Retrieve species in the database containing one or more chemical elements.
character, combination of elements, or list, elements in a chemical system
character, elements present in any ligands
character, filter the result on these state(s).
logical, add charge to the system?
logical, exclude groups from the result?
This function retrieves the species in the thermodynamic database (see
thermo) that have the indicated
A character value of
elements is interpreted as a combination of one or more elements that must be present in each species.
A list value of
elements is used to specify a chemical system – the species must contain one or more of the indicated elements, but no other elements.
ligands, if present, gives the elements that may be present in any ligands; this can be used to retrieve all species in a system bearing the
elements (usually a single metal).
The result includes charged species if
add.charge is TRUE (the default) or the user supplies the “element” of charge (Z).
Results can be filtered on physical state by setting the
Groups used in group-additivity calculations, which have names with square brackets (e.g. [-CH2-]), are excluded unless
hide.groups is FALSE.
A special argument value all can be used to retrieve all species in the thermodynamic database, including filtering on state and hiding of the groups.
The return value is a named integer vector giving the species index (i.e. rownumber(s) of
thermo()$OBIGT) with names corresponding to the chemical formulas of the species.
If the electron is in the result, its name (e-) is used instead of its chemical formula ((Z-1)).
An empty (length 0) integer value is returned if no
elements are specified or no species are retrieved.
To speed up operation, the function uses a precalculated stoichiometric matrix for the default database, which is loaded with the package (see
If the function detects a change to any chemical formulas in the database, it updates the stoichiometric matrix using
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 26
# species index of Ti-bearing minerals retrieve("Ti") # thermodynamic data for those minerals info(retrieve("Ti")) # all species that have Au retrieve("Au") # all species that have both Au and Cl retrieve(c("Au", "Cl")) # Au-Cl system: species that have Au and/or Cl, # including charged species, but no other elements retrieve(list("Au", "Cl")) # all Au-bearing species in the Au-Cl system retrieve("Au", "Cl") # all uncharged Au-bearing species in the Au-Cl system retrieve("Au", "Cl", add.charge = FALSE) # minerals in the system SiO2-MgO-CaO-CO2 retrieve(list("Si", "Mg", "Ca", "C", "O"), state="cr") # an Eh-pH diagram for Mn-bearing aqueous species basis(c("Mn+2", "H2O", "H+", "e-")) iMn <- retrieve("Mn", c("O", "H"), "aq") species(iMn) a <- affinity(pH = c(6, 14), Eh = c(-1, 1)) diagram(a, fill = "terrain")
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