Courses: The GoldSim Contaminant Transport Module:

Unit 5 - Building a Simple Model of a Well-Mixed Environmental Compartment

Lesson 4 - Defining the Contaminant Species

The first step in building a contaminant transport model is to define the species that you wish to simulate. GoldSim allows you to simulate an unlimited number of species. In the example we will build here, we will create two species (named X and Y).

The Species element is used to add, delete, and edit species. It is used to define a list of species that you wish to simulate, and specify their properties (in particular, those relating to the possible decay of the species)

It is important to understand that for the most part, GoldSim does not inherently understand anything about the chemistry of the species you are simulating.  You define these properties and can name the species anything you want.  In fact, although the species in a GoldSim model will typically represent chemicals (man-made or naturally occurring), you can also use GoldSim to model the transport of other types of mass in an environmental system, such as bacteria, viruses or particulate matter.

The one exception to this is if you are using the RT Module to simulate the transport of radionuclides.  In this case, you can take advantage of a built-in database that specifies the various decay chains and properties (e.g., atomic weight) of various radionuclides.  For those of you interested in doing so, we will discuss this in Unit 10.

The Species element can be found inside the Material Container.  Go there now and double-click on the element:

The dialog above is what you will see if you are using the CT Module.  If you are using the RT Module, the dialog for the Species element is more complex (offering a number of additional options and features required when modeling radionuclides):

We don’t need these other specialized options for this example (and the others we will discuss in subsequent Units), so if you are using the RT Module, you don’t need to be concerned about these other options right now.  We will discuss the various options available only when using the RT Module (including the ability to access a database of radionuclides when defining your species) in Unit 10.

Unlike any other element in GoldSim, you cannot rename the Species element (you will note that the Element ID is grayed out). The lower part of the dialog displays a list of all of the species in the model. By default, a single species named Species1 exists when you create a new model.

Double-click on Species1 in the list.  The dialog for that species looks like this:

If you are using the RT Module, you will note two differences from what you see here: 1) the bottom part of the dialog will not be completely grayed out (you can specify daughter products in the RT Module, but not the CT Module); and 2) the Radioactive checkbox is not grayed out. Again, we will discuss the various options available only when using the RT Module in Unit 10.

For each species, we can do the following:

  1. Change the Species ID;
  2. Specify whether or not it is an Isotope;
  3. Specify a Molecular (or Atomic) Weight; and
  4. Specify a Half-life.

Note: What we refer to in GoldSim as the Molecular (or Atomic) Weight is actually the molar mass (the mass of one mole of the substance). Strictly, the term “molecular (or atomic) weight” refers to the mass of a single molecule or atom (typically expressed in terms of atomic mass units).

For this species, all we are going to do here is change the Species ID from “Species1” to “X”.

Specifying a species as an isotope is necessary only if you are simulating multiple species that are isotopes of the same element (this is critical when modeling the transport of radioisotopes). In almost all cases, this is only of interest if you are using the RT Module, and we will discuss this in detail Unit 10. The Molecular (or Atomic) Weight is used to properly model reactions (only available in the RT Module).  It is also used when specifying solubilities in terms of molar concentrations. We will discuss this in Unit 7. For now, it will not actually be used anywhere in our model, so we can leave it at its default value (1 g/mol). We said that X did not decay, so we will not specify a Half-life.

Note: The default Half-life is zero.  Physically, of course, a zero half-life would indicate that the species decays instantaneously (and hence would be meaningless).  In GoldSim, a zero half-life indicates that the species does not decay at all (i.e., it indicates a decay rate, λ, of zero). This is indicated in the dialog for the species, where “No decay” is displayed if the half-life is set to zero.

Note: At the top of the Species dialog is an option labeled Specify decay.  The default option is “Half-lives”.  You could optionally select to specify decay in terms of “Decay Rates” (decay coefficients).  Recall that the half-life is simply equal to ln(2)/decay rate.

After renaming Species1 to X, close the dialog. Then press the Add… button to add a new species.  It will default to “Species2”.  Rename it “Y”.  We also need to add the Half-life:

After changing the name and specifying the Half-life, close the dialog. When you are done, the Species dialog will look like this:

You can now close this dialog (and save the model file).

One final note on the Species element: Unlike other element types in GoldSim, you will almost always have only a single Species element in a GoldSim model.  In fact, you cannot insert or copy a Species element. There are, however, special cases where you can create additional Species elements (via a process called cloning) in the same model (i.e., in situations where the decay properties of the species being simulated vary spatially in a system). We will discuss this special case in Unit 12.