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Geochemist's Workbench Support Forum

Melika Sharifi

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Posts posted by Melika Sharifi


  1. Hi Abdulaziz,

    The main purpose of The Geochemist’s Workbench® software package is geochemical reaction modeling and reactive transport modeling using parameters like rate constants and diffusion constants. You may estimate their optimum values by trial and error, though. For example, the Microbial Populations lesson on the GWB Online Academy describes how to adjust the rate constant to visually match experimental data. 

    You can set most basis entries as bulk or free constraints. For a bulk constraint, the value you set refers to the entire thermodynamic component, whereas for a free constraint, it refers to the particular species only. The Ca++ component, for example, might include the Ca++ species, as well as Ca(OH)2(aq), CaHCO3(aq), etc. If you set 10 “mg/kg” Ca++, the concentration is for the sum of those species. If you set 10 “free mg/kg” Ca++, though, the concentration refers only to the individual Ca++ species.

    If you are looking at the reaction between the fluid, and the rock, as the fluid traverse through it, you don't probably need to equilibrate the fluid and rock. For more information, please read section 3.10 in the GWB Reaction Modeling Guide.

    In a spherical domain, the length of the domain is r2-r1. Please read section 3.1 in the GWB Reactive Transport Modeling Guide.

    In future, please don't post your question in different topics. If you need further help, please attach your script.

    Thanks,

    Melika Sharifi

    Aqueous Solutions LLC


  2. Hi Helge, 

    I'm not sure which dataset you are using, so I am not able to give you an exact response. It looks like in your script, you have not decoupled Tc(VII) from Tc(IV). If you use "aqueous" in your command, it will give you the free concentration of that specific species in solution. Consider thermo.tdat dataset when Fe(II) is not decoupled from Fe(III),  myGWB.results('concentration aqueous Fe++', 'molal')[0], will give you the concentration of Fe++ aqueous species, and myGWB.results('concentration aqueous Fe+++', 'molal')[0] will give you the concentration of Fe+++ aqueous species. While myGWB.results('concentration Fe++', 'molal')[0], will give you the total concentration of component Fe(II), and myGWB.results('concentration Fe+++', 'molal')[0] will give you the total concentration of component Fe(III) (i.e. all species with Fe(III) such as Fe(OH)3, Fe+++, Fe2O3, etc).

    Hope this helps.

    Bests,

    Melika Sharifi

    Aqueous Solutions LLC


  3. Hi Helge,

    Concentration H+, molal will give you the concentration of component H+ which refers to the sum of all species with H+, such as HSO4-, OH-, Mg(OH)3, etc. If you want to get the concentration of a particular species, such as H+ which is called free H+, you will need to add "aqueous" to your command (i.e. ('concentration aqueous H+', 'molal').

    Hope this helps.

     

    Bests,

    Melika Sharifi

    Aqueous Solutions LLC


  4. Hello,

    Log K values are derived from the thermo dataset used in the calculation. To see which dataset is currently loaded for your calculation in each app, go to File – File Properties – Thermo data. The Q values for a reaction, however, depend on the activities of species involved in that reaction which are dependent on the thermodynamic data for all other dissolved species in the solution matrix. To overall, Q is a quantity that changes as the reaction approaches equilibrium (K).

    Hope this helps.

     

    Bests,

    Melika Sharifi

    Aqueous Solutions LLC


  5. Dear Gustavo,

    The GWB comes with a set of thermo datasets that you can load each into any GWB app using File-->Open-->Thermo Data... . Thermo.com.V8.R6 dataset, for example, includes a couple of rare earth elements. To check the elements, basis species, redox couple, minerals, and gases included in each of the thermos datasets distributed by GWB, you can use TEdit app.  If you can’t find a particular species, it’s a simple matter to add the necessary reactions and log Ks to the GWB thermo datasets. I think you will find TEdit app very useful for making these modifications. Sections 9.2.3 and 9.2.4 in the GWB Essentials Guide describe how to add reactions to your thermo dataset using TEdit. You can access the Users Guides from the Help menu of any GWB app.

    In future, please make sure that your question is posted in the main section of the GWB forum, and not the archive section.

     

    Bests,

    Melika Sharifi

    Aqueous Solutions LLC


  6. Hello,

    Each thermo dataset in the GWB has a set of basis species, redox species, aqueous species, minerals, oxides, and gases; you can load each into any GWB app using File--> Open--> Thermo Data... . In SpecE8 or any other apps in the GWB software, only basis species of the loaded thermo dataset are directly available on the pulldown list. You can alter the basis species to reflect the geochemical constraints in your system by clicking the pulldown next to the species and choosing the aqueous species of your interest.

    If you can not find the aqueous species of your interest in the database and are interested in adding new aqueous species/reactions along with their log Ks to each thermo dataset, you can use TEdit program which is a thermo data editor. Sections 9.2.3 and 9.2.4 in the GWB Essentials Guide describe how to add reactions to your thermo dataset using TEdit.

    Hope this helps.

     

    Bests,

    Melika Sharifi

    Aqueous Solutions LLC

    • Upvote 1

  7. Dear Mulyanto,

    Thank you for your question. You can certainly set activity ratios for X and Y axes in the Basis pane in Act2 program. To do so, you'll need to swap an activity ratio into the basis. For your problem, for example, you need to select "K+" for the x-axis species  and "Na+" for the y-axis species, then click on the swap button next to each and select Ratio... . In the Species Activity Ratio box set H+ as the denominator with power 1.

    For more information, please read Using Act2 section in the GWB Essentials Guide. All GWB Users Guides can be accessed from the Help menu of any GWB app.

