Models

Models is the branch of the project tree that holds what is being described — the chemistry, or the mathematics. A study runs on a model; the model itself does not run.

Two kinds live here:

  • a PHREEQC lab, which is the subject of this chapter;

  • a function model, a set of named mathematical expressions, for problems with no chemistry in them. Function models are useful in their own right and are what the “analytic” examples use to show a study type without PHREEQC in the way.

Earlier versions of GibbsStudio called this branch Chemistries.

The PHREEQC lab

A lab is a self-contained PHREEQC setting: the databases available to it, the chemical components defined in it, the input models, and the selected outputs that say what to record. A project can hold more than one, and they are independent — two labs can use different databases without interfering.

A new project is created with a lab already in it, carrying phreeqc.dat, a default selected output and a simple input model, so there is something to run from the start.

Under a lab:

Parameters

Parameters local to this lab. They behave as project Parameters do, but are scoped here.

Databases

The thermodynamic databases, and which is the default. See PHREEQC Databases.

Components

The chemistry defined once and reused: Solutions, Equilibrium Phases and Selected Outputs.

Components

A component is a piece of PHREEQC chemistry held as an entity rather than as text, so it can be named, reused by several models, and pointed at by parameters.

Solutions

Water compositions.

Equilibrium Phases

The minerals and gases a solution is allowed to equilibrate with.

Defining these as components rather than writing them into the input is what lets a parametric study vary them: a parameter in a component’s field is swept, fitted or sampled like any other.

Selected outputs

A selected output says what PHREEQC should record from each simulation. It is not a detail — it decides what exists afterwards. Nothing that is not in the selected output is available later to a filter, a table or a plot, whatever the simulation computed internally.

Choose the database first, then pick the fields from the list it offers.

Species, phases and totals written directly in the input file do not appear in that list, because the list comes from the database rather than from your input. They can still be recorded: type them into the box. They are shown in amber in the selected list as a warning that they were not recognised, and they will appear in the output if the simulation produces them. Amber here means “not checked”, not “wrong” — but it is also where a typo hides, since a misspelt name simply produces nothing.

Recording everything is tempting and expensive: the selected output is written for every simulation of every run, so a parametric study of a thousand simulations writes it a thousand times. Record what you will use.

Input models

A PHREEQC input model is the PHREEQC input itself, written in the editor. It is analogous to a PHREEQC input file, with the restrictions described under Studies.

Examples