Brian Farrell

Hello Shawen, Here is a similar thread which discusses this very topic. For Eh-pH and other diagrams in general, you might try taking a look at the Diagrams and Tutorials pages on our website. There, you can view a number of diagrams made with the GWB, and even click the GWB icons to load pre-calculated diagrams on your computer. The GWB Essentials Modeling Guide will also be very useful to read through. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi Jonathan, When you say you've run SpecE8, GSS, and React after changing the preferences, are these instances that are already open? I think if you have one instance of GWB open (any app) and change the preferences, as long as you close that instance and reopen GWB, the preferences change should take. If GWB is already open, however, I don't think the preferences will be updated. If you want to change the thermo data in only the current GWB application, you should go to File - Open - Thermo Data... This will take effect right away. Please let me know if you are still having issues with setting the default thermo data under Preferences. Best, Brian Farrell Aqueous Solutions LLC

Hello, Instead of swapping HS- in for SO4--, I think you'll want to decouple the HS-/ SO4-- and CH3COO-/ HCO3- redox pairs. That way, you can add both the reactants and products (likely a small, but nonzero concentration) to your Basis. Depending on your interests, you might set a kinetic rate law which describes the rate of sulfate reduction. The GWB User's Guides describe redox/ microbial kinetics and include some simple examples. For more on the theory, you should take a look at Chapter 7 (Redox disequilibrium), Chapter 17 (Redox kinetics), and Chapter 18 (Microbial kinetics) in Craig Bethke's Geochemical and Biogeochmical Reaction Modeling text. If you're not particularly interested in how fast the reaction occurs, but just how the pe changes with different activities of SO4-- and HS-, you might try a parametric model, in which reactant species are titrated out of the system and product species are titrated in. An example for microbial iron reduction is described here. In either case, React should include in its output a calculated Nernst Eh/ pe for the decoupled redox pairs (HS-/ SO4-- and CH3COO-/ HCO3-). Hope this helps. Brian Farrell Aqueous Solutions LLC

Hi Akram, What sort of species are you hoping to consider in your diagram? Do you know the oxidation state of Fe and Hg in this species? Once you have the appropriate information, you can start adding entries to your thermo data. The Appendix I've mentioned is a good place to see how this should be done. An example in which Phenol(aq) is added to a thermo dataset is given in our Tutorials webpage (go to Using GWB - How do I edit thermo datasets?). For your information, Phenol is a carbon molecule in a different oxidation state from HCO3-, the default Basis species used to represent carbon. It is added as a new Redox species, which is basically a Basis species in an alternative oxidation state. Since you're interested in Fe, take a look at some of the Fe species in the thermo datasets. Fe++ is a Basis species and Fe+++ is a redox species. All aqueous species and minerals which include ferrous iron (like FeCl2 and Siderite) are written in terms of Fe++, while those which contain ferric iron (FeCl3 and Hematite) are written in terms of Fe+++. Magnetite is an interesting case, in that it includes both ferrous and ferric iron. If you take a look at the entry for Magnetite in the thermo data, you'll see that it is written in terms of both Fe++ and Fe+++. Try looking through the thermo data in this way. You'll need to go through the above-mentioned Appendix as well. Finally, I would encourage you to read Chapter 7 (Redox disequilibrium) of Craig Bethke's Geochemical and Biogeochemical Reaction Modeling text. Hope this helps, Brian