     

    Bests,

    Melika Sharifi

    Aqueous Solutions LLC


  8. Hello,

    Thanks for attaching your scripts. From your scripts, it looks like the concentration of some elements in the inlet fluid, such as silica SiO2(aq), is too high for seawater. Please double check the concentration of all elements and make sure you are using the correct unit.

    Hope this helps.

     

    Bests,

    Melika Sharifi

    Aqueous Solutions LLC


  9. Hello,

    In x2t, to plot porosity or permeability(along x or y), you can either plot them as a color map to see their variations over the domain at a specific time step. Or, you can plot them VS. time or position as an XY plot.

    Hope this helps. If you need more assistance, please attach your script so I can take a closer look at it.

    Thanks,

    Melika Sharifi

    Aqueous Solutions LLC


  10. Hi Polo729,

    We are not sure what the problem could be. Please make sure that when you want to paste your data into Excel, you single left-click on a cell to select the cell. If you double click on a cell, and then paste your data, all your data will be pasted in that cell.

    Please let us know if you keep having any issues.

     

    Thanks,

    Melika Sharifi

    Aqueous Solutions LLC


  11. Dear John,

    From the dataset you sent us, it looks like Biotite has not been properly added to the dataset. To add a mineral or an aqueous species, you'll need to supply the necessary reaction between the new species/mineral and the basis species in the dataset, as well as the log Ks (from literature) for that reaction at different temperatures.

    Sections 9.2.3 and 9.2.4 in the GWB Essentials guide describe how to add reactions to your dataset using TEdit. I think you'll also find the tutorial entitled "How do I add new elements, species, and reactions" helpful.

     

    Bests,

    Melika Sharifi

    Aqueous Solutions LLC


  12. Dear Betty,

    Act2 can be useful for understanding the geochemical conditions under which various mineral are stable. It calculates and plots activity-activity diagrams. This class of diagrams shows the stability of minerals and the predominance of aqueous species in chemical systems. A species activity, gas fugacity, activity or fugacity ratio, pH, Eh, or pe may serve as an axis variable. 

    If you are trying to simulate reaction paths and precipitation/dissolution of minerals, you may need to use React. You specify the concentration of fluid components in your initial system, define a reaction path, and React computes the change in your initial system as it undergoes the defined reaction.

    Hope this helps.

    Bests,

    Melika Sharifi,

    Aqueous Solutions LLC


  13. Dear John,

    Act2, shows the stability of minerals and predominance of aqueous species for a single “element” or component, the diagram species, over the chosen axes: pH and Eh in your case. They’re allowed to complex with any of the ligands that you specify in the “in the presence of” field. Thus, when you add Fe++ to the "in the presence of field", you define the activity of Fe++ and allow it to make complexes with your main species. Thus, theoretically, you should get a different plot from when you don't have Fe++However, there are a few things in your plot that I think might not be set correctly:

    1. If you are looking at the speciation of sulfur, there is no need to swap Pyrite in. Pyrite will show up on your plot if it is stable over the defined pH-Eh range.

    2. if you know that your complexing species reacts under changing Eh or pH, you can include that in your graph using the "speciate over x”, “speciate over y”, or “speciate over x-y" options from the pulldown next to where you define your complexing species activity. For example., Fe++ would speciate and/or change oxidation state in response to changing pH and Eh.

    Finally, to check your simulated environment go to the “plot” plane --> “view results” to see all the reactions and the activity of species in your system.

    Hope this helps.

    Bests,

    Melika Sharifi

    Aqueous Solutions LLC


  14. Dear Erik,

    GWB does not determine which species to include as a promoting or inhibiting one, but it is the user who has an option to do so based on data from literature or from their lab experiments. For more information, please read section 4.2.1 "Promoting and inhibiting species" in the GWB Reaction Modeling Guide.

    Bests,

    Melika Sharifi,

    Aqueous Solutions, LLC


  15. Hi Erik,

    Thanks for providing the additional information. If you see rapid dissolution of minerals in your system, they should not be set as being in equilibrium with your initial system. You can, instead, put them on the Reactants pane as kinetic minerals. Another thing that you might find helpful is to set Cl- as the balance species.

    Bests,

    Melika Sharifi,

    Aqueous Solutions, LLC


  16. Dear Zsofia,

    The GWB's default thermo dataset, thermo.tdat, is compiled along the steam saturation curve from 0 -300 C. we don't currently account for the effects of pressure on the stability of species and you cannot control the pressure independently from the temperature, but you can certainly set the partial pressure or fugacity of gases in the initial system , but there are no "sliding partial pressure" paths. 

    Hope this helps.

     

    Bests,

    Melika Sharifi,

    Aqueous Solutions, LLC


  17. Hello Elg0086,

    Thanks for attaching your X2 script. I took a look at it and noticed a few issues:

    1. You have constrained your initial system with  several minerals that are quite unstable at the pH/T/oxidation state defined for your system. For example, Anorthite is not very stable at the pH-T of your initial system.

    2. There are not many environments in which magnetite is in equilibrium with a very oxidizing solution/atmosphere. Thus, magnetite puts a lot of ferrous iron into the system. Even after removing magnetite from your system, you still have a solution which is way too concentrated with Cl-, SO4--, Na+, and Ca++.

    I would recommend that you start with React and check the initial state (Run-->Go initial) of your X2T initial system as well as your inlet fluids before moving to X2T. 

    Hope this helps.

     

    Bests,

    Melika Sharifi,

    Aqueous Solutions, LLC

     

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