Department of Geosciences
North Dakota State University
GEOLOGY 428/628:
Geochemistry
Instructions for PHREEQC on abacus

The version of phreeqc installed on abacus is v. 2.3. Note, this is not the most recent version available. This includes the database, llnl.dat, "that implements most of the inorganic aqueous species and minerals in the thermodynamic data compiled by Jim Johnson of the Lawrence Livermore National Laboratory. This compilation includes many elements not available in any other PHREEQC database. Many of the aqueous species and minerals, but not all, are fit over the temperature range 0-300. The database llnl.dat should give results essentially equivalent to EQ3/6 and Geochemist's Workbench. The database llnl.dat requires version 2.3 because it relies on a new keyword LLNL_AQUEOUS_MODEL_PARAMETERS to define the activity coefficient parameters and their temperature dependence for the Lawrence Livermore model for activity coefficients." (D.L. Parkhurst, email of 2 Jan 2001 to phreeqc users list). Version 2.3 also has capabilities to simulate dispersion (or diffusion) and stagnant zones in 1D-transport calculations, to model kinetic reactions with user-defined rate expressions, to allow the number of surface or exchange sites to vary with the dissolution or precipitation of minerals or kinetic reactants, and other neat things as described by Parkhurst et al. at the PHREEQC web site.

1. In order to run PHREEQC on abacus, the links to it must be installed in your account.

To do this, type

/usr/local/phreeqc/bin/setup

at the sytem prompt. Only do this once, the first time you log on.

2. Once you have done this, there will be examples of input files installed in your account: ex1, ex2, etc. These are taken from the manual for PHREEQC, available online at http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/html/final.html, with a PDF version at ftp://water.usgs.gov/pub/software/geochemical/phreeqc/doc/manual.pdf (copies of which are in the back of room 134).

3. Use the program "pico" (or another text editor of your choice) to view the example files, and to construct files for your problem. For example, to view the input file ex1, type "pico ex1" at the system prompt. Commands for moving the cursor, deleting lines etc., are given at the bottom of the screen. Construct your input file, save it and give it a name. Below is an example input file for seawater:

TITLE Speciate seawater.
SOLUTION 1  SIMPLIFIED SEAWATER FROM NORDSTROM ET AL. (1979)
        units   ppm
        pH      8.22
        pe      8.451
        density 1.023
        temp    25.0
        Ca              412.3
        Mg              1291.8
        Na              10768.0
        K               399.1
        Fe              0.002
        Si              4.28
        Cl              19353.0
        Alkalinity      141.682 as HCO3
        S(6)            2712.0
END

4. To run PHREEQC, type phreeqc [return]. The program will ask you for an input file name, an output file name, and which database you wish to use, phreeqc.dat, wateq4f.dat, or llnl.dat.

5. To view your output file, type pico filename.out. Use the cursor controls to see the relevant parts of the output file. You may wish to cut and paste relevant parts to a wordprocessor for incorporation into a report.

The USGS has put up a useful web page of PHREEQC Frequently Asked Questions. Also, have a look at "STATUS OF PHREEQC". Check out both these pages.

I'm sure there will be questions. You can reach me at 701-231-8785 or bernhardt.saini-eidukat@ndsu.nodak.edu