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1-D pyrite oxidation model


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I am trying to reproduce the simulation of pyrite oxidation in 1-D porous media flow system by Xu et al (2000) for the training of GWB.

Given conditions for the simulation are as below, only.



length (x), 2m; height (z), 1cm; width (y), 1.0 cm; nodes, 40; discharge, 0.02m/day



porosity, 40%



Kinetic; Pyrite, 9 volume%

surface area, 0.587 cm2/g

rate constant, 4e-15 mol/cm2 sec, or (range from 2e-17 to 2e-14 mol/cm2 sec)



O2(aq), 1.0e-70 mol/L

time, 3 days



O2(aq), 2.53e-4 mol/L


Although I conducted the X1t simulation, I cannot acquired the result; even if I tried the simulation with the addition of the values of Fe++ and SO-- (demanded by the program), H+(initially pH 7, maybe), Na+ and Cl- (demanded by the program for charge balance) and so on, according to error messages.

Final error message is about large residual, and of course no plot data.


The result of the paper shows that the pH value of the water changed from nutrality to around 3.8.

I hope to acquire the result of the variation of pH derived from pyrite oxidation with time.

How should I deal with this case?




Xu et al (2000) Transport in Porous Media 39: 25-56.

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Hi Maki,


Could you please post your script (.x1t file) so people can take a look?


It's always a good idea to start with a simple system and add complexity as you go. Starting with a reaction path model (mixing two fluids) also helps quite a bit. I would use the pickup command in React to model mixing of an initial and inlet fluid. Setting up this system may help you with constraining your reactive transport simulation.


Hope this helps,


Brian Farrell

Aqueous Solutions LLC

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Thank you for the response.


I posted my scripts (v01, with minimum conditions provided by the paper; v02, with additional parameters demanded by the program).


Note: In the paper, specific surface area used is 58.7 m2 m-3. On the other hand, in the X1t, I input the value as 0.587 cm2 g-1 without considering the density of pyrite.


Best regards,





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Hi Maki,


I would like to spend some more time looking at your problem, but here a few things to consider right away. The second script is much closer to what is needed for a fully constrained model. Because you have Pyrite in your model, you need to include Fe++ and SO4-- in your Initial system and Inlet fluid (in order to form the Pyrite). As for charge balance, people commonly add both Na+ and Cl- (to balance each other initially) in a concentration much higher than you have here, but not so high as to have a large effect on activity coefficients (by increasing ionic strength).


If you make these changes you'll get a simulation that runs (and has lower pH near the inlet), but it could still use some work. You might experiment with swapping minerals into the Initial system (i.e. Pyrite or Hematite) rather than just assuming a very small concentration of Fe++, for example.


Hope this helps,



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Hi, Brian.


Thank you for your advice.


According to your suggestion, I have conducted many trials while varying the concentrations of Cl- and Na+ and swapping Fe++ to Pyrite or Fe++ to Hematite with SO4-- to Pyrite, and so on. However, the program has not worked yet. Although I didn't understand the reason and the process, the error messages depended on the combination of the Cl- and Na+.

If you have any other idea to run the calculation, could you give me that?


Thank you for your time.


Best regards,



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