In this pane all properties of chemical species are set.
The names of chemical species can be modified. No two species of any kind can have the same name.
The type of chemical species can not be modified.
A species is selected by clicking on the appropriate row of the table.
Stoichiometric coefficients are entered for the mass action and the mole balance equations. The user has to ensure consistency with the stoichiometric data entered in the "Chemical reactions" pane.
A new chemical species can be added by invoking the
"Add new species" button.
A dialog box will appear that requires the input of the name and the type
of the species. The checkbox "Kinetic species" needs to be activated when
this species is the product of a kinetic reaction. By default a new
species is assumed to be an equilibrium species, i.e. the product species
of an equilibrium reaction. Pressing Cancel or closing the
window will abort the addition of the new species.
Note: An ion exchanged species can only be added after at least
one ion exchange site was defined. This is done in the pane
Ion exchange.
The selected species can be removed by invoking the "Remove selected species" button when the following condition is met:
The species does not participate in any chemical or microbial reaction. (Chemical reactions are set up in the input panel Chemical reactions, microbial reactions in the input panel Microbial reactions.)If this condition is not met, the labeling of the button "Remove selected species" will appear in red. Clicking the button will display a message with a listing of the reasons why this species can not be removed. You need to fix all of these violations of the above listed rule before you can remove the species.
Initial conditions are assigned only to kinetic species. They are displayed if the selected species is kinetic. When the initial concentration is not homogeneous, a spreadsheet editor can be invoked. Boundary conditions are only assigned to mobile kinetic species. Therefore, they are only displayed if the selected species is mobile and kinetic.
A more detailed description of initial conditions is here.
A more detailed description of boundary conditions is here.
Last Modified:
Jin-Ping Gwo, email: jgwo@umbc.edu