Hi, Could you let me know which version of GWB you're using? If you're using version 9.0, you might have the same problem (values off by 1000) described in this forum thread. Assuming this is the same problem, updating to our latest maintenance release (9.0.3 as of Jan 09, 2013) should solve this problem. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi Allison, A few things. In general, if you have an analysis, including pH measurement, for the initial rainwater/ groundwater sample, I would use that as the starting point for my calculation (the initial system which you define in the Basis pane) rather than a completely arbitrary fluid composition. For example, if you're going to constrain pH by swapping the H+ component out for CO2(g) and setting its fugacity, you need a good idea of the total HCO3- component concentration (so that GWB can calculate the free HCO3- species activity, which fixes pH according the reaction H+ + HCO3- = CO2(g) + H2O). In this case, however, it looks like the huge amount of reactant minerals you add comes to dominate the chemistry eventually anyway. I'm not too sure what you mean by seeing the elements of interest in the output file. As for changing the step size, ideally this shouldn't be too big of a factor in your results. Under normal conditions decreasing or increasing the step size can increase or decrease, respectively, the resolution of your model. The increasingly smaller steps taken by React here, however, indicate it is having a hard time converging on a solution. Try taking a look at the Mass H2O vs. Reaction progress. You'll find that all of your solvent water is used up, causing the run to crash. As Michal states, as long as there is a large supply of O2(aq), Pyrrhotite will remain unstable and continue to oxidize, adding SO4-- to your system. This is not an artifact of the step size. Hope this helps, Brian

Hi, One more item to note. You've swapped Fe(s) for Fe++, and specified an activity of 0.0001. This is not much different from saying the activity of Fe(OH)3(s) or Hematite is 0.0001 - it's a tricky thing to do. Specifying the activity of an aqueous species, like Fe++, is much easier however. Since this is a redox pH diagram, Act2 will use combinations of the Basis species Fe++, O2(aq) (or e-), H+, and H2O to form all of the species, minerals, and gases which can appear on the diagram. In your case, Fe+++, Fe++, Fe(OH)3(s), FeO(s), and Fe(s) are predominant. Thus, there is no need to swap in Fe(s) to ensure it appears in your diagram. Cheers, Brian

Hi Akram, You've selected Fe as the main system to diagram, on Eh pH axes, in the presence of CO2 and H2S. Every species, mineral, or gas which will plot on this diagram must include Fe, and can optionally include H, O, C, or S. If you unsuppressed Siderite (FeCO3) or Troilite (FeS), for example, these could form. Hg does not form any sort of aqueous complex, gaseous species, or mineral with Fe, at least according to the currently loaded thermo data, so adding Hg++ to the basis (in the "in the presence of" field) will not affect your diagram. To see this, you can look read through the thermo dataset itself (go to File - View - thermo....) or, a little easier, go to Config - Show..., choose Fe++ (or Hg++) as the filter, and a list of all species which include Fe++ (or Hg++) will appear. There are none which include both Fe and Hg, so nothing with Hg will show up on your diagram. If you are aware of some species that exists, you would need to add this to the thermo data. (Keep in mind that surface species are not considered in these types of diagrams, so Act2 will not consider a surface complex of Hg++ onto an iron mineral like HFO). Hope this helps, Brian

Hi, There are a number of ways to approach this problem. You might start out by using Rxn to balance dissolution reactions, and calculating the equilibrium constant at various temperatures. Creating simple activity diagrams with Act2 or Tact is quick and easy, but can be very helpful. Finally, you might use React to construct a reaction path model of gas dissolution into a brine. You'll probably want to familiarize yourself with some concepts from the Geochemical and Biogeochemical Reaction Modeling textbook, or the GWB User's Guides. I would look into simple titration models, and sliding fugacity and polythermal runs, for example. If you're using GWB 9, you might be interested in gas transfer kinetics as well. If you go to our diagrams webpage, you'll see a number of example models calculated using Act2, Tact, and React. Take a look at some of these, including the "gas solubility" and "heating and cooling" examples. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi, If you're having a hard time adding Fe to the thermo dataset, could you please attach what you have so far so I can take a look? In the meantime, I would use thermo.com.v8.r6+.dat, which does have an entry for elemental Fe. You'll need to do a few things to make the elemental Fe field visible on your plot. First, you'll need to uncheck the "water limits" option so that Act2 will consider the areas where conditions are either so reducing or so oxidizing that water is not stable. You do this by right-clicking your plot and selecting "View...", then uncheck "water limits". Next make sure the range of your axes is appropriate to consider where Fe would be stable. I'm not sure what you mean by swapping e- for CO2 OR H2O instead of O2(aq). Try taking a look at some of the examples on our Diagrams webpage. If you click the Act2 icon, you'll open up Act2 with all of the necessary commands already specified. You can then adjust the plot to suit your needs. Hope this helps, Brian

