.. _example-phreeqc-manual-01:

01 - Speciation calculation
===========================

The simplest thing PHREEQC does, and the foundation of everything else: take
an analysis of a water and work out what is actually in it.

A laboratory reports total concentrations -- so much calcium, so much
sulfate. A speciation calculation turns those totals into the distribution of
*species* they imply: free Ca²⁺, the ion pair CaSO₄, CaHCO₃⁺ and the rest,
each with its activity. From that it computes a saturation index for every
mineral it knows, which says whether the water would dissolve or precipitate
each one.

The water here is seawater, from the analysis of Nordstrom and others (1979).


The input
---------

.. raw:: html
   :file: PhreeqcStudy.html

Two things in it are worth pointing out.

**Redox is specified, twice over.** The solution carries ``pe 8.451``, but
also ``redox O(0)/O(-2)``, telling PHREEQC which couple to use as the master
redox variable -- and then individual elements override it:
``Mn 0.0002 pe`` uses pe itself, and ``U 3.3 ppb N(5)/N(-3)`` uses the
nitrate-ammonium couple. Natural waters are rarely at redox equilibrium, and
different couples give different answers, so PHREEQC makes you say which one
governs each element rather than quietly picking one.

**The database is extended in the input.** Seawater contains uranium, and
``phreeqc.dat`` has none -- which is what the first Database example finds.
So the input carries ``SOLUTION_MASTER_SPECIES``, ``SOLUTION_SPECIES`` and
``PHASES`` blocks that add uranium to the database for this run only.

That is the pattern for working with a species a database lacks: add it where
the model is, not by editing the database. The addition travels with the
input, and the database stays the one everyone else is using.


What to look at
---------------

The results are a table rather than a figure. Two parts of it carry the
interest.

The **species distribution** shows how little of a total is usually free.
Seawater's calcium is not all Ca²⁺: a substantial part is paired with
sulfate and carbonate, and it is the free ion's activity, not the total, that
determines whether a mineral precipitates.

The **saturation indices** say what seawater is in equilibrium with. Values
near zero mean equilibrium; positive means the mineral could precipitate,
negative that it would dissolve. Seawater is supersaturated with respect to
calcite and dolomite -- which it famously is, without precipitating them,
because the kinetics are slow and the surfaces are poisoned. A saturation
index says what is thermodynamically possible, never what will happen or how
fast.


Where this goes next
--------------------

Every other example in this set starts from a speciation like this one and
then does something to it: changes the temperature
(:ref:`example-phreeqc-manual-02`), mixes it with another water
(:ref:`example-phreeqc-manual-03`), reacts it
(:ref:`example-phreeqc-manual-05`) or transports it
(:ref:`example-phreeqc-manual-11`).

The Monte Carlo example in the Statistics set takes this same seawater and
asks what the uncertainty in its inputs does to the answer.


Source
------

* Parkhurst, D. L. and Appelo, C. A. J. (2013). *Description of input and
  examples for PHREEQC version 3.* U.S. Geological Survey Techniques and
  Methods, book 6, chapter A43. This is Example 1 of that manual.
* Nordstrom, D. K. and others (1979). The seawater analysis used here.