HydroGeoSphere/Solute Definition

These instructions can be used to add a new solute (i.e. species) to the system. HydroGeoSphere is able to handle more than one solute per simulation, and straight and branching decay chains are also supported. An example of a straight decay chain is the following system:



Uranium^{234} \rightarrow Thorium^{230} \rightarrow Radium^{226} $$

which indicates that the decay of the radioactive isotope Uranium234 produces the daughter product Thorium230, which in turn decays to form Radium226. For an example of a straight decay chain see Section 4.5.1. Branching decay chains can have a single isotope which decays into one or more daughter products, or daughter products which have one or more parents.

Note that a solute can have different values for the decay constant and distribution coefficient (retardation factor for fractured media) in porous, dual or fractured media or from zone to zone in a single medium.

Solute
Causes grok to begin reading a group of solute definition instructions until it encounters an End instruction.
 * &bull; &bull; &bull;

The available instructions are:

Name

 * 1) spname Solute name.

Changes the solute name, which defaults to Species n, where n is the current solute number.
 * &bull; &bull; &bull;

Free-solution diffusion coefficient

 * 1) diffrac Free-solution diffusion coefficient [L2 T−1], $$D_{free}$$ in Equation 2.97.

Assigns a new value for the free-solution diffusion coefficient, which defaults to 0.0 (zero).
 * &bull; &bull; &bull;

Parents

 * 1) npa Number of parent species for the current species. If the current species has one or more parents, enter the following npa times (i.e. once for each parent):
 * (a) kparen, aparen Parent species number and the mass fraction.

Assigns a value for the number of parent species, which defaults to 0. The mass fraction is a number between 0 and 1 which defines how much of the parent species transforms into the daughter species (i.e. the current species).
 * &bull; &bull; &bull;

The following parameters affect porous media solute properties:

Decay constant

 * 1) clambda First-order decay constant [T−1], $${\lambda}$$ in Equation 2.95.

Assigns a uniform value for the solute first-order decay constant for all porous media zones in the domain. The default value is 0.0 (no decay).
 * &bull; &bull; &bull;

Zoned decay constant

 * 1) clambda(i,j),j=1,nzones_prop First-order decay constant [T−1] for species i for each porous media zone j, $${\lambda}$$ in Equation 2.95.

Assigns a unique value for the solute first-order decay constant to each porous media zone in the domain. The default value is 0.0 (no decay).
 * &bull; &bull; &bull;

Distribution coefficient

 * 1) dkd Distribution coefficient, $$K^\prime$$ in Equation 2.96.

Assigns a uniform value for the solute distribution coefficient for all porous media zones in the domain. The default value is 0.0 (no attenuation).
 * &bull; &bull; &bull;

Zoned distribution coefficient

 * 1) dkd(i,j),j=1,nzones_prop Distribution coefficient for species i for each porous media zone j, $$K^\prime$$ in Equation 2.96.

Assigns a unique value for the distribution coefficient to each porous media zone in the domain. The default value is 0.0 (no attenuation).
 * &bull; &bull; &bull;

Dual decay constant

 * 1) clambda First-order decay constant [T−1], $${\lambda}_d$$ in Equation 2.103.

Assigns a uniform value for the solute first-order decay constant for all dual continua zones in the domain. The default value is 0.0 (no decay).
 * &bull; &bull; &bull;

Zoned dual decay constant

 * 1) clambda(i,j),j=1,nzones_prop First-order decay constant [T−1] for species i for each dual continua zone j, $${\lambda}_d$$ in Equation 2.103.

Assigns a unique value for the solute first-order decay constant to each zone in the domain. The default value is 0.0 (no decay).
 * &bull; &bull; &bull;

Dual distribution coefficient

 * 1) dkd Distribution coefficient, $$K^\prime_d$$ in Equation 2.104.

Assigns a uniform value for the solute distribution coefficient for all dual continua zones in the domain. The default value is 0.0 (no attenuation).
 * &bull; &bull; &bull;

Zoned dual distribution coefficient

 * 1) dkd(i,j),j=1,nzones_prop Distribution coefficient for species i for each dual continua zone j, $$K^\prime_d$$ in Equation 2.104.

Assigns a unique value for the distribution coefficient to each dual continua zone in the domain. The default value is 0.0 (no attenuation).
 * &bull; &bull; &bull;

The following parameters affect fractured media solute properties:

Fracture Decay constant

 * 1) clambda_f First-order decay constant [T−1], $${\lambda}_f$$ in Equation 2.99.

