Define the species of interest in a system; modify their physical states and logarithms of activities.
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
logical, return the affected rownumbers of
After defining the
basis species of your system you can use
species to identify for the program the species of interest. A species is operationally a combination of a
state, which are columns of the thermodynamic database in
thermo$obigt. The function operates on one or more character values of
species. For each first match of
species (optionally restricted to a
state among aq, cr, gas, liq) to the name of a species or a formula or abbreviation in the thermodynamic database, a row is added to
The data frame in
thermo$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, and reference settings for the logarithms of activities or fugacities used in calculations of
affinity. The default values for logarithms of activities are -3 for aqueous (aq) species and 0 for others.
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 n'th matching duplicate) species is used. Note that the
states of species representing phases of minerals that undergo phase transitions are coded as cr1, 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
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.
species.basis is the function used by
species to calculate the coefficients of reactions to form the species from the basis species. It accepts one or more species formulas or indices, and produces an error if either the basis species are not defined, or they do not contain all of the elements in any of the species.
With no arguments or when adding species,
species returns the value of
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.
info to search the thermodynamic database without adding species to the system.
basis is a prerequisite for
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
# set up the basis species basis("CHNOS") # show the formation reactions of some species ispecies <- info(c("glutamic acid","phenylalanine")) species.basis(ispecies) # 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