Jump to content
Geochemist's Workbench Support Forum

All Activity

This stream auto-updates     

  1. Yesterday
  2. Jia Wang

    Kozoite log K recalculation

    Hi Kaizen, Thanks for attaching the file and the additional Rxn screenshot. The Log K value in reaction balancing using Rxn should match the resulting Log K for the mineral in TEdit. I see that the Log K value from reaction balancing using Rxn is -21.1 at 25C, which does not match the initial Log K value of -24.3 in your original post above. Using the database attached, I tried adding the kozoite into the database with the Log K value of -24.3 for the reaction LaOHCO3 = La+++ + OH- + CO3—and got 0.0289 as the new resulting Log K value for the reaction Kozoite + 2H+ = La+++ + H2O + HCO3-. Perhaps you entered -21.1 for your Log K value accidentally when you were creating the new mineral instead of the intended Log K of -24.3? You can modify your entry by deleting the basis species under ‘species in reaction’ and then re-enter the correct Log K value and select the corresponding aqueous species(CO3—and OH-) and basis species (La+++). You can also simply delete the entry and re-add kozoite as a new mineral. Hope this helps. Best, Jia
  3. Kaizen

    Kozoite log K recalculation

    Looked at Rxn (screenshot attached) and seems okay, but appreciate if you could check the database previously attached.
  4. Last week
  5. Kaizen

    Kozoite log K recalculation

    Hi Jia, Thanks for the prompt response. I am going to add in some other minerals so best I get this right before I proceed further. Attached is the modified database for you to check. The original reaction as entered is: LaOHCO3 → La + OH + CO3 logK = −24.1 ± 0.3 Many thanks thermo.com.V8.R6+.tdat
  6. Brian Farrell

    Pourbaix diagram using Phase2

    Hi Frank and Andrew, Act2 uses a simple analytical method to calculate equilibrium lines and assemble them into Pourbaix diagrams, so there's no difficulty in creating a diagram that spans large Eh and pH ranges. If you wanted, you could set the Eh and pH to span the range -100 to 100, and it would draw the diagram. With Phase2, however, you're setting up numerical reaction path models. In a model of the aqueous phase, working far outside the stability limits of water (i.e., the bottom left and top right corners of an Eh-pH diagram) can be difficult. To investigate your calculations, try overlaying some contour plots on your 2D diagram, or better yet, just look at a simple xy plot of the diagram’s left edge. You can select the left-most vertical cross-section through the entire diagram, use the “Go Y” option in Phase2 to calculate only the left edge of the diagram, or set up a React script to reproduce the left edge of the calculation. Whatever you choose, start out by plotting the Mass of Solution or Fluid volume vs. Eh. You'll see they're initially enormous. If you make a plot of species concentration, you’ll see it’s due to the extremely high concentration of H2(aq) that would exist under your initial conditions, which are far outside the stability range of water. Next, try plotting the concentration of your metal component of interest (U++++ or Al+++ in the system) and you should see that your initial conditions are honored. In the U example, U++++ was set to 1e-10 mol/l, but under the initial conditions that’s equivalent to .19 molal! That’s why so many minerals are stable throughout the diagram, compared to the Act2 calculation. As for the Al example, Al+++ was set to 1e-5 mol, and there’s still 1 kg of solvent in the system, so the initial Al+++ molal concentration isn’t skewed the way the U++++ was. You didn’t attach an Act2 script, Andrew, but presumably it’s not as different as the U calculations were. As for the failures you’re encountering, unfortunately it’s likely to happen when you’re so far outside water’s stability region, as in the corners of an Eh-pH diagram with a traditional range. In a log f O2(g)-pH diagram, by contrast, you don’t have to include such extreme conditions. Since a large portion of the area in an Eh-pH diagram is likely to be masked, log f O2(g)-pH diagrams can be a nice alternative in that they fill more of the plot area with useful information, rather than blank space. If you need to know the Eh, you can always plot contours on the log f O2(g) diagram. Whatever diagram you choose, it’s common to use a narrower range in these types of diagrams. I think when you do that you’ll find that you can reproduce an Act2 diagram much more closely. There will still be differences, of course. Boundary lines can be somewhat curved, rather than straight, reflecting the fact that Phase2 is solving a complete multicomponent calculation at each point in the grid instead of drawing equilibrium lines. It includes mass balance and activity calculations, unlike Act2. And whereas an Act2 diagram shows the stability of minerals and predominance of aqueous species (in terms of highest activity), Phase2/P2plot’s predominance map strictly shows the species accounting for the most mass at each point in the diagram. In other words, a mineral’s stability field (which you can see with an assemblage map) can be slightly larger than the area in which that mineral predominates all other species. Sorry for the delay in responding. It looks like we missed the original post. Hope this helps, Brian Farrell Aqueous Solutions
  7. Jia Wang