Assigns a uniform value for the solute first-order decay constant for all discrete fracture zones in the domain. The default value is 0.0 (no decay).
 * &bull; &bull; &bull;

Zoned fracture decay constant

 * 1) clambda_f(i,j),j=1,nzones_prop First-order decay constant [T−1] for species i for each discrete fracture zone j, $${\lambda}_f$$ in Equation 2.99.

Assigns a unique value for the solute first-order decay constant to each discrete fracture zone in the domain. The default value is 0.0 (no decay).
 * &bull; &bull; &bull;

Fracture retardation factor

 * 1) rfrac Fracture retardation factor, $$R_f$$ in Equation 2.100.

Assigns a uniform value for the fracture retardation factor for all discrete fracture zones in the domain. The default value is 1.0 (no attenuation).
 * &bull; &bull; &bull;

Zoned fracture retardation factor

 * 1) rfrac(i,j),j=1,nzones_prop Retardation factor for species i for each discrete fracture zone j, $$R_f$$ in Equation 2.100.

Assigns a unique value for the fracture retardation factor to each discrete fracture zone in the domain. The default value is 1.0 (no attenuation).
 * &bull; &bull; &bull;

The following parameters affect overland media solute properties:

Overland Decay constant

 * 1) clambda_o First-order decay constant [T−1], $${\lambda}_f$$ in Equation 2.110.

Assigns a uniform value for the solute first-order decay constant for all overland flow zones in the domain. The default value is 0.0 (no decay).
 * &bull; &bull; &bull;

Zoned overland decay constant

 * 1) clambda_o(i,j),j=1,nzones_prop First-order decay constant [T−1] for species i for each overland flow zone j, $${\lambda}_f$$ in Equation 2.99.

Assigns a unique value for the solute first-order decay constant to each overland flow zone in the domain. The default value is 0.0 (no decay).
 * &bull; &bull; &bull;

Overland retardation factor

 * 1) rolf Overland flow retardation factor, $$R_o$$ in Equation 2.100.

Assigns a uniform value for the overland retardation factor for all overland zones in the domain. The default value is 1.0 (no attenuation).
 * &bull; &bull; &bull;

Zoned overland retardation factor

 * 1) rfrac(i,j),j=1,nzones_prop retardation factor for species i for each overland flow zone j, $$R_o$$ (similar to $$R_f$$ in Equation 2.100).

Assigns a unique value for the overland flow retardation factor to each overland zone in the domain. The default value is 1.0 (no attenuation).
 * &bull; &bull; &bull;

The following instructions can be used to identify certain species. This is especially important to calculate fluid density and viscosity (for variable-density transport) from individual species concentrations and temperature. Note that fluid temperature is treated as a mobile species.

Sodium species
The presently defined species is identified as sodium, $${Na^+}$$
 * &bull; &bull; &bull;

The following instructions can be used likewise to identify other species:


 * Potassium species


 * Calcium species


 * Magnesium species


 * Chloride species


 * Sulphate species


 * Hydrogencarbonate species


 * Carbonate species


 * Salt mass fraction


 * Temperature species

By default, no species impacts fluid density or viscosity. This default can be changed with the following instruction:

Affects fluid properties
With this instruction, the presently defined species has an impact on both fluid density and viscosity. This instruction can only be applied to the following species: $$Na^+, K^+, Ca^{2+}, Mg^{2+}, Cl^-, SO_4^{2-}, CO_3^{2-} $$ and $$HCO_3^-$$, fluid temperature $$T$$ and salt mass fraction $$smf$$. Note that, for the moment, if salt mass fraction affects fluid properties, no other species can impact fluid properties.
 * &bull; &bull; &bull;

Placement of instructions
Note that instructions like decay constant and zoned decay constant are mutually exclusive for a given solute, and should not appear in the same Solute. . . End solute block. This also applies to distribution coefficient definitions for all types of media. You can however, define a solute with decay or attenuation properties which are uniform throughout the domain while a second solute has a zoned behaviour.

Since a new species is created each time the instruction solute is used, any instructions (e.g. make fractures, specified concentration , specified third-type concentration , etc. which depend on it should be placed after it in the prefix.grok file.

Example solute definitions
The following simple example shows how to define a single, conservative, non-decaying solute called 'Species 1' with a free-solution diffusion coefficient of zero (0.0):

An example of a more complex system with two solutes and 7 material zones is shown in Figure 5.7 for the first solute, called DCB, which only decays in zone 1, and has distribution coefficients which vary from zone to zone:


 * Figure 5.7: Definition of a Parent Solute With Zoned Properties

Figure 5.8 shows how to define the second solute, called BAM, which is a daughter product of DCB, and does not decay. This solute has the same zoned distribution coefficients as the first solute:


 * Figure 5.8: Definition of a Daughter Solute With Zoned Properties