For only $200 you can provide up to 20 students on your university course roster with semester-long GWB licenses for their laptops. You must be a faculty member and have licensed the latest release of GWB Essentials, Standard, or Professional. Annual licenses for computer classrooms are also available. Learn more here. Regards, Brian Farrell Aqueous Solutions LLC

Hi Alison, Do you know anything about the initial chemistry of your water (before reaction with the waste pile)? Regards, Brian

Hello, Your scripts appear to run, at least on my copy of the GWB. Which version are you using? A few things seem a little strange, however. Why are you adding both CO2(aq) and HCO3- to your system? In the first part of the example, you swap CO2(aq) in for HCO3-, then you constrain the CO2(aq) - this is normal. By adding HCO3-, you undo the basis swap and replace your original constraint for CO2(aq) with one for HCO3-. Keep in mind that you are adding in total components here, not the free CO2(aq) or HCO3- species. GWB will take that HCO3- component (total amount of carbon) and use it to form each possible species (CO2, HCO3-, CO3--, NaHCO3, etc.). Is there a reason you divide the calculation into so many separate steps? It seems that you have just one fluid composition and one mineral assemblage, and that they could be added together in one step at 150 C. Regards, Brian Farrell Aqueous Solutions LLC

Hi Allison, Increasing the number of steps is sometimes quite useful, but if you're getting up to 300,000 there may be some other issues which need to be addressed. If you attach the .rea file I can try to take a look at your problem. Regards, Brian

Hi, By default React will trace reaction paths in 100 steps, using a step size of 0.01 to advance the reaction progress from 0 (beginning) to 1 (completion). Under Config - Stepping..., you can change this default setting using the variable delxi. You might tell React to take smaller steps, say delxi = 0.001, so that the reaction path will be solved in 1000 steps. You can change the maximum number of iterations taken at each step from the Config - Iterations... menu using the itmax (normal steps) and itmax0 (solving for initial system only) keywords. Section 2.7 (Settable variables) in the GWB Reaction Modeling Guide lists a number of additional variables that you might adjust for your runs. You can find more information about each of these variables in the GWB Reference Manual's section on React. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi rvs, If you have a closed system, then all of the Al present at the beginning of the simulation should be present at the end, although it may be in a different form. I would add up all the moles of Al in the various species and minerals to verify this. If you're looking at the printed output file, try checking the Original basis total moles section for Al+++, or the Elemental composition section for Aluminum. Regards, Brian

Hi Akram, Depending on the dataset you're using, Fe++ and O2(aq) are likely to be Basis species. You'll need as well H2O and H+ to balance the reaction. The conventions you'll need to follow are described in the Thermo Datasets Appendix to the GWB Reference Manual. You might take a look at the reaction for Fe as it's written in thermo.com.V8.R6+.dat. Negative coefficients indicate that the balancing Basis species should appear on the left side of the reaction, along with whatever species or mineral you're interested in - Fe here. You'll likely want to verify that the equilibrium constants are appropriate for your application. You might search for log K's in the literature (be sure they're for reactions balanced the same way you enter the reaction in the dataset), or for standard state free energies of formation so that you can calculate a log K. Editing the database this way will allow you to make redox-pH diagrams, but for more in-depth analyses of redox chemistry, you might want to take a look at this topic, and the Redox Equilibrium chapter in the Geochemical and Biogeochemical Reaction Modeling text. Hope this helps, Brian