    Kozoite log K recalculation

    Hello Kaizen, The GWB apps expect all reactions to be written in terms of basis species, so TEdit performs reaction balancing to swap out the aqueous species to do so. Please see 9.2.7 Basis swapping in the GWB Essentials Guide for a description and example. I used the thermo.com.V8.R6+.tdat dataset and tested out the procedures you described and I got a different result. But that can be due to different Log K values for the carbonate and hydroxyl reactions that you might have entered in your database different from the default values? You can check your entry using Rxn, by swapping CO3—and OH- for HCO3- and H2O respectively, to see if you get the original Log K value when you balance the equation. See section 4.1 in the GWB Essentials User's guide for more information on Balancing reactions in Rxn. Please attach your database if you need further assistance. Best, Jia
  8. Hi, I added a new mineral, kozoite into my database using the reaction: LaOHCO3 = La+++ + OH- + CO3--. Upon entering the log K of -24.3 and the "Species in reaction" pane of La, OH and CO3, there was an automatic recalculation to give a reaction: Kozoite + 2H+ = La+++ + H2O + HCO3- with a new log K of +3.2239. Please refer to the attached screenshot. I gather that this was all done to reflect a dissolution reaction via H+ addition but I am wanting to check that I did not introduce an error along the way and I am okay to proceed. Many thanks for any advice/feedback
  9. Dear GWB users, We are pleased to announce our latest maintenance release, GWB 12.0.5. The 12.0.5 update features an important update to Flexera license manager, better user and administrator support for network floating licenses, Python 3 support for the GWB Plugin feature (ChemPlugin already supported Python 3), better ability of the time marching apps to back up and recover convergence failure, tracking and reporting of the number of pore volumes displaced in React, fixes for tab-completion feature in Command pane, and resolution of all known issues arising since the GWB 12.0.4 release. Update from 12.0.0-12.0.4 at no charge to ensure you have all the newest features and bug fixes. Existing installations should automatically update to this release, unless auto-update is disabled. In that case, users should update their installations from the Help menu of any GWB app. Regards, Jia Wang Aqueous Solutions
  10. Earlier
  11. Andrew Knight

    Pourbaix diagram using Phase2

    Hi, I have the same issue as Frank as seen above. I am try to model the Al-Na-Cl-H2O-CO2 system and look at the Pourbaix diagram over the entire eH pH range as mentioned above. I am able to do the calculation from pH = 0 to pH =9, and from Eh = -0.55 to Eh = 0.75, but anything outside of the range crashes and the program must be restarted. Also as Frank mentioned if I use Act2 to try to replicate the Phase2 calculation, the results are not entirely consistent. What are some tricks or ways to run the Phase2 at a full Eh/pH range? Thanks, Andrew Eh pH diagram.ph2
  12. Usman Abdullahi Usman

    New user: Solubility phase diagrams and Durov diagram

    Dear Jia, I will try and follow your suggestions. Thank you so much for the brilliant guide. I will get back to you. Best regard Usman
  13. Jia Wang

