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Define the species of interest in a system; modify their physical states and logarithms of activities.
species(species = NULL, state = NULL, delete = FALSE, index.return = FALSE)character, names or formulas of species to add to the species definition; numeric, rownumbers of species to modify or delete
character, physical states; numeric, logarithms of activities or fugacities
logical, delete the species identified by numeric values of species (all species if that argument is missing)?
logical, return the affected rownumbers of thermo()$species instead of its contents?
With no arguments or when adding species, species returns the value of thermo()$species, unless index.return is TRUE, when the function returns the rownumbers of thermo()$species having the new species.
With delete=TRUE, the value is the definition that existed prior the deletion; with delete=TRUE and species not NULL, the number of species remaining after the selected ones have been deleted, or NULL if no species remain.
After defining the basis species of your system you can use species to identify the species of interest.
A species is operationally a combination of a name and state, which are columns of the thermodynamic database in thermo$obigt.
The function operates on one or more character values of species.
For each first match of species (optionally restricted to a state among aq, cr, gas, liq) to the name of a species or a formula or abbreviation in the thermodynamic database, a row is added to thermo()$species.
The data frame in thermo()$species holds the identifying characteristics of the species as well as the stoichiometric reaction coefficients for the formation of each of the species from the basis species, the logarithms of activities or fugacities that are used by affinity.
The default values for logarithms of activities are -3 for aqueous (aq) species and 0 for others.
If state is NULL (the default), species in any state can be matched in the thermodynamic database.
If there are multiple matches for a species, the one that is in the state given by thermo()$opt$state is chosen, otherwise the matching (or states of species representing phases of minerals that undergo phase transitions are coded as cr (lowest-T phase), cr2, cr3, ... (phases with increasing temperature).
If state is cr when one of these minerals is matched, all the phase species are added.
To modify the logarithms of activities of species (logarithms of fugacities for gases) provide one or more numeric values of species referring to the rownumbers of the species dataframe, or species NULL, to modify all currently defined species.
The values in state, if numeric, are interpreted as the logarithms of activities, or if character are interpreted as states to which the species should be changed.
If species is numeric and delete is TRUE, the rows representing these species are deleted from the dataframe; if the only argument is delete and it is TRUE, all the species are removed.
Use info to search the thermodynamic database without adding species to the system. basis is a prerequisite for species.
# NOT RUN {
# set up the basis species
basis("CHNOS")
# add, modify, delete species
species(c("CO2","NH3")) # aqueous species
species(c("CO2","NH3"),"gas") # gases
# delete the first couple of species
species(1:2,delete=TRUE)
# modify the logarithms of activities (actually
# fugacities) of the remaining species
species(1:2,c(-2,-5))
# set the species to aqueous
species(1:2,"aq")
# delete all the species (returns the existing species
# definition, then deletes the species)
sd <- species(delete=TRUE)
# changing the elements in the basis definition
# causes species to be deleted
basis(c("CaO", "CO2", "H2O", "SiO2", "MgO", "O2"))
species(c("dolomite", "quartz", "calcite", "forsterite"))
basis(c("CO2", "H2O", "O2"))
species() # NULL
# }
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