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How to add two species with the same element?


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Hi Jia,

    I'm study the case "AsenateReduction.rea" about Microbial populations recently. But i found i can't add AsO4 --- and As(OH)4- at the same time by the button of swapping. Looking forward to your help.

    It seems that I have done the problem. I add As(OH)4- first, then I choose config→redox, finally I can add AsO4 ---. But I have no idea that whether it is different between swapping and non-swapping.

Best wishes,

Wen Qiu.

 

ArsenateReduction.rea

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Hello Wen Qiu,

In your example, species As(OH)4- and AsO4--- are both arsenic species with different valences. Typically in geochemical databases, one species is chosen as a basis species and the other species of the same element is formed by balancing a redox reaction. In this case, the species As(OH)4- is chosen as the basis species and AsO4--- is written as a redox reaction of the basis. The GWB by default only allows users to add basis species in the Basis pane as the constraints for each component. Please see more details regarding thermo datasets in section 9. TEdit of the GWB Essentials User Guide.

You can decouple the redox couple (e.g. As(OH)4- and AsO4---) for a specific simulation such that you can constrain the concentration of each oxidation state separately. Unless you decouple the reaction before the simulation, React will assume redox equilibrium when calculating the distribution of mass to each redox state. For more information on redox disequilibrium, please see section 7.3 in the GWB Essentials User Guide. You can also permanently decouple reactions in your thermo dataset and save it as a custom dataset if you find yourself needing to decouple the same redox reactions all the time. For more information on working with datasets, please refer to section 9.2 in the GWB Essentials User Guide.


Basis swapping allows the user flexibility to use other reactions in the datasets to set your chemical constraints. For example, if you can safely assume a mineral or a gas is in equilibrium with your system, you can swap it in for a corresponding basis species. A specific example of this may be swapping in the Quartz for SiO2(aq). For aqueous or redox species, occasionally, you may need to swap in more dominant form of the component to help the program to converge. For example, if you have a really reduced system where you have a large quantity of sulfide but no sulfate, you may want to swap in H2S(aq) for SO4--. You can find more information on how to configure the initial system in the GWB in section 2 of the GWB Essentials User Guide. For more examples on swapping, please see section 7.2 Equilibrium Models in the GWB Essentials User Guide.


Hope this helps,
Jia Wang 

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Hello Jia,

       Very excited to receive your reply. I met a problem again. When running plot results, I found that the rate changes. The figure shows in steady state after 10 days(Figure1,2,3). I never change the parameters in AsenateReduction.rea. So whether there is a change of rate in different editions of software?

1.jpg

2.jpg

3.jpg

4.jpg

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Hello Wen Qiu,

I don't believe this is an issue with the different software editions. The React input file provided is just a starting point for the user. If you follow the lesson on the GWB Academy further, you can see that running the file as provided is predicting results far from the experimental data. You would need to adjust the rate constant, KD, KA values to get a better fit. Please also note that the simulation in the exercise is set to 60 hours and not days. 

Also note that the last image posted in your last post is just plotting the experimental data from GSS and not the simulation result. You can superimpose the experimental data from GSS onto the simulation in Gtplot by dragging “As_reduction_scatter.gss” from your desktop folder into your Gtplot window. This way, you can visually assess the fit of the simulation result as you change the parameters and rerun.

Hope this helps,
Jia
 

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Hello Wen Qiu,

I would like add to the response to my previous post. The best description of thermo datasets is in the Thermo Datasets chapter of the GWB Reference Manual. If you do not find what you need in the GWB Essentials User Guide, please see the Reference Manual. 

Best regards,
Jia 

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