Sandbox monod reaction not behaving similar to microbial reaction

[Bisesh Joshi]

Hi all,

I'm trying to simulate NH4+ uptake in the root zone by using the Reaction Sandbox with the following input block, where I'm using total concentrations.

REACTION_SANDBOX

  NH4_UPTAKE_MATERIALIDS

    NH4_UPTAKE_RATE_CONSTANT 8.0d-09

    NH4_UPTAKE_HALF_SATURATION_CONSTANT 5.d-5

    NH4_UPTAKE_THRESHOLD_CONCENTRATION 1.d-30

    NH4_UPTAKE_MATERIAL_IDS 5  1 2 3 4 12  

    !output Tracer1

  END  

END

Previously, I was  using  microbial equations with biomass as a placeholder for these layers with the following block:

MICROBIAL_REACTION

    REACTION    1.0000 NH4+ <-> 1.00 Tracer1

    RATE_CONSTANT 8.d-12 #TL_uptake

#    ACTIVATION_ENERGY      80.d3 

    MONOD

      SPECIES_NAME NH4+ 

      HALF_SATURATION_CONSTANT 5E-5         ! A is the donor

      THRESHOLD_CONCENTRATION 1.d-30

    /    

      BIOMASS

      SPECIES_NAME TL

      YIELD 0.00d0

    /    

/

The initial biomass of TL in this zone is 1.d3

I'm using the same seasonal multipliers to rate constants on these reactions for seasonal NH4 uptake in separate monthly input files. I was expecting the same results, but I'm getting different results.

Please let me know if anyone has any suggestions regarding this.

Thank you,

Bisesh

--

Bisesh Joshi

PhD student

Water Science and Policy

Graduate College

University of Delaware

901-297-6761

[Hammond, Glenn E]

Bisesh,

Please help me better understand the implementation in your reaction sandbox. I need that before I can provide input.

Glenn

From: pflotra...@googlegroups.com <pflotra...@googlegroups.com> on behalf of Bisesh Joshi <bjo...@udel.edu>
Date: Monday, June 15, 2026 at 11:12 AM
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Subject: [pflotran-users: 8794] Sandbox monod reaction not behaving similar to microbial reaction

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[Bisesh Joshi]

Hi Glenn,

Thank you so much for your response.

I'm implementing a reaction sandbox for localized microbial reactions that simulate plant uptake in root zones. I'm using simple monod reaction in the reaction sandbox for area specified by material IDs: 

Reaction is: 1. NH4+ > 1. Tracer1

Looking forward to hear from you.

Bisesh Joshi

PhD student

Water Science and Policy

Graduate College

University of Delaware

901-297-6761

To view this discussion visit https://groups.google.com/d/msgid/pflotran-users/BY3PR09MB755549AF6BC29D77F1FAB8339AEF2%40BY3PR09MB7555.namprd09.prod.outlook.com.

[Hammond, Glenn E]

Bisesh,

To identify differences between implementations, I recommend starting with a single grid cell (batch) scenario using identical concentrations. By doing so, you can directly compare the results from each approach. Incorporate print statements to monitor the rate in the sandbox and then compare it to the rate in the microbial reaction. For reference, consult the following section of the code: https://bitbucket.org/pflotran/pflotran/src/5470dad5ecb6a85575b60f051c3502f5c6a121d4/src/pflotran/reaction_microbial.F90#lines-385. Be sure to verify that the rate units are consistent (mole/sec in reaction_microbial). Begin with a single time step and gradually increase complexity as needed.

Glenn

From: pflotra...@googlegroups.com <pflotra...@googlegroups.com> on behalf of Bisesh Joshi <bjo...@udel.edu>

Date: Monday, June 22, 2026 at 4:25 PM
To: pflotra...@googlegroups.com <pflotra...@googlegroups.com>
Subject: Re: [pflotran-users: 8804] Sandbox monod reaction not behaving similar to microbial reaction

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