O2(g) diffusion inhibiting SOM mineralization in Richards Mode

[Bisesh Joshi]

Hi all,

I'm trying to equilibrate the top surface layers with atmospheric O2, and I have a water level close to the surface. I'm using the Millington Quirk Tortuosity model for diffusion with a diffusion constant of 2d-5. I'm testing without a reaction network with SOM-ammonium mineralization from the database.

However, I'm unable to get ammonium mineralization with O2(g) in the system, while I get it when the O2(g) fluid property is turned off. I'm wondering what is causing this inhibition. I have tested scenarios by taking off CO2 and H+ suspecting if they are causing the issue, but I did not help. Shouldn't O2(g) diffusion in the saturated zone be near to zero

Please let me know if you have any ideas on this.

In input file I'm using: this for surface cells.

In the database, I have the following reactions of interest:

for O2 :

'O2(g)' 0.0000 1 1.0000 'O2(aq)' -2.6567 -2.8983 -3.0633 -3.1076 -3.0354 -2.8742 -2.6488 -2.3537 31.9988

for SOM

'SOM02' 125.52 7 -0.5 'H2O' 5.0 'Ac-'   0.441  'NH4+'  0.5 'DOM1' 0.5 'CO2(aq)*' 4.559 'H+' 0.441 'Tracer6' -24.32 -25.01 -25.73 -26.27 -26.81 -27.24 -27.60 -27.89 373.31

Thank you.

--

Bisesh Joshi

PhD student

Water Science and Policy

Graduate College

University of Delaware

901-297-6761

[Bisesh Joshi]

Hi all,

Just a gentle reminder.

Anybody have any thoughts on this?

Thank you.

Bisesh

[Hammond, Glenn E]

Bisesh,

Please send you input deck.

Glenn

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Date: Monday, February 23, 2026 at 7:36 AM
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Subject: [pflotran-users: 8675] Re: O2(g) diffusion inhibiting SOM mineralization in Richards Mode

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[Bisesh Joshi]

Hi Glenn,

Thanks for your reply.

Here, I have attached my input file and its dependencies for you review.

Thank you.

Best regards,

Bisesh

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[Bisesh Joshi]

Hi Glenn,

Hope you are doing well.

Just wondering if you have time to look into my input deck.

NH4+ is being produced from SOM mineralization.

Even in the model without a reaction network, this is the pattern I'm getting with O2 (g) with diffusion in the model for total NH4+ in the mostly saturated system.

Versus this pattern in the model without O2(g) diffusion 

I was expecting the first plot to be somewhat similar to the second. Please let me know your thoughts on this.

Thanks in advance!

Best regards,

Bisesh

[Hammond, Glenn E]

Bisesh,

I've spent some time reviewing your issue and now have a clearer understanding, though I don't yet have a definitive solution. One important consideration is that you cannot simply add new species to a mineral precipitation-dissolution rate expression based on transition state theory and expect unchanged results—in your case, this applies to the addition of Tracer6.

I suggest two possible approaches: First, you could create a new mineral that includes Tracer6 instead of NH4+. Alternatively, you might use the OVERRIDE_MINERAL_MASS_ACTION option to reset the mass action equation to its original value from the database; Tracer6 would still be updated according to the stoichiometry.

For reference, here are some helpful resources:

https://bitbucket.org/pflotran/pflotran/src/6ee92553c9cca7eb8cf670939b6e80e298845ac6/regression_tests/default/column/calcite_override.in#lines-23

https://documentation.pflotran.org/user_guide/cards/subsurface/chemistry/override_mineral_mass_action_card.html?highlight=override_min

Glenn

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[Bisesh Joshi]

Hi Glenn,

Thank you very much for taking the time to look into this matter and for your helpful suggestions regarding the tracer.

I observed a similar pattern for Total NH₄⁺ as seen for Tracer 6 when gas diffusivity is turned off. Specifically, the ammonium concentrations in the system are considerably higher when gas diffusivity is disabled and only liquid diffusivity is active.

I have attached the corresponding plot for your reference.

Best regards,

Bisesh

 

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