PRIMARY_SPECIES
The first primary species must always be H2O, and the second one must be H+. Other primary species may be entered in any order.
Example:
The PRIMARY_SPECIES keyword block is used to specify the primary component species for a particular problem. Borrowing from the tradition of EQ3/EQ6, there is a list of "database primary species" given in the first section of any database file. The list of "database primary species" serves as the building blocks of reactions in the main part of the database. From the point of view of CrunchODiTi, however, primary species are any that are so designated in the input file. The user may list any mathematically valid set of primary species which spans the concentration space for a particular problem. If aqueous kinetic reactions are included in the problem, then these must be made up entirely of the user's choice of primary species (not necessarily those found in the database). It should be noted, however, that some choices of primary species will result in non-intuitive components, making it difficult to specify initial and boundary conditions for a particular problem. The primary component species (or basis species) are the chemical building blocks for a particular problem. The concentrations of the primary species are the major unknowns in the chemistry part of a reactive transport problem. The partial differential equations for the conservation of chemical mass in the system are written in terms of the total concentration of these primary component species. This formulation, which has been widely discussed by a number of workers, is used instead of equations for the conservation of the various chemical elements.
The format of the PRIMARY_SPECIES keyword block is simple, consisting of a list of species name to be used. In contrast to other keyword parameters in the input file, the species names are case-sensitive. This is to remove the ambiguity which may arise from various species and compounds have similar names (for example, carbon monoxide or CO and cobalt or Co). The list of species in the PRIMARY_SPECIES keyword block is important in that it defines the chemical space for a particular problem (thus the term "component species"). When geochemical conditions are given, all of the primary species listed in the PRIMARY_SPECIES keyword block must be specified in each of the conditions. In this respect, CrunchODiTi differs from a code like PHREEQC (Parkhurst, 1995) where solutions may be mixed which have different sets of non-zero chemical concentrations specified (PHREEQC presumably sets unmentioned concentrations to 0). Since CrunchODiTi grew out of a standard finite-difference approach to solving partial differential equations rather than out of reaction path approaches, it requires a consistent set of primary species for each cell within the domain and for the system boundaries.