Hello, To make sure all of your Aluminum adds up you might start by looking at the amount of the Al+++ component in the fluid phase and tied up in minerals ("component in rock"). Once you're sure it's all accounted for, try looking at individual species or minerals with Al+++. Keep in mind they will have different mole weights and amounts of Al+++, so you'll want to choose appropriate units for making comparisons. If you can't explain the lack of Analcime after checking this you can post your script here. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi Elisabeth, Sorry for the delayed response. To calculate the pH of mixtures in GSS, there are a few things you need to do. First, define the chemistry of each of your samples (including pH and temperature) then set the mass of each sample (+ analyte - System parameters - Mass Solution) so that you can specify your mixing ratios. Then you need to calculate the concentration of total H+ component in the fluid (+ analyte - Calculate... - Components in fluid - H+). Next mix your samples (Analysis - Mix Samples), being sure to check "Save as sample". This treats your mixed fluid as a new sample which can be manipulated like any of the original fluids. Then just calculate the pH (+ analyte - System parameters - pH). GSS will give a warning that pH is already known for your original samples, just go ahead and say Yes to all, and the pH of the mixture will be calculated. There is an error in the current release, unfortunately, in the step where GSS calculates the amount of H+ component. The calculated value is total moles of H+, but the unit that shows up right now is molal. You'll want to change the unit without performing a unit conversion, since you'll want to preserve the calculated value. To do so, right-click the unit field for the H+ component and select units - mol, then when GSS asks to convert from molal to moles say no. GSS will then correctly solve for pH of the mixed sample given solution mass and total moles H+. The temperature and component concentrations of your mixed fluid will be calculated automatically, as will the mass of the mixed fluid. To find the concentration of an individual species in the mixture, just go to + analyte - Calculate - Species concentrations. In this way you can calculate the pH, temperature, and concentration of various species in a mixture of samples. Just change the solutions mass, then repeat the above steps, to consider various proportions. You can also use React to mix two fluids together. First define a fluid in the Basis pane. Once you run the equilibrium model, you can "pick up" the results to be used as a reactant, which will be titrated into a new, second fluid which you define in the now empty Basis pane. Now when you run the model, a small amount of the reactant fluid will be added incrementally to the fluid in the Basis pane. In the Reactants pane, you can set a value for "reactants times" to specify the final proportions of the two fluids. In this way you set up a reaction path in which one fluid is gradually added to another, allowing you to see how the pH, temperature, and speciation change. The flash option is a variant of this calculation type. With the flash option, you can mix two fluids in any mixing ratio - from one end-member to the other. For more information and examples, you should look at section 3.4.4 (Mixing samples) of the GWB Essentials Guide and sections 3.7 ("flash diagrams") and 3.9 (Picking up the results of a run) in the GWB Reaction Modeling Guide. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi, When you choose Fe++ as the main "diagram species" in Act2, you're considering not only the free Fe++ species, but any Fe complexes or minerals in the thermo dataset that can be formed from the current Basis. The Basis will include Fe++, your diagram axes (O2(aq) and H+, for redox state and pH, respectively), and any additional complexing species ("in the presence of" field). Since you have Fe++ (ferrous iron) and oxygen in your system, you can combine these to consider the various Fe+++(ferric iron) species and minerals. You should also be able to consider Fe(0), metallic iron, in the same way as long as it is listed in the thermo data. The default GWB dataset, thermo.dat, does not have an entry for Fe(0) but thermo.com.v8.r6+.dat does. Try loading this dataset and making a redox pH diagram for Fe++. You'll need to turn the "water limits" off in order to see where Fe(0) will plot. If you wanted to edit your own thermo dataset to include Fe(0), you would need to add a reaction for a new mineral "Fe(0)" written in terms of the default Basis species - likely Fe++ and O2(aq). You should take a look at a few sections of the GWB User's Guides for more information. The Act2 section of the GWB Essentials Guide will be very useful. In the Reference Manual, try looking up the "water_limits" keyword and the Thermo Datasets Appendix for details on editing a thermo dataset. Hope this helps, Brian

Hello Akram, Could you specify what type of diagram you are hoping to create? Some sort of redox-pH diagram or a solubility diagram, for example? Are you referring to metallic iron, Fe(0), or some iron oxide minerals? Regards, Brian Farrell Aqueous Solutions LLC