    New user: Solubility phase diagrams and Durov diagram

    Dear Usman, The Durov diagram currently cannot be modified to include alternate axes variables, such as Fe concentration. You can alternatively try to use one of the other diagrams such as Ternary, Stiff, or Bar graph. In these types of diagrams, you can select the species on each axis. Please refer to section 3.6 of the Essential Guide for information on plotting your data. To create diagrams with activity ratios as the axis variable, you would simply swap an activity ratio into the basis as described in section 5.1-5.2 in the GWB Essentials Guide. The procedure is essentially the same for K+/H+, Ca++/H+^2, and Mg++/H+^2. You can overlay your data points in GSS data sheet to the Activity diagram. Go to 'File' --> 'Open' --> 'Scatter Data' and select the GSS file with your data. Act2 diagrams are plotted in terms of species’ activities and fugacities, not chemical concentrations. You can calculate activities of your species in GSS directly or supply values as user defined analytes. Please refer for section 5.6 of the GWB Essentials Guide for more information on Scatter Data and section 3.3.4 for Calculated values. Hope this helps. Best, Jia
  14. Dear Brian/all members, Please help me at your convenient time, I will be much happy if you can solve my problems. I have never use geochemist workbench software before, my challenging areas follows: 1. I want to swap and replace my pH values with total iron (Fet) values in the Durov diagram so that i can discuss the relationship between the high Fe concentration with the fluid compositions. 2. Aluminum solubility phase diagram, Mg silicate phase stability diagram (Log Mg++/H+ VS pH), K silicate phase stability diagram (Log K+/H+ Vs Log a SiO2(aq)) and Na+/H+ Vs Log a SiO2(aq). I have tried to plot these 4 diagrams, the first challenge I don't understand mg++/H+, K+/H+ data. So I tried to plot Al, Vs pH for aluminum solubility, K Vs Si for K-silicate stability phase, etc. 1. Mg silicate phase stability diagram (Log a Si Vs Log a Mg/H+) I Have tried to plot the Magnesium silicate phase stability diagram, but I feel like is not correct. I want to know how to plot my scatter data to overlap on the diagram like Aluminium solubility diagram. Attached is the data file. Thank you. Best regard Usman
  15. Dear ALL,

    I'm a postgraduate research student at the University of Malaya in Malaysia. This is my first time using GWB, the version of my GWB is standard (12.0.4).

    The things that I want to know are as follows:

    1. How can I swap and replace the pH values with the dissolved trace metal (Fe) concentration values of my groundwater samples on Durov diagram, so that I can relate them with the groundwater composition?

    2. How can I import and overlap my pH and pe values and appear on the pH Vs pe phase diagram using GSS, Excell or notepad? I have used excel and GSS but if I try to import them it shows "the file does not match". I used notepad but the symbol of my sample is not appearing it only shows sample 1, Sample 2, etc with a micro symbol. 

    Please, I need your help so that I can continue with my work.

    Best regard

    Usman

    1. Brian Farrell

      Brian Farrell

      HI Usman,

      Please go to the font page of the forum, https://forum.gwb.com/index.php?/forum/23-the-geochemists-workbench/, and click "Start New Topic", then post your question there. Please attach your Act2, gss, and .txt files. That way we'll be able to troubleshoot why your scatter data is not plotting.

