Define Basis Species
Define the basis species of a chemical system. Change their physical states or chemical activities or fugacities. Get the stoichiometries of the basis species in selected species of interest.
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character, names or formulas of species, or numeric, indices of species
character, physical states or names of buffers
numeric, logarithms of activities or fugacities
logical, delete the current basis species definition?
numeric, indices of species (rownumbers of
character, a keyword identifying a preset basis definition
basis is used to define the basis species in a system of interest, and in many workflows is followed by calls to
diagram for making equilibrium chemical activity diagrams. The other functions documented here are supporting functions for
basis and generally are not intended to be called by the user.
The basis species represent the possible range of chemical compositions for all the species of interest. Any valid set of basis species used here must meet two conditions: 1) the number of basis species is the same as the number of chemical elements (including charge) in those species and 2) the square matrix representing the elemental stoichiometries of the basis species has a real inverse. Basis species might, but do not always (and not if a charged basis species is present), correspond to the thermodynamic components of a system.
To create a basis definition, call
basis with the names or formulas of the basis species in the first argument. Alternatively, the first argument may consist of numeric values indicating the species indices (rownumbers in
thermo$obigt), but a mixture of character and numeric values will generate an error. The special names pH, pe and Eh can be included in the
species argument; they get translated into the names of the proton (H+) and electron (e-) as appropriate.
If the new basis definition meets all requirements, it is stored in
thermo$basis, replacing any previous basis definition;
put.basis does the actual storing of the basis definition.
The physical states or logarithms of activities of species in the basis definition can be changed directly using
mod.basis but usually more conveniently by calling
basis with the formulas of species that are in the basis set, or their species indices. If either of the second or third arguments to
basis is of type character, it refers to the name of a state (if present in
thermo$obigt$state) or to the name of a chemical activity
buffer (if present in
thermo$buffers$name). If either of these arguments is numeric it specifies the logarithms of activities (or fugacities for gases) of the basis species. In case pH, pe or Eh are named, the logarithm of activity of the basis species is converted from these values. (For example, a value of 7 for pH is stored as a logarithm of activity of -7).
basis is called with NULL values of both
logact, the new set of species, if they are a valid basis set, completely replaces any existing basis definition. If this occurs, any existing species definition (created by the
species function) is deleted. However,
swap.basis can be used to change the species (the compositions and/or physical states thereof) in the basis set while maintaining the list of species of interest, with the added benefit of equivalence of the chemical potentials of the elements before and after the swap.
delete set to TRUE to clear the basis definition. Any current basis definition (before being deleted) is returned by this call or by calling
basis with all default arguments.
If the value of
basis is one of the keywords in the following table, the corresponding set of basis species is loaded (defined in
preset.basis), and their activities set to reference values (defined in
preset.logact). This approach is used by many of the examples in the package. The basis species identified by these keywords are aqueous except for H2O (liq), O2 (gas) and Fe2O3 (hematite, cr1).
||CO2, H2O, NH3, H2S, O2|
||CO2, H2O, NH3, H2S, O2, H+|
||CO2, H2O, NH3, H2S, e-, H+|
||CO2, H2O, NH3, H3PO4, H2S, e-, H+|
||Mg+2, CO2, H2O, NH3, H3PO4, H2S, e-, H+|
||Fe2O3, CO2, H2O, NH3, H2S, O2|
||Fe2O3, CO2, H2O, NH3, H2S, O2, H+|
||cysteine, glutamic acid, glutamine, H2O, O2|
basis returns the value of
thermo$basis after any modifications; or, if
delete is TRUE, its value before deletion.
info to query the thermodynamic database in order to find what species are available.
makeup is used by
basis to generate the stoichiometric matrix from chemical formulas.
species is the usual next step after
swap.basis is used to change the chemical compounds (species formulas) used in the basis definition while keeping the chemical potentials of the elements unaltered.
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## define basis species # one, two and three element examples basis("O2") basis(c("H2O", "O2")) basis(c("H2O", "O2", "H+")) ## clear the basis species basis(delete=TRUE) ## Not run: ## marked dontrun because they produce errors # fewer species than elements basis(c("H2O", "H+")) # more species than elements basis(c("H2O", "O2", "H2", "H+")) # non-independent species basis(c("CO2", "H2O", "HCl", "Cl-", "H+")) ## End(Not run) ## specify activities and states basis(c("H2O", "O2", "CO2"), c(-2, -78, -3), c("liq", "aq", "aq")) # change logarithms of activities/fugacities basis(c("H2O", "O2"), c(0, -80)) # change state of CO2 basis("CO2", "gas")