Hi Anastasia, Thanks for sending your thermo dataset. If you look at the Results pane, you should see the list of Loaded species, minerals, gases, etc. This list is controlled by the components in the Basis pane, the temperature range of the run, and the list of suppresses species. At 25 C, I believe 46 aqueous species were loaded, but at 26 C only 28. Since your Basis is the same, and you're not suppressing anything, the only difference is that some species are not being loaded because there is no thermo data outside 25 C. The "extrapolate" option can be useful here for troubleshooting because it ensures that you will consider the same species in your runs at various temperatures. In your case, using the extrapolate option does not make your model converge at 25 C. In fact, it makes the model fail at T>25 C as well. This gives me an indication that some of the species or minerals that were being considered in the 25 C run, but not the others, were the source of the problem. To check this, I can make a list of all possible species that can form at 25 C (46 species), and those which form at T>25 C (28 species). The subset which are loaded at 25 C only can be suppressed (not considered/ loaded), and the model rerun, to see whether a solutions can be found. By suppressing these species, the model will converge at 25 C and higher. You typically don't want to suppress species for no good reason, however, so you might unsuppress species one at a time to find out which one(s) cause the model to fail. After doing this, it looks like Fe(CO3)2-- is the culprit. With your knowledge of your system, or of the custom thermo dataset, perhaps you will be able to determine why this is the case. Is the equilibrium constant for the reaction specified in the thermo dataset (Fe(CO3)2-- + 2 H+ = Fe++ + 2 HCO3-) correct? You might consider whether Fe(CO3)2-- is likely to be important in your system, or whether it can safely be ignored (suppressed). Hope this helps, Brian

Hi, There are a couple ways to do this. In GSS, you can add multiple samples, each with a different temperature and solution mass (to specify the mixing ratios). Then just find the Analysis tab near the top and select "Mix Samples". Choose which samples you would like to mix and GWB will calculate the temperature of the mixture. If you're mixing two fluids in React, you'll need to define one fluid in the Basis pane and another in the Reactants pane. To define the Reactants fluid, you might enter its composition in the Basis pane, then run your model and "pickup" the results as Reactants. The Basis pane will now be free so that you can define your second fluid. Once the fluids in the Basis pane (the initial system) and the Reactants pane are set, go to the bottom of the Basis pane and fine the "+" button next to temperature. Set a temperature for the initial system (the fluid in the Basis pane) and the reactant fluid. As the reactant fluid is added into the initial fluid, React will calculate the temperature of the mixture using the mass and temperature of each fluid. React will use the heat capacity values you specify for a general "fluid" and "mineral". You might look into Sections 3.4 and 3.9 of the GWB Reaction Modeling Guide, or find the keywords "cpw" and "cpr" in the GWB Reference Manual. Chapter 14 of the Geochemical and Biogeochemical Reaction Modeling text will also be helpful here. Hope this helps, Brian Farrell Aqueous Solutions LLC

Dear GWB Users, Please join us August 24-25 in Florence, Italy for a workshop on reactive transport modeling using the GWB. Then stay on in Florence for the Goldschmidt 2013 conference. Regards, Brian Farrell Aqueous Solutions LLC

Hi Anastasia, Sorry for the delay in response. I have been out of the office the past couple weeks conducting training. If the model converges at 26 C but not 25 C the problem is likely not due to changes in the stability of certain minerals or species, but rather from differences in what minerals and species are loaded at the different temperatures. For example, if data is available at 25 C for a particular species, but not at 60 C, then it will be considered in runs at 25 C exactly but not in runs anywhere between 25 and 60 C. You might try using the extrapolate function to test whether this fixes your problem (type "extrapolate on" in the command pane). Without your custom dataset, however, I can't test this myself. Take a look at this and if it still fails to run perhaps you could post your thermo dataset or send it to support@gwb.com. Hope this helps, Brian Farrell Aqueous Solutions LLC