      Regards,

      Brian

  16. Jia Wang

    Change nucleus density in X1t

    Dear Misato, I would recommend using the ‘script’ or ‘script file’ option for setting the nucleus density rather than an ‘equation’. Using a script or script file would allow you to set 10 [cm2/cm3] if Time is less than 3000000 seconds and after that, the equation desired. It would look something like this: IF Time < 3000000 THEN 20 ELSE 40 20: nucleus = 10 GOTO 60 40: nucleus = 10*(1/2)^((Time-3e6)/150000) 60: RETURN nucleus As you’ve done, you need to check the “transient” option to evaluate the variable at each time step. Please refer to section 5.2 of the GWB Reaction Modeling Guide and the Heterogeneity Appendix to the GWB Reactive Transport Modeling Guide for more information. Please note that the nucleus density option prescribes a minimum value for a supersaturated mineral’s surface area over the calculation. The program calculates the actual surface area from the mineral’s current mass and specific surface area and uses this whenever it exceeds the nucleus density. Best, Jia Wang
  17. Hello Jeonghwan, Thank you for attaching your script. Suppress is a very useful feature to allow for less thermodynamically favorable minerals or species to form in your system by suppressing the more stable minerals from forming. React consider all minerals available from the database when making calculations unless otherwise specified. You can refer to the GWB Command Guide and the Reaction Modeling guide to learn more about this feature. With regards to your first question, you can certainly suppress AlO2- in your model but does this make sense in the context of the system you’re modeling and your field observations? I am not sure what your system is so it is difficult to determine what would be the most appropriate to suppress. Perhaps your field data will help to give you some suggestions with regards to what is appropriate for suppressing? I also noticed that you have unchecked precipitation in REACT0928.rea. This restricts minerals from precipitating even when they are supersaturated. Is this a constraint you meant to set? As for your second question, I think you mean to ask if your model has a pH of 8.3 at equilibrium? In simple reaction paths, where one or more reactants are gradually added to the system is called a “titration path”. The system’s equilibrium state is calculated as it steps forward in reaction progress. So React actually calculates the equilibrium state of your reaction at every time step. You can refer to chapter 3.1 “Titration paths” for more information. Hope this helps. Best Regards, Jia Wang
  18. Hi. I have question about change of nucleus density with time in X1t. I would like to set nucleus density of a precipitates 10 [cm2/cm3] before 3000000 seconds. After 3000000 seconds, I would like to set nucleus density this equation: 10*(1/2)^((Time-3e6)/150000) [cm2/cm3] How can I make it ? Screen shot of the reactants field is attached. Thank you. gwb.pptx
  19. Drew

    P2Plot data output

    Hi Brian, I've done some more work on my code to make it more general to detect both the left and right edge of a mineral solubility area from GWB. I edited the post to reflect this. Drew
  20. Brian Farrell

    Kinetic Mineral Custom Rate Law

    Hi Erik, I'm happy to hear you figured it out after more troubleshooting. Regards, Brian
  21. elg0086

    Kinetic Mineral Custom Rate Law

    Hi Brian, Thanks for the reply. Further troubleshooting may have solved the problem. If there is still an issue after the current model run is complete I will upload the script. Thank you. ~Erik
  22. Jeonghwan Hwang

    Why does pH in my model rapidly decrease?

    Hello, thank you for your help. I find that AlO2- mainly affect to decrease pH in my model. So, I made a model which i want to make by suppress the AlO2-. Next time, i wanted to know whether my react model can be an equilibrium condition . So, I extended my model time from 30 yr to 500 yr. And I find that pH of my model converged to 8.3 after almost 100 yr. I have 2 questions in my model. 1) Can i suppress AlO2- in my model? Is there any physical or chemical problem of my model to represent real environment? I don't know well of suppress... 2) Can I say that my model has an equilibrium condition of pH? Thank you Sincerely Jeonghwan Hwang REACT0928.rea
  23. Brian Farrell

