcite in 1M sodium chloride solution at 25 °C until water is saturated:
calcite 0 0.2
#-marker can be used for note writing: any text on the line after it is not taken as command.
Output-file contains first the parameters and elemental composition used in the calculations, then all the possible species for those elements found from the database and their calculated concentrations and in the end all the possible solid and gaseous phases that can be formed from the elements and their saturation indices (so all calculations with water have the possibility of formation of ice, H2O(g), O2(g), H2(g)...)