Defining Spatially Variable Decay Rates

In general, the properties of a Species element must, by definition, be constant throughout your model (e.g., you would not want the Molecular Weight of a Species to take on different values in different locations in your model). As a result, when you create a model using the Contaminant Transport Module, a single Species element is automatically created. This element can be moved, but cannot be deleted. Moreover, GoldSim does not allow you to insert additional Species elements.

There are, however, two Species element properties, the Decay Rate and the associated Stoichiometries,that you occasionally may wish to take on different values at different locations in your model. For example, you may want a species to decay only in certain pathways (e.g., a pathway representing anoxic sediments; or a pathway representing the liver in a pharmacokinetic model).

Because pathway and Source elements automatically link to the Species element, and the Decay Rate and Stoichiometries are properties of the Species element, the only way to allow these inputs to have different values in different pathways (or Sources) is to create multiple Species elements (with different Decay Rates and/or Stoichiometries) in different Containers such that different pathways (and Sources) link to different Species elements. As pointed out above, however, GoldSim does not allow you to insert additional Species elements. You can, however, create clones of the Species element, and this allows you to accomplish exactly what is outlined above.

Note: In order to understand how to spatially vary the Decay Rate or Stoichiometries in your model, you must be comfortable with cloning elements and localizing Containers.

Cloned elements automatically mimic each other, such that if you change a property of a clone, the property is automatically changed in all of the other clones. Hence, cloning a Species element does not create inconsistencies in your model, since if you change a property (such as the Atomic Weight) in one clone, it is automatically changed in all the other clones. How, then, can you use a clone to vary the Decay Rate or Stoichiometries in different clone species?

This can be accomplished because you can enter a link (a reference to another element's output), rather than just entering a number when defining a Decay Rate or a Stoichiometry. If you enter a link ID into an input field for a clone element, the same ID will appear in the corresponding input field of all of the clone elements. If, however, different elements having that same ID exist at the locations (Containers) where the clones are, each clone will link to a different element defining the Decay Rate or Stoichiometry, allowing that parameter to be different in each Container.