    Input organics

    Hello, Sure, there are many calculations you can do involving dissolved organics: You can set the total concentration of a dissolved organic and determine its speciation in solution. For example, you can look at a ligand like EDTA or acetate to see how much is present in free form, in various protonated or deprotonated forms, and complexed with various metals, and see how the distribution of mass changes as a function of pH, temperature, concentration, etc.. You can create Eh-pH or Pourbaix diagrams to see under what conditions a dissolved organic is stable and when it would tend to mineralize to inorganic carbon, or form various other organic compounds. You can also set up disequilibrium simulations in which a dissolved organic is oxidized or reduced with time, at a rate determined by a kinetic rate law you specify. You can account for abiotic reactions in solution, catalysis on mineral surfaces, biodegradation (a simple model of enzymatic catalysis), or microbial catabolism coupled to growth and decay. The program does not currently consider non-aqueous phase organics, however. You can’t find the solubility of an organic in water the same way you would a mineral, unless you create a fictive “organic mineral” with a log K to control the solubility. To set up a simulations involving organics, you’ll first need to load a thermodynamic dataset that contains your organics of interest. The GWB’s default dataset, thermo.tdat, does not have any data for hexane. However, the thermo.com.V8.R6+.tdat dataset, a later release from Lawrence Livermore National Lab, does contain data for one hexane isomer, n-Hexane(aq), along with many other organic species. Many organic species are found in the redox coupling reactions section of the dataset, in a reaction with inorganic carbon. Please note that there is only one reaction for n-hexane, though. I’m not familiar with the chemistry of hexane, but if you expect it to form complexes, you might need to modify one of the existing thermo dataset. You can do so in a text editor like Notepad, or in the GWB’s graphical thermo data editor, the TEdit app. Next, you’ll have to decide in the GWB app (e.g. React) what redox reactions should be in equilibrium. To look at speciation of acetate as a function of oxidation state and pH, for example, assuming equilibrium with inorganic carbon, you’d load thermo.com.V8.R6+.tdat into React, add basis entries HCO3-, O2(aq), H+, and constrain those values. In a redox equilibrium model, the HCO3- component includes inorganic carbon species as well as various organics. The oxidation state you specify determines how much is present at equilibrium as inorganic carbon, how much as acetate, methane, ethanol, benzene, and so on (all reactions are considered by default). You can disable one or more redox coupling reactions if you’d like. If you disable all coupling reactions involving carbon except for the one involving acetate, you can look at the distribution of mass between inorganic carbon and acetate. And you decouple all coupling reactions. In that case, you can add acetate directly, without needing to specify the oxidation state or amount of inorganic carbon. Then, you can look at speciation as a function of T, pH, concentration, etc., as mentioned above. For more information, please see sections 2.1 Configuring a calculation, 2.4 Redox couples, 7.2 Equilibrium models, and 7.3 Redox disequilibrium in the GWB Essentials Guide. Please see as well section 4.6 Kinetics of redox reactions in the GWB Reaction Modeling Guide, and the Thermo datasets chapter in the GWB Reference Manual. Hope this helps, Brian Farrell Aqueous Solutions
  24. Hello Jeonghwan, Thank you for attaching your script. I have looked at your script and noticed a couple of things that might help explain why the pH decreases initially. If you look at the primary dissolution of Montmor-Ca with its default species using Rxn, then you do indeed expect the reaction to consume H+ and consequently for the pH to increase. However, in your React model, the output text file shows that the pre-dominant Al species is AlO2-. When you swap the Al+++ species with AlO2- and recalculate the reaction for Montmor-Ca dissolution in Rxn, you will see H+ is on the right hand side of the equation and thus indicating the production of H+ in your system. Additionally, other minerals precipitating in your React model might also influence the consumption or the production of H+ in your system. For example, you can see that the initial system is saturated with respect to Talc and precipitates in React’s calculation. (For more information about React’s treatment of the initial system , please refer to section 2.3 in the GWB Reaction Modeling Guide.) If you return to the Rxn application, you can balance the reaction with Talc using the predominant species in fluid and see that the precipitation of Talc will increase H+ in solution. Your model subsequently precipitates other minerals such as Diaspore, Saponite-Ca, Stilbite, etc with the addition of Montmor-Ca. I would suggest you check whether the precipitation of these minerals is consuming or producing H+ using Rxn as mentioned above. This will most definitely influence the pH of your system. Lastly, it is rare to constrain the initial H+ concentration in mg/kg. Did you get this from a calculation? Perhaps check if the pH of your field measurements matches with what you entered for the H+ constraint? Hope this helps. Best regards, Jia Wang
  25. Brian Farrell

    P2Plot data output

    Hi Drew, I'm happy to hear that you have Phase2 output up and running with Igor Pro. Thanks for providing your code. Most likely someone in the geochemistry community will find it useful. Cheers, Brian
  26. Brian Farrell

    Kinetic Mineral Custom Rate Law

    Hi Erik, Can you please attach your script? Thanks, Brian Farrell Aqueous Solutions
  27. waters2018

    Input organics

    Can I simulate organics dissolve in water under various chemistry conditions? e.g. hexane in water under different pH
  28. Hi, I am testing out a custom rate law script file in an X2t model. The model has 4 injection wells and 100 nodes. However, the model does not acknowledge the conditional statement (pH) in any of the nodes except the injection well nodes. The injection solution has a pH less than 6. The kinetic mineral is present in all the nodes. Am I missing something in the script? IF pH < 6 THEN 20 ELSE 40 20: rate = 0.00000000052481 * totmoles ("H+") ^ 0.72 GOTO 60 40: rate = 0.0 60: RETURN rate Regards, Erik
  1. Load more activity
×